Identification of a Locus Involved in the Utilization of Iron by Haemophilus influenzae

Size: px
Start display at page:

Download "Identification of a Locus Involved in the Utilization of Iron by Haemophilus influenzae"

Transcription

1 INFECrION AND IMMUNITY, OCt. 1994, p /94/$ Copyright 1994, American Society for Microbiology Vol. 62, No. 10 Identification of a Locus Involved in the Utilization of Iron by Haemophilus influenzae JERRY D. SANDERS, LESLIE D. COPE, AND ERIC J. HANSEN* Department of Microbiology, University of Texas Southwestem Medical Center, Dallas, Texas Received 3 May 1994/Accepted 21 July 1994 Haemophilus influenzae has an absolute requirement for heme for aerobic growth. This organism can satisfy this requirement by synthesizing heme from iron and protoporphyrin IX (PPIX). H. influenzae type b (Hib) strain DL42 was found to be unable to form single colonies when grown on a medium containing free iron and PPIX in place of heme. In contrast, the nontypeable H. influenzae (NTHI) strain TN106 grew readily on the same medium. A genomic library from NTHI strain TN106 was used to transform Hib strain DL42, and recombinants were selected on a medium containing iron and PPIX in place of heme. A recombinant plasmid with an 11.5-kb NTHI DNA insert was shown to confer on Hib strain DLA2 the ability to grow on iron and PPIX. Nucleotide sequence analysis revealed that this NTHI DNA insert contained three genes, designated hita, hitb, and hitc, which encoded products similar to the SfuABC proteins of Serratia marcescens, which have been shown to constitute a periplasmic binding protein-dependent iron transport system in this enteric organism. The NTHI HitA protein also was 69%o identical to the ferric-binding protein ofneisseria gonorrhoeae. Inactivation of the cloned NTHI hitc gene by insertion of an antibiotic resistance cartridge eliminated the ability of the recombinant plasmid to complement the growth deficiency of Hib DL42. Construction of an isogenic NTHI TN106 mutant lacking a functional hitc gene revealed that this mutation prevented this strain from growing on a medium containing iron and PPIX in place of heme. This NTHI hitc mutant was also unable to utilize either iron bound to transferrin or iron chelates. These results suggest that the products encoded by the hitabc genes are essential for the utilization of iron by NTHI. The best-known phenotypic trait of Haemophilus influenzae is its absolute requirement for both heme and NAD (i.e., the classical X and V factors, respectively) for aerobic growth (16). This heme requirement is caused by the inability of H. influenzae to carry out the sequence of biochemical reactions necessary to convert 8-amino-levulinic acid to protoporphyrin IX (PPIX), the immediate biosynthetic precursor of heme (18, 58). H. influenzae does possess the ability to take up PPIX and convert it to heme via the activity of the enzyme ferrochelatase, which inserts a single molecule of iron into the PPIX molecule. Accordingly, PPIX can satisfy the heme requirement of H. influenzae in vitro only if a utilizable form of iron is available in the growth medium (18, 58). H. influenzae possesses the ability to utilize many different sources of iron, including both heme (43) and iron-loaded transferrin (25). In the latter instance, it would appear that H. influenzae, in a manner similar to Neisseria gonorrhoeae and Neisseria meningitidis (7, 50), binds the iron-loaded transferrin molecule to its cell surface (49) and then, by an undefined mechanism(s), extracts the iron from the transferrin and transports it into the cell. It is also known that, in the absence of heme, iron salts and chelates can suffice to provide iron for H. influenzae, provided that PPIX is also available as the source of the porphyrin ring (43, 60). However, there is no information available concerning how iron actually enters the H. influenzae cell after transferrin, heme, or iron chelates are taken up. In this study, we describe the identification of an iron utilization system in H. influenzae that is similar to a periplas- * Corresponding author. Mailing address: Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX Phone: (214) Fax: (214) mic binding protein-dependent iron transport system in Serratia marcescens (2, 3, 63). Mutant analysis was used to prove that this system is required for the utilization of iron by H. influenzae when PPIX is substituted for heme in the growth medium. MATERUILS AND METHODS Bacterial strains and culture media. H. influenzae type b (Hib) strain DL42 and nontypeable H. influenzae (NTHI) strain TN106 have both been described in detail (12, 37). The other Hib and NTHI strains used for Western blot (immunoblot) and Southern blot analyses have also been described (11). Mutant and recombinant strains derived from Hib strain DM42 and NTHI strain TN106 are listed in Table 1. H. influenzae strains were routinely grown by using brain heart infusion medium (Difco Laboratories, Detroit, Mich.) supplemented with Levinthal's base (1) (BHIs) at 37 C with aeration (for broth cultures) or at the same temperature in an atmosphere of 5% C02-95% air (for agar plates). The ability of H. influenzae strains to utilize iron and PPIX to satisfy their heme requirement was assessed by using BHI agar plates containing NAD (10,g/ml) and PPIX (20 pug/ml); there is sufficient free iron in this medium for growth of H. influenzae using PPIX in place of heme. Antimicrobial agent supplementation for H. influenzae strains included kanamycin (20,ug/ml), tetracycline (5,ug/ml), or chloramphenicol at either 0.8,ug/ml (for mutants with a cat cartridge insertion in the chromosome) or 2.0,ug/ml (for strains with plasmids containing the cat cartridge). The Escherichia coli cloning host HB101 was grown in LB medium (34) with appropriate antimicrobial agent supplementation. Assessment of utilization of various iron sources by wildtype and mutant NTHI strains. The basal medium was BHI agar containing NAD (10,ug/ml) and deferoxamine mesylate

2 4516 SANDERS ET AL. INFECT. IMMUN. TABLE 1. Bacterial strains and plasmids used in this study Strain or plasmid Relevant characteristic(s) Source or reference Strains Hib DL42 Virulent wild-type strain; cannot grow on iron and PPIX 20 DLA2(pJDS150) DL42 containing pjds150; can grow on iron and PPIX This study DL42(pJDS151) DM42 containing pjds151; cannot grow on iron and PPIX This study DL42(pJDS152) DL42 containing pjds152; can grow on iron and PPIX This study DLA2(pJDS153) DM42 containing pjds153; cannot grow on iron and PPIX This study DL42(pJDS154) DM42 containing pjds154; can grow on iron and PPIX This study DL42(pJDS155) DM42 containing pjds155; cannot grow on iron and PPIX This study H. influenzae Rd DB117 Recombination-deficient (rec-1) mutant strain used as a host for library construction 51 and certain subcloning experiments NTHI TN106 Isolate from a transtracheal aspirate from a patient with NTHI pneumonia; wild-type 47 strain which can grow on iron and PPIX TN TN106 with the hitc gene inactivated, accomplished by transforming TN106 with This study linearized pjds155; cannot grow on iron and PPIX TN T TN transformed with the 6.5-kb PstI fragment from recombinant plasmid This study pjds152; has a functional hitc gene and can grow on iron and PPIX E. coli HB101 Used as host strain for pbluescript II SK+ 46 Plasmids pls88 Shuttle vector capable of replication in E. coli and H. infiuenzae 61 pgjb103 Shuttle vector capable of replication in E. coli and H. influenzae S pbluescript II SK+ Plasmid vector Stratagene pjds150 pls88 with an 11.5-kb EcoRI fragment of NTHI TN106 DNA containing the intact This study hita, hitb, and hitc genes pjds151 pgjb103 containing a 7.5-kb EcoRI-ClaI fragment derived from the 11.5-kb insert in This study pjds150; contains intact hita and hitb genes pjds152 pgjb103 with the 6.5-kb PstI fragment derived from the 11.5-kb insert in pjds150; This study contains intact hitb and hitc genes pjds153 pgjb103 with the 4.5-kb PvuII-PstI fragment derived from the 6.5-kb PstI insert in This study pjds152; contains an intact hitc gene pjds154 pgjb103 with the 5.8-kb PstI-PvuII fragment derived from the 6.5-kb PstI insert in This study pjds152; contains intact hitb and hitc genes pjds155 pgjb103 with the ClaI sites of the vector removed and the 6.5-kb PstI fragment of This study pjds152 ligated into the PstI site; a cat cartridge was then ligated into the ClaI site within the hitc gene in this insert (Desferal; Ciba-Geigy Ltd., Basel, Switzerland) at a final concentration of either 0.04 or 0.08 mm. A suspension of H. influenzae from a BHIs plate was suspended in BHI broth, centrifuged at 4,000 x g for 10 min at 4 C, and resuspended in BHI broth to yield a Klett-Summerson colorimeter reading (Klett Manufacturing Company, New York, N.Y.) of 35 (equivalent to a final concentration of approximately 2 x 107 CFU/ml). This suspension of organisms was diluted 1:10 in BHI broth, and a 0.1-ml portion of this final suspension was spread on the surface of the test plate. After 30 min, sterile filter paper disks (4-mm diameter) were placed on the surface of the agar, the various iron sources (10,ul) were spotted onto these disks, and the plate was incubated overnight. The iron sources included heme (250,ug/ml), PPIX (250,ug/ml; a negative control), iron-loaded human transferrin (98% iron saturated; Sigma Chemical Co., St. Louis, Mo.) (20 mg/ml), ferric ammonium citrate (5.2 mg/ml), and ferric nitrate (8 mg/ml). Plasmids. The plasmid pbluescript II SK+ was obtained from Stratagene (La Jolla, Calif.). The plasmid shuttle vector pgjb103 (5, 53) was obtained from Gerard J. Barcak, and the plasmid shuttle vector pls88 (61) was provided by William L. Albritton. Recombinant DNA methods. Standard recombinant DNA methods including restriction enzyme digestions, ligation reactions, agarose gel electrophoresis, and plasmid purifications were performed as described previously (34, 46). Restriction enzymes, DNA polymerase Klenow fragment, and BglII, ClaI, and PstI linkers were purchased from New England Biolabs (Beverly, Mass.). The cat gene encoding chloramphenicol acetyltransferase and lacking an internal EcoRI site was derived from the plasmid puc4decat, which was kindly provided by Bruce A. Green. After excision from puc4decat with EcoRI, ClaI linkers were added to the cat cartridge (21). Construction of an NTHI strain TN106 genomic DNA library. Chromosomal DNA purified from NTHI strain TN106 by the method of Marmur (35) was partially digested with EcoRI. DNA fragments (6 to 15 kb) isolated by sucrose density gradient centrifugation were ligated into the EcoRI site of plasmid pls88 (61). This ligation reaction mixture was used to transform H. influenzae Rd strain DB117 as described previously (12, 20), yielding 166,000 recombinants. These recombinants were pooled and grown in BHIs broth, and plasmids representing the NTHI TN106 genomic DNA library were purified from this culture as described previously (12). H. influenzae genetic transformation methods. The glycerol-

3 VOL. 62, 1994 lactate shock method (52) was used to transform Hib strain DL42 with the shuttle vectors pls88 and pgjb103 and recombinant plasmids derived from these vectors. Transformants were selected on BHIs agar plates containing either kanamycin (20 p.g/ml) (when pls88-based plasmids were used) or tetracycline (5,ug/ml) (for pgjb103-derived plasmids). For transformation of NTHI with linear DNA molecules, either the M1v-based method of Herriott (26) or the BHIs agar plate-based method of Sanders et al. (47) was used. With the latter method, the segregation and outgrowth step was not performed in BHIs broth but instead was accomplished using BHIs agar plates. The resultant bacterial growth was suspended in BHI broth, serially diluted, and plated on appropriate selective media. MAbs. Monoclonal antibody (MAb) 6B8 is directed against the 40-kDa H. influenzae iron-regulated protein previously described as being located in the periplasmic space of this organism (24) and which was designated HitA in this study. To produce a MAb with this antigenic specificity, the HitA protein was purified from Hib strain DL42 for use as an immunogen. Whole cells of this strain, grown overnight on BHI agar plates containing NAD (10,ug/ml), PPIX (0.5,ug/ml), and deferoxamine mesylate (0.8 mm), were disrupted by sonication, and the cell envelopes were pelleted by centrifugation. The resultant supernatant fluid was concentrated by means of a Centriprep concentrator (Amicon, Beverly, Mass.) and analyzed by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE). The most abundant protein in this preparation had an apparent molecular mass of 40 kda in SDS-PAGE. N-terminal amino acid sequence analysis of this protein revealed that 13 of the first 14 amino acids were identical to those of the iron-regulated 40-kDa periplasmic protein of H. influenzae (24). This protein was eluted from the gel and used to immunize mice. Spleen cells from these immunized mice were fused with SP2/0-Agl4 plasmacytoma cells, and lymphocyte hybridomas were selected as described previously (44). Culture supernatants from these hybridomas were screened in Western blot analysis using the gel-purified 40-kDa Hib DL42 protein (HitA) as the antigen. MAb 6B8 reacted with a single antigen (approximate molecular mass of 37 to 40 kda) of every Hib and NTHI strain tested to date in Western blot analysis (data not shown). N-terminal amino acid sequence analysis. The HitA protein present in the supernatant from sonicated Hib DL42 cells was subjected to SDS-PAGE by the method of Hunkapiller et al. (29). The gel-resolved HitA protein band was transferred to a polyvinylidene difluoride membrane by the method of Matsudaira (36) and subjected to N-terminal amino acid analysis as described previously (22). Western blot analysis. Detection of the reactivity of the murine MAb 6B8 with the H. influenzae HitA protein in Western blot analysis was accomplished as described previously (30). Nucleotide sequence analysis. H. influenzae DNA inserts contained in pbluescript II SK+ were sequenced by standard techniques, including the use of nested deletions (46). In all cases, both strands were sequenced in their entirety. DNA sequence information was analyzed using the Intelligenetics Suite package and programs from the University of Wisconsin Genetics Computer Group software sequence analysis package (15). Southern blot analysis. Chromosomal DNA purified from wild-type, mutant, and transformant H. influenzae strains was digested to completion with appropriate restriction enzymes and probed in Southern blot analysis (46). The DNA probes used in these experiments included the 1.3-kb cat cartridge H. INFLUENZAE IRON UTILIZATION SYSTEM 4517 Hib DL42 NTHI TN 106 Hib DL42(pLS88) Hib DL42(pJDS1 50) (A) HEME (B) PPIX FIG. 1. Growth of wild-type and recombinant H. influenzae strains on BHI-NAD agar containing either heme (10,ug/ml) (A) or PPIX (20,ug/ml) (B). Mid-logarithmic- hase cultures in BHIs medium were diluted to 1 x 103 to 3 x 103 CFU/ml, and 0.1-ml portions of these suspensions were plated on the two types of solidified media and then incubated overnight as described in Materials and Methods. The strains tested in this experiment included the wild-type Hib strain DL42, the wild-type NTHI strain TN106, Hib DL42 carrying the plasmid shuttle vector pls88, and Hib DL42 carrying the recombinant plasmid pjds150. For the last two strains, the growth medium also contained kanamycin (20,ug/ml). from puc4decat, a 0.89-kb PstI-SspI fragment containing the majority of the hita gene, a 0.64-kb MunI-PvuII fragment containing half of the hitb gene, and a 0.57-kb BsrBI fragment from the hitc gene. RESULTS Growth of H. influenzae strains on iron and PPIX. In preliminary experiments examining the ability of selected Hib and NTHI strains to utilize heme compounds and precursors, it was noted that Hib strain DM42, which grows readily on BHI-NAD medium containing heme (Fig. 1A), could not form single colonies on BHI-NAD agar plates containing iron and PPIX in place of heme (Fig. 1B). Varying the concentration of PPIX in the medium from 0.5 to 100 p,g/ml still did not allow this Hib strain to grow, a finding which indicated that some sort of toxicity associated with relatively high levels of PPIX was not responsible for this phenotype. This finding in itself was not surprising, in that it had been previously reported that 8% of H. influenzae strains could not use iron and PPIX in place of

4 4518 SANDERS ET AL. INFECT. IMMUN. pjds C1 o L-.0 u C - 4-' 0.~ = QCL~ -=l.r--0 QOCLC(A o9rfi1 I orf 2 hita orf 3 [ ~ m U f) hitb orf 4 hitc orf 5 Iorf 61F orf7 = (a g 4it5 pjds1 51 pjds1 52 pjds1 53 pjds1 54 pjds Kb FIG. 2. Partial restriction enzyme map of the NTHI DNA inserts in pjds150 and related plasmids. All of the DNA extending from the AvaI site located 5' from ORF 1 to the PvuII site beyond ORF 7 in pjds150 was sequenced, and the ORFs detected in this region are depicted together with arrows indicating the predicted direction of transcription of each ORF. The plus and minus signs to the right of each plasmid's DNA insert indicate the ability of that plasmid to transform Hib DL42 to the ability to grow on BHI-NAD plates containing iron and PPIX in place of heme. The triangle beneath the insert from pjds155 indicates the ClaI site where a cat cartridge was inserted into the hitc gene within this plasmid's NTHI DNA insert. heme (25). In contrast, an NTHI strain (TN106) used routinely in this laboratory grew well on the same medium containing iron and PPIX (Fig. 1B). As expected, this same NTHI strain grew well on BHI-NAD agar containing heme (Fig. 1A). Cloning of an NTHI locus that permits growth of Hib DL42 on iron and PPIX. A genetic approach was used to address the interesting difference between Hib DL42 and NTHI TN106 in their relative abilities to grow on iron and PPIX. A genomic library constructed from NTHI strain TN106 in the shuttle vector pls88 was used to transform Hib strain DL42. The transformation reaction mixture was plated on BHI-NAD agar containing PPIX (20,ug/ml) and kanamycin and yielded 32 colonies. Each of these transformants was purified by singlecolony isolation, and their respective recombinant plasmids were isolated by a miniprep technique and used to transform Hib DML2. This second set of transformation reaction mixtures was plated on BHIs agar plates containing kanamycin (to avoid selecting possible spontaneous mutants able to utilize iron and PPIX). One transformant from each reaction mixture was purified and tested for its ability to grow on iron and PPIX. Only 2 of the 32 new transformants grew on iron and PPIX. The recombinant plasmids from these two transformants had very large NTHI DNA inserts of 11.5 and 16 kb. The plasmid with the smaller insert was selected for further study and designated pjds150 (Fig. 2). The recombinant Hib strain DL42(pJDS150) grew readily on iron and PPIX (Fig. 1B), whereas DL42 containing only the shuttle vector pls88 could not form single colonies on the same medium (Fig. 1B). Localization of the relevant genetic locus. Subcloning of restriction fragments from the 11.5-kb NTHI DNA insert in pjds150 involved the use of the shuttle vector pgjb103 which, in the experience of this laboratory, is more amenable for use in transforming both the H. influenzae Rd strain DB117 and Hib strain DL42 (data not shown). Neither the 7.5-kb EcoRI-Clal fragment in pjds151 nor the 4.5-kb PvuII-PstI segment in pjds153 could transform DL42 to grow on iron and PPIX (Fig. 2). However, the 6.5-kb PstI fragment contained in pjds152 was as effective as pjds150 in conferring on Hib DL42 the ability to form single colonies on iron and PPIX (Fig. 2). One additional subcloning experiment which resulted in the construction of pjds154 revealed that the 0.8-kb PvuII-PstI fragment in pjds152 was not involved in converting Hib strain DL42 to this altered phenotype (Fig. 2). Nucleotide sequence analysis. Three fragments of the NTHI insert in pjds150 were subcloned into pbluescript II SK+ for sequencing. These included the 2.7-kb AvaI-PstI, the 2.0-kb + +

5 VOL. 62, 1994 PstI-PvuII, and the 3.8-kb PvuII-PvuII fragments (Fig. 2). Upon evaluation of the nucleotide sequences of these three fragments, it appeared that a small DNA fragment located between the AvaI-PstI and PstI-PvuII fragments was missing, and therefore, double-stranded DNA sequencing of this region in pjds151 was performed. This analysis revealed the presence of a small (76-bp) PstI fragment located between these two fragments (Fig. 2). Seven open reading frames (ORFs) were readily identifiable within the 8.5 kb of DNA sequence (Fig. 2). Five of these ORFs were arranged sequentially on one strand, with the other two in tandem on the opposite strand. The first ORF (ORF 1 in Fig. 2) encoded a predicted protein with a calculated molecular weight of 26,598 which was 52% identical to the 24.5-kDa hypothetical protein from Pseudomonas aeruginosa suggested to be involved in proline biosynthesis (57). The protein encoded by the second ORF (ORF 2 in Fig. 2) had no significant homology with any proteins in the available data bases. On the opposite DNA strand, ORF 6 encoded a protein with a molecular weight of 30,470 which was 24% identical to the D-alanine-D-alanine ligase B of E. coli (45), while the protein encoded by ORF 7 on the same DNA strand had a calculated molecular weight of 41,470 and was 61% identical to the succinyl-diaminopimelate desuccinylase of E. coli (8, 62). Identification ofh. influenzae proteins putatively involved in iron utilization. The three ORFs in the middle of the sequenced DNA (ORFs 3 to 5 in Fig. 2) encoded proteins with significant similarity to a set of proteins (SfuA, SfuB, and SfuC) from S. marcescens that are involved in a periplasmic binding protein-dependent iron transport system (2, 3, 63). The protein encoded by ORF 3 had a calculated molecular weight of 36,218 and was 38% identical to the SfuA protein of S. marcescens (see Fig. 4) (2). This S. marcescens protein is the periplasmic binding component of this iron transport system (2, 3). The H. influenzae protein encoded by ORF 3 was also 69% identical to the major iron-regulated protein of N. gonorrhoeae, designated as ferric-binding protein (Fbp) (6). Because of the similarity between this H. influenzae protein and both the SfuA and Fbp molecules and because the last two proteins are involved in iron transport in their respective organisms (2, 3, 10), we tentatively designated the protein encoded by ORF 3 as H. influenzae iron transport protein A (HitA). A MAb (6B8) raised against the 40-kDa iron-regulated periplasmic protein from Hib strain DL42 reacted with the recombinant NTHI HitA protein expressed in E. coli (data not shown). Hydrophobicity analysis of the N-terminal region of the NTHI HitA protein indicated that the first 23 amino acids formed a hydrophobic domain similar to that of leader peptides (54). N-terminal amino acid sequence analysis of the 40-kDa periplasmic, iron-regulated protein expressed by Hib strain DL42 revealed that the N-terminal sequence of this mature Hib protein was identical to that of residues 24 to 37 of the NTHI HitA protein (Fig. 3) and nearly identical to the N terminus of the periplasmic iron-regulated protein from another H. influenzae strain (24), suggesting that the NTHI HitA protein was synthesized with a leader peptide. It was also noted that the hita gene was preceded by a 19-nucleotide sequence that weakly resembled (11 of 19 matches) the E. coli Fur consensus binding sequence (33). Whether this sequence plays a role in the expression of the HitA protein is not known. The fourth ORF detected in the sequenced DNA started approximately 120 nucleotides downstream from the stop codon in hita. The protein encoded by ORF 4 had a calculated molecular weight of 51,232 and was 37% identical to the S. marcescens SfuB protein (Fig. 4), which functions as an integral H. INFLUENZAE IRON UTILIZATION SYSTEM 4519 cytoplasmic membrane protein in the S. marcescens iron transport system (2). This protein encoded by ORF 4 was designated HitB. The putative start codon for this ORF was TTG (Fig. 3), based on the observation that the deduced amino acid sequence following this codon was similar to the N-terminal region of the SfuB protein (Fig. 4). ORF 5, the last of these three ORFs, overlapped the extreme 3' end of ORF 4 and encoded a protein with a molecular weight of 40,410. This protein exhibited 38% identity with the SfuC protein of S. marcescens (Fig. 4), which functions as an ATP-binding protein in the S. marcescens iron transport system (2), and was designated HitC. Similarly to SfuC, the HitC protein possessed the consensus A and B regions common to nucleotide-binding proteins of ABC transporters (17, 27) (Fig. 4). In addition, it should be noted that the start codon for the hitc gene overlaps the end of the hitb gene (Fig. 3). In S. marcescens, the start codon for the sfuc gene similarly overlaps the stop codon of the sfub gene (2). Use of mutant analysis to demonstrate involvement of the hitabc genes in utilization of iron and PPIX. The subcloning experiments described above had localized the genetic locus in pjds150 which allowed Hib strain DM42 to utilize iron and PPIX to the 5.8 kb PstI-PvuII fragment in pjds154. The possible involvement of the NTHI hitabc genes in this complementation activity was investigated directly by mutant analysis. A cat cartridge was inserted into the ClaI site within the hitc gene in pjds152, resulting in the mutated plasmid pjds155 (Fig. 2). When pjds155 was transformed into Hib strain DML2, the resultant recombinant could not grow on BHI-NAD agar plates containing iron and PPIX (Fig. 2). Construction of an isogenic NTHI hitc mutant. The inabilities of pjds155 and pjds151 to allow growth of Hib strain DM42 on medium containing iron and PPIX raised the possibility that the hitc gene product was directly involved in the growth of H. influenzae on this medium. To investigate this, pjds155 with the mutated hitc gene was linearized by digestion with BglII and used to transform the wild-type NTHI strain TN106. Transformants were selected on BHIs medium containing chloramphenicol. From a total of 52 chloramphenicol-resistant transformants, eight were tested for growth on BHI-NAD agar containing iron and PPIX in place of heme and found to be incapable of forming single colonies on this medium. One of these, designated TN , was selected for further study. To confirm that proper allelic exchange had occurred in this mutant strain, chromosomal DNA preparations from the wildtype NTHI strain TN106 and the mutant strain TN were digested with PstI and probed in Southern blot analysis with probes for both the hitc gene and the cat cartridge. When the wild-type chromosomal DNA was probed with a 0.57-kb BsrBI fragment from the hitc gene, a 6.5-kb PstI fragment bound this probe, as expected (Fig. 5, panel 1, lane A). In contrast, the chromosomal DNA from the mutant strain TN had a 7.8-kb PstI fragment that hybridized with this hitc probe (Fig. 5, panel 1, lane B), consistent with the presence of the 1.3-kb cat cartridge within the hitc gene in the chromosome of this mutant. The presence of the cat cartridge within the hitc gene of the mutant strain was confirmed by the use of the cat cartridge probe (Fig. 5, panel 2, lane B). As expected, the DNA of the wild-type strain did not bind this probe (Fig. 5, panel 2, lane A). Utilization of iron sources by the wild-type and mutant NTHI strains. To determine directly whether the hitc gene product was involved in iron utilization, the mutant and wild-type NTHI strains were plated on BHI-NAD agar containing PPIX (as the porphyrin source) and deferoxamine

6 4520 SANDERS ET AL. INFECT. IMMUN CAATGATAAATTGATTGATGAAACTTATGATTGCAGTGAGTTATTTAATGCGCTTTGTGATGTATTAACAAATTTAGGTTATATCCAGCCTGCAAACCTATAATCTGTGGACGGTGCGTGTTATGTA SD 254 CCGTTTTGTTTTTCATCTAAATATCAAT TTAAAAAATT6,""''...'MAGGCATAG AATAG-CTGC AATTCAG GCTTAACTGAATATTTGCACTCAACATAAGGAGCTTTTCA ATG CAA TTT AAA CAT TTC AAA CTT GCT ACC CTT GCT GCA GCA CTT GCT TTT TCT GCT MT AGT TTT GCT GAT ATT ACC GTT TAT MT GGT CAG CAC M Q F K H F K L A T L A A A L A F S A N S F A D I T V Y N G Q 351 H 446 AAA GM GCC GCT GCT GCA GTG GCA AAA GCC TTT GM CAG GM ACA GGC ATT AAA GTT ACG CTA MT AGC GGG AM AGT GCG CM CTT GCA GGT CM K E A A A A V A K A F E Q E T G I K V T L N S G K S A Q L A G Q TTA AAA GM GM GGC GAT AAA ACA CCC GCC GAT GTT TTC TAT ACT GM CM ACA GCG ACT TTT GCT GAT CTT TCT GM GCA GGG CTT TTA GCA CCA L K E E G D K T P A D V F Y T E Q T A T F A D L S E A G L L A P ATT TCA GM CM ACA ATT AAA CM ACT GCA CM AAA GGC GTA CCA CTT GCA CCG AAA AAA GAC TGG GTT GCA TTA AGT GGC CGT TCT CGC GTA GTG I S E Q T I K Q T A Q K G V P L A P K K D W V A L S G R S R V V GTT TAC GAT CAC ACT AAA TTA TCT GM AAA GAT ATG GM AAA TCA GTG CTT GAT TAT GCA ACA CCA AAA TGG AAA GGC AAA ATC GGT TAT GTA TCA V Y D H T K L S E K D M E K S V L D Y A T P K W K G K I G Y V S ACT TCT GGT GCG TTC TTA GAG CM GTT GTT GCT TTA AGC AAA ATG AAA GGG GAC AAA GTT GCG CTT MT TGG TTA AAA GGC TTA AAA GAG MC GGT T S G A F L E Q V V A L S K M K G D K V A L N W L K G L K E N G AAA CTT TAT GCT AAA MT AGT GTG GCA TTA CM GCG GTC GM MT GGT GM GTG CCT GCT GCG TTA ATC MT MC TAT TAT TGG TAT MC CTT GCA K L Y A K N S V A L Q A V E N G E V P A A L I N N Y Y W Y N L A AAA GAA AAA GGC GTG GM MT CTA AAA AGC CGT CTT TAT TTT GTT CGC CAC CM GAT CCA GGT GCG TTA GTT AGC TAT TCA GGT GCA GCA GTA TTA K E K G V E N L K S R L Y F V R H Q D P G A L V S Y S G A A V L AAA GCC TCT AAA MT CM GCT GM GCA CM AAA TTC GTT GAT TTC TTA GCA AGT AAA AAA GGT CM GM GCA TTA GTG GCA GTG CGT GCA GM TAT K A S K N Q A E A Q K F V D F L A S K K G Q E A L V A V R A E Y CCA TTA CGC GCT GAT GTG GTT TCG CCA TTT MT CTT GM CCT TAT GM AAA TTA GM GCA CCA GTG GTA TCC GCA ACA ACA GCT CM GAT AAA GAG P L R A D V V S P F N L E P Y E K L E A P V V S A T T A Q D K E CAT GCG ACC AAA TTA ATT GM GM GCT GGA TTG AAA TM TCCAAATATTGCGTGTGTGGATTTGAAAAMTTCACGCACGCGTTTACMTTCTCTACCAAAATTMCCGCTTGC H A T K L I E E A G L K 1329 SD 1433 GTGCGTGMCTGAAATGTTCACATTCCTAAAAGGATTTAACT TTG CCT CGC AGA CCG CCA TTC TGG CTT ACT TTA CTT ATC ATC TTA ATC GGA CTT CCG TTA TGT M P R R P P F W L T L L I I L I G L P L C TTG CCG TTT CTG TAT GTC ATT TTG CGT GCG ACA GM GTG GGA TTA ACG CGA AGT GTT GAG CTA TTG TTT CGC CCT CGA ATG GCT GM TTA TTA AGC L P F L Y V I L R A T E V G L T R S V E L L F R P R M A E L L S MT ACA ATG CTT TTA ATG GTT TGT GTA ACT ATT GGT GCT ATT TCA CTT GGT ACG CTT TGT GCT TTT TTA CTT GM CGT TAT CGC TTT TTC GGT AAA N T M L L M V C V T I G A I S L G T L C A F L L E R Y R F F G K GCT TTT TTT GM GTG GCG ATG ACG TTA CCC CTT TGT ATT CCC GCC TTT GTA AGT TGT TTT ACT TGG ATC AGC CTC ACA TTC CGC GTT GAG GGT TTT A F F E V A M T L P L C I P A F V S C F T W I S L T F R V E G F TGG GGA ACA ATT GGT ATT ATG ACA TTA AGT TCA TTT CCT TTG GCT TAT TTG CCC GTT TCC GCC ATA CTA AAA AGA CTT GAT CGT TCT CTT GM GAA W G T I G I M T L S S F P L A Y L P V S A I L K R L D R S L E E GTA AGC CTT TCG CTT GGT AAA AGC CCT GTG TAT ACC TTT TGG TAT GCT ATT TTT CCG CAA CTT AAA CCC GCC ATT GGT AGT AGT ATC TTA CTG ATT V S L S L G K S P V Y T F W Y A I F P Q L K P A I G S S I L L I GCT TTA CAT ATG TTG GTC GM TTT GGT GCA GTG TCA ATT TTA AAT TAT CM ACC TTT ACC ACT GCC ATT TTC CM GM TAT GM ATG TCT TTT MC A L H M L V E F G A V S I L N Y Q T F T T A I F Q E Y E M S F N MC AGC ACT GCT GCA TTA TTA TCT GCC GTT TTA ATG GCG ATT TGT ATA CTT ATT GTT TTT GGG GM ATT TTC TTT CGT GGA AAA CM ACA CTT TAC N S T A A L L S A V L M A I C I L I V F G E I F F R G K Q T L Y CAC AGT GGA AAA GGT GTT ATG CGT CCT TAT CTC GTA AAA ACA CTT TCC TTT GGA AAA CM TGT TTA ACC TTC GGA TTT TTC TCT AGC ATA TTC ATT H S G K G V M R P Y L V K T L S F G K Q C L T F G F F S S I F I TTA AGC ATT GGC GTG CCT GTG ATT ATG TTA ATT TAC TGG CTT ATT GTG GGA ACT TCA CTC GM AGT GCG GGT GAT TTT TCA GM TTT TTA TCG GCA L S I G V P V I M L I Y W L I V G T S L E S A G D F S E F L S A Nucleotide sequence of a 4.2-kb segment of NTHI TN106 DNA from pjds150 containing the hitabc genes; the deduced amino acid FIG. 3. sequence is listed below the nucleotide sequence. The ORF for hita extends from nucleotides 255 to 1253, the ORF for hitb extends from nucleotides 1371 to 2891, and the ORF for hitc extends from nucleotides 2878 to Putative -35 regions, -10 regions, and Shine-Dalgarno sites are indicated in front of each ORF. A possible Fur box is indicated upstream from hita by shading. An inverted repeat immediately downstream from the hitc gene is indicated by opposing arrows. The putative leader peptide for the HitA protein is indicated by underlining.

7 VOL. 62, 1994 H. INFLUENZAE IRON UTILIZATION SYSTEM TTC AGC MT TCA TTT ATC ATT TCA GGC TTA GGC GCA TTG CTT ACC GTA ATG TGC GCC TTG CCA TTA GTT TGG GCA GCT GTT CGT TAC CGT AGT TAT F S N S F I I S G L G A L L T V M C A L P L V W A A V R Y R S Y TTA ACG ATT TGG ATC GAC CGC TTG CCA TAT CTA TTG CAC GCT GTG CCA GGC TTA GTC ATT GCC TTA TCA TTA GTC TAT TTT TCC ATC CAT TAC GCT L T I W I D R L P Y L L H A V P G L V I A L S L V Y F S I H Y A MC GAC CTA TAT CAA ACC TTT TTT GTG ATT ATC ATT GCC TAC TTT ATG CTC TAT TTG CCA ATG GCA CM ACT ACA TTA AGA GCG TCT TTA GAG CM N D L Y Q T F F V I I I A Y F M L Y L P M A Q T T L R A S L E Q CTT TCC GAT CAA ATT GM AAA GTC GGA CM AGT CTT GGG CGA MC CCT TTC TAT ATT TTT CGC ACC TTG ACG CTA CCA GCC ATA TTA CCC GGT GTG L S D Q I E K V G Q S L G R N P F Y I F R T L T L P A I L P G V GCA GCC GCA TTT GCT TTG GTT TTT TTG MT TTA ATG AAA GAG CTT ACC GCG ACG CTT TTG CTC ACA TCA MT GAT ATT MA ACC TTA TCC ATT GCT A A A F A L V F L N L M K E L T A T L L L T S N D I K T L S I A GTG TGG GM CAT ACC AGC GAT GCA CAA TAT GCT GCC GCC ACC CCT TAT GCG TTA ATG CTC GTT CTT TTT TCG GGT ATT CCT GTA TTT TTA TTG AAA V W E H T S D A Q Y A A A T P Y A L M L V L F S G I P V F L L K AAA TAT GCG TTT AAA TAAA ATG ATA MT MT CCG TTA CTA ACC GTT AAA MT CTC MT MA TTT TTT MT GAA CM CM GTT CTG CAC GAT ATT TCA K Y A F K M R L N K M I N N P L L T V K N L N K F F N E Q Q V L H D I S TTC AGC TTA CM CGC GGA GM ATC CTC TTT TTA CTT GGT GCT TCA GGC TGT GGC AAA ACT ACA TTA TTA CGT GCC ATT GCA GGT TTT GM CM CCC F S L Q R G E I L F L L G A S G C G K T T L L R A I A G F E Q P TCT MT GGC GM ATT TGG CTA AAA GAG CGG TTA ATT TTT GGC GAG MT TTT MT CTT CCA ACG CM CM CGC CAT CTC GGT TAT GTG GTG CM GAG S N G E I W L K E R L I F G E N F N L P T Q Q R H L G Y V V Q E GGC ATA CTT TTT CCT CAC TTA MT GTC TAT CGC MC ATT GCT TAC GGA TTA GGC MC GGC AAA GGA AAA MT AGC GM GM AAA ACG CGG ATT GM G I L F P H L N V Y R N I A Y G L G N G K G K N S E E K T R I E CM ATA ATG CAA CTA ACG GGT ATT TTT GM CTG GCG GAT CGC TTT CCA CAT CM CTT TCA GGC GGA CM CM CM CGC GTA GCA TTG GCG CGT GCT Q I M Q L T G I F E L A D R F P H Q L S G G Q Q Q R V A L A R A TTA GCC CCT MT CCA GM CTG ATT TTA TTA GAC GAG CCT TTC AGT GCC TTA GAC GAG CAT CTT CGC CM CM ATT CGC CM GAG ATG CTC CM GCA L A P N P E L I L L D E P F S A L D E H L R Q Q I R Q E M L Q A CTT CGC CM AGC GGT GCT TCC GCA ATT TTC GTT ACT CAC GAC CGT GAT GM GCC TTA CGC TAC GCT GAT AAA ATC GCC ATT ATT CAG CM GGT AAA L R Q S G A S A I F V T H D R D E A L R Y A D K I A I I Q Q G K ATT TTA CM ATC GAT ACG CCT CGC ACC CTT TAT TGG TCG CCT MT CAT CTT GM ACA GCA AAA TTT ATG GGG GM AGT ATT GTT TTG CCT GCA MT I L Q I D T P R T L Y W S P N H L E T A K F M G E S I V L P A N CTA CTC GAT GM MT ACC GCT CM TGC CM TTA GGC MT ATT CCT ATA AAA MT AAA TCA ATC TCA CAA MT CM GGT AGG ATT TTG CTT CGT CCA L L D E N T A Q C Q L G N I P I K N K S I S Q N Q G R I L L R P GM CM TTT AGC CTG TTT AAA ACA TCA GAA MT CCA ACC GCA CTT TTT MT GGA CM ATA AAA CM ATT GM TTT AAA GGA AAA ATT ACC TCC ATT E Q F S L F K T S E N P T A L F N G Q I K Q I E F K G K I T S I CM ATT GM ATT MT GGC TAC GCA ATA TGG ATT GAG MC GTT ATT TCT CCC GAT TTA TCT ATT GGC GAT MT TTG CCT GTT TAT TTA CAT AAA AAA Q I E I N G Y A I W I E N V I S P D L S I G D N L P V Y L H K K GGG CTT TTT TAC GCT TM CMTAAAGCCTTATCTTCACGATMGGCTTATTTTTAMCMTATATTCGGMAAAATTTGTTCMGATGTGATATTAAACAGTCTGTGCCTAAAATATTTTC G L F Y A -- > < CCCTTTCCACGCCTGTTGCAAAATCTCTGGAGAAAATTGCTGGCTTGCTAATTCAGCTAACGGCAAATAACTGATATGCCAAGGCTCCCGCCCCACTTTCTTATTGGACTGCATATTCATAAAAGGC FIG. 3.-Continued. mesylate (to chelate free iron in the medium). Filter paper BHI-NAD agar plates containing iron and PPIX. All 30 disks containing various iron sources were then placed on the transformants that were obtained in this experiment were surface of these agar plates. The wild-type TN106 strain was chloramphenicol sensitive, a finding which suggested that able to use all of the iron sources tested, including heme, allelic exchange had replaced the mutated hitc gene with the transferrin, ferric ammonium citrate, and ferric nitrate, and wild-type allele in each of these strains. This was confirmed by exhibited a readily detectable zone of growth around the disks Southern blot analysis of one of these transformants, desigcontaining these compounds (Fig. 6). In contrast, the mutant nated TN T (Fig. 5, panels 1 and 2, lanes C). As strain TN , while it could use heme, was unable to expected, this transformant strain was able to utilize all of the utilize the other three iron sources described above for growth iron sources that could not be utilized by the hitc mutant (Fig. on this medium (Fig. 6). 6). Elimination of the hitc mutation in the mutant strain Detection of hitabc genes in other H. influenzae strains. TN To reconstitute the wild-type genotype, mutant Chromosomal DNA preparations from two NTHI strains TN was transformed with the 6.5-kb PstI fragment of (TN106 and AAR200) and three Hib strains (DM42, DL63, NTHI chromosomal DNA from pjds152 and the desired and ) were digested with PstI and used in Southern blot transformants were selected by virtue of their ability to grow on analysis together with probes for the hitabc genes. A single

8 4522 SANDERS ET AL. INFECT. IMMUN HitA HItA MQFKHFKL---ATLA--AALAFSA-NS FAD-- ITVYNGQHKEAAAAVAKAFEQETG IKVTLNSGKSAQLAGQ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~1 HM SfuA MKLRISSLGPVALLASSMMLAFGAQAASADQGIVIYNAQHENLVKSWVDGFTKDTGIKVTLRNGGDSELGNQ HitB SfuB LKEEGDKTPADVFYTEQTATFADLSEAGLLAPISEQTIKQTAQKGVPLAPKKDWVALSGRSRVVVYDHTKLS if, 011 H ll, , Ill LVQEGSASPADVFLTENSPAMVLVDNAKLFAPLDAATLAQVEPQYRP--SSHGRWIGIAARSTVFVYNPAKLS EKDMEKSVLDYATPKWKGKIGYVSTSGA-FLEQVVALSKMKGDKVALNWLKGLKENGKLYAKNSVALQAVEN DAQLPKSLLDLAKPEWKG-RWAASPSGADFQAIVSALLELKGEKATLAWLKAMKTNFTAYKGNSTVMKAVNA GEVPAALINNYYWYNLAKEKGVENLKSRLYFVRHQDPGALVSYSGAAVLKASKNQAEAQKFVDFLASKKGQE I' 10 H, I'll Ill 11 I 'l 11 I'l1 111! GQVDSGVIYHYYPFVDGAKTGENSNNIKLYYFKHQDPGAFVSISGGGVLASSKHQQQAQAFIKWITGKQGQE x ALVAVPA-EYPLRADVVSPFNLEPYEKLEAPVVSATTAQDKEHATKLIEEAGLK I ILIE O OIILV 'I L V T ILRTNNAFEYAVGVGAASNPKLVPLKDLDAPKVDAAQLNSK-KVVELMTEAGLL MPR--RPPFWLTLLIILIGLPLCLPFLYVILRATEVGLTRSVELLFRPRMAELLSNTMLLMVCVTIGAISLGTLC VPRHPRPGAIVVVSAVLLSLLALLPLGFVIGVAFETGWQTVKALVFRPRVAELLLNTLLLVVLTLPICAVLGVAL AFLLERYRFFGKAFFEVAMTLPLCIPAFVSCFTWISLTFRVEGFWGTIGIMTLSSFPLAYLPVSAILKRLDRSLE AWLTERTTLPGRRLWAVLATAPLAVPAFVQSYAWIISLVPSMHGLGAGVFISVLAYFPFIYLPAAAVLRRLDPGIE EVSLSLGKSPVYTFWYAIFPQLKPAIGSSILLIALHMLVEFGAVSILNYQTFTTAIFQEYEMSFNNSTAALLSAV DVATSLGSRPPAVFFRVVLPQLKLAVWGGSLLIALHLLAEYGLYAMIRFDTFTTAIFDQFQSTFNGPAANMLAGV LMAICILIVFGEIFFRGKQTLYHSGKGVMRPYLVKTLSFGKQCLTFGFFSSIFILSIGVPVIMLLIYWLIVG---- LVLCCLGLLLLEAISRGRARYARVGSGSARSQTPRRLSPPLAALALLLPIALTALALGVPFITLARWLWLGGFEV TSLESAGDFSEFLSAFSNSFI ISGLGALLTVMCALPLVWAAVRYRSYLTIWIDRLPYLLHAVPGLVIALSLV WRNAELWPALWQTLSLSA AGALLITLCAIPMAWLSVRYPARLYRVLEGCNYVTSSLPGIVVALALV YFSIHYANDLYQTFFVIIIAYFMLYLPMAQTTLRASLEQLSDQIEKVGQSLGRNPFYIFRTLTLPAILPGVAAAF TITIHSFRPIYQTEITLLLAYLLMFMPRALINLRAGIAQAPVELENVARSLGKSPAQALWSTTLRLAAPGVAAGA x ALVFLNLMKELTATLLLTSNDIKTLSIAVWEHTSDAQYAAATPYALMLVLFSGIPVFLL----KKYAFK llll 'l ALVFLAIANELTATLLLAPNGTRSTLATGFWALTSEIDYVAAAPYALIMVALSLPLTWLLYSQSKRTAGL x HitC NPLLTVKNLNKFFNEQQVLHDISFSLQRGEILFLLGASGCGKTTLLRAIAGFEQPSNGEIWLKERLIFGENFN SfuC MSTLELHGIGKSYNAIRVLEHIDLQVAA.SRTAIV9P8GS0R4 LLRIIAGFEIPDCGQILLQGQAMGNGSGW LPTQQRHLGYVVQEGILFPHLNVYRNIAYGLGNGKGKNSEEKTRIEQIM-QLTGIFELADRFPHQLSGGQQQR VPAHLRGIGFVPQDGALFPHFTVAGNIGFGL---KGGKREKQRRIEALMEMVALDRRLAALWPHELSGGQQQR VALARALAPNPELILLDEPFSALDEHLRQQIRQEHLQALRQSGASAIFVTHDRDEALRYADKIAIIQQGKILQ VAAASQRt''t)ZFSALDTGLRAATRKAVAELLTEAKVAS ILVTHDQSEALSFADQVAVMRSGRLAQ IDTPRTLYWSPNHLETAKFMGESIVLPANLLDENTAQCQLGNIPIKNKSISQNQGRILLRPEQFSLFKTSENP VGAPQDLYLRPVDEPTASFLGETLVLTA-ELAHGWADCALGRIAVDDRQRS-GPARIMLRPEQ--IQIGLSDP x TALFNGQIKQIEFKG--KITSIQIEINGYAIWIENVISPDLSIGDNLPVYLHKKGLFYA AQRGQAVITGIDFAGFVSTLNLQMAATGAQLEIKTVSREGLRPG--AQVTLNVMGQAHIFAG x 8kb 6 kb ABC _ ABC 1 2 FIG. 5. Southern blot analysis of PstI-digested chromosomal DNA from the wild-type, mutant, and transformant strains of NTHI TN106. DNA preparations from the wild-type strain (lanes A), the hitc mutant strain TN (lanes B), and the transformant strain TN T (lanes C) were probed either with a 0.57-kb BsrBI fragment from the hitc gene (panel 1) or with the cat cartridge (panel 2). Size position markers (in kilobases) are indicated on the left. possessed a PstI fragment of approximately 9.5 kb that hybridized these three probes (Fig. 7). DISCUSSION The paucity of free iron in the human body (9, 55, 56) requires that colonizing or invading microorganisms possess a mechanism(s) to obtain iron from host factors that sequester 2 4 ABCA FIG. 4. Comparison of the deduced amino acid sequences of the H. influenzae HitA, HitB, and HitC proteins with those of the SfuA, SfuB, and SfuC proteins of S. marcescens, respectively. The deduced amino acid sequences of the three S. marcescens proteins were published previously (2). The shaded regions in the SfuC protein indicate the FIG. 6. Utilization of iron sources by wild-type NTHI strain consensus A and B regions common to nucleotide-binding proteins of TN106, hitc mutant strain TN , and transformant strain ABC transporters (17, 27). TN1O6.155.T. Suspensions of 2 x 105 CFU of the wild-type (A), mutant (B), and transformant (C) strains were spread onto BHI-NAD agar plates containing PPIX (as the source of porphyrin) and deferoxamine mesylate (to chelate free iron in the medium). Filter paper disks were placed on these plates and spotted with the following compounds: DNA fragment from each strain bound all three probes. row Wlth 1, heme; row 2, PPIX (a negative control); row 3, ferric nitrate; NTHI strain TN1O6, this fragment was 6.5 kb in size, as would row 4, iron-loaded human transferrin; row 5, ferric ammonium citrate. be expected from the restriction map of pjds150 (Fig. 2). In The plates were incubated overnight as described in Materials and contrast, the other NTHI strain and the three Hib strains all Methods.

9 VOL. 62, 1994 H. INFLUENZAE IRON UTILIZATION SYSTEM 4523 gkb - 6kb AB C DE A B C D E A B C D E hydrophilic protein with nucleotide-binding domains (SfuC) (2, 3). The exact function of the SfuA molecule has been VW -t- inferred to be the binding of ferric iron (3), which enters the S. marcescens cell as a complex with citrate (2, 3, 63). Similarly, Sue the gonococcal Fbp protein, which is 37% identical to the SfuA molecule, has been shown to at least transiently bind iron (10). It should be noted that Fbp and HitA are even more similar to each other (69% identity) than they are to SfuA. This fact and the localization of the HitA protein to the periplasmic compartment of H. influenzae (24) reinforce the likely role of HitA 2 3 as the ligand-binding component of an iron transport system FIG. 7. Reactivity of the N' THI TN106 hita, hitb, and hitc gene that appears to be a member of the ABC transporter family probes with chromosomal DNA from wild-type NTHI and Hib strains. (17, 27). Chromosomal DNA preparatioins from NTHI strain TN106 (lanes A), The successful construction of an NTHI hitc mutant per- NTHI strain AAR200 (lanes B) H,ib strain DL42 (lanes C), Hib strain mitted in vitro testing that demonstrated directly the functional DL63 (lanes D), and Hib strair (lanes E) were digested with involvement of the protein products of the hitabc gene cluster PstI and probed in Southern blc t analysis with the following probes: a in iron utilization by H. influenzae. In contrast, several attempts 0.89-kb PstI-SspI fragment contaming the majority of the hita gene to use allelic exchange to introduce a mutated hita gene (panel 1), a 0.64-kb MunI-PvuII fragment from the hitb gene (panel 2), and a 0.57-kb BsrBI fragment fr om the hitc gene (panel 3). Molecular containing a cat cartridge into H. influenzae have met with size markers (in kilobases) are indicated on the left. failure (data not shown), suggesting that a functional HitA protein may be essential for the growth of H. influenzae. Similarly, mutant analysis of the function of Fbp, a HitA homolog, in the gonococcus has not been achieved to date this essential element. Graam-negative enteric bacteria and because attempts to construct anfbp mutant have been unsucccomplish this task by means of cessful (10). Whether N. gonorrhoeae also contains HitB and pseudomonads generally a( siderophore production andithe TonB-dependent transport of HitC homologs is not known with certainty, but the 136 bp of the siderophore-iron compil[ex into the bacterial cell (14, 19, published nucleotide sequence immediately downstream from 41). The mechanisms by wrhich siderophore-bound iron are the stop codon for the gonococcal fbp gene (6) encodes an transported across the out( er membrane, periplasmic space, incomplete polypeptide that has 57% identity with the N- and cytoplasmic membrane have been the subject of many terminal region of HitB (data not shown). elegant studies (4, 19, 41). The fact that the presence of the NTHI TN106 hitabc genes Other bacterial pathogenss, including both H. influenzae and in trans allowed Hib strain DML2 to grow on BHI-NAD agar pathogenic Neisseria specie, s, possess a siderophore-indepen- plates containing iron and PPIX indicates that this Hib strain dent mechanism(s) for iron, acquisition that involves the direct likely is deficient in its ability to transport iron. However, binding of iron-carrying sernim glycoproteins (e.g., transferrin) Southern blot analysis (Fig. 7) revealed that Hib strain DM42 to the bacterial cell (42). This binding of transferrin to the cell possessed chromosomal DNA regions that hybridized to the surface involves two proteinis, designated Tbpl and Thp2, and NTHI hita, hitb, and hitc gene probes. Moreover, Western the former protein from both N. gonorrhoeae (13) and N. blot analysis using the HitA-specific MAb 6B8 indicated that meningitidis (32) has been shown to possess similarity to Hib strain DLM2 does express a 40-kDa protein reactive with TonB-dependent outer meimbrane proteins. A recent study this MAb (data not shown); whether this Hib HitA protein is suggests that, in these path ogenic Neisseria species, once the functional has not yet been determined. However, the fact that iron has been removed from transferrin and gains access to the the mutation in the hitc gene in the recombinant plasmid periplasmic space, it is bounid by Fbp as part of the process of pjds155 eliminated the ability of this plasmid to complement transporting the iron molecaule across the cytoplasmic mem- the growth deficiency of Hib strain DM42 suggests that this Hib brane (10). It should also be noted that Fbp has been shown to strain may simply lack a functional HitC protein. be the major iron-repressib] le protein of both N. gonorrhoeae The results of the present study indicate that the H. influ- enzae HitA, HitB, and HitC proteins are likely involved in the and N. meningitidis (6, 38, 3i9). While studies involving eitther the regulation of H. influenzae utilization of iron once this element has gained access to the outer membrane protein expression by environmental iron periplasmic space. Elimination, by mutation, of a functional levels (31, 40, 59) or the identification of H. influenzae outer HitC protein resulted in an NTHI strain that could not utilize membrane proteins that bin d iron-containing compounds (23, iron chelates or iron bound to transferrin while still retaining 28, 31, 48, 49) have beer1 published, there has been no the ability to use heme as a source of iron (Fig. 6). Whether the identification to date of an JH. influenzae gene product(s) that HitA and HitB proteins are essential for iron utilization was is essential for the utilization of iron in any form. In the present not addressed directly in this study, and the inability to study, it was shown that an NITHI hitc mutant could not utilize construct a viable hita mutant (data not shown) may preclude either free or protein-bound iron (Fig. 6). Moreover, the ability genetic analysis of the role of HitA in this process. Nonetheof H. influenzae to utilize Fi'PIX as a source of porphyrin in less, it is clear that, at least in vitro, utilization of transferrinplace of heme appeared to b)e dependent on the presence of a bound iron by H. influenzae is dependent on the presence of a functional hitabc gene cluster. functional HitC protein. The H. influenzae hitabc lgene products proved to be similar to the proteins encoded by tile sfuabc operon in S. marcescens (2, 3). These three proteins ( of this enteric organism have been ACKNOWLEDGMENTS implicated in a periplasmic binding protein-dependent iron transport system (2, 3). Thlis system involves a periplasmic ligand-binding protein (SfuLA), a very hydrophobic protein localized to the cytoplasmic membrane (SfuB), and a rather This study was supported by Public Health Service grants A and A to E.J.H. L.D.C. was supported by NCI training grant CA We are grateful to Cindy Patterson for her assistance in the

10 4524 SANDERS ET AL. preparation of the manuscript and to Gregory Jarosik, Isobel Maciver, and Julia Klesney-Tait for their helpful comments. REFERENCES 1. Alexander, H. E The Haemophilus group, p In R. J. Dubos and J. G. Hirsch (ed.), Bacterial and mycotic infections of man. J. B. Lippincott Co., Philadelphia. 2. Angerer, A., S. Gaisser, and V. Braun Nucleotide sequences of the sfua, sfub, and sfuc genes of Serratia marcescens suggest a periplasmic-binding-protein-dependent iron transport mechanism. J. Bacteriol. 172: Angerer, A., B. Klupp, and V. Braun Iron transport systems of Serratia marcescens. J. Bacteriol. 174: Bagg, A., and J. B. Neilands Molecular mechanism of regulation of siderophore-mediated iron assimilation. Microbiol. Rev. 51: Barcak, G. J., M. S. Chandler, R. J. Redfield, and J.-F. Tomb Genetic systems in Haemophilus influenzae. Methods Enzymol. 204: Berish, S. A., T. A. Mietzner, L. W. Mayer, C. A. Genco, B. P. Holloway, and S. A. Morse Molecular cloning and characterization of the structural gene for the major iron-regulated protein expressed by Neisseria gonorrhoeae. J. Exp. Med. 171: Blanton, K. J., G. D. Biswas, J. Tsai, J. Adams, D. W. Dyer, S. M. Davis, G. G. Koch, P. K. Sen, and P. F. Sparling Genetic evidence that Neisseria gonorrhoeae produces specific receptors for transferrin and lactoferrin. J. Bacteriol. 172: Bouvier, J., C. Richaud, W. Higgins, 0. Bogler, and P. Stragier Cloning, characterization, and expression of the dape gene of Escherichia coli. J. Bacteriol. 174: Bullen, J. J., H. J. Rogers, and E. Grifliths Role of iron in bacterial infection. Curr. Top. Microbiol. Immunol. 80: Chen, C. Y., S. A. Berish, S. A. Morse, and T. A. Mietzner The ferric iron-binding protein of pathogenic Neisseria ssp. functions as a periplasmic transport protein in iron acquisition from human transferrin. Mol. Microbiol. 10: Cope, L. D., S. E. Thomas, J. L. Latimer, C. A. Slaughter, U. Muller-Eberhard, and E. J. Hansen. The 100 kda heme:hemopexin-binding protein of Haemophilus influenzae. Mol. Microbiol., in press. 12. Cope, L. D., R. Yogev, J. Mertsola, J. L. Latimer, M. S. Hanson, G. H. McCracken, Jr., and E. J. Hansen Molecular cloning of a gene involved in lipopolysaccharide biosynthesis and virulence expression by Haemophilus influenzae type b. Mol. Microbiol. 5: Cornelissen, C. N., G. D. Biswas, and P. F. Sparling Expression of gonococcal transferrin-binding protein 1 causes Escherichia coli to bind human transferrin. J. Bacteriol. 175: Crosa, J. H Genetics and molecular biology of siderophoremediated iron transport in bacteria. Microbiol. Rev. 53: Devereux, J., P. Haeberli, and 0. Smithies A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12: Evans, N. M., D. D. Smith, and A. J. Wicken Haemin and nicotinamide adenine dinucleotide requirements of Haemophilus influenzae and Haemophilus parainfluenzae. J. Med. Microbiol. 7: Faith, M. J., and R. Kolter ABC transporters: bacterial exporters. Microbiol. Rev. 57: Granick, S., and H. Gilder The porphyrin requirements of Haemophilus influenzae and some functions of the vinyl and propionic acid side chains of heme. J. Gen. Physiol. 30: Griffiths, E Iron and bacterial virulence-a brief overview. Biol. Metals 4: Hansen, E. J., F. R. Gonzales, N. R. Chamberlain, M. V. Norgard, E. E. Miller, L. D. Cope, S. E. Pelzel, B. Gaddy, and A. Clausell Cloning of the gene encoding the major outer membrane protein of Haemophilus influenzae type b. Infect. Immun. 56: Hansen, E. J., J. L. Latimer, S. E. Thomas, M. E. Helminen, W. L. Albritton, and J. D. Radolf Use of electroporation to INFECT. IMMUN. construct isogenic mutants of Haemophilus ducreyi. J. Bacteriol. 174: Hansen, E. J., S. E. Pelzel, K. Orth, C. R. Moomaw, J. D. Radolf, and C. A. Slaughter Structural and antigenic conservation of the P2 porin protein among strains of Haemophilus influenzae type B. Infect. Immun. 57: Hanson, M. S., S. E. Pelzel, J. L. Latimer, U. Muller-Eberhard, and E. J. Hansen Identification of a genetic locus of Haemophilus infiuenzae type b necessary for the binding and utilization of heme bound to human hemopexin. Proc. Natl. Acad. Sci. USA 89: Harkness, R. E., P. Chong, and M. H. Klein Identification of two iron-repressed periplasmic proteins in Haemophilus influenzae. J. Bacteriol. 174: Herrington, D. A., and P. F. Sparling Haemophilus influenzae can use human transferrin as a sole source for required iron. Infect. Immun. 48: Herriott, R. M., E. M. Meyer, and M. J. Vogt Defined non-growth media for stage II development of competence in Haemophilus influenzae. J. Bacteriol. 101: Higgins, C. F., M. P. Gallagher, M. L. Mimmack, and S. R. Pearce A family of closely related ATP-binding subunits from prokaryotic and eukaryotic cells. Bioessays 8: Holland, J., P. R. Langford, K. J. Towner, and P. Williams Evidence for in vivo expression of transferrin-binding proteins in Haemophilus influenzae type b. Infect. Immun. 60: Hunkapiller, M. W., E. Lujan, F. Ostrander, and L. E. Hood Isolation of microgram quantities of proteins from polyacrylamide gels for amino acid sequence analysis. Methods Enzymol. 91: Kimura, A., P. A. Gulig, G. H. McCracken, Jr., T. A. Loftus, and E. J. Hansen A minor high-molecular-weight outer membrane protein of Haemophilus influenzae type b is a protective antigen. Infect. Immun. 47: Lee, B. C Isolation of an outer membrane hemin-binding protein of Haemophilus influenzae type b. Infect. Immun. 60: Legrain, M., V. Mazarin, S. W. Irwin, B. Bouchon, M.-J. Quentin- Millet, and A. B. Schryvers Cloning and characterization of Neisseria meningitidis genes encoding the transferrin-binding proteins Tbpl and Thp2. Gene 130: Litwin, C. M., and S. B. Calderwood Role of iron in regulation of virulence genes. Clin. Microbiol. Rev. 6: Maniatis, T., E. F. Fritsch, and J. Sambrook Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. 35. Marmur, J A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J. Mol. Biol. 3: Matsudaira, P Sequence from picomole quantities of proteins electroblotted onto polyvinylidene difluoride membranes. J. Biol. Chem. 262: McGehee, J. L., J. D. Radolf, G. B. Toews, and E. J. Hansen Effect of primary immunization on clearance of nontypable Haemophilus infiuenzae. Am. J. Respir. Cell Mol. Biol. 1: Mietzner, T. A., G. Bolan, G. K. Schoolnik, and S. A. Morse Purification and characterization of the major iron-regulated protein expressed by pathogenic Neisseriae. J. Exp. Med. 165: Morse, S. A., C. Y. Chen, A. LeFaou, and T. A. Mietzner A potential role for the major iron-regulated protein expressed by pathogenic Neisseria species. Rev. Infect. Dis. 10(Suppl. 2):S306- S Morton, D. J., and P. Williams Characterization of the outer-membrane proteins of Haemophilus parainfluenzae expressed under iron-sufficient and iron-restricted conditions. J. Gen. Microbiol. 135: Payne, S. M Iron and virulence in the family Enterobacteriaceae. Crit. Rev. Microbiol. 16: Payne, S. M., and K. M. Lawlor Molecular studies on iron acquisition by non-escherichia coli species, p In B. H. Iglewski and V. L. Clark. (ed.), Molecular basis of bacterial pathogenesis. Academic Press, San Diego, Calif. 43. Pidcock, K. A., J. A. Wooten, B. A. Daley, and T. L. Stull

11 VOL. 62, 1994 Iron acquisition by Haemophilus influenzae. Infect. Immun. 56: Robertson, S. M., C. F. Frisch, P. A. Gulig, J. R. Kettman, K. H. Johnston, and E. J. Hansen Monoclonal antibodies directed against a cell surface-exposed outer membrane protein of Haemophilus influenzae type b. Infect. Immun. 36: Robinson, A. C., D. J. Kenan, J. Sweeney, and W. D. Donachie Further evidence for overlapping transcriptional units in an Escherichia coli cell envelope-cell division gene cluster: DNA sequence and transcriptional organization of the ddlftsq region. J. Bacteriol. 167: Sambrook, J., E. F. Fritsch, and T. Maniatis Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. 47. Sanders, J. D., L. D. Cope, G. P. Jarosik, I. Maciver, J. L. Latimer, G. B. Toews, and E. J. Hansen Reconstitution of a porin-deficient mutant of Haemophilus influenzae type b with a porin gene from nontypeable H. influenzae. Infect. Immun. 61: Schryvers, A. B Characterization of the human transferrin and lactoferrin receptors in Haemophilus influenzae. Mol. Microbiol. 2: Schryvers, A. B Identification of the transferrin- and lactoferrin-binding proteins in Haemophilus influenzae. J. Med. Microbiol. 29: Schryvers, A. B., and B. C. Lee Comparative analysis of the transferrin and lactoferrin binding proteins in the family Neisseriaceae. Can. J. Microbiol. 35: Setlow, J. K., D. C. Brown, M. E. Boling, A. Mattingly, and M. P. Gordon Repair of deoxyribonucleic acid in Haemophilus influenzae. J. Bacteriol. 95: Stuy, J. H., and R. B. Walter Effect of glycerol on plasmid transfer in genetically competent Haemophilus influenzae. Mol. Gen. Genet. 203: Tomb, J.-F., G. J. Barcak, M. S. Chandler, R. J. Redfield, and H. INFLUENZAE IRON UTILIZATION SYSTEM 4525 H. 0. Smith Transposon mutagenesis, characterization, and cloning of transformation genes of Haemophilus influenzae Rd. J. Bacteriol. 171: von Heijne, G The signal peptide. J. Membr. Biol. 115: Weinberg, E. D Iron withholding, a defense against infection and disease. Physiol. Rev. 64: Weinberg, E. D The iron-withholding defense system. ASM News 59: Whitchurch, C. B., M. Hobbs, S. P. Livingston, V. Krishnapillai, and J. S. Mattick Characterisation of a Pseudomonas aeruginosa twitching mobility gene and evidence for a specialised protein export system widespread in eubacteria. Gene 101: White, D. C., and S. Granick Hemin biosynthesis in Haemophilus. J. Bacteriol. 85: Williams, P., and M. R. W. Brown Influence of iron restriction on growth and the expression of outer membrane proteins by Haemophilus influenzae and H. parainfluenzae. FEMS Microbiol. Lett. 33: Williams, P., D. J. Morton, K J. Towner, P. Stevenson, and E. Griffiths Utilization of enterobactin and other exogenous iron sources by Haemophilus influenzae, H. parainfluenzae, and H. paraphrophilus. J. Gen. Microbiol. 136: Willson, P. J., W. L. Albritton, L. Slaney, and J.K Setlow Characterization of a multiple antibiotic resistance plasmid from Haemophilus ducreyi. Antimicrob. Agents Chemother. 33: Wu, B. W., C. Georgopoulos, and D. Ang The essential Escherichia coli msgb gene, a multicopy suppressor of a temperature-sensitive allele of the heat shock gene grpe, is identical to dape. J. Bacteriol. 174: Zimmermann, L., A. Angerer, and V. Braun Mechanically novel iron(iii) transport system in Serratia marcescens. J. Bacteriol. 171: Downloaded from on October 3, 2018 by guest

SUPPORTING INFORMATION FOR. SEquence-Enabled Reassembly of β-lactamase (SEER-LAC): a Sensitive Method for the Detection of Double-Stranded DNA

SUPPORTING INFORMATION FOR. SEquence-Enabled Reassembly of β-lactamase (SEER-LAC): a Sensitive Method for the Detection of Double-Stranded DNA SUPPORTING INFORMATION FOR SEquence-Enabled Reassembly of β-lactamase (SEER-LAC): a Sensitive Method for the Detection of Double-Stranded DNA Aik T. Ooi, Cliff I. Stains, Indraneel Ghosh *, David J. Segal

More information

Practical Bioinformatics

Practical Bioinformatics 5/2/2017 Dictionaries d i c t i o n a r y = { A : T, T : A, G : C, C : G } d i c t i o n a r y [ G ] d i c t i o n a r y [ N ] = N d i c t i o n a r y. h a s k e y ( C ) Dictionaries g e n e t i c C o

More information

High throughput near infrared screening discovers DNA-templated silver clusters with peak fluorescence beyond 950 nm

High throughput near infrared screening discovers DNA-templated silver clusters with peak fluorescence beyond 950 nm Electronic Supplementary Material (ESI) for Nanoscale. This journal is The Royal Society of Chemistry 2018 High throughput near infrared screening discovers DNA-templated silver clusters with peak fluorescence

More information

SUPPLEMENTARY DATA - 1 -

SUPPLEMENTARY DATA - 1 - - 1 - SUPPLEMENTARY DATA Construction of B. subtilis rnpb complementation plasmids For complementation, the B. subtilis rnpb wild-type gene (rnpbwt) under control of its native rnpb promoter and terminator

More information

Supporting Information for. Initial Biochemical and Functional Evaluation of Murine Calprotectin Reveals Ca(II)-

Supporting Information for. Initial Biochemical and Functional Evaluation of Murine Calprotectin Reveals Ca(II)- Supporting Information for Initial Biochemical and Functional Evaluation of Murine Calprotectin Reveals Ca(II)- Dependence and Its Ability to Chelate Multiple Nutrient Transition Metal Ions Rose C. Hadley,

More information

Clay Carter. Department of Biology. QuickTime and a TIFF (Uncompressed) decompressor are needed to see this picture.

Clay Carter. Department of Biology. QuickTime and a TIFF (Uncompressed) decompressor are needed to see this picture. QuickTime and a TIFF (Uncompressed) decompressor are needed to see this picture. Clay Carter Department of Biology QuickTime and a TIFF (LZW) decompressor are needed to see this picture. Ornamental tobacco

More information

Characterization of Pathogenic Genes through Condensed Matrix Method, Case Study through Bacterial Zeta Toxin

Characterization of Pathogenic Genes through Condensed Matrix Method, Case Study through Bacterial Zeta Toxin International Journal of Genetic Engineering and Biotechnology. ISSN 0974-3073 Volume 2, Number 1 (2011), pp. 109-114 International Research Publication House http://www.irphouse.com Characterization of

More information

Crick s early Hypothesis Revisited

Crick s early Hypothesis Revisited Crick s early Hypothesis Revisited Or The Existence of a Universal Coding Frame Ryan Rossi, Jean-Louis Lassez and Axel Bernal UPenn Center for Bioinformatics BIOINFORMATICS The application of computer

More information

Supplementary Information for

Supplementary Information for Supplementary Information for Evolutionary conservation of codon optimality reveals hidden signatures of co-translational folding Sebastian Pechmann & Judith Frydman Department of Biology and BioX, Stanford

More information

SEQUENCE ALIGNMENT BACKGROUND: BIOINFORMATICS. Prokaryotes and Eukaryotes. DNA and RNA

SEQUENCE ALIGNMENT BACKGROUND: BIOINFORMATICS. Prokaryotes and Eukaryotes. DNA and RNA SEQUENCE ALIGNMENT BACKGROUND: BIOINFORMATICS 1 Prokaryotes and Eukaryotes 2 DNA and RNA 3 4 Double helix structure Codons Codons are triplets of bases from the RNA sequence. Each triplet defines an amino-acid.

More information

Advanced topics in bioinformatics

Advanced topics in bioinformatics Feinberg Graduate School of the Weizmann Institute of Science Advanced topics in bioinformatics Shmuel Pietrokovski & Eitan Rubin Spring 2003 Course WWW site: http://bioinformatics.weizmann.ac.il/courses/atib

More information

NSCI Basic Properties of Life and The Biochemistry of Life on Earth

NSCI Basic Properties of Life and The Biochemistry of Life on Earth NSCI 314 LIFE IN THE COSMOS 4 Basic Properties of Life and The Biochemistry of Life on Earth Dr. Karen Kolehmainen Department of Physics CSUSB http://physics.csusb.edu/~karen/ WHAT IS LIFE? HARD TO DEFINE,

More information

Supplemental data. Pommerrenig et al. (2011). Plant Cell /tpc

Supplemental data. Pommerrenig et al. (2011). Plant Cell /tpc Supplemental Figure 1. Prediction of phloem-specific MTK1 expression in Arabidopsis shoots and roots. The images and the corresponding numbers showing absolute (A) or relative expression levels (B) of

More information

Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1

Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1 Supplementary Figure 1 Zn 2+ -binding sites in USP18. (a) The two molecules of USP18 present in the asymmetric unit are shown. Chain A is shown in blue, chain B in green. Bound Zn 2+ ions are shown as

More information

SSR ( ) Vol. 48 No ( Microsatellite marker) ( Simple sequence repeat,ssr),

SSR ( ) Vol. 48 No ( Microsatellite marker) ( Simple sequence repeat,ssr), 48 3 () Vol. 48 No. 3 2009 5 Journal of Xiamen University (Nat ural Science) May 2009 SSR,,,, 3 (, 361005) : SSR. 21 516,410. 60 %96. 7 %. (),(Between2groups linkage method),.,, 11 (),. 12,. (, ), : 0.

More information

Number-controlled spatial arrangement of gold nanoparticles with

Number-controlled spatial arrangement of gold nanoparticles with Electronic Supplementary Material (ESI) for RSC Advances. This journal is The Royal Society of Chemistry 2016 Number-controlled spatial arrangement of gold nanoparticles with DNA dendrimers Ping Chen,*

More information

Supporting Information

Supporting Information Supporting Information T. Pellegrino 1,2,3,#, R. A. Sperling 1,#, A. P. Alivisatos 2, W. J. Parak 1,2,* 1 Center for Nanoscience, Ludwig Maximilians Universität München, München, Germany 2 Department of

More information

Supplemental Figure 1.

Supplemental Figure 1. A wt spoiiiaδ spoiiiahδ bofaδ B C D E spoiiiaδ, bofaδ Supplemental Figure 1. GFP-SpoIVFA is more mislocalized in the absence of both BofA and SpoIIIAH. Sporulation was induced by resuspension in wild-type

More information

evoglow - express N kit distributed by Cat.#: FP product information broad host range vectors - gram negative bacteria

evoglow - express N kit distributed by Cat.#: FP product information broad host range vectors - gram negative bacteria evoglow - express N kit broad host range vectors - gram negative bacteria product information distributed by Cat.#: FP-21020 Content: Product Overview... 3 evoglow express N -kit... 3 The evoglow -Fluorescent

More information

Electronic supplementary material

Electronic supplementary material Applied Microbiology and Biotechnology Electronic supplementary material A family of AA9 lytic polysaccharide monooxygenases in Aspergillus nidulans is differentially regulated by multiple substrates and

More information

ydci GTC TGT TTG AAC GCG GGC GAC TGG GCG CGC AAT TAA CGG TGT GTA GGC TGG AGC TGC TTC

ydci GTC TGT TTG AAC GCG GGC GAC TGG GCG CGC AAT TAA CGG TGT GTA GGC TGG AGC TGC TTC Table S1. DNA primers used in this study. Name ydci P1ydcIkd3 Sequence GTC TGT TTG AAC GCG GGC GAC TGG GCG CGC AAT TAA CGG TGT GTA GGC TGG AGC TGC TTC Kd3ydcIp2 lacz fusion YdcIendP1 YdcItrgP2 GAC AGC

More information

evoglow - express N kit Cat. No.: product information broad host range vectors - gram negative bacteria

evoglow - express N kit Cat. No.: product information broad host range vectors - gram negative bacteria evoglow - express N kit broad host range vectors - gram negative bacteria product information Cat. No.: 2.1.020 evocatal GmbH 2 Content: Product Overview... 4 evoglow express N kit... 4 The evoglow Fluorescent

More information

Building a Multifunctional Aptamer-Based DNA Nanoassembly for Targeted Cancer Therapy

Building a Multifunctional Aptamer-Based DNA Nanoassembly for Targeted Cancer Therapy Supporting Information Building a Multifunctional Aptamer-Based DNA Nanoassembly for Targeted Cancer Therapy Cuichen Wu,, Da Han,, Tao Chen,, Lu Peng, Guizhi Zhu,, Mingxu You,, Liping Qiu,, Kwame Sefah,

More information

6.047 / Computational Biology: Genomes, Networks, Evolution Fall 2008

6.047 / Computational Biology: Genomes, Networks, Evolution Fall 2008 MIT OpenCourseWare http://ocw.mit.edu 6.047 / 6.878 Computational Biology: Genomes, Networks, Evolution Fall 2008 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms.

More information

Supplementary Information

Supplementary Information Electronic Supplementary Material (ESI) for RSC Advances. This journal is The Royal Society of Chemistry 2014 Directed self-assembly of genomic sequences into monomeric and polymeric branched DNA structures

More information

Table S1. Primers and PCR conditions used in this paper Primers Sequence (5 3 ) Thermal conditions Reference Rhizobacteria 27F 1492R

Table S1. Primers and PCR conditions used in this paper Primers Sequence (5 3 ) Thermal conditions Reference Rhizobacteria 27F 1492R Table S1. Primers and PCR conditions used in this paper Primers Sequence (5 3 ) Thermal conditions Reference Rhizobacteria 27F 1492R AAC MGG ATT AGA TAC CCK G GGY TAC CTT GTT ACG ACT T Detection of Candidatus

More information

Supplemental Table 1. Primers used for cloning and PCR amplification in this study

Supplemental Table 1. Primers used for cloning and PCR amplification in this study Supplemental Table 1. Primers used for cloning and PCR amplification in this study Target Gene Primer sequence NATA1 (At2g393) forward GGG GAC AAG TTT GTA CAA AAA AGC AGG CTT CAT GGC GCC TCC AAC CGC AGC

More information

TM1 TM2 TM3 TM4 TM5 TM6 TM bp

TM1 TM2 TM3 TM4 TM5 TM6 TM bp a 467 bp 1 482 2 93 3 321 4 7 281 6 21 7 66 8 176 19 12 13 212 113 16 8 b ATG TCA GGA CAT GTA ATG GAG GAA TGT GTA GTT CAC GGT ACG TTA GCG GCA GTA TTG CGT TTA ATG GGC GTA GTG M S G H V M E E C V V H G T

More information

Regulatory Sequence Analysis. Sequence models (Bernoulli and Markov models)

Regulatory Sequence Analysis. Sequence models (Bernoulli and Markov models) Regulatory Sequence Analysis Sequence models (Bernoulli and Markov models) 1 Why do we need random models? Any pattern discovery relies on an underlying model to estimate the random expectation. This model

More information

Modelling and Analysis in Bioinformatics. Lecture 1: Genomic k-mer Statistics

Modelling and Analysis in Bioinformatics. Lecture 1: Genomic k-mer Statistics 582746 Modelling and Analysis in Bioinformatics Lecture 1: Genomic k-mer Statistics Juha Kärkkäinen 06.09.2016 Outline Course introduction Genomic k-mers 1-Mers 2-Mers 3-Mers k-mers for Larger k Outline

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION DOI:.8/NCHEM. Conditionally Fluorescent Molecular Probes for Detecting Single Base Changes in Double-stranded DNA Sherry Xi Chen, David Yu Zhang, Georg Seelig. Analytic framework and probe design.. Design

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION DOI:.38/NCHEM.246 Optimizing the specificity of nucleic acid hyridization David Yu Zhang, Sherry Xi Chen, and Peng Yin. Analytic framework and proe design 3.. Concentration-adjusted

More information

Evolvable Neural Networks for Time Series Prediction with Adaptive Learning Interval

Evolvable Neural Networks for Time Series Prediction with Adaptive Learning Interval Evolvable Neural Networs for Time Series Prediction with Adaptive Learning Interval Dong-Woo Lee *, Seong G. Kong *, and Kwee-Bo Sim ** *Department of Electrical and Computer Engineering, The University

More information

3. Evolution makes sense of homologies. 3. Evolution makes sense of homologies. 3. Evolution makes sense of homologies

3. Evolution makes sense of homologies. 3. Evolution makes sense of homologies. 3. Evolution makes sense of homologies Richard Owen (1848) introduced the term Homology to refer to structural similarities among organisms. To Owen, these similarities indicated that organisms were created following a common plan or archetype.

More information

The role of the FliD C-terminal domain in pentamer formation and

The role of the FliD C-terminal domain in pentamer formation and The role of the FliD C-terminal domain in pentamer formation and interaction with FliT Hee Jung Kim 1,2,*, Woongjae Yoo 3,*, Kyeong Sik Jin 4, Sangryeol Ryu 3,5 & Hyung Ho Lee 1, 1 Department of Chemistry,

More information

Protein Threading. Combinatorial optimization approach. Stefan Balev.

Protein Threading. Combinatorial optimization approach. Stefan Balev. Protein Threading Combinatorial optimization approach Stefan Balev Stefan.Balev@univ-lehavre.fr Laboratoire d informatique du Havre Université du Havre Stefan Balev Cours DEA 30/01/2004 p.1/42 Outline

More information

Re- engineering cellular physiology by rewiring high- level global regulatory genes

Re- engineering cellular physiology by rewiring high- level global regulatory genes Re- engineering cellular physiology by rewiring high- level global regulatory genes Stephen Fitzgerald 1,2,, Shane C Dillon 1, Tzu- Chiao Chao 2, Heather L Wiencko 3, Karsten Hokamp 3, Andrew DS Cameron

More information

Codon Distribution in Error-Detecting Circular Codes

Codon Distribution in Error-Detecting Circular Codes life Article Codon Distribution in Error-Detecting Circular Codes Elena Fimmel, * and Lutz Strüngmann Institute for Mathematical Biology, Faculty of Computer Science, Mannheim University of Applied Sciences,

More information

The Trigram and other Fundamental Philosophies

The Trigram and other Fundamental Philosophies The Trigram and other Fundamental Philosophies by Weimin Kwauk July 2012 The following offers a minimal introduction to the trigram and other Chinese fundamental philosophies. A trigram consists of three

More information

Encoding of Amino Acids and Proteins from a Communications and Information Theoretic Perspective

Encoding of Amino Acids and Proteins from a Communications and Information Theoretic Perspective Jacobs University Bremen Encoding of Amino Acids and Proteins from a Communications and Information Theoretic Perspective Semester Project II By: Dawit Nigatu Supervisor: Prof. Dr. Werner Henkel Transmission

More information

The 3 Genomic Numbers Discovery: How Our Genome Single-Stranded DNA Sequence Is Self-Designed as a Numerical Whole

The 3 Genomic Numbers Discovery: How Our Genome Single-Stranded DNA Sequence Is Self-Designed as a Numerical Whole Applied Mathematics, 2013, 4, 37-53 http://dx.doi.org/10.4236/am.2013.410a2004 Published Online October 2013 (http://www.scirp.org/journal/am) The 3 Genomic Numbers Discovery: How Our Genome Single-Stranded

More information

ChemiScreen CaS Calcium Sensor Receptor Stable Cell Line

ChemiScreen CaS Calcium Sensor Receptor Stable Cell Line PRODUCT DATASHEET ChemiScreen CaS Calcium Sensor Receptor Stable Cell Line CATALOG NUMBER: HTS137C CONTENTS: 2 vials of mycoplasma-free cells, 1 ml per vial. STORAGE: Vials are to be stored in liquid N

More information

Why do more divergent sequences produce smaller nonsynonymous/synonymous

Why do more divergent sequences produce smaller nonsynonymous/synonymous Genetics: Early Online, published on June 21, 2013 as 10.1534/genetics.113.152025 Why do more divergent sequences produce smaller nonsynonymous/synonymous rate ratios in pairwise sequence comparisons?

More information

Supplementary Information

Supplementary Information Supplementary Information Arginine-rhamnosylation as new strategy to activate translation elongation factor P Jürgen Lassak 1,2,*, Eva Keilhauer 3, Max Fürst 1,2, Kristin Wuichet 4, Julia Gödeke 5, Agata

More information

Biology 112 Practice Midterm Questions

Biology 112 Practice Midterm Questions Biology 112 Practice Midterm Questions 1. Identify which statement is true or false I. Bacterial cell walls prevent osmotic lysis II. All bacterial cell walls contain an LPS layer III. In a Gram stain,

More information

Biosynthesis of Bacterial Glycogen: Primary Structure of Salmonella typhimurium ADPglucose Synthetase as Deduced from the

Biosynthesis of Bacterial Glycogen: Primary Structure of Salmonella typhimurium ADPglucose Synthetase as Deduced from the JOURNAL OF BACTERIOLOGY, Sept. 1987, p. 4355-4360 0021-9193/87/094355-06$02.00/0 Copyright X) 1987, American Society for Microbiology Vol. 169, No. 9 Biosynthesis of Bacterial Glycogen: Primary Structure

More information

Near-instant surface-selective fluorogenic protein quantification using sulfonated

Near-instant surface-selective fluorogenic protein quantification using sulfonated Electronic Supplementary Material (ESI) for rganic & Biomolecular Chemistry. This journal is The Royal Society of Chemistry 2014 Supplemental nline Materials for ear-instant surface-selective fluorogenic

More information

part 3: analysis of natural selection pressure

part 3: analysis of natural selection pressure part 3: analysis of natural selection pressure markov models are good phenomenological codon models do have many benefits: o principled framework for statistical inference o avoiding ad hoc corrections

More information

FliZ Is a Posttranslational Activator of FlhD 4 C 2 -Dependent Flagellar Gene Expression

FliZ Is a Posttranslational Activator of FlhD 4 C 2 -Dependent Flagellar Gene Expression JOURNAL OF BACTERIOLOGY, July 2008, p. 4979 4988 Vol. 190, No. 14 0021-9193/08/$08.00 0 doi:10.1128/jb.01996-07 Copyright 2008, American Society for Microbiology. All Rights Reserved. FliZ Is a Posttranslational

More information

Evolutionary dynamics of abundant stop codon readthrough in Anopheles and Drosophila

Evolutionary dynamics of abundant stop codon readthrough in Anopheles and Drosophila biorxiv preprint first posted online May. 3, 2016; doi: http://dx.doi.org/10.1101/051557. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. All rights reserved.

More information

Sex-Linked Inheritance in Macaque Monkeys: Implications for Effective Population Size and Dispersal to Sulawesi

Sex-Linked Inheritance in Macaque Monkeys: Implications for Effective Population Size and Dispersal to Sulawesi Supporting Information http://www.genetics.org/cgi/content/full/genetics.110.116228/dc1 Sex-Linked Inheritance in Macaque Monkeys: Implications for Effective Population Size and Dispersal to Sulawesi Ben

More information

160, and 220 bases, respectively, shorter than pbr322/hag93. (data not shown). The DNA sequence of approximately 100 bases of each

160, and 220 bases, respectively, shorter than pbr322/hag93. (data not shown). The DNA sequence of approximately 100 bases of each JOURNAL OF BACTEROLOGY, JUlY 1988, p. 3305-3309 0021-9193/88/073305-05$02.00/0 Copyright 1988, American Society for Microbiology Vol. 170, No. 7 Construction of a Minimum-Size Functional Flagellin of Escherichia

More information

Pathways and Controls of N 2 O Production in Nitritation Anammox Biomass

Pathways and Controls of N 2 O Production in Nitritation Anammox Biomass Supporting Information for Pathways and Controls of N 2 O Production in Nitritation Anammox Biomass Chun Ma, Marlene Mark Jensen, Barth F. Smets, Bo Thamdrup, Department of Biology, University of Southern

More information

Diversity of Chlamydia trachomatis Major Outer Membrane

Diversity of Chlamydia trachomatis Major Outer Membrane JOURNAL OF ACTERIOLOGY, Sept. 1987, p. 3879-3885 Vol. 169, No. 9 0021-9193/87/093879-07$02.00/0 Copyright 1987, American Society for Microbiology Diversity of Chlamydia trachomatis Major Outer Membrane

More information

Cloning, Nucleotide Sequencing, and Expression of the Clostridium perfringens Enterotoxin Gene in Eschenichia coli

Cloning, Nucleotide Sequencing, and Expression of the Clostridium perfringens Enterotoxin Gene in Eschenichia coli INFECTION AND IMMUNIrY, Aug. 1993, p. 3429-3439 0019-9567/93/083429-11$02.00/0 Copyright 1993, American Society for Microbiology Vol. 61, No. 8 Cloning, Nucleotide Sequencing, and Expression of the Clostridium

More information

Timing molecular motion and production with a synthetic transcriptional clock

Timing molecular motion and production with a synthetic transcriptional clock Timing molecular motion and production with a synthetic transcriptional clock Elisa Franco,1, Eike Friedrichs 2, Jongmin Kim 3, Ralf Jungmann 2, Richard Murray 1, Erik Winfree 3,4,5, and Friedrich C. Simmel

More information

ANALYZING THE DIVERSITY OF A SMALL ANTIBODY MIMIC LIBRARY. Nick Empey. Chapel Hill 2010

ANALYZING THE DIVERSITY OF A SMALL ANTIBODY MIMIC LIBRARY. Nick Empey. Chapel Hill 2010 ANALYZING THE DIVERSITY OF A SMALL ANTIBODY MIMIC LIBRARY Nick Empey A thesis submitted to the faculty of the University of North Carolina at Chapel Hill in partial fulfillment of the requirements for

More information

Chain-like assembly of gold nanoparticles on artificial DNA templates via Click Chemistry

Chain-like assembly of gold nanoparticles on artificial DNA templates via Click Chemistry Electronic Supporting Information: Chain-like assembly of gold nanoparticles on artificial DNA templates via Click Chemistry Monika Fischler, Alla Sologubenko, Joachim Mayer, Guido Clever, Glenn Burley,

More information

evoglow yeast kit distributed by product information Cat.#: FP-21040

evoglow yeast kit distributed by product information Cat.#: FP-21040 evoglow yeast kit product information distributed by Cat.#: FP-21040 Flavin-mononucleotide-based Fluorescent Protein (FbFP) evoglow basic kit Cat.# FP-21010 Quantity 20 µg each General Information Fluorescent

More information

evoglow basic kit product information

evoglow basic kit product information evoglow basic kit product information Cat. No.: 2.1.010 Flavin-mononucleotide-based Fluorescent Protein (FbFP) evoglow basic kit Catalog No. evo-2.1.010 Quantity 20 µg each General Information Fluorescent

More information

AtTIL-P91V. AtTIL-P92V. AtTIL-P95V. AtTIL-P98V YFP-HPR

AtTIL-P91V. AtTIL-P92V. AtTIL-P95V. AtTIL-P98V YFP-HPR Online Resource 1. Primers used to generate constructs AtTIL-P91V, AtTIL-P92V, AtTIL-P95V and AtTIL-P98V and YFP(HPR) using overlapping PCR. pentr/d- TOPO-AtTIL was used as template to generate the constructs

More information

DNA sequence analysis of the imp UV protection and mutation operon of the plasmid TP110: identification of a third gene

DNA sequence analysis of the imp UV protection and mutation operon of the plasmid TP110: identification of a third gene QD) 1990 Oxford University Press Nucleic Acids Research, Vol. 18, No. 17 5045 DNA sequence analysis of the imp UV protection and mutation operon of the plasmid TP110: identification of a third gene David

More information

Illegitimate translation causes unexpected gene expression from on-target out-of-frame alleles

Illegitimate translation causes unexpected gene expression from on-target out-of-frame alleles Illegitimate translation causes unexpected gene expression from on-target out-of-frame alleles created by CRISPR-Cas9 Shigeru Makino, Ryutaro Fukumura, Yoichi Gondo* Mutagenesis and Genomics Team, RIKEN

More information

Supporting Information. An Electric Single-Molecule Hybridisation Detector for short DNA Fragments

Supporting Information. An Electric Single-Molecule Hybridisation Detector for short DNA Fragments Supporting Information An Electric Single-Molecule Hybridisation Detector for short DNA Fragments A.Y.Y. Loh, 1 C.H. Burgess, 2 D.A. Tanase, 1 G. Ferrari, 3 M.A. Maclachlan, 2 A.E.G. Cass, 1 T. Albrecht*

More information

Evolutionary Analysis of Viral Genomes

Evolutionary Analysis of Viral Genomes University of Oxford, Department of Zoology Evolutionary Biology Group Department of Zoology University of Oxford South Parks Road Oxford OX1 3PS, U.K. Fax: +44 1865 271249 Evolutionary Analysis of Viral

More information

part 4: phenomenological load and biological inference. phenomenological load review types of models. Gαβ = 8π Tαβ. Newton.

part 4: phenomenological load and biological inference. phenomenological load review types of models. Gαβ = 8π Tαβ. Newton. 2017-07-29 part 4: and biological inference review types of models phenomenological Newton F= Gm1m2 r2 mechanistic Einstein Gαβ = 8π Tαβ 1 molecular evolution is process and pattern process pattern MutSel

More information

Supplemental Figure 1. Phenotype of ProRGA:RGAd17 plants under long day

Supplemental Figure 1. Phenotype of ProRGA:RGAd17 plants under long day Supplemental Figure 1. Phenotype of ProRGA:RGAd17 plants under long day conditions. Photo was taken when the wild type plant started to bolt. Scale bar represents 1 cm. Supplemental Figure 2. Flowering

More information

From DNA to protein, i.e. the central dogma

From DNA to protein, i.e. the central dogma From DNA to protein, i.e. the central dogma DNA RNA Protein Biochemistry, chapters1 5 and Chapters 29 31. Chapters 2 5 and 29 31 will be covered more in detail in other lectures. ph, chapter 1, will be

More information

Supplementary Materials for

Supplementary Materials for www.sciencetranslationalmedicine.org/cgi/content/full/4/148/148ra116/dc1 Supplementary Materials for Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing

More information

Aoife McLysaght Dept. of Genetics Trinity College Dublin

Aoife McLysaght Dept. of Genetics Trinity College Dublin Aoife McLysaght Dept. of Genetics Trinity College Dublin Evolution of genome arrangement Evolution of genome content. Evolution of genome arrangement Gene order changes Inversions, translocations Evolution

More information

PROTEIN SYNTHESIS INTRO

PROTEIN SYNTHESIS INTRO MR. POMERANTZ Page 1 of 6 Protein synthesis Intro. Use the text book to help properly answer the following questions 1. RNA differs from DNA in that RNA a. is single-stranded. c. contains the nitrogen

More information

P. syringae and E. coli

P. syringae and E. coli CHAPTER 6 A comparison of the recd mutant phenotypes of P. syringae and E. coli 6.1 INTRODUCTION The RecBCD complex is essential for recombination mediated repair of double strand breaks (DSBs) of DNA

More information

Insects act as vectors for a number of important diseases of

Insects act as vectors for a number of important diseases of pubs.acs.org/synthbio Novel Synthetic Medea Selfish Genetic Elements Drive Population Replacement in Drosophila; a Theoretical Exploration of Medea- Dependent Population Suppression Omar S. Abari,,# Chun-Hong

More information

dead, a New Escherichia coli Gene Encoding a Presumed

dead, a New Escherichia coli Gene Encoding a Presumed JOURNAL OF BACTERIOLOGY, June 1991, p. 3291-3302 0021-9193/91/113291-12$02.00/0 Copyright 1991, American Society for Microbiology Vol. 173, No. 11 dead, a New Escherichia coli Gene Encoding a Presumed

More information

Introduction to Molecular Phylogeny

Introduction to Molecular Phylogeny Introduction to Molecular Phylogeny Starting point: a set of homologous, aligned DNA or protein sequences Result of the process: a tree describing evolutionary relationships between studied sequences =

More information

THE MATHEMATICAL STRUCTURE OF THE GENETIC CODE: A TOOL FOR INQUIRING ON THE ORIGIN OF LIFE

THE MATHEMATICAL STRUCTURE OF THE GENETIC CODE: A TOOL FOR INQUIRING ON THE ORIGIN OF LIFE STATISTICA, anno LXIX, n. 2 3, 2009 THE MATHEMATICAL STRUCTURE OF THE GENETIC CODE: A TOOL FOR INQUIRING ON THE ORIGIN OF LIFE Diego Luis Gonzalez CNR-IMM, Bologna Section, Via Gobetti 101, I-40129, Bologna,

More information

Supporting Information

Supporting Information Supporting Information Mixed DNA-functionalized Nanoparticle Probes for Surface Enhanced Raman Scattering-based Multiplex DNA Detection Zhiliang Zhang, a, b Yongqiang Wen,* a Ying Ma, a Jia Luo, a Lei

More information

Gene expression in prokaryotic and eukaryotic cells, Plasmids: types, maintenance and functions. Mitesh Shrestha

Gene expression in prokaryotic and eukaryotic cells, Plasmids: types, maintenance and functions. Mitesh Shrestha Gene expression in prokaryotic and eukaryotic cells, Plasmids: types, maintenance and functions. Mitesh Shrestha Plasmids 1. Extrachromosomal DNA, usually circular-parasite 2. Usually encode ancillary

More information

CCHS 2015_2016 Biology Fall Semester Exam Review

CCHS 2015_2016 Biology Fall Semester Exam Review Biomolecule General Knowledge Macromolecule Monomer (building block) Function Energy Storage Structure 1. What type of biomolecule is hair, skin, and nails? 2. What is the polymer of a nucleotide? 3. Which

More information

Supplementary Figure 1. Schematic of split-merger microfluidic device used to add transposase to template drops for fragmentation.

Supplementary Figure 1. Schematic of split-merger microfluidic device used to add transposase to template drops for fragmentation. Supplementary Figure 1. Schematic of split-merger microfluidic device used to add transposase to template drops for fragmentation. Inlets are labelled in blue, outlets are labelled in red, and static channels

More information

CCHS 2016_2017 Biology Fall Semester Exam Review

CCHS 2016_2017 Biology Fall Semester Exam Review CCHS 2016_2017 Biology Fall Semester Exam Review Biomolecule General Knowledge Macromolecule Monomer (building block) Function Structure 1. What type of biomolecule is hair, skin, and nails? Energy Storage

More information

It is the author's version of the article accepted for publication in the journal "Biosystems" on 03/10/2015.

It is the author's version of the article accepted for publication in the journal Biosystems on 03/10/2015. It is the author's version of the article accepted for publication in the journal "Biosystems" on 03/10/2015. The system-resonance approach in modeling genetic structures Sergey V. Petoukhov Institute

More information

Supplementary information. Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization.

Supplementary information. Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization. Supplementary information Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization. Benjamin Cressiot #, Sandra J. Greive #, Wei Si ^#,

More information

Isolation of the hemf Operon Containing the Gene for the Escherichia coli Aerobic Coproporphyrinogen III Oxidase by

Isolation of the hemf Operon Containing the Gene for the Escherichia coli Aerobic Coproporphyrinogen III Oxidase by JOURNAL OF BACrERIOLOGY, Feb. 1994, p. 673-680 0021-9193/94/$04.00+0 Copyright X) 1994, American Society for Microbiology Vol. 176, No. 3 Isolation of the hemf Operon Containing the Gene for the Escherichia

More information

Characterization of Multiple-Antimicrobial-Resistant Salmonella Serovars Isolated from Retail Meats

Characterization of Multiple-Antimicrobial-Resistant Salmonella Serovars Isolated from Retail Meats APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Jan. 2004, p. 1 7 Vol. 70, No. 1 0099-2240/04/$08.00 0 DOI: 10.1128/AEM.70.1.1 7.2004 Copyright 2004, American Society for Microbiology. All Rights Reserved. Characterization

More information

Objective: You will be able to justify the claim that organisms share many conserved core processes and features.

Objective: You will be able to justify the claim that organisms share many conserved core processes and features. Objective: You will be able to justify the claim that organisms share many conserved core processes and features. Do Now: Read Enduring Understanding B Essential knowledge: Organisms share many conserved

More information

Evidence for RNA editing in mitochondria of all major groups of

Evidence for RNA editing in mitochondria of all major groups of Proc. Natl. Acad. Sci. USA Vol. 91, pp. 629-633, January 1994 Plant Biology Evidence for RNA editing in mitochondria of all major groups of land plants except the Bryophyta RUDOLF HIESEL, BRUNO COMBETTES*,

More information

CHAPTER 13 PROKARYOTE GENES: E. COLI LAC OPERON

CHAPTER 13 PROKARYOTE GENES: E. COLI LAC OPERON PROKARYOTE GENES: E. COLI LAC OPERON CHAPTER 13 CHAPTER 13 PROKARYOTE GENES: E. COLI LAC OPERON Figure 1. Electron micrograph of growing E. coli. Some show the constriction at the location where daughter

More information

Symmetry Studies. Marlos A. G. Viana

Symmetry Studies. Marlos A. G. Viana Symmetry Studies Marlos A. G. Viana aaa aac aag aat caa cac cag cat aca acc acg act cca ccc ccg cct aga agc agg agt cga cgc cgg cgt ata atc atg att cta ctc ctg ctt gaa gac gag gat taa tac tag tat gca gcc

More information

Newly made RNA is called primary transcript and is modified in three ways before leaving the nucleus:

Newly made RNA is called primary transcript and is modified in three ways before leaving the nucleus: m Eukaryotic mrna processing Newly made RNA is called primary transcript and is modified in three ways before leaving the nucleus: Cap structure a modified guanine base is added to the 5 end. Poly-A tail

More information

Analysis of Escherichia coli amino acid transporters

Analysis of Escherichia coli amino acid transporters Ph.D thesis Analysis of Escherichia coli amino acid transporters Presented by Attila Szvetnik Supervisor: Dr. Miklós Kálmán Biology Ph.D School University of Szeged Bay Zoltán Foundation for Applied Research

More information

Phosphotransferase Transport System from

Phosphotransferase Transport System from INFECTION AND IMMUNITY, Apr. 1994, p. 1156-1165 Vol. 62, No. 4 0019-9567/94/$04.00+0 Copyright 1994, American Society for Microbiology Sequence and Expression of the Genes for HPr (ptsh) and Enzyme I (ptsi)

More information

Glucosylglycerate phosphorylase, a novel enzyme specificity involved in compatible solute metabolism

Glucosylglycerate phosphorylase, a novel enzyme specificity involved in compatible solute metabolism Supplementary Information for Glucosylglycerate phosphorylase, a novel enzyme specificity involved in compatible solute metabolism Jorick Franceus, Denise Pinel, Tom Desmet Corresponding author: Tom Desmet,

More information

Chemical Biology on Genomic DNA: minimizing PCR bias. Electronic Supplementary Information (ESI) for Chemical Communications

Chemical Biology on Genomic DNA: minimizing PCR bias. Electronic Supplementary Information (ESI) for Chemical Communications Electronic Supplementary Material (ESI) for ChemComm. This journal is The Royal Society of Chemistry 2014 Chemical Biology on Genomic DA: minimizing PCR bias Gordon R. McInroy, Eun-Ang Raiber, & Shankar

More information

Regulation of the Bacillus subtilis Heat Shock Gene htpg Is under Positive Control

Regulation of the Bacillus subtilis Heat Shock Gene htpg Is under Positive Control JOURNAL OF BACTERIOLOGY, Jan. 2003, p. 466 474 Vol. 185, No. 2 0021-9193/03/$08.00 0 DOI: 10.1128/JB.185.2.466 474.2003 Copyright 2003, American Society for Microbiology. All Rights Reserved. Regulation

More information

BIOL 502 Population Genetics Spring 2017

BIOL 502 Population Genetics Spring 2017 BIOL 502 Population Genetics Spring 2017 Lecture 1 Genomic Variation Arun Sethuraman California State University San Marcos Table of contents 1. What is Population Genetics? 2. Vocabulary Recap 3. Relevance

More information

MicroGenomics. Universal replication biases in bacteria

MicroGenomics. Universal replication biases in bacteria Molecular Microbiology (1999) 32(1), 11±16 MicroGenomics Universal replication biases in bacteria Eduardo P. C. Rocha, 1,2 Antoine Danchin 2 and Alain Viari 1,3 * 1 Atelier de BioInformatique, UniversiteÂ

More information

Appendix B Protein-Signaling Networks from Single-cell Fluctuations and Information Theory Profiling B.1. Introduction

Appendix B Protein-Signaling Networks from Single-cell Fluctuations and Information Theory Profiling B.1. Introduction 92 Appendix B Protein-Signaling Networks from Single-cell Fluctuations and Information Theory Profiling B.1. Introduction Protein-signaling pathways play important roles in tissue processes ranging from

More information

Structure of the Mycobacterium tuberculosis Antigen 88, a Protein Related to the Escherichia coli PstA Periplasmic

Structure of the Mycobacterium tuberculosis Antigen 88, a Protein Related to the Escherichia coli PstA Periplasmic NFECrlON AND MMUNTY, Mar. 1994, p. 849-854 0019-9567/94/$04.00+0 Copyright 1994, American Society for Microbiology Vol. 62, No. 3 Structure of the Mycobacterium tuberculosis Antigen 88, a Protein Related

More information

RNA Synthesis and Processing

RNA Synthesis and Processing RNA Synthesis and Processing Introduction Regulation of gene expression allows cells to adapt to environmental changes and is responsible for the distinct activities of the differentiated cell types that

More information