Analysis of rpos mrna in Salmonella dublin: Identification of Multiple Transcripts with Growth-Phase-Dependent Variation in Transcript Stability

Size: px
Start display at page:

Download "Analysis of rpos mrna in Salmonella dublin: Identification of Multiple Transcripts with Growth-Phase-Dependent Variation in Transcript Stability"

Transcription

1 JOURNAL OF BACTERIOLOGY, Feb. 1999, p Vol. 181, No /99/$ Copyright 1999, American Society for Microbiology. All Rights Reserved. Analysis of rpos mrna in Salmonella dublin: Identification of Multiple Transcripts with Growth-Phase-Dependent Variation in Transcript Stability G. PAESOLD 1 * AND M. KRAUSE 2 Institute of Microbiology, Swiss Federal Institute of Technology, ETH-Zentrum, CH-8092 Zürich, 1 and Medical Clinic, Kantonsspital Münsterlingen, CH-8596 Münsterlingen, 2 Switzerland Received 8 June 1998/Accepted 25 November 1998 In Salmonella dublin, rpos encodes an alternative sigma factor of the RNA polymerase that activates a variety of stationary-phase-induced genes, including some virulence-associated genes. In this work, we studied the regulation and transcriptional organization of rpos during growth. We found two transcripts, 2.3 and 1.6 kb in length, that represent the complete rpos sequence. The 2.3-kb transcript is a polycistronic message that also includes the upstream nlpd gene. It is driven by a weak promoter with increasing activity when cells enter early stationary growth. The 1.6-kb message includes 566 bp upstream of the rpos start codon. It is transcribed from a strong 70 RNA polymerase-dependent promoter which is independent of growth. The decay of this transcript decreases substantially in early stationary growth, resulting in a significant net increase in rpos mrna levels. These levels are approximately 10-fold higher than the levels of the 2.3-kb mrna, indicating that the 1.6-kb message is mainly responsible for RpoS upregulation. In addition to the 2.3- and 1.6-kb transcripts, two smaller 1.0- and 0.4-kb RNA species are produced from the nlpd-rpos locus. They do not allow translation of full-length RpoS; hence their significance for rpos regulation remains unclear. We conclude that of four transcripts arising from the nlpd-rpos locus, only one plays a significant role in rpos expression in S. dublin. Its upregulation when cells enter stationary growth is due primarily to an increase in transcript stability. Many bacteria adapt to changing growth conditions by using alternative sigma factors that mediate the expression of particular sets of genes. In enteric bacteria such as Escherichia coli and Salmonella, Shigella, and Yersinia spp., 70 is the housekeeping sigma factor responsible for the transcription from the majority of the promoters (13). During transition to the stationary growth phase, RpoS is produced as an alternative sigma factor, also known as S or 38 (30, 31). RpoS rapidly triggers the expression of a variety of genes which enhance the viability under various stress conditions (reviewed in references 14, 24, and 25). In virulent, nontyphoid Salmonella, RpoS was also found to be responsible for the expression of the Salmonella plasmid virulence (spv) genes (6, 10, 12, 17). Most studies concerning the regulation of rpos itself were carried out in E. coli, where the expression of rpos is induced during the transition from exponential to stationary growth phase (22). At least two promoters controlling rpos transcription have been identified. The major promoter is located in the coding region of the nlpd gene upstream of rpos, whereas the second promoter is upstream of the nlpd gene, resulting in a polycistronic transcript of nlpd and rpos (20, 35). Whereas transcription from the rpos main promoter was found to be induced during transition to stationary phase, nlpd expression was not induced during growth (21, 22). The cellular concentrations of RpoS are further controlled at the translational and posttranslational levels by mechanisms involving several protein factors (2, 4, 5, 28, 29, 36) as well as some nonprotein regulatory factors (15, 20, 22). In this study, we determined the DNA sequence upstream of rpos in Salmonella dublin Lane and studied the regulation of * Corresponding author. Mailing address: Institute of Microbiology, Swiss Federal Institute of Technology, ETH-Zentrum, Schmelzbergstrasse 7, CH-8092 Zürich, Switzerland. Phone: Fax: paesold@micro.biol.ethz.ch. rpos expression throughout growth of batch cultures. Although the sequence including the corresponding nlpd gene was found to be very similar to that of E. coli, we identified some distinct differences between the two species in the control of rpos expression. Northern and immunoblot analyses and mrna decay assays revealed that the initiation of rpos expression in the late exponential growth phase is due primarily to an increase in mrna stability. MATERIALS AND METHODS Bacterial strains and culture conditions. The strains used in this study are listed in Table 1. S. dublin Lane is a clinical blood isolate which contains the virulence plasmid psdl2. S. dublin LD842 is the psdl2-cured avirulent derivative of S. dublin Lane (7). CC1002 and CC1003 are rpos mutants of S. dublin Lane and LD842, respectively (6). E. coli TB1 (2) and SK383 (37) were used for cloning and plasmid constructions. To transform S. dublin, plasmids were first passed through the restriction-deficient S. typhimurium LB5000 (9). Bacterial cultures were grown in Luria-Bertani (LB) broth. When required, appropriate antibiotics were added to the following final concentrations: penicillin G, 200 g/ml; chloramphenicol, 20 g/ml; and tetracycline 2 g/ml. To ensure that the bacteria were in exponential growth, overnight cultures were diluted 1:100 in fresh LB medium and incubated at 37 C with vigorously shaking (300 rpm). After 1 h, the cultures were diluted again 1:100. The growth of the bacterial cultures was monitored by measuring the optical density at 600 nm (OD 600 ). DNA manipulations. Plasmid clone analysis, cleavage with restriction endonucleases, agarose gel electrophoresis, ligations, and transformations were performed according to standard methods (32). For DNA sequencing, a T7 sequencing kit (Pharmacia) and [ - 35 S]thio-dATP ( 1,000 Ci/mmol; Amersham) were used. Sequencing of the complementary strand was performed to confirm all sequences. Plasmids. The plasmids used in this study are listed in Table 1. pbb4 is a ptrc99a (1) derivative which carries a 1,069-bp BclI-BspHI fragment containing the first 23 bp of the S. dublin rpos coding region and the upstream region of the rpos gene. prsp70 is a prs551-based (33) transcriptional fusion of a 389-bp RsaI fragment containing the putative rpos promoter and the transcriptional start site with the lacz gene. A 477-bp-long fragment containing the putative promoter, the translational start site, and the first 358 bp of the Salmonella nlpd gene was amplified by PCR using the primers 5 -TTTCCTGGTTATTCCGGT GG-3 and 5 -GTACTGCCACCCGTATAGC-3. Cloning of this fragment into prs551 resulted in the transcriptional fusion vector prsnl. 1264

2 VOL. 181, 1999 rpos TRANSCRIPTION IN S. DUBLIN 1265 TABLE 1. Strains and plasmids used in this study Strain or plasmid Characteristics Reference Strains E. coli TB1 JM83 hsdr (r K m K ) 3 SK383 dam-4 37 S. typhimurium r LT r SA r SB 9 LB5000 S. dublin CC1002 rpos mutant of S. dublin Lane 6 CC1003 rpos mutant of S. dublin 6 LD842 Lane Wild type, contains the 11 virulence plasmid psdl2 LD842 Plasmid-cured S. dublin Lane 7 Plasmids pbb4 ptrc99a containing the 1,069- bp BclI-BspHI region upstream of rpos prsp70 prs551 containing a 389-bp RsaI fragment carrying the rpos promoter prsnl prs551 containing a 477-bp PCR fragment carrying the nlpd promoter RNA preparation and Northern blotting. Total RNA from samples of about 10 9 cells was isolated as described earlier (18, 23). The RNA was precipitated overnight with ethanol, and the pellet was stored at 80 C until further use. Prior to electrophoresis the RNA pellet was dissolved in 5 l of 25 mm EDTA 0.1% sodium dodecyl sulfate, and 25 l of electrophoresis sample buffer (50% deionized formamide, 16% formaldehyde, and 7% glycerol in 20 mm MOPS 5 mm sodium acetate 1 mm EDTA) was added. The samples were normalized to equal amounts of total RNA. After heating for 15 min at 65 C, the samples were electrophoresed on horizontal denaturing formaldehyde-agarose gels and transferred to a Nytran N nylon membrane (Schleicher & Schuell). The probes were randomly labeled by using a Rediprime kit (Amersham). The membranes were manipulated according to the Rapid-hyb buffer protocol (Amersham). Primer extension. The oligonucleotides used as primers were 5 -CTTTCAG CGTATTCTGAC-3 (complementary to the 5 end of the rpos gene) and 5 -C CTGTTGTTCCCGGACCAGC-3 plus 5 -GTTGGTGCCGTTACAGGCG C-3 (complementary to regions 185 and 482 bp upstream of the rpos start codon). From each primer, a fragment of approximately 300 bp was run on the gels. The primers (10 pmol) were labeled by using a 5 -end labeling kit (Amersham), precipitated, and resuspended in 4 l of sterile H 2 O. The RNA was resuspended in 4 l of sterile H 2 O and mixed with the labeled primers; 5 annealing buffer (2 M NaCl, 5 mm PIPES [ph 7.0]) was added, and the mixture was heated to 100 C for 3 min, incubated for 5 min at 65 C, and then slowly cooled to 42 C; 40 l of 1.25 avian myeloblastosis virus reverse transcriptase buffer containing 1 mm each deoxynucleoside triphosphate and 10 U of avian myeloblastosis virus reverse transcriptase was added, and the mixture was incubated for1hat42 C. The reaction was stopped by addition of 5 l of 3 M sodium acetate (ph 6.0) and 150 l of cold ethanol; the pellet was washed and dissolved in 2 l of 0.1 M NaOH. Finally 4 l of formaldehyde stop and loading buffer (Pharmacia) was added, and the samples were loaded on 8% polyacrylamide 7 M urea or 6% Long Ranger 7 M urea (FMC Bioproducts) sequencing gels. Determination of the rpos mrna half-life. Rifampin, a potent inhibitor of RNA synthesis, was added to a final concentration of 300 g per ml of cell culture. The cells were incubated at 37 C with vigorous shaking; after 3, 6, 9, and 12 min, samples of about 10 9 cells were taken and total RNA was prepared as described above. The samples were stored at 80 C until used for Northern blot analysis. The experiments were performed two to four times. Protein analysis by immunoblotting. Specific polyclonal antibodies against S. dublin RpoS were kindly provided by A. El-Gedaily. The specificity of the antibodies was tested by immunoblot analysis of whole-cell extracts of the S. dublin rpos mutant strain CC1002 as a control (8). Western immunoblotting was performed as previously described (19). Proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (10 to 15% polyacrylamide) and transferred electrophoretically to nitrocellulose membranes. The samples were standardized to equal amounts of total protein. All samples were prepared under reducing conditions. After transfer to nitrocellulose membranes, nonspecific antibody binding was blocked by incubation in 4% (wt/vol) dried milk in Tris-buffered saline (ph 7.5) containing 0.05% (vol/vol) Tween 20. The blots FIG. 1. Comparison of the levels of RpoS protein (A) and rpos mrna (B) along the growth curve. Arrows mark the protein and mrna main band, respectively. The samples were standardized to equal amounts of total cellular protein and total RNA, respectively. were probed with rabbit polyclonal antibodies against RpoS. Binding of the primary antibody was detected by using horseradish peroxidase-labeled secondary antibodies and enhanced chemiluminescence detection reagents (Amersham) followed by exposure to a radiographic film. The intensities of the protein bands were determined by densitometry (model GS-700 densitometer [Bio-Rad]; Molecular Analyst software). To construct the figures, the blots were scanned with Adobe Photoshop 3.0 software. -Galactosidase activity. The standard procedure described by Miller (26) was used for quantitative measurements of -galactosidase activity. Each experiment was performed at least three times on different days. Nucleotide sequence accession number. The sequence determined has been deposited in the EMBL nucleotide sequence database under accession no. AJ RESULTS Cellular content of RpoS during growth. We first established that RpoS concentrations increase in S. dublin when bacteria enter stationary phase. S. dublin had been grown to different OD 600 values, and equal protein amounts of whole-cell extracts were analyzed by immunoblotting using specific anti-rpos antibodies (Fig. 1A). The course of RpoS expression was characterized by (i) a low initial baseline in early logarithmic growth until an OD 600 of 0.4, (ii) a sharp 10-fold rise between OD 600 of 0.4 and 0.5, (iii) a plateau until an OD 600 of 0.8, and (iv) a final approximately threefold rise at an OD 600 of 2.2. These data clearly confirm that RpoS synthesis in S. dublin is growth regulated and suggest that at least two events at OD 600 of approximately 0.4 to 0.5 and 0.8 to 2.2 result in significant increase of RpoS levels. Determination of the rpos upstream sequence in S. dublin Lane. The 1.5-kb upstream region of the rpos coding region of S. dublin was sequenced and found to be very similar to the DNA sequence of E. coli that contained the nlpd gene. Sequence analysis revealed an 1,131-bp open reading frame oriented in the same direction as rpos and an intergenic region of 350 bp. The deduced sequence of 377 amino acids revealed 88% identity to NlpD of E. coli. The signal sequence at the N terminus, the lipidation consensus sequence, and the 206 C- terminal amino acids of S. dublin and E. coli were conserved. Significant variations were found after the signal sequence between amino acid residues 62 and 93. In E. coli, this region has a high content of proline and glutamine arranged in characteristic repeats (16). In S. dublin Lane, no significant repeats were detected, although the content of prolines and glutamines was comparable to that in the E. coli protein. Interestingly, the putative nlpd promoter region of S. dublin was substantially different from that of E. coli by the absence of a typical 10

3 1266 PAESOLD AND KRAUSE J. BACTERIOL. FIG. 3. Mapping of the different rpos mrna transcripts. (A) The probes (A to E) used for the mapping. (B) Band patterns with the different probes. Lanes A to E correspond to probes A to E; bands 1 to 4 corresponds to the 2.3-, 1.6-, 1.0-, and 0.4-kb transcripts. (After longer exposure, the 2.3-kb band was also visualized in lanes D and E.) (C) Alignment of the identified transcripts to the DNA sequence. The arrowhead defines the 3 end of the 1.6-kb main transcript. FIG. 2. (A) Comparison of the nlpd promoter regions of S. dublin and E. coli (21). The two transcriptional start sites in E. coli and the translational start site are shaded; the 10 and 35 regions of the two promoters determined in E. coli are underlined; the corresponding sequences in S. dublin are marked. The 10 region of the promoter P1 is absent in S. dublin. (B) Determination of the 5 end of the 1.6-kb main transcript by primer extension. The arrow shows the transcriptional start site. The 10 and 35 regions of the putative 70 RNA polymerase-dependent promoter are also marked. Lanes A, C, G, and T represent the sequencing ladder using the same primer as used for the primer extension reaction. consensus sequence in the Salmonella promoter region (Fig. 2A). Mapping of the rpos mrna in S. dublin Lane. To analyze the rpos mrna, we extracted total RNA from S. dublin Lane that had been grown to early stationary phase. The RNA was separated by electrophoresis and blotted on a membrane, and the blots were probed with an rpos-specific probe that encompassed the complete rpos gene including the 350-bp upstream region that overlaps the 3 end of the nlpd gene. We identified four different bands with lengths of approximately 2.3, 1.6, 1.0, and 0.4 kb. To map these bands, we used four new probes corresponding to different regions of the rpos mrna (Fig. 3). The signal of the 2.3-kb transcript was fairly weak. It was found to be a polycistronic message including nlpd and rpos. The most intense signal was provided by the 1.6-kb band, which corresponded to the complete rpos gene including a large upstream segment. The precise transcriptional start of this message was identified by primer extension at 566 bp upstream of the ATG start codon of rpos (Fig. 2B). The start site was at the same position as the start in E. coli and was preceded by a typical 70 RNA polymerase-dependent promoter consensus sequence (22, 35). The remaining 1.0- and 0.4-kb bands encompassed only fragments of the rpos main mrna and do not allow translation of full-length RpoS. Thus, only the nlpd and rpos promoters of the 2.3- and 1.6-kb mrnas, respectively, control transcription of a complete rpos message. Cellular levels of rpos mrna during growth. To evaluate the role of rpos transcription during the course of RpoS expression, we determined the amount of the specific rpos mrna along the growth curve. The mrna from aliquots of approximately 10 9 cells at OD 600 of 0.2, 0.4, 0.5, 0.7, 0.8, and 2.2 was extracted, and the 2.3- and 1.6-kb rpos bands were analyzed by densitometry. We found that the 1.6- and 2.3-kb messages followed the same course, with intensities at a stable ratio of approximately 10:1 throughout the growth cycle. This clearly indicated that the 1.6-kb transcript is mainly responsible for RpoS production. It was remarkable that even in early exponential growth significant amounts of rpos mrna were present (Fig. 1B). Between an OD 600 of 0.4 and 0.5 we observed a significant (approximately threefold) increase. During continued growth the rpos mrna level decreased slightly, and in late stationary phase it had declined to about two-thirds of the maximum level. The distinct peak of mrna at an OD 600 of 0.5 corresponds well with the cellular RpoS, indicating that at this growth stage the sharp increase of RpoS is basically the result of increased transcription. At an OD 600 of 2.2, however, the levels of rpos mrna and RpoS proteins diverge, indicating that at that stage, RpoS is regulated mainly translationally or posttranslationally. Analysis of nlpd and rpos promoter activity. Next, we analyzed the activities of the rpos and nlpd promoters, which are responsible for generation of the 1.6- and 2.3-kb transcripts, respectively. The transcriptional lacz fusion vectors prsp70 and prsnl, containing 389- and 477-bp fragments from the upstream regions of rpos and nlpd, respectively, were transferred into S. dublin Lane, and -galactosidase levels were determined at time points along the growth curve (Fig. 4). The activity pattern of the nlpd promoter was found to be growth phase dependent. After a twofold increase at an OD 600 of 0.4 to 0.5, a gradual decrease during prolonged growth was observed. The -galactosidase levels from the rpos 1.6-kb tran-

4 VOL. 181, 1999 rpos TRANSCRIPTION IN S. DUBLIN 1267 FIG. 4. Transcriptional activities of the nlpd and rpos promoters. The activities were monitored by measuring the -galactosidase activities from the transcriptional lacz fusion vectors prsnl ( ) and prsp70 (}), respectively, and are presented as percentages of the basal transcription level during early exponential phase. The dashed line represents the OD 600 during growth. Each measurement was performed at least three times. script promoter were approximately 5- to 10-fold higher and, in contrast to the 2.3-kb transcript, were found to be constant throughout the whole cycle. Even in the very early exponential phase, we found high levels of activity (approximately 20,000 Miller units) that remained constant until late stationary phase. This finding was verified by Northern blot analysis using a probe complementary to the lacz mrna (data not shown), confirming that the rate of transcription was not growth phase dependent. Whereas the nlpd promoter activity corresponds well with the 2.3-kb mrna levels, there exists an obvious discrepancy between the activity of the rpos promoter and the amount of 1.6-kb message, indicating that the cellular level of this transcript is posttranscriptionally regulated. rpos mrna was stabilized during stationary phase. Since the transcriptional activity at the rpos promoter was not upregulated at an OD 600 of 0.4, we postulated that the rise of rpos mrna was due to a decreased decay. To examine the stability of the rpos mrna during the growth curve, we determined the half-life of the mrna at different growth phases. Rifampin, a potent inhibitor of RNA synthesis in bacterial cells, was added to cultures at OD 600 of 0.3, 0.8, and 2.3. Total RNA was prepared at different time points after rifampin addition and analyzed by quantitative Northern blot analysis (Fig. 5). We found an approximately twofold increase in the stability of the rpos mrna between an OD 600 of 0.3 and 0.8, with half-lives of 2.5 and 4.5 min, respectively. At an OD 600 of 2.3, the half-life decreased to 3.5 min. DISCUSSION In this work, we studied the regulation of rpos transcription in S. dublin. We identified four distinct rpos-specific transcripts 2.3, 1.6, 1.0, and 0.4 kb in size that were mapped within the nlpd-rpos locus. Only the 2.3- and 1.6-kb messages encompassed the complete rpos gene. The 2.3-kb transcript was a polycistronic message that included nlpd upstream of rpos, whereas the 1.6-kb transcript contained a 566-bp upstream segment in addition to rpos. The smaller 1.0- and 0.4-kb RNA fragments did not allow generation of a complete RpoS protein. They align with a part of the rpos coding region and the untranslated rpos upstream region, respectively. The finding of 2.3- and 1.6-kb messages that allow transcription of a full-length RpoS indicates that rpos transcription in S. FIG. 5. Stability of the rpos mrna main transcript along the growth curve. The half-life of the 1.6-kb rpos mrna was measured at OD , 0.8, and 2.3. (A) Relative amounts of rpos mrna after addition of rifampin depicted on a semilogarithmic graph. (B) Calculated half-lives (in minutes) and a typical Northern blot. Each experiment was carried out two to four times. dublin is controlled by two different promoter regions. Both transcript levels peak substantially during late exponential growth at an OD 600 of 0.4 to 0.5 (Fig. 1B). This upregulation is accompanied by a significant increase in cellular RpoS concentrations, indicating that the increase of rpos-specific mrna available for translation is the pivotal regulatory event at this point of growth. After the peak at OD to 0.5, the mrna levels of both 2.3- and 1.6-kb transcripts decreased continuously until late stationary phase. Although the courses of the net levels of the 2.3- and 1.6-kb mrnas were very similar along the growth curve, we surprisingly found that the two promoters are regulated differently. Transcription from the promoter region upstream of nlpd was found to be growth regulated. In accordance with the course of the 2.3-kb mrna, transcriptional activity increased about twofold during late exponential phase and then returned gradually to the baseline level (Fig. 4). Growth dependence was corroborated by the observation that in an rpos mutant growth regulation was abolished, and this suggested further the presence of a positive autoregulation. In contrast, the transcriptional rate from the rpos promoter producing the 1.6-kb transcript was found to be growth independent. A high and constant promoter activity was measured throughout the growth cycle, consistent with the finding of a transcriptional start that is preceded by a typical 70 RNA polymerase-dependent promoter consensus sequence (Fig. 2B). Hence, the significant increase of the 1.6-kb mrna levels in late exponential phase can be explained only by posttranscriptional regulation. We found a substantial rise in mrna stability that occurred together with the sharp rise of mrna, increasing the mrna half-life from 2.5 to 4.5 min. The molecular mechanism of this increased stability is not known. Possibly the unusually long untranslated upstream region of the 1.6-kb transcript plays a significant role; however, experimental evidence for this is lacking. Although the nlpd-rpos nucleotide sequences of E. coli and S. dublin are very closely related, we discovered significant

5 1268 PAESOLD AND KRAUSE J. BACTERIOL. differences in rpos regulation between the two species. First, the relative contributions of the 2.3- and 1.6-kb messages to rpos expression differed significantly from the findings reported for E. coli. Whereas in E. coli transcription from the nlpd promoter contributes up to 40% to rpos expression (20, 21), we found only a minor portion (10%) arising from the nlpd promoter in S. dublin (Fig. 1B). This lower activity might be explained by the finding that the 10 region of one of the two nlpd promoters in E. coli was virtually absent in S. dublin. Second, the rpos promoter responsible for the 1.6-kb main message showed high transcriptional activity even during early exponential growth. In contrast to E. coli (20), no significant induction of the transcription rate was observed when the cells entered the stationary phase. Third, nlpd, which is known in E. coli to be a growth-independent regulated gene (21), was found to be induced significantly during transition into stationary growth in S. dublin. This might be due to the differences that we found in the sequence upstream of the translational start site. Fourth, the smaller 1.0- and 0.4-kb RNAs have not been described for E. coli. Their possible function for rpos regulation in S. dublin remains unclear. It is conceivable that they represent stable degradation products of the 1.6-kb transcript from an endonucleolytic cleavage or are transcribed autonomously and function as regulatory RNA (27, 34). Although E. coli and S. dublin are closely related species, they differ significantly in terms of pathogenicity and the ability to survive in specific hosts. Therefore, differences in regulation of rpos expression are not unexpected, particularly since RpoS plays a significant role in the regulation of Salmonella virulence (6, 10, 12, 17). Our study emphasizes that based on homologous DNA sequences alone, we must not anticipate that even closely related species have identical regulatory pathways. ACKNOWLEDGMENTS We thank P. Vermeij and M. Kertesz for their interest and critical reading of the manuscript. We thank T. Leisinger, in whose laboratories this work was carried out. Financial support was provided by the Swiss National Research Foundation (grant to M.K.). REFERENCES 1. Amann, E., B. Ochs, K.-J. Abel Tightly regulated tac promoter vectors useful for the expression of unfused and fused proteins in Escherichia coli. Gene 69: Bearson, S. M. D., W. H. Benjamin, Jr., W. E. Swords, and J. W. Foster Acid shock induction of RpoS is mediated by the mouse virulence gene mvia of Salmonella typhimurium. J. Bacteriol. 178: Bethesda Research Laboratories E. coli TB1 host for puc plasmids. Focus 6: Brown, L., and T. Elliott Efficient translation of the RpoS sigma factor in Salmonella typhimurium requires host factor I, an RNA-binding protein encoded by the hfq gene. J. Bacteriol. 178: Brown, L., and T. Elliott Mutations that increase expression of the rpos gene and decrease its dependence on hfq function in Salmonella typhimurium. J. Bacteriol. 179: Chen, C.-Y., N. A. Buchmeier, S. Libby, F. C. Fang, M. Krause, and D. G. Guiney Central regulatory role for the RpoS sigma factor in expression of Salmonella dublin plasmid virulence genes. J. Bacteriol. 177: Chikami, G. K., J. Fierer, and D. G. Guiney Plasmid-mediated virulence in Salmonella dublin demonstrated by use of a Tn5-oriT construct. Infect. Immun. 50: El-Gedaily, A Regulation and subcellular location of the plasmid encoded virulence (Spv) proteins in wild-type Salmonella dublin. Ph.D. thesis. University of Zurich, Zurich, Switzerland. 9. Fang, F. C., M. Krause, C. Roudier, and D. G. Guiney Growth regulation of a Salmonella plasmid gene essential for virulence. J. Bacteriol. 173: Fang, F. C., S. J. Libby, N. A. Buchmeier, P. C. Loewen, J. Switala, J. Harwood, and D. G. Guiney The alternative factor KatF (RpoS) regulates Salmonella virulence. Proc. Natl. Acad. Sci. USA 89: Fierer, J., and W. Fleming Distinctive biochemical features of Salmonella dublin isolated in California. J. Clin. Microbiol. 17: Heiskanen, P., S. Taira, and M. Rhen Role of rpos in the regulation of Salmonella plasmid virulence (spv) genes. FEMS Microbiol. Lett. 123: Helmann, J. D., and M. J. Chamberlin Structure and function of bacterial sigma factors. Annu. Rev. Biochem. 57: Hengge-Aronis, R Back to log phase: S as a global regulator in the osmotic control of gene expression in Escherichia coli. Mol. Microbiol. 21: Huisman, G. W., and R. Kolter Sensing starvation: a homoserine lactone-dependent signaling pathway in Escherichia coli. Science 265: Ichikawa, J. K., C. Li, J. Fu, and S. Clarke A gene at 59 minutes on the Escherichia coli chromosome encodes a lipoprotein with unusual amino acid repeat sequences. J. Bacteriol. 176: Kowarz, L., C. Coynault, V. Robbe-Saule, and F. Norel The Salmonella typhimurium katf (rpos) gene: cloning, nucleotide sequence, and regulation of spvr and spvabcd virulence plasmid genes. J. Bacteriol. 176: Krause, M., F. C. Fang, and D. G. Guiney Regulation of plasmid virulence gene expression in Salmonella dublin involves an unusual operon structure. J. Bacteriol. 174: Krause, M., F. C. Fang, A. El-Gedaily, S. Libby, and D. G. Guiney Mutational analysis of SpvR binding to DNA in the regulation of the Salmonella plasmid virulence operon. Plasmid 34: Lange, R., D. Fischer, and R. Hengge-Aronis Identification of transcriptional start sites and the role of ppgpp in the expression of rpos, the structural gene for the 38 subunit of RNA polymerase in Escherichia coli. J. Bacteriol. 177: Lange, R., and R. Hengge-Aronis The nlpd gene is located in an operon with rpos on the Escherichia coli chromosome and encodes a novel lipoprotein with a potential function in cell wall formation. Mol. Microbiol. 13: Lange, R., and R. Hengge-Aronis The cellular concentration of the 38 subunit of RNA-polymerase in Escherichia coli is controlled at the levels of transcription, translation and protein stability. Genes Dev. 8: Laoide, B. M., and A. Ullmann Virulence dependent and independent regulation of the Bordetella pertussis cya operon. EMBO J. 9: Lee, I., J. Lin, H. K. Hall, B. Bearson, and J. W. Foster The stationaryphase sigma factor S (RpoS) is required for a sustained acid tolerance response in virulent Salmonella typhimurium. Mol. Microbiol. 17: Loewen, P. C., and R. Hengge-Aronis The role of the sigma factor S (KatF) in bacterial global regulation. Annu. Rev. Microbiol. 48: Miller, J. H Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. 27. Mudd, E. A., H. M. Krisch, and C. F. Higgins RNase E, an endoribonuclease, has a general role in the chemical decay of Escherichia coli mrna: evidence that rne and ams are the same genetic locus. Mol. Microbiol. 4: Muffler, A., D. Fischer, and R. Hengge-Aronis The RNA-binding protein HF-I, known as a host factor for phage Q RNA replication, is essential for rpos translation in Escherichia coli. Genes Dev. 10: Muffler, A., D. Fischer, S. Altuvia, G. Storz, and R. Hengge-Aronis The response regulator RssB controls stability of the S subunit of RNA polymerase in Escherichia coli. EMBO J. 15: Mulvey, M. R., and P. C. Loewen Nucleotide sequence of katf of Escherichia coli suggests KatF is a novel transcription factor. Nucleic Acids Res. 17: Prince, R. W., Y. Xu, S. J. Libby, and F. C. Fang Cloning and sequencing of the gene encoding the RpoS (KatF) factor from Salmonella typhimurium 14028s. Biochim. Biophys. Acta 1219: Sambrook, J., E. F. Fritsch, and T. Maniatis Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. 33. Simons, R. W., F. Houman, and N. Kleckner Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene 53: Sledjeski, D. D., A. Gupta, and S. Gottesman The small RNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in Escherichia coli. EMBO J. 15: Takayanagi, Y., K. Tanaka, H. Takahashi Structure of the 5 upstream region and the regulation of the rpos gene of Escherichia coli. Mol. Gen. Genet. 243: Zgurskaya, H. I., M. Keyhan, and A. Matin The S level in starving Escherichia coli cells increases solely as a result of its increased stability, despite decreased synthesis. Mol. Microbiol. 24: Zieg, J., V. F. Maples, and S. R. Kushner Recombination levels of Escherichia coli K-12 mutants deficient in various replication, recombination, or repair genes. J. Bacteriol. 134:

Introduction. Gene expression is the combined process of :

Introduction. Gene expression is the combined process of : 1 To know and explain: Regulation of Bacterial Gene Expression Constitutive ( house keeping) vs. Controllable genes OPERON structure and its role in gene regulation Regulation of Eukaryotic Gene Expression

More information

Bacterial strains, plasmids, and growth conditions. Bacterial strains and

Bacterial strains, plasmids, and growth conditions. Bacterial strains and I Text I Materials and Methods acterial strains, plasmids, and growth conditions. acterial strains and plasmids used in this study are listed in I Table. almonella enterica serovar Typhimurium strains

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

Optimization of Immunoblot Protocol for Use with a Yeast Strain Containing the CDC7 Gene Tagged with myc

Optimization of Immunoblot Protocol for Use with a Yeast Strain Containing the CDC7 Gene Tagged with myc OPTIMIZATION OF IMMUNOBLOT PROTOCOL 121 Optimization of Immunoblot Protocol for Use with a Yeast Strain Containing the CDC7 Gene Tagged with myc Jacqueline Bjornton and John Wheeler Faculty Sponsor: Anne

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

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

Name: SBI 4U. Gene Expression Quiz. Overall Expectation:

Name: SBI 4U. Gene Expression Quiz. Overall Expectation: Gene Expression Quiz Overall Expectation: - Demonstrate an understanding of concepts related to molecular genetics, and how genetic modification is applied in industry and agriculture Specific Expectation(s):

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

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

Name Period The Control of Gene Expression in Prokaryotes Notes

Name Period The Control of Gene Expression in Prokaryotes Notes Bacterial DNA contains genes that encode for many different proteins (enzymes) so that many processes have the ability to occur -not all processes are carried out at any one time -what allows expression

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

Vital Statistics Derived from Complete Genome Sequencing (for E. coli MG1655)

Vital Statistics Derived from Complete Genome Sequencing (for E. coli MG1655) We still consider the E. coli genome as a fairly typical bacterial genome, and given the extensive information available about this organism and it's lifestyle, the E. coli genome is a useful point of

More information

Evidence for Transcription Attenuation Rendering Cryptic a

Evidence for Transcription Attenuation Rendering Cryptic a JOURNAL OF BACTERIOLOGY, Nov. 1997, p. 7169 7173 Vol. 179, No. 22 0021-9193/97/$04.00 0 Copyright 1997, American Society for Microbiology Evidence for Transcription Attenuation Rendering Cryptic a S -Dependent

More information

Data Sheet. Azide Cy5 RNA T7 Transcription Kit

Data Sheet. Azide Cy5 RNA T7 Transcription Kit Cat. No. Size 1. Description PP-501-Cy5 10 reactions à 40 µl For in vitro use only Quality guaranteed for 12 months Store all components at -20 C. Avoid freeze and thaw cycles. DBCO-Sulfo-Cy5 must be stored

More information

Topic 4 - #14 The Lactose Operon

Topic 4 - #14 The Lactose Operon Topic 4 - #14 The Lactose Operon The Lactose Operon The lactose operon is an operon which is responsible for the transport and metabolism of the sugar lactose in E. coli. - Lactose is one of many organic

More information

Organization of Genes Differs in Prokaryotic and Eukaryotic DNA Chapter 10 p

Organization of Genes Differs in Prokaryotic and Eukaryotic DNA Chapter 10 p Organization of Genes Differs in Prokaryotic and Eukaryotic DNA Chapter 10 p.110-114 Arrangement of information in DNA----- requirements for RNA Common arrangement of protein-coding genes in prokaryotes=

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

mrna Isolation Kit for Blood/Bone Marrow For isolation mrna from blood or bone marrow lysates Cat. No

mrna Isolation Kit for Blood/Bone Marrow For isolation mrna from blood or bone marrow lysates Cat. No For isolation mrna from blood or bone marrow lysates Cat. No. 1 934 333 Principle Starting material Application Time required Results Key advantages The purification of mrna requires two steps: 1. Cells

More information

Phenol-Chloroform reagents. Selection guide. OH ; MW : High quality reagents for use in nucleic acid purification.

Phenol-Chloroform reagents. Selection guide. OH ; MW : High quality reagents for use in nucleic acid purification. Phenol-Chloroform reagents Extraction with phenol and phenol/chloroform mixtures is a universal method for purification of DNA and RNA. Proteins and restriction enzymes are removed by phenol and chloroform

More information

16 CONTROL OF GENE EXPRESSION

16 CONTROL OF GENE EXPRESSION 16 CONTROL OF GENE EXPRESSION Chapter Outline 16.1 REGULATION OF GENE EXPRESSION IN PROKARYOTES The operon is the unit of transcription in prokaryotes The lac operon for lactose metabolism is transcribed

More information

Bacterial Genetics & Operons

Bacterial Genetics & Operons Bacterial Genetics & Operons The Bacterial Genome Because bacteria have simple genomes, they are used most often in molecular genetics studies Most of what we know about bacterial genetics comes from the

More information

Regulation of Gene Expression in Bacteria and Their Viruses

Regulation of Gene Expression in Bacteria and Their Viruses 11 Regulation of Gene Expression in Bacteria and Their Viruses WORKING WITH THE FIGURES 1. Compare the structure of IPTG shown in Figure 11-7 with the structure of galactose shown in Figure 11-5. Why is

More information

Production of Recombinant Annexin V from plasmid pet12a-papi

Production of Recombinant Annexin V from plasmid pet12a-papi Tait Research Laboratory Page 1 of 5 Principle Production of Recombinant Annexin V from plasmid pet12a-papi Annexin V is expressed cytoplasmically in BL21(DE3) E. coli (Novagen) with the pet vector system

More information

Fitness constraints on horizontal gene transfer

Fitness constraints on horizontal gene transfer Fitness constraints on horizontal gene transfer Dan I Andersson University of Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala, Sweden GMM 3, 30 Aug--2 Sep, Oslo, Norway Acknowledgements:

More information

Transcription of the SsrAB Regulon Is Repressed by Alkaline ph and Is Independent of PhoPQ and Magnesium Concentration

Transcription of the SsrAB Regulon Is Repressed by Alkaline ph and Is Independent of PhoPQ and Magnesium Concentration JOURNAL OF BACTERIOLOGY, Mar. 2002, p. 1493 1497 Vol. 184, No. 5 0021-9193/02/$04.00 0 DOI: 10.1128/JB.184.5.1493 1497.2002 Copyright 2002, American Society for Microbiology. All Rights Reserved. Transcription

More information

CHAPTER : Prokaryotic Genetics

CHAPTER : Prokaryotic Genetics CHAPTER 13.3 13.5: Prokaryotic Genetics 1. Most bacteria are not pathogenic. Identify several important roles they play in the ecosystem and human culture. 2. How do variations arise in bacteria considering

More information

Supporting online material

Supporting online material Supporting online material Materials and Methods Target proteins All predicted ORFs in the E. coli genome (1) were downloaded from the Colibri data base (2) (http://genolist.pasteur.fr/colibri/). 737 proteins

More information

A Competitive Microflora Increases the Resistance of Salmonella typhimurium to Inimical Processes: Evidence for a Suicide Response

A Competitive Microflora Increases the Resistance of Salmonella typhimurium to Inimical Processes: Evidence for a Suicide Response APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Apr. 1998, p. 1323 1327 Vol. 64, No. 4 0099-2240/98/$04.00 0 Copyright 1998, American Society for Microbiology A Competitive Microflora Increases the Resistance

More information

Controlling Gene Expression

Controlling Gene Expression Controlling Gene Expression Control Mechanisms Gene regulation involves turning on or off specific genes as required by the cell Determine when to make more proteins and when to stop making more Housekeeping

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

Quantification of Protein Half-Lives in the Budding Yeast Proteome

Quantification of Protein Half-Lives in the Budding Yeast Proteome Supporting Methods Quantification of Protein Half-Lives in the Budding Yeast Proteome 1 Cell Growth and Cycloheximide Treatment Three parallel cultures (17 ml) of each TAP-tagged strain were grown in separate

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

Interactions between Mutations Mecting Ribosome Synthesis in Escherichia coli

Interactions between Mutations Mecting Ribosome Synthesis in Escherichia coli Journal of General Microbiology (1 989, 131, 945-949. Printed in Great Britain 945 Interactions between Mutations Mecting Ribosome Synthesis in Escherichia coli By PETER D. BUTLER, EMILIO CATTANEO AND

More information

Plasmid Partition System of the P1par Family from the pwr100 Virulence Plasmid of Shigella flexneri

Plasmid Partition System of the P1par Family from the pwr100 Virulence Plasmid of Shigella flexneri JOURNAL OF BACTERIOLOGY, May 2005, p. 3369 3373 Vol. 187, No. 10 0021-9193/05/$08.00 0 doi:10.1128/jb.187.10.3369 3373.2005 Plasmid Partition System of the P1par Family from the pwr100 Virulence Plasmid

More information

Reading Assignments. A. Genes and the Synthesis of Polypeptides. Lecture Series 7 From DNA to Protein: Genotype to Phenotype

Reading Assignments. A. Genes and the Synthesis of Polypeptides. Lecture Series 7 From DNA to Protein: Genotype to Phenotype Lecture Series 7 From DNA to Protein: Genotype to Phenotype Reading Assignments Read Chapter 7 From DNA to Protein A. Genes and the Synthesis of Polypeptides Genes are made up of DNA and are expressed

More information

Lecture 18 June 2 nd, Gene Expression Regulation Mutations

Lecture 18 June 2 nd, Gene Expression Regulation Mutations Lecture 18 June 2 nd, 2016 Gene Expression Regulation Mutations From Gene to Protein Central Dogma Replication DNA RNA PROTEIN Transcription Translation RNA Viruses: genome is RNA Reverse Transcriptase

More information

2. What was the Avery-MacLeod-McCarty experiment and why was it significant? 3. What was the Hershey-Chase experiment and why was it significant?

2. What was the Avery-MacLeod-McCarty experiment and why was it significant? 3. What was the Hershey-Chase experiment and why was it significant? Name Date Period AP Exam Review Part 6: Molecular Genetics I. DNA and RNA Basics A. History of finding out what DNA really is 1. What was Griffith s experiment and why was it significant? 1 2. What was

More information

2. Yeast two-hybrid system

2. Yeast two-hybrid system 2. Yeast two-hybrid system I. Process workflow a. Mating of haploid two-hybrid strains on YPD plates b. Replica-plating of diploids on selective plates c. Two-hydrid experiment plating on selective plates

More information

Three types of RNA polymerase in eukaryotic nuclei

Three types of RNA polymerase in eukaryotic nuclei Three types of RNA polymerase in eukaryotic nuclei Type Location RNA synthesized Effect of α-amanitin I Nucleolus Pre-rRNA for 18,.8 and 8S rrnas Insensitive II Nucleoplasm Pre-mRNA, some snrnas Sensitive

More information

Genetic Variation: The genetic substrate for natural selection. Horizontal Gene Transfer. General Principles 10/2/17.

Genetic Variation: The genetic substrate for natural selection. Horizontal Gene Transfer. General Principles 10/2/17. Genetic Variation: The genetic substrate for natural selection What about organisms that do not have sexual reproduction? Horizontal Gene Transfer Dr. Carol E. Lee, University of Wisconsin In prokaryotes:

More information

Lecture 4: Transcription networks basic concepts

Lecture 4: Transcription networks basic concepts Lecture 4: Transcription networks basic concepts - Activators and repressors - Input functions; Logic input functions; Multidimensional input functions - Dynamics and response time 2.1 Introduction The

More information

Boolean models of gene regulatory networks. Matthew Macauley Math 4500: Mathematical Modeling Clemson University Spring 2016

Boolean models of gene regulatory networks. Matthew Macauley Math 4500: Mathematical Modeling Clemson University Spring 2016 Boolean models of gene regulatory networks Matthew Macauley Math 4500: Mathematical Modeling Clemson University Spring 2016 Gene expression Gene expression is a process that takes gene info and creates

More information

Chapter 16 Lecture. Concepts Of Genetics. Tenth Edition. Regulation of Gene Expression in Prokaryotes

Chapter 16 Lecture. Concepts Of Genetics. Tenth Edition. Regulation of Gene Expression in Prokaryotes Chapter 16 Lecture Concepts Of Genetics Tenth Edition Regulation of Gene Expression in Prokaryotes Chapter Contents 16.1 Prokaryotes Regulate Gene Expression in Response to Environmental Conditions 16.2

More information

Molecular Biology (9)

Molecular Biology (9) Molecular Biology (9) Translation Mamoun Ahram, PhD Second semester, 2017-2018 1 Resources This lecture Cooper, Ch. 8 (297-319) 2 General information Protein synthesis involves interactions between three

More information

(starvation). Description a. Predicted operon members b. Gene no. a. Relative change in expression (n-fold) mutant vs. wild type.

(starvation). Description a. Predicted operon members b. Gene no. a. Relative change in expression (n-fold) mutant vs. wild type. 1 Table S1. Genes whose expression differ in the phyr mutant 8402 and/or in the ecfg mutant 8404 compared with the wild type when grown to the mid-exponential phase (OD600 0.5-0.7) in rich medium (PSY)

More information

Bio 119 Bacterial Genomics 6/26/10

Bio 119 Bacterial Genomics 6/26/10 BACTERIAL GENOMICS Reading in BOM-12: Sec. 11.1 Genetic Map of the E. coli Chromosome p. 279 Sec. 13.2 Prokaryotic Genomes: Sizes and ORF Contents p. 344 Sec. 13.3 Prokaryotic Genomes: Bioinformatic Analysis

More information

Tetracycline Induces Stabilization of mrna in Bacillus subtilis

Tetracycline Induces Stabilization of mrna in Bacillus subtilis JOURNAL OF BACTERIOLOGY, Feb. 2002, p. 889 894 Vol. 184, No. 4 0021-9193/02/$04.00 0 DOI: 10.1128/JB.184.4.889 894.2002 Copyright 2002, American Society for Microbiology. All Rights Reserved. Tetracycline

More information

Characterization of the RpoS Status of Clinical Isolates of Salmonella enterica

Characterization of the RpoS Status of Clinical Isolates of Salmonella enterica APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Aug. 2003, p. 4352 4358 Vol. 69, No. 8 0099-2240/03/$08.00 0 DOI: 10.1128/AEM.69.8.4352 4358.2003 Copyright 2003, American Society for Microbiology. All Rights Reserved.

More information

Introduction. Summary. genetic strategies of survival and cellular adaptation to the environment used by Salmonella.

Introduction. Summary. genetic strategies of survival and cellular adaptation to the environment used by Salmonella. Molecular Microbiology(2014) doi:10.1111/mmi.12610 The Salmonella enterica serovar Typhi ltrr-ompr-ompc-ompf genes are involved in resistance to the bile salt sodium deoxycholate and in bacterial transformation

More information

Biology. Biology. Slide 1 of 26. End Show. Copyright Pearson Prentice Hall

Biology. Biology. Slide 1 of 26. End Show. Copyright Pearson Prentice Hall Biology Biology 1 of 26 Fruit fly chromosome 12-5 Gene Regulation Mouse chromosomes Fruit fly embryo Mouse embryo Adult fruit fly Adult mouse 2 of 26 Gene Regulation: An Example Gene Regulation: An Example

More information

A Gene (sleb) Encoding a Spore Cortex-Lytic Enzyme from Bacillus subtilis and Response of the Enzyme to

A Gene (sleb) Encoding a Spore Cortex-Lytic Enzyme from Bacillus subtilis and Response of the Enzyme to JOURNAL OF BACTERIOLOGY, Oct. 1996, p. 6059 6063 Vol. 178, No. 20 0021-9193/96/$04.00 0 Copyright 1996, American Society for Microbiology A Gene (sleb) Encoding a Spore Cortex-Lytic Enzyme from Bacillus

More information

Big Idea 3: Living systems store, retrieve, transmit and respond to information essential to life processes. Tuesday, December 27, 16

Big Idea 3: Living systems store, retrieve, transmit and respond to information essential to life processes. Tuesday, December 27, 16 Big Idea 3: Living systems store, retrieve, transmit and respond to information essential to life processes. Enduring understanding 3.B: Expression of genetic information involves cellular and molecular

More information

Revisiting the Central Dogma The role of Small RNA in Bacteria

Revisiting the Central Dogma The role of Small RNA in Bacteria Graduate Student Seminar Revisiting the Central Dogma The role of Small RNA in Bacteria The Chinese University of Hong Kong Supervisor : Prof. Margaret Ip Faculty of Medicine Student : Helen Ma (PhD student)

More information

Prokaryotic Regulation

Prokaryotic Regulation Prokaryotic Regulation Control of transcription initiation can be: Positive control increases transcription when activators bind DNA Negative control reduces transcription when repressors bind to DNA regulatory

More information

Isolation of Total RNA and mrna from Plant Tissues

Isolation of Total RNA and mrna from Plant Tissues Promega Notes Magazine Number 54, 1995, p.02 Isolation of Total RNA and mrna from Plant Tissues By: Isabel Murillo, Dora Raventos, Estelle Jaeck, Blanca San Segundo* Centro de Investigacion y Desarrollo

More information

E.Z.N.A. MicroElute Clean-up Kits Table of Contents

E.Z.N.A. MicroElute Clean-up Kits Table of Contents E.Z.N.A. MicroElute Clean-up Kits Table of Contents Introduction... 2 Kit Contents... 3 Preparing Reagents/Storage and Stability... 4 Guideline for Vacuum Manifold... 5 MicroElute Cycle-Pure - Spin Protocol...

More information

TrioMol Isolation Reagent

TrioMol Isolation Reagent TrioMol Isolation Reagent Technical Manual No. 0242 Version 06142007 I Description... 1 II Key Features... 1 III Storage..... 1 IV General Protocol Using Triomol Isolation Reagent 1 V Troubleshooting.

More information

56:198:582 Biological Networks Lecture 8

56:198:582 Biological Networks Lecture 8 56:198:582 Biological Networks Lecture 8 Course organization Two complementary approaches to modeling and understanding biological networks Constraint-based modeling (Palsson) System-wide Metabolism Steady-state

More information

TrioMol Isolation Reagent

TrioMol Isolation Reagent TrioMol Isolation Reagent Technical Manual No. 0242 Version 06142007 I Description... 1 II Key Features... 1 III Storage..... 1 IV General Protocol Using Triomol Isolation Reagent 1 V Troubleshooting.

More information

Translation and Operons

Translation and Operons Translation and Operons You Should Be Able To 1. Describe the three stages translation. including the movement of trna molecules through the ribosome. 2. Compare and contrast the roles of three different

More information

the noisy gene Biology of the Universidad Autónoma de Madrid Jan 2008 Juan F. Poyatos Spanish National Biotechnology Centre (CNB)

the noisy gene Biology of the Universidad Autónoma de Madrid Jan 2008 Juan F. Poyatos Spanish National Biotechnology Centre (CNB) Biology of the the noisy gene Universidad Autónoma de Madrid Jan 2008 Juan F. Poyatos Spanish National Biotechnology Centre (CNB) day III: noisy bacteria - Regulation of noise (B. subtilis) - Intrinsic/Extrinsic

More information

Gene Switches Teacher Information

Gene Switches Teacher Information STO-143 Gene Switches Teacher Information Summary Kit contains How do bacteria turn on and turn off genes? Students model the action of the lac operon that regulates the expression of genes essential for

More information

Chapter 12. Genes: Expression and Regulation

Chapter 12. Genes: Expression and Regulation Chapter 12 Genes: Expression and Regulation 1 DNA Transcription or RNA Synthesis produces three types of RNA trna carries amino acids during protein synthesis rrna component of ribosomes mrna directs protein

More information

4. Why not make all enzymes all the time (even if not needed)? Enzyme synthesis uses a lot of energy.

4. Why not make all enzymes all the time (even if not needed)? Enzyme synthesis uses a lot of energy. 1 C2005/F2401 '10-- Lecture 15 -- Last Edited: 11/02/10 01:58 PM Copyright 2010 Deborah Mowshowitz and Lawrence Chasin Department of Biological Sciences Columbia University New York, NY. Handouts: 15A

More information

Supplementary Figure 1

Supplementary Figure 1 Supplementary Figure 1 Supplementary Figure 1. HSP21 expression in 35S:HSP21 and hsp21 knockdown plants. (a) Since no T- DNA insertion line for HSP21 is available in the publicly available T-DNA collections,

More information

Biology 105/Summer Bacterial Genetics 8/12/ Bacterial Genomes p Gene Transfer Mechanisms in Bacteria p.

Biology 105/Summer Bacterial Genetics 8/12/ Bacterial Genomes p Gene Transfer Mechanisms in Bacteria p. READING: 14.2 Bacterial Genomes p. 481 14.3 Gene Transfer Mechanisms in Bacteria p. 486 Suggested Problems: 1, 7, 13, 14, 15, 20, 22 BACTERIAL GENETICS AND GENOMICS We still consider the E. coli genome

More information

REGULATION OF GENE EXPRESSION. Bacterial Genetics Lac and Trp Operon

REGULATION OF GENE EXPRESSION. Bacterial Genetics Lac and Trp Operon REGULATION OF GENE EXPRESSION Bacterial Genetics Lac and Trp Operon Levels of Metabolic Control The amount of cellular products can be controlled by regulating: Enzyme activity: alters protein function

More information

Introduction to Microbiology BIOL 220 Summer Session I, 1996 Exam # 1

Introduction to Microbiology BIOL 220 Summer Session I, 1996 Exam # 1 Name I. Multiple Choice (1 point each) Introduction to Microbiology BIOL 220 Summer Session I, 1996 Exam # 1 B 1. Which is possessed by eukaryotes but not by prokaryotes? A. Cell wall B. Distinct nucleus

More information

BME 5742 Biosystems Modeling and Control

BME 5742 Biosystems Modeling and Control BME 5742 Biosystems Modeling and Control Lecture 24 Unregulated Gene Expression Model Dr. Zvi Roth (FAU) 1 The genetic material inside a cell, encoded in its DNA, governs the response of a cell to various

More information

3.B.1 Gene Regulation. Gene regulation results in differential gene expression, leading to cell specialization.

3.B.1 Gene Regulation. Gene regulation results in differential gene expression, leading to cell specialization. 3.B.1 Gene Regulation Gene regulation results in differential gene expression, leading to cell specialization. We will focus on gene regulation in prokaryotes first. Gene regulation accounts for some of

More information

AP Bio Module 16: Bacterial Genetics and Operons, Student Learning Guide

AP Bio Module 16: Bacterial Genetics and Operons, Student Learning Guide Name: Period: Date: AP Bio Module 6: Bacterial Genetics and Operons, Student Learning Guide Getting started. Work in pairs (share a computer). Make sure that you log in for the first quiz so that you get

More information

GENE REGULATION AND PROBLEMS OF DEVELOPMENT

GENE REGULATION AND PROBLEMS OF DEVELOPMENT GENE REGULATION AND PROBLEMS OF DEVELOPMENT By Surinder Kaur DIET Ropar Surinder_1998@ yahoo.in Mob No 9988530775 GENE REGULATION Gene is a segment of DNA that codes for a unit of function (polypeptide,

More information

15.2 Prokaryotic Transcription *

15.2 Prokaryotic Transcription * OpenStax-CNX module: m52697 1 15.2 Prokaryotic Transcription * Shannon McDermott Based on Prokaryotic Transcription by OpenStax This work is produced by OpenStax-CNX and licensed under the Creative Commons

More information

The Gene The gene; Genes Genes Allele;

The Gene The gene; Genes Genes Allele; Gene, genetic code and regulation of the gene expression, Regulating the Metabolism, The Lac- Operon system,catabolic repression, The Trp Operon system: regulating the biosynthesis of the tryptophan. Mitesh

More information

UCLA igem 2014 REAGENTS LIST

UCLA igem 2014 REAGENTS LIST [The following are a list of REAGENTS that are necessary to perform the collection of recombinant silk protocols. Each section is subdivided into their respective categories, along with amounts and catalog

More information

Supplementary materials Quantitative assessment of ribosome drop-off in E. coli

Supplementary materials Quantitative assessment of ribosome drop-off in E. coli Supplementary materials Quantitative assessment of ribosome drop-off in E. coli Celine Sin, Davide Chiarugi, Angelo Valleriani 1 Downstream Analysis Supplementary Figure 1: Illustration of the core steps

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

A sensitive whole-cell biosensor for the simultaneous detection of a broad-spectrum of toxic heavy metal ions

A sensitive whole-cell biosensor for the simultaneous detection of a broad-spectrum of toxic heavy metal ions Electronic Supplementary Material (ESI) for ChemComm. This journal is The Royal Society of Chemistry 2015 SUPPORTING INFORMATION A sensitive whole-cell biosensor for the simultaneous detection of a broad-spectrum

More information

Gene regulation II Biochemistry 302. Bob Kelm February 28, 2005

Gene regulation II Biochemistry 302. Bob Kelm February 28, 2005 Gene regulation II Biochemistry 302 Bob Kelm February 28, 2005 Catabolic operons: Regulation by multiple signals targeting different TFs Catabolite repression: Activity of lac operon is restricted when

More information

REVIEW SESSION. Wednesday, September 15 5:30 PM SHANTZ 242 E

REVIEW SESSION. Wednesday, September 15 5:30 PM SHANTZ 242 E REVIEW SESSION Wednesday, September 15 5:30 PM SHANTZ 242 E Gene Regulation Gene Regulation Gene expression can be turned on, turned off, turned up or turned down! For example, as test time approaches,

More information

Regulation of Gene Expression

Regulation of Gene Expression Chapter 18 Regulation of Gene Expression Edited by Shawn Lester PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley

More information

Introduction to Molecular and Cell Biology

Introduction to Molecular and Cell Biology Introduction to Molecular and Cell Biology Molecular biology seeks to understand the physical and chemical basis of life. and helps us answer the following? What is the molecular basis of disease? What

More information

RNA-Solv Reagent. R preps R preps R preps

RNA-Solv Reagent. R preps R preps R preps RNA-Solv Reagent R6830-00 5 preps R6830-01 100 preps R6830-02 200 preps March 2013 RNA-Solv Reagent Table of Contents Introduction...2 Kit Contents/Storage and Stability...3 Before Beginning...4 Analysis

More information

RNA-Solv Reagent. R preps R preps R preps

RNA-Solv Reagent. R preps R preps R preps RNA-Solv Reagent R6830-00 5 preps R6830-01 100 preps R6830-02 200 preps March 2013 RNA-Solv Reagent Table of Contents Introduction...2 Kit Contents/Storage and Stability...3 Before Beginning...4 Analysis

More information

BACTERIAL PHYSIOLOGY SMALL GROUP. Monday, August 25, :00pm. Faculty: Adam Driks, Ph.D. Alan Wolfe, Ph.D.

BACTERIAL PHYSIOLOGY SMALL GROUP. Monday, August 25, :00pm. Faculty: Adam Driks, Ph.D. Alan Wolfe, Ph.D. BACTERIAL PHYSIOLOGY SMALL GROUP Monday, August 25, 2014 1:00pm Faculty: Adam Driks, Ph.D. Alan Wolfe, Ph.D. Learning Goal To understand how bacterial physiology applies to the diagnosis and treatment

More information

Quorum sensing in Escherichia coli and Salmonella typhimurium

Quorum sensing in Escherichia coli and Salmonella typhimurium Proc. Natl. Acad. Sci. USA Vol. 95, pp. 7046 7050, June 1998 Microbiology Quorum sensing in Escherichia coli and Salmonella typhimurium MICHAEL G. SURETTE* AND BONNIE L. BASSLER *Department of Microbiology

More information

Sequence, Regulation, and Functions of fis in Salmonella typhimurium

Sequence, Regulation, and Functions of fis in Salmonella typhimurium JOURNAL OF BACTERIOLOGY, Apr. 1995, p. 2021 2032 Vol. 177, No. 8 0021-9193/95/$04.00 0 Copyright 1995, American Society for Microbiology Sequence, Regulation, and Functions of fis in Salmonella typhimurium

More information

2012 Univ Aguilera Lecture. Introduction to Molecular and Cell Biology

2012 Univ Aguilera Lecture. Introduction to Molecular and Cell Biology 2012 Univ. 1301 Aguilera Lecture Introduction to Molecular and Cell Biology Molecular biology seeks to understand the physical and chemical basis of life. and helps us answer the following? What is the

More information

Flow of Genetic Information

Flow of Genetic Information presents Flow of Genetic Information A Montagud E Navarro P Fernández de Córdoba JF Urchueguía Elements Nucleic acid DNA RNA building block structure & organization genome building block types Amino acid

More information

UNIVERSITY OF YORK. BA, BSc, and MSc Degree Examinations Department : BIOLOGY. Title of Exam: Molecular microbiology

UNIVERSITY OF YORK. BA, BSc, and MSc Degree Examinations Department : BIOLOGY. Title of Exam: Molecular microbiology Examination Candidate Number: Desk Number: UNIVERSITY OF YORK BA, BSc, and MSc Degree Examinations 2017-8 Department : BIOLOGY Title of Exam: Molecular microbiology Time Allowed: 1 hour 30 minutes Marking

More information

Chapter 17 The Mechanism of Translation I: Initiation

Chapter 17 The Mechanism of Translation I: Initiation Chapter 17 The Mechanism of Translation I: Initiation Focus only on experiments discussed in class. Completely skip Figure 17.36 Read pg 521-527 up to the sentence that begins "In 1969, Joan Steitz..."

More information

Integration and amplification of the Bacillus sp cellulase gene in the Bacillus subtilis 168 chromosome

Integration and amplification of the Bacillus sp cellulase gene in the Bacillus subtilis 168 chromosome J. Gen. Appl. Microbiol., 44, 107 111 (1998) Short Communication Integration and amplification of the Bacillus sp. 79-23 cellulase gene in the Bacillus subtilis 168 chromosome Kyung Hwa Jung, Dae-Hee Lee,

More information

THE ROLE OF THE SIGMA FACTOR cys (KatF) BACTERIAL GLOBAL REGULATION

THE ROLE OF THE SIGMA FACTOR cys (KatF) BACTERIAL GLOBAL REGULATION Annu. Rev. Microbiol. 1994. 48:53-80 Copyright 1994 by Annual Reviews Inc. All rights reserved THE ROLE OF THE SIGMA FACTOR cys (KatF) BACTERIAL GLOBAL REGULATION Peter C. Loewen Department of Microbiology,

More information

12-5 Gene Regulation

12-5 Gene Regulation 12-5 Gene Regulation Fruit fly chromosome 12-5 Gene Regulation Mouse chromosomes Fruit fly embryo Mouse embryo Adult fruit fly Adult mouse 1 of 26 12-5 Gene Regulation Gene Regulation: An Example Gene

More information

Protocol for 2D-E. Protein Extraction

Protocol for 2D-E. Protein Extraction Protocol for 2D-E Protein Extraction Reagent 1 inside the ReadyPrep TM Sequential Extraction kit (in powder form) 50ml of deionized water is used to dissolve all the Reagent 1. The solution is known as

More information

Prokaryotic Gene Expression (Learning Objectives)

Prokaryotic Gene Expression (Learning Objectives) Prokaryotic Gene Expression (Learning Objectives) 1. Learn how bacteria respond to changes of metabolites in their environment: short-term and longer-term. 2. Compare and contrast transcriptional control

More information

Chapter 15 Active Reading Guide Regulation of Gene Expression

Chapter 15 Active Reading Guide Regulation of Gene Expression Name: AP Biology Mr. Croft Chapter 15 Active Reading Guide Regulation of Gene Expression The overview for Chapter 15 introduces the idea that while all cells of an organism have all genes in the genome,

More information

Lesson Overview. Gene Regulation and Expression. Lesson Overview Gene Regulation and Expression

Lesson Overview. Gene Regulation and Expression. Lesson Overview Gene Regulation and Expression 13.4 Gene Regulation and Expression THINK ABOUT IT Think of a library filled with how-to books. Would you ever need to use all of those books at the same time? Of course not. Now picture a tiny bacterium

More information

Molecular Biology, Genetic Engineering & Biotechnology Operons ???

Molecular Biology, Genetic Engineering & Biotechnology Operons ??? 1 Description of Module Subject Name?? Paper Name Module Name/Title XV- 04: 2 OPERONS OBJECTIVES To understand how gene is expressed and regulated in prokaryotic cell To understand the regulation of Lactose

More information

Multiple Choice Review- Eukaryotic Gene Expression

Multiple Choice Review- Eukaryotic Gene Expression Multiple Choice Review- Eukaryotic Gene Expression 1. Which of the following is the Central Dogma of cell biology? a. DNA Nucleic Acid Protein Amino Acid b. Prokaryote Bacteria - Eukaryote c. Atom Molecule

More information