Research Survey of human mitochondrial diseases using new genomic/proteomic tools

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1 Research Survey of human mitochondrial diseases using new genomic/proteomic tools 6D =I 2 =IJAHAH 6A F A 5 EJD V JJ+ DH W )@@HAIIAI *E A?K =H- CE AAHE C4AIA=H?D+A A J B2D=H =? CO * IJ 7 ELAHIEJO5?D B A@E?E A & - +? H@5JHAAJ * IJ ) & 75) V *E A?K =H- CE AAHE C4AIA=H?D+A JAH * IJ 7 ELAHIEJO+ ACA B- CE AAHE C!$ +K E CJ 5JHAAJ * IJ ) # 75) W *E A?K =H- CE AAHE C4AIA=H?D+A A J B+DA EIJHO * IJ 7 ELAHIEJO #'+ MA= JD)LA KA * IJ ) # 75) + 5? JJ+ DH - =E DH(@=HME >K A@K Published: 1 June 2001 Genome Biology 2001, 2(6):research The electronic version of this article is the complete one and can be found online at Plasterer et al., licensee BioMed Central Ltd (Print ISSN ; Online ISSN ) Abstract Background: We have constructed Bayesian prior-based, amino-acid sequence profiles for the complete yeast mitochondrial proteome and used them to develop methods for identifying and characterizing the context of protein mutations that give rise to human mitochondrial diseases. (Bayesian priors are conditional probabilities that allow the estimation of the likelihood of an event - such as an amino-acid substitution - on the basis of prior occurrences of similar events.) Because these profiles can assemble sets of taxonomically very diverse homologs, they enable identification of the structurally and/or functionally most critical sites in the proteins on the basis of the degree of sequence conservation. These profiles can also find distant homologs with determined threedimensional structures that aid in the interpretation of effects of missense mutations. Results: This survey reports such an analysis for 15 missense mutations, one insertion and three deletions involved in Leber s hereditary optic neuropathy, Leigh syndrome, mitochondrial neurogastrointestinal encephalomyopathy, Mohr-Tranebjaerg syndrome, iron-storage disorders related to Friedreich s ataxia, and hereditary spastic paraplegia. We present structural correlations for seven of the mutations. Conclusions: Of the 19 mutations analyzed, 14 involved changes in very highly conserved parts of the affected proteins. Five out of seven structural correlations provided reasonable explanations for the malfunctions. As additional genetic and structural data become available, this methodology can be extended. It has the potential for assisting in identifying new disease-related genes. Furthermore, profiles with structural homologs can generate mechanistic hypotheses concerning the underlying biochemical processes - and why they break down as a result of the mutations. Background )IMA LAE J JDAF IJ CA AAH= >E E B H =JE?IJ I FH LE@A = F MAHBK A= I B HC= E E C E JACH=JE C E B H =JE HA =JA@J DAHA@EJ=HO@EIA=IAI 9AFHAIA JDAHA =FH J JOFAIJK@O BJDEI=FFH =?D 7IE C=@=J=>=IA B= Received: 8 February 2001 Revised: 3 April 2001 Accepted: 26 April 2001 E@A JEBE=> AFH JAE IJD=J? JHE>KJAJ H >E IO JDAIEI BOA=IJ5=??D=H O?AI?AHALEIE=A MAD=LACA AH=JA@= E>H=HO BFH JAE FH BE AI JD=J A => AIKIJ E@A JEBOD CIE =ME@AH= CA BCA AI E? K@E C DK = )I = HAIK J MA D=LA =L=E => A IAJI B comment reviews reports deposited research refereed research interactions information

2 2 Genome Biology Vol 2 No 6 2 =IJAHAHAJ= DECD O =??KH=JA = E =?E@ IAGKA?A = EC A JI LAH JDA? IAHLA@ HACE I JD=J? J JDAIA FH BE AI *O =FFE C M DK HA =JA@ KJ=JE I J JDAIA = EC A JI MA?= E LAIJEC=JA JDA HA =JE IDEFI J IAGKA?A? IAHL=JE J IAGKA?A L=HE=JE I 1 JDA?=IAI MDAHA A H HA B JDA E@A JEBEA@ D CI D=I E A@IJHK?JKHA JDAIA KJ=JE I?= >AE JAHFHAJA@E IJHK?JKH= JAH I = ME A?D= EIJE?E BAHA?AI 9AD=LAKIA@FH BE A= = OIEI>=IA@ *=OAIE= FHE = FH >=>E EJEAIJD=J= MJDAAIJE =JE BJDA E A E B= ALA J JDA>=IEI BFHE H??KHHA?AI BIE E =H ALA JI J = A JDEI E>H=HO B IAGKA?A FH BE AI 6DA IJHA CJD B FHE H >=IA@ FH BE A = = OIEI EAI E EJI =>E EJO J?=FJKHA D C KI FH =E I =I HA =JA@ > A?JI -=?D@ =E EIHAFHAIA JA@=I= =JHEN B= E =?E@FH > =>E EJEAI HA FHA?EIA O C E A L= KAI MDAHA A=?D F IEJE E JDA@ =E D=I= AIJE =JA@FH >=>E EJO B>AE C??KFEA@ >O = O F=HJE?K =H = E =?E@ 6DA IE E =HEJEAI B HAIE@KA? IAHL=JE >AJMAA D C KI IAGKA?AIHALA= F IEJE I?HEJE?= B HFH JAE BK?JE ) FH BE A K JEF A = EC A =OI E KJ=> AF IEJE I FDOIE??DA E?= O? IAHLA@F IEJE I DECD O L=HE=> A F IEJE I 6DA AN= F AI FHAIA JA@ E JDEI F=FAH ID M D M IK?D = EC A JI FH LE@A E IECDJ E J DK = F=JD CEAI FH JAE I=HA= =JJH=?JELAIK>IAJ BJDA?A K =HFH JA AJ = = O A>A?=KIAJDAOFAHB H = K >AH B? HHA =JA@ BK?JE I E JAH=?J ANJA IELA O MEJD A = JDAH 6DAEHFH HHAB A?J= E JACH=JA@ IOIJA B@EBBAHA J KJ=JE =?D= CAI?= >A A= E CBK O?H II? F=HA@ 6DAIKHLAO BJDEI E E= JKHAFH JA AID = O BJDABA=JKHAIJD=J?D=H =?JAHE A JDA =HCAH? F AJA FH JA AI B AK =HO JE??A JOFAI F=JD CEAI = I FHAIA J K EGKA O? F ANAL KJE AJE?BA=JKHAI=I=HAIK J BJDAEH HECE MEJDE HC= A AI@AHELA@BH =?EA JIO >E JDA IJHE?J O =JAH = E DAHEJ=?A F=JJAH B MA@ >O = E F HJ= JIK>IAJ BJDAHA AL= JCA AI Mitochondrial genome overview 6DA CA AEJIA B CA AI 6DA =HCAIJ CA LAHA@ BJDAFH JEIJ4A? E =I = AHE?= H '%CA JAE 4 )IE = IF= B $'!" >=IA F=EHI 0K = )EI K?DI = AH C!%CA JAE I H4 J4 )I LAH$ #$'>=IAF=EHI! ) JAE I=HA@EHA?J OE L LA@E NE@=JELA FD IFD HO =JE E? K@A? F A JI B? F AN 1 CA =IA IK>K EJI,,,!,",",#,$? F AN111?OJ?DH A>? F AN 18?OJ?DH A NE@=IA IK>K EJI F AN8 )62=IAIK>K " ) JDAH DK = CA AI C FH JAE I J J= AIJE =JA@=J=H # =HAJH= I?HE>A@E JDA K? AKI JH= I =JA@ E JDA?OJ F =I JDAEH E F HJA@ E J 6DA E JAHF =O >AJMAA HC= A K? A=HCA AI=?? K JIB H= =HCAF=HJ B JDA@ELAHIEJOE F=JD CEAI -=?D DK =?A? J=E I K JEF A = E?= O E JAH? A?JA@ E =? F AN HAJE?K =H AJM H $ % A=?D =O? J=E JA H HA ) J, ) A?K AI 7IK= O =? FEAI B J, ) =HA E@A JE?= = IJ=JA M =I D F =I O??=IE = O D MALAH J, ) KJ=JE I??KH JDAHA =HEIA JM H HA F FK =JE I B J, ) = IJ=JA?= A@ DAJAH F =I O " 1 B=?J DAJAH F =I E? J, ) KCDJJ >A HA =JELA O?? IE@AHE CJD=JDK = J, ) KJ=JAI JE AI B=IJAH JD= K? A=H, ) =I = HAIK J B E =@A GK=JAFH BHA=@E C>O )F O AH=IAI " E EJA@ J, )HAF=EH?=F=>E EJO 6DEIANFA?J=JE EIJ I AANJA J> H A KJ>OJDAHA =JELAFH E A?A H@AHI=HEIE CBH KJ=JE IE JDA J, ) = JD KCD EJ EI = I E F HJ= J J JA JD=J IK?D KJ=JE I >AE C? F=H=JELA OA=IOJ E@A JEBO>OIAGKA?E C ME =J KH= OD=LA>AA = CJDABEHIJJ >A?D=H=?JAHE A@ Disease classification 5?D=FEH=D=I@ALEIA@=? =IIEBE?=JE I?DA AB H & >=IA@FHE =HE O MDAJDAH H JJDA=BBA?JA@ CA A O E L LA@ E NE@=JELA FD IFD HO = J, ) H K? A=H, ) )FHE =HO@ABA?JE NE@=JELAFD IFD HO AI? =II 1,EIJE?J F=JD CEAI =O LAH =F HAJD= A? =II B HAN= F A AIAA>A M 5K>? =II 1=E? K@AI@EIA=IAI=HEIE CBH KJ=JE IE J, )CA AI C IK>K EJI B FH JAE I E L LA@ E NE@=JELA FD I FD HO =JE J4 ) CA AI H4 ) CA AI 6DEI IK>? =II D=I JDHAA HA C JDA =JKHA B JDA OE C KJ=JE I E =HCA I?= A J, AJE E?=JE I EE F E J KJ=JE I I = HA=HH= CA A JI E FH C J, ) HACE I EEE I = I?= A J, ) KJ=JE I E J4 )CA AI & 1 H@AHB H=? =II1=F=JD CO J FHAIA JEJIA B JDA J, ) KJ=JE KIJ??KHE =IEC EB E?= J BH=?JE B JDA DAJAH F =I E? J, ) F FK =JE =I DECD=I$B H J, )@A AJE I ' 1= KFJ '#B HJ4 ) KJ=JE I1= EEE + KJ=JE IE = O K? A=H CA CFH JAE IK>K EJIE L LA@E NE@=JELAFD I FD HO =JE # 6DAIA KJ=JE I?=??KH E AN I H E JH I=IMA =IFH JAHI + =II H@AHI IJA E NE@=JELA FD IFD HO =JE + =II 11= CA AJE? F=JD CEAI=HA?D=H=?JAHE A@>O KJ=JE IE K? A=H FH JAE CA AI MD IA =HA E F HJA@ E J JDA >KJ =HA J IK>K EJI B JDA NE@=JELA

3 FD IFD HO =JE =FF=H=JKI 6DAHA =HA B KH IK>JOFAI E J, )=> H = EJO@KAJ KJ=JE IE K? A=HCA AI=BBA?J E C J, )JH= I?HEFJE JH= I =JE HHAF E?=JE EE@EHA?J J, =CA E J, ) HAF=EH NE@=JELA FD IFD HO =JE IK>K EJ E F HJ NE@=JELA FD IFD HO =JE IK>K EJ =IIA > O & 6OFA 11> F=JD CEAI=HEIABH CA CA KIJ NE I Results 6=> A IK =HE AI JDA AN= F >A M 6DAO E? K@A =?=IAI B H MDE?D IKBBE?EA J O IFA?EBE? KJ=JE = E B H =JE ANEIJIJ A => AABBA?JELAKIA BJDAFH BE AJ Primary mutational disorders of oxidative phosphorylation (class I) Leber s hereditary optic neuropathy A>AH\I DAHA@EJ=HO FJE? AKH F=JDO 0 JDA IJ??=KIA B = A=@ AI?A J> AII EI=JJHE>KJA@J KJ=JE IE J, )CA CIK>K EJI B? F AN1 CA =IA, = JAH =JELA O JAH A@ ),0 + 3 HA@K?J=IA 6DA IJBHAGKA J OA? K JAHA@ KJ=JE # B?=IAI = C -KH FA= I '# = C )IE= I EI /%%&) E," )HC!" 0EI )@@EJE = O /!"$) ) =# 6DH E, > JD 6""&"+ AJ$" 8= =% 8= E,$H= = CJDA JDAH FHE =HO 0 =II?E=JA@ KJ=JE I " Table 1 Selected mutations associated with human mitochondrial disorders )IIAA E ECKHA JDA=HCE E AHAIE@KA=JF IEJE!"E JDADK = IAGKA?AB H," 7" 07 ) MDE?D? H J F IEJE! B JDA FH BE A EI =>I KJA O? IAHLA@ =?H II /H= F IEJELA 4L!#% /H= AC=JELA -+ %% =H?D=A= 2)*"! AK =HO JE? J=N= 7" 07 ) =@" 24) 6DA F=JD CA E? KJ= JE B =HCE E A J DEIJE@E A =J JDEI F IEJE HAFHAIA JI O IEC EBE?= E IAGKA?A IK>IJEJKJE C = E E@= ACH KFB H=CK= E@E CH KF 6DAJM = E =?E@IE@A?D=E I@EBBAHE ID=FA DO@H CA C?=F=>E B F IEJELA?D=HCA =HCE E A = M=OI >AE C F IE JELA O?D=HCA@ =J FDOIE CE?= F0 DEIJE@E A O D=LE C = F IEJELA?D=HCA=> KJD= BJDAJE A 6DA? EIIA IA IK>IJEJKJE E, JD=J A=@I J 0 ) =# AI JD=LA=I >LE KI= ANF = = JE B HEJIABBA?J 1 IFA?JE BJDAIAJ B= EC A@IAGKA?AI ECKHA ID MI JD=J JDEI F IEJE J AH=JAI C O?E A AJDE E A=IMA =I= = E A 5K>IJEJKJE C=JDHA E AB H JDA = = E A E JDA DK = IAGKA?A =@@I = >AJ= >H=?DA@ = E =?E@?=F=> A C?= JAHJE=HO IJHK?JKHA H F IIE> O E JAHIK>K EJ E JAH=?JE I 6DA DO@H NO CH KF B JDA JDHA E A =O = I B H DO@H CA AECD> HE C= E =?E@HAIE@KAII =IJ =@@J JDEI F JA KHJDAH IJHK?JKH= IJK@O B? F AN 1 ME >A HAGKEHA@ J ANF =E D M JDEI KJ=JE? JHE>KJAIJ 0 Disorder Affected protein DNA change Protein change Evolutionary conservation Structural environment LHON ND4 G11778A R340H Absolute N/A ND1 G3460A A52T Slight N/A ND6 T14484C M64V Moderate N/A G14459A A72V High N/A Leigh syndrome ATP6 T8993G L156R Absolute Subunit interface PDHA1 C892G R263G Slight Near active site SURF1 G385A G124E Absolute N/A T751C I246T High Predicted β-sheet SDHA C1684T R554W High Surface-exposed MNGIE TP G1419A G145R High Near active site G1443A G153S Absolute Near active site A2744G K222S Absolute Near active site A3371 E289A Absolute Not in active site Deafness-dystonia DDP1 T151del (1 nt) Truncation - see text High N/A A183del (10 nt) Truncation - see text High NA C198G C66W Absolute N/A Iron-storage ABCB7 ATT ATG I400M High Predicted tight turn HSP Paraplegin 784del (2 nt) 60% truncated High N/A 2228ins (1 nt = A) 7.2% Truncated Moderate N/A ABCB7, ATP-binding cassette, subfamily B, member 7; ATP4, adenosine triphosphate synthase subunit 4 (ATP6 subunit 6); DDP1, deafness-dystonia peptide 1, del, deletion; HSP, hereditary spastic paraplegia; ins, insertion; LHON, Leber s hereditary optic neuropathy; MNGIE, mitochondrial neurogastrointestinal encephalomyopathy; N/A, not available; ND, NADH dehydrogenase; ND1 NDn, ND subunits 1 n; nt, nucleotide; PDHA1, pyruvate dehydrogenase subunit E1α; SDHA, succinate dehydrogenase subunit A; SURF1, surfeit locus protein 1; TP, thymidine phosphorylase. comment reviews reports deposited research refereed research interactions information

4 4 Genome Biology Vol 2 No 6 2 =IJAHAHAJ= (a) Rv3157 EC2277 PAB1402 NU4M_HUMAN nad4_pra (b) PATTERN hhxfxfaxhh axxhxaffff jxxfxxxxir XfXXXXGaXs XfXfXXXXXf Rv3157 GSTLYMLNHG LSTAAVFLIA GFLIARRGSR SIADYGGVQK VAPILAGTFM EC2277 GAVIQMIAHG LSAAGLFILC GQLYERIHTR DMRMMGGLWS KMKWLPALSL PAB1402 AALFHLINHA IAKALLFLAV GVFIHVAGSR NIDDLAGLGR KMPITTFSLA NU4M_HUMAN GAVILMIAHG LTSSLLFCLA NSNYERTHSR IMILSQGLQT LLPLMAFWWL nad4_pra GSILLMLSHG IVSSALFLCI GVLYDRHKTR LLKYYSGVVQ TMPIFATLFM Conserved Arg340 His Figure 1 Profile-induced multiple alignment of NADH dehydrogenase, subunit 4. (a) Protein domain diagram. Profile-aligned regions (in red) set the boundaries for sequence domains. Gaps are indicated by gray interruptions in the red bars. Coordinates in the domain diagram are based on the aligned set of sequences. Amino-acid position is given on the scale above. (b) The zoomed-in aligned region marked by the yellow box on the domain diagram (see Additional data files). The alignment is colored according to amino-acid class assignments, with red indicating identity. Coordinates in the aligment are taken from the position in the profile. For more details see [48,53]. Sequences are obtained from Mycobacterium tuberculosis (Rv3157), Escherichia coli (EC2277), Pyrococcus abyssi (PAB1402), Homo sapiens mitochondrion (NU4M_HUMAN) and Reclinomonas americana mitochondrion (nad4_pra). 6DA JM? F=JD CA E? KJ=JE I E,$ AJ$" 8= =% 8= A=@J = B H B 0 HAIFA?JELA O )I O? >=?JAHEK JK>AH?K IEI = HA=@O KIAI = L= E A E F IEJE $" ECKHA! EJ A JD=J JDA AJ$" 8= IK>IJEJKJE ID = AII FDA JOFA 1 F IEJE % O = = E AJDE E AD=LA>AA IAA = CJDAE@A JEBEA@ D CI )I IK?D JDA E B L= E A =@@I = β >H=?DA@ = E =?E@ =J =? IAHLA@ β >H=?DA@ DO@H FD >E? F IEJE )@@EJE = O JDA JM AK =HO JAI :A FKI =ALEI 0 I=FEA I D=LA? IAHLA@ JDA = = E A MDAHA=I JDA J O HA =JA@ IFA?EAI =? IAHLA= AJDE E A 9DAHA=I O A BJDA CA =IAIK>K EJ KJ=JE I??KHI=J= =>I KJA O? IAHLA@ F IEJE JDAHA=HAHA=I => AANF = =JE IB HD MJDA JDAH KJ=JE I? = EBAIJJDAEH E A OF=JD CO Leigh syndrome AECD A = I M =I IK>=?KJA A?H JE E C A?AFD= OA F=JDOEI= JDAH? J, ) H@AH BHAGKA J O =II?E=JA@ MEJD?OJ?DH A NE@=IA + :@ABE?EA?O! JD HA =JA@ KJ=JE I BJDA J, ) :IK>K EJID=LA>AA HAF HJA@ ) IE C A6 J /JH= ILAHIE =J J, )F IEJE & ''!?D= CAI AK?E A#$ B)62IO JD=IAIK>K EJ$J =HCE E A AK#$ )HC " ECKHA "= MAH? FO K >AHI BJDEI KJ=JE %=HA=II?E=JA@ MEJD AKH F=JDO =J=NE= HAJE EJEI FEC A J I= )42 MDAHA=IDECD? FO K >AHI 'CELAHEIAJ A # KJ=JE C JDA? IAHLA@ AK?E A J =HCE E A =J F IEJE #$ EI C = γ >H=?DA@ = EFD=JE? HAIE@KA MEJD = >=IE? CK= E@E CH KF = = H?DA E?= FHAIK => O IJHK?JKH= IK>IJEJKJE 1 => AIAA ECKHA A=H O JDA AO?=JE B JDEI HAIE@KA =J JDA FH JAE FH JAE E JAHB=?A BJM BJDAIK>K EJI BJDA? F A J B? F AN8)62IO JD=IA KJ=JE IB =J A=IJJM K? A=HCA AI= I? HHA =JA MEJD AECD A A B H = IK>K EJ B JDA CA =IA? F AN A B H IKHBAEJ?KI FH JAE

5 Rv3152 EC2282 AF1831 nad1_pra NU1M_HUMAN PATTERN naxhxfqxrx GPXXVhggXX GXaQXfADXf nffxrexfxx XXXsXXfdXX Rv3152 KLLGRMQLRP GPNRVG--PK GALQSLADGI KLALKESITP GGIDRFVYFV EC2282 RLLGLFQNRY GPNRVG--WG GSLQLVADMI KMFFKEDWIP KFSDRVIFTL AF1831 KLTARIQWRV GPLEVARPIR GAIQALADGI RYFFQEAIVH REAHRPYFVQ nad1_pra KVIAAMQQRK GPNVVG--VF GLLQPLADGL KLLLKETIVP TRANSAIFIL NU1M_HUMAN KILGYMQLRK GPNVVG--PY GLLQPFADAM KLFTKEPLKP ATSTITLYIT Non-conserved Ala52 Figure 2 Domain diagram and partial alignment for NADH dehydrogenase, subunit 1 (ND1). The column indicated by the arrow at the bottom is position 52 of NU1M_HUMAN. Sequences are from M. tuberculosis (Rv3152), E. coli (EC2282), Archaeoglobus fulgidus (AF1831), H. sapiens mitochondrion (NU1M_HUMAN) and R. americana mitochondrion (nad1_pra). Colors are as in Figure MDE?DEIE L LA@E JDA=IIA > O B?OJ?DH A? NE@=IA )IJDAIA=HA J NE@=JELAFD IFD HO =JE FH JAE I JDA KJ=JE IGK= EBO=I? =II11@EI H@AHI ) EIIA IA KJ= JE )HC $! / OE JDA-α IK>K EJ BFOHKL=JA@ADO@H CA =IA 2,0) D=I >AA =II?E=JA@ MEJD AECD A ECKHA # 6DEI KJ=JE IAA I J =BBA?J =IIA > O B JDA -α -β DAJAH JAJH= AH $ 6DA CA A\I?=JE JDA :?DH I A? F E?=JAI EJI ANFHAIIE F=JJAH E BA = AI =I=HAIK J F=JJAH B:E =?JEL=JE % 9DAHA=I OJDADK = IAGKA?AKIAI=HCE E A=JJDEIF IE JE = JDAH J=N= KIA = =HCA DO@H FD >E? = E =?E@ AEJDAH JOH IE A H AK?E A JA JD=J ALA = =HCE E A IE@A?D=E D=I=IK>IJ= JE= DO@H FD >E?IAC A J>A=HE CEJIJAH E = CK= E@E CH KF 5K>IJEJKJE CJDAI = JKH B H E C C O?E A HAIE@KA? D=LA = IEC EBE?= J E F=?J FH FAH C B JDEI IK>K EJ )I ID M E ECKHA #> )HC $! EI?=JA@GKEJA? IAJ JDA=?JELAIEJA BJDAA O A =HACE BJDAIJHK?JKHAMDAHAALA I = FAHJKH>=JE I? =HCAABBA?JI =?JELEJO 6DACA AB =OI KJ=JE I/ O " / 1 A "$ 6DHJD=J?= = I A=@J A & ' Thr ) K >AH AJE I IAA E I =I MA 6DA / O " / =>I KJA O? IAHLA@ C O?E AJD=J IJFH >=> OF=HJE?EF=JAIE =JKH ECKHA $ 6DA 1 A "$ 6DH KJ=JE??KHI E FH >=> HKFJI = FHA@E?JA@ β IDAAJ >A EALA@ J >A FHAIA J E JDEI FH JAE BH = DECDAHAK =HO JAI 1J??KHIJ M=H@JDA?=H > NO JAH E KI B JDA DK = FH JAE EI JDA HACE? LAHA@>OJDAFH BE A =HAB A?JE BIAGKA?A@ELAH CA?A>AJMAA AK =HO =HO JAIE JDEIHACE KJ=JE I CELE C HEIA J AECD A D=LA = I E JDA B =L FH JAE IK>K EJ F H 5,0) B JDA IK??E CA =IA? F AN 5,0 6DA KJ= JLAHIE +$&"6 )HC##" 6HF ECKHA %= B5,0) D=I = H = E B H = =JA >KJ EI K?D HA IA M HACK =JE >O N= =?AJ=JA )) KJ=JE CJDA? IAHLA@=HCE E AHAIE@KA=JF IEJE ##"J = JHOFJ FD=?=KIAI= II B=F =?A A J MEJD= K?D =HCAH=H =JE?CH KF 1JEI J=FF=HA JBH JDA?=JE BJDEIHAIE@KAE JDAIJHK?JKHA ECKHA %>MDO JDEI?D= CAID ABBA?J BK?JE 1J EAI JDA IKHB=?A =J =? IE@AH=> BH JDA =?JELA IEJA comment reviews reports deposited research refereed research interactions information

6 6 Genome Biology Vol 2 No 6 2 =IJAHAHAJ= nad6_pra NU6M_HUMAN Rv3154 EC2280 NU6M_XENLA PATTERN fhffxffayx GhfffaFXdX XfffXXXXXo XXXsXXXXXX XXXaXXXfXX nad6_pra IAMIFIMVYV GAIAVLFLFV VMMLNVRLVQ FNVNMLRYLP LGGVIGLIFL NU6M_HUMAN MGLMVFLIYL GGMMVVFGYT TAMAIEEYPE AWGSGVEVLV SVLVGLAMEV Rv3154 LGVVQVVVYT GAVMMLFLFV LMLIGVDSAE SLKETLRGQR VAAVLTGVGF EC2280 AGALEIIVYA GAIMVLFVFV VMMLNLGGSE IEQERQWLKP QVWIGPAIL S NU6M_XENLA LSIVLFLIYL GGMLVVFAYS AARA-KPYPE AWGS--WSVV FYVLVYLIGV Semi-conserved Met64 Val Eukaryotic-conserved Ala72 Val Figure 3 Domain diagram and partial alignment for NADH dehydrogenase, subunit 6 (ND6). The columns indicated with arrows at the bottom are positions 64 and 72 of NU6M_HUMAN. Sequences are from M. tuberculosis (Rv3154), Escherichia coli (EC2280), X. laevis mitochondrion (NUAM6_XENLA), H. sapiens mitochondrion (NU6M_HUMAN) and R. americana mitochondrion (nad6_pra). Colors are as in Figure 1. AI JD=LA= O=FF=HA JH AE IK>K EJ IK>K EJE JAH =?JE I 1 B=?J D MALAH JDADECD@ACHAA BIAGKA?A? IAH L=JE LAHJDEIA JEHAHACE ECKHA %=IKCCAIJIJD=J5,0) EIB=EH OE J AH= J B KJ=JE IDAHA 2H FAHE JAH=?JE MEJD JDA EFE@>E =OAH =OF=HJ OANF =E JDAFDA A Secondary mutational disorders in oxidative phosphorylation (class II) Mitochondrial neurogastrointestinal encephalomyopathy + =II H@AHI J KJ=JE I E K? A=H FH JAE CA AI AKH C=IJH E JAIJE = A?AFD= O F=JDO /1- EI?D=H=?JAH E A@ >O FJ IEI FH CHAIIELA ANJAH = FDJD= F ACE= C=IJH E JAIJE JE EJO JDE D=>EJKI FAHEFDAH= AKH F=JDO O F=JDO AK A?AFD= K JEF A J, )@A AJE I H J, )@AF AJE H > JD 1J EI =? =II 11 J, H@AH 1J EI >A EALA@JD=JJDAF=JD CA E? A?D= EI HA =JAIJ =>AHH= J JDO E@E A AJ=> EI CELE CHEIAJ E F=EHA@ J, )HAF E?=JE H J, ) =E JA =?A EIIA IA KJ= JE IE JDAA O AJDO E@E AFD IFD HO =IA62/ O"# )HC / O#! 5AH OI 5AH / K &' ) = = BAM JDAHI D=LA >AA B E K JEF A /1- F=JEA JI EALA@J?=KIAJDAF=JD CO 62?=J= O AI = IJAF E JDA I= L=CA F=JDM=O B H JDO E A JDO E@E A FD IFD=JA JDO E NO, HE> IA FD IFD=JA 1 DECDAH AK =HO JAI 62 F =OI JDA H A B F JDA E=?A CH MJDB=?J H! ALE@A J O >O LEHJKA B JDA B=?J JD=J NOHE> IA IKC=H EI KIA@ =I = = CE CA AIEI C B=?J H " 62 = I D=I C E IJ=JE =?JELEJO 2H BE A K JEF A = EC A JI B JDEI FH JAE ID M = B? IAHL=JE LAH JDA F=JD CA E? F IEJE I F=HJE?K =H O B H JDA / O#! 5AH KJ=JE ECKHA & / O?E AEI=>I KJA OFHAIAHLA@=JJDEI F IEJE CJD=JEJ =O>A?HEJE?= B HFH C 5K>IJEJKJE C=IAHE A? = JD KCD=FHA?A@ E C C O?E A =O F=HJE= O? FA I=JA 6DA / O"# )HC AI J@EIHKFJ= =>I KJA O? IAHLA@F IE JE =I IAHE A EI = I FAH EJJA@ >KJ EJ E = =HCA >=IE? F=HJ O DO@H FD >E? HAIE@KA JD=J FHAIK => E EIDAI =J A=IJ A AO BK?JE B 62 OI 5AH / K &' ) = > =>I KJA O? IAHLA@ IAGKA?AF IEJE I JDAB H AH BMDE?D EAI JDAFAHEFDAHO

7 (a) EC3738 ATP6_HUMAN HP0828 Q0085 Rv PATTERN fxxxxxxfxf ffxipxasxf hnxaslhfrl XhNIgXGXXf ffaafxfg-g EC3738 PFNHWAFIPV NLILEGVSLL SKPVSLGLRL FGNMYAGELI FILIAGLLPW ATP6_HUMAN QGTPTPLIPM LVIIETISLL IQPMALAVRL TANITAGHLL MHLIGSA--- HP0828 AGPVKWLAPF MFPIEIISHF SRIVSLSFRL FGNI-KGDDM FLLIMLL--- Q0085 AGTPLPLVPL LVIIETLSYF ARAISLGLRL GSNILAGHLL MVILAGL--- Rv1304 IKLLKGHVTL LAPINLVEEV AKPISLSLRL FGNIFAGGIL VALIALFP-P (b) Conserved Leu156 1 Arg Figure 4 Domain diagram and structure of ATP synthase. (a) Domain diagram and partial alignment for ATP synthase, subunit 6 (ATP6). The column indicated by the arrow at the bottom corresponds to position 156 of ATP6_HUMAN. Sequences are obtained from M. tuberculosis (Rv1304), Helicobacter pylori (HP0828), E. coli (EC3738), S. cerevisiae mitochondrion (Q0085) and H. sapiens mitochondrion (ATP6_HUMAN). Colors are as in Figure 1. (b) Ribbon diagram showing the structure of ATP synthase subunits: ATP6 (a-chain, green) and ATP9 (c-chain, red). Leucine 156 (1) is shown as a space-filling model. The structure comes from the Protein Data Bank (code: 1C17). comment reviews reports deposited research refereed research interactions information

8 8 Genome Biology Vol 2 No 6 2 =IJAHAHAJ= (a) CT245 bsubtilis-pdha YER178W APE1677 ODPA_HUMAN PATTERN sxxfxxxxxg -galgxdxfx XfXXXXXAXr XfXsXXhPXa aexxxxrfxj CT245 SQAISYGLSS ITLNGFDLFN SLIGFREAYH HMQQTGSPII VEALCSRFRG bsubtilis-pdha KAVAAGIVGV -QVDGMDPLA VYAATAEARE RAINGEGPTL IETLTFRYGP YER178W RGQYIPGLK- --VNGMDILA VYQASKFAKD WCLSGKGPLV LEYETYRYGG APE1677 KGLAYGVPGV -RIDGNDVMV VYKIVSDAAE KARRGGGPTL IEAVTYRLGP ODPA_HUMAN RGDFIPGLR- --VDGMDILC VREATRFAAA YCRSGKGPIL MELQTYRYHG Non-conserved Arg263 Gly (b) Chain B Chain A Thiamine diphosphate Figure 5 Structures of pyruvate dehydrogenase E1-α subunit and branched-chain α-ketoacid dehydrogenase α subunit. (a) Domain diagram and partial alignment for pyruvate dehydrogenase E1-α subunit (PDHA1). The column indicated by the arrow at the bottom corresponds to position 263 of ODPA_HUMAN. Sequences come from Chlamydia trachomatis (CT245), Bacillus subtilis (bsubtilis-pdha), S. cerevisiae (YER178W), Aeropyrum pernix (APE1677) and H. sapiens (ODPA_HUMAN). Colors are as in Figure 1. (b) Ribbon diagram of branched-chain α-ketoacid dehydrogenase α subunit (H. sapiens) - a close homolog to PDHA1 (Z-score 73.2). The structure comes from the Protein Data Bank ([49]; code: 1DTWA). Chain A is colored red, chain B gray. A space-filling model of thiamine diphosphate (TPP) (center) indentifies the enzyme active site. Below and slightly to the left, the catalytic group Glu92 is also shown in space-filling representation (1), and further down (directly under the TPP) Tyr262 is similarly shown (2). Arg263 occupies this position in ODPA_HUMAN. Helix H3 is the second helix at the lower left (3).

9 CT27995 PA0110 RP733 Rv2235 SUR1_HUMAN YGR112W PATTERN gxxxfg--gs XfXDXXdXnV XfsGrdXXrX sfff-xxr CT27995 LPDDL----T DLAQMEYRLV KIRGRFLHDK EMRL-GPRSL IRPDGVETQG PA0110 -PGQL----E GLRDPAYVRV RLHGRFDERH TLLL-DNR RP L---EK VQENLLYHKV KITGQFLPNK DIYLYGIR Rv2235 LKTLLPQQDS SAPDAQWRRV TATGQYLPDV QVLA-RLR SUR1_HUMAN LPADPM---- ELKNLEYRPV KVRGCFDHSK ELYM-MPRTM VDPVRE---- YGR112W LPKSFT--PD MCEDWEYRKV ILTGHFLHNE EMFV-GPR Conserved Gly124 Glu Figure 6 Domain diagram and partial alignment for surfeit locus protein 1 (SURF1). The column indicated by an arrow at the bottom corresponds to position 124 of SUR1_HUMAN. Sequences come from Drosophila melanogaster (CT27995), Pseudomonas aeruginosa (PA0110), Rickettsia prowazekii (RP733), M. tuberculosis (Rv2235), H. sapiens (SUR1_HUMAN) and S. cerevisiae (YGR112W). Colors are as in Figure 1. B JDA =?JELA J ID M / K &' F=HJE?EF=JAI E I A F=HJ O >KHEA@? IAHLA@ E E? E JAH=?JE I HA JD= JBH JDA=?JELAIEJA@=J= JID M Deafness-dystonia,A=B E= H DH 6H= A> =AHC A EI = FH JAE E F H@AH KJ=JE I E= FAFJE@A A=@ E= 1 JM?=IAI IAA = AJE E AN 6#@A HAIK JI E = BH= AIDEBJ A=@E C J E? HF H=JE B # AM = E =?E@I =BJAH / K!& B MA@ >O = IJ 1 = = >F@A AJE E AN?=KIAI=BH= AIDEBJ=J AJ"& A=@E C J E? HF H=JE B AM HAIE@KAI = IJ # 6DAIAFH JAE I=HA D C KIJ JDAOA=IJ E F HJFH JAE 6E &F; 4!#9 ) $ )IIAA E ECKHA ' > JDBH= AIDEBJ KJ=JE I A=@J A E E = JE B=DECD O? IAHLA@ JEB +8F4 =,6 A=HJDA?=H > NO JAH E KI BJDAFAFJE@A =HACE JD=J KIJ>A?HEJE?= J FH FAHBK?JE C 6DAHA?A JFK> E?=JE BJDABEHIJ,,2 EIIA IA KJ=JE +OI$$ 6HF % IJH C O IKF F HJI JDEI FHE H?? KIE >=IA@ JDA BH= AIDEBJI )I AEJDAH6E &F H= O? IAD CD=IOAJD=@EJIIJHK? JKHA@AJAH E A@ MA?= JE BAH@AJ=E A@IJHK?JKHA BK?JE HA =JE IDEFI 6E JDA E JAH A >H= E AJDA?=JE B6E 'F 6E 'F EI?=JA@ AEJDAH E JDA %,= E F HJ? F AN >AJMAA JDA A >H= AI H JDA!,= 61? F AN A >A@@A@ E JDA E AH A >H= A &,A AJE I B6E &F=BBA?JJDA=>E EJOJ E F HJ FH JAE I JD=J >A? A A >A@@A@ E JDA E AH A >H= A ' 1J EI F IIE> A JD=J JDA BH= AIDEBJ KJ=JE I IAA E= E JAHBAHA MEJD JDA E JAHB=?A >AJMAA 6E Iron-storage disorders HEA@HAE?D\I =J=NE= = I B= I E J JDA?=JAC HO B =? =II 11 J, =CA H@AH 1J EI?D=H=?JAHE A@ >O comment reviews reports deposited research refereed research interactions information

10 10 Genome Biology Vol 2 No 6 2 =IJAHAHAJ= (a) YKL148C YJL045W Rv3318 AF0681 CEC03G5_1 DHSA_HUMAN RP128 PATTERN YKL148C YJL045W Rv3318 AF0681 CEC03G5_1 DHSA_HUMAN RP XrsXXrasXX EKTFDDVKTT DKTFEDVHVS KERYSRITVH KERYRNVEIN YKDQAHLNVA YGDLKHLKTF RNRYKDIKIN 510 DnhXXdNiDL 520 XsXaEaXXfL 530 XXAXXXffhA 540 XXRrESRGhH DRSMIWNSDL VETLELQNLL TCASQTAVSA ANRKESRGAH DKSMIWNSDL VETLELQNLL TCATQTAVSA SKRKESRGAH DKGKRFNTDL LEAIELGFLL ELAEVTVVGA LNRKESRGGH DKSRGFNTDL TSAIEIGYML DLAEVVAIGA LKRQESRGAH DKGLVWNSDL IETLELQNLL INATQTIVAA ENREESRGAH DRGMVWNTDL VETLELQNLM LCALQTIYGA EARKESRGAH DKSLIWNSDL VEALELDNLL DQALVTVCSA AARKESRGAH Conserved Arg554 Trp (b) Flavinadenine dinucleotide 1 Figure 7 Structures of the flavoprotein subunits of succinate dehydrogenase and fumarate reductase. (a) Domain diagram and alignment for the flavoprotein subunit of succinate dehydrogenase (SDHA). The column indicated by the arrow on the bottom corresponds to position 554 of DHSA_HUMAN. Sequences come from S. cerevisiae (YKL148W and YJL045W), M. tuberculosis (Rv3318), A. fulgidus (AF0681), Caenorhabditis elegans (CEC03G5_1), H. sapiens (DHSA_HUMAN) and R. prowazekii (RP128). Colors are as in Figure 1. (b) Ribbon diagram of the flavoprotein subunit of fumarate reductase (E. coli) - a very close homolog of SDH Fp (Z-score 175.8). The structure comes from the Protein Data Bank (code: 1FUMA). Flavin adenine dinucleotide can be seen (in space-filling representation) in the middle of the structure and Thr494 is similarly indicated at the right-hand end of the bottom-most helix (1). Arg554 occupies this position in DHSA_HUMAN.

11 (a) TYPH_HUMAN TYPH_MYCPI MJ0667 EC PATTERN XXXaXXXShR haxxxhgtfd XaEXaXXXsX XXXXXsgrXa XrXXjffafG TYPH_HUMAN GCKVPMISGR GLGHTGGTLD KLESIPGFNV IQSPEQMQVL LDQAGCCIVG TYPH_MYCPI DLGVAKLSGR GLGFTGGTID KLESINVNTD IDLKNS-KKI LNIANMFIVG MJ0667 GLKIPKTSSR AITSAAGTAD VVEVLTRVDL TIEEIK-RVV KETNGCMVWG EC4382 GGYIPMISGR GLGHTGGTLD KLESIPGFDI FPDDNRFREI IKDVGVAIIa Semi-conserved Gly145 Arg Conserved Gly153 Ser (b) 2 1 Figure 8 Domain diagram and structure of thymidine phosphorylase (TP). (a) Domain diagram and partial alignment for thymidine phosphorylase. The columns indicated by arrows at the bottom correspond to positions 145 and 153 of TYPH_HUMAN. Sequences are obtained from H. sapiens (TYPH_HUMAN), Mycoplasma pyrum (TYPH_MYCPI), Methanococcus jannaschii (MJ0667) and E. coli (EC4382). Colors are as in Figure 1. (b) Ribbon diagram of TP (E. coli). Structure from the Protein Data Bank (code: 2TPT). Space-filling representations show a sulfate ion (center) (3) and two conserved glycines (left), the lower of which (1) aligns with Gly145 in TYPH_HUMAN and the other (2) with Gly153 in TYPH_HUMAN. 3 comment reviews reports deposited research refereed research interactions information

12 12 Genome Biology Vol 2 No 6 2 =IJAHAHAJ= CEY39A3C_83_D CT4964 YJR135W-A DDP_HUMAN PATTERN XsXfXXXXXX rxoaxsfaxx EssKXrfpXX ahofspacdr KCfXsXXg-X CEY39A3C_83_D MDSA--DPQL NRFLQQ-LQA ETQRQKFTEQ VHTLTGRCWD VCFADYRPPS CT4964 MSDFENLSGN DKELQEFLLI EKQKAQVNAQ IHEFNEICWE KCIGKPS--T YJR135W-A SDLASLDDTS KKEIATFLEG ENSKQKVQMS IHQFTNICFK KCVESVND-S DDP_HUMAN SSSAAGLGAV DPQLQHFIEV ETQKQRFQQL VHQMTELCWE KCMDKPG--P PATTERN rlssxxexcf XNCVpRFaDT sxxixpxfxp X CEY39A3C_83_D KMDGKTQTCI QNCVNRMIDA SNFMVEHLSK M CT4964 KLDHATETCL SNCVDRFIDT SLLITQRFAQ M YJR135W-A NLSSQEEQCL SNCVNRFLDT NIRIVNGLQN T DDP_HUMAN KLDSRAEACF VNCVERFIDT SQFILNRLEQ T Codon-39 frameshift Codon-49 frameshift Conserved Cys66 Trp Figure 9 Domain diagram and complete alignment for Tim8p. The columns indicated by the two arrows on the right correspond to positions 39 and 49 of DDP_HUMAN. Sequences are obtained from C. elegans (CEY39A3C_83_D), D. melanogaster (CT4964), H. sapiens (DDP_HUMAN) and S. cerevisiae (YJR135W-A). Colors are as in Figure 1. FH CHAIIELA C=EJ E > =J=NE= =? B HAB FOH= E@= MA= AII E E BAHE H E >I! =? B BH=J=NE FH JAE?=KIAI = KF B EH E JDA =JHEN IF=?AI B JDA )I EH =??K K =JAI EJ? FAJAI MEJD?=J= =IA B H DO@H CA FAH NE@A B H I DO@H NO H=@E?= I A 0 A! 0 0 I?= A@HA=?JELA NOCA IFA?EAIJD=J?= =JJ=? J, ) A >H= A EFE@I?=H> DO@H=JAI FH JAE I =CA JDA A JEHA NE@=JELA FD IFD HO =JE IOIJA AIFA?E= O JDA DECD O LK AH=> A EH IK BKH?A JAHI 6DA ID HJ=CA B AI JHAIK JBH B H =JE B KJ= JFH JAE I >KJH=JDAHBH ANF= IE B=/))HAFA=JE JDABEHIJE JH B JDA BH=J=NE CA A 6DEI HAFA=J EI >A EALA@ J B H?= E A@4 JAHBAHAMEJD JH= I?HEFJE!! ;BDF ;, 9 JDA BH=J=NE D C E OA=IJ E JAH=?JI MEJD JDA OA=IJ E JAH A@E=JAFAFJE@=IA?J ;!"+J MAH =JHENEH??A FAJEJE!! H = EH D A IJ=IEI E E = JOFA BH=J=NE J? JH ABB KN * JD FH JA OJE?? A=L=CALE= H1 2? F E DA F J 052% 5I? F E A >H= A JH=BBE? E C H C=HA AA@A@B HJDA =JKHABH=J=NE FH JAE J =HHELA =J =JE E JDA =JHEN E EJI FH FAH? B H =JE 1H ABB JDAEH IK BKH? KIJAHJH= I F HJAH)J F; 4!+ ) EIIA IA KJ=JE E )>?>% H D)*+% JDADK = D C B)J F 1 A" AJ D=I >AA E F E?=JA@E : E A@IE@AH > =IJE?= A H@AH? IA O HA =JA@ J HEA@HAE?D\I =J=NE= ECKHA IK =HE AI JDA IAGKA?A FDO CA AJE?? JANJ B H JDEI F=JD CA E??D= CA ANFAHE A J= IJHK? =HA =L=E => A IJ=JA I!#!$ 0 0A /?) 5 EJD = KI?HEFJE FHAF=H=JE B H A >H= AFH JAE I? A=H KJ=JE B= I E = ANJH=?A K =H JECDJ JKH >AJMAA JH= I A >H= ADA )F=EH B?=JE JH= IF HJAHI J; J ;2 "+E OA=IJ? JH IEH E B KNE J JDA 6DEI JDAH D= B B EH D A IJ=IEI? = I A=IE O D=LA=H AE E A@IE@AH > =IJE? = A E= Hereditary spastic paraplegia 0AHA@EJ=HOIF=IJE?F=H=F ACE=052 =? =II11=IIA > O@EI H@AH EI?D=H=?JAHE A@>OFH CHAIIELA KIK= OIALAHA MAH ANJHA AH=JE BJDA C=N I B JDA?A JH= AHL KI IOIJA MDE A JDA?A HA =E E J=?J 1 DAHEJ=?A?= >A=KJ I E = J =KJ I = HA?AIIELA H: E A@ 5 A?=IAI B052HAIK JBH KJ= JE I E JDA CA A B H F=H=F ACE = K? A=H AJ= FH JA=IA E? K@E C = AJE =J F IEJE %&" MDE?D?=KIAI=BH= AIDEBJJD=JA E E =JAI$ BJDAFH JAE =@A E AE IAHJE =JF IEJE & B JDAF=H=F ACE?, ) MDE?D?HA=JAI=BH= AIDEBJHAIK JE CE JHK?=JE BJDA =IJ#%HAIE@KAI BJDEI%'# HAIE@KAFH JAE!% )I ID M E ECKHA JDAHA =HA LAHO BAM MA? IAHLA@F IEJE IE JDA@A AJA@#% HAIE@KAJ=E E F OE CJD=J JDEI =O>A=? F=H=JELA O@EI H@AHA@F=HJ BJDAFH JAE EIIA IA KJ=JE ID=LA>AA B DK = F=H=F A CE 6DEI FH JAE HAIA > AI JDHAA OA=IJ FH JAE I MDE?D BK?JE =I?D=FAH E I H FH JA=IAI )BC!F ;-4%+ 4?=F ; 4&'+ ; AF ;24 "9 6DAOF=HJE?EF=JAE HA?O? E CJDA? F A JI B? F AN8 )62 IO JD=IA =I MA =I E EJI =IIA > O 6DA B 4&'+ = AKFJDA =@A IE A JHEFD IFD=J=IA ))) FH JA=IA? F AN MDE?D EI A >A@@A@E JDAE AH A >H= AB=?E CJDA =JHEN ;24 "9 JDA E ))) FH JA=IA? F AN MDE?DB=?AIJDAE JAH A >H= AIF=?A 6DAOA=IJ )))FH JA=IA? F ANEIEJIA BHACK =JA@>OJM FH DE>EJE FH JAE I 2D> ;/4! + 2D> ;/4!+!& 2=H=F ACE D CI = = C KIJ JDAOA=IJF=H= CI

13 ABC7_HUMAN RP205 YMR301C PATTERN LXXYrshXXK 270 XisiLhfLNX Figure 10 Domain diagram and partial alignment for the Fe-S cluster transporter Atm1p. The column indicated by the arrow at the bottom corresponds to position 400 of ABC7_HUMAN. Sequences are obtained from H. sapiens (ABC7_HUMAN), R. prowazekii (RP205) and S. cerevisiae (YMR301C). Colors are as in Figure 1. )BC!F 4?=F ; AF KIJ = IJ?AHJ=E O ANEIJ DK = FH DE>EJE I =O>AANFA?JA@=IMA 2 E J KJ=JE I E? IAHLA@ HACE I B JDAIA FH JAE I?= >A ANFA?JA@ J?=KIA EIIA IA KJ=JE I =JE = JHK?=JE IJD=J ME = I A=@J DAHA@EJ=HOIF=IJE?F=H=F ACE= Discussion 6DA FH?AII C CA JOFE?= O FH?AA@I JDH KCD JDHAA IJ=CAI BEHIJ HA? C EJE B IJ=JA AE? K@E =FFE C BJDAHA =JA@ KJ=JE I A K?E@=JE B JDA >E?DA E?= >E FDOIE?= A?D= EI A=@E CJ JDA@EIA=IAFDA JOFA 5E? A?A = A E=FH LE@AI JDA? =IIE? AN= F A 1 JDA?=IA JDAHA =HA I 1!' 16 2 " 9756 # MA>IEJAI =? F=H=> A CH ME C K >AH B KJ=JE I & )I = H 0 JDA?=KI=JELA KJ=JE I =HA J A?AII=HE O? BE A@ J = IE C A FH CCA A HALA J JDA K? A=HLAHIKIJDA CA A J O JDAHA EI A J A =FFE C >AJMAA KJ=JE I H ALA MD A CA AI = F=HJE?K A@@EIA=IAA JEJO 6DKI A=?D@EIA=IAIFA?JHK =O? H J IALAH= IAJI B KJ=JE I A=?D IAJ =BBA?JE C A FH JAE HFH JAE IK>K EJ >LE KI O KJ=JE IE J J4 ) 280 GQsfIfiXhL 290 XhfMffhXsh 300 axxjsfxvgd ABC7_HUMAN LKTYETASLK STSTLAMLNF GQSAIFSVGL TAIMVLASQG IVAGTLTVGD RP205 LQAYEKSATK ITNSLSILNI GQDVIISLGL VSLMILSVNA INQNKMMVGD YMR301C LMNYRDSQIK VSQSLAFLNS GQNLIFTTAL TAMMYMGCTG VIGGNLTVGD Conserved Ile400 Met J H4 JAE IJD=J=BBA?J CA AANFHAI IE ME = I F JA JE= OD=LAF AE JH FE?ABBA?JI 6DAHAIK JIFHAIA JA@DAHA=@@HAIIJDAJDEH@IJ=CA CCA AJE?@EIA=IA = A OJDA?D=H=?JAHE =JE FDA JOFA =J JDA A?K =H ALA MEJD = LEAM J ANF =E E C EJI >E?DA E?= A?D= EI 1 FHE?EF A JDA =FFH =?D?= >A =FF EA@ J = O KJ=JA@ FH C CA A 9DA IJHK?JKH= E B H =JE EI =L=E => A JDA AN=?J A?D= EI B@EIA=IA?=KI=JE =O>A=I?AHJ=E => A=JJDA A?K =H ALA A>O A= I B?=HABK OJ=HCAJA@ ANFAHE A JI ) BKHJDAH ANJA IE B JDEI >=IE? M A@CA =FFH =?D EAIE JDA@EHA?JE B A?K =HAL KJE )IMA ME ID M A IAMDAHA K FK> EIDA@ >IAHL=JE I JDA IAJI B D CI =IIA > A@ KIE CFHE H >=IA@FH BE AIFH LE@A=HE?DI KH?A BFDO CA AJE? E B H =JE J O ID EJ >A F IIE> A J I AJ?D KJJDADEIJ HO BJDA@ALA F A J B@EBBAHA J>E?DA E?= =?DE AHEAI EJ ID = I >A F IIE> A J AIJ=> EID MDE?D F=HJI BJDAFH JAE I=HA IJ?HEJE?= J BK?JE JDA>=IEI B = E =?E@ IAGKA?A? IAHL=JE? HHA =JA@ MEJD JDA IJHK?JKH=? JANJI M A@CAC=E A@>OJDA=FFH =?D@AI?HE>A@DAHAD=I >LE KI =FF E?=JE J > JDJDA@E=C = KJ=JE D=I >AA?D=H=?JAHE A@ JDA AN=?J comment reviews reports deposited research refereed research interactions information

14 14 Genome Biology Vol 2 No 6 2 =IJAHAHAJ= YER017C YPR024W YMR089C bsubtilis-ftsh hum paraplegin hum parapleg_ins XF PATTERN alxkrxkrar XfhpXLLrXE XasXXpfXXa fxxxxxjxg- -gxrxxxxxx XXD YER017C LLTKNLDKVD LVAKELLRKE AITREDMIRL LGPRPFKE-- --RNEAFEKY LDP YPR024W LLTKKNVELH RLAQGLIEYE TLDAHEIEQV CKGEKLDKLK TSTNTVVEGP DSD YMR089C LLKEKAEDVE KIAQVLLKKE VLTREDMIDL LGKRPFPE-- --RNDAFDKY LND bsubtilis-ftsh ILTENRDKLE LIAQTLLKVE TLDAEQIKHL IDHGTLPE-- --RNFSDDEK NDD paraplegin VLQDNLDKLQ ALANALLEKE VINYEDIEAL IGPPPHGP-- --KKMIAPQR WID paraplegin_ins VLQDNLDKLQ ALANALLEKE VIN XF0093 ILADNLDKLH AMSQLLLQYE TIDAPQIDAI MEGREPPPPV GWGKPSDNGS DDD Figure 11 Domain diagram and partial alignment for the mitochondrial AAA-proteases. Sequences are obtained from H. sapiens (paraplegin and paraplegin_ins containing the adenine insertion), B. subtilis (bsubtilis-ftsh), Xylella fastidiosa (XF0093) and S. cerevisiae (YER017C, YPR024W and YMR089C). Colors are as in Figure 1. =JKHA BJDA=II?E=JA@E AIIEI M MEJDFHA?EIE 6DEI D=I = >A=HE C KF?D E?A B JDAH=FO = MI = K?D HAAN=?JFH C IEIJD= =?D=H=?JAHE =JE IE F O=I I=O A 1 =@@EJE JDAE B H =JE BH IAGKA?A = EC A JID=IFHA@E?JELAF MAH KJ=JE I JOAJHA? H@A@ E JDA EJAH=JKHA ECDJJKH KF=J AOF IEJE IE I A BJDA FH JAE I M J >A =BBA?JA@ I?=HHOE C IK?D?D= CAI ECDJ >A = AHJA@ J JDA F IIE> A D=H BK? IAGKA?AI J= A MD=JALAH FHA?=K JE =HO A=IKHAIIAA =FFH FHE=JA JAJD=JIK>IJEJKJE I E JDA DK = IAGKA?A JD=J =J?D = E =?E@ HAIE@KAI B =J JDA? C?=JE I E J=N E?= JIAGKA?AI=HA AII E A OJ FH LAD=H BK JD=? F AJA O LA IK>IJEJKJE I 6DEI =FF E?=JE B E B H OCH ME E F HJ=?A=I=?GKEIEJE B=@@E JE = IE C A K? A JE@AF O HFDEI 5 2@=J=>A? AI E?HA=IE C O? AM F=H= CI HJD CI =HA =@@A@ J JDA E C JDA =JKHA B JDA =BBA?JA@ FH JAE JDA BHAGKA?O B??KH HA?A I EJ =O>AF IIE> AJ H=JJA FJI=JH=JE HCA AJDAH=FO 6DAM H HAF HJA@DAHAHAFHAIA JI=FHA E E =HO LAHLEAM B JDA -LA JK= O = AND=KIJELA IKHLAO ID >A? F AJA@? JE K KI O KF@=JA@ =@A FK> E? O =L=E => A 6D=J ME HAGKEHA FHA?EIA?D=H=?JAHE =JE B = O HA KJ=JE I=IMA =IANF= IE BJDA@=J=>=IA B FH JAE FH BE IJHK?JA@KIE C 5K?DABB Materials and methods Yeast mitochondrial protein database (YMPD) 9A?HA=JA@=@=J=>=IA B "!OA=IJ FH JAE I KIE C>E?DA E?= AOM H@IA=H?DAIB H M FH?AIIAI BH JDA 5=??D=H O?AI /A A,=J=>=IA " JDA K E?D1 B H =JE +A JAHB H2H JAE 5AGKA?AI " JDA;A=IJ2H JA A,=J=>=IA "! EJ*)5- "" >O EJ HE C JDA?KHHA J EJAH=JKHA -=?D A >AH B JDEI IAJ B FH JAE I EI?D=H=?JAHE A@ >O =J A=IJ A FHE H >=IA@ FH BE A JD=JHAFHAIA JIJDA IJ? IAHLA@HACE I )I AI J KIA =?= E?= F AN 1 MA D=LA IK>IJEJKJA@ JDA CA =IA FH JAE IK>K EJIBH 4 = AHE?= = J E EJE= E AJDAIAFH BE AI Developing prior-based profiles 2HE H >=IA@FH BE AI JDAFHE?EF= J IKIA@E JDEIM H HAFHAIA J AL KJE =HE O? IAHLA@ IAGKA?A >=IA@ BK? JE =E I?A?HA=JA@ A=?D FH BE A?= >A KIA@ J

15 IA=H?D = =L=E => E = =JJA FJ J?=JA = D C KIIAGKA?A =J?DAI MDE?DE E@A=?=IAI? HHA IE C AFH =E I BD C KIIAGKA?AIEIJDA K JEF O= EC A@KIE CJDAFH BE A=I = JA F =JA 6DA IAJ B K JEF O = EC A@ AI =E > = MI FKJ=JELA BK?JE = =IIEC A JI B H FHALE KI O K E@A JEBEA@ FH JAE I DECD ECDJI AO? IAHLA@ HAIE@KAI B A >AHI B = D C KI IAJ BFH JAE I )I AI >A? A =L=E => A KH IAJ B FH BE AI?= E@A JEBO JDA =@@E JE = D CIMEJDDECDIA The profile-defining set E C IAJ MEJD = ME@A J=N E? IFHA=@ ID >A FJE = B H?=JE C@EIJ= JD CIBH =I = OIFA?EAI =I F IIE> A 1@A= FH BE AI D=LA E C IAJ? F IA@ B A FH JAE A=?D BH = AK =HO JA = =H?D=A = /H= F IEJELA>=?JAHEK AC=JELA>=?JAHEK A OA=IJ FH JAE 6?HA=JA E C IAJ B H A=?D FH BE A MA AIJ=> EIDA@ = IKFAHIAJ B F JA JE= B= E O A >AHIKIE C* )56IA=H?DAI "# =C=E IJ KH*E A?K =H - CE AAHE C 4AIA=H?D +A JAH * -4+ = CA 5MEII 2H J "$ -=?D E@A JEBEA@ OA=IJ FH JAE IAHLAI=I=[IAA@\E EJE= E E CFH JAE B H= * )56 IA=H?D 6DA?KJ BB I? HAI =HA IAJ =J = ANFA?J=JE L= KA B- `$ 7BE JAHIB H M? F ANEJO HACE I "% H JDAIA * )56 DEJI MA IA A?JA@ JDA E E C IAJ B =NE K J=N E? IFHA=@ 1 I A?=IAI * )56 B=E I J?=JA IAGKA?A D CI JD=J CHA=J O BH JDA IAA@ FH JAE 9A JDA KIA@ = EJAH=JELA FH?A@KHA J CA AH=JA = FH BE A KIE = E? FH CH= E C J =NE E AJDAE B H =JE? JA J HIK?D?=IAI JDAE EJE= FH BE AEIHK =C=E IJJDA= CA = E?FH CH= E C 6DA JDA ANJDECDAIJI? HE C A >AHBH =@EBBAHA J E C@ EI=@@A@J JDA@ABE E C IAJ 9AEJAH=JA@JDEIFH?AIIK JE JDAE@A= J=N E?IFHA=@ M=I =?DEALA@ H JDA E B H =JE? JA J B JDA FH BE FFA@>A MJA = E =?E@AGKEL= A?EAI "& Expanding the set of profile homologs?a = FH BE A EI >KE J MA =JJA FJ J = IAGKA?AI ID=HE C JDEI =E 6DEI A >O DAKHEIJE? HAND=KIJELA=FFH =?DAI 1 JDADAKHEIJE?=FFH =?DJDA FH BE AIA=H?DAI* -4+\I= CA 2H J>OBE JAHE CJDA =HCAH@=J=>=IAIKIE C* )56MEJD= ANFA?J=JE L= KA?KJ BB B- ` B MA@>O=ID HJ E CFH BE A IA=H?D 1 JDAAND=KIJELA=FFH =?D JDAFH BE AIA=H?DAIJDA = CA H JDA?KHHA J LAHIE B 5MEII 2H J KIE CID HJ E C@O = E?FH CH= E C Multiple alignment sets -=?DFH BE K JEF A= EC A JB H= OIAJ BFH JAE IJD=J? J=E EJ 6DAFH BE AI O= EC JD IAIK>HACE I B=FH JAE JD=JJDAO =J?D 6DAIAHACE IE? HF H=JAJDA IJ? IAHLA@= E =?E@F IEJE I= CJDAIAGKA?AI JD=J = A KF JDA FH BE E C IAJ 9A D=LA?D E C IAJI JD=J? J=E JDA ID HJAIJ E B H =JELA FH JAE IAGKA?A E H@AH J =NE E A JDA?D=?A B C IE C =E FH BE A > A?JI ) CAH IAGKA?A E E CIAJ ECDJ = A=I ECDJ ODECDAH I? HE CFH BE A>O JDA =@@EJE B = BAM?=H> NO H = E JAH E = HAIE@KAI >KJ O =J JDA HEI B EIIE C I ECDJ O ID HJAH A >AHI B JDAIAJMDA JDAFH BE AEIKIA@J IA=H?DJDA@=J=>=IAI Homologous structures from the Protein Data Bank 9A H KJE A O IA=H?D JDA 4+5* 2H JAE,=J= *= "' B H F JA JE= IJHK?JKH= D CI 2H BE A =J?DAIMEJD I? HAI => LA=HAHAJ=E = EC JDAFH BE A =J?DA@ HACE J =E 6DAIAFH BE A JKH= = EC A JI?= >A LEIK= E A@ E 4=I # E =CAI>KE JKIE C I?HEFJ # # Additional data files 6DA B ME C =@@EJE BE AI =HA =L=E => A MEJD JDEI F=FAH E A? F AJA = EC A JI B H JDA FH BE A? LAHA@ HACE I B JDA IAGKA?AI ID M E ECKHA ECKHA ECKHA! ECKHA " ECKHA # ECKHA $ ECKHA % ECKHA & ECKHA ' ECKHA ECKHA Acknowledgements We thank Greg McAllister for helpful discussions of transmembrane protein structures. This work was partially supported by US Department of Energy Grant DE-FG02-98ER62558 and NSF Grant DBI References 1. Das S, Smith, TF: Identifying nature s protein Lego set. In Advances in Protein Chemistry. Edited by Richards FM, Eisenberg DS, Kim PS. San Diego: Academic Press; 2000: Lang BF, Burger G, O Kelly CJ, Cedergren R, Golding GB, Lemieux C, Sankoff D, Turmel M, Gray MW: An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature 1997, 387: Taanman JW: The mitochondrial genome: structure, transcription, translation and replication. Biochim Biophys Acta 1999, 1410: Leonard JV, Schapira AH: Mitochondrial respiratory chain disorders I: mitochondrial DNA defects. Lancet 2000, 355: Mitochondrial disorders [ 6. Rizzuto R, Pinton P, Carrington W, Fay FS, Fogarty KE, Lifshitz LM, Tuft RA, Pozzan T: Close contacts with the endoplasmic reticulum as determinants of mitochondrial Ca 2+ responses. Science 1998, 280: Skulachev VP: Mitochondrial filaments and clusters as intracellular power-transmitting cables. Trends Biochem Sci 2001, 26: Schapira AH: Mitochondrial disorders. Biochim Biophys Acta 1999, 1410: Hayashi J, Ohta S, Kikuchi A, Takemitsu M, Goto Y, Nonaka I: Introduction of disease-related mitochondrial DNA deletions into HeLa cells lacking mitochondrial DNA results in mitochondrial dysfunction. Proc Natl Acad Sci USA 1991, 88: Chomyn A, Martinuzzi A, Yoneda M, Daga A, Hurko O, Johns D, Lai ST, Nonaka I, Angelini C, Attardi G: MELAS mutation in mtdna binding site for transcription termination factor causes defects in protein synthesis and in respiration but no comment reviews reports deposited research refereed research interactions information

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