Volume 6 Supplement 1
In silico identification of a multi-functional regulatory protein involved in Holliday junction resolution in bacteria
© Zhang et al.; licensee BioMed Central Ltd. 2012
Published: 16 July 2012
Homologous recombination is a fundamental cellular process that is most widely used by cells to rearrange genes and accurately repair DNA double-strand breaks. It may result in the formation of a critical intermediate named Holliday junction, which is a four-way DNA junction and needs to be resolved to allow chromosome segregation. Different Holliday junction resolution systems and enzymes have been characterized from all three domains of life. In bacteria, the RuvABC complex is the most important resolution system.
In this study, we conducted comparative genomics studies to identify a novel DNA-binding protein, YebC, which may serve as a key transcriptional regulator that mainly regulates the gene expression of RuvABC resolvasome in bacteria. On the other hand, the presence of YebC orthologs in some organisms lacking RuvC implied that it might participate in other biological processes. Further phylogenetic analysis of YebC protein sequences revealed two functionally different subtypes: YebC_I and YebC_II. Distribution of YebC_I is much wider than YebC_II. Only YebC_I proteins may play an important role in regulating RuvABC gene expression in bacteria. Investigation of YebC-like proteins in eukaryotes suggested that they may have originated from YebC_II proteins and evolved a new function as a specific translational activator in mitochondria. Finally, additional phylum-specific genes associated with Holliday junction resolution were predicted.
Overall, our data provide new insights into the basic mechanism of Holliday junction resolution and homologous recombination in bacteria.
Homologous recombination is a fundamental mechanism in biology that rearranges genes within and between chromosomes, promotes DNA repair, and guides segregation of chromosomes at division. This process is common to all forms of life and involves the exchange (i.e., breakage and reunion) of DNA sequences between two chromosomes or DNA molecules [1–4]. Such exchange provides a valid evolutionary force that contributes to promote genetic diversity and to conserve genetic identity. In addition, homologous recombination is also used in horizontal gene transfer to exchange genetic material between different strains and species of bacteria and viruses .
Although homologous recombination varies widely among different organisms and cell types, most forms of it involve the same basic steps: (i) after a DNA break occurs, sections of DNA around the break on the 5' end of the damaged chromosome are removed in a process called resection; (ii) in the strand invasion step that follows, an overhanging 3' end of the damaged chromosome then "invades" an undamaged homologous chromosome; (iii) after strand invasion, one or two cross-shaped structures (called Holliday junctions) are formed to connect the two chromosomes. Holliday junction (or four-way junction) has been generally assumed as a key intermediate in genetic recombination and DNA repair since its discovery in 1964 . They are highly conserved structures from prokaryotes to mammals, which adjoin two DNA duplexes, forming a branch point where four helices are interconnected by strand exchange [7, 8].
Because Holliday junctions provide a covalent linkage between chromosomes, their efficient resolution is essential for proper chromosome segregation. Enzymes that resolve Holliday junctions by endonucleolytic cleavage have been isolated from bacteriophages, bacteria, archaea and certain eukaryotes [9–12]. In Escherichia coli, the enzymes that are involved in resolution of Holliday junction include RuvABC, RecU, RecG, and RusA [13–15]. The RuvABC proteins (or RuvABC resolvasome) constitute a simple and the most widely used system for the processing of Holliday junctions. RuvAB proteins catalyze the branch migration whereas RuvC endonuclease resolves the Holliday junction into duplex products [15, 16]. RecU, a RuvC functional analog, was found to serve as a Holliday junction resolvase in some firmicutes and mollicutes that lack RuvC [17, 18]. The RecG protein is a DNA helicase and may promote branch migration of a variety of branched DNAs including Holliday junctions [19, 20]. The RusA protein is a homodimeric Holliday junction-specific endonuclease and can bind a variety of branched DNA structures [21, 22]. RecG may be required by RusA to branch migrate Holliday junctions to cleavable sequences .
Homologs of RuvABC, RecU, RecG, and RusA are absent from almost all sequenced archaea and eukaryotes. In archaea, the Hjc protein, a distantly related member of the type II restriction endonuclease family, has been characterized to serve as a Holliday junction resolving enzyme [23, 24]. Little is known about the mechanism of eukaryotic Holliday junction resolution and the enzymes involved. It was reported that Saccharomyces cerevisiae contains a Holliday junction resolvase Cce1 [25, 26], an equivalent enzyme from Schizosaccharomyces pombe (named Ydc2) has also been found . These enzymes are targeted to the mitochondria, suggesting that they can only cleave junctions formed during recombination of mitochondrial DNA. Very recently, a nuclear Holliday junction resolvase was first identified from both humans and yeast . These resolvases (GEN1 in human and its yeast ortholog Yen1) represent a new subclass of the the Rad2/XPG family of nucleases, and promote Holliday junction resolution in a manner similar to that shown by the E. coli RuvC [29, 30]. However, the precise mechanism regulating the activities of these enzymes is unknown and the factors involved remain unidentified.
In this study, we carried out comparative genomics approaches to investigate the mechanisms of Holliday junction resolution in prokaryotes. Occurrence of known components of Holliday junction resolution (e.g., RuvABC and RecU) could be easily identified by comparative genomics. Our analysis also generated evidence for a novel DNA-binding regulatory protein family involved in Holliday junction resolution in bacteria. Homologs of this family were detected in a variety of eukaryotes and are predicted to be localized in mitochondria. Overall, these data provide new insight for better understanding the basic mechanism of homologous recombination in nature.
Results and discussion
Distribution of the RuvABC/RecU Holliday junction resolution system in prokaryotes
Except a very small number of organisms (less than 2%) with small and condensed genomes (mostly parasites), all sequenced bacteria contain RuvA and RuvB genes. As RuvAB complex may catalyze both Holliday junction branch migration and replication fork reversal [31, 32], the occurrence of their genes may not precisely reflect the Holliday junction resolution trait. Thus, we used the co-occurrence of RuvABC or RuvAB/RecU as a signature for the presence of RuvABC/RecU-dependent Holliday junction resolution trait.
In contrast to bacteria, only two closely related archaea in Methanomicrobiales (Methanoregula boonei and Methanospirillum hungatei) were found to have RuvABC system, suggesting that they recently acquired this system from bacteria by horizontal gene transfer. No RecU homolog could be detected in archaea.
Identification of a new family involved in RuvABC-dependent Holliday junction resolution in bacteria
STRING analysis of genes functionally associated with RuvABC resolvasome.
Considering that YebC might be functionally associated with RuvABC resolvasome, we further analyzed the distribution of this protein family in all sequenced prokaryotes. Homologs of YebC were not detected in archaea, implying that YebC may either have evolved in bacteria or lost in the ancestors of archaea. In bacteria, the distribution of YebC appeared to be wider than RuvABC system (Figure 1). Almost all sequenced organisms (98%) possess YebC genes, suggesting that YebC may be also involved in other processes independent of RuvABC system. However, the facts that all RuvC-containing organisms have YebC, and that YebC and RuvC genes are located in the same operon in approximately half of the RuvC-containing organisms (Figure 1), indicate a strong relationship between them. These results were consistent with a previous study of some "hypothetical" genes expressed in Haemophilus influenzae, which also suggested a potential association of YebC with RuvABC in this organism .
Phylogeny and functional classification of YebC family
Prediction of the function of YebC proteins
Although YebC is a large family of widespread conserved proteins whose function is unknown, this group of proteins has been extensively characterized from the structural perspective. To date, the crystal structures of YebC proteins from Aquifex aeolicus (YebC_I), E. coli (YebC_I), and Helicobacter pylori (YebC_II) have been solved (PDB ID codes 1LFP, 1KON, and 1MW7, respectively). A previous structural analysis of A. aeolicus YebC revealed a large cavity with a predominance of negatively charged residues on the surface of this protein . Interestingly, all three structure-solved proteins have a putative DNA binding function, suggesting that YebC proteins may serve as a potential transcription factor. A recent study reported that the YebC protein in Pseudomonas aeruginosa (PA0964, YebC_I) may be involved in negatively regulating the quorum-sensing response regulator pqsR of the PQS system by binding at its promoter region . This result implied the complexity of the function of YebC in nature.
Although the function of YebC proteins and the biological pathways they are involved in are unclear, our current studies provide some useful information for this widely used protein family: (i) both YebC_I and YebC_II subgroups may bind DNA; (ii) YebC_I proteins may serve as a multi-functional transcription regulator mainly involved in regulating the expression of RuvABC genes as well as other genes such as pqsR; (iii) YebC_II might have evolved from YebC_I by gene duplication and have novel function independent of Holliday junction resolution or even DNA recombination. A future challenge would be to understand the DNA binding patterns of YebC_I and YebC_II proteins as well as additional processes they may regulate.
Investigation of YebC-like proteins in eukaryotes
Significant YebC homologs were also detected in a variety of eukaryotes, including fungi, plants and animals (Table S2 [see additional file 2]). Very recently, it was reported that a mutation in the human gene encoding a YebC homolog (named CCDC44, localized to the mitochondria) led to a specific defect in the synthesis of the mitochondrial DNA-encoded cytochrome c oxidase subunit I (COX I) . Thus, the human CCDC44 protein was renamed as TACO1, which may serve as a mammalian mitochondrial translational activator of COX I. Possible mechanisms of TACO1 action to ensure translation of COX 1 were also considered: (i) securing an accurate start of translation; (ii) stabilizing the elongating polypeptide; and (iii) interacting with the peptide release factor [41, 42].
We analyzed the sequences of all eukaryotic YebC-like proteins and the evolutionary relationship with their bacterial counterparts. All detected YebC-like proteins in eukaryotes have mitochondrial signal sequences, suggesting that they are mitochondria-targeted proteins. Phylogenetic analysis of bacterial YebC and eukaryotic YebC-like proteins showed that the eukaryotic YebC-like proteins were clustered with YebC_II subfamilies (Figure 2), implying that these YebC-like proteins (including human TACO1) might have evolved from ancient YebC_II proteins. The mitochondrial signal sequences were then added to target them into the mitochondria as a specific translational activator, at least in metazoan mitochondrial genome. As eukaryotes lack the RuvABC resolvasome, it is unclear whether these YebC-like proteins are involved in homologous recombination in mitochondria, or whether they still have the capacity to bind mitochondrial DNA. Further studies are required to determine the substrates and function of YebC-like proteins in other organisms as well as their relationship with DNA repair and recombination in mitochondria.
Prediction of additional phylum-specific genes associated with RuvABC resolvasome
Comparative genomics studies also suggested additional candidate genes involved in RuvABC-dependent Holliday junction resolution in certain bacterial phyla. In Firmicutes/Clostridia, most organisms possess a conserved hypothetical protein (CTC02214 in Clostridium tetani, a distant homolog of pfam08955, BofC C-terminal domain) whose gene is always located next to either YebC or RuvC gene, implying a potential functional link with them. However, orthologs of this protein family were exclusively detected in Clostridia, suggesting that this protein might be newly evolved in this phylum. Similarly, another conserved hypothetical protein (DUF208 super family; COG1636, uncharacterized protein conserved in bacteria) was also identified in a variety of distantly related organisms where its gene is often located close to either YebC or RuvABC genes (data not shown). Further studies, however, are needed to verify their function and the relationship between these genes and genetic recombination in bacteria.
In this study, we carried out comparative genomics to identify a novel DNA-binding regulatory protein family, YebC, which was strongly linked to Holliday junction resolution in bacteria. Phylogenetic analysis revealed that YebC might be divided into two functionally different subgroups: YebC_I and YebC_II. YebC_I may serve as a multi-functional transcriptional regulator that mainly regulates the gene expression of RuvABC resolvasome in bacteria. It could not be excluded that YebC_II is involved in homologous recombination, but current evidence does not provide strong support for this possibility. Further studies on eukaryotic YebC-like proteins suggested that they may have evolved from YebC_II subgroup and have different function to serve as a specific translational activator in mitochondria.
Genomes, sequences and resources
Fully sequenced genomes from the Entrez Genome Database at NCBI were used in this study . Because of the large number of strains for some bacterial species, only one strain was selected for each species. A total of 1549 bacteria, 97 archaea and 330 eukaryotes were analyzed (as of October 2011).
We used E. coli RuvA (COG0632, Holliday junction resolvasome DNA-binding subunit), RuvB (COG2255, Holliday junction resolvasome helicase subunit), RuvC (COG0817, Holliday junction resolvasome endonuclease subunit) and Bacillus subtilis RecU (pfam03838, recombination protein U) sequences as queries to search for RuvABC or RuvAB/RecU-dependent Holliday junction resolution trait. For each of these proteins, TBLASTN  was initially used to identify genes coding for homologs with a cutoff of E-value ≤ 0.1. Orthologous proteins were then defined using the conserved domain (COG/Pfam) database and bidirectional best hits .
The STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) database and programs  were used to identify gene candidates that may be functionally related to RuvABC resolvasome. Different parameters were used for better performance.
Multiple sequence alignment and phylogenetic analysis
Sequence alignments were performed with CLUSTALW  using default parameters. Ambiguous alignments in highly variable (gap-rich) regions were excluded. The resulting multiple alignments were then checked for conservation of residues and manually edited. Phylogenetic analyses were performed using PHYLIP programs . Pairwise distance matrices were calculated by PROTDIST to estimate the expected amino acid replacements per position. Neighbor-joining trees were obtained with NEIGHBOR and the most parsimonious trees were determined with PROTPARS.
List of abbreviations
- COX I:
cytochrome c oxidase subunit I
Search Tool for the Retrieval of Interacting Genes/Proteins.
Acknowledgements and funding
We are grateful to Dr. Vadim N. Gladyshev (Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA) for the insightful suggestion and comments. This work was supported by the National Natural Science Foundation of China under NO. 31171233 (Y.Z.).
This article has been published as part of BMC Systems Biology Volume 6 Supplement 1, 2012: Selected articles from The 5th IEEE International Conference on Systems Biology (ISB 2011). The full contents of the supplement are available online at http://www.biomedcentral.com/bmcsystbiol/supplements/6/S1.
- Shinohara A, Ogawa T: Homologous recombination and the roles of double-strand breaks. Trends Biochem Sci. 1995, 20: 387-391. 10.1016/S0968-0004(00)89085-4.View ArticlePubMedGoogle Scholar
- Camerini-Otero RD, Hsieh P: Homologous recombination proteins in prokaryotes and eukaryotes. Annu Rev Genet. 1995, 29: 509-552. 10.1146/annurev.ge.29.120195.002453.View ArticlePubMedGoogle Scholar
- Kuzminov A: DNA replication meets genetic exchange: chromosomal damage and its repair by homologous recombination. Proc Natl Acad Sci USA. 2001, 98: 8461-8468. 10.1073/pnas.151260698.PubMed CentralView ArticlePubMedGoogle Scholar
- Yanowitz J: Meiosis: making a break for it. Curr Opin Cell Biol. 2010, 22: 744-751. 10.1016/j.ceb.2010.08.016.PubMed CentralView ArticlePubMedGoogle Scholar
- Lawrence JG, Retchless AC: The interplay of homologous recombination and horizontal gene transfer in bacterial speciation. Methods Mol Biol. 2009, 532: 29-53. 10.1007/978-1-60327-853-9_3.View ArticlePubMedGoogle Scholar
- Holliday R: A mechanism for gene conversion in fungi. Genet Res. 1964, 5: 282-304. 10.1017/S0016672300001233.View ArticleGoogle Scholar
- Constantinou A, Davies AA, West SC: Branch migration and Holliday junction resolution catalyzed by activities from mammalian cells. Cell. 2001, 104: 259-268. 10.1016/S0092-8674(01)00210-0.View ArticlePubMedGoogle Scholar
- Ho PS, Eichman BF: The crystal structures of DNA Holliday junctions. Curr Opin Struct Biol. 2001, 11: 302-308. 10.1016/S0959-440X(00)00219-0.View ArticlePubMedGoogle Scholar
- Sharples GJ, Ingleston SM, Lloyd RG: Holliday junction processing in bacteria: insights from the evolutionary conservation of RuvABC, RecG, and RusA. J Bacteriol. 1999, 181: 5543-5550.PubMed CentralPubMedGoogle Scholar
- White MF: Homologous recombination in the archaea: the means justify the ends. Biochem Soc Trans. 2011, 39: 15-19. 10.1042/BST0390015.View ArticlePubMedGoogle Scholar
- Sharples GJ: The X philes: structure-specific endonucleases that resolve Holliday junctions. Mol Microbiol. 2001, 39: 823-834. 10.1046/j.1365-2958.2001.02284.x.View ArticlePubMedGoogle Scholar
- Déclais AC, Lilley DM: New insight into the recognition of branched DNA structure by junction-resolving enzymes. Curr Opin Struct Biol. 2008, 18: 86-95. 10.1016/j.sbi.2007.11.001.View ArticlePubMedGoogle Scholar
- West SC: Enzymes and molecular mechanisms of genetic recombination. Annu Rev Biochem. 1992, 61: 603-640. 10.1146/annurev.bi.61.070192.003131.View ArticlePubMedGoogle Scholar
- Kowalczykowski SC, Dixon DA, Eggleston AK, Lauder SD, Rehrauer WM: Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev. 1994, 58: 401-465.PubMed CentralPubMedGoogle Scholar
- West SC: The RuvABC proteins and Holliday junction processing in Escherichia coli. J Bacteriol. 1996, 178: 1237-1241.PubMed CentralPubMedGoogle Scholar
- Donaldson JR, Courcelle CT, Courcelle J: RuvABC is required to resolve holliday junctions that accumulate following replication on damaged templates in Escherichia coli. J Biol Chem. 2006, 281: 28811-28821. 10.1074/jbc.M603933200.View ArticlePubMedGoogle Scholar
- Sanchez H, Kidane D, Reed P, Curtis FA, Cozar MC, Graumann PL, Sharples GJ, Alonso JC: The RuvAB branch migration translocase and RecU Holliday junction resolvase are required for double-stranded DNA break repair in Bacillus subtilis. Genetics. 2005, 171: 873-883. 10.1534/genetics.105.045906.PubMed CentralView ArticlePubMedGoogle Scholar
- Rocha EP, Cornet E, Michel B: Comparative and evolutionary analysis of the bacterial homologous recombination systems. PLoS Genet. 2005, 1: e15-10.1371/journal.pgen.0010015.PubMed CentralView ArticlePubMedGoogle Scholar
- Lloyd RG, Sharples GJ: Dissociation of synthetic Holliday junctions by E. coli RecG protein. EMBO J. 1993, 12: 17-22.PubMed CentralPubMedGoogle Scholar
- McGlynn P, Lloyd RG: Genome stability and the processing of damaged replication forks by RecG. Trends Genet. 2002, 18: 413-419. 10.1016/S0168-9525(02)02720-8.View ArticlePubMedGoogle Scholar
- Sharples GJ, Chan SN, Mahdi AA, Whitby MC, Lloyd RG: Processing of intermediates in recombination and DNA repair: identification of a new endonuclease that specifically cleaves Holliday junctions. EMBO J. 1994, 13: 6133-6142.PubMed CentralPubMedGoogle Scholar
- Chan SN, Vincent SD, Lloyd RG: Recognition and manipulation of branched DNA by the RusA Holliday junction resolvase of Escherichia coli. Nucleic Acids Res. 1998, 26: 1560-1566. 10.1093/nar/26.7.1560.PubMed CentralView ArticlePubMedGoogle Scholar
- Komori K, Sakae S, Shinagawa H, Morikawa K, Ishino Y: A Holliday junction resolvase from Pyrococcus furiosus: functional similarity to Escherichia coli RuvC provides evidence for conserved mechanism of homologous recombination in Bacteria, Eukarya, and Archaea. Proc Natl Acad Sci USA. 1999, 96: 8873-8878. 10.1073/pnas.96.16.8873.PubMed CentralView ArticlePubMedGoogle Scholar
- Daiyasu H, Komori K, Sakae S, Ishino Y, Toh H: Hjc resolvase is a distantly related member of the type II restriction endonuclease family. Nucleic Acids Res. 2000, 28: 4540-4543. 10.1093/nar/28.22.4540.PubMed CentralView ArticlePubMedGoogle Scholar
- Kleff S, Kemper B, Sternglanz R: Identification and characterization of yeast mutants and the gene for a cruciform cutting endonuclease. EMBO J. 1992, 11: 699-704.PubMed CentralPubMedGoogle Scholar
- White MF, Lilley DM: The resolving enzyme CCE1 of yeast opens the structure of the four-way DNA junction. J Mol Biol. 1997, 266: 122-134. 10.1006/jmbi.1996.0795.View ArticlePubMedGoogle Scholar
- White MF, Lilley DM: Characterization of a Holliday junction-resolving enzyme from Schizosaccharomyces pombe. Mol Cell Biol. 1997, 17: 6465-6471.PubMed CentralView ArticlePubMedGoogle Scholar
- Ip SC, Rass U, Blanco MG, Flynn HR, Skehel JM, West SC: Identification of Holliday junction resolvases from humans and yeast. Nature. 2008, 456: 357-361. 10.1038/nature07470.View ArticlePubMedGoogle Scholar
- Svendsen JM, Harper JW: GEN1/Yen1 and the SLX4 complex: Solutions to the problem of Holliday junction resolution. Genes Dev. 2010, 24: 521-536. 10.1101/gad.1903510.PubMed CentralView ArticlePubMedGoogle Scholar
- Rass U, Compton SA, Matos J, Singleton MR, Ip SC, Blanco MG, Griffith JD, West SC: Mechanism of Holliday junction resolution by the human GEN1 protein. Genes Dev. 2010, 24: 1559-1569. 10.1101/gad.585310.PubMed CentralView ArticlePubMedGoogle Scholar
- Baharoglu Z, Petranovic M, Flores MJ, Michel B: RuvAB is essential for replication forks reversal in certain replication mutants. EMBO J. 2006, 25: 596-604. 10.1038/sj.emboj.7600941.PubMed CentralView ArticlePubMedGoogle Scholar
- Bradley AS, Baharoglu Z, Niewiarowski A, Michel B, Tsaneva IR: Formation of a stable RuvA protein double tetramer is required for efficient branch migration in vitro and for replication fork reversal in vivo. J Biol Chem. 2011, 286: 22372-22383. 10.1074/jbc.M111.233908.PubMed CentralView ArticlePubMedGoogle Scholar
- West SC: Processing of recombination intermediates by the RuvABC proteins. Annu Rev Genet. 1997, 31: 213-244. 10.1146/annurev.genet.31.1.213.View ArticlePubMedGoogle Scholar
- Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P: Toward automatic reconstruction of a highly resolved tree of life. Science. 2006, 311: 1283-1287. 10.1126/science.1123061.View ArticlePubMedGoogle Scholar
- The STRING web server. [http://string.embl.de/]
- Zhuang Z, Song F, Martin BM, Dunaway-Mariano D: The YbgC protein encoded by the ybgC gene of the tol-pal gene cluster of Haemophilus influenzae catalyzes acyl-coenzyme A thioester hydrolysis. FEBS Lett. 2002, 516: 161-163. 10.1016/S0014-5793(02)02533-4.View ArticlePubMedGoogle Scholar
- Sturgis JN: Organisation and evolution of the tol-pal gene cluster. J Mol Microbiol Biotechnol. 2001, 3: 113-122.PubMedGoogle Scholar
- Kolker E, Makarova KS, Shabalina S, Picone AF, Purvine S, Holzman T, Cherny T, Armbruster D, Munson RS, Kolesov G, Frishman D, Galperin MY: Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. Nucleic Acids Res. 2004, 32: 2353-2361. 10.1093/nar/gkh555.PubMed CentralView ArticlePubMedGoogle Scholar
- Shin DH, Yokota H, Kim R, Kim SH: Crystal structure of conserved hypothetical protein Aq1575 from Aquifex aeolicus. Proc Natl Acad Sci USA. 2002, 99: 7980-7985. 10.1073/pnas.132241399.PubMed CentralView ArticlePubMedGoogle Scholar
- Liang H, Li L, Dong Z, Surette MG, Duan K: The YebC family protein PA0964 negatively regulates the Pseudomonas aeruginosa quinolone signal system and pyocyanin production. J Bacteriol. 2008, 190: 6217-6227. 10.1128/JB.00428-08.PubMed CentralView ArticlePubMedGoogle Scholar
- Weraarpachai W, Antonicka H, Sasarman F, Seeger J, Schrank B, Kolesar JE, Lochmüller H, Chevrette M, Kaufman BA, Horvath R, Shoubridge EA: Mutation in TACO1, encoding a translational activator of COX I, results in cytochrome c oxidase deficiency and late-onset Leigh syndrome. Nat Genet. 2009, 41: 833-837. 10.1038/ng.390.View ArticlePubMedGoogle Scholar
- Galperin MY, Koonin EV: From complete genome sequence to 'complete' understanding?. Trends Biotechnol. 2010, 28: 398-406. 10.1016/j.tibtech.2010.05.006.PubMed CentralView ArticlePubMedGoogle Scholar
- The NCBI Genome Table. [http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi]
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410.View ArticlePubMedGoogle Scholar
- Tatusov RL, Galperin MY, Natale DA, Koonin EV: The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000, 28: 33-36. 10.1093/nar/28.1.33.PubMed CentralView ArticlePubMedGoogle Scholar
- Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22: 4673-4680. 10.1093/nar/22.22.4673.PubMed CentralView ArticlePubMedGoogle Scholar
- Felsenstein J: PHYLIP: Phylogeny Inference Package (Version 3.2). Cladistics. 1989, 5: 164-166.Google Scholar