Bacterial Syntenies: an Exact Approach with Gene Quorum

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2011 May 25

PMID 21605461

Citations 8

Authors

Yves-Pol Denielou

Marie-France Sagot

Frederic Boyer

Alain Viari

Affiliations

Soon will be listed here.

Abstract

Background: The automatic identification of syntenies across multiple species is a key step in comparative genomics that helps biologists shed light both on evolutionary and functional problems.

Results: In this paper, we present a versatile tool to extract all syntenies from multiple bacterial species based on a clear-cut and very flexible definition of the synteny blocks that allows for gene quorum, partial gene correspondence, gaps, and a partial or total conservation of the gene order.

Conclusions: We apply this tool to two different kinds of studies. The first one is a search for functional gene associations. In this context, we compare our tool to a widely used heuristic--I-ADHORE--and show that at least up to ten genomes, the problem remains tractable with our exact definition and algorithm. The second application is linked to evolutionary studies: we verify in a multiple alignment setting that pairs of orthologs in synteny are more conserved than pairs outside, thus extending a previous pairwise study. We then show that this observation is in fact a function of the size of the synteny: the larger the block of synteny is, the more conserved the genes are.

Citing Articles

Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes.

Cifuente J, Colleoni C, Kalscheuer R, Guerin M Chem Rev. 2024; 124(8):4863-4934.

PMID: 38606812 PMC: 11046441. DOI: 10.1021/acs.chemrev.3c00811.

Pan-genome analyses of model fungal species.

McCarthy C, Fitzpatrick D Microb Genom. 2019; 5(2).

PMID: 30714895 PMC: 6421352. DOI: 10.1099/mgen.0.000243.

CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts.

Zaharia A, Labedan B, Froidevaux C, Denise A BMC Bioinformatics. 2019; 20(1):19.

PMID: 30630411 PMC: 6327494. DOI: 10.1186/s12859-018-2542-2.

Identification and Characterization of Differentially-Regulated Type IVb Pilin Genes Necessary for Predation in Obligate Bacterial Predators.

Avidan O, Petrenko M, Becker R, Beck S, Linscheid M, Pietrokovski S Sci Rep. 2017; 7(1):1013.

PMID: 28432347 PMC: 5430801. DOI: 10.1038/s41598-017-00951-w.

Finding approximate gene clusters with Gecko 3.

Winter S, Jahn K, Wehner S, Kuchenbecker L, Marz M, Stoye J Nucleic Acids Res. 2016; 44(20):9600-9610.

PMID: 27679480 PMC: 5175365. DOI: 10.1093/nar/gkw843.

References

Remm M, Storm C, Sonnhammer E . Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol. 2001; 314(5):1041-52. DOI: 10.1006/jmbi.2000.5197. View

Rodelsperger C, Dieterich C . Syntenator: multiple gene order alignments with a gene-specific scoring function. Algorithms Mol Biol. 2008; 3:14. PMC: 2590594. DOI: 10.1186/1748-7188-3-14. View

Lin S, Hanson R, Cronan J . Biotin synthesis begins by hijacking the fatty acid synthetic pathway. Nat Chem Biol. 2010; 6(9):682-8. PMC: 2925990. DOI: 10.1038/nchembio.420. View

Lemoine F, Lespinet O, Labedan B . Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data. BMC Evol Biol. 2007; 7:237. PMC: 2238764. DOI: 10.1186/1471-2148-7-237. View

Boyer F, Morgat A, Labarre L, Pothier J, Viari A . Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data. Bioinformatics. 2005; 21(23):4209-15. DOI: 10.1093/bioinformatics/bti711. View

Ogata H, Fujibuchi W, Goto S, Kanehisa M . A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. Nucleic Acids Res. 2000; 28(20):4021-8. PMC: 110779. DOI: 10.1093/nar/28.20.4021. View

He X, Goldwasser M . Identifying conserved gene clusters in the presence of homology families. J Comput Biol. 2005; 12(6):638-56. DOI: 10.1089/cmb.2005.12.638. View

Calabrese P, Chakravarty S, Vision T . Fast identification and statistical evaluation of segmental homologies in comparative maps. Bioinformatics. 2003; 19 Suppl 1:i74-80. DOI: 10.1093/bioinformatics/btg1008. View

Ling X, He X, Xin D, Han J, Han J . Efficiently identifying max-gap clusters in pairwise genome comparison. J Comput Biol. 2008; 15(6):593-609. DOI: 10.1089/cmb.2008.0010. View

10.

Koonin E, Wolf Y . Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res. 2008; 36(21):6688-719. PMC: 2588523. DOI: 10.1093/nar/gkn668. View

11.

Dandekar T, Snel B, Huynen M, Bork P . Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci. 1998; 23(9):324-8. DOI: 10.1016/s0968-0004(98)01274-2. View

12.

Tesler G . GRIMM: genome rearrangements web server. Bioinformatics. 2002; 18(3):492-3. DOI: 10.1093/bioinformatics/18.3.492. View

13.

Altenhoff A, Dessimoz C . Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol. 2009; 5(1):e1000262. PMC: 2612752. DOI: 10.1371/journal.pcbi.1000262. View

14.

Haas B, Delcher A, Wortman J, Salzberg S . DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics. 2004; 20(18):3643-6. DOI: 10.1093/bioinformatics/bth397. View

15.

Rodionov D, Mironov A, Gelfand M . Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea. Genome Res. 2002; 12(10):1507-16. PMC: 187538. DOI: 10.1101/gr.314502. View

16.

Pasek S, Bergeron A, Risler J, Louis A, Ollivier E, Raffinot M . Identification of genomic features using microsyntenies of domains: domain teams. Genome Res. 2005; 15(6):867-74. PMC: 1142477. DOI: 10.1101/gr.3638405. View

17.

Simillion C, Vandepoele K, Saeys Y, Van de Peer Y . Building genomic profiles for uncovering segmental homology in the twilight zone. Genome Res. 2004; 14(6):1095-106. PMC: 419788. DOI: 10.1101/gr.2179004. View

18.

Wang X, Shi X, Li Z, Zhu Q, Kong L, Tang W . Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice. BMC Bioinformatics. 2006; 7:447. PMC: 1626491. DOI: 10.1186/1471-2105-7-447. View

19.

Itoh T, Takemoto K, Mori H, Gojobori T . Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol Biol Evol. 1999; 16(3):332-46. DOI: 10.1093/oxfordjournals.molbev.a026114. View

20.

Montero M, Almagro G, Eydallin G, Viale A, Munoz F, Bahaji A . Escherichia coli glycogen genes are organized in a single glgBXCAP transcriptional unit possessing an alternative suboperonic promoter within glgC that directs glgAP expression. Biochem J. 2010; 433(1):107-17. DOI: 10.1042/BJ20101186. View