Crossing Isorthology and Microsynteny to Resolve Multigenic Families Functional Annotation

Despite the increasing availability of complete genomes and detailed protein annotations, highly paralogous gene families suffer the lack of precise functional annotation. Consequently, those genes are poorly or erroneously annotated in most genome releases. With the thousands of upcoming prokaryotic genomes, automated methods for the reliable transfer of annotation to sequences fulfilling the same function are becoming key to fully benefit these data. We present a generic strategy to identify, across multiple genomes, sets of genes most likely to have kept the same biological function.

[1]  S. Pongor,et al.  The quest for orthologs: finding the corresponding gene across genomes. , 2008, Trends in genetics : TIG.

[2]  B. Bassler,et al.  Regulation of Uptake and Processing of the Quorum-Sensing Autoinducer AI-2 in Escherichia coli , 2005, Journal of bacteriology.

[3]  D. P. Wall,et al.  Detecting putative orthologs , 2003, Bioinform..

[4]  Sven Bergmann,et al.  Iterative signature algorithm for the analysis of large-scale gene expression data. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[5]  A. Hosie,et al.  A Member of the Second Carbohydrate Uptake Subfamily of ATP-Binding Cassette Transporters Is Responsible for Ribonucleoside Uptake in Streptococcus mutans , 2006, Journal of bacteriology.

[6]  Yves Quentin,et al.  ABCdb: an online resource for ABC transporter repertories from sequenced archaeal and bacterial genomes. , 2006, FEMS microbiology letters.

[7]  Jue Chen,et al.  Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems , 2008, Microbiology and Molecular Biology Reviews.

[8]  Christophe Dessimoz,et al.  Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods , 2009, PLoS Comput. Biol..

[9]  M E J Newman,et al.  Finding and evaluating community structure in networks. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[10]  J. Griffith,et al.  Differential Single-stranded DNA Binding Properties of the Paralogous SsbA and SsbB Proteins from Streptococcus pneumoniae* , 2005, Journal of Biological Chemistry.

[11]  W. Fitch Homology a personal view on some of the problems. , 2000, Trends in genetics : TIG.

[12]  R. Overbeek,et al.  The use of gene clusters to infer functional coupling. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[13]  D. Lipman,et al.  A genomic perspective on protein families. , 1997, Science.

[14]  T. Gabaldón Large-scale assignment of orthology: back to phylogenetics? , 2008, Genome Biology.

[15]  P. Henderson,et al.  Molecular genetics of a receptor protein for D-xylose, encoded by the gene xylF, in Escherichia coli. , 1995, Receptors & channels.

[16]  G L Hazelbauer,et al.  Characterization of the mgl operon of Escherichia coli by transposon mutagenesis and molecular cloning , 1983, Journal of bacteriology.

[17]  Stijn van Dongen,et al.  Graph Clustering Via a Discrete Uncoupling Process , 2008, SIAM J. Matrix Anal. Appl..

[18]  E. Koonin Orthologs, Paralogs, and Evolutionary Genomics 1 , 2005 .

[19]  E. Koonin Orthologs, paralogs, and evolutionary genomics. , 2005, Annual review of genetics.

[20]  Christian E. V. Storm,et al.  Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. , 2001, Journal of molecular biology.