title: Segmentally variable genes: a new perspective on adaptation.
abstract: Genomic sequence variation is the hallmark of life and is key to understanding diversity and adaptation among the numerous microorganisms on earth. Analysis of the sequenced microbial genomes suggests that genes are evolving at many different rates. We have attempted to derive a new classification of genes into three broad categories: lineage-specific genes that evolve rapidly and appear unique to individual species or strains; highly conserved genes that frequently perform housekeeping functions; and partially variable genes that contain highly variable regions, at least 70 amino acids long, interspersed among well-conserved regions. The latter we term segmentally variable genes (SVGs), and we suggest that they are especially interesting targets for biochemical studies. Among these genes are ones necessary to deal with the environment, including genes involved in host-pathogen interactions, defense mechanisms, and intracellular responses to internal and environmental changes. For the most part, the detailed function of these variable regions remains unknown. We propose that they are likely to perform important binding functions responsible for protein-protein, protein-nucleic acid, or protein-small molecule interactions. Discerning their function and identifying their binding partners may offer biologists new insights into the basic mechanisms of adaptation, context-dependent evolution, and the interaction between microbes and their environment.
authors.affiliation: Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, USA. zhengyu@bu.edu
authors.forename: Yu
authors.initials: Y
authors.lastname: Zheng
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Roberts
authors.forename: Simon
authors.initials: S
authors.lastname: Kasif
mesh_terms: D000064:Acclimatization; D001412:Bacillus subtilis / Q000235:genetics; D001425:Bacterial Outer Membrane Proteins / Q000378:metabolism; D001692:Biological Transport; D019070:Cell Lineage; D004247:DNA / Q000737:chemistry; D030541:Databases, Genetic; D019143:Evolution, Molecular; D020440:Gene Duplication; D014644:Genetic Variation; D016680:Genome, Bacterial; D016480:Helicobacter pylori / Q000378:metabolism; D015233:Models, Statistical; D005810:Multigene Family; D017434:Protein Structure, Tertiary; D012313:RNA / Q000737:chemistry; D015398:Signal Transduction; D014158:Transcription, Genetic
chemical_list: D001425:Bacterial Outer Membrane Proteins; D012313:RNA; D004247:DNA