title: Predicting gene expression levels from codon biases in alpha-proteobacterial genomes.
abstract: Predicted highly expressed (PHX) genes in five currently available high G+C complete alpha-proteobacterial genomes are analyzed. These include: the nitrogen-fixing plant symbionts Sinorhizobium meliloti (SINME) and Mesorhizobium loti (MESLO), the nonpathogenic aquatic bacterium Caulobacter crescentus (CAUCR), the plant pathogen Agrobacterium tumefaciens (AGRTU), and the mammalian pathogen Brucella melitensis (BRUME). Three of these genomes, SINME, AGRTU, and BRUME, contain multiple chromosomes or megaplasmids (>1 Mb length). PHX genes in these genomes are concentrated mainly in the major (largest) chromosome with few PHX genes found in the secondary chromosomes and megaplasmids. Tricarboxylic acid cycle and aerobic respiration genes are strongly PHX in all five genomes, whereas anaerobic pathways of glycolysis and fermentation are mostly not PHX. Only in MESLO (but not SINME) and BRUME are most glycolysis genes PHX. Many flagellar genes are PHX in MESLO and CAUCR, but mostly are not PHX in SINME and AGRTU. The nonmotile BRUME also carries many flagellar genes but these are generally not PHX and all but one are located in the second chromosome. CAUCR stands out among available prokaryotic genomes with 25 PHX TonB-dependent receptors. These are putatively involved in uptake of iron ions and other nonsoluble compounds.
authors.affiliation: Department of Mathematics, Stanford University, Stanford, CA 94305, USA. karlin@math.stanford.edu
authors.forename: Samuel
authors.initials: S
authors.lastname: Karlin
authors.forename: Melanie J
authors.initials: MJ
authors.lastname: Barnett
authors.forename: Allan M
authors.initials: AM
authors.lastname: Campbell
authors.forename: Robert F
authors.initials: RF
authors.lastname: Fisher
authors.forename: Jan
authors.initials: J
authors.lastname: Mrazek
mesh_terms: D016960:Agrobacterium tumefaciens / Q000235:genetics / Q000378:metabolism; D020561:Alphaproteobacteria / Q000235:genetics* / Q000378:metabolism; D001482:Base Composition; D017347:Brucella melitensis / Q000235:genetics / Q000378:metabolism; D016935:Caulobacter crescentus / Q000235:genetics / Q000378:metabolism; D002952:Citric Acid Cycle / Q000235:genetics; D003062:Codon / Q000235:genetics*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004734:Energy Metabolism / Q000235:genetics; D005407:Flagella / Q000235:genetics; D015870:Gene Expression; D016680:Genome, Bacterial; D008658:Inactivation, Metabolic / Q000235:genetics; D005810:Multigene Family; D009586:Nitrogen Fixation / Q000235:genetics; D016962:Sinorhizobium meliloti / Q000235:genetics / Q000378:metabolism; D013045:Species Specificity
chemical_list: D003062:Codon; D004269:DNA, Bacterial