ArticleProceedings of the National Academy of Sciences of the United States of America2003
Predicting gene expression levels from codon biases in alpha-proteobacterial genomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 44 citations in OpenAlex.
- Article
- Identification of common highly expressed genes of Salmonella Enteritidis by in silico prediction of gene expression and in vitro transcriptomic analysis.Poultry science · 2019Article
- RegA, the regulator of the two-component system RegB/RegA of Brucella suis, is a controller of both oxidative respiration and denitrification required for chronic infection in mice.Infection and immunity · 2013Article
- Article
- Relationship between amino acid composition and gene expression in the mouse genome.BMC research notes · 2011Article
- The systemic imprint of growth and its uses in ecological (meta)genomics.PLoS genetics · 2010Article
- Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5.BMC genomics · 2009Article
- Predicting gene expression level from relative codon usage bias: an application to Escherichia coli genome.DNA research : an international journal for rapid publication of reports on genes and genomes · 2009Article
- Protein disorder is positively correlated with gene expression in Escherichia coli.Journal of proteome research · 2008Article
- HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection.Nucleic acids research · 2008Article
- Proteomic identification of tmRNA substrates.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Prediction of highly expressed genes in microbes based on chromatin accessibility.BMC molecular biology · 2007Article
- Analysis of the terminus region of the Caulobacter crescentus chromosome and identification of the dif site.Journal of bacteriology · 2006Article
- Distinguishing features of delta-proteobacterial genomes.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- Identification of Sinorhizobium meliloti early symbiotic genes by use of a positive functional screen.Applied and environmental microbiology · 2006Article
- Salmonella enterica highly expressed genes are disease specific.Infection and immunity · 2006Article
- An environmental signature for 323 microbial genomes based on codon adaptation indices.Genome biology · 2006Article
- Development of a functional genomics platform for Sinorhizobium meliloti: construction of an ORFeome.Applied and environmental microbiology · 2005Article
- Predicted highly expressed genes in archaeal genomes.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae.Nucleic acids research · 2005Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.