This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Karlin, S.
Right arrow Articles by Kaiser, D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Karlin, S.
Right arrow Articles by Kaiser, D.

 Previous Article  |  Next Article 

Journal of Bacteriology, September 2001, p. 5025-5040, Vol. 183, No. 17
0021-9193/01/$04.00+0   DOI: 10.1128/JB.183.17.5025-5040.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.

Characterizations of Highly Expressed Genes of Four Fast-Growing Bacteria

Samuel Karlin,1,* Jan Mrázek,1 Allan Campbell,2 and Dale Kaiser3

Department of Mathematics, Stanford University, Stanford, California 94305-21251; Department of Biological Sciences, Stanford University, Stanford, California 94305-20502; and Department of Biochemistry, Stanford University, Stanford, California 94305-53073

Received 25 January 2001/Accepted 7 May 2001

Predicted highly expressed (PHX) genes are characterized for the completely sequenced genomes of the four fast-growing bacteria Escherichia coli, Haemophilus influenzae, Vibrio cholerae, and Bacillus subtilis. Our approach to ascertaining gene expression levels relates to codon usage differences among certain gene classes: the collection of all genes (average gene), the ensemble of ribosomal protein genes, major translation/transcription processing factors, and genes for polypeptides of chaperone/degradation complexes. A gene is predicted highly expressed (PHX) if its codon frequencies are close to those of the ribosomal proteins, major translation/transcription processing factor, and chaperone/degradation standards but strongly deviant from the average gene codon frequencies. PHX genes identified by their codon usage frequencies among prokaryotic genomes commonly include those for ribosomal proteins, major transcription/translation processing factors (several occurring in multiple copies), and major chaperone/degradation proteins. Also PHX genes generally include those encoding enzymes of essential energy metabolism pathways of glycolysis, pyruvate oxidation, and respiration (aerobic and anaerobic), genes of fatty acid biosynthesis, and the principal genes of amino acid and nucleotide biosyntheses. Gene classes generally not PHX include most repair protein genes, virtually all vitamin biosynthesis genes, genes of two-component sensor systems, most regulatory genes, and most genes expressed in stationary phase or during starvation. Members of the set of PHX aminoacyl-tRNA synthetase genes contrast sharply between genomes. There are also subtle differences among the PHX energy metabolism genes between E. coli and B. subtilis, particularly with respect to genes of the tricarboxylic acid cycle. The good agreement of PHX genes of E. coli and B. subtilis with high protein abundances, as assessed by two-dimensional gel determination, is verified. Relationships of PHX genes with stoichiometry, multifunctionality, and operon structures are also examined. The spatial distribution of PHX genes within each genome reveals clusters and significantly long regions without PHX genes.

* Corresponding author. Mailing address: Department of Mathematics, Stanford University, Stanford, CA 94305-2125. Phone: (650) 723-2204. Fax: (650) 725-2040. E-mail: karlin{at}math.stanford.edu.

Journal of Bacteriology, September 2001, p. 5025-5040, Vol. 183, No. 17
0021-9193/01/$04.00+0   DOI: 10.1128/JB.183.17.5025-5040.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.


This article has been cited by other articles:

  • Golovina, A. Y., Sergiev, P. V., Golovin, A. V., Serebryakova, M. V., Demina, I., Govorun, V. M., Dontsova, O. A. (2009). The yfiC gene of E. coli encodes an adenine-N6 methyltransferase that specifically modifies A37 of tRNA1Val(cmo5UAC). RNA 15: 1134-1141 [Abstract] [Full Text]  
  • Roymondal, U., Das, S., Sahoo, S. (2009). Predicting Gene Expression Level from Relative Codon Usage Bias: An Application to Escherichia coli Genome. DNA Res 16: 13-30 [Abstract] [Full Text]  
  • Suzuki, H., Brown, C. J., Forney, L. J., Top, E. M. (2008). Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria. DNA Res 15: 357-365 [Abstract] [Full Text]  
  • LaRocque, R. C., Krastins, B., Harris, J. B., Lebrun, L. M., Parker, K. C., Chase, M., Ryan, E. T., Qadri, F., Sarracino, D., Calderwood, S. B. (2008). Proteomic Analysis of Vibrio cholerae in Human Stool. Infect. Immun. 76: 4145-4151 [Abstract] [Full Text]  
  • Puigbo, P., Romeu, A., Garcia-Vallve, S. (2008). HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection. Nucleic Acids Res 36: D524-D527 [Abstract] [Full Text]  
  • Henry, I., Sharp, P. M. (2007). Predicting Gene Expression Level from Codon Usage Bias. Mol Biol Evol 24: 10-12 [Abstract] [Full Text]  
  • Karlin, S., Brocchieri, L., Mrazek, J., Kaiser, D. (2006). Distinguishing features of {delta}-proteobacterial genomes. Proc. Natl. Acad. Sci. USA 103: 11352-11357 [Abstract] [Full Text]  
  • Rollenhagen, C., Bumann, D. (2006). Salmonella enterica Highly Expressed Genes Are Disease Specific. Infect. Immun. 74: 1649-1660 [Abstract] [Full Text]  
  • Meinersmann, R. J., Phillips, R. W., Hiett, K. L., Fedorka-Cray, P. (2005). Differentiation of Campylobacter Populations as Demonstrated by Flagellin Short Variable Region Sequences. Appl. Environ. Microbiol. 71: 6368-6374 [Abstract] [Full Text]  
  • Karlin, S. (2005). Colloquium Perspective: Statistical signals in bioinformatics. Proc. Natl. Acad. Sci. USA 102: 13355-13362 [Abstract] [Full Text]  
  • Wu, G., Culley, D. E., Zhang, W. (2005). Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermitilis and the implications for their metabolism. Microbiology 151: 2175-2187 [Abstract] [Full Text]  
  • Gurvich, O. L., Baranov, P. V., Gesteland, R. F., Atkins, J. F. (2005). Expression Levels Influence Ribosomal Frameshifting at the Tandem Rare Arginine Codons AGG_AGG and AGA_AGA in Escherichia coli. J. Bacteriol. 187: 4023-4032 [Abstract] [Full Text]  
  • Karlin, S., Mrazek, J., Ma, J., Brocchieri, L. (2005). Predicted highly expressed genes in archaeal genomes. Proc. Natl. Acad. Sci. USA 102: 7303-7308 [Abstract] [Full Text]  
  • Lithwick, G., Margalit, H. (2005). Relative predicted protein levels of functionally associated proteins are conserved across organisms. Nucleic Acids Res 33: 1051-1057 [Abstract] [Full Text]  
  • Martin-Galiano, A. J., Wells, J. M., de la Campa, A. G. (2004). Relationship between codon biased genes, microarray expression values and physiological characteristics of Streptococcus pneumoniae. Microbiology 150: 2313-2325 [Abstract] [Full Text]  
  • Kolker, E., Makarova, K. S., Shabalina, S., Picone, A. F., Purvine, S., Holzman, T., Cherny, T., Armbruster, D., Munson, R. S. Jr, Kolesov, G., Frishman, D., Galperin, M. Y. (2004). Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. Nucleic Acids Res 32: 2353-2361 [Abstract] [Full Text]  
  • Karlin, S., Theriot, J., Mrazek, J. (2004). Comparative analysis of gene expression among low G+C gram-positive genomes. Proc. Natl. Acad. Sci. USA 101: 6182-6187 [Abstract] [Full Text]  
  • Bausch, C., Ramsey, M., Conway, T. (2004). Transcriptional Organization and Regulation of the L-Idonic Acid Pathway (GntII System) in Escherichia coli. J. Bacteriol. 186: 1388-1397 [Abstract] [Full Text]  
  • Lithwick, G., Margalit, H. (2003). Hierarchy of Sequence-Dependent Features Associated With Prokaryotic Translation. Genome Res 13: 2665-2673 [Abstract] [Full Text]  
  • Karlin, S., Barnett, M. J., Campbell, A. M., Fisher, R. F., Mrazek, J. (2003). Predicting gene expression levels from codon biases in {alpha}-proteobacterial genomes. Proc. Natl. Acad. Sci. USA 100: 7313-7318 [Abstract] [Full Text]  
  • Jansen, R., Bussemaker, H. J., Gerstein, M. (2003). Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models. Nucleic Acids Res 31: 2242-2251 [Abstract] [Full Text]  
  • Kleerebezem, M., Boekhorst, J., van Kranenburg, R., Molenaar, D., Kuipers, O. P., Leer, R., Tarchini, R., Peters, S. A., Sandbrink, H. M., Fiers, M. W. E. J., Stiekema, W., Lankhorst, R. M. K., Bron, P. A., Hoffer, S. M., Groot, M. N. N., Kerkhoven, R., de Vries, M., Ursing, B., de Vos, W. M., Siezen, R. J. (2003). Complete genome sequence of Lactobacillus plantarum WCFS1. Proc. Natl. Acad. Sci. USA 100: 1990-1995 [Abstract] [Full Text]  
  • Ma, J., Campbell, A., Karlin, S. (2002). Correlations between Shine-Dalgarno Sequences and Gene Features Such as Predicted Expression Levels and Operon Structures. J. Bacteriol. 184: 5733-5745 [Abstract] [Full Text]  
  • Akashi, H., Gojobori, T. (2002). Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc. Natl. Acad. Sci. USA 99: 3695-3700 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»