Using codon usage to predict genes origin: is the Escherichia coli outer membrane a patchwork of products from different genomes?

Analysis of the codon usage of genes coding for the structural components of the outer membrane in Escherichia coli, is consistent with the requirement for high expression of these genes. Because porins (which constitute the major protein component of the outer membrane), and LPS (which constitute the major outermost constituent of the outer membrane), are synthesized from genes displaying widely different codon usage, it is possible to investigate the origin of the outer membrane. The analysis predicts that the outer membrane might originate from a genome other than the genome coding for the major part of the cell. Such a special origin would explain in structural terms, the likely lethality of porins if they were inadvertently inserted within the inner membrane, giving rise to the Gram-negative bacterial type, having an envelope comprising two membranes, instead of a single cytoplasmic membrane and a murein sacculus.

[1]  R. Hancock,et al.  Lipopolysaccharide-free Escherichia coli OmpF and Pseudomonas aeruginosa protein P porins are functionally active in lipid bilayer membranes , 1986, Journal of bacteriology.

[2]  M. Hill.  Correspondence Analysis: A Neglected Multivariate Method , 1974 .

[3]  V. Emilsson,et al.  Growth rate dependence of transfer RNA abundance in Escherichia coli. , 1990, The EMBO journal.

[4]  Alain Hénaut,et al.  Merging of distance matrices and classification by dynamic clustering , 1988, Comput. Appl. Biosci..

[5]  F. Neidhardt,et al.  Linkage Map of Escherichia coli K-12 , 1987 .

[6]  Toshimichi Ikemura,et al.  Detection of genes in Escherichia coli sequences determined by genome projects and prediction of protein production levels, based on multivariate diversity in codon usage , 1996, Comput. Appl. Biosci..

[7]  W. Dowhan,et al.  Investigations on the association of phosphatidylserine synthase with the ribosomal component from Escherichia coli. , 1980, The Journal of biological chemistry.

[8]  A. Danchin,et al.  Comparison between the Escherichia coli and Bacillus subtilis genomes suggests that a major function of polynucleotide phosphorylase is to synthesize CDP. , 1997, DNA research : an international journal for rapid publication of reports on genes and genomes.

[9]  M. Gouy,et al.  Codon usage in bacteria: correlation with gene expressivity. , 1982, Nucleic acids research.

[10]  A Danchin,et al.  Colibri: a functional data base for the Escherichia coli genome. , 1993, Microbiological reviews.

[11]  K. Matsumoto,et al.  A regulatory mechanism for the balanced synthesis of membrane phospholipid species in Escherichia coli. , 1996, Bioscience, biotechnology, and biochemistry.

[12]  D. Zusman,et al.  The pss and psd genes are required for motility and chemotaxis in Escherichia coli , 1993, Journal of bacteriology.

[13]  R. Morona,et al.  Escherichia coli K-12 outer membrane protein (OmpA) as a bacteriophage receptor: analysis of mutant genes expressing altered proteins , 1984, Journal of bacteriology.

[14]  C. Funk,et al.  The pgpA and pgpB genes of Escherichia coli are not essential: evidence for a third phosphatidylglycerophosphate phosphatase , 1992, Journal of bacteriology.

[15]  T. Ikemura.  Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. , 1981, Journal of molecular biology.

[16]  D S Goodsell,et al.  Inside a living cell. , 1991, Trends in biochemical sciences.

[17]  A. Danchin,et al.  Evidence for horizontal gene transfer in Escherichia coli speciation. , 1991, Journal of molecular biology.

[18]  K. Matsumoto,et al.  Unbalanced membrane phospholipid compositions affect transcriptional expression of certain regulatory genes in Escherichia coli , 1997, Journal of bacteriology.

[19]  V. Emilsson,et al.  Growth-rate-dependent accumulation of twelve tRNA species in Escherichia coli. , 1993, Journal of molecular biology.

[20]  R. Macnab,et al.  Flagella and motility , 1996 .

[21]  N. Mackman,et al.  Genetics and biochemistry of the assembly of proteins into the outer membrane of E. coli. , 1987, Progress in biophysics and molecular biology.

[22]  T. Ikemura.  Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. , 1981, Journal of molecular biology.

[23]  B. Lugtenberg,et al.  Complete nucleotide sequence of phoE, the structural gene for the phosphate limitation inducible outer membrane pore protein of Escherichia coli K12. , 1983, Journal of molecular biology.