Selection for Unequal Densities of σ70 Promoter-Like Signals in Different Regions of Large Bacterial Genomes
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Julio Collado-Vides | Enrique Morett | Araceli M Huerta | M. Pilar Francino | J. Collado-Vides | E. Morett | M. P. Francino | A. M. Huerta
[1] D. K. Hawley,et al. Compilation and analysis of Escherichia coli promoter DNA sequences. , 1983, Nucleic acids research.
[2] J. Gralla,et al. Escherichia coli promoter opening and −10 recognition: mutational analysis of σ70 , 2000 .
[3] W. Reznikoff,et al. The lactose operon‐controlling elements: a complex paradigm , 1992, Molecular microbiology.
[4] G. Mittenhuber. An inventory of genes encoding RNA polymerase sigma factors in 31 completely sequenced eubacterial genomes. , 2002, Journal of molecular microbiology and biotechnology.
[5] M. Madan Babu. Did the loss of sigma factors initiate pseudogene accumulation in M. leprae? , 2003, Trends in microbiology.
[6] J. Collado-Vides,et al. Bacterial regulatory networks are extremely flexible in evolution , 2006, Nucleic acids research.
[7] C. Waldburger,et al. Changes in conserved region 2 of Escherichia coli sigma 70 affecting promoter recognition. , 1990, Journal of molecular biology.
[8] N. Moran,et al. Calibrating bacterial evolution. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[9] Sarath Chandra Janga,et al. Conservation of adjacency as evidence of paralogous operons. , 2004, Nucleic acids research.
[10] W. McClure,et al. Competing promoters in prokaryotic transcription. , 1991, Trends in biochemical sciences.
[11] Jason E Stajich,et al. The effects of selection against spurious transcription factor binding sites. , 2003, Molecular biology and evolution.
[12] J. Gralla,et al. Escherichia coli promoter opening and -10 recognition: mutational analysis of sigma70. , 2000, The EMBO journal.
[13] Jacques van Helden,et al. Regulatory Sequence Analysis Tools , 2003, Nucleic Acids Res..
[14] Larry Wall,et al. Programming Perl , 1991 .
[15] N. Moran,et al. Consequences of reductive evolution for gene expression in an obligate endosymbiont , 2003, Molecular microbiology.
[16] N. Moran. Accelerated evolution and Muller's rachet in endosymbiotic bacteria. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[17] Julio Collado-Vides,et al. Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. , 2003, Journal of molecular biology.
[18] Gary D. Stormo,et al. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences , 1999, Bioinform..
[19] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[20] J. Paul Tremblay,et al. Discrete Mathematical Structures with Applications to Computer Science , 1975 .
[21] H. Margalit,et al. Compilation of E. coli mRNA promoter sequences. , 1993, Nucleic acids research.
[22] B. Barrell,et al. Massive gene decay in the leprosy , 2001 .
[23] John D. Helmann,et al. Protein family review - The sigma(70) family of sigma factors , 2003 .
[24] Takeshi Itoh,et al. Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[25] Jayanta Mukhopadhyay,et al. The sigma 70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter. , 2004, Nature structural & molecular biology.
[26] N. Moran,et al. Regulation of Transcription in a Reduced Bacterial Genome: Nutrient-Provisioning Genes of the Obligate Symbiont Buchnera aphidicola , 2005, Journal of bacteriology.
[27] C. Waldburger,et al. Changes in conserved region 2 of Escherichia coli σ70 affecting promoter recognition , 1990 .
[28] M. Gribskov,et al. The sigma 70 family: sequence conservation and evolutionary relationships , 1992, Journal of bacteriology.
[29] A. Mira,et al. The silencing of pseudogenes. , 2005, Molecular biology and evolution.
[30] B. Barrell,et al. Massive gene decay in the leprosy bacillus , 2001, Nature.
[31] N. Moran,et al. Genomic changes following host restriction in bacteria. , 2004, Current opinion in genetics & development.
[32] T. Smith,et al. Transcription unit conservation in the three domains of life: a perspective from Escherichia coli. , 2001, Trends in genetics : TIG.
[33] N. Zenkin,et al. The σ70 subunit of RNA polymerase induces lacUV5 promoter-proximal pausing of transcription , 2004, Nature Structural &Molecular Biology.
[34] D. Wall,et al. Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia. , 2003, Microbiology.
[35] W. Reznikoff,et al. The -45 region of the Escherichia coli lac promoter: CAP-dependent and CAP-independent transcription , 1997, Journal of bacteriology.
[36] Julio Collado-Vides,et al. RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions , 2005, Nucleic Acids Res..
[37] M. Wösten. Eubacterial sigma-factors. , 1998, FEMS microbiology reviews.
[38] M. Babu. Did the loss of sigma factors initiate pseudogene accumulation in M. leprae , 2003 .
[39] G. Stormo. Information content and free energy in DNA--protein interactions. , 1998, Journal of theoretical biology.
[40] J. Helmann,et al. The σ70family of sigma factors , 2003, Genome Biology.
[41] Julio Collado-Vides,et al. A powerful non-homology method for the prediction of operons in prokaryotes , 2002, ISMB.
[42] J. Stone,et al. Rapid evolution of cis-regulatory sequences via local point mutations. , 2001, Molecular biology and evolution.
[43] M. Susskind,et al. A mutant Escherichia coli sigma 70 subunit of RNA polymerase with altered promoter specificity. , 1989, Journal of molecular biology.
[44] M A Savageau,et al. Demand theory of gene regulation. I. Quantitative development of the theory. , 1998, Genetics.
[45] M. Shimizu,et al. Leaf-specifically expressed genes for polypeptides destined for chloroplasts with domains of sigma70 factors of bacterial RNA polymerases in Arabidopsis thaliana. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[46] J. A. Goodrich,et al. Regulation of open complex formation at the Escherichia coli galactose operon promoters. Simultaneous interaction of RNA polymerase, gal repressor and CAP/cAMP. , 1992, Journal of molecular biology.
[47] D. J. Funk,et al. A conservative test of genetic drift in the endosymbiotic bacterium Buchnera: slightly deleterious mutations in the chaperonin groEL. , 2003, Genetics.
[48] C. Gross,et al. Multiple sigma subunits and the partitioning of bacterial transcription space. , 2003, Annual review of microbiology.
[49] Jayanta Mukhopadhyay,et al. The σ70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter , 2004, Nature Structural &Molecular Biology.
[50] A. Dombroski. Recognition of the -10 promoter sequence by a partial polypeptide of sigma70 in vitro. , 1997, The Journal of biological chemistry.
[51] A A Deev,et al. Non-canonical sequence elements in the promoter structure. Cluster analysis of promoters recognized by Escherichia coli RNA polymerase. , 1997, Nucleic acids research.