Conservation and evolution of the rpsU‐dnaG‐rpoD macromolecular synthesis operon in bacteria

The macromolecular synthesis (MMS) operon contains three essential genes (rpsU, dnaG, rpoD) whose products (S21, primase, sigma‐70) are necessary for the initiation of protein, DNA, and RNA synthesis respectively. PCR amplifications with primers complementary to conserved regions within these three genes, and subsequent DNA sequencing of rpsU—dnaG PCR products, demonstrate that the three genes appear to be contiguous in 11 different Gram‐negative species. Within the Gram‐negative enteric bacterial lineage, the S21 amino acid sequence is absolutely conserved in 10 species examined. The putative nuteq antiterminator sequence in rpsU consists of two motifs, boxA and boxB, conserved in primary sequence and secondary structure. The terminator sequence, Ti, located between rpsU and dnaG is conserved at 31 positions in nine enterobacterial species, suggesting the importance of primary sequence in addition to secondary structure for transcription termination. The intergenic region between rpsU and dnaG varies in size owing to the presence or absence of the Enterobacterial Repetitive Intergenic Consensus (ERIC) DNA element. The rpoD gene contains rearrangements involving a divergent sequence, although two carboxy‐terminal regions which encode functional domains are conserved in primary sequence and spacing. Our data suggest that primary sequence divergence and DNA rearrangements in both coding and non‐coding sequences account for the interspecies variation in operon structure. However, MMS operon gene organization and cis‐acting regulatory sequences appear to be conserved in diverse bacteria.

[1]  Michael Zuker,et al.  Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..

[2]  Y Yang,et al.  Mini-prep in ten minutes. , 1990, BioTechniques.

[3]  P. Sharp,et al.  ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. , 1991, Molecular microbiology.

[4]  J. Lupski,et al.  Role of the 5' upstream sequence and tandem promoters in regulation of the rpsU-dnaG-rpoD macromolecular synthesis operon , 1988, Journal of bacteriology.

[5]  J. Lupski,et al.  In vitro stimulation of Escherichia coli RNA polymerase sigma subunit synthesis by NusA protein. , 1985, Gene.

[6]  J. Lupski,et al.  Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. , 1991, Nucleic acids research.

[7]  W. Konigsberg,et al.  Evidence for use of rare codons in the dnaG gene and other regulatory genes of Escherichia coli. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[8]  H. Sambrook.  Molecular cloning : a laboratory manual. Cold Spring Harbor, NY , 1989 .

[9]  M. Susskind,et al.  A mutant Escherichia coli sigma 70 subunit of RNA polymerase with altered promoter specificity. , 1989, Journal of molecular biology.

[10]  J. Lupski,et al.  Mutations in the Escherichia coli dnaG gene suggest coupling between DNA replication and chromosome partitioning , 1991, Journal of bacteriology.

[11]  D. Friedman,et al.  Transcription-dependent competition for a host factor: the function and optimal sequence of the phage lambda boxA transcription antitermination signal. , 1990, Genes & development.

[12]  N. Franklin,et al.  Effects of all single base substitutions in the loop of boxB on antitermination of transcription by bacteriophage lambda's N protein. , 1989, Nucleic acids research.

[13]  J. van Duin,et al.  Basepairing potential of the 3' terminus of 16S RNA: dependence on the functional state of the 30S subunit and the presence of protein S21. , 1981, Nucleic acids research.

[14]  D. Court,et al.  The relationship between function and DNA sequence in an intercistronic regulatory region in phage λ , 1978, Nature.

[15]  T. Baker,et al.  Initiation of enzymatic replication at the origin of the Escherichia coli chromosome: primase as the sole priming enzyme. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[16]  J. Hein.  Unified approach to alignment and phylogenies. , 1990, Methods in enzymology.

[17]  J. Lupski,et al.  Short, interspersed repetitive DNA sequences in prokaryotic genomes , 1992, Journal of bacteriology.

[18]  D. Mead,et al.  Single-stranded DNA 'blue' T7 promoter plasmids: a versatile tandem promoter system for cloning and protein engineering. , 1986, Protein engineering.

[19]  D. Court,et al.  Functional importance of sequence in the stem-loop of a transcription terminator. , 1991, Science.

[20]  R. Szittner,et al.  Multiple repetitive elements and organization of the lux operons of luminescent terrestrial bacteria , 1992, Journal of bacteriology.

[21]  K. Lark.  Genetic control over the initiation of the synthesis of the short deoxynucleotide chains in E. coli. , 1972, Nature: New biology.

[22]  J. Lupski,et al.  The rpsU-dnaG-rpoD macromolecular synthesis operon of E. coli , 1984, Cell.

[23]  C. Chiaruttini,et al.  RNA--protein cross-linking. , 1988, Methods in enzymology.

[24]  R. Haselkorn,et al.  Isolation and characterization of the gene encoding the principal sigma factor of the vegetative cell RNA polymerase from the cyanobacterium Anabaena sp. strain PCC 7120 , 1991, Journal of bacteriology.

[25]  S. Inouye.  Cloning and DNA sequence of the gene coding for the major sigma factor from Myxococcus xanthus , 1990, Journal of bacteriology.

[26]  R. Burgess,et al.  The operen that encodes the sigma subunit of RNA polymerase also encodes ribosomal protein S21 and DNA primase in E. coli K12 , 1983, Cell.

[27]  V. Koronakis,et al.  Expression of the E.coli hemolysin secretion gene hlyB involves transcript anti-termination within the hly operon. , 1988, Nucleic acids research.

[28]  R. G. Lloyd,et al.  A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes. , 1990, Nucleic acids research.

[29]  James C. Hu,et al.  Altered promoter recognition by mutant forms of the sigma 70 subunit of Escherichia coli RNA polymerase. , 1989, Journal of molecular biology.

[30]  Kan Tanaka,et al.  Cloning and analysis of the gene (rpoDA) for the principal σ factor of Pseudomonas aeruginosa , 1991 .

[31]  D. Friedman,et al.  Analysis of nutR: A region of phage lambda required for antitermination of transcription , 1982, Cell.

[32]  C. Gross,et al.  Polypeptides containing highly conserved regions of transcription initiation factor σ 70 exhibit specificity of binding to promoter DNA , 1992, Cell.

[33]  F. Segal,et al.  A CHARACTERIZATION OF FIBRANT SEGAL CATEGORIES , 2006, math/0603400.

[34]  T. W. Stone,et al.  A DNA analysis program designed for computer novices working in an industrial-research environment , 1984, Nucleic Acids Res..

[35]  R. Doi,et al.  Nucleotide sequence and organization of Bacillus subtilis RNA polymerase major sigma (sigma 43) operon. , 1986, Nucleic acids research.

[36]  C. Wada,et al.  Genetic suppression of a dnaG mutation in Escherichia coli , 1989, Journal of bacteriology.

[37]  L. Brakier-Gingras,et al.  The anti-Shine-Dalgarno region in Escherichia coli 16S ribosomal RNA is not essential for the correct selection of translational starts. , 1990, Biochemistry.

[38]  R. Colwell,et al.  Taxonomy of Some Recently Described Species in the Family Enterobacteriaceae , 1976 .

[39]  A. Das,et al.  How the phage lambda N gene product suppresses transcription termination: communication of RNA polymerase with regulatory proteins mediated by signals in nascent RNA , 1992, Journal of bacteriology.

[40]  H. Winkler,et al.  Isolation and characterization of the gene coding for the major sigma factor of Rickettsia prowazekii DNA-dependent RNA polymerase. , 1992, Gene.

[41]  D. Higgins,et al.  See Blockindiscussions, Blockinstats, Blockinand Blockinauthor Blockinprofiles Blockinfor Blockinthis Blockinpublication Clustal: Blockina Blockinpackage Blockinfor Blockinperforming Multiple Blockinsequence Blockinalignment Blockinon Blockina Minicomputer Article Blockin Blockinin Blockin , 2022 .

[42]  J. Lupski,et al.  Dna → DNA, and DNA → RNA → protein: Orchestration by a single complex operon , 1989, BioEssays : news and reviews in molecular, cellular and developmental biology.

[43]  Lloyd M. Smith,et al.  Fluorescence detection in automated DNA sequence analysis , 1986, Nature.

[44]  D. Wood,et al.  Characterization of the gene coding for the Rickettsia prowazekii DNA primase analogue. , 1993, Gene.

[45]  J. Lupski,et al.  Sequences of the Escherichia coli dnaG primase gene and regulation of its expression. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[46]  M. Gribskov,et al.  The sigma 70 family: sequence conservation and evolutionary relationships , 1992, Journal of bacteriology.

[47]  D. K. Hawley,et al.  Compilation and analysis of Escherichia coli promoter DNA sequences. , 1983, Nucleic acids research.

[48]  P. Sharp,et al.  ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria , 1991, Molecular microbiology.

[49]  J. Lupski,et al.  Use of the polymerase chain reaction for physical mapping of Escherichia coli genes , 1991, Journal of bacteriology.

[50]  C. Woese,et al.  Bacterial evolution , 1987, Microbiological reviews.

[51]  R. Burgess,et al.  The nudeotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E. coil K12 , 1981 .

[52]  R. Miller,et al.  One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[53]  M. Chamberlin,et al.  Structure and function of bacterial sigma factors. , 1988, Annual review of biochemistry.

[54]  M Gribskov,et al.  Sigma factors from E. coli, B. subtilis, phage SP01, and phage T4 are homologous proteins. , 1986, Nucleic acids research.

[55]  J. Devereux,et al.  A comprehensive set of sequence analysis programs for the VAX , 1984, Nucleic Acids Res..

[56]  J. Greenblatt,et al.  Structure and associated DNA-helicase activity of a general transcription initiation factor that binds to RNA polymerase II , 1989, Nature.

[57]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[58]  R. Brimacombe,et al.  RNA-protein cross-linking in Escherichia coli ribosomal subunits: localization of sites on 16S RNA which are cross-linked to proteins S17 and S21 by treatment with 2-iminothiolane. , 1986, Nucleic acids research.

[59]  R. Burgess,et al.  Nucleotide sequence of the rpsU-dnaG-rpoD operon from Salmonella typhimurium and a comparison of this sequence with the homologous operon of Escherichia coli. , 1985, Gene.