Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes.

The DNA sequence of 91.4 kilobases of the Escherichia coli K-12 genome, spanning the region between rrnC at 84.5 minutes and rrnA at 86.5 minutes on the genetic map (85 to 87 percent on the physical map), is described. Analysis of this sequence identified 82 potential coding regions (open reading frames) covering 84 percent of the sequenced interval. The arrangement of these open reading frames, together with the consensus promoter sequences and terminator-like sequences found by computer searches, made it possible to assign them to proposed transcriptional units. More than half the open reading frames correlated with known genes or functions suggested by similarity to other sequences. Those remaining encode still unidentified proteins. The sequenced region also contains several RNA genes and two types of repeated sequence elements were found. Intergenic regions include three "gray holes," 0.6 to 0.8 kilobases, with no recognizable functions.

[1]  B. Dujon,et al.  The complete DNA sequence of yeast chromosome III , 1992, Nature.

[2]  U. Meier-Dieter,et al.  Nucleotide sequence of the Escherichia coli rfe gene involved in the synthesis of enterobacterial common antigen. Molecular cloning of the rfe-rff gene cluster. , 1992, The Journal of biological chemistry.

[3]  M. Cashel,et al.  rhlB, a new Escherichia coli K-12 gene with an RNA helicase-like protein sequence motif, one of at least five such possible genes in a prokaryote. , 1991, The New biologist.

[4]  Y. Arakawa,et al.  Cloning and expression of the rfe–rff gene cluster of Escherichia coli , 1991, Molecular microbiology.

[5]  K. Rudd,et al.  deaD, a new Escherichia coli gene encoding a presumed ATP-dependent RNA helicase, can suppress a mutation in rpsB, the gene encoding ribosomal protein S2 , 1991, Journal of bacteriology.

[6]  H. Jörnvall,et al.  Characterization of the flavin reductase gene (fre) of Escherichia coli and construction of a plasmid for overproduction of the enzyme , 1991, Journal of bacteriology.

[7]  A. Shatkin,et al.  Escherichia coli kgtP encodes an alpha-ketoglutarate transporter. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[8]  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.

[9]  E. Meighen.  Molecular biology of bacterial bioluminescence , 1991 .

[10]  S. Harayama,et al.  Primary structure of xylene monooxygenase: similarities to and differences from the alkane hydroxylation system , 1991, Journal of bacteriology.

[11]  B. Bachmann,et al.  Linkage Map of Escherichia coli K-12, Edition 8 , 1991, Microbiological reviews.

[12]  C. Waldburger,et al.  Hierarchies of base pair preferences in the P22 ant promoter , 1991, Journal of bacteriology.

[13]  W Miller,et al.  Mapping sequenced E.coli genes by computer: software, strategies and examples. , 1991, Nucleic acids research.

[14]  J. Steitz,et al.  Alive with DEAD proteins , 1991, Nature.

[15]  R Wahl,et al.  Compilation of DNA sequences of Escherichia coli (update 1991). , 1991, Nucleic acids research.

[16]  P. Hantzopoulos,et al.  Sequence and transcriptional activity of the Escherichia coli K-12 chromosome region between rrnC and ilvGMEDA. , 1991, Gene.

[17]  E. Meighen,et al.  A new Vibrio fischeri lux gene precedes a bidirectional termination site for the lux operon , 1990, Journal of bacteriology.

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

[19]  H. Inokuchi,et al.  Nucleotide sequence between the fadB gene and the rrnA operon from Escherichia coli. , 1990, Nucleic acids research.

[20]  D. Lane,et al.  Identification of a putative RNA helicase in E.coli. , 1990, Nucleic acids research.

[21]  A. Christensen,et al.  A novel RNA helicase gene tightly linked to the Triplo-lethal locus of Drosophila. , 1990, Nucleic acids research.

[22]  N. Brot,et al.  Structure-function studies on Escherichia coli MetR protein, a putative prokaryotic leucine zipper protein. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[23]  W. Coleman,et al.  Cloning, expression, and characterization of the Escherichia coli K-12 rfaD gene , 1990, Journal of bacteriology.

[24]  G. Schiedner,et al.  Complete cDNA sequence of the human p68 protein. , 1990, Nucleic acids research.

[25]  D. Daniels.  The complete AvrII restriction map of the Escherichia coli genome and comparisons of several laboratory strains. , 1990, Nucleic acids research.

[26]  H. Azakami,et al.  A sulfur- and tyramine-regulated Klebsiella aerogenes operon containing the arylsulfatase (atsA) gene and the atsB gene , 1990, Journal of bacteriology.

[27]  S. Cole,et al.  Nucleotide sequence of the aroP gene encoding the general aromatic amino acid transport protein of Escherichia coli K-12: homology with yeast transport proteins. , 1990, Nucleic acids research.

[28]  M. Ikeda,et al.  Nucleotide sequence involving murD and an open reading frame ORF-Y spacing murF and ftsW in Escherichia coli. , 1990, Nucleic acids research.

[29]  E. Meighen,et al.  Delineation of the transcriptional boundaries of the lux operon of Vibrio harveyi demonstrates the presence of two new lux genes. , 1990, The Journal of biological chemistry.

[30]  A. Chakrabarty,et al.  Nucleotide sequencing and characterization of Pseudomonas putida catR: a positive regulator of the catBC operon is a member of the LysR family , 1990, Journal of bacteriology.

[31]  T. Imanaka,et al.  Nucleotide sequence and cloning in Bacillus subtilis of the Bacillus stearothermophilus pleiotropic regulatory gene degT , 1990, Journal of bacteriology.

[32]  S. Henikoff,et al.  Finding protein similarities with nucleotide sequence databases. , 1990, Methods in enzymology.

[33]  G. Salmond,et al.  The methane monooxygenase gene cluster of Methylococcus capsulatus (Bath). , 1990, Gene.

[34]  H. Berg.  Cold Spring Harbor Symposia on Quantitative Biology.: Vol. LII. Evolution of Catalytic Functions. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1987, ISBN 0-87969-054-2, xix + 955 pp., US $150.00. , 1989 .

[35]  M. Grenson,et al.  Nucleotide sequence of the Saccharomyces cerevisiae PUT4 proline-permease-encoding gene: similarities between CAN1, HIP1 and PUT4 permeases. , 1989, Gene.

[36]  P. Leadlay,et al.  Molecular characterization of a gene from Saccharopolyspora erythraea (Streptomyces erythraeus) which is involved in erythromycin biosynthesis , 1989, Molecular Microbiology.

[37]  P. Reeves,et al.  Identification and sequence of rfbS and rfbE, which determine antigenic specificity of group A and group D salmonellae , 1989, Journal of bacteriology.

[38]  M. Bölker,et al.  The Escherichia coli regulatory protein OxyR discriminates between methylated and unmethylated states of the phage Mu mom promoter. , 1989, The EMBO journal.

[39]  J. Hershey,et al.  Corrigendum: An elF-4A-like protein is a suppressor of an Escherichia coli mutant defective in 5OS ribosomal subunit assembly , 1989, Nature.

[40]  C. Scazzocchio,et al.  The proline transport protein of Aspergillus nidulans is very similar to amino acid transporters of Saccharomyces cerevisiae , 1989, Molecular microbiology.

[41]  P. Leroy,et al.  The protein encoded by a murine male germ cell-specific transcript is a putative ATP-dependent RNA helicase , 1989, Cell.

[42]  G. Storz,et al.  OxyR, a positive regulator of hydrogen peroxide-inducible genes in Escherichia coli and Salmonella typhimurium, is homologous to a family of bacterial regulatory proteins. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[43]  K. Titani,et al.  Primary structure and gene localization of human prolidase. , 1989, The Journal of biological chemistry.

[44]  C. Stein,et al.  Cloning and expression of human arylsulfatase A. , 1989, The Journal of biological chemistry.

[45]  G. Faye,et al.  Mitochondrial splicing requires a protein from a novel helicase family , 1989, Nature.

[46]  M. Kröger,et al.  Compilation of DNA sequences of Escherichia coli. , 1989, Nucleic acids research.

[47]  R. Shoeman,et al.  Regulation of methionine synthesis in Escherichia coli: effect of the MetR protein on the expression of the metE and metR genes. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[48]  J. Hershey,et al.  An eIF-4A-like protein is a suppressor of an Escherichia coli mutant defective in 50S ribosomal subunit assembly , 1988, Nature.

[49]  Y. Jan,et al.  A protein component of Drosophila polar granules is encoded by vasa and has extensive sequence similarity to ATP-dependent helicases , 1988, Cell.

[50]  P. Slonimski,et al.  Sequence of the genes TIF1 and TIF2 from Saccharomyces cerevisiae coding for a translation initiation factor. , 1988, Nucleic acids research.

[51]  D. Henner,et al.  Localization of Bacillus subtilis sacU(Hy) mutations to two linked genes with similarities to the conserved procaryotic family of two-component signalling systems , 1988, Journal of bacteriology.

[52]  M. Ashburner,et al.  The product of the Drosophila gene vasa is very similar to eukaryotic initiation factor-4A , 1988, Nature.

[53]  S Henikoff,et al.  A large family of bacterial activator proteins. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[54]  R. C. Dickson,et al.  Nucleotide sequence of the galactose gene cluster of Kluyveromyces lactis. , 1988, Nucleic acids research.

[55]  P. Matsumura,et al.  Flagellar transcriptional activators FlbB and FlaI: gene sequences and 5' consensus sequences of operons under FlbB and FlaI control , 1988, Journal of bacteriology.

[56]  F. Schmidt,et al.  Gene organization and structure of the Streptomyces lividans gal operon , 1988, Journal of bacteriology.

[57]  A. Ebert,et al.  Gene cluster for streptomycin biosynthesis in Streptomyces griseus: nucleotide sequence of three genes and analysis of transcriptional activity. , 1987, Nucleic acids research.

[58]  K. Isono,et al.  The physical map of the whole E. coli chromosome: Application of a new strategy for rapid analysis and sorting of a large genomic library , 1987, Cell.

[59]  K. Smith,et al.  Comparison of the rep-38 and mmrA1 mutations of Escherichia coli. , 1987, Mutation research.

[60]  C. Cantor,et al.  A physical map of the Escherichia coli K12 genome. , 1987, Science.

[61]  A. Chakrabarty,et al.  Pseudomonas aeruginosa infection in cystic fibrosis: nucleotide sequence and transcriptional regulation of the algD gene. , 1987, Nucleic acids research.

[62]  N. M. Kredich,et al.  DNA sequences of the cysB regions of Salmonella typhimurium and Escherichia coli. , 1987, The Journal of biological chemistry.

[63]  F. Blattner,et al.  Mapping using gene encyclopaedias , 1987, Nature.

[64]  C. Gilchrist,et al.  Escherichia coli rep gene: sequence of the gene, the encoded helicase, and its homology with uvrD. , 1987, Nucleic acids research.

[65]  Y. Kim,et al.  Primary structure of CTP:CMP-3-deoxy-D-manno-octulosonate cytidylyltransferase (CMP-KDO synthetase) from Escherichia coli. , 1986, The Journal of biological chemistry.

[66]  K. Shigesada,et al.  Autogenous regulation of the gene for transcription termination factor rho in Escherichia coli: localization and function of its attenuators , 1986, Journal of bacteriology.

[67]  A. Rehemtulla,et al.  Cloning and analysis of the sfrB (sex factor repression) gene of Escherichia coli K-12 , 1986, Journal of bacteriology.

[68]  G. W. Hatfield,et al.  Nucleotide sequence and in vivo expression of the ilvY and ilvC genes in Escherichia coli K12. Transcription from divergent overlapping promoters. , 1986, The Journal of biological chemistry.

[69]  H. Matsuo,et al.  Determination of the initiation sites of transcription and translation of the uvrD gene of Escherichia coli. , 1986, Journal of biochemistry.

[70]  H. Trachsel,et al.  Cloning of eukaryotic protein synthesis initiation factor genes: isolation and characterization of cDNA clones encoding factor eIF-4A. , 1985, Nucleic acids research.

[71]  T. Kobayashi,et al.  Nucleotide sequence of the pldB gene and characteristics of deduced amino acid sequence of lysophospholipase L2 in Escherichia coli. , 1985, Journal of Biochemistry (Tokyo).

[72]  D. Lipman,et al.  Rapid and sensitive protein similarity searches. , 1985, Science.

[73]  A. Danchin,et al.  The complete nucleotide sequence of the adenylate cyclase gene of Escherichia coli. , 1984, Nucleic acids research.

[74]  P. L. Deininger,et al.  DNA sequence and expression of the B95-8 Epstein—Barr virus genome , 1984, Nature.

[75]  M. Gribskov,et al.  The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression , 1984, Nucleic Acids Res..

[76]  D. Crothers,et al.  A computer graphics study of sequence-directed bending in DNA. , 1983, Journal of biomolecular structure & dynamics.

[77]  C. Raetz,et al.  A trans-acting regulatory mutation that causes overproduction of phosphatidylserine synthase in Escherichia coli. , 1983, The Journal of biological chemistry.

[78]  P. Stragier,et al.  Regulation of diaminopimelate decarboxylase synthesis in Escherichia coli. III. Nucleotide sequence and regulation of the lysR gene. , 1983, Journal of molecular biology.

[79]  J. Pinkham,et al.  The nucleotde sequence of the rho gene of E. coli K-12 , 1983 .

[80]  K. Smith,et al.  New mutation (mmrA1) in Escherichia coli K-12 that affects minimal medium recovery and postreplication repair after UV irradiation , 1983, Journal of bacteriology.

[81]  F. Sanger,et al.  Nucleotide sequence of bacteriophage lambda DNA. , 1982, Journal of molecular biology.

[82]  A. D. McLachlan,et al.  Codon preference and its use in identifying protein coding regions in long DNA sequences , 1982, Nucleic Acids Res..

[83]  F. Studier,et al.  Nucleotide sequence from the genetic left end of bacteriophage T7 DNA to the beginning of gene 4. , 1981, Journal of molecular biology.

[84]  G. W. Hatfield,et al.  Molecular basis of valine resistance in Escherichia coli K-12. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[85]  Y. Murooka,et al.  Comparative immunological studies on arylsulfatase in bacteria of the family Enterobacteriaceae: occurrence of latent arylsulfatase protein regulated by sulfur compounds and tyramine , 1978, Journal of bacteriology.

[86]  F. Sanger,et al.  Nucleotide sequence of bacteriophage φX174 DNA , 1977, Nature.

[87]  M. H. Park,et al.  Mutants in three genes affecting transport of magnesium in Escherichia coli: genetics and physiology , 1976, Journal of bacteriology.

[88]  日本農芸化学会.  Agricultural and biological chemistry , 1961 .