Compilation of DNA sequences of Escherichia coli (update 1993)

Biosynthesis of Arginine and Polyamines

Early investigations on arginine biosynthesis brought to light basic features of metabolic regulation. The most significant advances of the last 10 to 15 years concern the arginine repressor, its structure and mode of action in both E. coli and Salmonella typhimurium, the sequence analysis of all arg structural genes in E. coli and Salmonella typhimurium, the resulting evolutionary inferences, and the dual regulation of the carAB operon. This review provides an overall picture of the pathways, their interconnections, the regulatory circuits involved, and the resulting interferences between arginine and polyamine biosynthesis. Carbamoylphosphate is a precursor common to arginine and the pyrimidines. In both Escherichia coli and Salmonella enterica serovar Typhimurium, it is produced by a single synthetase, carbamoylphosphate synthetase (CPSase), with glutamine as the physiological amino group donor. This situation contrasts with the existence of separate enzymes specific for arginine and pyrimidine biosynthesis in Bacillus subtilis and fungi. Polyamine biosynthesis has been particularly well studied in E. coli, and the cognate genes have been identified in the Salmonella genome as well, including those involved in transport functions. The review summarizes what is known about the enzymes involved in the arginine pathway of E. coli and S. enterica serovar Typhimurium; homologous genes were identified in both organisms, except argF (encoding a supplementary OTCase), which is lacking in Salmonella. Several examples of putative enzyme recruitment (homologous enzymes performing analogous functions) are also presented.

Archaeon Pyrococcus kodakaraensis KOD1: application and evolution

Archaea is the third domain which is phylogenetically differentiated from the other two domains, bacteria and eucarya. Hyperthermophile within the archaea domain has evolved most slowly retaining many ancestral features of higher eukaryotes. Pyrococcus kodakaraensis KOD1, which grows at 95 degrees C optimally, is a newly isolated hyperthermophilc archaeon. The KOD1 strain possesses a circular genome, whose size is estimated to be approximately 2,036 kb. KOD1 enzymes involved in the genetic information processing system, such as DNA polymerase, Rec protein, aspartyl tRNA synthetase and molecular chaperonin, share features of eukaryotic enzymes. Rapid and accurate PCR method by KOD1 DNA polymerase and enzyme stabilization system by KOD1 chaperonin are also introduced in this article.

Compilation of DNA sequences of Escherichia coli K12: description of the interactive databases ECD and ECDC

We have compiled the DNA sequence data for Escherichia coli K12 available from the GenBank and EMBL data libraries and independently from the literature. We provide the most definitive version of the ECD Escherichia coli database now exclusively via the World Wide Web System (http://susi.bio.uni-giessen.de/ecdc.html ). Our database encloses the completed genome sequence recently published by two competing groups and an assembled set of all elder sequences. The organisation of the database allows precise physical location of each individual gene or regulatory region, even taking into consideration discrepancies in nomenclature. The WWW program allows to the user to branch into the original EMBL and SWISS-PROT datafiles. A number of links to other WWW servers dealing with E. coli is provided. A FASTA and BLAST search may be performed online. Besides the WWW format a flat file version may be obtained via ftp. A number of discrepancies between the two systematic sequence determinations and/or the literature have not yet been resolved. However, our database may serve as a reference source for resolution and/or the assignment of strain difference.

Compilation of DNA sequences of Escherichia coli K12: description of the interactive databases ECD and ECDC (update 1996)

We have compiled the DNA sequence data forEscherichia coliavailable from the GenBank and EMBL data libraries and independently from the literature. We provide the most definitive version of the ECDEscherichia colidatabase now exclusively via the World Wide Web System: http://susi.bio.uni-giessen.de/usr/local/www/ html/ecdc.html . Our database encloses an assembled set of contiguous sequences. Each of these contigs compiles all available sequence information, including those derived from a variety of elder sequences. The organisation of the database allows precise physical location of each individual gene or regulatory region, even taking into consideration discrepancies in nomenclature. The WWW program allows to branch into the original EMBL and SWISSPROT datafiles. A number of links to other WWW servers is provided. A FASTA and BLAST search may be performed online. Besides the WWW format a flat file version may be obtained via ftp. The ftp version may also be obtained from the EMBL data library as part of the CD-ROM issue of the EMBL sequence database, which is released and updated every 3 months. After deletion of all detected overlaps a total of 3 588 706 individual bp has been determined up to the end of September 1996. This corresponds to a total of 77.09% of the entire E.coli chromosome consisting of approximately 4655 kb. About 479 kb (10.3%) are additionally available from Kyoto (Japan). Another 94 kb (2%) are available, but mapping has not been confirmed. Thus the total may have reached 89.4%.

The world of archaea: genome analysis, evolution and thermostable enzymes

Pyrococcus sp. KOD1 is a newly isolated hyperthermophilic archaeon from a solfatara at a wharf on Kodakara Island, Kagoshima, Japan. A physical map of the KOD1 chromosome was constructed using pulsed-field gel electrophoresis of restriction fragments generated by AscI, PacI and PmeI. The order of the AscI fragments was deduced from Southern hybridization using the AscI, PmeI and PacI fragments as a probe. The derived physical map indicates that KOD1 possesses a circular-form genome and its size was estimated to be 2036 kb. Several cloned genes were hybridized to restriction fragments to locate their positions on the physical map. Some genes involved in the central dogma were located on the restricted segment of the genome. Novel characteristics of KOD1 enzymes are also introduced in this article.

Global analysis of proteins synthesized during phosphorus restriction in Escherichia coli

The pattern of proteins synthesized in Escherichia coli during steady-state growth in media with ample inorganic phosphate (Pi), upon limitation for Pi (without an alternative phosphorous compound), and during steady-state growth in media containing phosphonate (PHN) as the sole P source was examined by two-dimensional gel electrophoresis. Of 816 proteins monitored in these experiments, all those with differential synthesis rates greater than 2.0 or less than 0.5 upon phosphate limitation (P limitation) or during growth on PHN compared with their rates in the cultures with Pi were classified as belonging to the PL or PHN stimulon, respectively. The PL stimulon included 413 proteins, 208 showing induced synthesis and 205 showing repressed synthesis. The PHN stimulon was smaller: it included 257 proteins; 227 showed induced synthesis and 30 showed repressed synthesis. The overlap of the two stimulons included 137 proteins: most (118) were ones showing induced synthesis. The promoter regions of genes for several of the proteins with induced or repressed synthesis contained sequences which resembled the consensus sequence for PhoB binding. The aggregate mass of proteins responding to P limitation or growth on PHN was 30 to 40% of the cells' total mass. By comparing the proteins responding to P limitation with those responding to growth on PHN, one can speculate which proteins are likely involved in adapting cells to new P sources or in preparing cells to survive stationary phase.

Isolation of cmr, a novel Escherichia coli chloramphenicol resistance gene encoding a putative efflux pump

A novel gene designated cmr, which mapped to 18.8 min of the Escherichia coli K-12 genome, was shown to mediate resistance to chloramphenicol when it was expressed from a multicopy vector. The accumulation of chloramphenicol was significantly less in cells overexpressing cmr than in control cells harboring the vector without insert. After the addition of a proton motive force blocker, the level of accumulation of chloramphenicol in the resistant cells rapidly approached the levels found in sensitive cells carrying only the chromosomal cmr. Northern (RNA) blot analyses revealed that the cmr gene is expressed as a 1.3-kb transcript. This size corresponds very well with a predicted size of 1,293 nucleotides (nt) based on the mapping of the transcription initiation site to a G residue 24 nt upstream of the start codon and the presence of a putative rho-independent terminator sequence ending 36 nt downstream of the 1,233-nt open reading frame encoding the putative Cmr protein. The 411-residue-long derived amino acid sequence contains 12 putative transmembrane segments and displays significant sequence similarities to several known drug resistance protein sequences of the major facilitator family. We provide evidence strongly suggesting that the resistance mediated by Cmr involves active exclusion of chloramphenicol.

Compilation of DNA sequences of Escherichia coli K12 (ECD and ECDC; update 1995)

We have compiled the DNA sequence data for Escherichia coli available from the GenBank and EMBL data libraries and independently from the literature. Unlike the previous updates of our E.coli databases, we provide the most recent version preferentially via the World Wide Web System (use URL: http://susi.bio.unigiessen.de/usr/local/www++ +/html/ecdc.html). Our database includes an assembled set of contiguous sequences. Each of these contigs compiles all available sequence information, including those derived from a variety of elder sequences. The organization of the database allows one to find the exact physical location of each individual gene or regulatory region, even regarding discrepancies in nomenclature. The WWW program allows access into the original EMBL and SWISSPROT datafiles. A FASTA and BLAST search may be performed online. Besides the WWW format a flat file version may be obtained via ftp. The complete compilation, including a full set of genetic map data and the E.coli protein index, can be obtained in machine readable form from the EMBL data library as a part of the CD-ROM issue of the EMBL sequence database, released and updated every three months. After deletion of all detected overlaps a total of 3 333 878 individual bp was determined by the end of September 1995. This corresponds to a total of 71.71% of the entire E.coli chromosome consisting of about 4720 kbp. About 94 kbp (2%) are available additionally, but have not yet been definitely mapped.

A general genetic approach in Escherichia coli for determining the mechanism(s) of action of tumoricidal agents: application to DMP 840, a tumoricidal agent

We describe here a simple and easily manipulatable Escherichia coli-based genetic system that permits us to identify bacterial gene products that modulate the sensitivity of bacteria to tumoricidal agents, such as DMP 840, a bisnaphthalimide drug. To the extent that the action of these agents is conserved, these studies may expand our understanding agents is conserved, these studies may expand our understanding of how the agents work in mammalian cells. The approach briefly is to use a library of E. coli genes that are overexpressed in a high copy number vector to select bacterial clones that are resistant to the cytotoxic effects of drugs. AtolC bacterial mutant is used to maximize permeability of cells to hydrophobic organic molecules. By using DMP 840 to model the system, we have identified two genes, designated mdaA and mdaB, that impart resistance to DMP 840 when they are expressed at elevated levels. mdaB maps to E. coli map coordinate 66, is located between the parE and parC genes, and encodes a protein of 22 kDa. mdaA maps to E. coli map coordinate 18, is located adjacent to the glutaredoxin (grx) gene, and encodes a protein of 24 kDa. Specific and regulatable overproduction of both of these proteins correlates with DMP 840 resistance. Overproduction of the MdaB protein also imparts resistance to two mammalian topoisomerase inhibitors, Adriamycin and etoposide. In contrast, overproduction of the MdaA protein produces resistance only to Adriamycin. Based on its drug-resistance properties and its location between genes that encode the two subunits of the bacterial topoisomerase IV, we suggest that mdaB acts by modulating topoisomerase IV activity. The location of the mdaA gene adjacent to grx suggests it acts by a drug detoxification mechanism.

Identification and chromosomal distribution of DNA sequence segments conserved since divergence of Escherichia coli and Bacillus subtilis

DNA sequence segments conserved since divergence of Escherichia coli and Bacillus subtilis were identified, using the GenBank sequence database. Chromosomal locations of the conserved segments were compared between the two bacteria, and the following three features were observed. (1) Although the two genomes are nearly identical in size, chromosomal arrangements of the conserved segments are considerably different from each other. (2) In many cases, chromosomal locations of a conserved segment in the two species have deviated from each other by a multiple of 60 degrees. (3) There are many instances in which a contiguous segment in one genome is split into two or more segments located at distinct positions in the other genome, and these split segments were found to tend to lie on the E. coli or B. subtilis genome separated by distances of multiples of 60 degrees. On the basis of these observations, genome organizations of the two bacteria were discussed in terms of genome doublings as well as random chromosomal rearrangements.

Repression of lipopolysaccharide biosynthesis in Escherichia coli by an antisense RNA of Acetobacter methanolicus phage Acm1

Lysogenic Acetobacter methanolicus strains carrying the prophage Acm1 were found to be unable to synthesize both the capsular polysaccharide (CPS) and the O-specific side-chain of lipopolysaccharide (LPS) and to represent rough variants of the host bacterium. A 262 bp DNA fragment of phage Acm1, obviously required for interference with LPS biosynthesis, was cloned and expressed in Escherichia coli. Independently of the O-type, transformation of various E. coli strains with the recombinant DNA resulted in a suppression of biosynthesis of the O-specific chains. The DNA fragment of phage Acm1 contained three very short open reading frames of 21, 24, and 36 bp. However, attempts to express phage-encoded peptides were not successful. Instead, the Acm1-derived DNA fragment was shown to code for the synthesis of a trans-acting RNA molecule of 97 nucleotides, designated lbi (LPS biosynthesis-interfering) RNA. This RNA contains sequence complementarity to E. coli target RNA sequences and appears to have the ability to form intracellularly RNA hybrid duplexes with mRNA. The data presented in this study support the hypothesis that the phenotypic effect of conversion to rough-type LPS is accompanied by the expression of an antisense RNA of phage Acm1.

ECDC--a totally integrated and interactively usable genetic map of Escherichia coli K12

A printed version of the interactively usable genetic map of Escherichia coli K12 is provided together with some statistical information about the actual status of the respective genome sequencing project. A total of 3,179,967 bp corresponding to 68.38% of the genome is available through the ECDC database. Contigs as well as individual DNA sequences for each gene or open reading frame are provided. Access to a number of other databases is possible using World Wide Web or local programs.

DNA sequence changes in mutations in the tonB gene on the chromosome of Escherichia coli K12: insertion elements dominate the spontaneous spectra

To obtain insight into the nature and mechanisms of spontaneous mutations, Escherichia coli K12 strain TM31 was constructed to determine, by DNA sequencing, the mutational spectrum of the tonB gene on the chromosome. We inserted the chloramphenicol resistant gene 1.6 kb upstream of the tonB gene, thus making it possible to retrieve the mutated tonB gene from the chromosome by shotgun cloning using a drug-resistant marker. The spontaneous mutation frequency in the tonB gene, which was judged by its colicin B-resistant phenotype, is 3-10 x 10(-7). Spontaneous mutations were dominated by large insertions that are identified by DNA sequencing to be IS elements; IS1 dominated, but IS2, IS5, and IS10 were also obtained. In uvrA- strain, transposition of both IS10-R and IS10-L are equally increased, suggesting the interaction of the UvrA protein and IS10 transposition. The base substitutions are the second largest group of mutations, among which G:C-->A:T transition is predominant. Deletions also contribute significantly in wild type with regard to DNA repair and uvrA- strains, but not recA- strain, suggesting that the RecA protein is involved to some extent in deletion formation. Endpoints of these deletions do not always correlate with the presence of repeated sequences, indicating the absence of homologous recombination for deletion formation.

A hidden Markov model that finds genes in E. coli DNA

A hidden Markov model (HMM) has been developed to find protein coding genes in E. coli DNA using E. coli genome DNA sequence from the EcoSeq6 database maintained by Kenn Rudd. This HMM includes states that model the codons and their frequencies in E. coli genes, as well as the patterns found in the intergenic region, including repetitive extragenic palindromic sequences and the Shine-Delgarno motif. To account for potential sequencing errors and or frameshifts in raw genomic DNA sequence, it allows for the (very unlikely) possibility of insertions and deletions of individual nucleotides within a codon. The parameters of the HMM are estimated using approximately one million nucleotides of annotated DNA in EcoSeq6 and the model tested on a disjoint set of contigs containing about 325,000 nucleotides. The HMM finds the exact locations of about 80% of the known E. coli genes, and approximate locations for about 10%. It also finds several potentially new genes, and locates several places were insertion or deletion errors/and or frameshifts may be present in the contigs.

Intrinsic and extrinsic approaches for detecting genes in a bacterial genome

The unannotated regions of the Escherichia coli genome DNA sequence from the EcoSeq6 database, totaling 1,278 'intergenic' sequences of the combined length of 359,279 basepairs, were analyzed using computer-assisted methods with the aim of identifying putative unknown genes. The proposed strategy for finding new genes includes two key elements: i) prediction of expressed open reading frames (ORFs) using the GeneMark method based on Markov chain models for coding and non-coding regions of Escherichia coli DNA, and ii) search for protein sequence similarities using programs based on the BLAST algorithm and programs for motif identification. A total of 354 putative expressed ORFs were predicted by GeneMark. Using the BLASTX and TBLASTN programs, it was shown that 208 ORFs located in the unannotated regions of the E. coli chromosome are significantly similar to other protein sequences. Identification of 182 ORFs as probable genes was supported by GeneMark and BLAST, comprising 51.4% of the GeneMark 'hits' and 87.5% of the BLAST 'hits'. 73 putative new genes, comprising 20.6% of the GeneMark predictions, belong to ancient conserved protein families that include both eubacterial and eukaryotic members. This value is close to the overall proportion of highly conserved sequences among eubacterial proteins, indicating that the majority of the putative expressed ORFs that are predicted by GeneMark, but have no significant BLAST hits, nevertheless are likely to be real genes. The majority of the putative genes identified by BLAST search have been described since the release of the EcoSeq6 database, but about 70 genes have not been detected so far. Among these new identifications are genes encoding proteins with a variety of predicted functions including dehydrogenases, kinases, several other metabolic enzymes, ATPases, rRNA methyltransferases, membrane proteins, and different types of regulatory proteins.

The European Bioinformatics Institute (EBI) databases

This paper describes the databases and services of the European Bioinformatics Institute (EBI). In collaboration with DDBJ and GenBank/NCBI, the EBI maintains and distributes the EMBL Nucleotide Sequence Database, Europe's primary nucleotide sequence data resource. The EBI also maintains and distributes the SWISS-PROT Protein Sequence Database, in collaboration with Amos Bairoch of the University of Geneva. Over thirty additional specialist molecular biology databases, as well as software and documentation of interest to molecular biologists, are also available. The EBI network services include database searching, entry retrieval, and sequence similarity searching facilities.

ECD--a totally integrated database of Escherichia coli K12

We have compiled the DNA sequence data for E. coli available from the GENBANK and EMBL data libraries and independently from the literature. Starting with this update of our Escherichia coli database (ECD release 20) we provide major changes compared to previous issues. This update not only represents another substantial increase in sequence information, it also allows now to find the exact physical location of each individual gene or regulatory region, even regarding discrepancies in nomenclature. In order to save space this printed version does not contain the database itself anymore, but we provide several examples. The complete database is publically available in electronic form together with a self explaining application program or as a flat file. The complete compilation including a full set of genetic map data and the E. coli protein index can be obtained in machine readable form from the EMBL data library as a part of the CD-ROM issue of the EMBL sequence database, released and updated every three months. After deletion of all detected overlaps a total of 2,878,364 individual bp is found to be determined till the end of June 1994. This corresponds to a total of 60.98% of the entire E. coli chromosome consisting of about 4,720 kbp. This number may actually be higher by 9161 bp derived from other strains of E. coli.

Methionine as translation start signal: a review of the enzymes of the pathway in Escherichia coli

Methionine is the universal translation start but the first methionine is removed from most mature proteins. This review focuses on our present knowledge of the five enzymes sustaining the methionine pathway in translation initiation in Escherichia coli: methionyl-tRNA synthetase, methionyl-tRNA(fMet) formyltransferase, peptidyl-tRNA hydrolase, peptide deformylase and methionine aminopeptidase. The possible significance of retaining methionine as initiation signal is discussed.