Functions of the gene products of Escherichia coli

Riley, Matilda White

doi:10.1128/mr.57.4.862-952.1993

Cited by 224 publications

(6 citation statements)

References 1,717 publications

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“…All M.pneumoniae gene products were classified (Table 1 and 2), with some minor modifications, in accordance with criteria introduced for Escherichia coli (31) and adapted for the classification of putative genes from H.influenzae. We added 'cytadherence associated proteins' to the category of cell envelope-surface structures, since evidence is mounting, that M.pneumoniae possesses a cytoskeleton-like organization which stabilizes the bacterium and protects it against osmotic lysis (2).…”

Section: Resultsmentioning

confidence: 99%

Complete Sequence Analysis of the Genome of the Bacterium Mycoplasma Pneumoniae

Himmelreich

Hilbert

Plagens

et al. 1996

Nucleic Acids Research

1,054

932

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The entire genome of the bacterium Mycoplasma pneumoniae M129 has been sequenced. It has a size of 816,394 base pairs with an average G+C content of 40.0 mol%. We predict 677 open reading frames (ORFs) and 39 genes coding for various RNA species. Of the predicted ORFs, 75.9% showed significant similarity to genes/proteins of other organisms while only 9.9% did not reveal any significant similarity to gene sequences in databases. This permitted us tentatively to assign a functional classification to a large number of ORFs and to deduce the biochemical and physiological properties of this bacterium. The reduction of the genome size of M. pneumoniae during its reductive evolution from ancestral bacteria can be explained by the loss of complete anabolic (e.g. no amino acid synthesis) and metabolic pathways. Therefore, M. pneumoniae depends in nature on an obligate parasitic lifestyle which requires the provision of exogenous essential metabolites. All the major classes of cellular processes and metabolic pathways are briefly described. For a number of activities/functions present in M. pneumoniae according to experimental evidence, the corresponding genes could not be identified by similarity search. For instance we failed to identify genes/proteins involved in motility, chemotaxis and management of oxidative stress.

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Section: Resultsmentioning

confidence: 99%

Complete Sequence Analysis of the Genome of the Bacterium Mycoplasma Pneumoniae

Himmelreich

Hilbert

Plagens

et al. 1996

Nucleic Acids Research

1,054

932

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“…The potential protein-encoding genes whose function could be anticipated were classified into 14 categories, each with different biological roles, according to the principle of Riley. 24 The numbers of genes in each category are summarized in Table 1, and the name of each gene is listed in CyanoBase at http://www.kazusa.or.jp/cyanobase/. On the gene map in the Supplement section (Fig.…”

Section: Functional Assignment Of Protein-encoding Genesmentioning

confidence: 99%

Complete Genome Structure of the Thermophilic Cyanobacterium Thermosynechococcus elongatus BP-1

et al. 2002

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The entire genome of a thermophilic unicellular cyanobacterium, Thermosynechococcus elongatus BP-1, was sequenced. The genome consisted of a circular chromosome 2,593,857 bp long, and no plasmid was detected. A total of 2475 potential protein-encoding genes, one set of rRNA genes, 42 tRNA genes representing 42 tRNA species and 4 genes for small structural RNAs were assigned to the chromosome by similarity search and computer prediction. The translated products of 56% of the potential protein-encoding genes showed sequence similarity to experimentally identified and predicted proteins of known function, and the products of 34% of these genes showed sequence similarity to the translated products of hypothetical genes. The remaining 10% lacked significant similarity to genes for predicted proteins in the public DNA databases. Sixty-three percent of the T. elongatus genes showed significant sequence similarity to those of both Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120, while 22% of the genes were unique to this species, indicating a high degree of divergence of the gene information among cyanobacterial strains. The lack of genes for typical fatty acid desaturases and the presence of more genes for heat-shock proteins in comparison with other mesophilic cyanobacteria may be genomic features of thermophilic strains. A remarkable feature of the genome is the presence of 28 copies of group II introns, 8 of which contained a presumptive gene for maturase/reverse transcriptase. A trace of genome rearrangement mediated by the group II introns was also observed.

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“…Another automatic tool, based on the proposed functional classifications of genes in prokaryotic genomes (Riley 1993;Fleischmann et al 1995) and commentaries from SwissProt, has been used to classify the genes. The programme uses list of functional categories and the relevant keywords with assigned weights corresponding to each category for a given keyword.…”

Section: Genome Analysismentioning

confidence: 99%

Low-redundancy sequencing of the entire Lactococcus lactis IL1403 genome

Bolotin¹,

Mauger²,

Malarme³

et al. 1999

Lactic Acid Bacteria: Genetics, Metabolism and Applications

115

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Lactococcus lactis is an AT-rich gram positive bacterium phylogenetically close to the genus Streptococcus. Various strains of L. lactis are used in dairy industry as starters for cheese making. L. lactis is also one of the well characterized laboratory microorganisms, widely used for studies on physiology of lactic acid bacteria. We describe here a low redundancy sequence of the genome of the strain L. lactis IL1403. The strategy which we followed to determine the sequence consists of two main steps. First, a limited number of plasmids and -phages that carryrandom segments of the genome were sequenced. Second, sequences of the inserts were used for production of novel sequencing templates by applying Multiplex Long Accurate PCR protocols. Using of these PCR product sallowed to determine the sequence of the entire 2.35 Mb genome with a very low redundancy, close to 2. The error rate of the sequence is estimated to be below 1%. The correctness of the sequence assembly was confirmed by PCR amplification of the entire L. lactis IL1403 genome, using a set of 266 oligonucleotides. Anotation of the sequence was undertaken by using automatic gene prediction computer tools. This allowed to identify 1495protein-encoding genes, to locate them on the genome map and to classify their functions on the basis of homology to known proteins. The function of about 700 genes expected to encode proteins that lack homologs in data bases cannot be reliably predicted in this way. The approach which we used eliminates high redundancy sequencing and mapping efforts, needed to obtain detailed and comprehensive genetic and physical maps of a bacterium.Availability of detailed genetic and physical maps of the L. lactis IL1403 genome provides many entries to study metabolism and physiology of bacteria from this group. The presence of 42 copies of five different IS elements in the IL1403 genome confirms the importance of these elements for genetic exchange in Lactococci. These include two previously unknown elements, present at seven and fifteen copies and designated IS1077 and IS983, respectively. Five potential or rudimentary prophages were identified in the genome by detecting clusters of phage-related genes. The metabolic and regulatory potential of L. lactis was evaluated by inspecting gene sets classified into different functional categories.L. lactis has the genetic potential to synthesise 20 standard amino acids, purine and pyrimidine nucleotides and at least four cofactors. Some of these metabolites, which are usually present in chemically defined media, can probably be omitted. About twenty compounds can be used by L. lactis as a sole carbon source. Some 83 regulators were revealed, indicating a regulatory potential close to that of Haemophilus influenzae, a bacterium with a similar genome size. Unexpectedly, L. lactis has a complete set of late competence genes, which may have concerted transcriptional regulation and unleadered polycistronic mRNAs. These findings open new possibilities for developing genetic tools, useful for studi...

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Functions of the gene products of Escherichia coli

Cited by 224 publications

References 1,717 publications

Complete Sequence Analysis of the Genome of the Bacterium Mycoplasma Pneumoniae

Complete Sequence Analysis of the Genome of the Bacterium Mycoplasma Pneumoniae

Complete Genome Structure of the Thermophilic Cyanobacterium Thermosynechococcus elongatus BP-1

Low-redundancy sequencing of the entire Lactococcus lactis IL1403 genome

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