Nucleotide sequence of the metH gene of Escherichia coli K-12 and comparison with that of Salmonella typhimurium LT2

Old, Iain G.; Margarita, Danielle; Glass, Robert E.; Girons, Isabelle Saint

doi:10.1016/0378-1119(90)90490-i

Cited by 35 publications

(16 citation statements)

References 27 publications

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“…The ORF for cobyric acid synthase is not close to the formatetetrahydrofolate ligase gene in FN. Both FN and FNV contain ORFs for an efflux pump and the methyltransferase in the same orientation, but the methyltransferase is only about one-fourth the size of the E. coli ortholog (Old et al 1990). In both genomes, there are two ORFs for thymidylate synthase with the flanking genes rearranged.…”

Section: C1-carbon Metabolismmentioning

confidence: 99%

Genome Analysis of F. nucleatum sub spp vincentii and Its Comparison With the Genome of F. nucleatum ATCC 25586

Kapatral¹,

Ivanova²,

Anderson³

et al. 2003

Genome Res.

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We present the draft genome sequence and its analysis for Fusobacterium nucleatum sub spp. vincentii (FNV), and compare that genome with F. nucleatum ATCC 25586 (FN). A total of 441 FNV open reading frames (ORFs) with no orthologs in FN have been identified. Of these, 118 ORFs have no known function and are unique to FNV, whereas 323 ORFs have functional orthologs in other organisms. In addition to the excretion of butyrate, H 2 S and ammonia-like FN, FNV has the additional capability to excrete lactate and aminobutyrate. Unlike FN, FNV is likely to incorporate galactopyranose, galacturonate, and sialic acid into its O-antigen. It appears to transport ferrous iron by an anaerobic ferrous transporter. Genes for eukaryotic type serine/threonine kinase and phosphatase, transpeptidase E-transglycosylase Pbp1A are found in FNV but not in FN. Unique ABC transporters, cryptic phages, and three types of restriction-modification systems have been identified in FNV. ORFs for ethanolamine utilization, thermostable carboxypeptidase, ␥ glutamyl-transpeptidase, and deblocking aminopeptidases are absent from FNV. FNV, like FN, lacks the classical catalase-peroxidase system, but thioredoxin/glutaredoxin enzymes might alleviate oxidative stress. Genes for resistance to antibiotics such as acriflavin, bacitracin, bleomycin, daunorubicin, florfenicol, and other general multidrug resistance are present. These capabilities allow Fusobacteria to survive in a mixed culture in the mouth.

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Section: C1-carbon Metabolismmentioning

confidence: 99%

Genome Analysis of F. nucleatum sub spp vincentii and Its Comparison With the Genome of F. nucleatum ATCC 25586

Kapatral¹,

Ivanova²,

Anderson³

et al. 2003

Genome Res.

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“…An example of this adaptation mechanism can be seen on the 5-methyltetrahydrofolate (MTH) protein (34), which catalyzes methyltetrahydrofolate into methionine and tetrahydrofolate (35). This protein is part of a larger network that is involved in methionine metabolism, a process integral to the survival of both thermophiles and mesophiles.…”

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confidence: 99%

Natural selection of more designable folds: A mechanism for thermophilic adaptation

England

Shakhnovich

2003

Proc. Natl. Acad. Sci. U.S.A.

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An open question of great interest in biophysics is whether variations in structure cause protein folds to differ in the number of amino acid sequences that can fold to them stably, i.e., in their designability. Recently, we have shown that a novel quantitative measure of a fold's tertiary topology, called its contact trace, strongly correlates with the fold's designability. Here, we investigate the relationship between a fold's contact trace and its relative frequency of usage in mesophilic vs. thermophilic eubacteria. We observe that thermophilic organisms exhibit a bias toward using folds of higher contact trace when compared with mesophiles. We establish this difference both for the distributions of folds at the whole-proteome level and also through more focused structural comparisons of orthologous proteins. Our findings suggest that thermophilic adaptation in bacterial genomes occurs in part through natural selection of more designable folds, pointing to designability as a key component of protein fitness.U nderstanding the adaptations that enable thermophilic organisms to survive at extreme temperatures is a challenge that has interested researchers since 1897 (1), and great strides have been made along this line of inquiry since the recent publications of complete genomes for several hyperthermophilic species (2). However, most research in this area has focused on amino acid sequence variations that increase the thermodynamic stability of thermophilic proteins while leaving their structures unchanged (2, 3). Far less is known about what structural differences exist between thermophilic and mesophilic proteomes. One interesting possibility is that a thermophilic bias in structure may manifest as a preference for folds that are able to accommodate a large number of low-energy sequences, because such folds have a higher probability of being able to maintain their stability while adapting by mutation to new pressures. This hypothesis relates to another problem of great interest in biophysics: how the structural topology of a protein fold affects its designability (4-9). Here, we present results that point to an important connection between these two problems. Making use of what is known analytically about the relationship between a fold's topology and its designability and thermostability, we report an adaptation mechanism of thermophillic bacteria: one that proceeds by selection of more designable folds.Recently, a new theoretical treatment of designability has been developed within the framework of a residue-residue contact Hamiltonian (10). This Hamiltonian is a well established model for protein energetics that defines the conformational energy of a polypeptide chain as the sum of the pairwise interaction energies of all of the amino acid pairs whose ␣ carbons are separated by a distance less than some contact cutoff, typically chosen to be Ϸ7.5 Å (11). More formally, for a chain of length N with a monomer alphabet containing M amino acid types (of course, M ϭ 20 for real proteins), we can define the ene...

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“…As shown in Fig. 4, iclR is transcribed kOa: counterclockwise on the E. coli chromosome and was mapped on the same HindIII fragment as metH (16), which is transcribed clockwise (17).…”

Section: Resultsmentioning

confidence: 99%

“…A 5-kbp HindIlI fragment on pUWL100 (Fig. 4) showed the same arrangement of three EcoRV restriction sites as did a fragment on the E. coli K-12 chromosome, used for sequencing the metH gene by Old et al (17). We therefore sequenced the region around the HindIII site nearest the sor operon, which is located about 450 bp upstream of the stop codon for metH.…”

Section: Resultsmentioning

confidence: 99%

Cloning of the Escherichia coli sor genes for L-sorbose transport and metabolism and physical mapping of the genes near metH and iclR

1992

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The sor genes for L-sorbose (Sor) degradation of Escherichia coli EC3132, a wild-type strain, have been cloned on a 10.8-kbp fragment together with parts of the metH gene. The genes were mapped by restriction analysis, by deletion mapping, and by insertion mutagenesis with Tnl725. Seven sor genes with their corresponding gene products have been identified. They form an operon (gene order sorCpCDFBAME) inducible by L-sorbose, and their products have the following functions: SorC (36 kDa), regulatory protein with repressor-activator functions; SorD (29 kDa), D-glucitol-6-phosphate dehydrogenase; SorF and SorB (14 and 19 kDa, respectively), and SorA and SorM (27 and 29 kDa, respectively), two soluble and two membrane-bound proteins, respectively, of an L-sorbose phosphotransferase transport system; SorE (45 kDa), sorbose-lphosphate reductase. The sor operon from E. coli EC3132 thus is identical to the operon from Kiebsiella pneumoniae KAY2026. On the basis of restriction mapping followed by Southern hybridization experiments, the sor genes were mapped at 91.2 min on the chromosome, 3.3 kbp downstream of the metH-iciR gene cluster, and shown to be transcribed in a counterclockwise direction. The chromosomal map of the Sor+ strain EC3132 differs from that of the Sor-strain K-12 in approximately 8.6 kbp.

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Nucleotide sequence of the metH gene of Escherichia coli K-12 and comparison with that of Salmonella typhimurium LT2

Cited by 35 publications

References 27 publications

Genome Analysis of F. nucleatum sub spp vincentii and Its Comparison With the Genome of F. nucleatum ATCC 25586

Genome Analysis of F. nucleatum sub spp vincentii and Its Comparison With the Genome of F. nucleatum ATCC 25586

Natural selection of more designable folds: A mechanism for thermophilic adaptation

Cloning of the Escherichia coli sor genes for L-sorbose transport and metabolism and physical mapping of the genes near metH and iclR

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