Abstract:
:When the stop codons TGA, TAA, and TAG are found in the second and third reading frames of a protein-encoding gene, they are considered premature stop codons (PSC). Deinococcus radiodurans disproportionately favored TGA more than the other two triplets as a PSC. The TGA triplet was also found more often in noncoding regions and as a stop codon, though the bias was less pronounced. We investigated this phenomenon in 72 bacterial species with widely differing chromosomal GC contents. Although TGA and TAG were compositionally similar, we found a great variation in use of TGA but a very limited range of use of TAG. The frequency of use of TGA in the gene sequences generally increased with the GC content of the chromosome, while the frequency of use of TAG, like that of TAA, was inversely proportional to the GC content of the chromosome. The patterns of use of TAA, TGA and TAG as real stop codons were less biased and less influenced by the GC content of the chromosome. Bacteria with higher chromosomal GC contents often contained fewer PSC trimers in their genes. Phylogenetically related bacteria often exhibited similar PSC ratios. In addition, metabolically versatile bacteria have significantly fewer PSC trimers in their genes. The bias toward TGA but against TAG as a PSC could not be explained either by the preferential usage of specific codons or by the GC contents of individual chromosomes. We proposed that the quantity and the quality of the PSC in the genome might be important in bacterial evolution.
journal_name
J Bacterioljournal_title
Journal of bacteriologyauthors
Wong TY,Fernandes S,Sankhon N,Leong PP,Kuo J,Liu JKdoi
10.1128/JB.00682-08subject
Has Abstractpub_date
2008-10-01 00:00:00pages
6718-25issue
20eissn
0021-9193issn
1098-5530pii
JB.00682-08journal_volume
190pub_type
杂志文章abstract::CooA is a heme-containing transcriptional activator that enables Rhodospirillum rubrum to sense and grow on CO as a sole energy source. We have identified a number of CooA homologs through database searches, expressed these heterologously in Escherichia coli, and monitored their ability to respond to CO in vivo. Furth...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.186.5.1320-1329.2004
更新日期:2004-03-01 00:00:00
abstract::Pseudomonas aeruginosa and members of the Burkholderia cepacia complex often coexist in both the soil and the lungs of cystic fibrosis patients. To gain an understanding of how these different species affect each other's physiology when coexisting, we performed a screen to identify P. aeruginosa genes that are induced...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.186.8.2376-2384.2004
更新日期:2004-04-01 00:00:00
abstract::The first generalized transducing bacteriophage reported for Bacillus megaterium has been characterized. Optimum conditions for lysate production and transduction procedures were established so that transducing frequencies of 8 x 10(-6) and higher are now possible. The phage, MP13, has a head diameter of 97 nm and a c...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.149.3.1112-1119.1982
更新日期:1982-03-01 00:00:00
abstract::Mutants of Escherichia coli capable of growing in the presence of 10 microgram of mecillinam per ml were selected after intensive mutagenesis. Of these mutants, 1.4% formed normal, rod-shaped cells at 30 degrees C but grew as spherical cells at 42 degrees C. The phenotype of one of these rod(Ts) mutants was 88% cotran...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.136.3.1143-1158.1978
更新日期:1978-12-01 00:00:00
abstract::The transduction efficiency of Tn551, a staphylococcal transposon coding for erythromycin resistance (ermB), was increased by a factor of about five in acceptor strains carrying the gene for methicillin resistance (mec), as compared with methicillin-sensitive strains. This enhancement was independent of the generalize...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.154.1.533-535.1983
更新日期:1983-04-01 00:00:00
abstract::Bacteria in biofilms often undergo active dispersal events and revert to a free-swimming, planktonic state to complete the biofilm life cycle. The signaling molecule nitric oxide (NO) was previously found to trigger biofilm dispersal in the opportunistic pathogen Pseudomonas aeruginosa at low, nontoxic concentrations ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00975-09
更新日期:2009-12-01 00:00:00
abstract::Thirteen different serotypes of Listeria monocytogenes can be distinguished on the basis of variation in somatic and flagellar antigens. Although the known virulence genes are present in all serotypes, greater than 90% of human cases of listeriosis are caused by serotypes 1/2a, 1/2b, and 4b and nearly all outbreaks of...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.185.18.5573-5584.2003
更新日期:2003-09-01 00:00:00
abstract::Molecular typing of Mycobacterium tuberculosis by using IS6110 shows low discrimination when there are fewer than five copies of the insertion sequence. Using a collection of such isolates from a study of the epidemiology of tuberculosis in London, we have shown a substantial degree of congruence between IS6110 patter...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.185.8.2555-2562.2003
更新日期:2003-04-01 00:00:00
abstract::Production of Bacillus subtilis exoproteases is positively regulated by the DegS-DegU two-component regulatory system and other regulatory factors including DegR and ProB. It was shown that the expression of degR was virtually abolished in a sigD mutant and that the transcriptional initiation site in vivo is preceded ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.178.1.216-222.1996
更新日期:1996-01-01 00:00:00
abstract::Auxotrophs of Acinetobacter calcoaceticus blocked in each reaction of the synthetic pathway from chorismic acid to tryptophan were obtained after N-methyl-N'-nitro-N-nitrosoguanidine mutagenesis. One novel class was found to be blocked in both anthranilate and p-aminobenzoate synthesis; these mutants (trpG) require p-...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.112.2.797-805.1972
更新日期:1972-11-01 00:00:00
abstract::The recA441 mutant of Escherichia coli, which has been thought to have thermoinducible constitutive RecA protease activity, is known to have two mutations within recA. We show here that the mutation that alters codon 38 actually confers temperature-independent constitutive protease activity; the second mutation in rec...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.163.1.407-409.1985
更新日期:1985-07-01 00:00:00
abstract::Weiss, Emilio (Naval Medical Research Institute, Bethesda, Md.) and Harry R. Dressler. Increased resistance to chloramphenicol in Rickettsia prowazekii with a note on failure to demonstrate genetic interaction among strains. J. Bacteriol. 83:409-414. 1962.-A further effort to produce genetically labeled Rickettsia pro...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.83.2.409-414.1962
更新日期:1962-02-01 00:00:00
abstract::The mevalonate diphosphate decarboxylase is an enzyme which converts mevalonate diphosphate to isopentenyl diphosphate, the building block of isoprenoids. We used the Saccharomyces cerevisiae temperature-sensitive mutant defective for mevalonate diphosphate decarboxylase previously described (C. Chambon, V. Ladeveve, ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.179.15.4664-4670.1997
更新日期:1997-08-01 00:00:00
abstract::Lactobacillus plantarum is a highly versatile lactic acid bacterium found in various ecological niches, such as fermented vegetable, meat, and dairy products and the gastrointestinal tract. We sequenced the genome of L. plantarum NC8, a naturally plasmid-free strain, which has been used as a model strain in many labor...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00141-12
更新日期:2012-05-01 00:00:00
abstract::Nosocomial infections caused by antibiotic-resistant Klebsiella pneumoniae are emerging as a major health problem worldwide, while community-acquired K. pneumoniae infections present with a range of diverse clinical pictures in different geographic areas. In particular, an invasive form of K. pneumoniae that causes li...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00315-09
更新日期:2009-07-01 00:00:00
abstract::The major outer membrane protein of molecular weight 40,000 (the 40K protein) of a virulent isolate of Bordetella pertussis was purified to apparent homogeneity. The purified protein formed an oligomer band (of apparent molecular weight 90,000) on sodium dodecyl sulfate-polyacrylamide gels after solubilization at low ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.166.1.212-216.1986
更新日期:1986-04-01 00:00:00
abstract::Flavobacterium johnsoniae cells move rapidly over surfaces by gliding motility. Gliding results from the movement of adhesins such as SprB and RemA along the cell surface. These adhesins are delivered to the cell surface by a Bacteroidetes-specific secretion system referred to as the type IX secretion system (T9SS). G...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00333-13
更新日期:2013-07-01 00:00:00
abstract::We developed a procedure for isolating membrane vesicles from the homolactic fermentative bacterium Streptococcus cremoris. The membrane vesicles were shown to have a right-side-out orientation by freeze-etch electron microscopy and to be free of cytoplasmic constituents. The membrane vesicles retained their functiona...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.149.2.733-738.1982
更新日期:1982-02-01 00:00:00
abstract::Segregation was studied by measuring the positions of autoradiographic grain clusters in chains formed from single cells containing on average less than one radiolabeled chromosome strand. The degree to which chromosomal and cell wall material cosegregated was quantified by using the methods of S. Cooper and M. Weinbe...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.171.1.349-352.1989
更新日期:1989-01-01 00:00:00
abstract::Bacteroides fragilis synthesizes eight distinct capsular polysaccharides, more than any described bacterium outside the order Bacteroidales. Here, we show that this organism also produces a high-molecular-weight extracellular polysaccharide (EPS). Expression of the EPS results in the formation of a large polysaccharid...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.01519-07
更新日期:2008-02-01 00:00:00
abstract::Analysis of the deoxyribonucleic acid prepared from Proteus mirabilis, Escherichia coli, and Serratia marcescens in an alkaline CsCl gradient has shown that there is an asymmetric distribution of guanine plus thymine residues between the complementary strands of the deoxyribonucleic acid. ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.106.1.238-242.1971
更新日期:1971-04-01 00:00:00
abstract::Acinetobacter baumannii has emerged as a significant nosocomial pathogen worldwide. The increasing trend of carbapenem and fluoroquinolone resistance in A. baumannii severely limits the usage of therapeutic antimicrobial agents. Here we report the genome sequence of a multidrug-resistant A. baumannii strain, TCDC-AB07...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00244-11
更新日期:2011-05-01 00:00:00
abstract:UNLABELLED:The ubiquitous bacterial second messenger cyclic di-GMP (c-di-GMP) has recently become prominent as a trigger for biofilm formation in many bacteria. It is generated by diguanylate cyclases (DGCs; with GGDEF domains) and degraded by specific phosphodiesterases (PDEs; containing either EAL or HD-GYP domains)....
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00520-15
更新日期:2015-08-24 00:00:00
abstract::Eight different derivatives of R plasmid RP1 with thermosensitive mutations affecting maintenance in Escherichia coli and Pseudomonas aeruginosa were introduce into Rhizobium meliloti. None of the plasmids showed a thermosensitive character in R. meliloti. On the other hand, a certain deletion mutation in RP1 was foun...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.150.1.395-397.1982
更新日期:1982-04-01 00:00:00
abstract::The growth of Bacillus subtilis mutant betaA177 can be inhibited under special conditions in which not enough autolytic enzymes are produced for optimal growth. Electron microscopy studies show that during growth inhibition there is localized thickening of the cell wall at positions where cells bend. A model is propos...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.109.3.1247-1257.1972
更新日期:1972-03-01 00:00:00
abstract::The spoVM gene encodes a 26-amino-acid polypeptide that is essential for spore formation in Bacillus subtilis. A transposon insertion within the spoVM open reading frame has been shown to encode a chimeric protein which is biologically inactive and produces a phenotype identical to that of a deletion and insertion mut...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.179.17.5534-5542.1997
更新日期:1997-09-01 00:00:00
abstract::The plasmid nature of genes specifying degradation of nicotine and nicotinate in Pseudomas convexa strain 1 (Pc1) is indicated by mitomycin curing and conjugational transfer to other strains. The NIC plasmid appears to be compatible with other metabolic plasmids in Pseudomonas putida. ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.135.1.289-290.1978
更新日期:1978-07-01 00:00:00
abstract::Protein K is an outer membrane protein found in pathogenic encapsulated strains of Escherichia coli. We present evidence here that protein K is structurally and functionally related to the E. coli K-12 porin proteins (OmpF, OmpC, and PhoE). Protein K was found to cross-react with antibody to OmpF protein and to share ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.156.2.867-872.1983
更新日期:1983-11-01 00:00:00
abstract::Those genes in Escherichia coli defined by mutations which result in an inability to grow at high temperatures are designated htr, indicating a high temperature requirement. A new htr mutant of E. coli was isolated and characterized and is designated htrD. The htrD gene has been mapped to 19.3 min on the E. coli chrom...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.174.4.1240-1247.1992
更新日期:1992-02-01 00:00:00
abstract::Discadenine,3-(3-amino-3-carboxypropyl)-N6-delta 2-isopentenyladenine, which inhibits spore germination, was previously found in Dictyostelium discoideum. Studies on the distribution of discadenine in different species of cellular slime molds by high-pressure liquid chromatography showed that discadenine is present in...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.143.2.715-719.1980
更新日期:1980-08-01 00:00:00