Abstract:
:Comprehensive analysis of genome-wide expression patterns during growth of the hyperthermophilic bacterium Thermotoga maritima on 14 monosaccharide and polysaccharide substrates was undertaken with the goal of proposing carbohydrate specificities for transport systems and putative transcriptional regulators. Saccharide-induced regulons were predicted through the complementary use of comparative genomics, mixed-model analysis of genome-wide microarray expression data, and examination of upstream sequence patterns. The results indicate that T. maritima relies extensively on ABC transporters for carbohydrate uptake, many of which are likely controlled by local regulators responsive to either the transport substrate or a key metabolic degradation product. Roles in uptake of specific carbohydrates were suggested for members of the expanded Opp/Dpp family of ABC transporters. In this family, phylogenetic relationships among transport systems revealed patterns of possible duplication and divergence as a strategy for the evolution of new uptake capabilities. The presence of GC-rich hairpin sequences between substrate-binding proteins and other components of Opp/Dpp family transporters offers a possible explanation for differential regulation of transporter subunit genes. Numerous improvements to T. maritima genome annotations were proposed, including the identification of ABC transport systems originally annotated as oligopeptide transporters as candidate transporters for rhamnose, xylose, beta-xylan, and beta-glucans and identification of genes likely to encode proteins missing from current annotations of the pentose phosphate pathway. Beyond the information obtained for T. maritima, the present study illustrates how expression-based strategies can be used for improving genome annotation in other microorganisms, especially those for which genetic systems are unavailable.
journal_name
J Bacterioljournal_title
Journal of bacteriologyauthors
Conners SB,Montero CI,Comfort DA,Shockley KR,Johnson MR,Chhabra SR,Kelly RMdoi
10.1128/JB.187.21.7267-7282.2005keywords:
subject
Has Abstractpub_date
2005-11-01 00:00:00pages
7267-82issue
21eissn
0021-9193issn
1098-5530pii
187/21/7267journal_volume
187pub_type
杂志文章abstract::Davies, Helen C. (University of Pennsylvania, Philadelphia), Fred Karush, and Joanne H. Rudd. Effect of amino acids on steady-state growth of a group A hemolytic streptococcus. J. Bacteriol. 89:421-427. 1965.-A study has been made of amino acid utilization by a strain of type 4, group A streptococcus growing under ste...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:
更新日期:1965-02-01 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::We constructed mercury resistance operon-luciferase (mer-lux) transcriptional fusion plasmids to evaluate in vivo gene expression rates of the mer structural gene promoter (PTPCAD) of transposon Tn21. In vivo gene expression kinetics corresponded well with those previously determined in vitro, yielding an apparent K0....
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.174.24.8094-8101.1992
更新日期:1992-12-01 00:00:00
abstract::Sortases are transamidases that covalently link proteins to the peptidoglycan of gram-positive bacteria. The genome of the pathogenic bacterium Listeria monocytogenes encodes two sortases genes, srtA and srtB. The srtA gene product anchors internalin and some other LPXTG-containing proteins to the listerial surface. H...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.186.7.1972-1982.2004
更新日期:2004-04-01 00:00:00
abstract::Leuconostoc mesenteroides subsp. mesenteroides is one of the most predominant lactic acid bacterial groups during kimchi fermentation. Here, we report the complete genome sequence of L. mesenteroides subsp. mesenteroides J18, which was isolated from kimchi. The genome of the strain consists of a 1,896,561-bp chromosom...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.06498-11
更新日期:2012-02-01 00:00:00
abstract::Members of the carnobacteria have been extensively studied as probiotic cultures in aquacultures and protective cultures in seafood, diary, and meat. We report on the finished genome sequence of Carnobacterium sp. 17-4, which has been isolated from permanently cold seawater. The genetic information reveals a new circu...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.05113-11
更新日期:2011-07-01 00:00:00
abstract::The hutC gene in Pseudomonas putida encodes a repressor protein that negatively regulates the expression of all hut genes. We have overexpressed this cloned hutC gene in Escherichia coli to identify P. putida hut regions that could specifically bind the repressor. Ten restriction fragments, some of which were partiall...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.171.8.4189-4195.1989
更新日期:1989-08-01 00:00:00
abstract::One of the phosphatidyl glycerophosphate phosphatase genes of Escherichia coli, pgpA, was cloned, and its DNA sequence was determined. Its 507-base-pair open reading frame was consistent with the 18,000-molecular-weight product identified by a maxicell experiment. Between its possible promoter and methionine initiatio...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.170.11.5110-5116.1988
更新日期:1988-11-01 00:00:00
abstract::A fusion constructed between the putative attenuator plus the first 219 nucleotides of the ermC (erythromycin resistance) structural gene and a 5' terminally deleted lacZ gene produced a moderate, basal level of beta-galactosidase which was increased by erythromycin addition. Another construction containing an intact ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.159.1.381-384.1984
更新日期:1984-07-01 00:00:00
abstract::Acetyl coenzyme A synthetase (Acs) activates acetate to acetyl coenzyme A through an acetyladenylate intermediate; two other enzymes, acetate kinase (Ack) and phosphotransacetylase (Pta), activate acetate through an acetyl phosphate intermediate. We subcloned acs, the Escherichia coli open reading frame purported to e...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.177.10.2878-2886.1995
更新日期:1995-05-01 00:00:00
abstract::We used primer extension and mutational analysis to identify a promoter upstream of ilvB, the first gene in the ilv-leu operon of Bacillus subtilis. Between the promoter and ilvB, there is a 482-bp leader region which contains a sequence that resembles a factor-independent transcription terminator. In in vitro transcr...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.174.10.3212-3219.1992
更新日期:1992-05-01 00:00:00
abstract::Two isozymes of chorismate mutase (CA mutase(1) and CA mutase(2)) and two isozymes of prephenate dehydratase (PPA dehydratase(1) and PPA dehydratase(2)) have been found in Pseudomonas aeruginosa. The activities CA mutase(2)-PPA dehydratase(2) catalyzing phenylalanine biosynthesis have been purified almost 40-fold and ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.115.1.205-212.1973
更新日期:1973-07-01 00:00:00
abstract::Duerre, John A. (University of North Dakota, Grand Forks), and Patrick J. Buckley. Pigment production from tryptophan by an Achromobacter species. J. Bacteriol. 90:1686-1691. 1965.-A microorganism was isolated from the soil near the University of North Dakota. Biochemical and morphological characteristics indicated th...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.90.6.1686-1691.1965
更新日期:1965-12-01 00:00:00
abstract::Herbaspirillum sp. strain GW103 was isolated from rhizosphere soil of the reed Phragmites australis on reclaimed land. Here we report the 5.05-Mb draft genome sequence of the strain, providing bioinformation about the agronomic benefits of this strain, such as multiple traits relevant to plant root colonization and pl...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00806-12
更新日期:2012-08-01 00:00:00
abstract::Spo0A is a DNA binding protein in Bacillus subtilis required for the activation of spoIIG and other promoters at the onset of endospore formation. Activation of some of these promoters may involve interaction of Spo0A and the sigmaA subunit of RNA polymerase. Previous studies identified two single-amino-acid substitut...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.180.14.3578-3583.1998
更新日期:1998-07-01 00:00:00
abstract::MukBEF is a bacterial SMC (structural maintenance of chromosome) complex required for chromosome partitioning in Escherichia coli. We report that overproduction of MukBEF results in marked chromosome condensation. This condensation is rapid and precedes the effects of overproduction on macromolecular synthesis. Conden...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00313-06
更新日期:2006-06-01 00:00:00
abstract::The group A streptococcus (GAS), Streptococcus pyogenes, is an important human pathogen that causes infections ranging in severity from self-limiting pharyngitis to severe invasive diseases that are associated with significant morbidity and mortality. The pathogenic effects of GAS are mediated by the expression of vir...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00198-06
更新日期:2006-07-01 00:00:00
abstract::Haight, Rodger D. (Oregon State University, Corvallis), and Richard Y. Morita. Thermally induced leakage from Vibrio marinus, an obligately psychrophilic bacterium. J. Bacteriol. 92:1388-1393. 1966.-Leakage of various cellular components into the surrounding menstruum occurred when Vibrio marinus was subjected to temp...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.92.5.1388-1393.1966
更新日期:1966-11-01 00:00:00
abstract::The effect of a mutation in luxI (autoinducer synthetase gene) on transcription of luxR in the cloned Vibrio fischeri lux system (luxR, luxICDABE) was examined in Escherichia coli. For the luxI mutant, transcription from the luxR promoter (monitored with beta-galactosidase levels from a luxR::lacZ fusion, with LuxR su...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.171.6.3549-3552.1989
更新日期:1989-06-01 00:00:00
abstract::Clostridium perfringens enterotoxin was detected intracellularly about 3 hr after the inoculation of vegetative cells into sporulation medium. The subsequent increase in intracellular enterotoxin concentration roughly paralleled but followed by 2.5 to 5 hr the increase in number of heat-resistant spores. The increase ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.113.2.932-936.1973
更新日期:1973-02-01 00:00:00
abstract::A procedure for protoplast formation in Escherichia coli is described. Removal of the cell wall was confirmed by examination of cells in thin-section preparations. ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.128.2.668-670.1976
更新日期:1976-11-01 00:00:00
abstract::Hauge, Jens G. (National Institute for Public Health, Oslo, Norway). Glucose dehydrogenation in bacteria: a comparative study. J. Bacteriol. 82:609-614. 1961.-Extracts of a series of bacteria reported to convert glucose to gluconic acid via particulate enzyme systems were fractionated by differential centrifugation in...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.82.4.609-614.1961
更新日期:1961-10-01 00:00:00
abstract::Most bacteria are likely to face osmotic challenges, but there is yet much to learn about how such environmental changes affect the architecture of bacterial cells. Here, we report a cell-biological study in model organisms of the genus Streptomyces, which are actinobacteria that grow in a highly polarized fashion to ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00465-16
更新日期:2016-12-13 00:00:00
abstract::A polyacrylamide gel electrophoretic method was used for identification of L-forms in the genera Streptococcus, Staphylococcus, and Proteus, by comparing phenol-acetic acid-water extracts of homologous parent L-form pairs to one another and to other pairs. The method requires only milligram quantities of material for ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.100.1.71-77.1969
更新日期:1969-10-01 00:00:00
abstract::This paper describes the major transmutations of donor deoxyribonucleic acid (DNA) after uptake by competent Bacillus subtilis cells. Kinetic experiments confirm that after exposure to competent cells, donor DNA is converted to double-stranded fragments (DSF) which can be isolated as early as 30 s from the beginning o...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.116.1.154-162.1973
更新日期:1973-10-01 00:00:00
abstract::A positive selection method for isolation of nitrogenase-derepressed mutant strains of a filamentous cyanobacterium, Anabaena variabilis, is described. Mutant strains that are resistant to a glutamate analog, L-methionine-D,L-sulfoximine, were screened for their ability to produce and excrete NH4+ into medium. Mutant ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.165.2.412-419.1986
更新日期:1986-02-01 00:00:00
abstract::Quorum sensing of Sinorhizobium meliloti relies on N-acyl-homoserine lactones (AHLs) as autoinducers. AHL production increases at high population density, and this depends on the AHL synthase SinI and two transcriptional regulators, SinR and ExpR. Our study demonstrates that ectopic expression of the gene rne, coding ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.01471-13
更新日期:2014-04-01 00:00:00
abstract::Cells of the cyanobacterium Anabaena variabilis starved for phosphate for 3 days took up phosphate at about 100 times the rate of unstarved cells. Kinetic data suggested that a new transport system had been induced by starvation for phosphate. The inducible phosphate transport system was quickly repressed by addition ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.170.3.1143-1147.1988
更新日期:1988-03-01 00:00:00
abstract::A mutant of Escherichia coli resistant to serine hydroxamate which has a large increase in Km for serine of seryl-tRNA synthetase is described. The mutant serS gene was cloned and sequenced and was found to contain a single-base-pair mutation, resulting in the substitution of the residue alanine 262 by valine in motif...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.177.11.3347-3350.1995
更新日期:1995-06-01 00:00:00
abstract::Enterococcus faecalis ATCC 29212, a vancomycin-sensitive strain, has been extensively used as a representative control strain for clinical and laboratory experiments. Here we report the draft genome and annotation of this strain, containing 3,027,060 bp, with a G+C content of 37.2% in 126 contigs (≥ 500 bp). ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.01423-12
更新日期:2012-11-01 00:00:00