Abstract:
:Horizontal acquisition of novel chromosomal genes is considered to be a key process in the evolution of bacterial pathogens. However, the identification of gene presence or absence could be hindered by the inconsistencies in bacterial genome annotations. Here, we performed a cross-annotation of omnipresent core and mosaic accessory genes in the chromosome of Salmonella enterica serovar Typhimurium across a total of 20 fully assembled genomes deposited into GenBank. Cross-annotation resulted in a 32% increase in the number of core genes and a 3-fold decrease in the number of genes identified as mosaic genes (i.e., genes present in some strains only) by the original annotation. Of the remaining noncore genes, the vast majority were prophage genes, and 255 of the nonphage genes were actually of core origin but lost in some strains upon the emergence of the S Typhimurium serovar, suggesting that the chromosomal portion of the S Typhimurium genome acquired a very limited number of novel genes other than prophages. Only horizontally acquired nonphage genes related to bacterial fitness or virulence were found in four recently sequenced isolates, all located on three different genomic islands that harbor multidrug resistance determinants. Thus, the extensive use of antimicrobials could be the main selection force behind the new fitness gene acquisition and the emergence of novel Salmonella pathotypes. IMPORTANCE:Significant discrepancies in the annotations of bacterial genomes could mislead the conclusions about evolutionary origin of chromosomal genes, as we demonstrate here via a cross-annotation-based analysis of Salmonella Typhimurium genomes from GenBank. We conclude that despite being able to infect a broad range of vertebrate hosts, the genomic diversity of S Typhimurium strains is almost exclusively limited to gene loss and the transfer of prophage DNA. Only nonphage chromosomal genes acquired after the emergence of the serovar are linked to the genomic islands harboring multidrug resistance factors. Since the fitness factors could lead to increased virulence, this poses an important research question: could overuse or misuse of antimicrobials act as selection forces for the emergence of more pathogenic strains of Salmonella?
journal_name
J Bacterioljournal_title
Journal of bacteriologyauthors
Paul S,Sokurenko EV,Chattopadhyay Sdoi
10.1128/JB.00545-16subject
Has Abstractpub_date
2016-11-04 00:00:00pages
3152-3161issue
23eissn
0021-9193issn
1098-5530pii
JB.00545-16journal_volume
198pub_type
杂志文章abstract::Enger, M. D. (North Dakota State University, Fargo), and B. P. Sleeper. Multiple cellulase system from Streptomyces antibioticus. J. Bacteriol. 89:23-27. 1965.-Starch-block zone electrophoresis was used to isolate five electrophoretically distinct, active cellulolytic components (I to V) from the crude extracellular c...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.89.1.23-27.1965
更新日期:1965-01-01 00:00:00
abstract::When Azotobacter vinelandii was derepressed for nitrogenase synthesis in a N-free medium containing tungstate instead of molybdate, an inactive component I was synthesized. Although this inactive component I could be activated in vivo upon addition of molybdate to the medium, it could not be activated in vitro when mo...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.120.2.697-701.1974
更新日期:1974-11-01 00:00:00
abstract::Rohlfing, S. R. (Western Reserve University, Cleveland, Ohio), and I. P. Crawford. Purification and characterization of the beta-galactosidase of Aeromonas formicans. J. Bacteriol. 91:1085-1097. 1966.-The beta-galactosidase of Aeromonas formicans was purified by diethylaminoethyl cellulose chromatography and gel filtr...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.91.3.1085-1097.1966
更新日期:1966-03-01 00:00:00
abstract::The first step in the transfer of the Bacteroides conjugative transposon CTnDOT is excision of the integrated element from the chromosome to form a circular transfer intermediate. Excision occurs only after the bacteria are exposed to tetracycline. Previously, four excision genes were identified. One was the integrase...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.187.16.5732-5741.2005
更新日期:2005-08-01 00:00:00
abstract::The role of oxygen in the transcriptional regulation of the PN promoter that controls the bzd operon involved in the anaerobic catabolism of benzoate in the denitrifying Azoarcus sp. strain CIB has been investigated. In vivo experiments using PN::lacZ translational fusions, in both Azoarcus sp. strain CIB and Escheric...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.188.7.2343-2354.2006
更新日期:2006-04-01 00:00:00
abstract::The synthesis of cytosine deaminase in Salmonella typhimurium is repressed by pyrimidines. This repression is mediated by both a uridine and a cytidine compound, indicating a distinct difference in the regulation of synthesis of cytosine deaminase from the regulation of the de novo pyrimidine pathway enzymes. A salvag...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.149.3.1171-1174.1982
更新日期:1982-03-01 00:00:00
abstract::During sporulation in diploid Saccharomyces cerevisiae, spindle pole bodies acquire the so-called meiotic plaque, a prerequisite for spore formation. Mpc70p is a component of the meiotic plaque and is thus essential for spore formation. We show here that MPC70/mpc70 heterozygous strains most often produce two spores i...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.183.7.2372-2375.2001
更新日期:2001-04-01 00:00:00
abstract::In vivo assembly of the Klebsiella aerogenes urease nickel metallocenter requires the presence of UreD, UreF, and UreG accessory proteins and is further facilitated by UreE. Prior studies had shown that urease apoprotein exists in an uncomplexed form as well as in a series of UreD-urease (I.-S. Park, M.B. Carr, and R....
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.178.18.5417-5421.1996
更新日期:1996-09-01 00:00:00
abstract::Genetic exchange mechanisms, to our knowledge, have not been reported for Legionella pneumophila, and consequently, studies on the genetic organization of L. pneumophila have not appeared in the literature. Here, we describe gene transfer mediated by broad host range conjugative plasmids in Legionella spp. Escherichia...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.161.1.80-84.1985
更新日期:1985-01-01 00:00:00
abstract::A coordinated response to a complex and dynamic environment requires an organism to simultaneously monitor and interpret multiple signaling cues. In bacteria and some eukaryotes, environmental responses depend on the histidine autokinases (HKs). For example, VirA, a large integral membrane HK from Agrobacterium tumefa...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00459-07
更新日期:2007-08-01 00:00:00
abstract::The force required to rupture bonds between individual Staphylococcus aureus MSCRAMMs and surfaces coated with extracellular matrix molecules has been quantified by using optical tweezers. The observed binding forces between fibrinogen or fibronectin and S. aureus MSCRAMMs occurred as an approximate integer multiple o...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.185.6.2031-2035.2003
更新日期:2003-03-01 00:00:00
abstract::HtrA-type serine proteases participate in folding and degradation of aberrant proteins and in processing and maturation of native proteins. Mutation of the corresponding genes often confers a pleiotropic phenotype that can include temperature sensitivity, sensitivity to osmotic and oxidative stress, and attenuated vir...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.183.2.654-663.2001
更新日期:2001-01-01 00:00:00
abstract::In Salmonella enterica, the biosynthetic pathways for the generation of purines and the essential cofactor thiamine pyrophosphate branch after sharing five enzymatic steps. Phosphoribosyl amine (PRA) is the first intermediate in the common portion of the pathway and is generated from phosphoribosylpyrophosphate and gl...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00745-06
更新日期:2006-10-01 00:00:00
abstract::In Salmonella typhimurium, three groups of genes located in rfb, rfe, and rff clusters are known to be involved in the biosynthesis of the enterobacterial common antigen. We found that enzymatic synthesis of uridine diphosphate N-acetylmannosaminouric acid, the activated form of a constituent sugar of the common antig...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.136.1.227-233.1978
更新日期:1978-10-01 00:00:00
abstract::Utilization of heme as an iron source by Bradyrhizobium japonicum involves induction of the outer membrane heme receptor gene hmuR and other genes within the heme utilization locus. Here, we discovered the hmuP gene located upstream of hmuR and transcribed divergently from it along with hmuTUV. hmuP encodes a small pr...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00071-12
更新日期:2012-06-01 00:00:00
abstract::The ability to reduce Hg(II) to Hg(0), which is determined by a plasmid-borne gene in Escherichia coli, is conferred by a Hg(II)-inducible activity which is located in the cytoplasm rather than in the periplasmic space of the cell. This Hg(II)-reducing activity can be isolated from the supernatant of a 160,000 x g cen...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.119.1.242-249.1974
更新日期:1974-07-01 00:00:00
abstract::Pseudomonas sp. VLB120 uses styrene as a sole source of carbon and energy. The first step in this metabolic pathway is catalyzed by an oxygenase (StyA) and a NADH-flavin oxidoreductase (StyB). Both components have been isolated from wild-type Pseudomonas strain VLB120 as well as from recombinant Escherichia coli. StyA...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.186.16.5292-5302.2004
更新日期:2004-08-01 00:00:00
abstract::The steps in the biosynthetic transformation of GTP to 7,8-dihydro-D-erythro-neopterin (H2neopterin), the precursor to the modified folates found in the methanogenic archaea, has been elucidated for the first time in two members of the domain Archaea. In Methanococcus thermophila and Methanobacterium thermoautotrophic...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.179.16.5165-5170.1997
更新日期:1997-08-01 00:00:00
abstract::We have developed a rapid and sensitive fluorimetric method, based on the formation of a fluorescent product from nitrosation of 2,3-diaminonaphthalene, for measuring the ability of bacteria to catalyze nitrosation of amines. We have shown in Escherichia coli that nitrosation can be induced under anaerobic conditions ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.170.1.359-364.1988
更新日期:1988-01-01 00:00:00
abstract::The cheA locus of Escherichia coli encodes two similar proteins, CheAL (654 amino acids) and CheAS (557 amino acids), which are made by initiating translation from different in-frame start sites [start(L) and start(S)]. CheAL plays an essential role in chemotactic signaling. It autophosphorylates at a histidine residu...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.177.10.2713-2720.1995
更新日期:1995-05-01 00:00:00
abstract::Autoplaquing has been observed in Myxococcus strains freshly isolated from soil. Initial observations suggest that this phenomenon is not induced by elevated temperature or visible light; we suggest that it may be the result of a derangement in the developmental autolytic mechanism within the cell. ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.158.3.1163-1164.1984
更新日期:1984-06-01 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::Rhodobacter sphaeroides cells containing an in-frame deletion within ccmA lack detectable soluble and membrane-bound c-type cytochromes and are unable to grow under conditions where these proteins are required. Only strains merodiploid for ccmABCDG were found after attempting to generate cells containing either a ccmG...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.183.15.4643-4647.2001
更新日期:2001-08-01 00:00:00
abstract::Synthesis of the Salmonella typhimurium hook protein from the gene cloned on a multicopy plasmid results in partial suppression of the flagellar assembly defects of certain classes of Escherichia coli mutants (K. Ohnishi, M. Homma, K. Kutsukake, and T. Iino, J. Bacteriol, 169:1485-1488, 1987). This phenomenon allowed ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.169.4.1489-1492.1987
更新日期:1987-04-01 00:00:00
abstract::The PhoQ/PhoP two-component system is repressed by divalent cations, such as Mg(2+) and Ca(2+), in the growth medium and stimulated by low pH and certain cationic antimicrobial peptides. In Escherichia coli, it was recently shown that the histidine kinase PhoQ is also modulated by at least two additional factors, the ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.06055-11
更新日期:2012-03-01 00:00:00
abstract::A fragment of the Lactococcus lactis chromosome containing an open reading frame of 265 codons, denoted bglR, has been characterized. The polypeptide encoded by bglR shares 36 to 30% sequence identity with a family of regulatory proteins including ArbG from Erwinia chrysanthemi, BglG from Escherichia coli, and SacT an...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.176.18.5681-5685.1994
更新日期:1994-09-01 00:00:00
abstract::The Gram-positive bacterium Streptococcus pyogenes (also called group A Streptococcus [GAS]), is found strictly in humans and is capable of causing a wide variety of infections. Here we demonstrate that serine catabolism in GAS is controlled by the transcriptional regulator Spy49_0126c. We have designated this regulat...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.01516-10
更新日期:2011-04-01 00:00:00
abstract::We report the draft genome sequence of methicillin-resistant Staphylococcus aureus (MRSA) strain ST672, an emerging disease clone in India, from a septicemia patient. The genome size is about 2.82 Mb with 2,485 open reading frames (ORFs). The staphylococcal cassette chromosome mec (SCCmec) element (type V) and immune ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.01868-12
更新日期:2012-12-01 00:00:00
abstract::ZmaR is a resistance determinant of unusual abundance in the environment and confers on gram-positive and gram-negative bacteria resistance to zwittermicin A, a novel broad-spectrum antibiotic produced by species of Bacillus. The ZmaR protein has no sequence similarity to proteins of known function; thus, the purpose ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.181.17.5455-5460.1999
更新日期:1999-09-01 00:00:00
abstract::At specific times in the cell cycle, the bacterium Caulobacter crescentus assembles two major polar organelles, the flagellum and the stalk. Previous studies have shown that flbT mutants overproduce flagellins and are unable to form chemotaxis swarm rings. In this paper, we report alterations in both the stalk and the...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.172.4.2113-2123.1990
更新日期:1990-04-01 00:00:00