scholarly journals Comparativein silicoanalysis offtsZgene from different bacteria reveals the preference for core set of codons in coding sequence structuring and secondary structural elements determination

2019 ◽  
Author(s):  
Ayon Pal ◽  
Barnan Kr Saha ◽  
Jayanti Saha
Keyword(s):  
Bacterial Species ◽  
Gc Content ◽  
Gene Organization ◽  
Sequence Information ◽  
Antibacterial Drug ◽  
Bacterial Cell Division ◽  
Bacterial Gene ◽  
Coding Sequence ◽  
Ftsz Protein ◽  
Core Set

AbstractThe deluge of sequence information in the recent times provide us with an excellent opportunity to compare organisms on a large genomic scale. In this study we have tried to decipher the variation in the gene organization and structuring of a vital bacterial gene calledftsZwhich codes for an integral component of the bacterial cell division, the FtsZ protein. FtsZ is homologous to tubulin protein and has been found to be ubiquitous in eubacteria. FtsZ is showing increasing promise as a target for antibacterial drug discovery. Our study offtsZprotein from 143 different bacterial species spanning a wider range of morphological and physiological type demonstrates that theftsZgene of about ninety three percent of the organisms involved in our analyses show relatively biased codon usage profile and significant GC deviation from their genomic GC content. We have also detected a tendency among the different organisms to utilize a core set of codons in structuring theftsZcoding sequence. Our meticulous analysis of theftsZgene linked with the corresponding FtsZ protein show that there is a bias towards the use of specific synonymous codons particularly in the helix and strand regions of the multi-domain FtsZ protein. Overall our findings suggest that in an indispensable and vital protein such as FtsZ, there is an inherent tendency to maintain form and structure for optimized performance in spite of the extrinsic variability in coding features.

scholarly journals Structural Organization of Virulence-Associated Plasmids of Yersinia pestis

1998 ◽  
Vol 180 (19) ◽  
pp. 5192-5202 ◽  
Author(s):  
Ping Hu ◽  
Jeffrey Elliott ◽  
Paula McCready ◽  
Evan Skowronski ◽  
Jeffrey Garnes ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Bacterial Species ◽  
Gc Content ◽  
Single Copy ◽  
Hypothetical Protein ◽  
Gene Organization ◽  
Open Reading Frames ◽  
Virulence Determinants ◽  
Intact Gene ◽  
Anchoring Protein

ABSTRACT The complete nucleotide sequence and gene organization of the three virulence plasmids from Yersinia pestis KIM5 were determined. Plasmid pPCP1 (9,610 bp) has a GC content of 45.3% and encodes two previously known virulence factors, an associated protein, and a single copy of IS100. Plasmid pCD1 (70,504 bp) has a GC content of 44.8%. It is known to encode a number of essential virulence determinants, regulatory functions, and a multiprotein secretory system comprising the low-calcium response stimulation that is shared with the other two Yersinia species pathogenic for humans (Y. pseudotuberculosis and Y. enterocolitica). A new pseudogene, which occurs as an intact gene in the Y. enterocolitica and Y. pseudotuberculosis-derived analogues, was found in pCD1. It corresponds to that encoding the lipoprotein YlpA. Several intact and partial insertion sequences and/or transposons were also found in pCD1, as well as six putative structural genes with high homology to proteins of unknown function in other yersiniae. The sequences of the genes involved in the replication of pCD1 are highly homologous to those of the cognate plasmids in Y. pseudotuberculosisand Y. enterocolitica, but their localization within the plasmid differs markedly from those of the latter. Plasmid pMT1 (100,984 bp) has a GC content of 50.2%. It possesses two copies of IS100, which are located 25 kb apart and in opposite orientations. Adjacent to one of these IS100 inserts is a partial copy of IS285. A single copy of an IS200-like element (recently named IS1541) was also located in pMT1. In addition to 5 previously described genes, such as murine toxin, capsule antigen, capsule anchoring protein, etc., 30 homologues to genes of several bacterial species were found in this plasmid, and another 44 open reading frames without homology to any known or hypothetical protein in the databases were predicted.

Novel compound with potential of an antibacterial drug targets FtsZ protein

2009 ◽  
Vol 423 (1) ◽  
pp. e1-e3 ◽  
Author(s):  
Dipak Dasgupta
Keyword(s):  
Cell Division ◽  
Self Assembly ◽  
Drug Targets ◽  
Antibacterial Drug ◽  
Bacterial Cell Division ◽  
Normal Functioning ◽  
Ftsz Protein ◽  
Biochemical Journal ◽  
Z Ring ◽  
Dissociation Step

A dynamic bacterial cytoskeleton consisting of FtsZ and other proteins is a potential target for the development of antibacterial drugs. GTPase activity of FtsZ protein leads to self-assembly of the protein. The resultant circumferential dynamic Z-ring at the centre of the cell recruits other proteins during progression and completion of bacterial cell division. There are natural compounds inhibiting one or more of these steps. Such inhibition ultimately culminates in the arrest of cell division. In this issue of the Biochemical Journal, a paper by Beuria et al. highlights the importance of the dynamics of the Z-ring for cell division. The ligand-induced enhanced degree of stabilization of FtsZ protofilaments, leading to the absence of the subsequent dissociation step, would hamper the normal functioning of the Z-ring, leading to an inhibition of cell proliferation. A novel antibacterial agent, OTBA (3-{5-[4-oxo-2-thioxo-3-(3-trifluoromethylphenyl)-thiazolidin-5-ylidenemethyl]-furan-2-yl}-benzoic acid) works via this hitherto unreported pathway. It stabilizes the FtsZ polymers, suppressing the dynamics which, in turn, inhibits cell division.

scholarly journals Rapid Detection, Identification, and Enumeration ofEscherichia coli Cells in Municipal Water by Chemiluminescent In Situ Hybridization

2001 ◽  
Vol 67 (1) ◽  
pp. 142-147 ◽  
Author(s):  
Henrik Stender ◽  
Adam J. Broomer ◽  
Kenneth Oliveira ◽  
Heather Perry-O'Keefe ◽  
Jens J. Hyldig-Nielsen ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
16S Rrna ◽  
Sensitivity And Specificity ◽  
Bacterial Species ◽  
Rdna Sequence ◽  
Sequence Information ◽  
Sequence Alignments ◽  
E Coli ◽  
Municipal Water

ABSTRACT A new chemiluminescent in situ hybridization (CISH) method provides simultaneous detection, identification, and enumeration of culturableEscherichia coli cells in 100 ml of municipal water within one working day. Following filtration and 5 h of growth on tryptic soy agar at 35°C, individual microcolonies of E. coliwere detected directly on a 47-mm-diameter membrane filter using soybean peroxidase-labeled peptide nucleic acid (PNA) probes targeting a species-specific sequence in E. coli 16S rRNA. Within each microcolony, hybridized, peroxidase-labeled PNA probe and chemiluminescent substrate generated light which was subsequently captured on film. Thus, each spot of light represented one microcolony of E. coli. Following probe selection based on 16S ribosomal DNA (rDNA) sequence alignments and sample matrix interference, the sensitivity and specificity of the probe Eco16S07C were determined by dot hybridization to RNA of eight bacterial species. Only the rRNA of E. coli and Pseudomonas aeruginosa were detected by Eco16S07C with the latter mismatch hybridization being eliminated by a PNA blocker probe targetingP. aeruginosa 16S rRNA. The sensitivity and specificity for the detection of E. coli by PNA CISH were then determined using 8 E. coli strains and 17 other bacterial species, including closely related species. No bacterial strains other thanE. coli and Shigella spp. were detected, which is in accordance with 16S rDNA sequence information. Furthermore, the enumeration of microcolonies of E. coli represented by spots of light correlated 92 to 95% with visible colonies following overnight incubation. PNA CISH employs traditional membrane filtration and culturing techniques while providing the added sensitivity and specificity of PNA probes in order to yield faster and more definitive results.

Polyamine-mediated regulation of mouse ornithine decarboxylase is posttranslational

1989 ◽  
Vol 9 (12) ◽  
pp. 5484-5490
Author(s):  
T van Daalen Wetters ◽  
M Macrae ◽  
M Brabant ◽  
A Sittler ◽  
P Coffino
Keyword(s):  
Ornithine Decarboxylase ◽  
Translational Regulation ◽  
Feedback Inhibition ◽  
Chimeric Protein ◽  
Sequence Information ◽  
Pulse Label ◽  
Protein Coding ◽  
Coding Sequence ◽  
Series Of Experiments ◽  
The Difference

The activity of ornithine decarboxylase (ODC) is negatively regulated by intracellular polyamines, which thereby mediate a form of feedback inhibition of the initial enzyme in the pathway of their synthesis. This phenomenon has been believed to result, at least in part, from translational regulation. To investigate this further, we performed four series of experiments. First, we found that a chimeric protein encoded by an mRNA containing the ODC 5' leader sequence did not exhibit polyamine-dependent regulation. Second, we showed that transcripts containing the protein-coding sequence of ODC, but no other ODC-derived sequence information, exhibited regulation. Third, we found that the association of ODC mRNA with ribosomes was not altered when intracellular polyamine levels were modulated under conditions previously deemed to cause translational regulation. Last, we carried out experiments to measure the incorporation of [35S]methionine into ODC in polyamine-starved and polyamine-replete cells. Differential incorporation diminished progressively as pulse-label times were shortened; at the shortest labeling time used (4 min), the difference in favor of ODC in polyamine-starved cells was less than twofold. These findings suggest that it is necessary to reevaluate the question of whether polyamines cause alterations of translation of ODC mRNA.

scholarly journals Discovery of genes encoding a Streptolysin S-like toxin biosynthetic cluster in a select highly pathogenic methicillin resistant Staphylococcus aureus JKD6159 strain

2019 ◽  
Author(s):  
Trevor Kane ◽  
Katelyn E. Carothers ◽  
Yunjuan Bao ◽  
Won-Sik Yeo ◽  
Taeok Bae ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Gene Cluster ◽  
Virulence Factor ◽  
Gene Organization ◽  
Biosynthetic Gene ◽  
Bacterial Gene ◽  
Methicillin Resistant ◽  
Streptolysin S

AbstractBackgroundStaphylococcus aureus (S. aureus) is a major human pathogen owing to its arsenal of virulence factors, as well as its acquisition of multi-antibiotic resistance. Here we report the identification of a Streptolysin S (SLS) like biosynthetic gene cluster in a highly virulent community-acquired methicillin resistant S. aureus (MRSA) isolate, JKD6159. Examination of the SLS-like gene cluster in JKD6159 shows significant homology and gene organization to the SLS-associated biosynthetic gene (sag) cluster responsible for the production of the major hemolysin SLS in Group A Streptococcus.ResultsWe took a comprehensive approach to elucidating the putative role of the sag gene cluster in JKD6159 by constructing a mutant in which one of the biosynthesis genes (sagB homologue) was deleted in the parent JKD6159 strain. Assays to evaluate bacterial gene regulation, biofilm formation, antimicrobial activity, as well as complete host cell response profile and comparative in vivo infections in Balb/Cj mice were conducted.ConclusionsAlthough no significant phenotypic changes were observed in our assays, we postulate that the SLS-like toxin produced by this strain of S. aureus may be a highly specialized virulence factor utilized in specific environments for selective advantage; studies to better understand the role of this newly discovered virulence factor in S. aureus warrant further investigation.

scholarly journals The key bacterial cell division protein FtsZ as a novel antibacterial drug target

2020 ◽  
Author(s):  
Mujeeb Rahman ◽  
Ping Wang ◽  
Na Wang ◽  
Yaodong Chen
Keyword(s):  
Cell Division ◽  
Bacterial Cell ◽  
Drug Targets ◽  
Multidrug Resistant ◽  
Antibacterial Drug ◽  
Bacterial Cell Division ◽  
Bacterial Strains ◽  
Antimicrobial Drugs ◽  
Novel Antibiotics

The number of multidrug-resistant bacterial strains is currently increasing; thus, the determination of drug targets for the development of novel antimicrobial drugs is urgently needed. FtsZ, the prokaryotic homolog of the eukaryotic tubulin, is a GTP-dependent prokaryotic cytoskeletal protein that is conserved among most bacterial strains. In vitro studies revealed that FtsZ self-assembles into dynamic protofilaments or bundles, and it forms a dynamic Z-ring at the center of the cell, leading to septation and consequent cell division. The potential role of FtsZ in the blockage of cell division makes FtsZ a highly attractive target for developing novel antibiotics. Researchers have been working on synthetic molecules and natural products as inhibitors of FtsZ. Accumulating data suggest that FtsZ may provide the platform for the development of novel antibiotics. In this review, we summarize recent advances on the properties of FtsZ protein and bacterial cell division, as well as on the development of FtsZ inhibitors.

scholarly journals Draft Genome Sequence of Streptomyces mexicanus Strain Q0842, Isolated from Human Skin

2020 ◽  
Vol 9 (44) ◽  
Author(s):  
Manon Boxberger ◽  
Mariem Ben Khedher ◽  
Anthony Levasseur ◽  
Bernard La Scola
Keyword(s):  
Human Skin ◽  
Genome Sequencing ◽  
Genome Sequence ◽  
Bacterial Species ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Swab Sample ◽  
Partial Genome Sequence ◽  
Partial Genome

ABSTRACT In 2003, Streptomyces mexicanus was reported as a novel xylanolytic bacterial species isolated from soil; a partial genome sequence was determined. In 2019, a strain from the same species was isolated from a hand skin swab sample from a healthy French woman. Genome sequencing revealed an 8,011,832-bp sequence with a GC content of 72.5%.

scholarly journals Polyamine-mediated regulation of mouse ornithine decarboxylase is posttranslational.

1989 ◽  
Vol 9 (12) ◽  
pp. 5484-5490 ◽  
Author(s):  
T van Daalen Wetters ◽  
M Macrae ◽  
M Brabant ◽  
A Sittler ◽  
P Coffino
Keyword(s):  
Ornithine Decarboxylase ◽  
Translational Regulation ◽  
Feedback Inhibition ◽  
Chimeric Protein ◽  
Sequence Information ◽  
Pulse Label ◽  
Protein Coding ◽  
Coding Sequence ◽  
Series Of Experiments ◽  
The Difference

The activity of ornithine decarboxylase (ODC) is negatively regulated by intracellular polyamines, which thereby mediate a form of feedback inhibition of the initial enzyme in the pathway of their synthesis. This phenomenon has been believed to result, at least in part, from translational regulation. To investigate this further, we performed four series of experiments. First, we found that a chimeric protein encoded by an mRNA containing the ODC 5' leader sequence did not exhibit polyamine-dependent regulation. Second, we showed that transcripts containing the protein-coding sequence of ODC, but no other ODC-derived sequence information, exhibited regulation. Third, we found that the association of ODC mRNA with ribosomes was not altered when intracellular polyamine levels were modulated under conditions previously deemed to cause translational regulation. Last, we carried out experiments to measure the incorporation of [35S]methionine into ODC in polyamine-starved and polyamine-replete cells. Differential incorporation diminished progressively as pulse-label times were shortened; at the shortest labeling time used (4 min), the difference in favor of ODC in polyamine-starved cells was less than twofold. These findings suggest that it is necessary to reevaluate the question of whether polyamines cause alterations of translation of ODC mRNA.

scholarly journals Analysis of the Genome Sequence of Lactobacillus gasseri ATCC 33323 Reveals the Molecular Basis of an Autochthonous Intestinal Organism

2008 ◽  
Vol 74 (15) ◽  
pp. 4610-4625 ◽  
Author(s):  
M. Andrea Azcarate-Peril ◽  
Eric Altermann ◽  
Yong Jun Goh ◽  
Richard Tallon ◽  
Rosemary B. Sanozky-Dawes ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Native Species ◽  
Bacterial Species ◽  
Gc Content ◽  
Intestinal Epithelial ◽  
Growth And Survival ◽  
Lactobacillus Gasseri ◽  
Bacteriophage Infection ◽  
A Genome

ABSTRACT This study presents the complete genome sequence of Lactobacillus gasseri ATCC 33323, a neotype strain of human origin and a native species found commonly in the gastrointestinal tracts of neonates and adults. The plasmid-free genome was 1,894,360 bp in size and predicted to encode 1,810 genes. The GC content was 35.3%, similar to the GC content of its closest relatives, L. johnsonii NCC 533 (34%) and L. acidophilus NCFM (34%). Two identical copies of the prophage LgaI (40,086 bp), of the Sfi11-like Siphoviridae phage family, were integrated tandomly in the chromosome. A number of unique features were identified in the genome of L. gasseri that were likely acquired by horizontal gene transfer and may contribute to the survival of this bacterium in its ecological niche. L. gasseri encodes two restriction and modification systems, which may limit bacteriophage infection. L. gasseri also encodes an operon for production of heteropolysaccharides of high complexity. A unique alternative sigma factor was present similar to that of B. caccae ATCC 43185, a bacterial species isolated from human feces. In addition, L. gasseri encoded the highest number of putative mucus-binding proteins (14) among lactobacilli sequenced to date. Selected phenotypic characteristics that were compared between ATCC 33323 and other human L. gasseri strains included carbohydrate fermentation patterns, growth and survival in bile, oxalate degradation, and adhesion to intestinal epithelial cells, in vitro. The results from this study indicated high intraspecies variability from a genome encoding traits important for survival and retention in the gastrointestinal tract.

A Relationship Between GC Content and Coding-Sequence Length

1996 ◽  
Vol 43 (3) ◽  
pp. 216-223
Author(s):  
José L. Oliver ◽  
Antonio Marín
Keyword(s):  
Gc Content ◽  
Sequence Length ◽  
Coding Sequence
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