scholarly journals Sequence and genome context analysis of a new molecular class D beta-lactamase gene from Legionella pneumophila

2002 ◽  
Vol 50 (3) ◽  
pp. 331-338 ◽  
Author(s):  
M. B. Avison
Keyword(s):  
Legionella Pneumophila ◽  
Beta Lactamase ◽  
Context Analysis ◽  
Class D ◽  
Genome Context Analysis ◽  
Genome Context ◽  
Lactamase Gene

Genome-wide Analysis of the Distribution of Riboswitches and Function Analyses of the Corresponding Downstream Genes in Prokaryotes

2018 ◽  
Vol 14 (1) ◽  
pp. 53-61
Author(s):  
Xinfeng Li ◽  
Fang Chen ◽  
Jinfeng Xiao ◽  
Shan-Ho Chou ◽  
Xuming Li ◽  
...  
Keyword(s):  
Functional Categories ◽  
Gene Expressions ◽  
Context Analysis ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Prokaryotic Genomes ◽  
Genome Context Analysis ◽  
Genome Context ◽  
And Function

Background: Riboswitches are structured elements that usually reside in the noncoding regions of mRNAs, with which various ligands bind to control a wide variety of downstream gene expressions. To date, more than twenty different classes of riboswitches have been characterized to sense various metabolites, including purines and their derivatives, coenzymes, amino acids, and metal ions, etc. </P><P> Objective: This study aims to study the genome-wide analysis of the distribution of riboswitches and function analyses of the corresponding downstream genes in prokaryotes. Results: In this study, we have completed a genome context analysis of 27 riboswitches to elucidate their metabolic capacities of riboswitch-mediated gene regulation from the completely-sequenced 3,079 prokaryotic genomes. Furthermore, Cluster of Orthologous Groups of proteins (COG) annotation was applied to predict and classify the possible functions of corresponding downstream genes of these riboswitches. We found that they could all be successfully annotated and grouped into 20 different COG functional categories, in which the two main clusters &quot;coenzyme metabolism [H]&quot; and &quot;amino acid transport and metabolism [E]&quot; were the most significantly enriched. Conclusion: Riboswitches are found to be widespread in bacteria, among which three main classes of TPP-, cobalamin- and SAM-riboswitch were the most widely distributed. We found a wide variety of functions were associated with the corresponding downstream genes, suggesting that a wide extend of regulatory roles were mediated by these riboswitches in prokaryotes.

scholarly journals Complete Genome Sequencing of Acinetobacter sp. Strain LoGeW2-3, Isolated from the Pellet of a White Stork, Reveals a Novel Class D Beta-Lactamase Gene

2018 ◽  
Vol 6 (2) ◽  
Author(s):  
Ulrike Blaschke ◽  
Evelyn Skiebe ◽  
Michael Kaatz ◽  
Paul G. Higgins ◽  
Yvonne Pfeifer ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Complete Genome ◽  
White Stork ◽  
Whole Genome ◽  
Beta Lactamase ◽  
Ciconia Ciconia ◽  
Complete Genome Sequencing ◽  
Class D ◽  
Lactamase Gene

ABSTRACT Whole-genome sequencing of Acinetobacter sp. strain LoGeW2-3, isolated from the pellet of a white stork (Ciconia ciconia), reveals the presence of a plasmid of 179,399 bp encoding a CRISPR-Cas (clustered regularly interspaced short palindromic repeats and associated genes) system of the I-F type, and the chromosomally encoded novel class D beta-lactamase OXA-568.

Role of multiprotein bridging factor 1 in archaea: bridging the domains?

2009 ◽  
Vol 37 (1) ◽  
pp. 52-57 ◽  
Author(s):  
Bart de Koning ◽  
Fabian Blombach ◽  
Hao Wu ◽  
Stan J.J. Brouns ◽  
John van der Oost
Keyword(s):  
Yeast Genome ◽  
Terminal Part ◽  
Context Analysis ◽  
Eukaryotic Transcription ◽  
Translation Fidelity ◽  
Genome Context Analysis ◽  
Tata Box Binding Protein ◽  
Genome Context ◽  
Regulatory Dna

MBF1 (multiprotein bridging factor 1) is a highly conserved protein in archaea and eukaryotes. It was originally identified as a mediator of the eukaryotic transcription regulator BmFTZ-F1 (Bombyx mori regulator of fushi tarazu). MBF1 was demonstrated to enhance transcription by forming a bridge between distinct regulatory DNA-binding proteins and the TATA-box-binding protein. MBF1 consists of two parts: a C-terminal part that contains a highly conserved helix–turn–helix, and an N-terminal part that shows a clear divergence: in eukaryotes, it is a weakly conserved flexible domain, whereas, in archaea, it is a conserved zinc-ribbon domain. Although its function in archaea remains elusive, its function as a transcriptional co-activator has been deduced from thorough studies of several eukaryotic proteins, often indicating a role in stress response. In addition, MBF1 was found to influence translation fidelity in yeast. Genome context analysis of mbf1 in archaea revealed conserved clustering in the crenarchaeal branch together with genes generally involved in gene expression. It points to a role of MBF1 in transcription and/or translation. Experimental data are required to allow comparison of the archaeal MBF1 with its eukaryotic counterpart.

scholarly journals The Salmonella enterica serovar Typhimurium virulence factor STM3169 is a hexuronic acid binding protein component of a TRAP transporter

Microbiology ◽  
2020 ◽  
Vol 166 (10) ◽  
pp. 981-987 ◽  
Author(s):  
Reyme Herman ◽  
Cavan Bennett-Ness ◽  
Abbas Maqbool ◽  
Amna Afzal ◽  
Andrew Leech ◽  
...  
Keyword(s):  
Carbon Source ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Binding Protein ◽  
Context Analysis ◽  
Gene Coding ◽  
Serovar Typhimurium ◽  
Genes Encoding ◽  
Genome Context Analysis ◽  
Genome Context ◽  
Substrate Binding Protein

The intracellular pathogen S. Typhimurium is a leading cause of foodborne illness across the world and is known to rely on a range of virulence factors to colonize the human host and cause disease. The gene coding for one such factor, stm3169, was determined to be upregulated upon macrophage entry and its disruption reduces survival in the macrophage. In this study we characterize the STM3169 protein, which forms the substrate binding protein (SBP) of an uncharacterized tripartite ATP-independent periplasmic (TRAP) transporter. Genome context analysis of the genes encoding this system in related bacteria suggests a function in sugar acid transport. We demonstrate that purified STM3169 binds d-glucuronic acid with high affinity and specificity. S. Typhimurium LT2 can use this sugar acid as a sole carbon source and the genes for a probable catabolic pathway are present in the genome. As this gene was previously implicated in macrophage survival, it suggests a role for d-glucuronate as an important carbon source for S. Typhimurium in this environment.

scholarly journals Comprehensive analysis of protein acetyltransferases of human pathogen Mycobacterium tuberculosis

2019 ◽  
Vol 39 (12) ◽  
Author(s):  
Longxiang Xie ◽  
Wenmin Yang ◽  
Xiangyu Fan ◽  
Jianping Xie
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Comprehensive Analysis ◽  
Therapeutic Interventions ◽  
Lysine Acetylation ◽  
Human Pathogen ◽  
Tuberculosis Control ◽  
Context Analysis ◽  
H37rv Strain ◽  
Genome Context Analysis ◽  
Genome Context

Abstract Tuberculosis (TB), a leading infectious disease caused by Mycobacterium tuberculosis strain, takes four human lives every minute globally. Paucity of knowledge on M. tuberculosis virulence and antibiotic resistance is the major challenge for tuberculosis control. We have identified 47 acetyltransferases in the M. tuberculosis, which use diverse substrates including antibiotic, amino acids, and other chemical molecules. Through comparative analysis of the protein file of the virulent M. tuberculosis H37Rv strain and the avirulent M. tuberculosis H37Ra strain, we identified one acetyltransferase that shows significant variations with N-terminal deletion, possibly influencing its physicochemical properties. We also found that one acetyltransferase has three types of post-translation modifications (lysine acetylation, succinylation, and glutarylation). The genome context analysis showed that many acetyltransferases with their neighboring genes belong to one operon. By data mining from published transcriptional profiles of M. tuberculosis exposed to diverse treatments, we revealed that several acetyltransferases may be functional during M. tuberculosis infection. Insights obtained from the present study can potentially provide clues for developing novel TB therapeutic interventions.

scholarly journals A comparative study of class-D β-lactamases

1993 ◽  
Vol 292 (2) ◽  
pp. 555-562 ◽  
Author(s):  
P Ledent ◽  
X Raquet ◽  
B Joris ◽  
J Van Beeumen ◽  
J M Frère
Keyword(s):  
Active Site ◽  
Gene Sequence ◽  
Catalytic Properties ◽  
Ion Exchange Chromatography ◽  
Exchange Chromatography ◽  
Beta Lactamase ◽  
Serine Residue ◽  
Beta Lactamases ◽  
Class D ◽  
Burst Kinetics

Three class-D beta-lactamases (OXA2, OXA1 and PSE2) were produced and purified to protein homogeneity. 6 beta-Iodopenicillanate inactivated the OXA2 enzyme without detectable turnover. Labelling of the same beta-lactamase with 6 beta-iodo[3H]penicillanate allowed the identification of Ser-70 as the active-site serine residue. In agreement with previous reports, the apparent M(r) of the OXA2 enzyme as determined by molecular-sieve filtration, was significantly higher than that deduced from the gene sequence, but this was not due to an equilibrium between a monomer and a dimer. The heterogeneity of the OXA2 beta-lactamase on ion-exchange chromatography contrasted with the similarity of the catalytic properties of the various forms. A first overview of the enzymic properties of the three ‘oxacillinases’ is presented. With the OXA2 enzyme, ‘burst’ kinetics, implying branched pathways, seemed to prevail with many substrates.

scholarly journals Acquisition of Beta-Lactamase by Neisseria meningitidis through Possible Horizontal Gene Transfer

2018 ◽  
Vol 62 (9) ◽  
Author(s):  
Eva Hong ◽  
Ala-Eddine Deghmane ◽  
Muhamed-Kheir Taha
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genome Sequencing ◽  
Meningococcal Disease ◽  
Bacterial Species ◽  
Whole Genome ◽  
Beta Lactamase ◽  
Content Type ◽  
Beta Lactamases ◽  
Lactamase Gene

ABSTRACT We report the detection in France of a beta-lactamase-producing invasive meningococcal isolate. Whole-genome sequencing of the isolate revealed a ROB-1-type beta-lactamase gene that is frequently encountered in Haemophilus influenzae, suggesting horizontal transfer between isolates of these bacterial species. Beta-lactamases are exceptional in meningococci, with no reports for more than 2 decades. This report is worrying, as the expansion of such isolates may jeopardize the effective treatment against invasive meningococcal disease.

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