scholarly journals Functional Genotyping of Sulfurospirillum spp. in Mixed Cultures Allowed the Identification of a New Tetrachloroethene Reductive Dehalogenase

2013 ◽  
Vol 79 (22) ◽  
pp. 6941-6947 ◽  
Author(s):  
Géraldine F. Buttet ◽  
Christof Holliger ◽  
Julien Maillard
Keyword(s):  
Anaerobic Respiration ◽  
Bacterial Genomes ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
Bacterial Consortia ◽  
Sequence Identity ◽  
Reductive Dehalogenase Genes ◽  
High Level ◽  
Substrate Prediction ◽  
Groundwater Pollutant

ABSTRACTReductive dehalogenases are the key enzymes involved in the anaerobic respiration of organohalides such as the widespread groundwater pollutant tetrachloroethene. The increasing number of available bacterial genomes and metagenomes gives access to hundreds of new putative reductive dehalogenase genes that display a high level of sequence diversity and for which substrate prediction remains very challenging. In this study, we present the development of a functional genotyping method targeting the diverse reductive dehalogenases present inSulfurospirillumspp., which allowed us to unambiguously identify a new reductive dehalogenase from our tetrachloroethene-dechlorinating SL2 bacterial consortia. The new enzyme, named PceATCE, shows 92% sequence identity with the well-characterized PceA enzyme ofSulfurospirillum multivorans, but in contrast to the latter, it is restricted to tetrachloroethene as a substrate. Its apparent higher dechlorinating activity with tetrachloroethene likely allowed its selection and maintenance in the bacterial consortia among other enzymes showing broader substrate ranges. The sequence-substrate relationships within tetrachloroethene reductive dehalogenases are also discussed.

scholarly journals Complete Genome Sequence of Dehalococcoides mccartyi Strain FL2, a Trichloroethene-Respiring Anaerobe Isolated from Pristine Freshwater Sediment

2019 ◽  
Vol 8 (33) ◽  
Author(s):  
Jun Yan ◽  
Yi Yang ◽  
Xiuying Li ◽  
Frank E. Löffler
Keyword(s):  
Complete Genome Sequence ◽  
Reductive Dechlorination ◽  
Complete Genome ◽  
Hydrogen Oxidation ◽  
Protein Coding ◽  
Coding Sequences ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
Dehalococcoides Mccartyi ◽  
Reductive Dehalogenase Genes

Dehalococcoides mccartyi strain FL2 couples growth to hydrogen oxidation and reductive dechlorination of trichloroethene and cis- and trans-1,2-dichloroethenes. Strain FL2 has a 1.42-Mb genome with a G+C content of 47.0% and carries 1,465 protein-coding sequences, including 24 reductive dehalogenase genes.

scholarly journals Quantitative Analysis of the Relative Transcript Levels of Four Chlorophenol Reductive Dehalogenase Genes in Desulfitobacterium hafniense PCP-1 Exposed to Chlorophenols

2011 ◽  
Vol 77 (17) ◽  
pp. 6261-6264 ◽  
Author(s):  
Ariane Bisaillon ◽  
Réjean Beaudet ◽  
François Lépine ◽  
Richard Villemur
Keyword(s):  
Quantitative Analysis ◽  
Transcript Levels ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
Reductive Dehalogenase Genes ◽  
Desulfitobacterium Hafniense

ABSTRACTRelative to those of unexposed cultures, the transcript levels of the four CprA-type reductive dehalogenase genes (cprA2,cprA3,cprA4, andcprA5) inDesulfitobacterium hafniensePCP-1 were measured in cultures exposed to chlorophenols. In 2,4,6-trichlorophenol-amended cultures,cprA2andcprA3were upregulated, as wascprA5, but concomitantly with the appearance of 2,4-dichlorophenol (DCP). In 3,5-DCP-amended cultures, onlycprA5was upregulated. In pentachlorophenol-amended cultures grown for 12 h,cprA2andcprA3were upregulated but notcprA5. cprA4was not upregulated significantly in cultures containing any tested chlorophenols.

scholarly journals Genome-Guided Identification of Organohalide-RespiringDeltaproteobacteriafrom the Marine Environment

mBio ◽  
2018 ◽  
Vol 9 (6) ◽  
Author(s):  
Jie Liu ◽  
Max M. Häggblom
Keyword(s):  
Marine Environment ◽  
Gene Diversity ◽  
Anthropogenic Activities ◽  
Reductive Dehalogenation ◽  
Important Process ◽  
Organohalide Respiration ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
Comprehensive Survey ◽  
Reductive Dehalogenase Genes

ABSTRACTOrganohalide compounds are widespread in the environment as a result of both anthropogenic activities and natural production. The marine environment, in particular, is a major reservoir of organohalides, and reductive dehalogenation is thought to be an important process in the overall cycling of these compounds.Deltaproteobacteriaare important members of the marine microbiota with diverse metabolic capacities, and reductive dehalogenation has been observed in someDeltaproteobacteria. In this study, a comprehensive survey ofDeltaproteobacteriagenomes revealed that approximately 10% contain reductive dehalogenase (RDase) genes, which are found within a common gene neighborhood. The dehalogenating potential of select RDase A-containingDeltaproteobacteriaand their gene expression were experimentally verified. ThreeDeltaproteobacteriastrains isolated from marine environments representing diverse species,Halodesulfovibrio marinisediminis,Desulfuromusa kysingii, andDesulfovibrio bizertensis, were shown to reductively dehalogenate bromophenols and utilize them as terminal electron acceptors in organohalide respiration. Their debrominating activity was not inhibited by sulfate or elemental sulfur, and these species are either sulfate- or sulfur-reducing bacteria. The analysis of RDase A gene transcripts indicated significant upregulation induced by 2,6-dibromophenol. This study extends our knowledge of the phylogenetic diversity of organohalide-respiring bacteria and their functional RDase A gene diversity. The identification of reductive dehalogenase genes in diverseDeltaproteobacteriaand confirmation of their organohalide-respiring capability suggest thatDeltaproteobacteriaplay an important role in natural organohalide cycling.IMPORTANCEThe marine environment is a major reservoir for both anthropogenic and natural organohalides, and reductive dehalogenation is thought to be an important process in the overall cycling of these compounds. Here we demonstrate that the capacity of organohalide respiration appears to be widely distributed in members of marineDeltaproteobacteria. The identification of reductive dehalogenase genes in diverseDeltaproteobacteriaand the confirmation of their dehalogenating activity through functional assays and transcript analysis in select isolates extend our knowledge of organohalide-respiringDeltaproteobacteriadiversity. The presence of functional reductive dehalogenase genes in diverseDeltaproteobacteriaimplies that they may play an important role in organohalide respiration in the environment.

scholarly journals Design and Verification of a Pangenome Microarray Oligonucleotide Probe Set for Dehalococcoides spp.

2011 ◽  
Vol 77 (15) ◽  
pp. 5361-5369 ◽  
Author(s):  
Laura A. Hug ◽  
Maryam Salehi ◽  
Paulo Nuin ◽  
Elisabeth R. Tillier ◽  
Elizabeth A. Edwards
Keyword(s):  
Sequence Data ◽  
Molecular Techniques ◽  
Specific Probe ◽  
Original Design ◽  
16S Rrna Sequence ◽  
Microarray Probe ◽  
Content Type ◽  
Sequence Identity ◽  
High Level ◽  
Probe Set

ABSTRACTDehalococcoidesspp. are an industrially relevant group ofChloroflexibacteria capable of reductively dechlorinating contaminants in groundwater environments. ExistingDehalococcoidesgenomes revealed a high level of sequence identity within this group, including 98 to 100% 16S rRNA sequence identity between strains with diverse substrate specificities. Common molecular techniques for identification of microbial populations are often not applicable for distinguishingDehalococcoidesstrains. Here we describe an oligonucleotide microarray probe set designed based on clusteredDehalococcoidesgenes from five different sources (strain DET195, CBDB1, BAV1, and VS genomes and the KB-1 metagenome). This “pangenome” probe set provides coverage of coreDehalococcoidesgenes as well as strain-specific genes while optimizing the potential for hybridization to closely related, previously unknownDehalococcoidesstrains. The pangenome probe set was compared to probe sets designed independently for each of the fiveDehalococcoidesstrains. The pangenome probe set demonstrated better predictability and higher detection ofDehalococcoidesgenes than strain-specific probe sets on nontarget strains with <99% average nucleotide identity. Anin silicoanalysis of the expected probe hybridization against the recently releasedDehalococcoidesstrain GT genome and additional KB-1 metagenome sequence data indicated that the pangenome probe set performs more robustly than the combined strain-specific probe sets in the detection of genes not included in the original design. The pangenome probe set represents a highly specific, universal tool for the detection and characterization ofDehalococcoidesfrom contaminated sites. It has the potential to become a common platform forDehalococcoides-focused research, allowing meaningful comparisons between microarray experiments regardless of the strain examined.

scholarly journals Class A Carbapenemase FPH-1 from Francisella philomiragia

2012 ◽  
Vol 56 (6) ◽  
pp. 2852-2857 ◽  
Author(s):  
Marta Toth ◽  
Viktoria Vakulenko ◽  
Nuno T. Antunes ◽  
Hilary Frase ◽  
Sergei B. Vakulenko
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Sequence Identity ◽  
Content Type ◽  
E Coli ◽  
New Class ◽  
Sequence Identity ◽  
Class A ◽  
High Level ◽  
Level Resistance

ABSTRACTFPH-1 is a new class A carbapenemase fromFrancisella philomiragia. It produces high-level resistance to penicillins and the narrow-spectrum cephalosporin cephalothin and hydrolyzes these β-lactam antibiotics with catalytic efficiencies of 106to 107M−1s−1. When expressed inEscherichia coli, the enzyme confers resistance to clavulanic acid, tazobactam, and sulbactam and hasKivalues of 7.5, 4, and 220 μM, respectively, against these inhibitors. FPH-1 increases the MIC of the monobactam aztreonam 256-fold and the MIC of the broad-spectrum cephalosporin ceftazidime 128-fold, while the MIC of cefoxitin remains unchanged. MICs of the carbapenem antibiotics imipenem, meropenem, doripenem, and ertapenem are elevated 8-, 8-, 16-, and 64-fold, respectively, against anE. coliJM83 strain producing the FPH-1 carbapenemase. The catalytic efficiencies of the enzyme against carbapenems are in the range of 104to 105M−1s−1. FPH-1 is 77% identical to the FTU-1 β-lactamase fromFrancisella tularensisand has low amino acid sequence identity with other class A β-lactamases. Together with FTU-1, FPH-1 constitutes a new branch of the prolific and ever-expanding class A β-lactamase tree.

scholarly journals Evolution and Virulence Contributions of the Autotransporter Proteins YapJ and YapK of Yersinia pestis CO92 and Their Homologs in Y. pseudotuberculosis IP32953

2012 ◽  
Vol 80 (10) ◽  
pp. 3693-3705 ◽  
Author(s):  
Jonathan D. Lenz ◽  
Brenda R. S. Temple ◽  
Virginia L. Miller
Keyword(s):  
Yersinia Pestis ◽  
Yersinia Pseudotuberculosis ◽  
Systemic Infection ◽  
Content Type ◽  
Sequence Identity ◽  
Homologous Genes ◽  
C Terminus ◽  
Gastrointestinal Pathogen ◽  
Numerous Type ◽  
High Level

ABSTRACTYersinia pestis, the causative agent of plague, evolved from the gastrointestinal pathogenYersinia pseudotuberculosis. Both species have numerous type Va autotransporters, most of which appear to be highly conserved. InY. pestisCO92, the autotransporter genesyapKandyapJshare a high level of sequence identity. By comparingyapKandyapJto three homologous genes inY. pseudotuberculosisIP32953 (YPTB0365, YPTB3285, and YPTB3286), we show thatyapKis conserved inY. pseudotuberculosis, whileyapJis unique toY. pestis. All of these autotransporters exhibit >96% identity in the C terminus of the protein and identities ranging from 58 to 72% in their N termini. By extending this analysis to include homologous sequences from numerousY. pestisandY. pseudotuberculosisstrains, we determined that these autotransporters cluster into a YapK (YPTB3285) class and a YapJ (YPTB3286) class. The YPTB3286-like gene of mostY. pestisstrains appears to be inactivated, perhaps in favor of maintainingyapJ. Since autotransporters are important for virulence in many bacterial pathogens, includingY. pestis, any change in autotransporter content should be considered for its impact on virulence. Using established mouse models ofY. pestisinfection, we demonstrated that despite the high level of sequence identity,yapKis distinct fromyapJin its contribution to disseminatedY. pestisinfection. In addition, a mutant lacking both of these genes exhibits an additive attenuation, suggesting nonredundant roles foryapJandyapKin systemicY. pestisinfection. However, the deletion of the homologous genes inY. pseudotuberculosisdoes not seem to impact the virulence of this organism in orogastric or systemic infection models.

scholarly journals Mutations in fbiD (Rv2983) as a Novel Determinant of Resistance to Pretomanid and Delamanid in Mycobacterium tuberculosis

2020 ◽  
Vol 65 (1) ◽  
pp. e01948-20
Author(s):  
Dalin Rifat ◽  
Si-Yang Li ◽  
Thomas Ioerger ◽  
Keshav Shah ◽  
Jean-Philippe Lanoix ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Clinical Evidence ◽  
Clinical Samples ◽  
Loss Of Function ◽  
Wild Type ◽  
Content Type ◽  
Solid Media ◽  
High Level ◽  
Level Resistance

ABSTRACTThe nitroimidazole prodrugs delamanid and pretomanid comprise one of only two new antimicrobial classes approved to treat tuberculosis (TB) in 50 years. Prior in vitro studies suggest a relatively low barrier to nitroimidazole resistance in Mycobacterium tuberculosis, but clinical evidence is limited to date. We selected pretomanid-resistant M. tuberculosis mutants in two mouse models of TB using a range of pretomanid doses. The frequency of spontaneous resistance was approximately 10−5 CFU. Whole-genome sequencing of 161 resistant isolates from 47 mice revealed 99 unique mutations, of which 91% occurred in 1 of 5 genes previously associated with nitroimidazole activation and resistance, namely, fbiC (56%), fbiA (15%), ddn (12%), fgd (4%), and fbiB (4%). Nearly all mutations were unique to a single mouse and not previously identified. The remaining 9% of resistant mutants harbored mutations in Rv2983 (fbiD), a gene not previously associated with nitroimidazole resistance but recently shown to be a guanylyltransferase necessary for cofactor F420 synthesis. Most mutants exhibited high-level resistance to pretomanid and delamanid, although Rv2983 and fbiB mutants exhibited high-level pretomanid resistance but relatively small changes in delamanid susceptibility. Complementing an Rv2983 mutant with wild-type Rv2983 restored susceptibility to pretomanid and delamanid. By quantifying intracellular F420 and its precursor Fo in overexpressing and loss-of-function mutants, we provide further evidence that Rv2983 is necessary for F420 biosynthesis. Finally, Rv2983 mutants and other F420H2-deficient mutants displayed hypersusceptibility to some antibiotics and to concentrations of malachite green found in solid media used to isolate and propagate mycobacteria from clinical samples.

scholarly journals Complete Sequences of Two Plasmids Found in a Brazilian Bacillus thuringiensis Serovar israelensis Strain

2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Fabrício S. Campos ◽  
Fernando B. Cerqueira ◽  
Gil R. Santos ◽  
Eliseu J. G. Pereira ◽  
Roberto F. T. Corrêia ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Crucial Role ◽  
Bacterial Genomes ◽  
Content Type ◽  
Complete Sequences

Plasmids play a crucial role in the evolution of bacterial genomes by mediating horizontal gene transfer. In this work, we sequenced two plasmids found in a Brazilian Bacillus thuringiensis serovar israelensis strain which showed 100% nucleotide identities with Bacillus thuringiensis serovar kurstaki plasmids.

scholarly journals Understanding employee turnover in humanitarian organizations

2016 ◽  
Vol 48 (4) ◽  
pp. 208-214 ◽  
Author(s):  
Rameshwar Dubey ◽  
Angappa Gunasekaran ◽  
Nezih Altay ◽  
Stephen J Childe ◽  
Thanos Papadopoulos
Keyword(s):  
Employee Turnover ◽  
Factor Loading ◽  
Personal Factors ◽  
Related Factors ◽  
Content Type ◽  
Factors Affecting ◽  
Work Related ◽  
Humanitarian Organizations ◽  
Using Data ◽  
High Level

Purpose – At a time when the number and seriousness of disasters seems to be increasing, humanitarian organizations find that besides their challenging work they are faced with problems caused by a high level of turnover of staff. The paper aims to discuss these issues. Design/methodology/approach – Based on the 24 variables leading to employee turnover identified by Cotton and Tuttle (1986) the authors analyse the work-related, external and personal factors affecting employee turnover in humanitarian organizations, using a survey of members of the Indian National Institute of Disaster Management. Findings – Results indicated that the three factors are present. Of the external factors, only employment perception had a factor loading over 0.7; of the work-related factors, all were significant; of the personal factors, biographical information, marital status, number of dependants, aptitude and ability and intelligence had the highest loadings. It was also shown that behavioural intentions and net expectation were not significant. Originality/value – Only a few studies reported on employee turnover and its reasons are not well understood in the context of humanitarian organizations. To address this need, the aim of this paper is to explore the personal reasons impacting employee turnover in humanitarian organizations. In the study the authors have adopted 24 variables used in Cotton and Tuttle (1986) and classified into constructs to explain turnover, and further tested the model using data gathered from humanitarian organizations.

scholarly journals Whole-Genome Phylogenomic Heterogeneity of Neisseria gonorrhoeae Isolates with Decreased Cephalosporin Susceptibility Collected in Canada between 1989 and 2013

2014 ◽  
Vol 53 (1) ◽  
pp. 191-200 ◽  
Author(s):  
Walter Demczuk ◽  
Tarah Lynch ◽  
Irene Martin ◽  
Gary Van Domselaar ◽  
Morag Graham ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Large Scale ◽  
Epidemiological Studies ◽  
23S Rrna ◽  
Genome Comparison ◽  
Whole Genome ◽  
Content Type ◽  
Genomic Epidemiology ◽  
High Level ◽  
Sequence Types

A large-scale, whole-genome comparison of CanadianNeisseria gonorrhoeaeisolates with high-level cephalosporin MICs was used to demonstrate a genomic epidemiology approach to investigate strain relatedness and dynamics. Although current typing methods have been very successful in tracing short-chain transmission of gonorrheal disease, investigating the temporal evolutionary relationships and geographical dissemination of highly clonal lineages requires enhanced resolution only available through whole-genome sequencing (WGS). Phylogenomic cluster analysis grouped 169 Canadian strains into 12 distinct clades. While someN. gonorrhoeaemultiantigen sequence types (NG-MAST) agreed with specific phylogenomic clades or subclades, other sequence types (ST) and closely related groups of ST were widely distributed among clades. Decreased susceptibility to extended-spectrum cephalosporins (ESC-DS) emerged among a group of diverse strains in Canada during the 1990s with a variety of nonmosaicpenAalleles, followed in 2000/2001 with thepenAmosaic X allele and then in 2007 with ST1407 strains with thepenAmosaic XXXIV allele. Five genetically distinct ESC-DS lineages were associated withpenAmosaic X, XXXV, and XXXIV alleles and nonmosaic XII and XIII alleles. ESC-DS with coresistance to azithromycin was observed in 5 strains with 23S rRNA C2599T or A2143G mutations. As the costs associated with WGS decline and analysis tools are streamlined, WGS can provide a more thorough understanding of strain dynamics, facilitate epidemiological studies to better resolve social networks, and improve surveillance to optimize treatment for gonorrheal infections.

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