The VapBC1 toxin–antitoxin complex from<i>Mycobacterium tuberculosis</i>: purification, crystallization and X-ray diffraction analysis

Lu, Zuokun; Wang, Han; Zhang, Aili; Tan, Yusheng

doi:10.1107/s2053230x16007603

Cited by 4 publications

(2 citation statements)

References 27 publications

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“…Remarkably, the virulence‐associated protein (Vap) toxin‐antitoxin (TA) locus was also found in the unique gene category of the Ca. M. psychrophilus MAG, in which vapB encodes the proteolytically labile antitoxin (Lu et al ., 2016) and vapC encodes a stable ribonucleolytic toxin VapC. In addition, Ca.…”

Section: Resultsmentioning

confidence: 99%

Anaerobic methane oxidation linked to Fe(III) reduction in a Candidatus Methanoperedens‐enriched consortium from the cold Zoige wetland at Tibetan Plateau

Chen

Zhang

et al. 2021

Environmental Microbiology

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Summary Anaerobic oxidation of methane (AOM) is a microbial process degrading ample methane in anoxic environments, and Ca. Methanoperedens mediated nitrate‐ or metal‐reduction linked AOM is believed important in freshwater systems. This work, via 16S rRNA gene diversity survey and 16S rRNA quantification, found abundant Ca. Methanoperedens along with iron in the cold Zoige wetland at Tibetan Plateau. The wetland soil microcosm performed Fe(III) reduction, rather than nitrate‐ nor sulphate‐reduction, coupled methane oxidation (3.87 μmol d−1) with 32.33 μmol Fe(II) accumulation per day at 18°C, but not at 30°C. A metagenome‐assembled genome (MAG) recovered from the microcosm exhibits ~74% average nucleotide identity with the reported Ca. Methanoperedens spp. that perform Fe(III) reduction linked AOM, thus a novel species Ca. Methanoperedens psychrophilus was proposed. Ca. M. psychrophilus contains the whole suite of CO2 reductive methanogenic genes presumably involving in AOM via a reverse direction, and comparative genome analysis revealed its unique gene categories: the multi‐heme clusters (MHCs) cytochromes, the S‐layer proteins highly homologous to those recovered from lower temperature environments and type IV pili, those could confer Ca. M. psychrophilus of cold adaptability. Therefore, this work reports the first methanotroph implementing AOM in an alpine wetland.

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Section: Resultsmentioning

confidence: 99%

Anaerobic methane oxidation linked to Fe(III) reduction in a Candidatus Methanoperedens‐enriched consortium from the cold Zoige wetland at Tibetan Plateau

Chen

Zhang

et al. 2021

Environmental Microbiology

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“…vapB1 upstream insertion is selected as Moxifloxacin resistance marker. VapB1 is shown to be degraded in unfavorable conditions which causes toxin VapC1 release and subsequent inhibition of cell growth [75]. VapC21, a toxin from the same family, was associated with XDR in other studies [37].…”

Section: Discussionmentioning

confidence: 99%

Feature selection and aggregation for antibiotic resistance GWAS inMycobacterium tuberculosis: a comparative study

Reshetnikov

Bykova

Kuleshov

et al. 2022

Preprint

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Drug resistance (DR) remains a global healthcare concern. In contrast to other human bacterial pathogens, acquiring mutations in the genome is the main mechanism of drug resistance for Mycobacterium tuberculosis (MTB). For some antibiotics resistance of a particular isolate can be predicted with high confidence knowing whether specific mutations occurred, but for some antibiotics our knowledge of resistance mechanism is moderate. Statistical machine learning (ML) methods are used in attempts to infer new genes implicated in drug resistance. These methods use large collections of isolates with known whole-genome sequences and resistance status for different drugs. However, high correlations between the presence or absence of resistance to drugs that are used together in one treatment regimen complicate inference of causal mutations by traditional ML. Recently, several new methods were suggested to deal with the problem of correlations of response variables in training data. In this study, we applied the following methods to tackle the confounding effect of resistance co-occurrence in a dataset of approximately 13 000 complete genomes of MTB with characterized resistance status for 13 drugs: logistic regression with different regularization penalty functions, a polynomial-time algorithm for best-subset selection problem (ABESS), and "Hungry, Hungry SNPos" (HHS) method. We compared these methods by the ability to select known causal mutations for the resistance to each particular drug and not to select mutations in genes that are known to be associated with resistance to other drugs. ABESS significantly outperformed the others selecting more relevant sets of mutations. We also showed that aggregation of rare mutations into features indicating changes of PFAM domains increased the quality of prediction and these features were majorly selected by ABESS.

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Identification of four type II toxin-antitoxin systems in Actinobacillus pleuropneumoniae

Zheng

Zhao

Zhang

et al. 2017

FEMS Microbiology Letters

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Toxin-antitoxin (TA) systems are small genetic elements that are widely prevalent in the genomes of bacteria and archaea. These modules have been identified in various bacteria and proposed to play an important role in bacterial physiology and virulence. However, their presence in the genomes of Actinobacillus species has received no attention. In this study, we describe the identification of four type II TA systems in Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia. Reverse transcription PCR analysis revealed that the genes encoding the toxin and antitoxin are co-transcribed. Overexpression of each toxin inhibited the growth of Escherichia coli, and the toxic effect could be counteracted by its cognate antitoxin. The pull-down experiments demonstrated that each toxin interacts with its cognate antitoxin in vivo. The promoter activity assays showed that each antitoxin could autoregulate either positively or negatively the TA operon transcription. In addition, the APJL_0660/0659 TA system is present in half of the detected serovars of A. pleuropneumoniae, while the others are present in all. Collectively, we identified four type II TA systems in A. pleuropneumoniae, and this study has laid the foundation for further functional study of these TA systems.

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The VapBC1 toxin–antitoxin complex fromMycobacterium tuberculosis: purification, crystallization and X-ray diffraction analysis

Cited by 4 publications

References 27 publications

Anaerobic methane oxidation linked to Fe(III) reduction in a Candidatus Methanoperedens‐enriched consortium from the cold Zoige wetland at Tibetan Plateau

Anaerobic methane oxidation linked to Fe(III) reduction in a Candidatus Methanoperedens‐enriched consortium from the cold Zoige wetland at Tibetan Plateau

Feature selection and aggregation for antibiotic resistance GWAS inMycobacterium tuberculosis: a comparative study

Identification of four type II toxin-antitoxin systems in Actinobacillus pleuropneumoniae

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