Identification of a metagenomic gene cluster containing a new class A beta-lactamase and toxin-antitoxin systems
Article first published online: 22 JUL 2013
© 2013 The Authors. Microbiology Open published by John Wiley & Sons Ltd.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Volume 2, Issue 4, pages 674–683, August 2013
How to Cite
MicrobiologyOpen 2013; 2(4): 674–683
- Issue published online: 12 AUG 2013
- Article first published online: 22 JUL 2013
- Manuscript Accepted: 6 JUN 2013
- Manuscript Revised: 15 MAY 2013
- Manuscript Received: 30 JAN 2013
- 2009. Functional metagenomics reveals diverse beta-lactamases in a remote Alaskan soil. ISME J. 3:243–251. , , , , and .
- 2010. Call of the wild: antibiotic resistance genes in natural environments. Nat. Rev. Microbiol. 8:251–259. , , , , , and .
- 2011. Multilevel populations and the evolution of antibiotic resistance through horizontal gene transfer. FEMS Microbiol. Rev. 35:756–767. , , and .
- 2006. Co-selection of antibiotic and metal resistance. Trends Microbiol. 14:176–182. , , , and .
- 2008. Antibiotics and antibiotic resistance in water environments. Curr. Opin. Biotechnol. 19:260–265. , , and .
- 1991. A family of low and high copy replicative, integrative and single-stranded S. cerevisiae/E. coli shuttle vectors. Yeast 7:609–615. , , , , , and .
- 2008. Conserved water molecules stabilize the Omega-loop in class A beta-lactamases. Antimicrob. Agents Chemother. 52:1072–1079. , and .
- 1984. Regulation of ribosomal RNA promoters with a synthetic lac operator. Proc. Natl Acad. Sci. USA 81:6929–6933. , and .
- 1984. Association of metal tolerance with multiple antibiotic resistance of bacteria isolated from drinking water. Appl. Environ. Microbiol. 47:1238–1242. , , and .
- 1980. Analysis of gene control signals by DNA fusion and cloning in Escherichia coli. J. Mol. Biol. 138:179–207. , and .
- 2001. Revisiting the stringent response, ppGpp and starvation signaling. Curr. Opin. Microbiol. 4:160–165. , and .
- 2004. Delayed-relaxed response explained by hyperactivation of RelE. Mol. Microbiol. 53:587–597. , and .
- 2001. RelE, a global inhibitor of translation, is activated during nutritional stress. Proc. Natl. Acad. Sci. USA 98:14328–14333. , , , and .
- 2000. Horizontal gene transfer and the origin of species: lessons from bacteria. Trends Microbiol. 8:128–133. , and .
- 2012. The great screen anomaly: a new frontier in product discovery through functional metagenomics. Appl. Microbiol. Biotechnol. 93:1005–1020. , , , and .
- 2012. Adenylylation control by intra- or intermolecular active-site obstruction in Fic proteins. Nature 482:107–110. , , , , , , et al.
- 2011. Antimicrobial resistance of heterotrophic bacteria in sewage-contaminated rivers. Water Res. 45:788–796. , , , , , and .
- 2008. Doc of prophage P1 is inhibited by its antitoxin partner Phd through fold complementation. J. Biol. Chem. 283:30821–30827. , , , , , , et al.
- 2007. Quick and easy yeast transformation using the LiAc/SS carrier DNA/PEG method. Nat. Protoc. 2:35–37. , and .
- 2010. The global problem of antibiotic resistance. Crit. Rev. Immunol. 30:79–93.
- 2010. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 27:221–224. , , and .
- 2011. Metal toxicity. Metallomics 3:1095–1097. , , and .
- 1995. Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J. Bacteriol. 177:4121–4130. , , , and .
- 2004. Evolution of the serine beta-lactamases: past, present and future. Drug Resist. Updat. 7:111–123. , and .
- 2011. Toxins-antitoxins: diversity, evolution and function. Crit. Rev. Biochem. Mol. Biol. 46:386–408. , and .
- 2011. Switch or funnel: how RND-type transport systems control periplasmic metal homeostasis. J. Bacteriol. 193:2381–2387. , , , and .
- 2011. Antibiotic resistance gene abundances correlate with metal and geochemical conditions in archived Scottish soils. PLoS ONE 6:e27300. , , , , , and .
- 2010. Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis. Mol. Cell 37:311–320. , , and .
- 2010. Novel florfenicol and chloramphenicol resistance gene discovered in Alaskan soil by using functional metagenomics. Appl. Environ. Microbiol. 76:5321–5326. , , , , , and .
- 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948. , , , , , , et al.
- 2011. Diversity of bacterial type II toxin-antitoxin systems: a comprehensive search and functional analysis of novel families. Nucleic Acids Res. 39:5513–5525. , , , , , and .
- 2008. Structural mechanism of transcriptional autorepression of the Escherichia coli RelB/RelE antitoxin/toxin module. J. Mol. Biol. 380:107–119. , , , and .
- 2009. Inhibitory mechanism of Escherichia coli RelE-RelB toxin-antitoxin module involves a helix displacement near an mRNA interferase active site. J. Biol. Chem. 284:14628–14636. , , , and .
- 1999. Oxidative DNA damage mediated by copper(II), iron(II) and nickel(II) fenton reactions: evidence for site-specific mechanisms in the formation of double-strand breaks, 8-hydroxydeoxyguanosine and putative intrastrand cross-links. Mutat. Res. 424:23–36. , and .
- 1998. Corepression of the P1 addiction operon by Phd and Doc. J. Bacteriol. 180:6342–6351. , and .
- 2002. Molecular analysis of beta-lactamase structure and function. Int. J. Med. Microbiol. 292:127–137. , , and .
- 2011. Metabolic regulation of antibiotic resistance. FEMS Microbiol. Rev. 35:768–789. , and .
- 2009. A global view of antibiotic resistance. FEMS Microbiol. Rev. 33:44–65. , , , , , , et al.
- 2011. Functional metagenomics reveals previously unrecognized diversity of antibiotic resistance genes in gulls. Front. Microbiol. 2:238. , , , , and .
- 2007. A tale of two oxidation states: bacterial colonization of arsenic-rich environments. PLoS Genet. 3:e53. , , , , , , et al.
- 2009. RelB and RelE of Escherichia coli form a tight complex that represses transcription via the ribbon-helix-helix motif in RelB. J. Mol. Biol. 394:183–196. , , and .
- 2004. Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ. Microbiol. 6:981–989. , , and .
- 2010. Transcriptional switching in Escherichia coli during stress and starvation by modulation of sigma activity. FEMS Microbiol. Rev. 34:646–657. , and .
- 2010. The structural mechanism of the inhibition of archaeal RelE toxin by its cognate RelB antitoxin. Biochem. Biophys. Res. Commun. 400:346–351. , , , , , , et al.
- 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56:564–577. , and .
- 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731–2739. , , , , , and .
- 2011. Characterization of novel antibiotic resistance genes identified by functional metagenomics on soil samples. Environ. Microbiol. 13:1101–1114. , , , , , and .
- 2009. Functional metagenomics for enzyme discovery: challenges to efficient screening. Curr. Opin. Biotechnol. 20:616–622. , and .
- 1991. Residual guanosine 3′,5′-bispyrophosphate synthetic activity of relA null mutants can be eliminated by spoT null mutations. J. Biol. Chem. 266:5980–5990. , , , , , and .
- 2011. Plasmid metagenome reveals high levels of antibiotic resistance genes and mobile genetic elements in activated sludge. PLoS ONE 6:e26041. , , and .