Crystal Structures of Phd-Doc, HigA, and YeeU Establish Multiple Evolutionary Links between Microbial Growth-Regulating Toxin-Antitoxin Systems

Arbing, M.A.; Handelman, Samuel K.; Kuzin, A.P.; Verdon, Grégory; Wang, Chi; Su, Min; Rothenbacher, Francesca P.; Abashidze, M.; Liu, Mohan; Hurley, Jennifer M.; Xiao, Rong; Acton, Thomas; Inouye, Masayori; Montelione, Gaetano T.; Woychik, Nancy A.; Hunt, J.F.

doi:10.1016/j.str.2010.04.018

Cited by 63 publications

(63 citation statements)

References 69 publications

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“…S1 in the supplemental material). The crystal structure shows that Phd P1 forms a heterotetrameric 2:2 complex with Doc P1 (59). It has been shown for Phd P1 that the C-terminal domain (residues 52 to 73) harbors the site of interaction with Doc P1 and that this domain is sufficient to prevent Doc-mediated growth arrest (60).…”

Section: Discussionmentioning

confidence: 99%

Characterization of the phd-doc and ccd Toxin-Antitoxin Cassettes from Vibrio Superintegrons

et al. 2013

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c Toxin-antitoxin (TA) systems have been reported in the genomes of most bacterial species, and their role when located on the chromosome is still debated. TA systems are particularly abundant in the massive cassette arrays associated with chromosomal superintegrons (SI). Here, we describe the characterization of two superintegron cassettes encoding putative TA systems. The first is the phd-doc SI system identified in Vibrio cholerae N16961. We determined its distribution in 36 V. cholerae strains and among five V. metschnikovii strains. We show that this cassette, which is in position 72 of the V. cholerae N16961 cassette array, is functional, carries its own promoter, and is expressed from this location. Interestingly, the phd-doc SI system is unable to control its own expression, most likely due to the absence of any DNA-binding domain on the antitoxin. In addition, this SI system is able to cross talk with the canonical P1 phage system. The second cassette that we characterized is the ccd Vfi cassette found in the V. fischeri superintegron. We demonstrate that CcdB Vfi targets DNA-gyrase, as the canonical CcB F toxin, and that ccd Vfi regulates its expression in a fashion similar to the ccd F operon of the conjugative plasmid F. We also establish that this cassette is functional and expressed in its chromosomal context in V. fischeri CIP 103206T. We tested its functional interactions with the ccdAB F system and found that CcdA Vfi is specific for its associated CcdB Vfi and cannot prevent CcdB F toxicity. Based on these results, we discuss the possible biological functions of these TA systems in superintegrons.

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Section: Discussionmentioning

confidence: 99%

Characterization of the phd-doc and ccd Toxin-Antitoxin Cassettes from Vibrio Superintegrons

et al. 2013

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“…To date, three antitoxin⅐DNA structures have been reported: the chromosome-encoded hipBA module from E. coli (27), the plasmid-encoded ccdAB module from E. coli (55), and the chromosome-encoded fitAB module from Neisseria gonorrhoeae (56). HipB, like MqsA, is one of the few antitoxins identified to date that recognizes DNA via an XRE-HTH DNA-binding motif (19,27,57,58). Despite sharing a common DNA recognition fold, the sequence identity between the MqsA and HipB DNA-binding domains is only 16%.…”

Section: Discussionmentioning

confidence: 99%

Structure of the Escherichia coli Antitoxin MqsA (YgiT/b3021) Bound to Its Gene Promoter Reveals Extensive Domain Rearrangements and the Specificity of Transcriptional Regulation

Brown¹,

Wood

Peti³

et al. 2011

Journal of Biological Chemistry

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Bacterial cultures, especially biofilms, produce a small number of persister cells, a genetically identical subpopulation of wild type cells that are metabolically dormant, exhibit multidrug tolerance, and are highly enriched in bacterial toxins. The gene most highly up-regulated in Escherichia coli persisters is mqsR, a ribonuclease toxin that, along with mqsA, forms a novel toxin⅐antitoxin (TA) system. Like all known TA systems, both the MqsR⅐MqsA complex and MqsA alone regulate their own transcription. Despite the importance of TA systems in persistence and biofilms, very little is known about how TA modules, and antitoxins in particular, bind and recognize DNA at a molecular level. Here, we report the crystal structure of MqsA bound to a 26-bp fragment from the mqsRA promoter. We show that MqsA binds DNA predominantly via its C-terminal helix-turn-helix domain, with direct binding of recognition helix residues Asn 97 and Arg 101 to the DNA major groove. Unexpectedly, the structure also revealed that the MqsA N-terminal domain interacts with the DNA phosphate backbone. This results in a more than 105°rotation of the Nterminal domains between the free and complexed states, an unprecedented rearrangement for an antitoxin. The structure also shows that MqsA bends the DNA by more than 55°in order to achieve symmetrical binding. Finally, using a combination of biochemical and NMR studies, we show that the DNA sequence specificity of MqsA is mediated by direct readout.

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“…Doc Is a Kinase-Fic domains (alternately referred to as "Fido" for Fic and Doc (18)) are ϳ100 -140 amino acids in length and share a conserved ␣-helical core (15,18,20,28,29). For most Fic domain proteins, this core is composed of eight ␣-helices; six are arranged in an up and down bundle with two lying perpendicular to the bundle (18).…”

Section: Resultsmentioning

confidence: 99%

“…Existing clues to Doc function were derived from high resolution structures (8,15,16) and functional studies (17). However, the activity and intracellular target(s) of Doc are still unknown.…”

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confidence: 99%

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Doc Toxin Is a Kinase That Inactivates Elongation Factor Tu

Cruz

Rothenbacher

Maehigashi

et al. 2014

Journal of Biological Chemistry

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Background: Doc toxin, of the phd-doc toxin-antitoxin system, belongs to the Fic protein family found in all domains of life. Results: Doc inactivates elongation factor Tu by phosphorylation of a single amino acid. Conclusion: This phosphorylation event inhibits protein synthesis and thereby arrests cell growth. Significance: The phosphorylation activity of Doc toxin represents a new catalytic activity for members of the Fic protein family.

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Crystal Structures of Phd-Doc, HigA, and YeeU Establish Multiple Evolutionary Links between Microbial Growth-Regulating Toxin-Antitoxin Systems

Cited by 63 publications

References 69 publications

Characterization of the phd-doc and ccd Toxin-Antitoxin Cassettes from Vibrio Superintegrons

Characterization of the phd-doc and ccd Toxin-Antitoxin Cassettes from Vibrio Superintegrons

Structure of the Escherichia coli Antitoxin MqsA (YgiT/b3021) Bound to Its Gene Promoter Reveals Extensive Domain Rearrangements and the Specificity of Transcriptional Regulation

Doc Toxin Is a Kinase That Inactivates Elongation Factor Tu

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