Structure of the
            <i>Pseudomonas aeruginosa</i>
            transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis

Suzuki, Tateki; Nakamura, Akiyoshi; Kato, Kuniki; Söll, Dieter; Tanaka, Isao; Sheppard, Kelly; Yao, Min

doi:10.1073/pnas.1423314112

Cited by 34 publications

(51 citation statements)

References 44 publications

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“…(B) covariance‐assisted fragment‐assembly model of residues 72‐167. (C) The crystal structure of Primosomal Replication Protein N Klebsiella pneumonia (PDB code 4apv; ) D) the OB fold from subunit A of the structure of Pseudomonas aeruginosa Glutamyl‐tRNA(Gln) Amidotransferase (PDB code 4wj3; ). [Color figure can be viewed in the online issue, which is available at http://wileyonlinelibrary.com.…”

Section: Resultsmentioning

confidence: 99%

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Potential DNA binding and nuclease functions of ComEC domains characterized in silico

et al. 2016

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Bacterial competence, which can be natural or induced, allows the uptake of exogenous double stranded DNA (dsDNA) into a competent bacterium. This process is known as transformation. A multiprotein assembly binds and processes the dsDNA to import one strand and degrade another yet the underlying molecular mechanisms are relatively poorly understood. Here distant relationships of domains in Competence protein EC (ComEC) of Bacillus subtilis (Uniprot: P39695) were characterized. DNA‐protein interactions were investigated in silico by analyzing models for structural conservation, surface electrostatics and structure‐based DNA binding propensity; and by data‐driven macromolecular docking of DNA to models. Our findings suggest that the DUF4131 domain contains a cryptic DNA‐binding OB fold domain and that the β‐lactamase‐like domain is the hitherto cryptic competence nuclease. Proteins 2016; 84:1431–1442. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

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Section: Resultsmentioning

confidence: 99%

“…This is not seen in the top DALI match [Fig. (C)], but is seen in the structure of the ligase domain of the asparagine transamidosome from Pseudomonas aeruginosa [PDB code 4wj3; Fig. (D)] which matched the model with a DALI score of 6.6.…”

Section: Resultsmentioning

confidence: 99%

Potential DNA binding and nuclease functions of ComEC domains characterized in silico

et al. 2016

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“…Using Phyre2 23 we found that the closest 3D homologs of Tse8 are the Stenotrophomonas maltophilia Peptide amidase (Pam) 24 (sequence identity 29%), the Staphylococcus aureus Gln-tRNA(Gln) transamidosome subunit A (GatA) 25 (sequence identity 20%), the P. aeruginosa Asn-tRNA(Asn) transamidosome subunit A (GatA) 26 (sequence identity 25%), the Flavobacterium sp. 6-aminohexanoate cyclic dimer hydrolase (NylA) 27 (sequence identity 24%), the Bradyrhizobium japonicum malonamidase E2 (MAE2) 28 (sequence identity 25%), the Pseudomonas sp.…”

Section: Tradis Identifies Known and Novel H1-t6ss Toxin-immunity Pairsmentioning

confidence: 99%

“…The structure of the P. aeruginosa GatCAB transamidosome reveals it to be a symmetric complex comprising ND-AspRS, GatCAB, and tRNA Asn in a 2:2:2 stoichiometry 26 (as represented in Extended Data Fig. 8a).…”

Section: Tradis Identifies Known and Novel H1-t6ss Toxin-immunity Pairsmentioning

confidence: 99%

Discovery of aPseudomonas aeruginosaType VI secretion system toxin targeting bacterial protein synthesis using a global genomics approach

Nolan

Cain

Manoli

et al. 2019

Preprint

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19The Type VI secretion system (T6SS) is a bacterial weapon which delivers toxic 20 effectors to kill competitors or subvert some of their key functions. Here we use transposon 21 directed insertion-site sequencing (TraDIS) to identify T6SS toxins associated with the H1-22 T6SS, one of the three T6SS machines found in Pseudomonas aeruginosa. This approach 23 identified several putative toxin-immunity pairs, including Tse8-Tsi8. Full characterization of 24 this protein pair demonstrated that Tse8 is delivered by the VgrG1a spike complex into prey 25 cells where it targets the transamidosome, a multiprotein complex involved in protein synthesis 26 in bacteria lacking either one or both of the asparagine or glutamine tRNA synthases. Our data 27 suggests that Tse8 combines as a non-cognate component of the transamidosome complex, 28 reducing fitness by limiting the ability of the cell to synthesize proteins. This is the first 29 demonstration of a T6SS toxin affecting protein synthesis, expanding the range of cellular 30 components targeted by this bacterial weapon. The success of the current study validates the 31 use of our TraDIS approach as a tool to drastically expand the repertoire of T6SS toxins in any 32 T6SS-encoding bacterium. 33 34 3 Bacteria rarely exist in a single-species planktonic state and instead form complex 35 polymicrobial structures, called biofilms 1,2 . Within this context bacteria often compete with 36 other microorganisms to secure space and nutrients. The Type VI secretion system (T6SS) is a 37 Gram-negative bacterial weapon which delivers toxins into neighbouring competitors to either 38 kill or subvert their key functions in order to attain dominance within a given niche 3-5 . The 39 T6SS is composed of 13 core components, several of which are structurally related to proteins 40 from the T4 bacteriophage tail 6 . The Hcp tube-like structure is capped by a VgrG-PAAR tip 41 complex, or spike, and encapsulated within a TssBC, or VipAB, contractile sheath. Upon 42 extension of the sheath within the cytoplasm and subsequent contraction, the spike is thought 43 to facilitate the puncturing of the cell membranes of both the producing and target cells, 44 allowing delivery of the attached toxins 7,8 . T6SS toxins have been shown to be secreted in 45 association with the VgrG tip complex, the Hcp tube, or as extension domains of the VgrG, 46 PAAR or Hcp proteins 9-12 . Importantly, neighbouring bacterial sister cells are protected from 47 the effects of the toxins by production of cognate immunity proteins, which are usually encoded 48 adjacent to the toxin gene in the genome 13 . The major identified targets of T6SS toxins to date 49 are components of the cell wall, as well as the cell membrane and nucleic acids 14 . These T6SS 50 toxins have mainly been identified by searching in the genomic proximity of known T6SS 51 components, or by detection of toxins in the secretome 9,12,15 . 52 Pseudomonas aeruginosa is a highly antibiotic-resistant Gram-negative pathogen and 53 ranked second by the World...

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“…5). The transamidosome is a three protein complex (GatCAB) that is essential for the production of correctly charged tRNA in bacteria via the transfer of an ammonia from gutamine to acidic amino acid-charged tRNA (21). Deamination occurs in the active site of an amidase (GatA).…”

Section: Atze Is a 1-carboxybiuret Hydrolase -mentioning

confidence: 99%

An unexpected vestigial protein complex reveals the evolutionary origins of an s-triazine catabolic enzyme

Esquirol

Peat

Wilding

et al. 2018

Journal of Biological Chemistry

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Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis

Cited by 34 publications

References 44 publications

Potential DNA binding and nuclease functions of ComEC domains characterized in silico

Potential DNA binding and nuclease functions of ComEC domains characterized in silico

Discovery of aPseudomonas aeruginosaType VI secretion system toxin targeting bacterial protein synthesis using a global genomics approach

An unexpected vestigial protein complex reveals the evolutionary origins of an s-triazine catabolic enzyme

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