title: The CDI toxin of Yersinia kristensenii is a novel bacterial member of the RNase A superfamily.
abstract: Contact-dependent growth inhibition (CDI) is an important mechanism of inter-bacterial competition found in many Gram-negative pathogens. CDI+ cells express cell-surface CdiA proteins that bind neighboring bacteria and deliver C-terminal toxin domains (CdiA-CT) to inhibit target-cell growth. CDI+ bacteria also produce CdiI immunity proteins, which specifically neutralize cognate CdiA-CT toxins to prevent self-inhibition. Here, we present the crystal structure of the CdiA-CT/CdiIYkris complex from Yersinia kristensenii ATCC 33638. CdiA-CTYkris adopts the same fold as angiogenin and other RNase A paralogs, but the toxin does not share sequence similarity with these nucleases and lacks the characteristic disulfide bonds of the superfamily. Consistent with the structural homology, CdiA-CTYkris has potent RNase activity in vitro and in vivo. Structure-guided mutagenesis reveals that His175, Arg186, Thr276 and Tyr278 contribute to CdiA-CTYkris activity, suggesting that these residues participate in substrate binding and/or catalysis. CdiIYkris binds directly over the putative active site and likely neutralizes toxicity by blocking access to RNA substrates. Significantly, CdiA-CTYkris is the first non-vertebrate protein found to possess the RNase A superfamily fold, and homologs of this toxin are associated with secretion systems in many Gram-negative and Gram-positive bacteria. These observations suggest that RNase A-like toxins are commonly deployed in inter-bacterial competition.
authors.affiliation: Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, CA 92697, USA.
authors.forename: Gaëlle
authors.initials: G
authors.lastname: Batot
authors.affiliation: Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA.|Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.
authors.forename: Karolina
authors.initials: K
authors.lastname: Michalska
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA.
authors.forename: Greg
authors.initials: G
authors.lastname: Ekberg
authors.affiliation: Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, CA 92697, USA.
authors.forename: Ervin M
authors.initials: EM
authors.lastname: Irimpan
authors.affiliation: Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA.
authors.forename: Grazyna
authors.initials: G
authors.lastname: Joachimiak
authors.affiliation: Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Jedrzejczak
authors.affiliation: Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA.
authors.forename: Gyorgy
authors.initials: G
authors.lastname: Babnigg
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA.|Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA.
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Hayes
authors.affiliation: Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA.|Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.|Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Joachimiak
authors.affiliation: Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, CA 92697, USA.|Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA 92697, USA.
authors.forename: Celia W
authors.initials: CW
authors.lastname: Goulding
mesh_terms: D001427:Bacterial Toxins / Q000737:chemistry* / Q000378:metabolism; D018360:Crystallography, X-Ray; D004722:Endoribonucleases / Q000737:chemistry*; D008958:Models, Molecular; D011487:Protein Conformation; D012313:RNA / Q000378:metabolism; D012259:Ribonuclease, Pancreatic / Q000737:chemistry* / Q000378:metabolism; D015007:Yersinia / Q000201:enzymology*
chemical_list: D001427:Bacterial Toxins; C000622114:CDI toxin, Yersinia kristensenii; D012313:RNA; D004722:Endoribonucleases; D012259:Ribonuclease, Pancreatic