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Fallet M, Wilson R, Sarkies P. Cisplatin exposure alters tRNA-derived small RNAs but does not affect epimutations in C. elegans. BMC Biol 2023; 21:276. [PMID: 38031056 PMCID: PMC10688063 DOI: 10.1186/s12915-023-01767-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND The individual lifestyle and environment of an organism can influence its phenotype and potentially the phenotype of its offspring. The different genetic and non-genetic components of the inheritance system and their mutual interactions are key mechanisms to generate inherited phenotypic changes. Epigenetic changes can be transmitted between generations independently from changes in DNA sequence. In Caenorhabditis elegans, epigenetic differences, i.e. epimutations, mediated by small non-coding RNAs, particularly 22G-RNAs, as well as chromatin have been identified, and their average persistence is three to five generations. In addition, previous research showed that some epimutations had a longer duration and concerned genes that were enriched for multiple components of xenobiotic response pathways. These results raise the possibility that environmental stresses might change the rate at which epimutations occur, with potential significance for adaptation. RESULTS In this work, we explore this question by propagating C. elegans lines either in control conditions or in moderate or high doses of cisplatin, which introduces genotoxic stress by damaging DNA. Our results show that cisplatin has a limited effect on global small non-coding RNA epimutations and epimutations in gene expression levels. However, cisplatin exposure leads to increased fluctuations in the levels of small non-coding RNAs derived from tRNA cleavage. We show that changes in tRNA-derived small RNAs may be associated with gene expression changes. CONCLUSIONS Our work shows that epimutations are not substantially altered by cisplatin exposure but identifies transient changes in tRNA-derived small RNAs as a potential source of variation induced by genotoxic stress.
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Affiliation(s)
- Manon Fallet
- Department of Biochemistry, Evolutionary Epigenetics Group, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd., Oxford, OX1 3QU, UK.
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182, Örebro, Sweden.
| | - Rachel Wilson
- Department of Biochemistry, Evolutionary Epigenetics Group, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd., Oxford, OX1 3QU, UK
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Peter Sarkies
- Department of Biochemistry, Evolutionary Epigenetics Group, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd., Oxford, OX1 3QU, UK.
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2
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Benler S, Yutin N, Antipov D, Rayko M, Shmakov S, Gussow AB, Pevzner P, Koonin EV. Thousands of previously unknown phages discovered in whole-community human gut metagenomes. MICROBIOME 2021; 9:78. [PMID: 33781338 PMCID: PMC8008677 DOI: 10.1186/s40168-021-01017-w] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/02/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND Double-stranded DNA bacteriophages (dsDNA phages) play pivotal roles in structuring human gut microbiomes; yet, the gut virome is far from being fully characterized, and additional groups of phages, including highly abundant ones, continue to be discovered by metagenome mining. A multilevel framework for taxonomic classification of viruses was recently adopted, facilitating the classification of phages into evolutionary informative taxonomic units based on hallmark genes. Together with advanced approaches for sequence assembly and powerful methods of sequence analysis, this revised framework offers the opportunity to discover and classify unknown phage taxa in the human gut. RESULTS A search of human gut metagenomes for circular contigs encoding phage hallmark genes resulted in the identification of 3738 apparently complete phage genomes that represent 451 putative genera. Several of these phage genera are only distantly related to previously identified phages and are likely to found new families. Two of the candidate families, "Flandersviridae" and "Quimbyviridae", include some of the most common and abundant members of the human gut virome that infect Bacteroides, Parabacteroides, and Prevotella. The third proposed family, "Gratiaviridae," consists of less abundant phages that are distantly related to the families Autographiviridae, Drexlerviridae, and Chaseviridae. Analysis of CRISPR spacers indicates that phages of all three putative families infect bacteria of the phylum Bacteroidetes. Comparative genomic analysis of the three candidate phage families revealed features without precedent in phage genomes. Some "Quimbyviridae" phages possess Diversity-Generating Retroelements (DGRs) that generate hypervariable target genes nested within defense-related genes, whereas the previously known targets of phage-encoded DGRs are structural genes. Several "Flandersviridae" phages encode enzymes of the isoprenoid pathway, a lipid biosynthesis pathway that so far has not been known to be manipulated by phages. The "Gratiaviridae" phages encode a HipA-family protein kinase and glycosyltransferase, suggesting these phages modify the host cell wall, preventing superinfection by other phages. Hundreds of phages in these three and other families are shown to encode catalases and iron-sequestering enzymes that can be predicted to enhance cellular tolerance to reactive oxygen species. CONCLUSIONS Analysis of phage genomes identified in whole-community human gut metagenomes resulted in the delineation of at least three new candidate families of Caudovirales and revealed diverse putative mechanisms underlying phage-host interactions in the human gut. Addition of these phylogenetically classified, diverse, and distinct phages to public databases will facilitate taxonomic decomposition and functional characterization of human gut viromes. Video abstract.
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Affiliation(s)
- Sean Benler
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894 USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894 USA
| | - Dmitry Antipov
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, 199004 Russia
| | - Mikhail Rayko
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, 199004 Russia
| | - Sergey Shmakov
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894 USA
| | - Ayal B. Gussow
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894 USA
| | - Pavel Pevzner
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, 199004 Russia
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093 USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894 USA
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3
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Krishnan A, Burroughs AM, Iyer LM, Aravind L. Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems. Nucleic Acids Res 2020; 48:10045-10075. [PMID: 32894288 DOI: 10.1093/nar/gkaa726] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/17/2020] [Accepted: 08/20/2020] [Indexed: 12/13/2022] Open
Abstract
ABC ATPases form one of the largest clades of P-loop NTPase fold enzymes that catalyze ATP-hydrolysis and utilize its free energy for a staggering range of functions from transport to nucleoprotein dynamics. Using sensitive sequence and structure analysis with comparative genomics, for the first time we provide a comprehensive classification of the ABC ATPase superfamily. ABC ATPases developed structural hallmarks that unambiguously distinguish them from other P-loop NTPases such as an alternative to arginine-finger-based catalysis. At least five and up to eight distinct clades of ABC ATPases are reconstructed as being present in the last universal common ancestor. They underwent distinct phases of structural innovation with the emergence of inserts constituting conserved binding interfaces for proteins or nucleic acids and the adoption of a unique dimeric toroidal configuration for DNA-threading. Specifically, several clades have also extensively radiated in counter-invader conflict systems where they serve as nodal nucleotide-dependent sensory and energetic components regulating a diversity of effectors (including some previously unrecognized) acting independently or together with restriction-modification systems. We present a unified mechanism for ABC ATPase function across disparate systems like RNA editing, translation, metabolism, DNA repair, and biological conflicts, and some unexpected recruitments, such as MutS ATPases in secondary metabolism.
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Affiliation(s)
- Arunkumar Krishnan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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4
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Bacusmo JM, Orsini SS, Hu J, DeMott M, Thiaville PC, Elfarash A, Paulines MJ, Rojas-Benítez D, Meineke B, Deutsch C, Iwata-Reuyl D, Limbach PA, Dedon PC, Rice KC, Shuman S, Crécy-Lagard VD. The t 6A modification acts as a positive determinant for the anticodon nuclease PrrC, and is distinctively nonessential in Streptococcus mutans. RNA Biol 2017; 15:508-517. [PMID: 28726545 DOI: 10.1080/15476286.2017.1353861] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Endoribonuclease toxins (ribotoxins) are produced by bacteria and fungi to respond to stress, eliminate non-self competitor species, or interdict virus infection. PrrC is a bacterial ribotoxin that targets and cleaves tRNALysUUU in the anticodon loop. In vitro studies suggested that the post-transcriptional modification threonylcarbamoyl adenosine (t6A) is required for PrrC activity but this prediction had never been validated in vivo. Here, by using t6A-deficient yeast derivatives, it is shown that t6A is a positive determinant for PrrC proteins from various bacterial species. Streptococcus mutans is one of the few bacteria where the t6A synthesis gene tsaE (brpB) is dispensable and its genome encodes a PrrC toxin. We had previously shown using an HPLC-based assay that the S. mutans tsaE mutant was devoid of t6A. However, we describe here a novel and a more sensitive hybridization-based t6A detection method (compared to HPLC) that showed t6A was still present in the S. mutans ΔtsaE, albeit at greatly reduced levels (93% reduced compared with WT). Moreover, mutants in 2 other S. mutans t6A synthesis genes (tsaB and tsaC) were shown to be totally devoid of the modification thus confirming its dispensability in this organism. Furthermore, analysis of t6A modification ratios and of t6A synthesis genes mRNA levels in S. mutans suggest they may be regulated by growth phase.
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Affiliation(s)
- Jo Marie Bacusmo
- a Department of Microbiology and Cell Science, IFAS , University of Florida , Gainesville , FL , USA
| | - Silvia S Orsini
- a Department of Microbiology and Cell Science, IFAS , University of Florida , Gainesville , FL , USA
| | - Jennifer Hu
- b Center for Environmental Health Sciences, Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Michael DeMott
- b Center for Environmental Health Sciences, Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Patrick C Thiaville
- a Department of Microbiology and Cell Science, IFAS , University of Florida , Gainesville , FL , USA.,c Genetics and Genomics Graduate Program , University of Florida , Gainesville , USA.,d University of Florida Genetics Institute, University of Florida , Gainesville , FL , USA
| | - Ameer Elfarash
- a Department of Microbiology and Cell Science, IFAS , University of Florida , Gainesville , FL , USA.,e Genetic Department, Faculty of Agriculture , Assiut University , Assuit , Egypt
| | - Mellie June Paulines
- f Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry , University of Cincinnati , Cincinnati OH , USA
| | - Diego Rojas-Benítez
- g Centro de Regulación del Genoma. Facultad de Ciencias - Universidad de Chile , Santiago , Chile
| | - Birthe Meineke
- h Molecular Biology Program , Sloan-Kettering Institute , New York , NY , USA
| | - Chris Deutsch
- i Department of Chemistry , Portland State University , Portland , OR , USA
| | - Dirk Iwata-Reuyl
- i Department of Chemistry , Portland State University , Portland , OR , USA
| | - Patrick A Limbach
- f Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry , University of Cincinnati , Cincinnati OH , USA
| | - Peter C Dedon
- b Center for Environmental Health Sciences, Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Kelly C Rice
- a Department of Microbiology and Cell Science, IFAS , University of Florida , Gainesville , FL , USA
| | - Stewart Shuman
- h Molecular Biology Program , Sloan-Kettering Institute , New York , NY , USA
| | - Valérie de Crécy-Lagard
- a Department of Microbiology and Cell Science, IFAS , University of Florida , Gainesville , FL , USA.,d University of Florida Genetics Institute, University of Florida , Gainesville , FL , USA
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5
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Koonin EV, Zhang F. Coupling immunity and programmed cell suicide in prokaryotes: Life-or-death choices. Bioessays 2016; 39:1-9. [DOI: 10.1002/bies.201600186] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information; National Library of Medicine; Bethesda MD USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard; Cambridge MA USA
- Department of Health Sciences and Technology; Massachusetts Institute of Technology; Cambridge MA USA
- McGovern Institute for Brain Research at MIT; Cambridge MA USA
- Departments of Brain and Cognitive Science and Biological Engineering; Cambridge MA USA
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Burroughs AM, Aravind L. RNA damage in biological conflicts and the diversity of responding RNA repair systems. Nucleic Acids Res 2016; 44:8525-8555. [PMID: 27536007 PMCID: PMC5062991 DOI: 10.1093/nar/gkw722] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/08/2016] [Indexed: 12/16/2022] Open
Abstract
RNA is targeted in biological conflicts by enzymatic toxins or effectors. A vast diversity of systems which repair or ‘heal’ this damage has only recently become apparent. Here, we summarize the known effectors, their modes of action, and RNA targets before surveying the diverse systems which counter this damage from a comparative genomics viewpoint. RNA-repair systems show a modular organization with extensive shuffling and displacement of the constituent domains; however, a general ‘syntax’ is strongly maintained whereby systems typically contain: a RNA ligase (either ATP-grasp or RtcB superfamilies), nucleotidyltransferases, enzymes modifying RNA-termini for ligation (phosphatases and kinases) or protection (methylases), and scaffold or cofactor proteins. We highlight poorly-understood or previously-uncharacterized repair systems and components, e.g. potential scaffolding cofactors (Rot/TROVE and SPFH/Band-7 modules) with their respective cognate non-coding RNAs (YRNAs and a novel tRNA-like molecule) and a novel nucleotidyltransferase associating with diverse ligases. These systems have been extensively disseminated by lateral transfer between distant prokaryotic and microbial eukaryotic lineages consistent with intense inter-organismal conflict. Components have also often been ‘institutionalized’ for non-conflict roles, e.g. in RNA-splicing and in RNAi systems (e.g. in kinetoplastids) which combine a distinct family of RNA-acting prim-pol domains with DICER-like proteins.
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Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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7
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Niewoehner O, Jinek M. Structural basis for the endoribonuclease activity of the type III-A CRISPR-associated protein Csm6. RNA (NEW YORK, N.Y.) 2016; 22:318-29. [PMID: 26763118 PMCID: PMC4748810 DOI: 10.1261/rna.054098.115] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/30/2015] [Indexed: 05/14/2023]
Abstract
Prokaryotic CRISPR-Cas systems provide an RNA-guided mechanism for genome defense against mobile genetic elements such as viruses and plasmids. In type III-A CRISPR-Cas systems, the RNA-guided multisubunit Csm effector complex targets both single-stranded RNAs and double-stranded DNAs. In addition to the Csm complex, efficient anti-plasmid immunity mediated by type III-A systems also requires the CRISPR-associated protein Csm6. Here we report the crystal structure of Csm6 from Thermus thermophilus and show that the protein is a ssRNA-specific endoribonuclease. The structure reveals a dimeric architecture generated by interactions involving the N-terminal CARF and C-terminal HEPN domains. HEPN domain dimerization leads to the formation of a composite ribonuclease active site. Consistently, mutations of invariant active site residues impair catalytic activity in vitro. We further show that the ribonuclease activity of Csm6 is conserved across orthologs, suggesting that it plays an important functional role in CRISPR-Cas systems. The dimer interface of the CARF domains features a conserved electropositive pocket that may function as a ligand-binding site for allosteric control of ribonuclease activity. Altogether, our work suggests that Csm6 proteins provide an auxiliary RNA-targeting interference mechanism in type III-A CRISPR-Cas systems that operates in conjunction with the RNA- and DNA-targeting endonuclease activities of the Csm effector complex.
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Affiliation(s)
- Ole Niewoehner
- Department of Biochemistry, University of Zurich, Zurich CH-8057, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich CH-8057, Switzerland
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8
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Zhong J, Xiao C, Gu W, Du G, Sun X, He QY, Zhang G. Transfer RNAs Mediate the Rapid Adaptation of Escherichia coli to Oxidative Stress. PLoS Genet 2015; 11:e1005302. [PMID: 26090660 PMCID: PMC4474833 DOI: 10.1371/journal.pgen.1005302] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 05/27/2015] [Indexed: 11/18/2022] Open
Abstract
Translational systems can respond promptly to sudden environmental changes to provide rapid adaptations to environmental stress. Unlike the well-studied translational responses to oxidative stress in eukaryotic systems, little is known regarding how prokaryotes respond rapidly to oxidative stress in terms of translation. In this study, we measured protein synthesis from the entire Escherichia coli proteome and found that protein synthesis was severely slowed down under oxidative stress. With unchanged translation initiation, this slowdown was caused by decreased translation elongation speed. We further confirmed by tRNA sequencing and qRT-PCR that this deceleration was caused by a global, enzymatic downregulation of almost all tRNA species shortly after exposure to oxidative agents. Elevation in tRNA levels accelerated translation and protected E. coli against oxidative stress caused by hydrogen peroxide and the antibiotic ciprofloxacin. Our results showed that the global regulation of tRNAs mediates the rapid adjustment of the E. coli translation system for prompt adaptation to oxidative stress. All organisms need to respond quickly to sudden environmental changes. Translational regulation can occur in response to environmental stresses within minutes, which is much faster than transcriptional regulation, and thus normally provides immediate adaptation. Eukaryotic cells can manipulate their tRNA molecules, mainly in a reversible manner, to suppress translation. Here, we showed for the first time that bacteria respond to oxidative stress by adjusting the translational system in a manner that differs from that of eukaryotes. The bacteria nonspecifically, irreversibly, and enzymatically degrade tRNAs to block protein synthesis. Interestingly, we showed that elevated tRNA concentrations lead to opposing effects by causing increased protein aggregation, which impairs fitness under normal conditions but facilitates adaptation under oxidative stress, including that caused by antibiotics. Our results provide a new understanding of the role of global adjustments to the entire translation system during stress adaptation in bacteria. This mechanism may also be involved in the development of antibiotic resistance in bacteria.
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Affiliation(s)
- Jiayong Zhong
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Chuanle Xiao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Wei Gu
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Gaofei Du
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Xuesong Sun
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
- * E-mail: (QYH); (GZ)
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
- * E-mail: (QYH); (GZ)
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9
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Zhang D, Iyer LM, Burroughs AM, Aravind L. Resilience of biochemical activity in protein domains in the face of structural divergence. Curr Opin Struct Biol 2014; 26:92-103. [PMID: 24952217 DOI: 10.1016/j.sbi.2014.05.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/20/2014] [Indexed: 01/07/2023]
Abstract
Recent studies point to the prevalence of the evolutionary phenomenon of drastic structural transformation of protein domains while continuing to preserve their basic biochemical function. These transformations span a wide spectrum, including simple domains incorporated into larger structural scaffolds, changes in the structural core, major active site shifts, topological rewiring and extensive structural transmogrifications. Proteins from biological conflict systems, such as toxin-antitoxin, restriction-modification, CRISPR/Cas, polymorphic toxin and secondary metabolism systems commonly display such transformations. These include endoDNases, metal-independent RNases, deaminases, ADP ribosyltransferases, immunity proteins, kinases and E1-like enzymes. In eukaryotes such transformations are seen in domains involved in chromatin-related peptide recognition and protein/DNA-modification. Intense selective pressures from 'arms-race'-like situations in conflict and macromolecular modification systems could favor drastic structural divergence while preserving function.
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Affiliation(s)
- Dapeng Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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10
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Structure, mechanism, and specificity of a eukaryal tRNA restriction enzyme involved in self-nonself discrimination. Cell Rep 2014; 7:339-347. [PMID: 24726365 DOI: 10.1016/j.celrep.2014.03.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 02/26/2014] [Accepted: 03/11/2014] [Indexed: 11/22/2022] Open
Abstract
tRNA restriction by anticodon nucleases underlies cellular stress responses and self-nonself discrimination in a wide range of taxa. Anticodon breakage inhibits protein synthesis, which, in turn, results in growth arrest or cell death. The eukaryal ribotoxin PaT secreted by Pichia acaciae inhibits growth of Saccharomyces cerevisiae via cleavage of tRNA(Gln(UUG)). We find that recombinant PaT incises a synthetic tRNA(Gln(UUG)) stem-loop RNA by transesterification at a single site 3' of the wobble uridine, yielding 2',3'-cyclic phosphate and 5'-OH ends. Incision is suppressed by replacement of the wobble nucleobase with adenine or guanine. The crystal structure of PaT reveals a distinctive fold and active site, essential components of which are demonstrated by mutagenesis. Pichia acaciae evades self-toxicity via a distinctive intracellular immunity protein, ImmPaT, which binds PaT and blocks nuclease activity. Our results highlight the evolutionary diversity of tRNA restriction and immunity systems.
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11
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Klaiman D, Steinfels-Kohn E, Kaufmann G. A DNA break inducer activates the anticodon nuclease RloC and the adaptive immunity in Acinetobacter baylyi ADP1. Nucleic Acids Res 2013; 42:328-39. [PMID: 24062157 PMCID: PMC3874168 DOI: 10.1093/nar/gkt851] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Double-stranded DNA breaks (DSB) cause bacteria to augment expression of DNA repair and various stress response proteins. A puzzling exception educes the anticodon nuclease (ACNase) RloC, which resembles the DSB responder Rad50 and the antiviral, translation-disabling ACNase PrrC. While PrrC's ACNase is regulated by a DNA restriction-modification (R-M) protein and a phage anti-DNA restriction peptide, RloC has an internal ACNase switch comprising a putative DSB sensor and coupled ATPase. Further exploration of RloC's controls revealed, first, that its ACNase is stabilized by the activating DNA and hydrolysed nucleotide. Second, DSB inducers activated RloC's ACNase in heterologous contexts as well as in a natural host, even when R-M deficient. Third, the DSB-induced activation of the indigenous RloC led to partial and temporary disruption of tRNA(Glu) and tRNA(Gln). Lastly, accumulation of CRISPR-derived RNA that occurred in parallel raises the possibility that the adaptive immunity and RloC provide the genotoxicated host with complementary protection from impending infections.
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Affiliation(s)
- Daniel Klaiman
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv 69978, Israel
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Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Biol Direct 2013; 8:15. [PMID: 23768067 PMCID: PMC3710099 DOI: 10.1186/1745-6150-8-15] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 05/09/2013] [Indexed: 12/20/2022] Open
Abstract
Background The major role of enzymatic toxins that target nucleic acids in biological conflicts at all levels has become increasingly apparent thanks in large part to the advances of comparative genomics. Typically, toxins evolve rapidly hampering the identification of these proteins by sequence analysis. Here we analyze an unexpectedly widespread superfamily of toxin domains most of which possess RNase activity. Results The HEPN superfamily is comprised of all α-helical domains that were first identified as being associated with DNA polymerase β-type nucleotidyltransferases in prokaryotes and animal Sacsin proteins. Using sensitive sequence and structure comparison methods, we vastly extend the HEPN superfamily by identifying numerous novel families and by detecting diverged HEPN domains in several known protein families. The new HEPN families include the RNase LS and LsoA catalytic domains, KEN domains (e.g. RNaseL and Ire1) and the RNase domains of RloC and PrrC. The majority of HEPN domains contain conserved motifs that constitute a metal-independent endoRNase active site. Some HEPN domains lacking this motif probably function as non-catalytic RNA-binding domains, such as in the case of the mannitol repressor MtlR. Our analysis shows that HEPN domains function as toxins that are shared by numerous systems implicated in intra-genomic, inter-genomic and intra-organismal conflicts across the three domains of cellular life. In prokaryotes HEPN domains are essential components of numerous toxin-antitoxin (TA) and abortive infection (Abi) systems and in addition are tightly associated with many restriction-modification (R-M) and CRISPR-Cas systems, and occasionally with other defense systems such as Pgl and Ter. We present evidence of multiple modes of action of HEPN domains in these systems, which include direct attack on viral RNAs (e.g. LsoA and RNase LS) in conjunction with other RNase domains (e.g. a novel RNase H fold domain, NamA), suicidal or dormancy-inducing attack on self RNAs (RM systems and possibly CRISPR-Cas systems), and suicidal attack coupled with direct interaction with phage components (Abi systems). These findings are compatible with the hypothesis on coupling of pathogen-targeting (immunity) and self-directed (programmed cell death and dormancy induction) responses in the evolution of robust antiviral strategies. We propose that altruistic cell suicide mediated by HEPN domains and other functionally similar RNases was essential for the evolution of kin and group selection and cell cooperation. HEPN domains were repeatedly acquired by eukaryotes and incorporated into several core functions such as endonucleolytic processing of the 5.8S-25S/28S rRNA precursor (Las1), a novel ER membrane-associated RNA degradation system (C6orf70), sensing of unprocessed transcripts at the nuclear periphery (Swt1). Multiple lines of evidence suggest that, similar to prokaryotes, HEPN proteins were recruited to antiviral, antitransposon, apoptotic systems or RNA-level response to unfolded proteins (Sacsin and KEN domains) in several groups of eukaryotes. Conclusions Extensive sequence and structure comparisons reveal unexpectedly broad presence of the HEPN domain in an enormous variety of defense and stress response systems across the tree of life. In addition, HEPN domains have been recruited to perform essential functions, in particular in eukaryotic rRNA processing. These findings are expected to stimulate experiments that could shed light on diverse cellular processes across the three domains of life. Reviewers This article was reviewed by Martijn Huynen, Igor Zhulin and Nick Grishin
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Affiliation(s)
- Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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Meineke B, Kast A, Schwer B, Meinhardt F, Shuman S, Klassen R. A fungal anticodon nuclease ribotoxin exploits a secondary cleavage site to evade tRNA repair. RNA (NEW YORK, N.Y.) 2012; 18:1716-1724. [PMID: 22836353 PMCID: PMC3425785 DOI: 10.1261/rna.034132.112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 06/14/2012] [Indexed: 06/01/2023]
Abstract
PaOrf2 and γ-toxin subunits of Pichia acaciae toxin (PaT) and Kluyveromyces lactis zymocin are tRNA anticodon nucleases. These secreted ribotoxins are assimilated by Saccharomyces cerevisiae, wherein they arrest growth by depleting specific tRNAs. Toxicity can be recapitulated by induced intracellular expression of PaOrf2 or γ-toxin in S. cerevisiae. Mutational analysis of γ-toxin has identified amino acids required for ribotoxicity in vivo and RNA transesterification in vitro. Here, we report that PaOrf2 residues Glu9 and His287 (putative counterparts of γ-toxin Glu9 and His209) are essential for toxicity. Our results suggest a similar basis for RNA transesterification by PaOrf2 and γ-toxin, despite their dissimilar primary structures and distinctive tRNA target specificities. PaOrf2 makes two sequential incisions in tRNA, the first of which occurs 3' from the mcm(5)s(2)U wobble nucleoside and depends on mcm(5). A second incision two nucleotides upstream results in the net excision of a di-nucleotide. Expression of phage and plant tRNA repair systems can relieve PaOrf2 toxicity when tRNA cleavage is restricted to the secondary site in elp3 cells that lack the mcm(5) wobble U modification. Whereas the endogenous yeast tRNA ligase Trl1 can heal tRNA halves produced by PaOrf2 cleavage in elp3 cells, its RNA sealing activity is inadequate to complete the repair. Compatible sealing activity can be provided in trans by plant tRNA ligase. The damage-rescuing ability of tRNA repair systems is lost when PaOrf2 can break tRNA at both sites. These results highlight the logic of a two-incision mechanism of tRNA anticodon damage that evades productive repair by tRNA ligases.
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Affiliation(s)
- Birthe Meineke
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Alene Kast
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Friedhelm Meinhardt
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Roland Klassen
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany
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14
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Klaiman D, Steinfels-Kohn E, Krutkina E, Davidov E, Kaufmann G. The wobble nucleotide-excising anticodon nuclease RloC is governed by the zinc-hook and DNA-dependent ATPase of its Rad50-like region. Nucleic Acids Res 2012; 40:8568-78. [PMID: 22730290 PMCID: PMC3458546 DOI: 10.1093/nar/gks593] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The conserved bacterial anticodon nuclease (ACNase) RloC and its phage-excluding homolog PrrC comprise respective ABC-adenosine triphosphatase (ATPase) and ACNase N- and C-domains but differ in three key attributes. First, prrC is always linked to an ACNase silencing, DNA restriction–modification (R–M) locus while rloC rarely features such linkage. Second, RloC excises its substrate’s wobble nucleotide, a lesion expected to impede damage reversal by phage transfer RNA (tRNA) repair enzymes that counteract the nick inflicted by PrrC. Third, a distinct coiled-coil/zinc-hook (CC/ZH) insert likens RloC’s N-region to the universal DNA damage checkpoint/repair protein Rad50. Previous work revealed that ZH mutations activate RloC’s ACNase. Data shown here suggest that RloC has an internal ACNase silencing/activating switch comprising its ZH and DNA-break-responsive ATPase. The existence of this control may explain the lateral transfer of rloC without an external silencer and supports the proposed role of RloC as an antiviral contingency acting when DNA restriction is alleviated under genotoxic stress. We also discuss RloC’s possible evolution from a PrrC-like ancestor.
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Affiliation(s)
- Daniel Klaiman
- Department of Biochemistry, Tel Aviv University, Tel Aviv 69978, Israel
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15
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Meineke B, Shuman S. Structure-function relations in the NTPase domain of the antiviral tRNA ribotoxin Escherichia coli PrrC. Virology 2012; 427:144-50. [PMID: 22386822 DOI: 10.1016/j.virol.2012.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Revised: 02/08/2012] [Accepted: 02/11/2012] [Indexed: 01/26/2023]
Abstract
Breakage of tRNA by Escherichia coli anticodon nuclease PrrC (EcoPrrC) underlies a host antiviral response to phage T4 infection. Expression of EcoPrrC is cytocidal in yeast, signifying that PrrC ribotoxicity crosses phylogenetic domain boundaries. EcoPrrC consists of an N-terminal NTPase module that resembles ABC transporters and a C-terminal nuclease module that is sui generis. PrrC homologs are prevalent in many other bacteria. Here we report that Haemophilus influenzae PrrC is toxic in E. coli and yeast. To illuminate structure-activity relations, we conducted a new round of mutational analysis of EcoPrrC guided by primary structure conservation among toxic PrrC homologs. We indentify 17 candidate active site residues in the NTPase module that are essential for toxicity in yeast when EcoPrrC is expressed at high gene dosage. Their functions could be educed by integrating mutational data with the atomic structure of the transition-state complex of a homologous ABC protein.
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Affiliation(s)
- Birthe Meineke
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
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