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Vaysset H, Meers C, Cury J, Bernheim A, Sternberg SH. Evolutionary origins of archaeal and eukaryotic RNA-guided RNA modification in bacterial IS110 transposons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.599552. [PMID: 38948817 PMCID: PMC11213020 DOI: 10.1101/2024.06.21.599552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Transposase genes are ubiquitous in all domains of life and provide a rich reservoir for the evolution of novel protein functions. Here we report deep evolutionary links between bacterial IS110 transposases, which catalyze RNA-guided DNA recombination using bridge RNAs, and archaeal/eukaryotic Nop5-family proteins, which promote RNA-guided RNA 2'-O-methylation using C/D-box snoRNAs. Based on conservation in the protein primary sequence, domain architecture, and three-dimensional structure, as well as common architectural features of the non-coding RNA components, we propose that programmable RNA modification emerged via exaptation of components derived from IS110-like transposons. Alongside recent studies highlighting the origins of CRISPR-Cas9 and Cas12 in IS605-family transposons, these findings underscore how recurrent domestication events of transposable elements gave rise to complex RNA-guided biological mechanisms.
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Affiliation(s)
- Hugo Vaysset
- Institut Pasteur, CNRS UMR3525, Molecular Diversity of Microbes Lab, Paris, France
- AgroParisTech, Université Paris-Saclay, Paris, France
| | - Chance Meers
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Jean Cury
- Institut Pasteur, CNRS UMR3525, Molecular Diversity of Microbes Lab, Paris, France
| | - Aude Bernheim
- Institut Pasteur, CNRS UMR3525, Molecular Diversity of Microbes Lab, Paris, France
| | - Samuel H. Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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2
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Gu Y, Yang Y, Kou C, Peng Y, Yang W, Zhang J, Jin H, Han X, Wang Y, Shen X. Classical and novel properties of Holliday junction resolvase SynRuvC from Synechocystis sp. PCC6803. Front Microbiol 2024; 15:1362880. [PMID: 38699476 PMCID: PMC11063404 DOI: 10.3389/fmicb.2024.1362880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/29/2024] [Indexed: 05/05/2024] Open
Abstract
Cyanobacteria, which have a photoautotrophic lifestyle, are threatened by ultraviolet solar rays and the reactive oxygen species generated during photosynthesis. They can adapt to environmental conditions primarily because of their DNA damage response and repair mechanisms, notably an efficient homologous recombination repair system. However, research on double-strand break (DSB) repair pathways, including the Holliday junction (HJ) resolution process, in Synechocystis sp. PCC6803 is limited. Here, we report that SynRuvC from cyanobacteria Synechocystis sp. PCC6803 has classical HJ resolution activity. We investigated the structural specificity, sequence preference, and biochemical properties of SynRuvC. SynRuvC strongly preferred Mn2+ as a cofactor, and its cleavage site predominantly resides within the 5'-TG↓(G/A)-3' sequence. Interestingly, novel flap endonuclease and replication fork intermediate cleavage activities of SynRuvC were also determined, which distinguish it from other reported RuvCs. To explore the effect of SynRuvC on cell viability, we constructed a knockdown mutant and an overexpression strain of Synechocystis sp. PCC6803 (synruvCKD and synruvCOE) and assessed their survival under a variety of conditions. Knockdown of synruvC increased the sensitivity of cells to MMS, HU, and H2O2. The findings suggest that a novel RuvC family HJ resolvase SynRuvC is important in a variety of DNA repair processes and stress resistance in Synechocystis sp. PCC6803.
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Affiliation(s)
- Yanchao Gu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yantao Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Chunhua Kou
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ying Peng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenguang Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiayu Zhang
- Suzhou XinBio Co., Ltd., Suzhou, Jiangsu, China
| | - Han Jin
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaoru Han
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yao Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xihui Shen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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3
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Ahlqvist J, Tymecka-Mulik J, Burkiewicz K, Wallenberg R, Jasilionis A, Karlsson EN, Dabrowski S. DNA digestion and formation of DNA-network structures with Holliday junction-resolving enzyme Hjc_15-6 in conjunction with polymerase reactions. J Biotechnol 2024; 385:23-29. [PMID: 38408644 DOI: 10.1016/j.jbiotec.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 02/11/2024] [Accepted: 02/22/2024] [Indexed: 02/28/2024]
Abstract
The recently identified novel Holliday junction-resolving enzyme, termed Hjc_15-6, activity investigation results imply DNA cleavage by Hjc_15-6 in a manner that potentially enhances the molecular self-assembly that may be exploited for creating DNA-networks and nanostructures. The study also demonstrates Pwo DNA polymerase acting in combination with Hjc_15-6 capability to produce large amounts of DNA that transforms into large DNA-network structures even without DNA template and primers. Furthermore, it is demonstrated that Hjc_15-6 prefers Holliday junction oligonucleotides as compared to Y-shaped oligonucleotides as well as efficiently cleaves typical branched products from isothermal DNA amplification of both linear and circular DNA templates amplified by phi29-like DNA polymerase. The assembly of large DNA network structures was observed in real time, by transmission electron microscopy, on negative stained grids that were freshly prepared, and also on the same grids after incubation for 4 days under constant cooling. Hence, Hjc_15-6 is a promising molecular tool for efficient production of various DNA origamis that may be implemented for a wide range of applications such as within medical biomaterials, catalytic materials, molecular devices and biosensors.
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Affiliation(s)
- Josefin Ahlqvist
- Division of Biotechnology, Department of Chemistry, Lund University, PO Box 124, Lund SE-221 00, Sweden.
| | | | | | - Reine Wallenberg
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, PO Box 124, Lund SE-221 00, Sweden
| | - Andrius Jasilionis
- Division of Biotechnology, Department of Chemistry, Lund University, PO Box 124, Lund SE-221 00, Sweden
| | - Eva Nordberg Karlsson
- Division of Biotechnology, Department of Chemistry, Lund University, PO Box 124, Lund SE-221 00, Sweden
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4
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Nautiyal A, Thakur M. Prokaryotic DNA Crossroads: Holliday Junction Formation and Resolution. ACS OMEGA 2024; 9:12515-12538. [PMID: 38524412 PMCID: PMC10956419 DOI: 10.1021/acsomega.3c09866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/04/2024] [Accepted: 02/09/2024] [Indexed: 03/26/2024]
Abstract
Cells are continually exposed to a multitude of internal and external stressors, which give rise to various types of DNA damage. To protect the integrity of their genetic material, cells are equipped with a repertoire of repair proteins that engage in various repair mechanisms, facilitated by intricate networks of protein-protein and protein-DNA interactions. Among these networks is the homologous recombination (HR) system, a molecular repair mechanism conserved in all three domains of life. On one hand, HR ensures high-fidelity, template-dependent DNA repair, while on the other hand, it results in the generation of combinatorial genetic variations through allelic exchange. Despite substantial progress in understanding this pathway in bacteria, yeast, and humans, several critical questions remain unanswered, including the molecular processes leading to the exchange of DNA segments, the coordination of protein binding, conformational switching during branch migration, and the resolution of Holliday Junctions (HJs). This Review delves into our current understanding of the HR pathway in bacteria, shedding light on the roles played by various proteins or their complexes at different stages of HR. In the first part of this Review, we provide a brief overview of the end resection processes and the strand-exchange reaction, offering a concise depiction of the mechanisms that culminate in the formation of HJs. In the latter half, we expound upon the alternative methods of branch migration and HJ resolution more comprehensively and holistically, considering the historical research timelines. Finally, when we consolidate our knowledge about HR within the broader context of genome replication and the emergence of resistant species, it becomes evident that the HR pathway is indispensable for the survival of bacteria in diverse ecological niches.
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Affiliation(s)
- Astha Nautiyal
- Department
of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Manoj Thakur
- Sri
Venkateswara College, Benito Juarez Road, University of Delhi, New Delhi 110021, India
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5
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Biochemical and Structural Study of RuvC and YqgF from Deinococcus radiodurans. mBio 2022; 13:e0183422. [PMID: 36000732 DOI: 10.1128/mbio.01834-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Deinococcus radiodurans possesses robust DNA damage response and repair abilities, and this is mainly due to its efficient homologous recombination repair system, which incorporates an uncharacterized Holliday junction (HJ) resolution process. D. radiodurans encodes two putative HJ resolvase (HJR) homologs: RuvC (DrRuvC) and YqgF (DrYqgF). Here, both DrRuvC and DrYqgF were identified as essential proteins for the survival of D. radiodurans. The crystal structures and the biochemical properties of DrRuvC and DrYqgF were also studied. DrRuvC crystallized as a homodimer, while DrYqgF crystallized as a monomer. DrRuvC could preferentially cleave HJ at the consensus 5'-(G/C)TC↓(G/C)-3' sequence and could prefer using Mn2+ for catalysis in vitro, which would be different from the preferences of the other previously characterized RuvCs. On the other hand, DrYqgF was identified as a Mn2+-dependent RNA 5'-3' exo/endonuclease with a sequence preference for poly(A) and without any HJR activity. IMPORTANCE Deinococcus radiodurans is one of the most radioresistant bacteria in the world due to its robust DNA damage response and repair abilities, which are contributed by its efficient homologous recombination repair system. However, the late steps of homologous recombination, especially the Holliday junction (HJ) resolution process, have not yet been well-studied in D. radiodurans. We characterized the structural and biochemical features of the two putative HJ resolvases, DrRuvC and DrYqgF, in D. radiodurans. It was identified that DrRuvC and DrYqgF exhibit HJ resolvase (HJR) activity and RNA exo/endonuclease activity, respectively. Furthermore, both DrRuvC and DrYqgF digest substrates in a sequence-specific manner with a preferred sequence that is different from those of the other characterized RuvCs or YqgFs. Our findings provide new insights into the HJ resolution process and reveal a novel RNase involved in RNA metabolism in D. radiodurans.
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Wright LR, Wright DL, Weller SK. Viral Nucleases from Herpesviruses and Coronavirus in Recombination and Proofreading: Potential Targets for Antiviral Drug Discovery. Viruses 2022; 14:v14071557. [PMID: 35891537 PMCID: PMC9324378 DOI: 10.3390/v14071557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 02/05/2023] Open
Abstract
In this review, we explore recombination in two very different virus families that have become major threats to human health. The Herpesviridae are a large family of pathogenic double-stranded DNA viruses involved in a range of diseases affecting both people and animals. Coronaviridae are positive-strand RNA viruses (CoVs) that have also become major threats to global health and economic stability, especially in the last two decades. Despite many differences, such as the make-up of their genetic material (DNA vs. RNA) and overall mechanisms of genome replication, both human herpes viruses (HHVs) and CoVs have evolved to rely heavily on recombination for viral genome replication, adaptation to new hosts and evasion of host immune regulation. In this review, we will focus on the roles of three viral exonucleases: two HHV exonucleases (alkaline nuclease and PolExo) and one CoV exonuclease (ExoN). We will review the roles of these three nucleases in their respective life cycles and discuss the state of drug discovery efforts against these targets.
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Affiliation(s)
- Lee R. Wright
- Department of Pharmaceutical Sciences, University of Connecticut School of Pharmacy, Storrs, CT 06269, USA; (L.R.W.); (D.L.W.)
| | - Dennis L. Wright
- Department of Pharmaceutical Sciences, University of Connecticut School of Pharmacy, Storrs, CT 06269, USA; (L.R.W.); (D.L.W.)
| | - Sandra K. Weller
- Department of Molecular Biology and Biophysics, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
- Correspondence: ; Tel.: +1-(860)-679-2310; Fax: +1-(860)-679-1239
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7
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Aravind L, Iyer LM, Burroughs AM. Discovering Biological Conflict Systems Through Genome Analysis: Evolutionary Principles and Biochemical Novelty. Annu Rev Biomed Data Sci 2022; 5:367-391. [PMID: 35609893 DOI: 10.1146/annurev-biodatasci-122220-101119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biological replicators, from genes within a genome to whole organisms, are locked in conflicts. Comparative genomics has revealed a staggering diversity of molecular armaments and mechanisms regulating their deployment, collectively termed biological conflict systems. These encompass toxins used in inter- and intraspecific interactions, self/nonself discrimination, antiviral immune mechanisms, and counter-host effectors deployed by viruses and intragenomic selfish elements. These systems possess shared syntactical features in their organizational logic and a set of effectors targeting genetic information flow through the Central Dogma, certain membranes, and key molecules like NAD+. These principles can be exploited to discover new conflict systems through sensitive computational analyses. This has led to significant advances in our understanding of the biology of these systems and furnished new biotechnological reagents for genome editing, sequencing, and beyond. We discuss these advances using specific examples of toxins, restriction-modification, apoptosis, CRISPR/second messenger-regulated systems, and other enigmatic nucleic acid-targeting systems. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA;
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA;
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA;
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8
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Łabędzka-Dmoch K, Rażew M, Gapińska M, Piątkowski J, Kolondra A, Salmonowicz H, Wenda JM, Nowotny M, Golik P. The Pet127 protein is a mitochondrial 5'-to-3' exoribonuclease from the PD-(D/E)XK superfamily involved in RNA maturation and intron degradation in yeasts. RNA (NEW YORK, N.Y.) 2022; 28:711-728. [PMID: 35197365 PMCID: PMC9014873 DOI: 10.1261/rna.079083.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/31/2022] [Indexed: 06/01/2023]
Abstract
Pet127 is a mitochondrial protein found in multiple eukaryotic lineages, but absent from several taxa, including plants and animals. Distant homology suggests that it belongs to the divergent PD-(D/E)XK superfamily which includes various nucleases and related proteins. Earlier yeast genetics experiments suggest that it plays a nonessential role in RNA degradation and 5' end processing. Our phylogenetic analysis suggests that it is a primordial eukaryotic invention that was retained in diverse groups, and independently lost several times in the evolution of other organisms. We demonstrate for the first time that the fungal Pet127 protein in vitro is a processive 5'-to-3' exoribonuclease capable of digesting various substrates in a sequence nonspecific manner. Mutations in conserved residues essential in the PD-(D/E)XK superfamily active site abolish the activity of Pet127. Deletion of the PET127 gene in the pathogenic yeast Candida albicans results in a moderate increase in the steady-state levels of several transcripts and in accumulation of unspliced precursors and intronic sequences of three introns. Mutations in the active site residues result in a phenotype identical to that of the deletant, confirming that the exoribonuclease activity is related to the physiological role of the Pet127 protein. Pet127 activity is, however, not essential for maintaining the mitochondrial respiratory activity in C. albicans.
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Affiliation(s)
- Karolina Łabędzka-Dmoch
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw 02-106, Poland
| | - Michal Rażew
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
| | - Marta Gapińska
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
| | - Jakub Piątkowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw 02-106, Poland
| | - Adam Kolondra
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw 02-106, Poland
| | - Hanna Salmonowicz
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw 02-106, Poland
- Laboratory of Metabolic Quality Control, IMOL, Polish Academy of Sciences, Warsaw 00-783, Poland
| | - Joanna M Wenda
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw 02-106, Poland
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
| | - Paweł Golik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw 02-106, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
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Benler S, Koonin EV. Recruitment of Mobile Genetic Elements for Diverse Cellular Functions in Prokaryotes. Front Mol Biosci 2022; 9:821197. [PMID: 35402511 PMCID: PMC8987985 DOI: 10.3389/fmolb.2022.821197] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/08/2022] [Indexed: 12/15/2022] Open
Abstract
Prokaryotic genomes are replete with mobile genetic elements (MGE) that span a continuum of replication autonomy. On numerous occasions during microbial evolution, diverse MGE lose their autonomy altogether but, rather than being quickly purged from the host genome, assume a new function that benefits the host, rendering the immobilized MGE subject to purifying selection, and resulting in its vertical inheritance. This mini-review highlights the diversity of the repurposed (exapted) MGE as well as the plethora of cellular functions that they perform. The principal contribution of the exaptation of MGE and their components is to the prokaryotic functional systems involved in biological conflicts, and in particular, defense against viruses and other MGE. This evolutionary entanglement between MGE and defense systems appears to stem both from mechanistic similarities and from similar evolutionary predicaments whereby both MGEs and defense systems tend to incur fitness costs to the hosts and thereby evolve mechanisms for survival including horizontal mobility, causing host addiction, and exaptation for functions beneficial to the host. The examples discussed demonstrate that the identity of an MGE, overall mobility and relationship with the host cell (mutualistic, symbiotic, commensal, or parasitic) are all factors that affect exaptation.
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Ahlqvist J, Linares-Pastén JA, Håkansson M, Jasilionis A, Kwiatkowska-Semrau K, Friðjónsson ÓH, Kaczorowska AK, Dabrowski S, Ævarsson A, Hreggviðsson GÓ, Al-Karadaghi S, Kaczorowski T, Nordberg Karlsson E. Crystal structure and initial characterization of a novel archaeal-like Holliday junction-resolving enzyme from Thermus thermophilus phage Tth15-6. Acta Crystallogr D Struct Biol 2022; 78:212-227. [PMID: 35102887 PMCID: PMC8805305 DOI: 10.1107/s2059798321012298] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/19/2021] [Indexed: 11/10/2022] Open
Abstract
This study describes the production, characterization and structure determination of a novel Holliday junction-resolving enzyme. The enzyme, termed Hjc_15-6, is encoded in the genome of phage Tth15-6, which infects Thermus thermophilus. Hjc_15-6 was heterologously produced in Escherichia coli and high yields of soluble and biologically active recombinant enzyme were obtained in both complex and defined media. Amino-acid sequence and structure comparison suggested that the enzyme belongs to a group of enzymes classified as archaeal Holliday junction-resolving enzymes, which are typically divalent metal ion-binding dimers that are able to cleave X-shaped dsDNA–Holliday junctions (Hjs). The crystal structure of Hjc_15-6 was determined to 2.5 Å resolution using the selenomethionine single-wavelength anomalous dispersion method. To our knowledge, this is the first crystal structure of an Hj-resolving enzyme originating from a bacteriophage that can be classified as an archaeal type of Hj-resolving enzyme. As such, it represents a new fold for Hj-resolving enzymes from phages. Characterization of the structure of Hjc_15-6 suggests that it may form a dimer, or even a homodimer of dimers, and activity studies show endonuclease activity towards Hjs. Furthermore, based on sequence analysis it is proposed that Hjc_15-6 has a three-part catalytic motif corresponding to E–SD–EVK, and this motif may be common among other Hj-resolving enzymes originating from thermophilic bacteriophages.
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11
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Kaur G, Iyer LM, Burroughs AM, Aravind L. Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans. eLife 2021; 10:70394. [PMID: 34061031 PMCID: PMC8195603 DOI: 10.7554/elife.70394] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 05/23/2021] [Indexed: 12/12/2022] Open
Abstract
Several homologous domains are shared by eukaryotic immunity and programmed cell-death systems and poorly understood bacterial proteins. Recent studies show these to be components of a network of highly regulated systems connecting apoptotic processes to counter-invader immunity, in prokaryotes with a multicellular habit. However, the provenance of key adaptor domains, namely those of the Death-like and TRADD-N superfamilies, a quintessential feature of metazoan apoptotic systems, remained murky. Here, we use sensitive sequence analysis and comparative genomics methods to identify unambiguous bacterial homologs of the Death-like and TRADD-N superfamilies. We show the former to have arisen as part of a radiation of effector-associated α-helical adaptor domains that likely mediate homotypic interactions bringing together diverse effector and signaling domains in predicted bacterial apoptosis- and counter-invader systems. Similarly, we show that the TRADD-N domain defines a key, widespread signaling bridge that links effector deployment to invader-sensing in multicellular bacterial and metazoan counter-invader systems. TRADD-N domains are expanded in aggregating marine invertebrates and point to distinctive diversifying immune strategies probably directed both at RNA and retroviruses and cellular pathogens that might infect such communities. These TRADD-N and Death-like domains helped identify several new bacterial and metazoan counter-invader systems featuring underappreciated, common functional principles: the use of intracellular invader-sensing lectin-like (NPCBM and FGS), transcription elongation GreA/B-C, glycosyltransferase-4 family, inactive NTPase (serving as nucleic acid receptors), and invader-sensing GTPase switch domains. Finally, these findings point to the possibility of multicellular bacteria-stem metazoan symbiosis in the emergence of the immune/apoptotic systems of the latter.
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Affiliation(s)
- Gurmeet Kaur
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Lakshminarayan M Iyer
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - A Maxwell Burroughs
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - L Aravind
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
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12
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Thakur M, Mohan D, Singh AK, Agarwal A, Gopal B, Muniyappa K. Novel insights into ATP-Stimulated Cleavage of branched DNA and RNA Substrates through Structure-Guided Studies of the Holliday Junction Resolvase RuvX. J Mol Biol 2021; 433:167014. [PMID: 33933468 DOI: 10.1016/j.jmb.2021.167014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/05/2021] [Accepted: 04/23/2021] [Indexed: 11/18/2022]
Abstract
Much of our understanding of the homologous recombination (HR) machinery hinges on studies using Escherichia coli as a model organism. Interestingly enough, studies on the HR machinery in different bacterial species casts doubt on the universality of the E. coli paradigm. The human pathogen Mycobacterium tuberculosis encodes two Holliday junction (HJ)-resolvase paralogues, namely RuvC and RuvX; however, insights into their structural features and functional relevance is still limited. Here, we report on structure-guided functional studies of the M. tuberculosis RuvX HJ resolvase (MtRuvX). The crystalline MtRuvX is a dimer in the asymmetric unit, and each monomer has a RNAse H fold vis-à-vis RuvC-like nucleases. Interestingly, MtRuvX also contains some unique features, including the residues essential for ATP binding/coordination of Mg2+ ions. Indeed, MtRuvX exhibited an intrinsic, robust ATPase activity, which was further accentuated by DNA cofactors. Structure-guided substitutions of single residues at the ATP binding/Mg2+coordination sites while markedly attenuating the ATPase activity completely abrogated HJ cleavage, indicating an unanticipated relationship between ATP hydrolysis and DNA cleavage. However, the affinity of ATPase-deficient mutants for the HJ was not impaired. Contrary to RuvC, MtRuvX exhibits relaxed substrate specificity, cleaving a variety of branched DNA/RNA substrates. Notably, ATP hydrolysis plays a regulatory role, rendering MtRuvX from a canonical HJ resolvase to a DNA/RNA non-sequence specific endonuclease, indicating a link between HJ resolvase and nucleic acid metabolism. These findings provide novel insights into the structure and dual-functional activities of MtRuvX, and suggest that it may play an important role in DNA/RNA metabolism.
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Affiliation(s)
- Manoj Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Disha Mohan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ankur Kumar Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ankit Agarwal
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | | | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India.
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M. Iyer L, Anantharaman V, Krishnan A, Burroughs AM, Aravind L. Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts. Viruses 2021; 13:v13010063. [PMID: 33466489 PMCID: PMC7824862 DOI: 10.3390/v13010063] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 02/07/2023] Open
Abstract
Jumbo phages have attracted much attention by virtue of their extraordinary genome size and unusual aspects of biology. By performing a comparative genomics analysis of 224 jumbo phages, we suggest an objective inclusion criterion based on genome size distributions and present a synthetic overview of their manifold adaptations across major biological systems. By means of clustering and principal component analysis of the phyletic patterns of conserved genes, all known jumbo phages can be classified into three higher-order groups, which include both myoviral and siphoviral morphologies indicating multiple independent origins from smaller predecessors. Our study uncovers several under-appreciated or unreported aspects of the DNA replication, recombination, transcription and virion maturation systems. Leveraging sensitive sequence analysis methods, we identify novel protein-modifying enzymes that might help hijack the host-machinery. Focusing on host–virus conflicts, we detect strategies used to counter different wings of the bacterial immune system, such as cyclic nucleotide- and NAD+-dependent effector-activation, and prevention of superinfection during pseudolysogeny. We reconstruct the RNA-repair systems of jumbo phages that counter the consequences of RNA-targeting host effectors. These findings also suggest that several jumbo phage proteins provide a snapshot of the systems found in ancient replicons preceding the last universal ancestor of cellular life.
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Affiliation(s)
- Lakshminarayan M. Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (L.M.I.); (V.A.); (A.M.B.)
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (L.M.I.); (V.A.); (A.M.B.)
| | - Arunkumar Krishnan
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha 760010, India;
| | - A. Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (L.M.I.); (V.A.); (A.M.B.)
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (L.M.I.); (V.A.); (A.M.B.)
- Correspondence:
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Structure-Based Deep Mining Reveals First-Time Annotations for 46 Percent of the Dark Annotation Space of the 9,671-Member Superproteome of the Nucleocytoplasmic Large DNA Viruses. J Virol 2020; 94:JVI.00854-20. [PMID: 32999026 DOI: 10.1128/jvi.00854-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/16/2020] [Indexed: 12/20/2022] Open
Abstract
We conducted an exhaustive search for three-dimensional structural homologs to the proteins of 20 key phylogenetically distinct nucleocytoplasmic DNA viruses (NCLDV). Structural matches covered 429 known protein domain superfamilies, with the most highly represented being ankyrin repeat, P-loop NTPase, F-box, protein kinase, and membrane occupation and recognition nexus (MORN) repeat. Domain superfamily diversity correlated with genome size, but a diversity of around 200 superfamilies appeared to correlate with an abrupt switch to paralogization. Extensive structural homology was found across the range of eukaryotic RNA polymerase II subunits and their associated basal transcription factors, with the coordinated gain and loss of clusters of subunits on a virus-by-virus basis. The total number of predicted endonucleases across the 20 NCLDV was nearly quadrupled from 36 to 132, covering much of the structural and functional diversity of endonucleases throughout the biosphere in DNA restriction, repair, and homing. Unexpected findings included capsid protein-transcription factor chimeras; endonuclease chimeras; enzymes for detoxification; antimicrobial peptides and toxin-antitoxin systems associated with symbiosis, immunity, and addiction; and novel proteins for membrane abscission and protein turnover.IMPORTANCE We extended the known annotation space for the NCLDV by 46%, revealing high-probability structural matches for fully 45% of the 9,671 query proteins and confirming up to 98% of existing annotations per virus. The most prevalent protein families included ankyrin repeat- and MORN repeat-containing proteins, many of which included an F-box, suggesting extensive host cell modulation among the NCLDV. Regression suggested a minimum requirement for around 36 protein structural superfamilies for a viable NCLDV, and beyond around 200 superfamilies, genome expansion by the acquisition of new functions was abruptly replaced by paralogization. We found homologs to herpesvirus surface glycoprotein gB in cytoplasmic viruses. This study provided the first prediction of an endonuclease in 10 of the 20 viruses examined; the first report in a virus of a phenolic acid decarboxylase, proteasomal subunit, or cysteine knot (defensin) protein; and the first report of a prokaryotic-type ribosomal protein in a eukaryotic virus.
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15
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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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16
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Wilkinson OJ, Carrasco C, Aicart-Ramos C, Moreno-Herrero F, Dillingham MS. Bulk and single-molecule analysis of a bacterial DNA2-like helicase-nuclease reveals a single-stranded DNA looping motor. Nucleic Acids Res 2020; 48:7991-8005. [PMID: 32621607 PMCID: PMC7430649 DOI: 10.1093/nar/gkaa562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/12/2020] [Accepted: 06/19/2020] [Indexed: 11/14/2022] Open
Abstract
DNA2 is an essential enzyme involved in DNA replication and repair in eukaryotes. In a search for homologues of this protein, we identified and characterised Geobacillus stearothermophilus Bad, a bacterial DNA helicase-nuclease with similarity to human DNA2. We show that Bad contains an Fe-S cluster and identify four cysteine residues that are likely to co-ordinate the cluster by analogy to DNA2. The purified enzyme specifically recognises ss-dsDNA junctions and possesses ssDNA-dependent ATPase, ssDNA binding, ssDNA endonuclease, 5' to 3' ssDNA translocase and 5' to 3' helicase activity. Single molecule analysis reveals that Bad is a processive DNA motor capable of moving along DNA for distances of >4 kb at a rate of ∼200 bp per second at room temperature. Interestingly, as reported for the homologous human and yeast DNA2 proteins, the DNA unwinding activity of Bad is cryptic and can be unmasked by inactivating the intrinsic nuclease activity. Strikingly, our experiments show that the enzyme loops DNA while translocating, which is an emerging feature of processive DNA unwinding enzymes. The bacterial Bad enzymes will provide an excellent model system for understanding the biochemical properties of DNA2-like helicase-nucleases and DNA looping motor proteins in general.
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Affiliation(s)
- Oliver J Wilkinson
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Carolina Carrasco
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Mark S Dillingham
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, UK
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17
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Zhang L, Jiang D, Wu M, Yang Z, Oger PM. New Insights Into DNA Repair Revealed by NucS Endonucleases From Hyperthermophilic Archaea. Front Microbiol 2020; 11:1263. [PMID: 32714287 PMCID: PMC7343888 DOI: 10.3389/fmicb.2020.01263] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/18/2020] [Indexed: 12/22/2022] Open
Abstract
Hyperthermophilic Archaea (HA) thrive in high temperature environments and their genome is facing severe stability challenge due to the increased DNA damage levels caused by high temperature. Surprisingly, HA display spontaneous mutation frequencies similar to mesophilic microorganisms, thereby indicating that the former must possess more efficient DNA repair systems than the latter to counteract the potentially enhanced mutation rates under the harsher environment. Although a few repair proteins or enzymes from HA have been biochemically and structurally characterized, the molecular mechanisms of DNA repair of HA remain largely unknown. Genomic analyses of HA revealed that they lack MutS/MutL homologues of the mismatch repair (MMR) pathway and the recognition proteins of the nucleotide excision repair (NER) pathway. Endonucleases play an essential role in DNA repair. NucS endonuclease, a novel endonuclease recently identified in some HA and bacteria, has been shown to act on branched, mismatched, and deaminated DNA, suggesting that this endonuclease is a multifunctional enzyme involved in NER, MMR, and deaminated base repair in a non-canonical manner. However, the catalytic mechanism and the physiological function of NucS endonucleases from HA need to be further clarified to determine how they participate in the different DNA repair pathways in cells from HA. In this review, we focus on recent advances in our understanding of the function of NucS endonucleases from HA in NER, MMR, and deaminated DNA repair, and propose directions for future studies of the NucS family of endonucleases.
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Affiliation(s)
- Likui Zhang
- College of Environmental Science and Engineering, Marine Science and Technology Institute, Yangzhou University, Yangzhou, China.,Guangling College, Yangzhou University, Yangzhou, China
| | - Donghao Jiang
- College of Environmental Science and Engineering, Marine Science and Technology Institute, Yangzhou University, Yangzhou, China
| | - Mai Wu
- College of Environmental Science and Engineering, Marine Science and Technology Institute, Yangzhou University, Yangzhou, China
| | - Zhihui Yang
- College of Plant Protection, Agricultural University of Hebei, Baoding, China
| | - Philippe M Oger
- Univ Lyon, INSA de Lyon, CNRS UMR 5240, Villeurbanne, France
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18
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Chevigny N, Schatz-Daas D, Lotfi F, Gualberto JM. DNA Repair and the Stability of the Plant Mitochondrial Genome. Int J Mol Sci 2020; 21:E328. [PMID: 31947741 PMCID: PMC6981420 DOI: 10.3390/ijms21010328] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/27/2019] [Accepted: 01/01/2020] [Indexed: 12/13/2022] Open
Abstract
The mitochondrion stands at the center of cell energy metabolism. It contains its own genome, the mtDNA, that is a relic of its prokaryotic symbiotic ancestor. In plants, the mitochondrial genetic information influences important agronomic traits including fertility, plant vigor, chloroplast function, and cross-compatibility. Plant mtDNA has remarkable characteristics: It is much larger than the mtDNA of other eukaryotes and evolves very rapidly in structure. This is because of recombination activities that generate alternative mtDNA configurations, an important reservoir of genetic diversity that promotes rapid mtDNA evolution. On the other hand, the high incidence of ectopic recombination leads to mtDNA instability and the expression of gene chimeras, with potential deleterious effects. In contrast to the structural plasticity of the genome, in most plant species the mtDNA coding sequences evolve very slowly, even if the organization of the genome is highly variable. Repair mechanisms are probably responsible for such low mutation rates, in particular repair by homologous recombination. Herein we review some of the characteristics of plant organellar genomes and of the repair pathways found in plant mitochondria. We further discuss how homologous recombination is involved in the evolution of the plant mtDNA.
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Affiliation(s)
| | | | | | - José Manuel Gualberto
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67081 Strasbourg, France; (N.C.); (D.S.-D.); (F.L.)
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19
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Herpes simplex virus 1 ICP8 mutant lacking annealing activity is deficient for viral DNA replication. Proc Natl Acad Sci U S A 2018; 116:1033-1042. [PMID: 30598436 DOI: 10.1073/pnas.1817642116] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Most DNA viruses that use recombination-dependent mechanisms to replicate their DNA encode a single-strand annealing protein (SSAP). The herpes simplex virus (HSV) single-strand DNA binding protein (SSB), ICP8, is the central player in all stages of DNA replication. ICP8 is a classical replicative SSB and interacts physically and/or functionally with the other viral replication proteins. Additionally, ICP8 can promote efficient annealing of complementary ssDNA and is thus considered to be a member of the SSAP family. The role of annealing during HSV infection has been difficult to assess in part, because it has not been possible to distinguish between the role of ICP8 as an SSAP from its role as a replicative SSB during viral replication. In this paper, we have characterized an ICP8 mutant, Q706A/F707A (QF), that lacks annealing activity but retains many other functions characteristic of replicative SSBs. Like WT ICP8, the QF mutant protein forms filaments in vitro, binds ssDNA cooperatively, and stimulates the activities of other replication proteins including the viral polymerase, helicase-primase complex, and the origin binding protein. Interestingly, the QF mutant does not complement an ICP8-null virus for viral growth, replication compartment formation, or DNA replication. Thus, we have been able to separate the activities of ICP8 as a replicative SSB from its annealing activity. Taken together, our data indicate that the annealing activity of ICP8 is essential for viral DNA replication in the context of infection and support the notion that HSV-1 uses recombination-dependent mechanisms during DNA replication.
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20
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Alleman A, Hertweck KL, Kambhampati S. Random Genetic Drift and Selective Pressures Shaping the Blattabacterium Genome. Sci Rep 2018; 8:13427. [PMID: 30194350 PMCID: PMC6128925 DOI: 10.1038/s41598-018-31796-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 08/21/2018] [Indexed: 01/30/2023] Open
Abstract
Estimates suggest that at least half of all extant insect genera harbor obligate bacterial mutualists. Whereas an endosymbiotic relationship imparts many benefits upon host and symbiont alike, the intracellular lifestyle has profound effects on the bacterial genome. The obligate endosymbiont genome is a product of opposing forces: genes important to host survival are maintained through physiological constraint, contrasted by the fixation of deleterious mutations and genome erosion through random genetic drift. The obligate cockroach endosymbiont, Blattabacterium - providing nutritional augmentation to its host in the form of amino acid synthesis - displays radical genome alterations when compared to its most recent free-living relative Flavobacterium. To date, eight Blattabacterium genomes have been published, affording an unparalleled opportunity to examine the direction and magnitude of selective forces acting upon this group of symbionts. Here, we find that the Blattabacterium genome is experiencing a 10-fold increase in selection rate compared to Flavobacteria. Additionally, the proportion of selection events is largely negative in direction, with only a handful of loci exhibiting signatures of positive selection. These findings suggest that the Blattabacterium genome will continue to erode, potentially resulting in an endosymbiont with an even further reduced genome, as seen in other insect groups such as Hemiptera.
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Affiliation(s)
- Austin Alleman
- Department of Biology, University of Texas at Tyler, 3900 University Blvd., Tyler, Texas, 75799, United States.
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Johannes von Müller Weg 6, Mainz, 55128, Germany.
| | - Kate L Hertweck
- Department of Biology, University of Texas at Tyler, 3900 University Blvd., Tyler, Texas, 75799, United States
| | - Srini Kambhampati
- Department of Biology, University of Texas at Tyler, 3900 University Blvd., Tyler, Texas, 75799, United States
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21
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Valledor M, Myers RS, Schiller PC. Herpes ICP8 protein stimulates homologous recombination in human cells. PLoS One 2018; 13:e0200955. [PMID: 30110337 PMCID: PMC6093641 DOI: 10.1371/journal.pone.0200955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/04/2018] [Indexed: 12/11/2022] Open
Abstract
Recombineering has transformed functional genomic analysis. Genome modification by recombineering using the phage lambda Red homologous recombination protein Beta in Escherichia coli has approached 100% efficiency. While highly efficient in E. coli, recombineering using the Red Synaptase/Exonuclease pair (SynExo) in other organisms declines in efficiency roughly correlating with phylogenetic distance from E. coli. SynExo recombinases are common to double-stranded DNA viruses infecting a variety of organisms, including humans. Human Herpes virus 1 (HHV1) encodes a SynExo comprised of ICP8 synaptase and UL12 exonuclease. In a previous study, the Herpes SynExo was reconstituted in vitro and shown to catalyze a model recombination reaction. Here we describe stimulation of gene targeting to edit a novel fluorescent protein gene in the human genome using ICP8 and compared its efficiency to that of a "humanized" version of Beta protein from phage λ. ICP8 significantly enhanced gene targeting rates in HEK 293T cells while Beta was not only unable to catalyze recombineering but inhibited gene targeting using endogenous recombination functions, despite both synaptases being well-expressed and localized to the nucleus. This proof of concept encourages developing species-specific SynExo recombinases for genome engineering.
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Affiliation(s)
- Melvys Valledor
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Richard S. Myers
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Paul C. Schiller
- Department of Orthopaedics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Geriatric Research, Education, and Clinical Center and Research Service, Bruce W. Carter VAMC, Miami, Florida, United States of America
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22
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Liu Y, Freeman A, Déclais AC, Gartner A, Lilley DMJ. Biochemical and Structural Properties of Fungal Holliday Junction-Resolving Enzymes. Methods Enzymol 2018; 600:543-568. [PMID: 29458774 DOI: 10.1016/bs.mie.2017.11.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Four-way Holliday junctions in DNA are the central intermediates of genetic recombination and must be processed into regular duplex species. One mechanism for achieving this is called resolution, brought about by structure-selective nucleases. GEN1 is an important junction-resolving enzyme in eukaryotic cells, a member of the FEN1/EXO1 superfamily of nucleases. While human GEN1 is difficult to work with because of aggregation, orthologs from thermophilic fungi have been identified using bioinformatics and have proved to have excellent properties. Here, the expression and purification of this enzyme from Chaetomium thermophilum is described, together with the means of investigating its biochemical properties. The enzyme is quite similar to junction-resolving enzymes from lower organisms, binding to junctions in dimeric form, introducing symmetrical bilateral cleavages, the second of which is accelerated to promote productive resolution. Crystallization of C. thermophilum GEN1 is described, and the structure of a DNA-product complex. Juxtaposition of complexes in the crystal lattice suggests how the structure of a dimeric enzyme with an intact junction is organized.
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Affiliation(s)
- Yijin Liu
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - Alasdair Freeman
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - Anne-Cécile Déclais
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - Anton Gartner
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom.
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23
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Singh A. Guardians of the mycobacterial genome: A review on DNA repair systems in Mycobacterium tuberculosis. MICROBIOLOGY-SGM 2017; 163:1740-1758. [PMID: 29171825 DOI: 10.1099/mic.0.000578] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The genomic integrity of Mycobacterium tuberculosis is continuously threatened by the harsh survival conditions inside host macrophages, due to immune and antibiotic stresses. Faithful genome maintenance and repair must be accomplished under stress for the bacillus to survive in the host, necessitating a robust DNA repair system. The importance of DNA repair systems in pathogenesis is well established. Previous examination of the M. tuberculosis genome revealed homologues of almost all the major DNA repair systems, i.e. nucleotide excision repair (NER), base excision repair (BER), homologous recombination (HR) and non-homologous end joining (NHEJ). However, recent developments in the field have pointed to the presence of novel proteins and pathways in mycobacteria. Homologues of archeal mismatch repair proteins were recently reported in mycobacteria, a pathway previously thought to be absent. RecBCD, the major nuclease-helicase enzymes involved in HR in E. coli, were implicated in the single-strand annealing (SSA) pathway. Novel roles of archeo-eukaryotic primase (AEP) polymerases, previously thought to be exclusive to NHEJ, have been reported in BER. Many new proteins with a probable role in DNA repair have also been discovered. It is now realized that the DNA repair systems in M. tuberculosis are highly evolved and have redundant backup mechanisms to mend the damage. This review is an attempt to summarize our current understanding of the DNA repair systems in M. tuberculosis.
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Affiliation(s)
- Amandeep Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
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24
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25
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Gualberto JM, Newton KJ. Plant Mitochondrial Genomes: Dynamics and Mechanisms of Mutation. ANNUAL REVIEW OF PLANT BIOLOGY 2017; 68:225-252. [PMID: 28226235 DOI: 10.1146/annurev-arplant-043015-112232] [Citation(s) in RCA: 231] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The large mitochondrial genomes of angiosperms are unusually dynamic because of recombination activities involving repeated sequences. These activities generate subgenomic forms and extensive genomic variation even within the same species. Such changes in genome structure are responsible for the rapid evolution of plant mitochondrial DNA and for the variants associated with cytoplasmic male sterility and abnormal growth phenotypes. Nuclear genes modulate these processes, and over the past decade, several of these genes have been identified. They are involved mainly in pathways of DNA repair by homologous recombination and mismatch repair, which appear to be essential for the faithful replication of the mitogenome. Mutations leading to the loss of any of these activities release error-prone repair pathways, resulting in increased ectopic recombination, genome instability, and heteroplasmy. We review the present state of knowledge of the genes and pathways underlying mitochondrial genome stability.
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Affiliation(s)
- José M Gualberto
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, 67084 Strasbourg, France;
| | - Kathleen J Newton
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211;
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26
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Lilley DMJ. Holliday junction-resolving enzymes-structures and mechanisms. FEBS Lett 2017; 591:1073-1082. [PMID: 27990631 DOI: 10.1002/1873-3468.12529] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 12/12/2016] [Accepted: 12/13/2016] [Indexed: 12/15/2022]
Abstract
Holliday junction-resolving enzymes are nucleases that are highly specific for the structure of the junction, to which they bind in dimeric form. Two symmetrically disposed cleavages are made. These are not simultaneous, but the second cleavage is accelerated relative to the first, so ensuring that bilateral cleavage occurs during the lifetime of the DNA-protein complex. In eukaryotic cells there are two known junction-resolving activities. GEN1 is similar to enzymes from lower organisms. A crystallographic structure of a fungal GEN1 bound to the product of resolution has been determined. These complexes are dimerized within the crystal lattice such that the strands of the products may be simply reconnected to form a junction. These structures suggest a trajectory for the resolution process.
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Affiliation(s)
- David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, UK
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27
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Kingston AW, Ponkratz C, Raleigh EA. Rpn (YhgA-Like) Proteins of Escherichia coli K-12 and Their Contribution to RecA-Independent Horizontal Transfer. J Bacteriol 2017; 199:e00787-16. [PMID: 28096446 PMCID: PMC5350276 DOI: 10.1128/jb.00787-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/09/2017] [Indexed: 01/21/2023] Open
Abstract
Bacteria use a variety of DNA-mobilizing enzymes to facilitate environmental niche adaptation via horizontal gene transfer. This has led to real-world problems, like the spread of antibiotic resistance, yet many mobilization proteins remain undefined. In the study described here, we investigated the uncharacterized family of YhgA-like transposase_31 (Pfam PF04754) proteins. Our primary focus was the genetic and biochemical properties of the five Escherichia coli K-12 members of this family, which we designate RpnA to RpnE, where Rpn represents recombination-promoting nuclease. We employed a conjugal system developed by our lab that demanded RecA-independent recombination following transfer of chromosomal DNA. Overexpression of RpnA (YhgA), RpnB (YfcI), RpnC (YadD), and RpnD (YjiP) increased RecA-independent recombination, reduced cell viability, and induced the expression of reporter of DNA damage. For the exemplar of the family, RpnA, mutational changes in proposed catalytic residues reduced or abolished all three phenotypes in concert. In vitro, RpnA displayed magnesium-dependent, calcium-stimulated DNA endonuclease activity with little, if any, sequence specificity and a preference for double-strand cleavage. We propose that Rpn/YhgA-like family nucleases can participate in gene acquisition processes.IMPORTANCE Bacteria adapt to new environments by obtaining new genes from other bacteria. Here, we characterize a set of genes that can promote the acquisition process by a novel mechanism. Genome comparisons had suggested the horizontal spread of the genes for the YhgA-like family of proteins through bacteria. Although annotated as transposase_31, no member of the family has previously been characterized experimentally. We show that four Escherichia coli K-12 paralogs contribute to a novel RecA-independent recombination mechanism in vivo For RpnA, we demonstrate in vitro action as a magnesium-dependent, calcium-stimulated nonspecific DNA endonuclease. The cleavage products are capable of providing priming sites for DNA polymerase, which can enable DNA joining by primer-template switching.
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Abstract
Efficacy of de novo gene synthesis largely depends on the quality of overlapping oligonucleotides used as template for PCR assembly. The error rate associated with current gene synthesis protocols limits the efficient and accurate production of synthetic genes, both in the small and large scales. Here, we analysed the ability of different endonuclease enzymes, which specifically recognize and cleave DNA mismatches resulting from incorrect impairments between DNA strands, to remove mutations accumulated in synthetic genes. The gfp gene, which encodes the green fluorescent protein, was artificially synthesized using an integrated protocol including an enzymatic mismatch cleavage step (EMC) following gene assembly. Functional and sequence analysis of resulting artificial genes revealed that number of deletions, insertions and substitutions was strongly reduced when T7 endonuclease I was used for mutation removal. This method diminished mutation frequency by eightfold relative to gene synthesis not incorporating an error correction step. Overall, EMC using T7 endonuclease I improved the population of error-free synthetic genes, resulting in an error frequency of 0.43 errors per 1 kb. Taken together, data presented here reveal that incorporation of a mutation-removal step including T7 endonuclease I can effectively improve the fidelity of artificial gene synthesis.
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Sharaf A, Mercati F, Elmaghraby I, Elbaz RM, Marei EM. Functional and comparative genome analysis of novel virulent actinophages belonging to Streptomyces flavovirens. BMC Microbiol 2017; 17:51. [PMID: 28257628 PMCID: PMC5336643 DOI: 10.1186/s12866-017-0940-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 01/24/2017] [Indexed: 11/25/2022] Open
Abstract
Background Next Generation Sequencing (NGS) technologies provide exciting possibilities for whole genome sequencing of a plethora of organisms including bacterial strains and phages, with many possible applications in research and diagnostics. No Streptomyces flavovirens phages have been sequenced to date; there is therefore a lack in available information about S. flavovirens phage genomics. We report biological and physiochemical features and use NGS to provide the complete annotated genomes for two new strains (Sf1 and Sf3) of the virulent phage Streptomyces flavovirens, isolated from Egyptian soil samples. Results The S. flavovirens phages (Sf1 and Sf3) examined in this study show higher adsorption rates (82 and 85%, respectively) than other actinophages, indicating a strong specificity to their host, and latent periods (15 and 30 min.), followed by rise periods of 45 and 30 min. As expected for actinophages, their burst sizes were 1.95 and 2.49 virions per mL. Both phages were stable and, as reported in previous experiments, showed a significant increase in their activity after sodium chloride (NaCl) and magnesium chloride (MgCl2.6H2O) treatments, whereas after zinc chloride (ZnCl2) application both phages showed a significant decrease in infection. The sequenced phage genomes are parts of a singleton cluster with sizes of 43,150 bp and 60,934 bp, respectively. Bioinformatics analyses and functional characterizations enabled the assignment of possible functions to 19 and 28 putative identified ORFs, which included phage structural proteins, lysis components and metabolic proteins. Thirty phams were identified in both phages, 10 (33.3%) of them with known function, which can be used in cluster prediction. Comparative genomic analysis revealed significant homology between the two phages, showing the highest hits among Sf1, Sf3 and the closest Streptomyces phage (VWB phages) in a specific 13Kb region. However, the phylogenetic analysis using the Major Capsid Protein (MCP) sequences highlighted that the isolated phages belong to the BG Streptomyces phage group but are clearly separated, representing a novel sub-cluster. Conclusion The results of this study provide the first physiological and genomic information for S. flavovirens phages and will be useful for pharmaceutical industries based on S. flavovirens and future phage evolution studies.
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Affiliation(s)
- A Sharaf
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt. .,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czechia.
| | - F Mercati
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR) of Italy, 90129, Palermo, Italy
| | - I Elmaghraby
- Central Lab. of Organic Agriculture, Agricultural Research Center, Giza, 12619, Egypt
| | - R M Elbaz
- Botany and Microbiology Department, Faculty of Science, Helwan University, Ain-Helwan, Cairo, 11970, Egypt
| | - E M Marei
- Microbiology Department, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt
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Khavnekar S, Dantu SC, Sedelnikova S, Ayora S, Rafferty J, Kale A. Structural insights into dynamics of RecU-HJ complex formation elucidates key role of NTR and stalk region toward formation of reactive state. Nucleic Acids Res 2016; 45:975-986. [PMID: 27903910 PMCID: PMC5314769 DOI: 10.1093/nar/gkw1165] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 11/04/2016] [Accepted: 11/09/2016] [Indexed: 11/16/2022] Open
Abstract
Holliday junction (HJ) resolving enzyme RecU is involved in DNA repair and recombination. We have determined the crystal structure of inactive mutant (D88N) of RecU from Bacillus subtilis in complex with a 12 base palindromic DNA fragment at a resolution of 3.2 Å. This structure shows the stalk region and the essential N-terminal region (NTR) previously unseen in our DNA unbound structure. The flexible nature of the NTR in solution was confirmed using SAXS. Thermofluor studies performed to assess the stability of RecU in complex with the arms of an HJ indicate that it confers stability. Further, we performed molecular dynamics (MD) simulations of wild type and an NTR deletion variant of RecU, with and without HJ. The NTR is observed to be highly flexible in simulations of the unbound RecU, in agreement with SAXS observations. These simulations revealed domain dynamics of RecU and their role in the formation of complex with HJ. The MD simulations also elucidate key roles of the NTR, stalk region, and breathing motion of RecU in the formation of the reactive state.
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Affiliation(s)
- Sagar Khavnekar
- UM-DAE Centre for Excellence in Basic Science, University of Mumbai, Vidhyanagari Campus, Mumbai 400098, India
| | - Sarath Chandra Dantu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, IIT Bombay, Mumbai 400076, India
| | - Svetlana Sedelnikova
- The Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Sylvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 28049 Madrid, Spain
| | - John Rafferty
- The Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Avinash Kale
- UM-DAE Centre for Excellence in Basic Science, University of Mumbai, Vidhyanagari Campus, Mumbai 400098, India
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Hoff G, Bertrand C, Zhang L, Piotrowski E, Chipot L, Bontemps C, Confalonieri F, McGovern S, Lecointe F, Thibessard A, Leblond P. Multiple and Variable NHEJ-Like Genes Are Involved in Resistance to DNA Damage in Streptomyces ambofaciens. Front Microbiol 2016; 7:1901. [PMID: 27965636 PMCID: PMC5124664 DOI: 10.3389/fmicb.2016.01901] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 11/14/2016] [Indexed: 11/26/2022] Open
Abstract
Non-homologous end-joining (NHEJ) is a double strand break (DSB) repair pathway which does not require any homologous template and can ligate two DNA ends together. The basic bacterial NHEJ machinery involves two partners: the Ku protein, a DNA end binding protein for DSB recognition and the multifunctional LigD protein composed a ligase, a nuclease and a polymerase domain, for end processing and ligation of the broken ends. In silico analyses performed in the 38 sequenced genomes of Streptomyces species revealed the existence of a large panel of NHEJ-like genes. Indeed, ku genes or ligD domain homologues are scattered throughout the genome in multiple copies and can be distinguished in two categories: the “core” NHEJ gene set constituted of conserved loci and the “variable” NHEJ gene set constituted of NHEJ-like genes present in only a part of the species. In Streptomyces ambofaciens ATCC23877, not only the deletion of “core” genes but also that of “variable” genes led to an increased sensitivity to DNA damage induced by electron beam irradiation. Multiple mutants of ku, ligase or polymerase encoding genes showed an aggravated phenotype compared to single mutants. Biochemical assays revealed the ability of Ku-like proteins to protect and to stimulate ligation of DNA ends. RT-qPCR and GFP fusion experiments suggested that ku-like genes show a growth phase dependent expression profile consistent with their involvement in DNA repair during spores formation and/or germination.
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Affiliation(s)
- Grégory Hoff
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Claire Bertrand
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Lingli Zhang
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Emilie Piotrowski
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Ludovic Chipot
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Cyril Bontemps
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Fabrice Confalonieri
- Institute for Integrative Biology of the Cell (I2BC), CEA, Centre National de la Recherche Scientifique, Université Paris-Sud Orsay, France
| | - Stephen McGovern
- Institut Micalis, INRA, AgroParisTech, Université Paris-Saclay Jouy-en-Josas, France
| | - François Lecointe
- Institut Micalis, INRA, AgroParisTech, Université Paris-Saclay Jouy-en-Josas, France
| | - Annabelle Thibessard
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Pierre Leblond
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
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Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease. Structure 2016; 24:1960-1971. [PMID: 27773688 DOI: 10.1016/j.str.2016.09.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 08/08/2016] [Accepted: 09/28/2016] [Indexed: 01/17/2023]
Abstract
Archaeal NucS nuclease was thought to degrade the single-stranded region of branched DNA, which contains flapped and splayed DNA. However, recent findings indicated that EndoMS, the orthologous enzyme of NucS, specifically cleaves double-stranded DNA (dsDNA) containing mismatched bases. In this study, we determined the structure of the EndoMS-DNA complex. The complex structure of the EndoMS dimer with dsDNA unexpectedly revealed that the mismatched bases were flipped out into binding sites, and the overall architecture most resembled that of restriction enzymes. The structure of the apo form was similar to the reported structure of Pyrococcus abyssi NucS, indicating that movement of the C-terminal domain from the resting state was required for activity. In addition, a model of the EndoMS-PCNA-DNA complex was preliminarily verified with electron microscopy. The structures strongly support the idea that EndoMS acts in a mismatch repair pathway.
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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: 50] [Impact Index Per Article: 6.3] [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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McClung DJ, Calixto A, Mosera MN, Kumar R, Neidle EL, Elliott KT. Novel heterologous bacterial system reveals enhanced susceptibility to DNA damage mediated by yqgF, a nearly ubiquitous and often essential gene. MICROBIOLOGY-SGM 2016; 162:1808-1821. [PMID: 27527105 DOI: 10.1099/mic.0.000355] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite its presence in most bacteria, yqgF remains one of only 13 essential genes of unknown function in Escherichia coli. Predictions of YqgF function often derive from sequence similarity to RuvC, the canonical Holliday junction resolvase. To clarify its role, we deleted yqgF from a bacterium where it is not essential, Acinetobacter baylyi ADP1. Loss of yqgF impaired growth and increased the frequency of transformation and allelic replacement (TAR). When E. coli yqgF was inserted in place of its A. baylyi chromosomal orthologue, wild-type growth and TAR were restored. Functional similarities of yqgF in both gamma-proteobacteria were further supported by defective 16S rRNA processing by the A. baylyi mutant, an effect previously shown in E. coli for a temperature-sensitive yqgF allele. However, our data question the validity of deducing YqgF function strictly by comparison to RuvC. A. baylyi studies indicated that YqgF and RuvC can function in opposition to one another. Relative to the wild type, the ΔyqgF mutant had increased TAR frequency and increased resistance to nalidixic acid, a DNA-damaging agent. In contrast, deletion of ruvC decreased TAR frequency and lowered resistance to nalidixic acid. YqgF, but not RuvC, appears to increase bacterial susceptibility to DNA damage, including UV radiation. Nevertheless, the effects of yqgF on growth and TAR frequency were found to depend on amino acids analogous to catalytically required residues of RuvC. This new heterologous system should facilitate future yqgF investigation by exploiting the viability of A. baylyi yqgF mutants. In addition, bioinformatic analysis showed that a non-essential gene immediately upstream of yqgF in A. baylyi and E. coli (yqgE) is similarly positioned in most gamma- and beta-proteobacteria. A small overlap in the coding sequences of these adjacent genes is typical. This conserved genetic arrangement raises the possibility of a functional partnership between yqgE and yqgF.
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Affiliation(s)
- Dylan J McClung
- Department of Biology, The College of New Jersey, Ewing, NJ, USA
| | - Abigail Calixto
- Department of Biology, The College of New Jersey, Ewing, NJ, USA
| | | | - Raagni Kumar
- Department of Biology, The College of New Jersey, Ewing, NJ, USA
| | - Ellen L Neidle
- Department of Microbiology, University of Georgia, Athens, GA, USA
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Dizman YA, Muratoglu H, Sandalli C, Nalcacioglu R, Demirbag Z. Chilo iridescent virus (CIV) ORF 012L encodes a protein with both exonuclease and endonuclease functions. Arch Virol 2016; 161:3029-37. [PMID: 27496102 DOI: 10.1007/s00705-016-3007-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 08/01/2016] [Indexed: 10/21/2022]
Abstract
Chilo iridescent virus (CIV) is the type member of the genus Iridovirus within the family Iridoviridae. The virions of CIV contain a single linear dsDNA molecule that is circularly permuted and terminally redundant. The genome of CIV contains an open reading frame (ORF 012L) encoding a protein homologous to exonuclease II of Schizosaccharomyces pombe. In this study, we focused on the characterization of CIV ORF 012L. The target ORF was cloned into the pET28a vector, expressed in E. coli strain BL21 (DE3) pLysS with an N-terminal His tag and purified to homogeneity by using Ni-NTA affinity chromatography. Biochemical characterization of the purified CIV 012L confirmed that this viral protein is a functional 5'-3' exonuclease that digests 3'-biotin-labelled oligonucleotides and linear double-stranded DNA (dsDNA) molecules from their 5' termini in a highly processive manner. CIV 012L also has a potent endonuclease activity on dsDNA in vitro. In addition, CIV 012L converted supercoiled plasmid DNA (replicative form I, RFI) into the open circular form (RFII) and then open circular form into linear form (RFIII). Endonuclease activity of CIV 012L was optimal in the presence of 10 mM Mg(2+) or 30 mM Mn(2+) ions and at 150 mM NaCl or KCl salt concentrations. The highest endonuclease activity was obtained at pH 8, and it reached a maximum at 55 °C. The CIV 012L protein showed deficiencies for both double- and single-stranded RNAs.
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Affiliation(s)
- Yesim Akturk Dizman
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey.,Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdoğan University, 53100, Rize, Turkey
| | - Hacer Muratoglu
- Department of Molecular Biology and Genetic, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Cemal Sandalli
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdoğan University, 53100, Rize, Turkey
| | - Remziye Nalcacioglu
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey.
| | - Zihni Demirbag
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey
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Hoff G, Bertrand C, Piotrowski E, Thibessard A, Leblond P. Implication of RuvABC and RecG in homologous recombination in Streptomyces ambofaciens. Res Microbiol 2016; 168:26-35. [PMID: 27424811 DOI: 10.1016/j.resmic.2016.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/04/2016] [Accepted: 07/04/2016] [Indexed: 10/21/2022]
Abstract
Most bacterial organisms rely on homologous recombination to repair DNA double-strand breaks and for the post-replicative repair of DNA single-strand gaps. Homologous recombination can be divided into three steps: (i) a pre-synaptic step in which the DNA 3'-OH ends are processed, (ii) a recA-dependent synaptic step allowing the invasion of an intact copy and the formation of Holliday junctions, and (iii) a post-synaptic step consisting of migration and resolution of these junctions. Currently, little is known about factors involved in homologous recombination, especially for the post-synaptic step. In Escherichia coli, branch migration and resolution are performed by the RuvABC complex, but could also rely on the RecG helicase in a redundant manner. In this study, we show that recG and ruvABC are well-conserved among Streptomyces. ΔruvABC, ΔrecG and ΔruvABC ΔrecG mutant strains were constructed. ΔruvABC ΔrecG is only slightly affected by exposure to DNA damage (UV). We also show that conjugational recombination decreases in the absence of RuvABC and RecG, but that intra-chromosomal recombination is not affected. These data suggest that RuvABC and RecG are indeed involved in homologous recombination in Streptomyces ambofaciens and that alternative factors are able to take over Holliday junction in Streptomyces.
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Affiliation(s)
- Grégory Hoff
- Université de Lorraine, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France; INRA, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France.
| | - Claire Bertrand
- Université de Lorraine, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France; INRA, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France.
| | - Emilie Piotrowski
- Université de Lorraine, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France; INRA, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France.
| | - Annabelle Thibessard
- Université de Lorraine, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France; INRA, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France.
| | - Pierre Leblond
- Université de Lorraine, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France; INRA, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France.
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DNA Damage and Pulmonary Hypertension. Int J Mol Sci 2016; 17:ijms17060990. [PMID: 27338373 PMCID: PMC4926518 DOI: 10.3390/ijms17060990] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/01/2016] [Accepted: 06/16/2016] [Indexed: 01/21/2023] Open
Abstract
Pulmonary hypertension (PH) is defined by a mean pulmonary arterial pressure over 25 mmHg at rest and is diagnosed by right heart catheterization. Among the different groups of PH, pulmonary arterial hypertension (PAH) is characterized by a progressive obstruction of distal pulmonary arteries, related to endothelial cell dysfunction and vascular cell proliferation, which leads to an increased pulmonary vascular resistance, right ventricular hypertrophy, and right heart failure. Although the primary trigger of PAH remains unknown, oxidative stress and inflammation have been shown to play a key role in the development and progression of vascular remodeling. These factors are known to increase DNA damage that might favor the emergence of the proliferative and apoptosis-resistant phenotype observed in PAH vascular cells. High levels of DNA damage were reported to occur in PAH lungs and remodeled arteries as well as in animal models of PH. Moreover, recent studies have demonstrated that impaired DNA-response mechanisms may lead to an increased mutagen sensitivity in PAH patients. Finally, PAH was linked with decreased breast cancer 1 protein (BRCA1) and DNA topoisomerase 2-binding protein 1 (TopBP1) expression, both involved in maintaining genome integrity. This review aims to provide an overview of recent evidence of DNA damage and DNA repair deficiency and their implication in PAH pathogenesis.
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Singh A, Bhagavat R, Vijayan M, Chandra N. A comparative analysis of the DNA recombination repair pathway in mycobacterial genomes. Tuberculosis (Edinb) 2016; 99:109-119. [PMID: 27450012 DOI: 10.1016/j.tube.2016.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/19/2016] [Accepted: 04/28/2016] [Indexed: 10/21/2022]
Abstract
In prokaryotes, repair by homologous recombination provides a major means to reinstate the genetic information lost in DNA damage. Recombination repair pathway in mycobacteria has multiple differences as compared to that in Escherichia coli. Of about 20 proteins known to be involved in the pathway, a set of 9 proteins, namely, RecF, RecO, RecR, RecA, SSBa, RuvA, RuvB and RuvC was found to be indispensable among the 43 mycobacterial strains. A domain level analysis indicated that most domains involved in recombination repair are unique to these proteins and are present as single copies in the genomes. Synteny analysis reveals that the gene order of proteins involved in the pathway is not conserved, suggesting that they may be regulated differently in different species. Sequence conservation among the same protein from different strains suggests the importance of RecO-RecA and RecFOR-RecA presynaptic pathways in the repair of double strand-breaks and single strand-breaks respectively. New annotations obtained from the analysis, include identification of a protein with a probable Holliday junction binding role present in 41 mycobacterial genomes and that of a RecB-like nuclease, containing a cas4 domain, present in 42 genomes. New insights into the binding of small molecules to the relevant proteins are provided by binding pocket analysis using three dimensional structural models. Analysis of the various features of the recombination repair pathway, presented here, is likely to provide a framework for further exploring stress response and emergence of drug resistance in mycobacteria.
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Affiliation(s)
- Amandeep Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Raghu Bhagavat
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - M Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India.
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39
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Zhang D, Burroughs AM, Vidal ND, Iyer LM, Aravind L. Transposons to toxins: the provenance, architecture and diversification of a widespread class of eukaryotic effectors. Nucleic Acids Res 2016; 44:3513-33. [PMID: 27060143 PMCID: PMC4857004 DOI: 10.1093/nar/gkw221] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/22/2016] [Indexed: 01/13/2023] Open
Abstract
Enzymatic effectors targeting nucleic acids, proteins and other cellular components are the mainstay of conflicts across life forms. Using comparative genomics we identify a large class of eukaryotic proteins, which include effectors from oomycetes, fungi and other parasites. The majority of these proteins have a characteristic domain architecture with one of several N-terminal 'Header' domains, which are predicted to play a role in trafficking of these effectors, including a novel version of the Ubiquitin fold. The Headers are followed by one or more diverse C-terminal domains, such as restriction endonuclease (REase), protein kinase, HNH endonuclease, LK-nuclease (a RNase) and multiple distinct peptidase domains, which are predicted to carry their toxicity determinants. The most common types of these proteins appear to have originated from prokaryotic transposases (e.g. TN7 and Mu) and combine a CDC6/ORC1-STAND clade NTPase domain with a C-terminal REase domain. Other than the so-called Crinkler effectors of oomycetes and fungi, these effectors are encoded by other eukaryotic parasites such as trypanosomatids (the RHS proteins) and the rhizarian Plasmodiophora, and symbionts like Capsaspora Remarkably, we also find these proteins in free-living eukaryotes, including several viridiplantae, fungi, amoebozoans and animals. These versions might either still be transposons or function in other poorly understood eukaryote-specific inter-organismal and inter-genomic conflicts. These include the Medea1 selfish element of Tribolium that spreads via post-zygotic killing. We present a unified mechanism for the recombination-dependent diversification and action of this widespread class of molecular weaponry deployed across diverse conflicts ranging from parasitic to free-living forms.
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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
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Newton D Vidal
- 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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40
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Nautiyal A, Rani PS, Sharples GJ, Muniyappa K. Mycobacterium tuberculosis RuvX is a Holliday junction resolvase formed by dimerisation of the monomeric YqgF nuclease domain. Mol Microbiol 2016; 100:656-74. [PMID: 26817626 DOI: 10.1111/mmi.13338] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2016] [Indexed: 01/07/2023]
Abstract
The Mycobacterium tuberculosis genome possesses homologues of the ruvC and yqgF genes that encode putative Holliday junction (HJ) resolvases. However, their gene expression profiles and enzymatic properties have not been experimentally defined. Here we report that expression of ruvC and yqgF is induced in response to DNA damage. Protein-DNA interaction assays with purified M. tuberculosis RuvC (MtRuvC) and YqgF (MtRuvX) revealed that both associate preferentially with HJ DNA, albeit with differing affinities. Although both MtRuvC and MtRuvX cleaved HJ DNA in vitro, the latter displayed robust HJ resolution activity by symmetrically related, paired incisions. MtRuvX showed a higher binding affinity for the HJ structure over other branched recombination and replication intermediates. An MtRuvX(D28N) mutation, eliminating one of the highly conserved catalytic residues in this class of endonucleases, dramatically reduced its ability to cleave HJ DNA. Furthermore, a unique cysteine (C38) fulfils a crucial role in HJ cleavage, consistent with disulfide-bond mediated dimerization being essential for MtRuvX activity. In contrast, E. coli YqgF is monomeric and exhibits no branched DNA binding or cleavage activity. These results fit with a functional modification of YqgF in M. tuberculosis so that it can act as a dimeric HJ resolvase analogous to that of RuvC.
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Affiliation(s)
- Astha Nautiyal
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - P Sandhya Rani
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Gary J Sharples
- Department of Chemistry, School of Biological and Biomedical Sciences, Biophysical Sciences Institute, University of Durham, DH1 3LE, UK
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
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41
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Kumar A, Beloglazova N, Bundalovic-Torma C, Phanse S, Deineko V, Gagarinova A, Musso G, Vlasblom J, Lemak S, Hooshyar M, Minic Z, Wagih O, Mosca R, Aloy P, Golshani A, Parkinson J, Emili A, Yakunin AF, Babu M. Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli. Cell Rep 2016; 14:648-661. [PMID: 26774489 DOI: 10.1016/j.celrep.2015.12.060] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/08/2015] [Accepted: 12/10/2015] [Indexed: 11/27/2022] Open
Abstract
As antibiotic resistance is increasingly becoming a public health concern, an improved understanding of the bacterial DNA damage response (DDR), which is commonly targeted by antibiotics, could be of tremendous therapeutic value. Although the genetic components of the bacterial DDR have been studied extensively in isolation, how the underlying biological pathways interact functionally remains unclear. Here, we address this by performing systematic, unbiased, quantitative synthetic genetic interaction (GI) screens and uncover widespread changes in the GI network of the entire genomic integrity apparatus of Escherichia coli under standard and DNA-damaging growth conditions. The GI patterns of untreated cultures implicated two previously uncharacterized proteins (YhbQ and YqgF) as nucleases, whereas reorganization of the GI network after DNA damage revealed DDR roles for both annotated and uncharacterized genes. Analyses of pan-bacterial conservation patterns suggest that DDR mechanisms and functional relationships are near universal, highlighting a modular and highly adaptive genomic stress response.
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Affiliation(s)
- Ashwani Kumar
- Department of Computer Science, University of Regina, Regina, SK S4S 0A2, Canada
| | - Natalia Beloglazova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Cedoljub Bundalovic-Torma
- Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G OX4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sadhna Phanse
- Terrence Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Viktor Deineko
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Alla Gagarinova
- Terrence Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Gabriel Musso
- Department of Medicine, Harvard Medical School and Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - James Vlasblom
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Sofia Lemak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Mohsen Hooshyar
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Zoran Minic
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Omar Wagih
- Terrence Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Roberto Mosca
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, c/Baldiri i Reixac 10-12, Barcelona, 08028, Catalonia, Spain
| | - Patrick Aloy
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, c/Baldiri i Reixac 10-12, Barcelona, 08028, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, Barcelona, 08010, Catalonia, Spain
| | - Ashkan Golshani
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - John Parkinson
- Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G OX4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Andrew Emili
- Terrence Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada.
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42
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Chan YW, West S. GEN1 promotes Holliday junction resolution by a coordinated nick and counter-nick mechanism. Nucleic Acids Res 2015; 43:10882-92. [PMID: 26578604 PMCID: PMC4678824 DOI: 10.1093/nar/gkv1207] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/07/2015] [Accepted: 10/27/2015] [Indexed: 11/25/2022] Open
Abstract
Holliday junctions (HJs) that physically link sister chromatids or homologous chromosomes are formed as intermediates during DNA repair by homologous recombination. Persistent recombination intermediates are acted upon by structure-selective endonucleases that are required for proper chromosome segregation at mitosis. Here, we have purified full-length human GEN1 protein and show that it promotes Holliday junction resolution by a mechanism that is analogous to that exhibited by the prototypic HJ resolvase E. coli RuvC. We find that GEN1 cleaves HJs by a nick and counter-nick mechanism involving dual co-ordinated incisions that lead to the formation of ligatable nicked duplex products. As observed with RuvC, cleavage of the first strand is rate limiting, while second strand cleavage is rapid. In contrast to RuvC, however, GEN1 is largely monomeric in solution, but dimerizes on the HJ. Using HJs containing non-cleavable phosphorothioate-containing linkages in one strand, we show that the two incisions can be uncoupled and that the first nick occurs upon GEN1 dimerization at the junction. These results indicate that the mechanism of HJ resolution is largely conserved from bacteria to man, despite a lack of sequence homology between the resolvases.
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Affiliation(s)
- Ying Wai Chan
- Francis Crick Institute, Clare Hall Laboratories, South Mimms, Herts EN6 3LD, UK
| | - Stephen West
- Francis Crick Institute, Clare Hall Laboratories, South Mimms, Herts EN6 3LD, UK
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43
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Zhou C, Pourmal S, Pavletich NP. Dna2 nuclease-helicase structure, mechanism and regulation by Rpa. eLife 2015; 4. [PMID: 26491943 PMCID: PMC4716839 DOI: 10.7554/elife.09832] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/20/2015] [Indexed: 12/04/2022] Open
Abstract
The Dna2 nuclease-helicase maintains genomic integrity by processing DNA double-strand breaks, Okazaki fragments and stalled replication forks. Dna2 requires ssDNA ends, and is dependent on the ssDNA-binding protein Rpa, which controls cleavage polarity. Here we present the 2.3 Å structure of intact mouse Dna2 bound to a 15-nucleotide ssDNA. The nuclease active site is embedded in a long, narrow tunnel through which the DNA has to thread. The helicase domain is required for DNA binding but not threading. We also present the structure of a flexibly-tethered Dna2-Rpa interaction that recruits Dna2 to Rpa-coated DNA. We establish that a second Dna2-Rpa interaction is mutually exclusive with Rpa-DNA interactions and mediates the displacement of Rpa from ssDNA. This interaction occurs at the nuclease tunnel entrance and the 5’ end of the Rpa-DNA complex. Hence, it only displaces Rpa from the 5’ but not 3’ end, explaining how Rpa regulates cleavage polarity. DOI:http://dx.doi.org/10.7554/eLife.09832.001 DNA carries the genetic information that is essential for organisms to survive and reproduce. It is made of two strands that twist together to form a double helix. However, these strands can be damaged when the DNA is copied before a cell divides, or by exposure to radiation or hazardous chemicals. To prevent this damage from causing serious harm to an organism, cells activate processes that rapidly repair the damaged DNA. “Homologous recombination” is one way in which cells can repair damage that has caused both strands of the DNA to break in a particular place. In the first step, several enzymes trim one of the two DNA strands at each broken end to leave single stranded “tails”. Dna2 is one enzyme that is involved in making these tails, but it can only bind to single-stranded DNA so it only acts after another enzyme has made some initial cuts. The exposed single stranded DNA then searches for an intact copy of itself elsewhere in the genome, which promotes its repair. It is important that only one of the two DNA strands is trimmed at each end otherwise the repair will fail. A protein called Rpa is bound to the DNA and is required for Dna2 to correctly trim the DNA. However, it is not clear exactly how Rpa2 regulates Dna2. Zhou et al. used a technique called X-ray crystallography to analyze the three-dimensional structures of Dna2 when it is bound to single stranded DNA and when it is bound to Rpa. The experiments show that Dna2 adopts a cylindrical shape with a tunnel through which the single-stranded DNA passes through. The region of Dna2 that is capable of trimming DNA – which is called the nuclease domain – is embedded within the tunnel. The entrance to the tunnel is too narrow to allow double-stranded DNA to enter, so this explains why Dna2 can only act on double-stranded DNA that already has a small single-stranded section at the end. Inside the tunnel, Dna2 displaces Rpa from one of the strands, which allows Dna2 to trim the DNA. However, other molecules of Rpa remain firmly bound to the other strand to protect it from Dna2. These enzymes also act in a similar way to trim DNA before it is copied in preparation for cell division. Zhou et al.’s findings provide an explanation for how Rpa determines which strand of DNA is trimmed by Dna2. Further work is needed to understand how Dna2 and Rpa work with other enzymes to trim DNA. DOI:http://dx.doi.org/10.7554/eLife.09832.002
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Affiliation(s)
- Chun Zhou
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Sergei Pourmal
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Nikola P Pavletich
- Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, United States
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44
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Shmakov S, Abudayyeh OO, Makarova KS, Wolf YI, Gootenberg JS, Semenova E, Minakhin L, Joung J, Konermann S, Severinov K, Zhang F, Koonin EV. Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems. Mol Cell 2015; 60:385-97. [PMID: 26593719 DOI: 10.1016/j.molcel.2015.10.008] [Citation(s) in RCA: 775] [Impact Index Per Article: 86.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/01/2015] [Accepted: 10/02/2015] [Indexed: 02/06/2023]
Abstract
Microbial CRISPR-Cas systems are divided into Class 1, with multisubunit effector complexes, and Class 2, with single protein effectors. Currently, only two Class 2 effectors, Cas9 and Cpf1, are known. We describe here three distinct Class 2 CRISPR-Cas systems. The effectors of two of the identified systems, C2c1 and C2c3, contain RuvC-like endonuclease domains distantly related to Cpf1. The third system, C2c2, contains an effector with two predicted HEPN RNase domains. Whereas production of mature CRISPR RNA (crRNA) by C2c1 depends on tracrRNA, C2c2 crRNA maturation is tracrRNA independent. We found that C2c1 systems can mediate DNA interference in a 5'-PAM-dependent fashion analogous to Cpf1. However, unlike Cpf1, which is a single-RNA-guided nuclease, C2c1 depends on both crRNA and tracrRNA for DNA cleavage. Finally, comparative analysis indicates that Class 2 CRISPR-Cas systems evolved on multiple occasions through recombination of Class 1 adaptation modules with effector proteins acquired from distinct mobile elements.
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Affiliation(s)
- Sergey Shmakov
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia; NCBI, NLM, NIH, Bethesda, MD 20894, USA
| | - Omar O Abudayyeh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - Jonathan S Gootenberg
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ekaterina Semenova
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Leonid Minakhin
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Julia Joung
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Silvana Konermann
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Konstantin Severinov
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia; Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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45
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Abstract
DNA exonucleases, enzymes that hydrolyze phosphodiester bonds in DNA from a free end, play important cellular roles in DNA repair, genetic recombination and mutation avoidance in all organisms. This article reviews the structure, biochemistry, and biological functions of the 17 exonucleases currently identified in the bacterium Escherichia coli. These include the exonucleases associated with DNA polymerases I (polA), II (polB), and III (dnaQ/mutD); Exonucleases I (xonA/sbcB), III (xthA), IV, VII (xseAB), IX (xni/xgdG), and X (exoX); the RecBCD, RecJ, and RecE exonucleases; SbcCD endo/exonucleases; the DNA exonuclease activities of RNase T (rnt) and Endonuclease IV (nfo); and TatD. These enzymes are diverse in terms of substrate specificity and biochemical properties and have specialized biological roles. Most of these enzymes fall into structural families with characteristic sequence motifs, and members of many of these families can be found in all domains of life.
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46
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Lopes-Kulishev CO, Alves IR, Valencia EY, Pidhirnyj MI, Fernández-Silva FS, Rodrigues TR, Guzzo CR, Galhardo RS. Functional characterization of two SOS-regulated genes involved in mitomycin C resistance in Caulobacter crescentus. DNA Repair (Amst) 2015; 33:78-89. [DOI: 10.1016/j.dnarep.2015.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 06/24/2015] [Accepted: 06/26/2015] [Indexed: 10/23/2022]
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47
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Functional coupling of duplex translocation to DNA cleavage in a type I restriction enzyme. PLoS One 2015; 10:e0128700. [PMID: 26039067 PMCID: PMC4454674 DOI: 10.1371/journal.pone.0128700] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 04/29/2015] [Indexed: 11/20/2022] Open
Abstract
Type I restriction-modification enzymes are multifunctional heteromeric complexes with DNA cleavage and ATP-dependent DNA translocation activities located on motor subunit HsdR. Functional coupling of DNA cleavage and translocation is a hallmark of the Type I restriction systems that is consistent with their proposed role in horizontal gene transfer. DNA cleavage occurs at nonspecific sites distant from the cognate recognition sequence, apparently triggered by stalled translocation. The X-ray crystal structure of the complete HsdR subunit from E. coli plasmid R124 suggested that the triggering mechanism involves interdomain contacts mediated by ATP. In the present work, in vivo and in vitro activity assays and crystal structures of three mutants of EcoR124I HsdR designed to probe this mechanism are reported. The results indicate that interdomain engagement via ATP is indeed responsible for signal transmission between the endonuclease and helicase domains of the motor subunit. A previously identified sequence motif that is shared by the RecB nucleases and some Type I endonucleases is implicated in signaling.
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48
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Damke PP, Dhanaraju R, Marsin S, Radicella JP, Rao DN. The nuclease activities of both the Smr domain and an additional LDLK motif are required for an efficient anti-recombination function of Helicobacter pylori MutS2. Mol Microbiol 2015; 96:1240-56. [PMID: 25800579 DOI: 10.1111/mmi.13003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2015] [Indexed: 12/23/2022]
Abstract
Helicobacter pylori, a human pathogen, is a naturally and constitutively competent bacteria, displaying a high rate of intergenomic recombination. While recombination events are essential for evolution and adaptation of H. pylori to dynamic gastric niches and new hosts, such events should be regulated tightly to maintain genomic integrity. Here, we analyze the role of the nuclease activity of MutS2, a protein that limits recombination during transformation in H. pylori. In previously studied MutS2 proteins, the C-terminal Smr domain was mapped as the region responsible for its nuclease activity. We report here that deletion of Smr domain does not completely abolish the nuclease activity of HpMutS2. Using bioinformatics analysis and mutagenesis, we identified an additional and novel nuclease motif (LDLK) at the N-terminus of HpMutS2 unique to Helicobacter and related ε-proteobacterial species. A single point mutation (D30A) in the LDLK motif and the deletion of Smr domain resulted in ∼ 5-10-fold loss of DNA cleavage ability of HpMutS2. Interestingly, the mutant forms of HpMutS2 wherein the LDLK motif was mutated or the Smr domain was deleted were unable to complement the hyper-recombination phenotype of a mutS2(-) strain, suggesting that both nuclease sites are indispensable for an efficient anti-recombinase activity of HpMutS2.
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Affiliation(s)
- Prashant P Damke
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Rajkumar Dhanaraju
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Stéphanie Marsin
- Institute of Cellular and Molecular Radiobiology, CEA, Fontenay-aux-Roses, France.,INSERM UMR967, Fontenay-aux-Roses, France.,Universités Paris Diderot et Paris Sud, Fontenay-aux-Roses, France
| | - Juan Pablo Radicella
- Institute of Cellular and Molecular Radiobiology, CEA, Fontenay-aux-Roses, France.,INSERM UMR967, Fontenay-aux-Roses, France.,Universités Paris Diderot et Paris Sud, Fontenay-aux-Roses, France
| | - Desirazu N Rao
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
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49
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Huang Q, Li Y, Zeng C, Song T, Yan Z, Ni J, She Q, Shen Y. Genetic analysis of the Holliday junction resolvases Hje and Hjc in Sulfolobus islandicus. Extremophiles 2015; 19:505-14. [PMID: 25644236 DOI: 10.1007/s00792-015-0734-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/20/2015] [Indexed: 11/26/2022]
Abstract
The in vivo functions of Hje and Hjc, two Holliday junction resolvases in Sulfolobus islandicus were investigated. We found that deletion of either hje or hjc had no effect on normal cell growth, while deletion of both hje and hjc is lethal. Although Hjc is the conserved resolvase in all archaea, the hje deletion rather than hjc deletion rendered cells more sensitive to DNA-damaging agents such as hydroxyurea, cisplatin, and methyl methanesulfonate than the wild type (WT). Intriguingly, the sensitivity of Δhje could not be rescued by ectopic expression of Hje from a plasmid and Hje overexpression slowed growth and large cells appeared with more than two genome equivalents. We showed that Hje was maintained at a low level in WT cells. Furthermore, transcriptomic microarray analysis revealed that the abundance of transcripts of many genes including those involved in DNA replication, repair, transcription regulation, and cell division changed drastically in the Hje-overexpressed strain. However, only limited genes were up- or downregulated in the hje deletion strain. Our findings collectively suggest that Hje is the primary resolvase involved in DNA repair and its expression must be tightly controlled in cells.
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Affiliation(s)
- Qihong Huang
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nan Rd., Jinan, 250100, People's Republic of China
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Kurata T, Nakanishi S, Hashimoto M, Taoka M, Yamazaki Y, Isobe T, Kato JI. Novel essential gene Involved in 16S rRNA processing in Escherichia coli. J Mol Biol 2014; 427:955-965. [PMID: 25545592 DOI: 10.1016/j.jmb.2014.12.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 12/21/2022]
Abstract
Biogenesis of ribosomes is a complex process mediated by many factors. While its transcription proceeds, ribosomal RNA (rRNA) folds itself into a characteristic three-dimensional structure through interaction with ribosomal proteins, during which its ends are processed. Here, we show that the essential protein YqgF, a RuvC family protein with an RNase-H-like motif, is involved in the processing of pre-16S rRNA during ribosome maturation. Indeed, pre-16S rRNA accumulated in cells of a temperature-sensitive yqgF mutant (yqgF(ts)) cultured at a non-permissive temperature. In addition, purified YqgF was shown to process the 5' end of pre-16S rRNA within 70S ribosomes in vitro. Mass spectrometry analysis of the total proteins in the yqgF(ts) mutant cells showed that the expression of genes containing multiple Shine-Dalgarno-like sequences was observed to be lower than in wild type. These results are interpreted to indicate that YqgF is involved in a novel enzymic activity necessary for the processing of pre-16S rRNA, thereby affecting elongation of translation.
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Affiliation(s)
- Tatsuaki Kurata
- Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Shinobu Nakanishi
- Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Masayuki Hashimoto
- Institute of Molecular Medicine, Medical College, National Cheng-Kung University, Tainan City 704, Taiwan; Infectious Disease and Signal Transduction Center, Medical College, National Cheng-Kung University, Tainan City 704, Taiwan
| | - Masato Taoka
- Department of Chemistry, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Yukiko Yamazaki
- Genetic Informatics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Jun-Ichi Kato
- Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Tokyo 192-0397, Japan.
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