1
|
Wenck BR, Vickerman RL, Burkhart BW, Santangelo TJ. Archaeal histone-based chromatin structures regulate transcription elongation rates. Commun Biol 2024; 7:236. [PMID: 38413771 PMCID: PMC10899632 DOI: 10.1038/s42003-024-05928-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 02/16/2024] [Indexed: 02/29/2024] Open
Abstract
Many archaea encode and express histone proteins to compact their genomes. Archaeal and eukaryotic histones share a near-identical fold that permits DNA wrapping through select histone-DNA contacts to generate chromatin-structures that must be traversed by RNA polymerase (RNAP) to generate transcripts. As archaeal histones can spontaneously assemble with a single histone isoform, single-histone chromatin variants provide an idealized platform to detail the impacts of distinct histone-DNA contacts on transcription efficiencies and to detail the role of the conserved cleavage stimulatory factor, Transcription Factor S (TFS), in assisting RNAP through chromatin landscapes. We demonstrate that substitution of histone residues that modify histone-DNA contacts or the three-dimensional chromatin structure result in radically altered transcription elongation rates and pausing patterns. Chromatin-barriers slow and pause RNAP, providing regulatory potential. The modest impacts of TFS on elongation rates through chromatin landscapes is correlated with TFS-dispensability from the archaeon Thermococcus kodakarensis. Our results detail the importance of distinct chromatin structures for archaeal gene expression and provide a unique perspective on the evolution of, and regulatory strategies imposed by, eukaryotic chromatin.
Collapse
Affiliation(s)
- Breanna R Wenck
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Robert L Vickerman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Brett W Burkhart
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| |
Collapse
|
2
|
Caffrey PJ, Eckenroth BE, Burkhart BW, Zatopek KM, McClung CM, Santangelo TJ, Doublié S, Gardner AF. Thermococcus kodakarensis TK0353 is a novel AP lyase with a new fold. J Biol Chem 2024; 300:105503. [PMID: 38013090 PMCID: PMC10731606 DOI: 10.1016/j.jbc.2023.105503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 11/02/2023] [Accepted: 11/12/2023] [Indexed: 11/29/2023] Open
Abstract
Hyperthermophilic organisms thrive in extreme environments prone to high levels of DNA damage. Growth at high temperature stimulates DNA base hydrolysis resulting in apurinic/apyrimidinic (AP) sites that destabilize the genome. Organisms across all domains have evolved enzymes to recognize and repair AP sites to maintain genome stability. The hyperthermophilic archaeon Thermococcus kodakarensis encodes several enzymes to repair AP site damage including the essential AP endonuclease TK endonuclease IV. Recently, using functional genomic screening, we discovered a new family of AP lyases typified by TK0353. Here, using biochemistry, structural analysis, and genetic deletion, we have characterized the TK0353 structure and function. TK0353 lacks glycosylase activity on a variety of damaged bases and is therefore either a monofunctional AP lyase or may be a glycosylase-lyase on a yet unidentified substrate. The crystal structure of TK0353 revealed a novel fold, which does not resemble other known DNA repair enzymes. The TK0353 gene is not essential for T. kodakarensis viability presumably because of redundant base excision repair enzymes involved in AP site processing. In summary, TK0353 is a novel AP lyase unique to hyperthermophiles that provides redundant repair activity necessary for genome maintenance.
Collapse
Affiliation(s)
| | - Brian E Eckenroth
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA
| | - Brett W Burkhart
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | | | | | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA
| | | |
Collapse
|
3
|
Zatopek KM, Burkhart BW, Morgan RD, Gehring AM, Scott KA, Santangelo TJ, Gardner AF. The Hyperthermophilic Restriction-Modification Systems of Thermococcus kodakarensis Protect Genome Integrity. Front Microbiol 2021; 12:657356. [PMID: 34093470 PMCID: PMC8172983 DOI: 10.3389/fmicb.2021.657356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/20/2021] [Indexed: 11/18/2022] Open
Abstract
Thermococcus kodakarensis (T. kodakarensis), a hyperthermophilic, genetically accessible model archaeon, encodes two putative restriction modification (R-M) defense systems, TkoI and TkoII. TkoI is encoded by TK1460 while TkoII is encoded by TK1158. Bioinformative analysis suggests both R-M enzymes are large, fused methyltransferase (MTase)-endonuclease polypeptides that contain both restriction endonuclease (REase) activity to degrade foreign invading DNA and MTase activity to methylate host genomic DNA at specific recognition sites. In this work, we demonsrate T. kodakarensis strains deleted for either or both R-M enzymes grow more slowly but display significantly increased competency compared to strains with intact R-M systems, suggesting that both TkoI and TkoII assist in maintenance of genomic integrity in vivo and likely protect against viral- or plasmid-based DNA transfers. Pacific Biosciences single molecule real-time (SMRT) sequencing of T. kodakarensis strains containing both, one or neither R-M systems permitted assignment of the recognition sites for TkoI and TkoII and demonstrated that both R-M enzymes are TypeIIL; TkoI and TkoII methylate the N6 position of adenine on one strand of the recognition sequences GTGAAG and TTCAAG, respectively. Further in vitro biochemical characterization of the REase activities reveal TkoI and TkoII cleave the DNA backbone GTGAAG(N)20/(N)18 and TTCAAG(N)10/(N)8, respectively, away from the recognition sequences, while in vitro characterization of the MTase activities reveal transfer of tritiated S-adenosyl methionine by TkoI and TkoII to their respective recognition sites. Together these results demonstrate TkoI and TkoII restriction systems are important for protecting T. kodakarensis genome integrity from invading foreign DNA.
Collapse
Affiliation(s)
| | - Brett W Burkhart
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | | | | | - Kristin A Scott
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | | |
Collapse
|
4
|
Sanders TJ, Ullah F, Gehring AM, Burkhart BW, Vickerman RL, Fernando S, Gardner AF, Ben-Hur A, Santangelo TJ. Extended Archaeal Histone-Based Chromatin Structure Regulates Global Gene Expression in Thermococcus kodakarensis. Front Microbiol 2021; 12:681150. [PMID: 34054788 PMCID: PMC8155482 DOI: 10.3389/fmicb.2021.681150] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
Histone proteins compact and organize DNA resulting in a dynamic chromatin architecture impacting DNA accessibility and ultimately gene expression. Eukaryotic chromatin landscapes are structured through histone protein variants, epigenetic marks, the activities of chromatin-remodeling complexes, and post-translational modification of histone proteins. In most Archaea, histone-based chromatin structure is dominated by the helical polymerization of histone proteins wrapping DNA into a repetitive and closely gyred configuration. The formation of the archaeal-histone chromatin-superhelix is a regulatory force of adaptive gene expression and is likely critical for regulation of gene expression in all histone-encoding Archaea. Single amino acid substitutions in archaeal histones that block formation of tightly packed chromatin structures have profound effects on cellular fitness, but the underlying gene expression changes resultant from an altered chromatin landscape have not been resolved. Using the model organism Thermococcus kodakarensis, we genetically alter the chromatin landscape and quantify the resultant changes in gene expression, including unanticipated and significant impacts on provirus transcription. Global transcriptome changes resultant from varying chromatin landscapes reveal the regulatory importance of higher-order histone-based chromatin architectures in regulating archaeal gene expression.
Collapse
Affiliation(s)
- Travis J. Sanders
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Fahad Ullah
- Department of Computer Science, Colorado State University, Fort Collins, CO, United States
| | - Alexandra M. Gehring
- Molecular Enzymology Division, New England Biolabs, Inc., Ipswich, MA, United States
| | - Brett W. Burkhart
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Robert L. Vickerman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Sudili Fernando
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Andrew F. Gardner
- Molecular Enzymology Division, New England Biolabs, Inc., Ipswich, MA, United States
| | - Asa Ben-Hur
- Department of Computer Science, Colorado State University, Fort Collins, CO, United States
| | - Thomas J. Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| |
Collapse
|
5
|
Sas-Chen A, Thomas JM, Matzov D, Taoka M, Nance KD, Nir R, Bryson KM, Shachar R, Liman GLS, Burkhart BW, Gamage ST, Nobe Y, Briney CA, Levy MJ, Fuchs RT, Robb GB, Hartmann J, Sharma S, Lin Q, Florens L, Washburn MP, Isobe T, Santangelo TJ, Shalev-Benami M, Meier JL, Schwartz S. Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping. Nature 2020; 583:638-643. [PMID: 32555463 PMCID: PMC8130014 DOI: 10.1038/s41586-020-2418-2] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 03/26/2020] [Indexed: 12/14/2022]
Abstract
N4-acetylcytidine (ac4C) is an ancient and highly conserved RNA modification that is present on tRNA and rRNA and has recently been investigated in eukaryotic mRNA1-3. However, the distribution, dynamics and functions of cytidine acetylation have yet to be fully elucidated. Here we report ac4C-seq, a chemical genomic method for the transcriptome-wide quantitative mapping of ac4C at single-nucleotide resolution. In human and yeast mRNAs, ac4C sites are not detected but can be induced-at a conserved sequence motif-via the ectopic overexpression of eukaryotic acetyltransferase complexes. By contrast, cross-evolutionary profiling revealed unprecedented levels of ac4C across hundreds of residues in rRNA, tRNA, non-coding RNA and mRNA from hyperthermophilic archaea. Ac4C is markedly induced in response to increases in temperature, and acetyltransferase-deficient archaeal strains exhibit temperature-dependent growth defects. Visualization of wild-type and acetyltransferase-deficient archaeal ribosomes by cryo-electron microscopy provided structural insights into the temperature-dependent distribution of ac4C and its potential thermoadaptive role. Our studies quantitatively define the ac4C landscape, providing a technical and conceptual foundation for elucidating the role of this modification in biology and disease4-6.
Collapse
Affiliation(s)
- Aldema Sas-Chen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Justin M Thomas
- National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Donna Matzov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Kellie D Nance
- National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Ronit Nir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Keri M Bryson
- National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Ran Shachar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Geraldy L S Liman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Brett W Burkhart
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Chloe A Briney
- National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | | | - Ryan T Fuchs
- RNA Research Division, New England Biolabs, Inc, Ipswich, MA, USA
| | - G Brett Robb
- RNA Research Division, New England Biolabs, Inc, Ipswich, MA, USA
| | - Jesse Hartmann
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sunny Sharma
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Qishan Lin
- RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY, USA
| | | | | | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Moran Shalev-Benami
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Jordan L Meier
- National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
6
|
Gehring AM, Zatopek KM, Burkhart BW, Potapov V, Santangelo TJ, Gardner AF. Biochemical reconstitution and genetic characterization of the major oxidative damage base excision DNA repair pathway in Thermococcus kodakarensis. DNA Repair (Amst) 2020; 86:102767. [PMID: 31841800 PMCID: PMC8061334 DOI: 10.1016/j.dnarep.2019.102767] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/22/2019] [Accepted: 12/04/2019] [Indexed: 11/16/2022]
Abstract
Reactive oxygen species drive the oxidation of guanine to 8-oxoguanine (8oxoG), which threatens genome integrity. The repair of 8oxoG is carried out by base excision repair enzymes in Bacteria and Eukarya, however, little is known about archaeal 8oxoG repair. This study identifies a member of the Ogg-subfamily archaeal GO glycosylase (AGOG) in Thermococcus kodakarensis, an anaerobic, hyperthermophilic archaeon, and delineates its mechanism, kinetics, and substrate specificity. TkoAGOG is the major 8oxoG glycosylase in T. kodakarensis, but is non-essential. In addition to TkoAGOG, the major apurinic/apyrimidinic (AP) endonuclease (TkoEndoIV) required for archaeal base excision repair and cell viability was identified and characterized. Enzymes required for the archaeal oxidative damage base excision repair pathway were identified and the complete pathway was reconstituted. This study illustrates the conservation of oxidative damage repair across all Domains of life.
Collapse
Affiliation(s)
| | | | - Brett W Burkhart
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, United States
| | | | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, United States
| | | |
Collapse
|
7
|
Mattiroli F, Bhattacharyya S, Dyer PN, White AE, Sandman K, Burkhart BW, Byrne KR, Lee T, Ahn NG, Santangelo TJ, Reeve JN, Luger K. Structure of histone-based chromatin in Archaea. Science 2017; 357:609-612. [PMID: 28798133 DOI: 10.1126/science.aaj1849] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 05/16/2017] [Accepted: 07/05/2017] [Indexed: 12/16/2022]
Abstract
Small basic proteins present in most Archaea share a common ancestor with the eukaryotic core histones. We report the crystal structure of an archaeal histone-DNA complex. DNA wraps around an extended polymer, formed by archaeal histone homodimers, in a quasi-continuous superhelix with the same geometry as DNA in the eukaryotic nucleosome. Substitutions of a conserved glycine at the interface of adjacent protein layers destabilize archaeal chromatin, reduce growth rate, and impair transcription regulation, confirming the biological importance of the polymeric structure. Our data establish that the histone-based mechanism of DNA compaction predates the nucleosome, illuminating the origin of the nucleosome.
Collapse
Affiliation(s)
- Francesca Mattiroli
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Sudipta Bhattacharyya
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Pamela N Dyer
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Alison E White
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Kathleen Sandman
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Brett W Burkhart
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kyle R Byrne
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Thomas Lee
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Natalie G Ahn
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.,Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO 80523, USA
| | - John N Reeve
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Karolin Luger
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA. .,Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO 80523, USA.,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80309, USA
| |
Collapse
|
8
|
Gehring AM, Astling DP, Matsumi R, Burkhart BW, Kelman Z, Reeve JN, Jones KL, Santangelo TJ. Genome Replication in Thermococcus kodakarensis Independent of Cdc6 and an Origin of Replication. Front Microbiol 2017; 8:2084. [PMID: 29163389 PMCID: PMC5663688 DOI: 10.3389/fmicb.2017.02084] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/11/2017] [Indexed: 11/22/2022] Open
Abstract
The initiation of DNA replication is typically tightly regulated by proteins that form initiation complexes at specific sequences known as replication origins. In Archaea and Eukaryotes, Cdc6, a near-universally conserved protein binds and facilitates the origin-dependent assembly of the replicative apparatus. TK1901 encodes Cdc6 in Thermococcus kodakarensis but, as we report here, TK1901 and the presumed origin of replication can be deleted from the genome of this hyperthermophilic Archaeon without any detectable effects on growth, genetic competence or the ability to support autonomous plasmid replication. All regions of the genome were equally represented in the sequences generated by whole genome sequencing of DNA isolated from T. kodakarensis strains with or without TK1901, inconsistent with DNA initiation occurring at one or few origins, and instead suggestive of replication initiating at many sites distributed throughout the genome. We were unable to generate strains lacking the recombination factors, RadA or RadB, consistent with T. kodakarensis cells, that are oligoploid (7–19 genomes per cell), employing a recombination-based mechanism of DNA replication. Deletion of the previously presumed origin region reduced the long-term viability of cultures supporting the possibility that retaining an origin-based mechanism of DNA initiation provides a survival mechanism for stationary phase cells with only one genome.
Collapse
Affiliation(s)
- Alexandra M Gehring
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - David P Astling
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Rie Matsumi
- Department of Microbiology, Ohio State University, Columbus, OH, United States
| | - Brett W Burkhart
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Zvi Kelman
- Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD, United States
| | - John N Reeve
- Department of Microbiology, Ohio State University, Columbus, OH, United States
| | - Kenneth L Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| |
Collapse
|
9
|
Heider MR, Burkhart BW, Santangelo TJ, Gardner AF. Defining the RNaseH2 enzyme-initiated ribonucleotide excision repair pathway in Archaea. J Biol Chem 2017; 292:8835-8845. [PMID: 28373277 PMCID: PMC5448109 DOI: 10.1074/jbc.m117.783472] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 03/31/2017] [Indexed: 11/06/2022] Open
Abstract
Incorporation of ribonucleotides during DNA replication has severe consequences for genome stability. Although eukaryotes possess a number of redundancies for initiating and completing repair of misincorporated ribonucleotides, archaea such as Thermococcus rely only upon RNaseH2 to initiate the pathway. Because Thermococcus DNA polymerases incorporate as many as 1,000 ribonucleotides per genome, RNaseH2 must be efficient at recognizing and nicking at embedded ribonucleotides to ensure genome integrity. Here, we show that ribonucleotides are incorporated by the hyperthermophilic archaeon Thermococcus kodakarensis both in vitro and in vivo and a robust ribonucleotide excision repair pathway is critical to keeping incorporation levels low in wild-type cells. Using pre-steady-state and steady-state kinetics experiments, we also show that archaeal RNaseH2 rapidly cleaves at embedded ribonucleotides (200-450 s-1), but exhibits an ∼1,000-fold slower turnover rate (0.06-0.17 s-1), suggesting a potential role for RNaseH2 in protecting or marking nicked sites for further processing. We found that following RNaseH2 cleavage, the combined activities of polymerase B (PolB), flap endonuclease (Fen1), and DNA ligase are required to complete ribonucleotide processing. PolB formed a ribonucleotide-containing flap by strand displacement synthesis that was cleaved by Fen1, and DNA ligase sealed the nick for complete repair. Our study reveals conservation of the overall mechanism of ribonucleotide excision repair across domains of life. The lack of redundancies in ribonucleotide repair in archaea perhaps suggests a more ancestral form of ribonucleotide excision repair compared with the eukaryotic pathway.
Collapse
Affiliation(s)
| | - Brett W Burkhart
- the Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80521
| | - Thomas J Santangelo
- the Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80521
| | - Andrew F Gardner
- From New England Biolabs, Inc., Ipswich, Massachusetts 01938 and
| |
Collapse
|