1
|
Cohen R, Milo S, Sharma S, Savidor A, Covo S. Ribonucleotide reductase from Fusarium oxysporum does not Respond to DNA replication stress. DNA Repair (Amst) 2019; 83:102674. [PMID: 31375409 DOI: 10.1016/j.dnarep.2019.102674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/22/2019] [Accepted: 07/22/2019] [Indexed: 12/14/2022]
Abstract
Ribonucleotide reductase (RNR) catalyzes the rate limiting step in dNTP biosynthesis and is tightly regulated at the transcription and activity levels. One of the best characterized responses of yeast to DNA damage is up-regulation of RNR transcription and activity and consequently, elevation of the dNTP pools. Hydroxyurea is a universal inhibitor of RNR that causes S phase arrest. It is used in the clinic to treat certain types of cancers. Here we studied the response of the fungal plant pathogen Fusarium oxysporum to hydroxyurea in order to generate hypotheses that can be used in the future in development of a new class of pesticides. F. oxysporum causes severe damage to more than 100 agricultural crops and specifically threatens banana cultivation world-wide. Although the recovery of F. oxysporum from transient hydroxyurea exposure was similar to the one of Saccharomyces cerevisiae, colony formation was strongly inhibited in F. oxysporum in comparison with S. cerevisiae. As expected, genomic and phosphoproteomic analyses of F. oxysporum conidia (spores) exposed to hydroxyurea showed hallmarks of DNA replication perturbation and activation of recombination. Unexpectedly and strikingly, RNR was not induced by either hydroxyurea or the DNA-damaging agent methyl methanesulfonate as determined at the RNA and protein levels. Consequently, dNTP concentrations were significantly reduced, even in response to a low dose of hydroxyurea. Methyl methanesulfonate treatment did not induce dNTP pools in F. oxysporum, in contrast to the response of RNR and dNTP pools to DNA damage and hydroxyurea in several tested organisms. Our results are important because the lack of a feedback mechanism to increase RNR expression in F. oxysporum is expected to sensitize the pathogen to a fungal-specific ribonucleotide inhibitor. The potential impact of our observations on F. oxysporum genome stability and genome evolution is discussed.
Collapse
Affiliation(s)
- Rotem Cohen
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot, 76100, Israel
| | - Shira Milo
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot, 76100, Israel
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Alon Savidor
- de Botton Institute for Protein Profiling, the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Shay Covo
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot, 76100, Israel.
| |
Collapse
|
2
|
Pham B, Lindsay RJ, Shen T. Effector-Binding-Directed Dimerization and Dynamic Communication between Allosteric Sites of Ribonucleotide Reductase. Biochemistry 2019; 58:697-705. [PMID: 30571104 DOI: 10.1021/acs.biochem.8b01131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Proteins forming dimers or larger complexes can be strongly influenced by their effector-binding status. We investigated how the effector-binding event is coupled with interface formation via computer simulations, and we quantified the correlation of two types of contact interactions: between the effector and its binding pocket and between protein monomers. This was achieved by connecting the protein dynamics at the monomeric level with the oligomer interface information. We applied this method to ribonucleotide reductase (RNR), an essential enzyme for de novo DNA synthesis. RNR contains two important allosteric sites, the s-site (specificity site) and the a-site (activity site), which bind different effectors. We studied these different binding states with atomistic simulation and used their coarse-grained contact information to analyze the protein dynamics. The results reveal that the effector-protein dynamics at the s-site and dimer interface formation are positively coupled. We further quantify the resonance level between these two events, which can be applied to other similar systems. At the a-site, different effector-binding states (ATP vs dATP) drastically alter the protein dynamics and affect the activity of the enzyme. On the basis of these results, we propose a new mechanism of how the a-site regulates enzyme activation.
Collapse
Affiliation(s)
- Bill Pham
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Richard J Lindsay
- UT-ORNL Graduate School of Genome Science and Technology , Knoxville , Tennessee 37996 , United States
| | - Tongye Shen
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| |
Collapse
|
3
|
Misko TA, Wijerathna SR, Radivoyevitch T, Berdis AJ, Ahmad MF, Harris ME, Dealwis CG. Inhibition of yeast ribonucleotide reductase by Sml1 depends on the allosteric state of the enzyme. FEBS Lett 2016; 590:1704-12. [PMID: 27155231 DOI: 10.1002/1873-3468.12207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/19/2016] [Accepted: 04/29/2016] [Indexed: 11/05/2022]
Abstract
Sml1 is an intrinsically disordered protein inhibitor of Saccharomyces cerevisiae ribonucleotide reductase (ScRR1), but its inhibition mechanism is poorly understood. RR reduces ribonucleoside diphosphates to their deoxy forms, and balances the nucleotide pool. Multiple turnover kinetics show that Sml1 inhibition of dGTP/ADP- and ATP/CDP-bound ScRR follows a mixed inhibition mechanism. However, Sml1 cooperatively binds to the ES complex in the dGTP/ADP form, whereas with ATP/CDP, Sml1 binds weakly and noncooperatively. Gel filtration and mutagenesis studies indicate that Sml1 does not alter the oligomerization equilibrium and the CXXC motif is not involved in the inhibition. The data suggest that Sml1 is an allosteric inhibitor.
Collapse
Affiliation(s)
- Tessianna A Misko
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Sanath R Wijerathna
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Tomas Radivoyevitch
- Department of Quantitative Health Sciences, Cleveland Clinic Foundation, OH, USA
| | | | - Md Faiz Ahmad
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Chris G Dealwis
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| |
Collapse
|
4
|
Lin CY, Wu MY, Gay S, Marjavaara L, Lai MS, Hsiao WC, Hung SH, Tseng HY, Wright DE, Wang CY, Hsu GSW, Devys D, Chabes A, Kao CF. H2B mono-ubiquitylation facilitates fork stalling and recovery during replication stress by coordinating Rad53 activation and chromatin assembly. PLoS Genet 2014; 10:e1004667. [PMID: 25275495 PMCID: PMC4183429 DOI: 10.1371/journal.pgen.1004667] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 08/14/2014] [Indexed: 01/11/2023] Open
Abstract
The influence of mono-ubiquitylation of histone H2B (H2Bub) on transcription via nucleosome reassembly has been widely documented. Recently, it has also been shown that H2Bub promotes recovery from replication stress; however, the underling molecular mechanism remains unclear. Here, we show that H2B ubiquitylation coordinates activation of the intra-S replication checkpoint and chromatin re-assembly, in order to limit fork progression and DNA damage in the presence of replication stress. In particular, we show that the absence of H2Bub affects replication dynamics (enhanced fork progression and reduced origin firing), leading to γH2A accumulation and increased hydroxyurea sensitivity. Further genetic analysis indicates a role for H2Bub in transducing Rad53 phosphorylation. Concomitantly, we found that a change in replication dynamics is not due to a change in dNTP level, but is mediated by reduced Rad53 activation and destabilization of the RecQ helicase Sgs1 at the fork. Furthermore, we demonstrate that H2Bub facilitates the dissociation of the histone chaperone Asf1 from Rad53, and nucleosome reassembly behind the fork is compromised in cells lacking H2Bub. Taken together, these results indicate that the regulation of H2B ubiquitylation is a key event in the maintenance of genome stability, through coordination of intra-S checkpoint activation, chromatin assembly and replication fork progression. Eukaryotic DNA is organized into nucleosomes, which are the fundamental repeating units of chromatin. Coordination of chromatin structure is required for efficient and accurate DNA replication. Aberrant DNA replication results in mutations and chromosome rearrangements that may be associated with human disorders. Therefore, cellular surveillance mechanisms have evolved to counteract potential threats to DNA replication. These mechanisms include checkpoints and specialized enzymatic activities that prevent the replication and segregation of defective DNA molecules. We employed a genome-wide approach to investigate how chromatin structure affects DNA replication under stress. We report that coordination of chromatin assembly and checkpoint activity by a histone modification, H2B ubiquitylation (H2Bub), is critical for the cell response to HU-induced replication stress. In cells with a mutation that abolishes H2Bub, replication progression is enhanced, and the forks are more susceptible to damage by environmental insults. The replication proteins on replicating DNA are akin to a train on the tracks, and movement of this train is carefully controlled. Our data indicate that H2Bub helps organize DNA in the nuclei during DNA replication; this process plays a similar role to the brakes on a train, serving to slow down replication, and maintaining stable progression of replication under environmental stress.
Collapse
Affiliation(s)
- Chia-Yeh Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan
- Graduate Institute of Nutrition and Food Sciences, Fu-Jen Catholic University, Xinzhuang, New Taipei City, Taiwan
| | - Meng-Ying Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Sophie Gay
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), IFOM-IEO Campus, Milan, Italy
| | - Lisette Marjavaara
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Mong Sing Lai
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), IFOM-IEO Campus, Milan, Italy
| | - Wei-Chun Hsiao
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Shih-Hsun Hung
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Hsin-Yi Tseng
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Duncan Edward Wright
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Chen-Yi Wang
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan
- Institut de Génétique et de Biologie Moléculaire. CNRS UMR 7104, INSERM U 596, Université Louis Pasteur de Strasbourg, Illkirch, CU de Strasbourg, France
| | - Guoo-Shyng W. Hsu
- Graduate Institute of Nutrition and Food Sciences, Fu-Jen Catholic University, Xinzhuang, New Taipei City, Taiwan
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire. CNRS UMR 7104, INSERM U 596, Université Louis Pasteur de Strasbourg, Illkirch, CU de Strasbourg, France
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan
- * E-mail:
| |
Collapse
|
5
|
Andreson BL, Gupta A, Georgieva BP, Rothstein R. The ribonucleotide reductase inhibitor, Sml1, is sequentially phosphorylated, ubiquitylated and degraded in response to DNA damage. Nucleic Acids Res 2010; 38:6490-501. [PMID: 20566477 PMCID: PMC2965251 DOI: 10.1093/nar/gkq552] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Regulation of ribonucleotide reductase (RNR) is important for cell survival and genome integrity in the face of genotoxic stress. The Mec1/Rad53/Dun1 DNA damage response kinase cascade exhibits multifaceted controls over RNR activity including the regulation of the RNR inhibitor, Sml1. After DNA damage, Sml1 is degraded leading to the up-regulation of dNTP pools by RNR. Here, we probe the requirements for Sml1 degradation and identify several sites required for in vivo phosphorylation and degradation of Sml1 in response to DNA damage. Further, in a strain containing a mutation in Rnr1, rnr1-W688G, mutation of these sites in Sml1 causes lethality. Degradation of Sml1 is dependent on the 26S proteasome. We also show that degradation of phosphorylated Sml1 is dependent on the E2 ubiquitin-conjugating enzyme, Rad6, the E3 ubiquitin ligase, Ubr2, and the E2/E3-interacting protein, Mub1, which form a complex previously only implicated in the ubiquitylation of Rpn4.
Collapse
Affiliation(s)
- Bethany L Andreson
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | | | | | | |
Collapse
|
6
|
Zhang Z, Yang K, Chen CC, Feser J, Huang M. Role of the C terminus of the ribonucleotide reductase large subunit in enzyme regeneration and its inhibition by Sml1. Proc Natl Acad Sci U S A 2007; 104:2217-22. [PMID: 17277086 PMCID: PMC1892911 DOI: 10.1073/pnas.0611095104] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Ribonucleotide reductase maintains cellular deoxyribonucleotide pools and is thus tightly regulated during the cell cycle to ensure high fidelity in DNA replication. The Sml1 protein inhibits ribonucleotide reductase activity by binding to the R1 subunit. At the completion of each turnover cycle, the active site of R1 becomes oxidized and subsequently regenerated by a cysteine pair (CX2C) at its C-terminal domain (R1-CTD). Here we show that R1-CTD acts in trans to reduce the active site of its neighboring monomer. Both Sml1 and R1-CTD interact with the N-terminal domain of R1 (R1-NTD), which involves a conserved two-residue sequence motif in the R1-NTD. Mutations at these two positions enhancing the Sml1-R1 interaction cause SML1-dependent lethality. These results point to a model whereby Sml1 competes with R1-CTD for association with R1-NTD to hinder the accessibility of the CX2C motif to the active site for R1 regeneration.
Collapse
Affiliation(s)
- Zhen Zhang
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora, CO 80045
| | - Kui Yang
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora, CO 80045
| | - Chin-Chuan Chen
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora, CO 80045
| | - Jason Feser
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora, CO 80045
| | - Mingxia Huang
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora, CO 80045
- *To whom correspondence should be addressed. E-mail:
| |
Collapse
|
7
|
Abstract
The Lcd1p/Mec1p complex is crucial for normal S phase progression and for signaling DNA damage. We show that Lcd1p/Ddc2p and Mec1p in cell extracts bind to DNA ends. Although Lcd1p binds DNA independently of Mec1p, recruitment of Mec1p to DNA requires Lcd1p. DNA binding by Lcd1p is also independent of Rad9p, Rad17p, and Rad24p. Recombinant Lcd1p binds DNA, and this is impaired by Lcd1p mutations that abrogate its in vivo functions. Furthermore, Mec1p is recruited to cdc13-induced DNA damage and HO endonuclease-induced double-strand breaks in vivo. This requires Lcd1p, and recruitment of Lcd1p/Mec1p to cdc13-induced damage is abolished by Lcd1p mutations that abrogate its in vivo functions. Recruitment of Lcd1p to these lesions is independent of Mec1p and Rad9p/Rad24p. Thus, recruitment of Mec1p to DNA lesions by Lcd1p is crucial for the DNA damage response.
Collapse
Affiliation(s)
- John Rouse
- Wellcome Trust and Cancer Research UK, Institute of Cancer and Developmental Biology, University of Cambridge, Cambridge CB2 1QR, United Kingdom
| | | |
Collapse
|