1
|
Jin Y, Ke J, Zheng P, Zhang H, Zhu Z, Niu L. Structural and biochemical characterization of a nucleotide hydrolase from Streptococcus pneumonia. Structure 2024:S0969-2126(24)00135-7. [PMID: 38701795 DOI: 10.1016/j.str.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 12/14/2023] [Accepted: 04/08/2024] [Indexed: 05/05/2024]
Abstract
In this report, we structurally and biochemically characterized the unknown gene product SP1746 from Streptococcus pneumoniae serotype 4. Various crystal structures of SP1746 in the apo form and in complex with different nucleotides were determined. SP1746 is a globular protein, which belongs to the histidine-aspartate (HD) domain superfamily with two Fe3+ ions in the active site that are coordinated by key active site residues and water molecules. All nucleotides bind in a similar orientation in the active site with their phosphate groups anchored to the diiron cluster. Biochemically, SP1746 hydrolyzes different nucleotide substrates. SP1746 most effectively hydrolyzes diadenosine tetraphosphate (Ap4A) to two ADPs. Based on the aforementioned data, we annotated SP1746 as an Ap4A hydrolase, belonging to the YqeK family. Our in vitro data indicate a potential role for SP1746 in regulating Ap4A homeostasis, which requires validation with in vivo experiments in bacteria in the future.
Collapse
Affiliation(s)
- Yuping Jin
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Jiyuan Ke
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, 4090 Susong Rd, Hefei, Hefei Economic and Technological Development Zone, Hefei, Anhui 230601, China.
| | - Peiyi Zheng
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Haiyan Zhang
- Core Facility Center for Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Zhongliang Zhu
- Core Facility Center for Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Liwen Niu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China.
| |
Collapse
|
2
|
Zheng T, Jing M, Gong T, Yan J, Zeng J, Li Y. Deletion of the yqeK gene leads to the accumulation of Ap4A and reduced biofilm formation in Streptococcus mutans. Mol Oral Microbiol 2021; 37:9-21. [PMID: 34761536 DOI: 10.1111/omi.12356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/15/2021] [Accepted: 11/01/2021] [Indexed: 02/05/2023]
Abstract
Diadenosine-5',5'''-P1, P4-tetraphosphate (Ap4A) is a second messenger playing a crucial role in various life activities of bacteria. The increase of Ap4A expression is pleiotropic, resulting in an impairment in the formation of biofilm and other physiological functions in some bacteria. However, Ap4A function in Streptococcus mutans, an important pathogen related to dental caries, remains unknown. In this work, the Ap4A hydrolase, YqeK, was identified and characterized in S. mutans. Then, the effects of yqeK deletion on the growth, biofilm formation, and exopolysaccharide (EPS) quantification in S. mutans were determined by the assessment of the growth curve, crystal violet, and anthrone-sulfuric acid, respectively, and visualized by microscopy. The results showed that the in-frame deletion of the yqeK gene in S. mutans UA159 led to an increase in Ap4A levels, lag phase in the early growth, as well as decrease in biofilm formation and water-insoluble exopolysaccharide production. Global gene expression profile showed that the expression of 88 genes was changed in the yqeK mutant, and among these, 42 were upregulated and 46 were downregulated when compared with the wild-type S. mutans UA159. Upregulated genes were mainly involved in post-translational modification, protein turnover, and chaperones, while downregulated genes were mainly involved in carbohydrate transport and metabolism. Important virulence genes related to biofilms, such as gtfB, gtfC, and gbpC, were also significantly downregulated. In conclusion, these results indicated that YqeK affected the formation of biofilms and the expression of biofilm-related genes in S. mutans.
Collapse
Affiliation(s)
- Ting Zheng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Meiling Jing
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Tao Gong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jiangchuan Yan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| |
Collapse
|
3
|
Márquez-Moñino MÁ, Ortega-García R, Shipton ML, Franco-Echevarría E, Riley AM, Sanz-Aparicio J, Potter BVL, González B. Multiple substrate recognition by yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase through phosphate clamping. SCIENCE ADVANCES 2021; 7:7/17/eabf6744. [PMID: 33893105 PMCID: PMC8064635 DOI: 10.1126/sciadv.abf6744] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
The yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase DDP1 is a Nudix enzyme with pyrophosphatase activity on diphosphoinositides, dinucleotides, and polyphosphates. These substrates bind to diverse protein targets and participate in signaling and metabolism, being essential for energy and phosphate homeostasis, ATPase pump regulation, or protein phosphorylation. An exhaustive structural study of DDP1 in complex with multiple ligands related to its three diverse substrate classes is reported. This allowed full characterization of the DDP1 active site depicting the molecular basis for endowing multisubstrate abilities to a Nudix enzyme, driven by phosphate anchoring following a defined path. This study, combined with multiple enzyme variants, reveals the different substrate binding modes, preferences, and selection. Our findings expand current knowledge on this important structural superfamily with implications extending beyond inositide research. This work represents a valuable tool for inhibitor/substrate design for ScDDP1 and orthologs as potential targets to address fungal infections and other health concerns.
Collapse
Affiliation(s)
- María Ángeles Márquez-Moñino
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Raquel Ortega-García
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Megan L Shipton
- Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford Mansfield Road, Oxford OX1 3QT, UK
| | - Elsa Franco-Echevarría
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Andrew M Riley
- Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford Mansfield Road, Oxford OX1 3QT, UK
| | - Julia Sanz-Aparicio
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Barry V L Potter
- Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford Mansfield Road, Oxford OX1 3QT, UK
| | - Beatriz González
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain.
| |
Collapse
|
4
|
Ferguson F, McLennan AG, Urbaniak MD, Jones NJ, Copeland NA. Re-evaluation of Diadenosine Tetraphosphate (Ap 4A) From a Stress Metabolite to Bona Fide Secondary Messenger. Front Mol Biosci 2020; 7:606807. [PMID: 33282915 PMCID: PMC7705103 DOI: 10.3389/fmolb.2020.606807] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/19/2020] [Indexed: 01/14/2023] Open
Abstract
Cellular homeostasis requires adaption to environmental stress. In response to various environmental and genotoxic stresses, all cells produce dinucleoside polyphosphates (NpnNs), the best studied of which is diadenosine tetraphosphate (Ap4A). Despite intensive investigation, the precise biological roles of these molecules have remained elusive. However, recent studies have elucidated distinct and specific signaling mechanisms for these nucleotides in prokaryotes and eukaryotes. This review summarizes these key discoveries and describes the mechanisms of Ap4A and Ap4N synthesis, the mediators of the cellular responses to increased intracellular levels of these molecules and the hydrolytic mechanisms required to maintain low levels in the absence of stress. The intracellular responses to dinucleotide accumulation are evaluated in the context of the "friend" and "foe" scenarios. The "friend (or alarmone) hypothesis" suggests that ApnN act as bona fide secondary messengers mediating responses to stress. In contrast, the "foe" hypothesis proposes that ApnN and other NpnN are produced by non-canonical enzymatic synthesis as a result of physiological and environmental stress in critically damaged cells but do not actively regulate mitigating signaling pathways. In addition, we will discuss potential target proteins, and critically assess new evidence supporting roles for ApnN in the regulation of gene expression, immune responses, DNA replication and DNA repair. The recent advances in the field have generated great interest as they have for the first time revealed some of the molecular mechanisms that mediate cellular responses to ApnN. Finally, areas for future research are discussed with possible but unproven roles for intracellular ApnN to encourage further research into the signaling networks that are regulated by these nucleotides.
Collapse
Affiliation(s)
- Freya Ferguson
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom.,Materials Science Institute, Lancaster University, Lancaster, United Kingdom
| | - Alexander G McLennan
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Michael D Urbaniak
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
| | - Nigel J Jones
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Nikki A Copeland
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom.,Materials Science Institute, Lancaster University, Lancaster, United Kingdom
| |
Collapse
|
5
|
Raj P, Karthik S, Arif SM, Varshney U, Vijayan M. Plasticity, ligand conformation and enzyme action of Mycobacterium smegmatis MutT1. Acta Crystallogr D Struct Biol 2020; 76:982-992. [PMID: 33021500 DOI: 10.1107/s2059798320010992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/11/2020] [Indexed: 11/10/2022] Open
Abstract
Mycobacterium smegmatis MutT1 (MsMutT1) is a sanitation enzyme made up of an N-terminal Nudix hydrolase domain and a C-terminal domain resembling a histidine phosphatase. It has been established that the action of MutT1 on 8-oxo-dGTP, 8-oxo-GTP and diadenosine polyphosphates is modulated by intermolecular interactions. In order to further explore this and to elucidate the structural basis of its differential action on 8-oxo-NTPs and unsubstituted NTPs, the crystal structures of complexes of MsMutT1 with 8-oxo-dGTP, GMPPNP and GMPPCP have been determined. Replacement soaking was used in order to ensure that the complexes were isomorphous to one another. Analysis of the structural data led to the elucidation of a relationship between the arrangements of molecules observed in the crystals, molecular plasticity and the action of the enzyme on nucleotides. The dominant mode of arrangement involving a head-to-tail sequence predominantly leads to the generation of NDPs. The other mode of packing arrangement appears to preferentially generate NMPs. This work also provides interesting insights into the dependence of enzyme action on the conformation of the ligand. The possibility of modulating the enzyme action through differences in intermolecular interactions and ligand conformations makes MsMutT1 a versatile enzyme.
Collapse
Affiliation(s)
- Prateek Raj
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560 012, India
| | - S Karthik
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560 012, India
| | - S M Arif
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560 012, India
| | - U Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560 012, India
| | - M Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560 012, India
| |
Collapse
|
6
|
Gao A, Vasilyev N, Kaushik A, Duan W, Serganov A. Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH. Nucleic Acids Res 2020; 48:3776-3788. [PMID: 31960065 PMCID: PMC7144940 DOI: 10.1093/nar/gkaa024] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 01/06/2020] [Accepted: 01/18/2020] [Indexed: 12/23/2022] Open
Abstract
All enzymes face a challenge of discriminating cognate substrates from similar cellular compounds. Finding a correct substrate is especially difficult for the Escherichia coli Nudix hydrolase RppH, which triggers 5′-end-dependent RNA degradation by removing orthophosphate from the 5′-diphosphorylated transcripts. Here we show that RppH binds and slowly hydrolyzes NTPs, NDPs and (p)ppGpp, which each resemble the 5′-end of RNA. A series of X-ray crystal structures of RppH-nucleotide complexes, trapped in conformations either compatible or incompatible with hydrolysis, explain the low reaction rates of mononucleotides and suggest two distinct mechanisms for their hydrolysis. While RppH adopts the same catalytic arrangement with 5′-diphosphorylated nucleotides as with RNA, the enzyme hydrolyzes 5′-triphosphorylated nucleotides by extending the active site with an additional Mg2+ cation, which coordinates another reactive nucleophile. Although the average intracellular pH minimizes the hydrolysis of nucleotides by slowing their reaction with RppH, they nevertheless compete with RNA for binding and differentially inhibit the reactivity of RppH with triphosphorylated and diphosphorylated RNAs. Thus, E. coli RppH integrates various signals, such as competing non-cognate substrates and a stimulatory protein factor DapF, to achieve the differential degradation of transcripts involved in cellular processes important for the adaptation of bacteria to different growth conditions.
Collapse
Affiliation(s)
- Ang Gao
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Abhishek Kaushik
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Wenqian Duan
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Alexander Serganov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
- To whom correspondence should be addressed. Tel: +1 212 263 4446;
| |
Collapse
|
7
|
Frindert J, Zhang Y, Nübel G, Kahloon M, Kolmar L, Hotz-Wagenblatt A, Burhenne J, Haefeli WE, Jäschke A. Identification, Biosynthesis, and Decapping of NAD-Capped RNAs in B. subtilis. Cell Rep 2019; 24:1890-1901.e8. [PMID: 30110644 DOI: 10.1016/j.celrep.2018.07.047] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 07/02/2018] [Accepted: 07/13/2018] [Indexed: 11/30/2022] Open
Abstract
The ubiquitous coenzyme nicotinamide adenine dinucleotide (NAD) decorates various RNAs in different organisms. In the proteobacterium Escherichia coli, the NAD-cap confers stability against RNA degradation. To date, NAD-RNAs have not been identified in any other bacterial microorganism. Here, we report the identification of NAD-RNA in the firmicute Bacillus subtilis. In the late exponential growth phase, predominantly mRNAs are NAD modified. NAD is incorporated de novo into RNA by the cellular RNA polymerase using non-canonical transcription initiation. The incorporation efficiency depends on the -1 position of the promoter but is independent of sigma factors or mutations in the rifampicin binding pocket. RNA pyrophosphohydrolase BsRppH is found to decap NAD-RNA. In vitro, the decapping activity is facilitated by manganese ions and single-stranded RNA 5' ends. Depletion of BsRppH influences the gene expression of ∼13% of transcripts in B. subtilis. The NAD-cap stabilizes RNA against 5'-to-3'-exonucleolytic decay by RNase J1.
Collapse
Affiliation(s)
- Jens Frindert
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| | - Yaqing Zhang
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| | - Gabriele Nübel
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| | - Masroor Kahloon
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| | - Leonie Kolmar
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- Bioinformatics Group, Core Facility Genomics and Proteomics, German Cancer Research Center (DKFZ), DKFZ-Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, 69120 Heidelberg, Germany
| | - Jürgen Burhenne
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University, 69120 Heidelberg, Germany
| | - Walter E Haefeli
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University, 69120 Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany.
| |
Collapse
|
8
|
Mao FX, Luo CH, Chen HJ, Zhang YX, Zhang Q. CaSR is required for ischemia-induced proliferation and differentiation of white matter progenitor cells from neonatal rats. Brain Res Bull 2019; 154:116-126. [PMID: 31738973 DOI: 10.1016/j.brainresbull.2019.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 10/06/2019] [Accepted: 11/09/2019] [Indexed: 12/24/2022]
Abstract
This study was designed to investigate whether calcium-sensing receptor (CaSR) could induce immture white matter progenitor cells proliferation and differentiation into oligodendrocyte(OL) precursor cells after oxygen-glucose deprivation (OGD) in vitro. Progenitor cells of immature white matter originating from five-day-old newborn rats were divided into control, OGD, control + CaSR silencing, OGD + CaSR silencing, control + adenosine triphosphate magnesium chloride (ATP-MgCl2) and OGD + ATP-MgCl2 groups. Immunofluorescence, real-time RT-PCR, gene silencing, Hoechst 33342/propidium iodide (PI) and Flow cytometry tests were used to examine the proliferation, differentiation and survival of the white matter progenitor cells in the different treatment groups. The results showed that normal immature white matter progenitor cells have certain ability of self-proliferation and differentiation in vitro. OGD could further induce progenitor cells proliferation and differentiation into O4 + OL precursor cells by activating CaSR, but OGD also induced more necrosis and apoptosis of newborn cells and less MBP + OL formation. The addition of ATP-MgCl2 as an activating agent of CaSR further promoted cell proliferation and differentiation both under normal and OGD conditions and reduced OGD-induced apoptosis and necrosis, while CaSR silenced resulted in minimal cell proliferation, differentiation and survival. This study suggests that CaSR plays an important role in the induction of immature white matter progenitor cells proliferation and differentiation into OL precursor cells after OGD, which may provide a new angle to further study whether CaSR initiates the intrinsic repair potential of immature white matter after ischemia in vivo.
Collapse
Affiliation(s)
- Feng-Xia Mao
- The First Affiliated Hospital of Zhengzhou University, Jianshe East Road No.1, Zhengzhou, 450052, China
| | - Cheng-Han Luo
- The First Affiliated Hospital of Zhengzhou University, Jianshe East Road No.1, Zhengzhou, 450052, China
| | - Hui-Jin Chen
- Shanghai Institute for Pediatric Research, Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Kongjiang Road 1665, Shanghai, 200092, China
| | - Yi-Xia Zhang
- The First Affiliated Hospital of Zhengzhou University, Jianshe East Road No.1, Zhengzhou, 450052, China
| | - Qian Zhang
- The First Affiliated Hospital of Zhengzhou University, Jianshe East Road No.1, Zhengzhou, 450052, China.
| |
Collapse
|
9
|
Singh A, Mohammad Arif S, Biak Sang P, Varshney U, Vijayan M. Structural insights into the specificity and catalytic mechanism of mycobacterial nucleotide pool sanitizing enzyme MutT2. J Struct Biol 2018; 204:449-456. [PMID: 30312643 DOI: 10.1016/j.jsb.2018.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/04/2018] [Accepted: 10/07/2018] [Indexed: 12/29/2022]
Abstract
Mis-incorporation of modified nucleotides, such as 5-methyl-dCTP or 8-oxo-dGTP, in DNA can be detrimental to genomic integrity. MutT proteins are sanitization enzymes which function by hydrolyzing such nucleotides and regulating the pool of free nucleotides in the cytoplasm. Mycobacterial genomes have a set of four MutT homologs, namely, MutT1, MutT2, MutT3 and MutT4. Mycobacterial MutT2 hydrolyzes 5 m-dCTP and 8-oxo-dGTP to their respective monophosphate products. Additionally, it can hydrolyze canonical nucleotides dCTP and CTP, with a suggested role in sustaining their optimal levels in the nucleotide pool. The structures of M. smegmatis MutT2 and its complexes with cytosine derivatives have been determined at resolutions ranging from 1.10 Å to 1.73 Å. The apo enzyme and its complexes with products (dCMP, CMP and 5 m-dCMP) crystallize in space group P21212, while those involving substrates (dCTP, CTP and 5 m-dCTP) crystallize in space group P21. The molecule takes an α/β/α sandwich fold arrangement, as observed in other MutT homologs. The nucleoside moiety of the ligands is similarly located in all the complexes, while the location of the remaining tail exhibits variability. This is the first report of a MutT2-type protein in complex with ligands. A critical interaction involving Asp116 confers the specificity of the enzyme towards cytosine moieties. A conserved set of enzyme-ligand interactions along with concerted movements of important water molecules provide insights into the mechanism of action.
Collapse
Affiliation(s)
- Amandeep Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | | | - Pau Biak Sang
- Dept. of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Umesh Varshney
- Dept. of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - M Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
| |
Collapse
|
10
|
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.
Collapse
Affiliation(s)
- Amandeep Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| |
Collapse
|