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Kapoor I, Varshney U. Diverse roles of nucleoside diphosphate kinase in genome stability and growth fitness. Curr Genet 2020; 66:671-682. [PMID: 32249353 DOI: 10.1007/s00294-020-01073-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 01/01/2023]
Abstract
Nucleoside diphosphate kinase (NDK), a ubiquitous enzyme, catalyses reversible transfer of the γ phosphate from nucleoside triphosphates to nucleoside diphosphates and functions to maintain the pools of ribonucleotides and deoxyribonucleotides in the cell. As even a minor imbalance in the nucleotide pools can be mutagenic, NDK plays an antimutator role in maintaining genome integrity. However, the mechanism of the antimutator roles of NDK is not completely understood. In addition, NDKs play important roles in the host-pathogen interactions, metastasis, gene regulation, and various cellular metabolic processes. To add to these diverse roles of NDK in cells, a recent study now reveals that NDK may even confer mutator phenotypes to the cell by acting on the damaged deoxyribonucleoside diphosphates that may be formed during the oxidative stress. In this review, we discuss the roles of NDK in homeostasis of the nucleotide pools and genome integrity, and its possible implications in conferring growth/survival fitness to the organisms in the changing environmental niches.
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Affiliation(s)
- Indu Kapoor
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India. .,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India.
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Mathews CK. Enzyme organization in DNA precursor biosynthesis. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1993; 44:167-203. [PMID: 8434123 DOI: 10.1016/s0079-6603(08)60220-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- C K Mathews
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331
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Ji JP, Mathews CK. Analysis of mutagenesis induced by a thermolabile T4 phage deoxycytidylate hydroxymethylase suggests localized deoxyribonucleotide pool imbalance. MOLECULAR & GENERAL GENETICS : MGG 1991; 226:257-64. [PMID: 2034218 DOI: 10.1007/bf00273611] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To understand the molecular basis of mutation stimulated by deoxyribonucleotide pool imbalance, we studied a temperature-sensitive T4 phage gene 42 mutant (LB3), which specifies a thermolabile deoxycytidylate hydroxymethylase. Analysis of rII mutations, revertible to wild type along either GC-to-AT or AT-to-GC transition pathways, showed 8- to 80-fold stimulation of GC-to-AT mutations at a semi-permissive temperature (34 degrees C). One such marker, rII SN103, which showed the highest stimulation at 34 degrees C, was sequenced after amplification of the template by polymerase chain reaction. The mutant site in rII SN103 was identified at nucleotide position 265 from the rII B translational start as an AT-to-GC transition, which changes TCA to CCA. Sequence analysis of revertants and pseudorevertants generated at 34 degrees C showed that both cytosines within this triplet can undergo change to either thymine or adenine, consistent with the hypothesis that hydroxymethyldeoxycytidine triphosphate pools are depleted at replication sites. However, dNTP pool measurements in extracts of 34 degrees C cultures showed no significant deviations from values obtained at 30 degrees C, suggesting that pool imbalances occur only locally, close to replication forks. Our studies support the hypothesis that the mutator phenotype displayed by ts LB3 at semi-permissive temperature is a consequence of perturbation of the flow of nucleotide precursors into the DNA replication machinery. A putative localized depletion of hm-dCTP presumably enlarges effective dTTP/hm-dCTP and dATP/hm-dCTP pool ratios, resulting in the observed C-to-T transition and C-to-A transversion mutations.
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Affiliation(s)
- J P Ji
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331
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Bacteriophage T4 infection mechanisms. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/b978-0-444-80400-6.50013-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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7
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Manwaring JD, Fuchs JA. Relationship between deoxyribonucleoside triphosphate pools and deoxyribonucleic acid synthesis in an nrdA mutant of Escherichia coli. J Bacteriol 1979; 138:245-8. [PMID: 374367 PMCID: PMC218263 DOI: 10.1128/jb.138.1.245-248.1979] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A shift to 42 degrees C in an nrdA mutant causes a decrease in deoxyribonucleic acid synthesis without a concomitant decrease in deoxynucleotide triphosphate pools.
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Mathews CK, North TW, Prem veer Reddy G. Multienzyme complexes in DNA precursor biosynthesis. ADVANCES IN ENZYME REGULATION 1979; 17:133-56. [PMID: 393088 DOI: 10.1016/0065-2571(79)90011-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Morton D, Kutter EM, Guttman BS. Synthesis of T4 DNA and bacteriophage in the absence of dCMP hydroxymethylase. J Virol 1978; 28:262-9. [PMID: 212605 PMCID: PMC354265 DOI: 10.1128/jvi.28.1.262-269.1978] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Several lines of research have suggested that the dCMP hydroxymethylase (HMase) coded by bacteriophage T4 is an essential protein in a DNA replication complex, as well as a supplier of hydroxymethyl dCMP for phage DNA synthesis. We show that a mutant [HMase, dCTPase, endonuclease II, endonuclease IV] which lacked this enzyme made cytosine-containing DNA at about two-thirds of the normal rate. When coupled with an alc mutation which permitted synthesis of late proteins, a small burst of phage was produced whose DNA contained no hydroxymethylcytosine. This pentuple mutant made both early and late proteins with abnormal kinetics, whereas the HMase+ parent showed normal kinetics. However, intracellular phage DNA showed no gross abnormalities in alkaline sucrose gradients. We conclude that HMase is not required for DNA synthesis when hydroxymethyl dCMP is not needed as a substrate; however, its absence still impairs both replication and transcription.
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Chiu C, Ruettinger T, Flanegan J, Greenberg G. Role of deoxycytidylate deaminase in deoxyribonucleotide synthesis in bacteriophage T4 DNA replication. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(19)75263-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Chao J, Leach M, Karam J. In vivo functional interaction between DNA polymerase and dCMP-hydroxymethylase of bacteriophage T4. J Virol 1977; 24:557-63. [PMID: 562423 PMCID: PMC515967 DOI: 10.1128/jvi.24.2.557-563.1977] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Some mutations in the structural gene for T4 DNA polymerase (gene 43) behave as suppressors of a deficiency in T4 dCMP-hydroxymethylase (gene 42). The suppression appears to involve a functional interaction between the two enzymes at the level of DNA replication. The hydroxymethylase deficiency caused DNA structural abnormalities in replication, and DNA polymerase lesions appeared to partially reverse these abnormalities. The results do not necessarily imply protein-protein interactions between the two enzymes, although both enzymes appear to play roles in controlling the fidelity of phage DNA replication.
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Flanegan JB, Chiu CS, Greenberg GR. Inhibitory effect of agents altering the structure of DNA on the synthesis of pyrimidine deoxyribonucleotides in bacteriophage T4 DNA replication. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)40024-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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North TW, Mathews CK. T4 phage-coded deoxycytidylate hydroxymethylase: purification and studies on intermolecular interactions. Biochem Biophys Res Commun 1977; 77:898-904. [PMID: 332172 DOI: 10.1016/s0006-291x(77)80062-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Reddy GP, Singh A, Stafford ME, Mathews CK. Enzyme associations in T4 phage DNA precursor synthesis. Proc Natl Acad Sci U S A 1977; 74:3152-6. [PMID: 198773 PMCID: PMC431474 DOI: 10.1073/pnas.74.8.3152] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A DIRECT APPROACH IS DESCRIBED TO THE QUESTION: Are enzymes of DNA precursor synthesis organized into a supramolecular structure? This approach involved sedimentation analysis of several T4 phage-coded early enzyme activities in crude lysates of infected Escherichia coli. One-third to one-half of several activities tested-dCMP hydroxymethylase, dTMP synthetase, deoxynucleoside 5'-monophosphate kinase, deoxyuridine triphosphatase, and probably dCMP deaminase, but not dihydrofolate reductase or DNA polymerase-sedimented much more rapidly than expected from molecular weight. About 5% of the host cell nucleoside diphosphate kinase, known to participate in T4 DNA precursor synthesis, cosedimented with these activities. To show that this rapidly sedimenting material represents an organized enzyme complex rather than a nonspecific aggregate, we studied the kinetics of formation of dTTP with dUMP as the initial substrate. This three-step reaction sequence reached its maximal rate within a few seconds when catalyzed by enzymes in the aggregate, whereas an equivalent mixture of uncomplexed enzymes required nearly 20 min before dTTP synthesis reached its maximal rate. The effect of aggregation is evidently to decrease the volume into which intermediates are free to diffuse. Because there is reason to believe that intracellular concentration gradients of DNA precursors exist, the properties of this enzyme aggregate in vitro may help to explain how such gradients are maintained.
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Stafford ME, Reddy GP, Mathews CK. Further studies on bacteriophage T4 DNA synthesis in sucrose-plasmolyzed cells. J Virol 1977; 23:53-60. [PMID: 328926 PMCID: PMC515799 DOI: 10.1128/jvi.23.1.53-60.1977] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
This paper describes several technical improvements in the sucrose-plasmolyzed cell system used in earlier experiments on DNA synthesis in situ with Escherichia coli infected by DNA-defective mutants of bacteriophage T4 (W. L. Collinsworth and C. K. Mathews, J. Virol. 13:908-915, 1974). Using this system, which is based primarily on that of M. G. Wovcha et al. (Proc. Natl. Acad. Sci. U.S.A. 70:2196-2200, 1973), we reinvestigated the properties of mutants bearing lesions in genes 1, 41, and 62, and we resolved some disagreements with data reported from that laboratory. We also asked whether the DNA-delay phenotype of T4 mutants is related to possible early leakage of DNA precursors from infected cells. Such cells display defective DNA synthesis in situ, even when ample DNA precursors are made available. Thus, the lesions associated with these mutations seem to manifest themselves at the level of macromolecular metabolism. Similarly, we examined an E. coli mutant defective in its ability to support T4 production, apparently because of a lesion affecting DNA synthesis (L. Simon et al., Nature [London] 252:451-455). In the plasmolyzed cell system, reduced nucleotide incorporation is seen, indicating also that the genetic defect does not involve DNA precursor synthesis. The plasmolyzed cell system incorporates deoxynucleotide 5'-monophosphates into DNA severalfold more rapidly than the corresponding 5'-triphosphates. This is consistent with the idea that DNA precursor-synthesizing enzymes are functionally organized to shuttle substrates to their sites of utilization.
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Flanegan JB, Greenberg GR. Regulation of deoxyribonucleotide biosynthesis during in vivo bacteriophage T4 DNA replication. Intrinsic control of synthesis of thymine and 5-hydroxymethylcytosine deoxyribonucleotides at precise ratio found in DNA. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)40466-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Wovcha MG, Chiu CS, Tomich PK, Greenberg GR. Replicative bacteriophage DNA synthesis in plasmolyzed T4-infected cells: evidence for two independent pathways to DNA. J Virol 1976; 20:142-56. [PMID: 789911 PMCID: PMC354975 DOI: 10.1128/jvi.20.1.142-156.1976] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bacteriophage T4-infected Escherichia coli rendered permeable to nucleotides by sucrose plasmolysis exhibited two apparently separate pathways or channels to T4 DNA with respect to the utilization of exogenously supplied substrates. By one pathway, individual labeled ribonucleotides, thymidine (tdR), and 5-hydroxymethyl-dCMP could be incorporated into phage DNA. Incorporation of each of these labeled compounds was not dependent upon the addition of the other deoxyribonucleotide precursors, suggesting that a functioning de novo pathway to deoxyribonucleotides was being monitored. The second pathway or reaction required all four deoxyribonucleoside triphosphates or the deoxyribonucleoside monophosphates together with ATP. However, in this reaction, dTTP was not replaced by TdR. The two pathways were also distinguished on the basis of their apparent Mg2+ requirements and responses to N-ethylmaleimide, micrococcal nuclease, and to hydroxyurea, which is a specific inhibitor of ribonucleoside diphosphate reductase. Separate products were synthesized by the two channels, as shown by density-gradient experiments and velocity sedimentation analysis. Each of the pathways required the products of the T4 DNA synthesis genes. Furthermore, DNA synthesis by each pathway appeared to be coupled to the functioning of several of the phage-induced enzymes involved in deoxyribonucleotide biosynthesis. Both systems represent replicative phage DNA synthesis as determined by CsCl density-gradient analysis. Autoradiographic and other studies provided evidence that both pathways occur in the same cell. Further studies were carried out on the direct role of dCMP hydroxymethylase in T4 DNA replication. Temperature-shift experiments in plasmolyzed cells using a temperature-sensitive mutant furnished strong evidence that this gene product is necessary in DNA replication and is not functioning by allowing preinitiation of DNA before plasmolysis.
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