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Abstract
SAR11 clade members are among the most abundant bacteria on Earth. Their study is complicated by their great diversity and difficulties in being grown and manipulated in the laboratory. On the other hand, and due to their extraordinary abundance, metagenomic data sets provide enormous richness of information about these microbes. Given the major role played by phages in the lifestyle and evolution of prokaryotic cells, the contribution of several new bacteriophage genomes preying on this clade opens windows into the infection strategies and life cycle of its viruses. Such strategies could provide models of attack of large-genome phages preying on streamlined aquatic microbes. The SAR11 clade is one of the most abundant bacterioplankton groups in surface waters of most of the oceans and lakes. However, only 15 SAR11 phages have been isolated thus far, and only one of them belongs to the Myoviridae family (pelagimyophages). Here, we have analyzed 26 sequences of myophages that putatively infect the SAR11 clade. They have been retrieved by mining ca. 45 Gbp aquatic assembled cellular metagenomes and viromes. Most of the myophages were obtained from the cellular fraction (0.2 μm), indicating a bias against this type of virus in viromes. We have found the first myophages that putatively infect Candidatus Fonsibacter (freshwater SAR11) and another group putatively infecting bathypelagic SAR11 phylogroup Ic. The genomes have similar sizes and maintain overall synteny in spite of low average nucleotide identity values, revealing high similarity to marine cyanomyophages. Pelagimyophages recruited metagenomic reads widely from several locations but always much more from cellular metagenomes than from viromes, opposite to what happens with pelagipodophages. Comparing the genomes resulted in the identification of a hypervariable island that is related to host recognition. Interestingly, some genes in these islands could be related to host cell wall synthesis and coinfection avoidance. A cluster of curli-related proteins was widespread among the genomes, although its function is unclear. IMPORTANCE SAR11 clade members are among the most abundant bacteria on Earth. Their study is complicated by their great diversity and difficulties in being grown and manipulated in the laboratory. On the other hand, and due to their extraordinary abundance, metagenomic data sets provide enormous richness of information about these microbes. Given the major role played by phages in the lifestyle and evolution of prokaryotic cells, the contribution of several new bacteriophage genomes preying on this clade opens windows into the infection strategies and life cycle of its viruses. Such strategies could provide models of attack of large-genome phages preying on streamlined aquatic microbes.
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Scortecci JF, Serrão VHB, Cheleski J, Torini JR, Romanello L, DeMarco R, D'Muniz Pereira H. Spectroscopic and calorimetric assays reveal dependence on dCTP and two metals (Zn 2++Mg 2+) for enzymatic activity of Schistosoma mansoni deoxycytidylate (dCMP) deaminase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1326-1335. [PMID: 28807888 DOI: 10.1016/j.bbapap.2017.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 11/27/2022]
Abstract
The parasite Schistosoma mansoni possess all pathways for pyrimidine biosynthesis, whereby deaminases play an essential role in the thymidylate cycle, a crucial step to controlling the ratio between cytidine and uridine nucleotides. In this study, we heterologously expressed and purified the deoxycytidylate (dCMP) deaminase from S. mansoni to obtain structural, biochemical and kinetic information. Small-angle X-ray scattering of this enzyme showed that it is organized as a hexamer in solution. Isothermal titration calorimetry was used to determine the kinetic constants for dCMP-dUMP conversion and the role of dCTP and dTTP in enzymatic regulation. We evaluated the metals involved in activating the enzyme and show for the first time the dependence of correct folding on the interaction of two metals. This study provides information that may be useful for understanding the regulatory mechanisms involved in the metabolic pathways of S. mansoni. Thus, improving our understanding of the function of these essential pathways for parasite metabolism and showing for the first time the hitherto unknown deaminase function in this parasite.
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Affiliation(s)
| | - Vitor Hugo Balasco Serrão
- Physics Institute of São Carlos, University of São Paulo, São Carlos, SP CEP 13566-590, Brazil; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.
| | - Juliana Cheleski
- Physics Institute of São Carlos, University of São Paulo, São Carlos, SP CEP 13566-590, Brazil
| | - Juliana Roberta Torini
- Physics Institute of São Carlos, University of São Paulo, São Carlos, SP CEP 13566-590, Brazil
| | - Larissa Romanello
- Physics Institute of São Carlos, University of São Paulo, São Carlos, SP CEP 13566-590, Brazil
| | - Ricardo DeMarco
- Physics Institute of São Carlos, University of São Paulo, São Carlos, SP CEP 13566-590, Brazil
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Yang Y, Cai L, Ma R, Xu Y, Tong Y, Huang Y, Jiao N, Zhang R. A Novel Roseosiphophage Isolated from the Oligotrophic South China Sea. Viruses 2017; 9:v9050109. [PMID: 28505134 PMCID: PMC5454422 DOI: 10.3390/v9050109] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/22/2017] [Accepted: 05/10/2017] [Indexed: 12/30/2022] Open
Abstract
The Roseobacter clade is abundant and widespread in marine environments and plays an important role in oceanic biogeochemical cycling. In this present study, a lytic siphophage (labeled vB_DshS-R5C) infecting the strain type of Dinoroseobacter shibae named DFL12T, which is part of the Roseobacter clade, was isolated from the oligotrophic South China Sea. Phage R5C showed a narrow host range, short latent period and low burst size. The genome length of phage R5C was 77, 874 bp with a G+C content of 61.5%. Genomic comparisons detected no genome matches in the GenBank database and phylogenetic analysis based on DNA polymerase I revealed phylogenetic features that were distinct to other phages, suggesting the novelty of R5C. Several auxiliary metabolic genes (e.g., phoH gene, heat shock protein and queuosine biosynthesis genes) were identified in the R5C genome that may be beneficial to the host and/or offer a competitive advantage for the phage. Among siphophages infecting the Roseobacter clade (roseosiphophages), four gene transfer agent-like genes were commonly located with close proximity to structural genes, suggesting that their function may be related to the tail of siphoviruses. The isolation and characterization of R5C demonstrated the high genomic and physiological diversity of roseophages as well as improved our understanding of host-phage interactions and the ecology of the marine Roseobacter.
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Affiliation(s)
- Yunlan Yang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen 361102, Fujian, China.
| | - Lanlan Cai
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen 361102, Fujian, China.
| | - Ruijie Ma
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen 361102, Fujian, China.
| | - Yongle Xu
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen 361102, Fujian, China.
| | - Yigang Tong
- Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
| | - Yong Huang
- Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen 361102, Fujian, China.
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen 361102, Fujian, China.
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Li Y, Guo Z, Jin L, Wang D, Gao Z, Su X, Hou H, Dong Y. Mechanism of the allosteric regulation of Streptococcus mutans 2'-deoxycytidylate deaminase. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:883-91. [PMID: 27377385 DOI: 10.1107/s2059798316009153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 06/07/2016] [Indexed: 01/24/2023]
Abstract
In cells, dUMP is the intermediate precursor of dTTP in its synthesis during deoxynucleotide metabolism. In Gram-positive bacteria and eukaryotes, zinc-dependent deoxycytidylate deaminases (dCDs) catalyze the conversion of dCMP to dUMP. The activity of dCD is allosterically activated by dCTP and inhibited by dTTP. Here, the crystal structure of Streptococcus mutans dCD (SmdCD) complexed with dTTP is presented at 2.35 Å resolution, thereby solving the first pair of activator-bound and inhibitor-bound structures from the same species to provide a more definitive description of the allosteric mechanism. In contrast to the dTTP-bound dCD from the bacteriophage S-TIM5 (S-TIM5-dCD), dTTP-bound SmdCD adopts an inactive conformation similar to the apo form. A structural comparison suggests that the distinct orientations of the triphosphate group in S-TIM5-dCD and SmdCD are a result of the varying protein binding environment. In addition, calorimetric data establish that the modulators bound to dCD can be mutually competitively replaced. The results reveal the mechanism underlying its regulator-specific activity and might greatly enhance the understanding of the allosteric regulation of other dCDs.
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Affiliation(s)
- Yanhua Li
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Zhen Guo
- Key Laboratory of Molecular Biology on Infectious Disease, Chongqing Medical University, YiXueYuanlu-1, Chongqing, People's Republic of China
| | - Li Jin
- Key Laboratory of Molecular Biology on Infectious Disease, Chongqing Medical University, YiXueYuanlu-1, Chongqing, People's Republic of China
| | - Deqiang Wang
- Key Laboratory of Molecular Biology on Infectious Disease, Chongqing Medical University, YiXueYuanlu-1, Chongqing, People's Republic of China
| | - Zengqiang Gao
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xiaodong Su
- National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Science, Peking University, Beijing 100871, People's Republic of China
| | - Haifeng Hou
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yuhui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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Marx A, Alian A. The first crystal structure of a dTTP-bound deoxycytidylate deaminase validates and details the allosteric-inhibitor binding site. J Biol Chem 2014; 290:682-90. [PMID: 25404739 DOI: 10.1074/jbc.m114.617720] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Deoxycytidylate deaminase is unique within the zinc-dependent cytidine deaminase family as being allosterically regulated, activated by dCTP, and inhibited by dTTP. Here we present the first crystal structure of a dTTP-bound deoxycytidylate deaminase from the bacteriophage S-TIM5, confirming that this inhibitor binds to the same site as the dCTP activator. The molecular details of this structure, complemented by structures apo- and dCMP-bound, provide insights into the allosteric mechanism. Although the positioning of the nucleoside moiety of dTTP is almost identical to that previously described for dCTP, protonation of N3 in deoxythymidine and not deoxycytidine would facilitate hydrogen bonding of dTTP but not dCTP and may result in a higher affinity of dTTP to the allosteric site conferring its inhibitory activity. Further the functional group on C4 (O in dTTP and NH2 in dCTP) makes interactions with nonconserved protein residues preceding the allosteric motif, and the relative strength of binding to these residues appears to correspond to the potency of dTTP inhibition. The active sites of these structures are also uniquely occupied by dTMP and dCMP resolving aspects of substrate specificity. The methyl group of dTMP apparently clashes with a highly conserved tyrosine residue, preventing the formation of a correct base stacking shown to be imperative for deamination activity. The relevance of these findings to the wider zinc-dependent cytidine deaminase family is also discussed.
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Affiliation(s)
- Ailie Marx
- From the Faculty of Biology, Technion-Israel Institute of Technology, Haifa 320003, Israel
| | - Akram Alian
- From the Faculty of Biology, Technion-Israel Institute of Technology, Haifa 320003, Israel
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Crystal structures of Streptococcus mutans 2'-deoxycytidylate deaminase and its complex with substrate analog and allosteric regulator dCTP x Mg2+. J Mol Biol 2008; 377:220-31. [PMID: 18255096 DOI: 10.1016/j.jmb.2007.12.064] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2007] [Revised: 12/13/2007] [Accepted: 12/23/2007] [Indexed: 11/22/2022]
Abstract
2'-Deoxycytidylate deaminase [or deoxycytidine-5'-monophosphate (dCMP) deaminase, dCD] catalyzes the deamination of dCMP to deoxyuridine-5'-monophosphate to provide the main nucleotide substrate for thymidylate synthase, which is important in DNA synthesis. The activity of this homohexameric enzyme is allosterically regulated by deoxycytidine-5'-triphosphate (dCTP) as an activator and by deoxythymidine-5'-triphosphate as an inhibitor. In this article, we report the crystal structures of dCMP deaminase from Streptococcus mutans and its complex with dCTP and an intermediate analog at resolutions of 3.0 and 1.66 A. The protein forms a hexamer composed of subunits adopting a three-layer alpha/beta/alpha sandwich fold. The positive allosteric regulator dCTP mainly binds at the interface between two monomers in a molar ratio of 1:1 and rearranges the neighboring interaction networks. Structural comparisons and sequence alignments revealed that dCMP deaminase from Streptococcus mutans belongs to the cytidine deaminase superfamily, wherein the proteins exhibit a similar catalytic mechanism. In addition to the two conserved motifs involved in the binding of Zn(2+), a new conserved motif, (G(43)YNG(46)), related to the binding of dCTP was also identified. N-terminal Arg4, a key residue located between two monomers, binds strongly to the gamma phosphate group of dCTP. The regulation signal was transmitted by Arg4 from the allosteric site to the active site via modifications in the interactions at the interface where the substrate-binding pocket was involved and the relocations of Arg26, His65, Tyr120, and Arg121 to envelope the active site in order to stabilize substrate binding in the complex. Based on the enzyme-regulator complex structure observed in this study, we propose an allosteric mechanism for dCD regulation.
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Zhang Y, Maley F, Maley GF, Duncan G, Dunigan DD, Van Etten JL. Chloroviruses encode a bifunctional dCMP-dCTP deaminase that produces two key intermediates in dTTP formation. J Virol 2007; 81:7662-71. [PMID: 17475641 PMCID: PMC1933376 DOI: 10.1128/jvi.00186-07] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The chlorovirus PBCV-1, like many large double-stranded DNA-containing viruses, contains several genes that encode putative proteins involved in nucleotide biosynthesis. This report describes the characterization of the PBCV-1 dCMP deaminase, which produces dUMP, a key intermediate in the synthesis of dTTP. As predicted, the recombinant protein has dCMP deaminase activity that is activated by dCTP and inhibited by dTTP. Unexpectedly, however, the viral enzyme also has dCTP deaminase activity, producing dUTP. Typically, these two reactions are catalyzed by proteins in separate enzyme classes; to our knowledge, this is the first example of a protein having both deaminase activities. Kinetic experiments established that (i) the PBCV-1 enzyme has a higher affinity for dCTP than for dCMP, (ii) dCTP serves as a positive heterotropic effector for the dCMP deaminase activity and a positive homotropic effector for the dCTP deaminase activity, and (iii) the enzymatic efficiency of the dCMP deaminase activity is about four times higher than that of the dCTP deaminase activity. Inhibitor studies suggest that the same active site is involved in both dCMP and dCTP deaminations. The discovery that the PBCV-1 dCMP deaminase has two activities, together with a previous report that the virus also encodes a functional dUTP triphosphatase (Y. Zhang, H. Moriyama, K. Homma, and J. L. Van Etten, J. Virol. 79:9945-9953, 2005), means that PBCV-1 is the first virus to encode enzymes involved in all three known pathways to form dUMP.
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Affiliation(s)
- Yuanzheng Zhang
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583-0722, USA
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Liu Q, Liu J, Cao Q, Sha J, Zhou Z, Wang H, Li J. NYD-SP15: A Novel Gene Potentially Involved in Regulating Testicular Development and Spermatogenesis. Biochem Genet 2006; 44:409-23. [PMID: 16955368 DOI: 10.1007/s10528-006-9038-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2005] [Accepted: 02/23/2006] [Indexed: 10/24/2022]
Abstract
By hybridizing human adult testis cDNA microarrays with human adult and embryo testis cDNA probes, we identified a novel human testis gene, NYD-SP15. NYD-SP15 expression was 3.26-fold higher in adult than in fetal testis; however, there was almost no NYD-SP15 expression in the sperm. NYD-SP15 comprises 3364 base pairs, including a 1545 bp open reading frame encoding a 514 amino acid protein possessing 89% sequence identity with the mouse testis homologous protein. NYD-SP15 is located on human chromosome 13q14.2. The deduced structure of the protein contains two dCMP_cyt_deam domains, indicating a potential functional role for zinc ion binding. The gene is expressed variably in a wide range of tissues, with high expression levels in the testis. Sequence analysis revealed that NYD-SP15 is not a highly conserved protein, with its distribution in high-level species such as vertebrates including Homo, Mus, Rattus, and Canis. The results of semiquantitative polymerase chain reaction in mouse testis representing different developmental stages indicate that NYD-SP15 expression was developmentally regulated. These results suggest the putative NYD-SP15 protein may play an important role in testicular development and spermatogenesis and may be an important factor governing male infertility.
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Affiliation(s)
- Qinghuai Liu
- Lab of Reproductive Medicine, Department of Cell Biology and Medical Genetics, Nanjing Medical University, 140 Han Zhong Road, Nanjing, Jiangsu 210029, PR China
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Kim J, Shen R, Olcott MC, Rajagopal I, Mathews CK. Adenylate kinase of Escherichia coli, a component of the phage T4 dNTP synthetase complex. J Biol Chem 2005; 280:28221-9. [PMID: 15941717 DOI: 10.1074/jbc.m502201200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Adenylate kinase, which catalyzes the reversible ATP-dependent phosphorylation of AMP to ADP and dAMP to dADP, can also catalyze the conversion of nucleoside diphosphates to the corresponding triphosphates. Lu and Inouye (Lu, Q., and Inouye, M. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 5720-5725) showed that an Escherichia coli ndk mutant, lacking nucleoside diphosphate kinase, can use adenylate kinase as an alternative source of nucleoside triphosphates. Bacteriophage T4 can reproduce in an Escherichia coli ndk mutant, implying that adenylate kinase can meet a demand for deoxyribonucleoside triphosphates that increases by up to 10-fold as a result of T4 infection. In terms of kinetic linkage and specific protein-protein associations, NDP kinase is an integral component of T4 dNTP synthetase, a multienzyme complex containing phage-coded enzymes, which facilitates the synthesis of dNTPs and their flow into DNA. Here we asked whether, by similar criteria, adenylate kinase of the host cell is also a specific component of the complex. Experiments involving protein affinity chromatography, immunoprecipitation, optical biosensor measurements, and glutathione S-transferase pulldowns demonstrated direct interactions between adenylate kinase and several phage-coded enzymes, as well as E. coli nucleoside diphosphate kinase. These results identify adenylate kinase as a specific component of the complex. The rate of DNA synthesis after infection of an ndk mutant was found to be about 40% of the rate seen in wild-type infection, implying that complementation of the missing NDP kinase function by adenylate kinase is fairly efficient, but that adenylate kinase becomes rate-limiting for DNA synthesis when it is the sole source of dNTPs.
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Affiliation(s)
- Juhyun Kim
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305, USA
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Li H, Xu H, Graham DE, White RH. The Methanococcus jannaschii dCTP deaminase is a bifunctional deaminase and diphosphatase. J Biol Chem 2003; 278:11100-6. [PMID: 12538648 DOI: 10.1074/jbc.m212460200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most bacteria produce the dUMP precursor for thymine nucleotide biosynthesis using two enzymes: a dCTP deaminase catalyzes the formation of dUTP and a dUTP diphosphatase catalyzes pyrophosphate release. Although these two hydrolytic enzymes appear to catalyze very different reactions, they are encoded by homologous genes. The hyperthermophilic archaeon Methanococcus jannaschii has two members of this gene family. One gene, at locus MJ1102, encodes a dUTP diphosphatase, which can scavenge deoxyuridine nucleotides that inhibit archaeal DNA polymerases. The second gene, at locus MJ0430, encodes a novel dCTP deaminase that releases dUMP, ammonia, and pyrophosphate. Therefore this enzyme can singly catalyze both steps in dUMP biosynthesis, precluding the formation of free, mutagenic dUTP. Besides differing from the previously characterized Salmonella typhimurium dCTP deaminase in its reaction products, this archaeal enzyme has a higher affinity for dCTP and its steady-state turnover is faster than the bacterial enzyme. Kinetic studies suggest: 1) the archaeal enzyme specifically recognizes dCTP; 2) dCTP deamination and dUTP diphosphatase activities occur independently at the same active site, and 3) both activities depend on Mg(2+). The bifunctional activity of this M. jannaschii enzyme illustrates the evolution of a suprafamily of related enzymes that catalyze mechanistically distinct reactions.
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Affiliation(s)
- Hong Li
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0308, USA
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11
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Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Rüger W. Bacteriophage T4 genome. Microbiol Mol Biol Rev 2003; 67:86-156, table of contents. [PMID: 12626685 PMCID: PMC150520 DOI: 10.1128/mmbr.67.1.86-156.2003] [Citation(s) in RCA: 562] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene products. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods. The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition. Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level. The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments. Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the "cell-puncturing device," combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection. Despite these advances, nearly 130 potential T4 genes remain uncharacterized. Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli. T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex evolution and ecology of phages-the most abundant and among the most ancient biological entities on Earth.
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Affiliation(s)
- Eric S Miller
- Department of Microbiology, North Carolina State University, Raleigh, North Carolina 27695-7615, USA.
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Keefe RG, Maley GF, Saxl RL, Maley F. A T4-phage deoxycytidylate deaminase mutant that no longer requires deoxycytidine 5'-triphosphate for activation. J Biol Chem 2000; 275:12598-602. [PMID: 10777550 DOI: 10.1074/jbc.275.17.12598] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A deoxycytidylate (dCMP) deaminase encoded in T4-bacteriophage DNA that is induced on phage infection of Escherichia coli was shown earlier (Maley, G. F., Duceman, B. W., Wang, A. M., Martinez, J. M., and Maley, F. (1990) J. Biol. Chem. 265, 47-51) to be similar in size, properties, and amino acid composition to the T2-phage-induced deaminase. Neither enzyme is active in the absence of dCTP or its natural activator, 5-hydroxymethyl-dCTP. However, on changing the arginine (Arg) at residue 115 of the T4-deaminase to either a glutamate (R115E) or a glutamine (R115Q), the resulting mutant enzymes were active in the absence of dCTP, with each mutant possessing a turnover number or k(cat) that is about 15% that of the wild-type deaminase. When compared on the basis of specific activity, however, the mutants are about 40-50% of the wild-type (WT)-enzyme's specific activity. Molecular weight analysis on the wild-type and mutant deaminases using HPLC size exclusion chromatography revealed that the wild-type deaminase was basically a hexamer, particularly in the presence of dCTP, regardless of the extent of dilution. Under similar conditions, R115E remained a dimer, whereas R115Q and F112A varied from hexamers to dimers particularly at concentrations normally present in the assay solution. Activity measurements appear to support the conclusion that the hexameric form of the enzyme is activated by dCTP, while the dimer is not. Another feature emphasizing the difference between the WT and mutant deaminases was observed on their denaturation-renaturation in EDTA, which revealed the mutants to be restored to 50% of their original activities with the WT deaminase only marginally restored.
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Affiliation(s)
- R G Keefe
- Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509, USA
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13
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Porter DJ. Escherichia coli cytosine deaminase: the kinetics and thermodynamics for binding of cytosine to the apoenzyme and the Zn(2+) holoenzyme are similar. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1476:239-52. [PMID: 10669789 DOI: 10.1016/s0167-4838(99)00246-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Recombinant Escherichia coli cytosine deaminase is purified as a mixture of Zn(2+) and Fe(2+) forms of the enzyme. Fe(2+) is removed readily by o-phenanthroline to yield apoenzyme (apoCDase) that contains <0.2 mol of Zn(2+)per mol of subunit. ApoCDase was efficiently reconstituted to Zn(2+)CDase by treatment with ZnCl(2). The interaction of cytosine with apoCDase and Zn(2+)CDase was investigated at pH 7.5 and 25 degrees C by monitoring changes in intrinsic protein fluorescence. The values for the kinetic data K(1), k(2), and k(3) for Zn(2+)CDase were 0.25 mM, 80 s(-1), and 38 s(-1), respectively. The value for k(-2) was statistically indistinguishable from zero. The analogous values for K(1), k(2), and k(-2), (k(3)=0) for apoCDase were 0.157 mM, 186 s(-1) and approximately 0.8 s(-1), respectively. The overall dissociation constant of apoCDase for cytosine was 0.00069 mM, whereas the K(m) of Zn(2+)CDase for cytosine was 0.20 mM. The pre-steady state phase of the reaction was associated with an absorbance increase at 280 nm that was attributed to solvent perturbation of the spectrum of cytosine or enzyme. Formation of the Fe(2+)CDase-cytosine complex was too rapid to monitor by these techniques.
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Affiliation(s)
- D J Porter
- Glaxo Wellcome, 5 Moore Drive, Research Triangle Park, NC 27709, USA
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14
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Mian IS, Moser MJ, Holley WR, Chatterjee A. Statistical modelling and phylogenetic analysis of a deaminase domain. J Comput Biol 1998; 5:57-72. [PMID: 9541871 DOI: 10.1089/cmb.1998.5.57] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Deamination reactions are catalyzed by a variety of enzymes including those involved in nucleoside/nucleotide metabolism and cytosine to uracil (C-->U) and adenosine to inosine (A-->I) mRNA editing. The active site of the deaminase (DM) domain in these enzymes contains a conserved histidine (or rarely cysteine), two cysteines and a glutamate proposed to act as a proton shuttle during deamination. Here, a statistical model, a hidden Markov model (HMM), of the DM domain has been created which identifies currently known DM domains and suggests new DM domains in viral, bacterial and eucaryotic proteins. However, no DM domains were identified in the currently predicted proteins from the archaeon Methanococcus jannaschii and possible causes for, and a potential means to ameliorate this situation are discussed. In some of the newly identified DM domains, the glutamate is changed to a residue that could not function as a proton shuttle and in one instance (Mus musculus spermatid protein TENR) the cysteines are also changed to lysine and serine. These may be non-competent DM domains able to bind but not act upon their substrate. Phylogenetic analysis using an HMM-generated alignment of DM domains reveals three branches with clear substructure in each branch. The results suggest DM domains that are candidates for yeast, platyhelminth, plant and mammalian C-->U and A-->I mRNA editing enzymes. Some bacterial and eucaryotic DM domains form distinct branches in the phylogenetic tree suggesting the existence of common, novel substrates.
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Affiliation(s)
- I S Mian
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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15
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McGaughey KM, Wheeler LJ, Moore JT, Maley GF, Maley F, Mathews CK. Protein-protein interactions involving T4 phage-coded deoxycytidylate deaminase and thymidylate synthase. J Biol Chem 1996; 271:23037-42. [PMID: 8798492 DOI: 10.1074/jbc.271.38.23037] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The enzymes deoxycytidylate deaminase (EC) and thymidylate synthase (EC) are functionally associated with one another, since they catalyze sequential reactions. In T4 coliphage infection the two enzymes are found in dNTP synthetase, a multienzyme complex for deoxyribonucleotide biosynthesis. Protein-protein interactions involving the phage-coded forms of these two enzymes have been explored in three experiments that use the respective purified protein as an affinity ligand. First, an extract of radiolabeled T4 proteins was passed through a column of immobilized enzyme (either dTMP synthase or dCMP deaminase), and the specifically bound proteins were identified. Second, two mutant form of dCMP deaminase (H90N and H94N), altered in presumed zinc-binding sites, were analyzed similarly, with the results suggesting that some, but not all, interactions require normal structure near the catalytic site. Third, affinity chromatography using either enzyme as the immobilized ligand, revealed interactions between the two purified enzymes in the absence of other proteins. In these experiments we noted a significant effect of dCTP, an allosteric modifier of dCMP deaminase, upon the interactions.
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Affiliation(s)
- K M McGaughey
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7503, USA
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16
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Grosjean H, Auxilien S, Constantinesco F, Simon C, Corda Y, Becker HF, Foiret D, Morin A, Jin YX, Fournier M, Fourrey JL. Enzymatic conversion of adenosine to inosine and to N1-methylinosine in transfer RNAs: a review. Biochimie 1996; 78:488-501. [PMID: 8915538 DOI: 10.1016/0300-9084(96)84755-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Inosine (6-deaminated adenosine) is a characteristic modified nucleoside that is found at the first anticodon position (position 34) of several tRNAs of eukaryotic and eubacterial origins, while N1-methylinosine is found exclusively at position 37 (3' adjacent to the anticodon) of eukaryotic tRNA(Ala) and at position 57 (in the middle of the psi loop) of several tRNAs from halophilic and thermophilic archaebacteria. Inosine has also been recently found in double-stranded RNA, mRNA and viral RNAs. As for all other modified nucleosides in RNAs, formation of inosine and inosine derivative in these RNA is catalysed by specific enzymes acting after transcription of the RNA genes. Using recombinant tRNAs and T7-runoff transcripts of several tRNA genes as substrates, we have studied the mechanism and specificity of tRNA-inosine-forming enzymes. The results show that inosine-34 and inosine-37 in tRNAs are both synthesised by a hydrolytic deamination-type reaction, catalysed by distinct tRNA:adenosine deaminases. Recognition of tRNA substrates by the deaminases does not strictly depend on a particular "identity' nucleotide. However, the efficiency of adenosine to inosine conversion depends on the nucleotides composition of the anticodon loop and the proximal stem as well as on 3D-architecture of the tRNA. In eukaryotic tRNA(Ala), N1-methylinosine-37 is formed from inosine-37 by a specific SAM-dependent methylase, while in the case of N1-methylinosine-57 in archaeal tRNAs, methylation of adenosine-57 into N1-methyladenosine-57 occurs before the deamination process. The T psi-branch of fragmented tRNA is the minimalist substrate for the N1-methylinosine-57 forming enzymes. Inosine-34 and N1-methylinosine-37 in human tRNA(Ala) are targets for specific autoantibodies which are present in the serum of patients with inflammatory muscle disease of the PL-12 polymyositis type. Here we discuss the mechanism, specificity and general properties of the recently discovered RNA:adenosine deaminases/editases acting on double-stranded RNA, intron-containing mRNA and viral RNA in relation to those of the deaminases acting on tRNAs.
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Affiliation(s)
- H Grosjean
- CNRS, Laboratoire d'Enzymologie et de Biochimie Structurales, Gif-sur-Yvétte, France
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17
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MacGinnitie AJ, Anant S, Davidson NO. Mutagenesis of apobec-1, the Catalytic Subunit of the Mammalian Apolipoprotein B mRNA Editing Enzyme, Reveals Distinct Domains That Mediate Cytosine Nucleoside Deaminase, RNA Binding, and RNA Editing Activity. J Biol Chem 1995. [DOI: 10.1074/jbc.270.24.14768] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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18
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Navaratnam N, Bhattacharya S, Fujino T, Patel D, Jarmuz AL, Scott J. Evolutionary origins of apoB mRNA editing: catalysis by a cytidine deaminase that has acquired a novel RNA-binding motif at its active site. Cell 1995; 81:187-95. [PMID: 7736571 DOI: 10.1016/0092-8674(95)90328-3] [Citation(s) in RCA: 146] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The site-specific C to U editing of apolipoprotein B100 (apoB100) mRNA requires a 27 kDa protein (p27) with homology to cytidine deaminase. Here, we show that p27 is a zinc-containing deaminase, which operates catalytically like the E. coli enzyme that acts on monomeric substrate. In contrast with the bacterial enzyme that does not bind RNA, p27 interacts with its polymeric apoB mRNA substrate at AU sequences adjacent to the editing site. This interaction is necessary for editing. RNA binding is mediated through amino acid residues involved in zinc coordination, in proton shuttling, and in forming the alpha beta alpha structure that encompasses the active site. However, certain mutations that inactivate the enzyme do not affect RNA binding. Thus, RNA binding does not require a catalytically active site. The acquisition of polymeric substrate binding provides a route for the evolution of this editing enzyme from one that acts on monomeric substrates.
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Affiliation(s)
- N Navaratnam
- Medical Research Council Molecular Medicine Group, Royal Postgraduate Medical School, Hammersmith Hospital, London, England
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19
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Expression and characterization of p27, the catalytic subunit of the apolipoprotein B mRNA editing enzyme. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)32097-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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20
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Yamanaka S, Poksay K, Balestra M, Zeng G, Innerarity T. Cloning and mutagenesis of the rabbit ApoB mRNA editing protein. A zinc motif is essential for catalytic activity, and noncatalytic auxiliary factor(s) of the editing complex are widely distributed. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)31865-3] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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21
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Reizer J, Buskirk S, Bairoch A, Reizer A, Saier MH. A novel zinc-binding motif found in two ubiquitous deaminase families. Protein Sci 1994; 3:853-6. [PMID: 8061614 PMCID: PMC2142716 DOI: 10.1002/pro.5560030515] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Two families of deaminases, one specific for cytidine, the other for deoxycytidylate, are shown to possess a novel zinc-binding motif, here designated ZBS. We have (1) identified the protein members of these 2 families, (2) carried out sequence analyses that allow specification of this zinc-binding motif, and (3) determined signature sequences that will allow identification of additional members of these families as their sequences become available.
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Affiliation(s)
- J Reizer
- Department of Biology, University of California at San Diego, La Jolla 92093-0116
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22
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Bhattacharya S, Navaratnam N, Morrison JR, Scott J, Taylor WR. Cytosine nucleoside/nucleotide deaminases and apolipoprotein B mRNA editing. Trends Biochem Sci 1994; 19:105-6. [PMID: 8203015 DOI: 10.1016/0968-0004(94)90200-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- S Bhattacharya
- Medical Research Council Molecular Medicine Group, Royal Postgraduate Medical School, Hammersmith Hospital, London, UK
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23
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Navaratnam N, Morrison J, Bhattacharya S, Patel D, Funahashi T, Giannoni F, Teng B, Davidson N, Scott J. The p27 catalytic subunit of the apolipoprotein B mRNA editing enzyme is a cytidine deaminase. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(19)36836-x] [Citation(s) in RCA: 221] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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