1
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Nicastro GG, Burroughs AM, Iyer L, Aravind L. Functionally comparable but evolutionarily distinct nucleotide-targeting effectors help identify conserved paradigms across diverse immune systems. Nucleic Acids Res 2023; 51:11479-11503. [PMID: 37889040 PMCID: PMC10681802 DOI: 10.1093/nar/gkad879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
While nucleic acid-targeting effectors are known to be central to biological conflicts and anti-selfish element immunity, recent findings have revealed immune effectors that target their building blocks and the cellular energy currency-free nucleotides. Through comparative genomics and sequence-structure analysis, we identified several distinct effector domains, which we named Calcineurin-CE, HD-CE, and PRTase-CE. These domains, along with specific versions of the ParB and MazG domains, are widely present in diverse prokaryotic immune systems and are predicted to degrade nucleotides by targeting phosphate or glycosidic linkages. Our findings unveil multiple potential immune systems associated with at least 17 different functional themes featuring these effectors. Some of these systems sense modified DNA/nucleotides from phages or operate downstream of novel enzymes generating signaling nucleotides. We also uncovered a class of systems utilizing HSP90- and HSP70-related modules as analogs of STAND and GTPase domains that are coupled to these nucleotide-targeting- or proteolysis-induced complex-forming effectors. While widespread in bacteria, only a limited subset of nucleotide-targeting effectors was integrated into eukaryotic immune systems, suggesting barriers to interoperability across subcellular contexts. This work establishes nucleotide-degrading effectors as an emerging immune paradigm and traces their origins back to homologous domains in housekeeping systems.
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Affiliation(s)
- Gianlucca G Nicastro
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - A Maxwell Burroughs
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - Lakshminarayan M Iyer
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - L Aravind
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
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2
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Cui L, Balamkundu S, Liu CF, Ye H, Hourihan J, Rausch A, Hauß C, Nilsson E, Hoetzinger M, Holmfeldt K, Zhang W, Martinez-Alvarez L, Peng X, Tremblay D, Moinau S, Solonenko N, Sullivan M, Lee YJ, Mulholland A, Weigele P, de Crécy-Lagard V, Dedon P, Hutinet G. Four additional natural 7-deazaguanine derivatives in phages and how to make them. Nucleic Acids Res 2023; 51:9214-9226. [PMID: 37572349 PMCID: PMC10516641 DOI: 10.1093/nar/gkad657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/20/2023] [Accepted: 08/06/2023] [Indexed: 08/14/2023] Open
Abstract
Bacteriophages and bacteria are engaged in a constant arms race, continually evolving new molecular tools to survive one another. To protect their genomic DNA from restriction enzymes, the most common bacterial defence systems, double-stranded DNA phages have evolved complex modifications that affect all four bases. This study focuses on modifications at position 7 of guanines. Eight derivatives of 7-deazaguanines were identified, including four previously unknown ones: 2'-deoxy-7-(methylamino)methyl-7-deazaguanine (mdPreQ1), 2'-deoxy-7-(formylamino)methyl-7-deazaguanine (fdPreQ1), 2'-deoxy-7-deazaguanine (dDG) and 2'-deoxy-7-carboxy-7-deazaguanine (dCDG). These modifications are inserted in DNA by a guanine transglycosylase named DpdA. Three subfamilies of DpdA had been previously characterized: bDpdA, DpdA1, and DpdA2. Two additional subfamilies were identified in this work: DpdA3, which allows for complete replacement of the guanines, and DpdA4, which is specific to archaeal viruses. Transglycosylases have now been identified in all phages and viruses carrying 7-deazaguanine modifications, indicating that the insertion of these modifications is a post-replication event. Three enzymes were predicted to be involved in the biosynthesis of these newly identified DNA modifications: 7-carboxy-7-deazaguanine decarboxylase (DpdL), dPreQ1 formyltransferase (DpdN) and dPreQ1 methyltransferase (DpdM), which was experimentally validated and harbors a unique fold not previously observed for nucleic acid methylases.
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Affiliation(s)
- Liang Cui
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore
| | - Seetharamsing Balamkundu
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Hong Ye
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jacob Hourihan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Astrid Rausch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Christopher Hauß
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Emelie Nilsson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 391 82 Kalmar, Sweden
| | - Matthias Hoetzinger
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 391 82 Kalmar, Sweden
| | - Karin Holmfeldt
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 391 82 Kalmar, Sweden
| | - Weijia Zhang
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | | | - Xu Peng
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Denise Tremblay
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
- Félix d’Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Québec, Canada
| | - Sylvain Moinau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
- Félix d’Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Québec, Canada
| | - Natalie Solonenko
- Department of Microbiology, Ohio State University, Columbus, OH, USA
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Department of Civil, Environmental, and Geodetic Engineering, and Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
| | | | - Peter R Weigele
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
- University of Florida, Genetics Institute, Gainesville, FL 32610, USA
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
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3
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Xu J, Li J, Yan Y, Han P, Tong Y, Li X. SW16-7, a Novel Ackermannviridae Bacteriophage with Highly Effective Lytic Activity Targets Salmonella enterica Serovar Weltevreden. Microorganisms 2023; 11:2090. [PMID: 37630650 PMCID: PMC10458263 DOI: 10.3390/microorganisms11082090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Salmonella enterica serovar Weltevreden is a foodborne pathogen commonly transmitted through fresh vegetables and seafood. In this study, a lytic phage, SW16-7, was isolated from medical sewage, demonstrating high infectivity against S. Weltevreden, S. London, S. Meleagridis, and S. Give of Group O:3. In vitro inhibition assays revealed its effective antibacterial effect for up to 12 h. Moreover, analysis using the Comprehensive Antibiotic Resistance Database (CARD) and the Virulence Factor Database (VFDB) showed that SW16-7's genome does not contain any virulence factors or antibiotic resistance genes, indicating its potential as a promising biocontrol agent against S. Weltevreden. Additionally, a TSP gene cluster was identified in SW16-7's genome, with TSP1 and TSP2 showing a high similarity to lysogenic phages ε15 and ε34, respectively, in the C-terminal region. The whole-genome phylogenetic analysis classified SW16-7 within the Ackermannviridae family and indicated a close relationship with Agtrevirus, which is consistent with the ANI results.
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Affiliation(s)
- Jialiang Xu
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing 100048, China; (J.X.); (J.L.); (Y.Y.)
| | - Jia Li
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing 100048, China; (J.X.); (J.L.); (Y.Y.)
| | - Yi Yan
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing 100048, China; (J.X.); (J.L.); (Y.Y.)
| | - Pengjun Han
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (P.H.); (Y.T.)
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (P.H.); (Y.T.)
| | - Xu Li
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing 100048, China; (J.X.); (J.L.); (Y.Y.)
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4
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A Glimpse at the Anti-Phage Defenses Landscape in the Foodborne Pathogen Salmonella enterica subsp. enterica serovar Typhimurium. Viruses 2023; 15:v15020333. [PMID: 36851545 PMCID: PMC9958689 DOI: 10.3390/v15020333] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Bacteriophages, which specifically infect and kill bacteria, are currently used as additives to control pathogens such as Salmonella in human food (PhageGuard S®) or animal feed (SalmoFREE®, Bafasal®). Indeed, salmonellosis is among the most important zoonotic foodborne illnesses. The presence of anti-phage defenses protecting bacteria against phage infection could impair phage applications aiming at reducing the burden of foodborne pathogens such as Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) to the food industry. In this study, the landscape of S. Typhimurium anti-phage defenses was bioinformatically investigated in publicly available genomes using the webserver PADLOC. The primary anti-phage systems identified in S. Typhimurium use nucleic acid degradation and abortive infection mechanisms. Reference systems were identified on an integrative and conjugative element, a transposon, a putative integrative and mobilizable element, and prophages. Additionally, the mobile genetic elements (MGEs) containing a subset of anti-phage systems were found in the Salmonella enterica species. Lastly, the MGEs alone were also identified in the Enterobacteriaceae family. The presented diversity assessment of the anti-phage defenses and investigation of their dissemination through MGEs in S. Typhimurium constitute a first step towards the design of preventive measures against the spread of phage resistance that may hinder phage applications.
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5
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Bommisetti P, Young A, Bandarian V. Elucidation of the substrate of tRNA-modifying enzymes MnmEG leads to in vitro reconstitution of an evolutionarily conserved uridine hypermodification. J Biol Chem 2022; 298:102548. [PMID: 36181794 PMCID: PMC9626948 DOI: 10.1016/j.jbc.2022.102548] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 12/02/2022] Open
Abstract
The evolutionarily conserved bacterial proteins MnmE and MnmG collectively install a carboxymethylaminomethyl (cmnm) group at the fifth position of wobble uridines of several tRNA species. While the reaction catalyzed by MnmEG is one of the central steps in the biosynthesis of the methylaminomethyl (mnm) posttranscriptional tRNA modification, details of the reaction remain elusive. Glycine is known to be the source of the carboxy methylamino moiety of cmnm, and a tetrahydrofolate (THF) analog is thought to supply the one carbon that is appended to the fifth position of U. However, the nature of the folate analog remains unknown. This article reports the in vitro biochemical reconstitution of the MnmEG reaction. Using isotopically labeled methyl and methylene THF analogs, we demonstrate that methylene THF is the true substrate. We also show that reduced FAD is required for the reaction and that DTT can replace the NADH in its role as a reductant. We discuss the implications of these methylene-THF and reductant requirements on the mechanism of this key tRNA modification catalyzed by MnmEG.
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Affiliation(s)
- Praneeth Bommisetti
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Anthony Young
- Soliome Inc, 479 Jessie Street, San Francisco, CA 94103, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States.
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6
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Genome Sequence of SN1, a Bacteriophage That Infects Sphaerotilus natans and Pseudomonas aeruginosa. Microbiol Resour Announc 2022; 11:e0047822. [PMID: 35920671 PMCID: PMC9476957 DOI: 10.1128/mra.00478-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phage SN1 infects
Sphaerotilus natans
and
Pseudomonas aeruginosa
strains. Its genome consists of 61,858 bp (64.3% GC) and 89 genes, including 32 with predicted functions. SN1 genome is very similar to
Pseudomonas
phage M6, which contains hypermodified thymidines. Genome analyses revealed similar base-modifying genes as those found in M6.
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7
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Udupa S, Nagaraja V, Karambelkar S. Binding Affinity Quantifications of the Bacteriophage Mu DNA Modification Protein Mom Using Microscale Thermophoresis (MST). Bio Protoc 2022; 12:e4472. [PMID: 35978573 PMCID: PMC9350919 DOI: 10.21769/bioprotoc.4472] [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: 11/01/2021] [Revised: 05/15/2022] [Accepted: 06/11/2022] [Indexed: 12/29/2022] Open
Abstract
Epigenetic modifications play diverse roles in biological systems. Nucleic acid modifications control gene expression, protein synthesis, and sensitivity to nucleic acid-cleaving enzymes. However, the mechanisms underlying the biosynthesis of nucleic acid modifications can be challenging to identify. Studying protein-ligand interactions helps decipher biosynthetic and regulatory pathways underlying biological reactions. Here, we describe a fluorescence labeling-based quantitative method for unraveling the biomolecular interactions of bacteriophage Mu DNA modification protein Mom with its ligands, using microscale thermophoresis (MST). Compared to traditional methods for studying protein-biomolecular interactions, MST requires significantly lower sample amounts, volumes, and analysis time, thus allowing screening of a large number of candidates for interaction with a protein of interest. Another distinguishing feature of the method is that it obviates the need for protein purification, often a time- and resource-consuming step, and works well with whole or partially purified cell extracts. Importantly, the method is sensitive over a broad range of molecular affinities while offering great specificity and can be used to interrogate ligands ranging from metal ions to macromolecules. Although we established this method for a DNA modification protein, it can easily be adapted to study a variety of molecular interactions engaged by proteins.
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Affiliation(s)
- Shubha Udupa
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
,
Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
,
*For correspondence:
;
| | - Shweta Karambelkar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
,
Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
,
*For correspondence:
;
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8
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Gracias F, Ruiz-Larrabeiti O, Vaňková Hausnerová V, Pohl R, Klepetářová B, Sýkorová V, Krásný L, Hocek M. Homologues of epigenetic pyrimidines: 5-alkyl-, 5-hydroxyalkyl and 5-acyluracil and -cytosine nucleotides: synthesis, enzymatic incorporation into DNA and effect on transcription with bacterial RNA polymerase. RSC Chem Biol 2022; 3:1069-1075. [PMID: 35975001 PMCID: PMC9347353 DOI: 10.1039/d2cb00133k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/23/2022] [Indexed: 12/17/2022] Open
Abstract
Homologues of natural epigenetic pyrimidine nucleosides and nucleotides were designed and synthesized. They included 5-ethyl-, 5-propyl-, 5-(1-hydroxyethyl)-, 5-(1-hydroxypropyl)- and 5-acetyl- and 5-propionylcytosine and -uracil 2′-deoxyribonucleosides and their corresponding 5′-O-triphosphates (dNXTPs). The epimers of 5-(1-hydroxyethyl)- and 5-(1-hydroxypropyl)pyrimidine nucleosides were separated and their absolute configuration was determined by a combination of X-ray and NMR analysis. The modified dNXTPs were used as substrates for PCR synthesis of modified DNA templates used for the study of transcription with bacterial RNA polymerase. Fundamental differences in transcription efficiency were observed, depending on the various modifications. The most notable effects included pronounced stimulation of transcription from 5-ethyluracil-bearing templates (200% transcription yield compared to natural thymine) and an enhancing effect of 5-acetylcytosine versus inhibiting effect of 5-acetyluracil. In summary, these results reveal that RNA polymerase copes with dramatically altered DNA structure and suggest that these nucleobases could potentially play roles as artificial epigenetic DNA nucleobases. Nucleotides derived from homologues of epigenetic pyrimidine bases were prepared and used for polymerase synthesis of modified DNA templates. Interesting effects of the substituents on PCR and transcription have been observed.![]()
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Affiliation(s)
- Filip Gracias
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
| | - Olatz Ruiz-Larrabeiti
- Lab. of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Prague 4, Czech Republic
| | - Viola Vaňková Hausnerová
- Lab. of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Prague 4, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
| | - Blanka Klepetářová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
| | - Libor Krásný
- Lab. of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Prague 4, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843, Prague 2, Czech Republic
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9
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Hutinet G, Lee YJ, de Crécy-Lagard V, Weigele PR. Hypermodified DNA in Viruses of E. coli and Salmonella. EcoSal Plus 2021; 9:eESP00282019. [PMID: 34910575 PMCID: PMC11163837 DOI: 10.1128/ecosalplus.esp-0028-2019] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/26/2021] [Indexed: 12/23/2022]
Abstract
The DNA in bacterial viruses collectively contains a rich, yet relatively underexplored, chemical diversity of nucleobases beyond the canonical adenine, guanine, cytosine, and thymine. Herein, we review what is known about the genetic and biochemical basis for the biosynthesis of complex DNA modifications, also called DNA hypermodifications, in the DNA of tailed bacteriophages infecting Escherichia coli and Salmonella enterica. These modifications, and their diversification, likely arose out of the evolutionary arms race between bacteriophages and their cellular hosts. Despite their apparent diversity in chemical structure, the syntheses of various hypermodified bases share some common themes. Hypermodifications form through virus-directed synthesis of noncanonical deoxyribonucleotide triphosphates, direct modification DNA, or a combination of both. Hypermodification enzymes are often encoded in modular operons reminiscent of biosynthetic gene clusters observed in natural product biosynthesis. The study of phage-hypermodified DNA provides an exciting opportunity to expand what is known about the enzyme-catalyzed chemistry of nucleic acids and will yield new tools for the manipulation and interrogation of DNA.
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Affiliation(s)
- Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, Massachusetts, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Peter R. Weigele
- Research Department, New England Biolabs, Ipswich, Massachusetts, USA
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10
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Kaminski PA. Mechanisms supporting aminoadenine-based viral DNA genomes. Cell Mol Life Sci 2021; 79:51. [PMID: 34910247 PMCID: PMC11072226 DOI: 10.1007/s00018-021-04055-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/17/2021] [Accepted: 11/21/2021] [Indexed: 10/19/2022]
Abstract
Bacteriophage genomes are the richest source of modified nucleobases of any life form. Of these, 2,6 diaminopurine, which pairs with thymine by forming three hydrogen bonds violates Watson and Crick's base pairing. 2,6 diaminopurine initially found in the cyanophage S-2L is more widespread than expected and has also been detected in phage infecting Gram-negative and Gram-positive bacteria. The biosynthetic pathway for aminoadenine containing DNA as well as the exclusion of adenine are now elucidated. This example of a natural deviation from the genetic code represents only one of the possibilities explored by nature and provides a proof of concept for the synthetic biology of non-canonical nucleic acids.
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Affiliation(s)
- P A Kaminski
- Biologie des Bactéries Pathogènes à Gram-Positif, Institut Pasteur, CNRS-UMR 2001, Paris, France.
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