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Yuan Y, Hutinet G, Valera JG, Hu J, Hillebrand R, Gustafson A, Iwata-Reuyl D, Dedon PC, de Crécy-Lagard V. Identification of the minimal bacterial 2'-deoxy-7-amido-7-deazaguanine synthesis machinery. Mol Microbiol 2018; 110:469-483. [PMID: 30159947 DOI: 10.1111/mmi.14113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2018] [Indexed: 12/27/2022]
Abstract
The 7-deazapurine derivatives, 2'-deoxy-7-cyano-7-deazaguanosine (dPreQ0 ) and 2'-deoxy-7-amido-7-deazaguanosine (dADG) are recently discovered DNA modifications encoded by the dpd cluster found in a diverse set of bacteria. Here we identify the genes required for the formation of dPreQ0 and dADG in DNA and propose a biosynthetic pathway. The preQ0 base is a precursor that in Salmonella Montevideo, is synthesized as an intermediate in the pathway of the tRNA modification queuosine. Of the 11 genes (dpdA - dpdK) found in the S. Montevideo dpd cluster, dpdA and dpdB are necessary and sufficient to synthesize dPreQ0 , while dpdC is additionally required for dADG synthesis. Among the rest of the dpd genes, dpdE, dpdG, dpdI, dpdK, dpdD and possibly dpdJ appear to be involved in a restriction-like phenotype. Indirect competition for preQ0 base led to a model for dADG synthesis in which DpdA inserts preQ0 into DNA with the help of DpdB, and then DpdC hydrolyzes dPreQ0 to dADG. The role of DpdB is not entirely clear as it is dispensable in other dpd clusters. Our discovery of a minimal gene set for introducing 7-deazapurine derivatives in DNA provides new tools for biotechnology applications and demonstrates the interplay between the DNA and RNA modification machineries.
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Affiliation(s)
- Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Jacqueline Gamboa Valera
- Department of Biological Engineering and Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jennifer Hu
- Department of Biological Engineering and Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Roman Hillebrand
- Department of Biological Engineering and Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Andrew Gustafson
- Department of Chemistry, Portland State University, Portland, OR, 97201, USA
| | - Dirk Iwata-Reuyl
- Department of Chemistry, Portland State University, Portland, OR, 97201, USA
| | - Peter C Dedon
- Department of Biological Engineering and Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.,University of Florida Genetics Institute, Gainesville, Florida, 32610, USA
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The Sequence of Two Bacteriophages with Hypermodified Bases Reveals Novel Phage-Host Interactions. Viruses 2018; 10:v10050217. [PMID: 29695085 PMCID: PMC5977210 DOI: 10.3390/v10050217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages SP-15 and ΦW-14 are members of the Myoviridae infecting Bacillus subtilis and Delftia (formerly Pseudomonas) acidovorans, respectively. What links them is that in both cases, approximately 50% of the thymine residues are replaced by hypermodified bases. The consequence of this is that the physico-chemical properties of the DNA are radically altered (melting temperature (Tm), buoyant density and susceptibility to restriction endonucleases). Using 454 pyrosequencing technology, we sequenced the genomes of both viruses. Phage ΦW-14 possesses a 157-kb genome (56.3% GC) specifying 236 proteins, while SP-15 is larger at 222 kb (38.6 mol % G + C) and encodes 318 proteins. In both cases, the phages can be considered genomic singletons since they do not possess BLASTn homologs. While no obvious genes were identified as being responsible for the modified base in ΦW-14, SP-15 contains a cluster of genes obviously involved in carbohydrate metabolism.
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Restriction and modification of deoxyarchaeosine (dG +)-containing phage 9 g DNA. Sci Rep 2017; 7:8348. [PMID: 28827753 PMCID: PMC5567051 DOI: 10.1038/s41598-017-08864-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 07/18/2017] [Indexed: 11/08/2022] Open
Abstract
E. coli phage 9 g contains the modified base deoxyarchaeosine (dG+) in its genome. The phage encodes its own primase, DNA ligase, DNA polymerase, and enzymes necessary to synthesize and incorporate dG+. Here we report phage 9 g DNA sensitivity to >200 Type II restriction endonucleases (REases). Among the REases tested approximately 29% generated complete or partial digestions, while the remaining 71% displayed resistance to restriction. Phage 9 g restriction fragments can be degraded by DNA exonucleases or ligated by T3 and T4 DNA ligases. In addition, we examined a number of cytosine and adenine methyltransferases to generate double base modifications. M.AluI, M.CviPI, M.HhaI, and M.EcoGII were able to introduce 5mC or N6mA into 9 g DNA as confirmed by partial resistance to restriction and by liquid chromatography-mass spectrometry. A number of wild-type E. coli bacteria restricted phage 9 g, indicating natural restriction barriers exist in some strains. A BlastP search of GenBank sequences revealed five glutamine amidotransferase-QueC homologs in Enterobacteria and Pseudomonas phage, and distant homologs in other phage and bacterial genomes, suggesting that dG+ is not a rare modification. We also mapped phage 9 g DNA packaging (pac) site containing two 21-bp direct repeats and a major terminase cleavage site in the phage genome.
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Miller PB, Wakarchuk WW, Warren RA. alpha-Putrescinylthymine and the sensitivity of bacteriophage phi W-14 DNA to restriction endonucleases. Nucleic Acids Res 1985; 13:2559-68. [PMID: 2987859 PMCID: PMC341175 DOI: 10.1093/nar/13.7.2559] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The modified base alpha-putrescinylthymine (putT) in phi W-14 DNA blocks cleavage of the DNA by 17 of 32 Type II restriction endonucleases. The enzymes cleaving the DNA do so to widely varying extents. The frequencies of cleavage of three altered forms of the DNA show that putT blocks recognition sites either when it occurs within the site or when it is in a sequence flanking the site. The blocking is dependent on both charge and steric factors. The charge effects can be greater than the steric effects for some of the enzymes tested. All the enzymes cleaving phi W-14 DNA release discrete fragments, showing that the distribution of putT is ordered. The cleavage frequencies for different enzymes suggest that the sequence CAputTG occurs frequently in the DNA. Only TaqI of the enzymes tested appeared not to be blocked by putT, but it was slowed down. TaqI generated fragments are joinable by T4 DNA ligase.
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