1
|
Abstract
Toxin-antitoxin (TA) systems are ubiquitous genetic elements in bacteria that consist of a growth-inhibiting toxin and its cognate antitoxin. These systems are prevalent in bacterial chromosomes, plasmids, and phage genomes, but individual systems are not highly conserved, even among closely related strains. The biological functions of TA systems have been controversial and enigmatic, although a handful of these systems have been shown to defend bacteria against their viral predators, bacteriophages. Additionally, their patterns of conservation-ubiquitous, but rapidly acquired and lost from genomes-as well as the co-occurrence of some TA systems with known phage defense elements are suggestive of a broader role in mediating phage defense. Here, we review the existing evidence for phage defense mediated by TA systems, highlighting how toxins are activated by phage infection and how toxins disrupt phage replication. We also discuss phage-encoded systems that counteract TA systems, underscoring the ongoing coevolutionary battle between bacteria and phage. We anticipate that TA systems will continue to emerge as central players in the innate immunity of bacteria against phage. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Michele LeRoux
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; .,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| |
Collapse
|
2
|
Flodman K, Corrêa IR, Dai N, Weigele P, Xu SY. In vitro Type II Restriction of Bacteriophage DNA With Modified Pyrimidines. Front Microbiol 2020; 11:604618. [PMID: 33193286 PMCID: PMC7653180 DOI: 10.3389/fmicb.2020.604618] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/05/2020] [Indexed: 01/09/2023] Open
Abstract
To counteract host-encoded restriction systems, bacteriophages (phages) incorporate modified bases in their genomes. For example, phages carry in their genomes modified pyrimidines such as 5-hydroxymethyl-cytosine (5hmC) in T4gt deficient in α- and β-glycosyltransferases, glucosylated-5-hydroxymethylcytosine (5gmC) in T4, 5-methylcytosine (5mC) in Xp12, and 5-hydroxymethyldeoxyuridine (5hmdU) in SP8. In this work we sequenced phage Xp12 and SP8 genomes and examined Type II restriction of T4gt, T4, Xp12, and SP8 phage DNAs. T4gt, T4, and Xp12 genomes showed resistance to 81.9% (186 out of 227 enzymes tested), 94.3% (214 out of 227 enzymes tested), and 89.9% (196 out of 218 enzymes tested), respectively, commercially available Type II restriction endonucleases (REases). The SP8 genome, however, was resistant to only ∼8.3% of these enzymes (17 out of 204 enzymes tested). SP8 DNA could be further modified by adenine DNA methyltransferases (MTases) such as M.Dam and M.EcoGII as well as a number of cytosine DNA MTases, such as CpG methylase. The 5hmdU base in SP8 DNA was phosphorylated by treatment with a 5hmdU DNA kinase to achieve ∼20% phosphorylated 5hmdU, resulting resistance or partially resistant to more Type II restriction. This work provides a convenient reference for molecular biologists working with modified pyrimidines and using REases. The genomic sequences of phage Xp12 and SP8 lay the foundation for further studies on genetic pathways for 5mC and 5hmdU DNA base modifications and for comparative phage genomics.
Collapse
Affiliation(s)
| | - Ivan R Corrêa
- New England Biolabs, Inc., Ipswich, MA, United States
| | - Nan Dai
- New England Biolabs, Inc., Ipswich, MA, United States
| | - Peter Weigele
- New England Biolabs, Inc., Ipswich, MA, United States
| | | |
Collapse
|
3
|
Yaung SJ, Esvelt KM, Church GM. CRISPR/Cas9-mediated phage resistance is not impeded by the DNA modifications of phage T4. PLoS One 2014; 9:e98811. [PMID: 24886988 PMCID: PMC4041780 DOI: 10.1371/journal.pone.0098811] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 05/07/2014] [Indexed: 12/26/2022] Open
Abstract
Bacteria rely on two known DNA-level defenses against their bacteriophage predators: restriction-modification and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) systems. Certain phages have evolved countermeasures that are known to block endonucleases. For example, phage T4 not only adds hydroxymethyl groups to all of its cytosines, but also glucosylates them, a strategy that defeats almost all restriction enzymes. We sought to determine whether these DNA modifications can similarly impede CRISPR-based defenses. In a bioinformatics search, we found naturally occurring CRISPR spacers that potentially target phages known to modify their DNA. Experimentally, we show that the Cas9 nuclease from the Type II CRISPR system of Streptococcus pyogenes can overcome a variety of DNA modifications in Escherichia coli. The levels of Cas9-mediated phage resistance to bacteriophage T4 and the mutant phage T4 gt, which contains hydroxymethylated but not glucosylated cytosines, were comparable to phages with unmodified cytosines, T7 and the T4-like phage RB49. Our results demonstrate that Cas9 is not impeded by N6-methyladenine, 5-methylcytosine, 5-hydroxymethylated cytosine, or glucosylated 5-hydroxymethylated cytosine.
Collapse
Affiliation(s)
- Stephanie J. Yaung
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical Engineering & Medical Physics, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Kevin M. Esvelt
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, United States of America
| | - George M. Church
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
4
|
Opalka N, Brown J, Lane WJ, Twist KAF, Landick R, Asturias FJ, Darst SA. Complete structural model of Escherichia coli RNA polymerase from a hybrid approach. PLoS Biol 2010; 8. [PMID: 20856905 PMCID: PMC2939025 DOI: 10.1371/journal.pbio.1000483] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 08/04/2010] [Indexed: 11/25/2022] Open
Abstract
A combination of structural approaches yields a complete atomic model of the highly biochemically characterized Escherichia coli RNA polymerase, enabling fuller exploitation of E. coli as a model for understanding transcription. The Escherichia coli transcription system is the best characterized from a biochemical and genetic point of view and has served as a model system. Nevertheless, a molecular understanding of the details of E. coli transcription and its regulation, and therefore its full exploitation as a model system, has been hampered by the absence of high-resolution structural information on E. coli RNA polymerase (RNAP). We use a combination of approaches, including high-resolution X-ray crystallography, ab initio structural prediction, homology modeling, and single-particle cryo-electron microscopy, to generate complete atomic models of E. coli core RNAP and an E. coli RNAP ternary elongation complex. The detailed and comprehensive structural descriptions can be used to help interpret previous biochemical and genetic data in a new light and provide a structural framework for designing experiments to understand the function of the E. coli lineage-specific insertions and their role in the E. coli transcription program. Transcription, or the synthesis of RNA from DNA, is one of the most important processes in the cell. The central enzyme of transcription is the DNA-dependent RNA polymerase (RNAP), a large, macromolecular assembly consisting of at least five subunits. Historically, much of our fundamental information on the process of transcription has come from genetic and biochemical studies of RNAP from the model bacterium Escherichia coli. More recently, major breakthroughs in our understanding of the mechanism of action of RNAP have come from high resolution crystal structures of various bacterial, archaebacterial, and eukaryotic enzymes. However, all of our high-resolution bacterial RNAP structures are of enzymes from the thermophiles Thermus aquaticus or T. thermophilus, organisms with poorly characterized transcription systems. It has thus far proven impossible to obtain a high-resolution structure of E. coli RNAP, which has made it difficult to relate the large collection of genetic and biochemical data on RNAP function directly to the available structural information. Here, we used a combination of approaches—high-resolution X-ray crystallography of E. coli RNAP fragments, ab initio structure prediction, homology modeling, and single-particle cryo-electron microscopy—to generate complete atomic models of E. coli RNAP. Our detailed and comprehensive structural models provide the heretofore missing structural framework for understanding the function of the highly characterized E. coli RNAP.
Collapse
Affiliation(s)
- Natacha Opalka
- The Rockefeller University, New York, New York, United States of America
| | - Jesse Brown
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - William J. Lane
- Department of Pathology, Brigham & Women's Hospital, Boston, Massachusetts, United States of America
| | | | - Robert Landick
- Departments of Biochemistry and Bacteriology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Francisco J. Asturias
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail: (FJA); (SAD)
| | - Seth A. Darst
- The Rockefeller University, New York, New York, United States of America
- * E-mail: (FJA); (SAD)
| |
Collapse
|
5
|
Hirano N, Ohshima H, Sakashita H, Takahashi H. The Ser176 of T4 endonuclease IV is crucial for the restricted and polarized dC-specific cleavage of single-stranded DNA implicated in restriction of dC-containing DNA in host Escherichia coli. Nucleic Acids Res 2007; 35:6692-700. [PMID: 17913749 PMCID: PMC2175332 DOI: 10.1093/nar/gkm722] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Endonuclease (Endo) IV encoded by denB of bacteriophage T4 is an enzyme that cleaves single-stranded (ss) DNA in a dC-specific manner. Also the growth of dC-substituted T4 phage and host Escherichia coli cells is inhibited by denB expression presumably because of the inhibitory effect on replication of dC-containing DNA. Recently, we have demonstrated that an efficient cleavage by Endo IV occurs exclusively at the 5′-proximal dC (dC1) within a hexameric or an extended sequence consisting of dC residues at the 5′-proximal and the 3′-proximal positions (dCs tract), in which a third dC residue within the tract affects the polarized cleavage and cleavage rate. Here we isolate and characterize two denB mutants, denB(W88R) and denB(S176N). Both mutant alleles have lost the detrimental effect on the host cell. Endo IV(W88R) shows no enzymatic activity (<0.4% of that of wild-type Endo IV). On the other hand, Endo IV(S176N) retains cleavage activity (17.5% of that of wild-type Endo IV), but has lost the polarized and restricted cleavage of a dCs tract, indicating that the Ser176 residue of Endo IV is implicated in the polarized cleavage of a dCs tract which brings about a detrimental effect on the replication of dC-containing DNA.
Collapse
Affiliation(s)
| | | | | | - Hideo Takahashi
- *To whom correspondence should be addressed. +81 466 84 3350+81 466 84 3698
| |
Collapse
|
6
|
Hirano N, Ohshima H, Takahashi H. Biochemical analysis of the substrate specificity and sequence preference of endonuclease IV from bacteriophage T4, a dC-specific endonuclease implicated in restriction of dC-substituted T4 DNA synthesis. Nucleic Acids Res 2006; 34:4743-51. [PMID: 16971463 PMCID: PMC1635256 DOI: 10.1093/nar/gkl553] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Endonuclease IV encoded by denB of bacteriophage T4 is implicated in restriction of deoxycytidine (dC)-containing DNA in the host Escherichia coli. The enzyme was synthesized with the use of a wheat germ cell-free protein synthesis system, given a lethal effect of its expression in E.coli cells, and was purified to homogeneity. The purified enzyme showed high activity with single-stranded (ss) DNA and denatured dC-substituted T4 genomic double-stranded (ds) DNA but exhibited no activity with dsDNA, ssRNA or denatured T4 genomic dsDNA containing glucosylated deoxyhydroxymethylcytidine. Characterization of Endo IV activity revealed that the enzyme catalyzed specific endonucleolytic cleavage of the 5' phosphodiester bond of dC in ssDNA with an efficiency markedly dependent on the surrounding nucleotide sequence. The enzyme preferentially targeted 5'-dTdCdA-3' but tolerated various combinations of individual nucleotides flanking this trinucleotide sequence. These results suggest that Endo IV preferentially recognizes short nucleotide sequences containing 5'-dTdCdA-3', which likely accounts for the limited digestion of ssDNA by the enzyme and may be responsible in part for the indispensability of a deficiency in denB for stable synthesis of dC-substituted T4 genomic DNA.
Collapse
Affiliation(s)
| | | | - Hideo Takahashi
- To whom correspondence should be addressed. Tel: +81 466 84 3350; Fax: +81 466 84 3698;
| |
Collapse
|
7
|
Petrov VM, Nolan JM, Bertrand C, Levy D, Desplats C, Krisch HM, Karam JD. Plasticity of the gene functions for DNA replication in the T4-like phages. J Mol Biol 2006; 361:46-68. [PMID: 16828113 DOI: 10.1016/j.jmb.2006.05.071] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Revised: 05/24/2006] [Accepted: 05/31/2006] [Indexed: 10/24/2022]
Abstract
We have completely sequenced and annotated the genomes of several relatives of the bacteriophage T4, including three coliphages (RB43, RB49 and RB69), three Aeromonas salmonicida phages (44RR2.8t, 25 and 31) and one Aeromonas hydrophila phage (Aeh1). In addition, we have partially sequenced and annotated the T4-like genomes of coliphage RB16 (a close relative of RB43), A. salmonicida phage 65, Acinetobacter johnsonii phage 133 and Vibrio natriegens phage nt-1. Each of these phage genomes exhibited a unique sequence that distinguished it from its relatives, although there were examples of genomes that are very similar to each other. As a group the phages compared here diverge from one another by several criteria, including (a) host range, (b) genome size in the range between approximately 160 kb and approximately 250 kb, (c) content and genetic organization of their T4-like genes for DNA metabolism, (d) mutational drift of the predicted T4-like gene products and their regulatory sites and (e) content of open-reading frames that have no counterparts in T4 or other known organisms (novel ORFs). We have observed a number of DNA rearrangements of the T4 genome type, some exhibiting proximity to putative homing endonuclease genes. Also, we cite and discuss examples of sequence divergence in the predicted sites for protein-protein and protein-nucleic acid interactions of homologues of the T4 DNA replication proteins, with emphasis on the diversity in sequence, molecular form and regulation of the phage-encoded DNA polymerase, gp43. Five of the sequenced phage genomes are predicted to encode split forms of this polymerase. Our studies suggest that the modular construction and plasticity of the T4 genome type and several of its replication proteins may offer resilience to mutation, including DNA rearrangements, and facilitate the adaptation of T4-like phages to different bacterial hosts in nature.
Collapse
Affiliation(s)
- Vasiliy M Petrov
- Department of Biochemistry SL43, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | | | | | | | | | | | | |
Collapse
|
8
|
Mamoon NM, Song Y, Wellman SE. Binding of histone H1 to DNA is described by an allosteric model. Biopolymers 2004; 77:9-17. [PMID: 15558656 DOI: 10.1002/bip.20172] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Equilibrium binding data were analyzed to characterize the interaction of the linker histone H1 degrees with unmodified T4 phage DNA. Data were cast into the Scatchard-type plot described by McGhee and von Hippel and fit to their eponymous model for nonspecific binding of ligand to DNA. The data were not fit by the simple McGhee-von Hippel model, nor fit satisfactorily by the inclusion of a cooperativity parameter. Instead, the interaction appeared to be well described by Crothers' allosteric model, in which the higher affinity of the protein for one conformational form of the DNA drives an allosteric transition of the DNA to the conformational form with higher affinity (form 2). At 214 mM Na(+), the observed affinity K for an isolated site on unmodified T4 bacteriophage DNA in the form 2 conformation is 4.5 x 10(7) M(-1). The binding constant for an isolated site on DNA in the conformation with lower affinity, form 1, appears to be about 10-fold lower. Binding affinity is dependent on ion concentration: the magnitude of K is about 10-fold higher at 14 mM (5.9 x 10(8) M(-1) for form 2 DNA) than at 214 mM Na(+) concentration.
Collapse
Affiliation(s)
- Naila M Mamoon
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, 2500 N. State Street, Jackson, MS 39216-4505, USA
| | | | | |
Collapse
|
9
|
Amitsur M, Benjamin S, Rosner R, Chapman-Shimshoni D, Meidler R, Blanga S, Kaufmann G. Bacteriophage T4-encoded Stp can be replaced as activator of anticodon nuclease by a normal host cell metabolite. Mol Microbiol 2003; 50:129-43. [PMID: 14507369 DOI: 10.1046/j.1365-2958.2003.03691.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The bacterial tRNALys-specific anticodon nuclease is known as a phage T4 exclusion system. In the uninfected host cell anticodon nuclease is kept latent due to the association of its core protein PrrC with the DNA restriction-modification endonuclease EcoprrI. Stp, the T4-encoded peptide inhibitor of EcoprrI activates the latent enzyme. Previous in vitro work indicated that the activation by Stp is sensitive to DNase and requires added nucleotides. Biochemical and mutational data reported here suggest that Stp activates the latent holoenzyme when its EcoprrI component is tethered to a cognate DNA substrate. Moreover, the activation is driven by GTP hydrolysis, possibly mediated by the NTPase domain of PrrC. The data also reveal that Stp can be replaced as the activator of latent anticodon nuclease by certain pyrimidine nucleotides, the most potent of which is dTTP. The activation by dTTP likewise requires an EcoprrI DNA substrate and GTP hydrolysis but involves a different form of the latent holoenzyme/DNA complex. Moreover, whereas Stp relays its activating effect through EcoprrI, dTTP targets PrrC. The activation of the latent enzyme by a normal cell constituent hints that anticodon nuclease plays additional roles, other than warding off phage T4 infection.
Collapse
Affiliation(s)
- Michal Amitsur
- Department of Biochemistry, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | | | | | | | | | | | | |
Collapse
|
10
|
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: 555] [Impact Index Per Article: 26.4] [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.
Collapse
Affiliation(s)
- Eric S Miller
- Department of Microbiology, North Carolina State University, Raleigh, North Carolina 27695-7615, USA.
| | | | | | | | | | | |
Collapse
|
11
|
Abstract
Transcription termination in Escherichia coli is controlled by many factors. The sequence of the DNA template, the structure of the transcript, and the actions of auxiliary proteins all play a role in determining the efficiency of the process. Termination is regulated and can be enhanced or suppressed by host and phage proteins. This complex reaction is rapidly yielding to biochemical and structural analysis of the interacting factors. Below we review and attempt to unify into basic principles the remarkable recent progress in understanding transcription termination and anti-termination.
Collapse
Affiliation(s)
- Evgeny Nudler
- Department of Biochemistry, NYU Medical Center, New York, NY 10016, USA.
| | | |
Collapse
|
12
|
Sagawa H, Ohshima A, Kato I. Sse8387I, a useful eight base cutter for mammalian genome analysis (influence of methylation on the activity of Sse8387I). Nucleic Acids Res 1995; 23:2367-70. [PMID: 7630713 PMCID: PMC307039 DOI: 10.1093/nar/23.13.2367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
To develop restriction enzymes that are useful for genome analysis, we previously performed screening and isolated Sse8387I from Streptomyces sp. strain 8387. Sse8387I is a restriction enzyme that recognizes 5'-CCTGCA/GG-3' and cleaves DNA at the site shown by the diagonal (Nucleic Acid Res., 18, 5637-5640). The present study evaluated the effects of methylation that is important when Sse8387I is used for genome analysis. Sse8387I lost cleavage activity after methylation of adenine or methylation of cytosine at any site in the recognition sequence. However, the recognition sequence of Sse8387I contains no CG sequence, which is the mammalian methylation sequence. In addition, we evaluated the effects of methylation of CG at sites other than the recognition sequence. The cleavage activity of Sse8387I was maintained even when CG sequences were present immediately before or after, or near the recognition sequence, and cytosine was methylated. These results suggest that CG methylation does not affect the cleavage activity of Sse8387I. Therefore, Sse8387I seems to be very useful for mammalian genome analysis.
Collapse
Affiliation(s)
- H Sagawa
- Genetic Engineering Section II, Biotechnology Research Laboratories, Takara Shuzo Co. Ltd, Shiga, Japan
| | | | | |
Collapse
|
13
|
Morad I, Chapman-Shimshoni D, Amitsur M, Kaufmann G. Functional expression and properties of the tRNA(Lys)-specific core anticodon nuclease encoded by Escherichia coli prrC. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(19)74188-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
14
|
Kashlev M, Nudler E, Goldfarb A, White T, Kutter E. Bacteriophage T4 Alc protein: A transcription termination factor sensing local modification of DNA. Cell 1993. [DOI: 10.1016/s0092-8674(05)80091-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
15
|
Carlson K, Krabbe M, Nyström A, Kosturko L. DNA determinants of restriction. Bacteriophage T4 endonuclease II-dependent cleavage of plasmid DNA in vivo. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)52959-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
16
|
Krabbe M, Carlson K. In vivo restriction. Sequence and structure of endonuclease II-dependent cleavage sites in bacteriophage T4 DNA. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)54511-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
17
|
Drivdahl RH, Kutter EM. Inhibition of transcription of cytosine-containing DNA in vitro by the alc gene product of bacteriophage T4. J Bacteriol 1990; 172:2716-27. [PMID: 2185231 PMCID: PMC208917 DOI: 10.1128/jb.172.5.2716-2727.1990] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The alc gene product (gpalc) of bacteriophage T4 inhibits the transcription of cytosine-containing DNA in vivo. We examined its effect on transcription in vitro by comparing RNA polymerase isolated from Escherichia coli infected with either wild-type T4D+ or alc mutants. A 50 to 60% decline in RNA polymerase activity, measured on phage T7 DNA, was observed by 1 min after infection with either T4D+ or alc mutants; this did not occur when the infecting phage lacked gpalt. In the case of the T4D+ strain but not alc mutants, this was followed by a further decrease. By 5 min after infection the activity of alc mutants was 1.5 to 2.5 times greater than that of the wild type on various cytosine-containing DNA templates, whereas there was little or no difference in activity on T4 HMdC-DNA, in agreement with the in vivo specificity. Effects on transcript initiation and elongation were distinguished by using a T7 phage DNA template. Rifampin challenge, end-labeling with [gamma-32P]ATP, and selective initiation with a dinucleotide all indicate that the decreased in vitro activity of the wild-type polymerase relative to that of the alc mutants was due to inhibition of elongation, not to any difference in initiation rates. Wild-type (but not mutated) gpalc copurified with RNA polymerase on heparin agarose but not in subsequent steps. Immunoprecipitation of modified RNA polymerase also indicated that gpalc was not tightly bound to RNA polymerase intracellularly. It thus appears likely that gpalc inhibits transcript elongation on cytosine-containing DNA by interacting with actively transcribing core polymerase as a complex with the enzyme and cytosine-rich stretches of the template.
Collapse
Affiliation(s)
- R H Drivdahl
- Evergreen State College, Olympia, Washington 98505
| | | |
Collapse
|
18
|
Selick HE, Kreuzer KN, Alberts BM. The bacteriophage T4 insertion/substitution vector system. A method for introducing site-specific mutations into the virus chromosome. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)37963-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
19
|
Snustad DP, Haas N, Oppenheimer DG. The bacteriophage T4 regulatory protein gpunf/alc binds to DNA in the absence of RNA polymerase. J Virol 1986; 60:1145-7. [PMID: 3783815 PMCID: PMC253370 DOI: 10.1128/jvi.60.3.1145-1147.1986] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
DNA-cellulose chromatography and two-dimensional gel electrophoresis have been used to demonstrate the DNA-binding capacity of bacteriophage T4 gpunf/alc. The unf/alc protein does not bind to DNA via an association with RNA polymerase; gpunf/alc was shown to bind to DNA after separation from RNA polymerase and other large proteins by Sephadex chromatography.
Collapse
|
20
|
Valerie K, Stevens J, Lynch M, Henderson EE, de Riel JK. Nucleotide sequence and analysis of the 58.3 to 65.5-kb early region of bacteriophage T4. Nucleic Acids Res 1986; 14:8637-54. [PMID: 3024113 PMCID: PMC311883 DOI: 10.1093/nar/14.21.8637] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The complete 7.2-kb nucleotide sequence from the 58.3 to 65.5-kb early region of bacteriophage T4 has been determined by Maxam and Gilbert sequencing. Computer analysis revealed at least 20 open reading frames (ORFs) within this sequence. All major ORFs are transcribed from the left strand, suggesting that they are expressed early during infection. Among the ORFs, we have identified the ipIII, ipII, denV and tk genes. The ORFs are very tightly spaced, even overlapping in some instances, and when ORF interspacing occurs, promoter-like sequences can be implicated. Several of the sequences preceding the ORFs, in particular those at ipIII, ipII, denV, and orf61.9, can potentially form stable stem-loop structures.
Collapse
|
21
|
Abstract
The DNA of bacteriophage T4 normally has a substituted base, hydroxymethylcytosine, instead of the usual cytosine. The bacteriophage shuts off host transcription after infection presumably by specifically blocking transcription of cytosine DNA. If T4 incorporates cytosine into its own DNA, this shutoff mechanism is directed back at itself and blocks its own transcription. Mutations which overcome this transcriptional block are in the T4 alc gene, and alc mutations allow the propagation of T4 with cytosine in their DNA (L. Snyder, L. Gold, and E. Kutter, Proc. Natl. Acad. Sci. USA 73:3098-3102, 1976). By genetic criteria, alc is the same as another gene, unf, whose product is required for the unfolding of the bacterial nucleoid after infection (K. Sirotkin, J. Wei, and L. Snyder, Nature [London] 265:28-32, 1977; D. P. Snustad, M. A. Tigges, K. A. Parson, C. J. H. Bursch, F. M. Caron, J. F. Koerner, and D. J. Tutas, J. Virol. 17:622-641, 1976; M. Tigges, C. J. H. Bursch, and D. P. Snustad, J. Virol. 24:775-785, 1977). The product of the alc gene has been identified as a 19-kilodalton protein (R. E. Herman, N. Haas, and D. P. Snustad, Genetics 108:305-317, 1984; E. Kutter, R. Drivdahl, and K. Rand, Genetics 108:291-304, 1984), and an open reading frame has been proposed to be the alc gene based on its size and map position (E. Kutter, R. Drivdahl, and K. Rand, Genetics 108:291-304, 1984). We used marker rescue techniques and DNA sequencing to confirm that this open reading frame is the alc gene. We also present a molecular proof that alc and unf are the same gene. While these results do not rigorously exclude the possibility that Unf and Alc are different activities of the same protein, they strongly support the conclusion that the unfolding of the bacterial nucleoid the blockage of transcription are but different manifestations of the same activity.
Collapse
|
22
|
Huang WM. Nucleotide sequence of a type II DNA topoisomerase gene. Bacteriophage T4 gene 39. Nucleic Acids Res 1986; 14:7751-65. [PMID: 3022233 PMCID: PMC311794 DOI: 10.1093/nar/14.19.7751] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
T4 DNA topoisomerase is a type II enzyme and is thought to be required for normal T4 DNA replication T4 gene 39 codes for the largest of the three subunits of T4 DNA topoisomerase. I have determined the nucleotide sequence of a region of 2568 nucleotides of T4 DNA which includes gene 39. The location of the gene was established by the identification of the first fifteen amino acids in the large open reading frame in the DNA sequence as those found at the amino-terminus of the purified 39-protein. The coding region of gene 39 has 1560 bases, and it is followed by two in-frame stop codons. The gene is preceded by a typical Shine-Dalgarno sequence as well as possible promoter sequences for E. coli RNA polymerase. T4 39-protein consists of 520 amino acids, and it has a calculated molecular weight of 58,478. By comparing the amino acid sequences, T4 39-protein is found to share homology with the gyrB subunit of DNA gyrase. This suggests that these topoisomerase subunits may be equivalent functionally. Some of the characteristics of the 39-protein and its structural features predicted from the DNA sequence data are discussed.
Collapse
|
23
|
Huang WM. The 52-protein subunit of T4 DNA topoisomerase is homologous to the gyrA-protein of gyrase. Nucleic Acids Res 1986; 14:7379-90. [PMID: 3020513 PMCID: PMC311757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
T4 gene 52 encodes one of the three subunits of T4 DNA topoisomerase. The T4 enzyme is required for normal phage DNA replication. I have cloned the entire gene, and it is expressed in uninfected E. coli cells. The sequence of 1966 nucleotides of T4 deletion delta sa9 surrounding gene 52 has been determined. The reading frame of the gene was established by identifying the first ten amino acids in the large open reading frame derived from the DNA sequence as those at the amino-terminus of the purified 52-protein. Based on the DNA sequence, 52-protein has 441 amino acids and a calculated peptide molecular weight of 50,583 daltons. This T4 topoisomerase subunit shares significant amino acid sequence homology with the gyrA subunit of bacterial gyrases and the carboxyl-half of yeast topoisomerase II in spite of the large differences in their sizes, confirming their functional equivalence in type II enzyme directed DNA topoisomerization. Amino acid sequence homology is highest in the amino-terminal portions of the equivalent peptides. The homology alignment suggests a consensus sequence organization surrounding the reactive tyrosine which is used to form the transient protein-DNA intermediate in the double-stranded DNA passing reaction. The delta sa9 deletion in T4 brings gene 52 to a location 30 nucleotides 3' from the rIIB gene whose C-terminal 167 codons are also reported here.
Collapse
|
24
|
Expression of a cloned denV gene of bacteriophage T4 in Escherichia coli. Proc Natl Acad Sci U S A 1985; 82:4763-7. [PMID: 2991891 PMCID: PMC390985 DOI: 10.1073/pnas.82.14.4763] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A 713-base-pair Hae III fragment from bacteriophage T4 encompassing the denV gene with its preceding promoter has been cloned in a pBR322-derived positive-selection vector and introduced into a variety of DNA repair-deficient uvr and rec and uvr,rec Escherichia coli strains. The denV gene was found to be expressed, probably from its own promoter, causing pyrimidine dimer incision-deficient uvrA, uvrB, uvrC strains to be rescued by the denV gene. A uvrD (DNA helicase II) strain was also complemented, but to a lesser extent. A wild-type strain did not seem to be affected at the UV doses tested. Surprisingly, all recA, recB, and recC strains tested also showed an increased UV resistance, perhaps by reinforcement of the intact uvr system in these strains. Complementation of denV- T4 strains and host-cell reactivation of lambda phage was also observed in denV+ E. coli strains. Equilibrium sedimentation showed that DNA repair synthesis occurred in a UV-irradiated uvrA E. coli strain carrying the cloned denV gene. Southern blotting confirmed our earlier results [Valerie, K., Henderson, E. E. & de Riel, J. K. (1984) Nucleic Acids Res. 12, 8085-8096] that the denV gene is located at 64 kilobases on the T4 map. Phage T2 (denV-) did not hybridize to a denV-specific probe.
Collapse
|
25
|
Abstract
Partially replicated bacteriophage T4 DNA containing cytosine was isolated from cells 6.5 and 7 min after infection and cleaved with restriction endonuclease BglII or BamHI. Positions of replication eyes relative to the cleavage sites were observed by electron microscopy. Four groups of eyes were found. They are consistent with replication from origins located at map positions 34, 60, 73, and 86 kilobases. In individual molecules that contained two or three eyes, the distribution of the eyes agreed with the initiation of replication at more than one of these four assigned origins and possibly at two additional origins located near 15 and 110 kilobases, which were reported by P. M. Macdonald, R. M. Seaby, W. Brown, and G. Mosig (p. 111-116, in D. Schlessinger, ed., Microbiology--1983, 1983) and M. E. Halpern, T. Mattson, and A. W. Kozinski (Proc. Natl. Acad. Sci. U.S.A. 76:6137-6141, 1979).
Collapse
|
26
|
Herman RE, Snustad DP. Bacteriophage T4 unf (=alc) gene function is required for late replication in the presence of plasmid pR386. J Virol 1985; 53:430-9. [PMID: 2578570 PMCID: PMC254654 DOI: 10.1128/jvi.53.2.430-439.1985] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The bacteriophage T4 unf gene, known to be involved in the arrest of transcription from cytosine-containing DNA, is unessential except in Escherichia coli strains containing plasmid pR386. Comparative genetic and biochemical analyses of parameters of unf+ and unf- phage growth in host cells isogenic except for the presence or absence of plasmid pR386 have shown that unf gene function is required for late phage DNA synthesis in the presence of the plasmid. Shutoff of host DNA, RNA, and protein syntheses, degradation of host DNA, adsorption, injection, and early phage DNA, RNA, and protein syntheses all occurred with normal or near-normal kinetics in unf- infections, even in the presence of the plasmid. The switch from early to late protein synthesis occurred in plasmid pR386-containing cells infected with unf+ or unf- phage. However, this switchover was slow in both cases and may be slower in unf- infections than in unf+ infections. Net incorporation of [3H]thymidine terminated at about 30 min after infection of pR386-containing cells with unf- phage at 30 degrees C. Alkaline sucrose gradient studies of the intracellular pools of replicative DNA in unf-infected plasmid pR386-containing cells indicated that this DNA is not detectably nickel or cleaved at the time that DNA synthesis aborts. The addition of chloramphenicol subsequent to early enzyme synthesis prevented the arrest of DNA synthesis in plasmid-containing cells infected with unf-phage.
Collapse
|
27
|
Miller PB, Warren RA. DNA synthesis in Pseudomonas acidovorans infected with mutants of bacteriophage phi W-14 defective in the synthesis of alpha-putrescinylthymine. J Virol 1984; 52:1036-8. [PMID: 6492260 PMCID: PMC254638 DOI: 10.1128/jvi.52.3.1036-1038.1984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Normal levels of the hypermodified pyrimidine, alpha-putrescinylthymine, which is formed from hydhydroxymethyluracil at the polynucleotide level (Maltman et al., J. Virol. 34:354-359, 1984), are not required in bacteriophage luminal diameterW-14 DNA for the DNA to serve as a replicative template in luminal diameterW-14-infected cells.
Collapse
|
28
|
Herman RE, Haas N, Snustad DP. Identification of the bacteriophage T4 unf ( = alc) gene product, a protein involved in the shutoff of host transcription. Genetics 1984; 108:305-17. [PMID: 6389257 PMCID: PMC1202407 DOI: 10.1093/genetics/108.2.305] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The introduction of plasmid pR386 into E. coli cells renders them restrictive to the growth of phage T4 unf ( = alc) mutants. This system has been used to isolate Unf+ revertants, which, along with the mutant parental strains, have been used to identify the unf gene product by two-dimensional gel electrophoresis. Synthesis of the unf gene product, a polypeptide of just over 18,000 daltons in size, begins within 1 min after infection and terminates at about 12 min after infection at 30 degrees. Gene dosage experiments suggest that the unf protein functions catalytically.
Collapse
|
29
|
Kutter E, Drivdahl R, Rand K. Identification and characterization of the alc gene product of bacteriophage T4. Genetics 1984; 108:291-304. [PMID: 6389256 PMCID: PMC1202406 DOI: 10.1093/genetics/108.2.291] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Bacteriophage T4 infection rapidly and almost completely inhibits transcription of host and other phage DNAs. Two processes have been implicated to date in this inhibition: (1) ADP ribosylation of the alpha subunits of the RNA polymerase, involving gpalt (which is injected with the phage DNA) and, later, gpmod; and (2) the action of the T4 alc/unf gene product, synthesized immediately after infection. The latter unfolds the host genome and also blocks transcription of cytosine-containing DNA. Here, we describe the identification on two-dimensional polyacrylamide gels of gpalc/unf, the more precise mapping of the gene and the identification and analysis of the appropriate DNA sequence from an Unf+ alc mutant.
Collapse
|
30
|
Kassavetis GA, Geiduschek EP. Defining a bacteriophage T4 late promoter: bacteriophage T4 gene 55 protein suffices for directing late promoter recognition. Proc Natl Acad Sci U S A 1984; 81:5101-5. [PMID: 6382259 PMCID: PMC391645 DOI: 10.1073/pnas.81.16.5101] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The RNA polymerase from bacteriophage T4-infected Escherichia coli, which specifically initiates transcription at phage T4 late promoters, is extensively modified by ADP-ribosylation of core subunits and by binding several virus-encoded subunits. We show here that one of these subunits, the phage T4 gene 55 protein, designated gp55, alone endows unmodified RNA polymerase core enzyme from uninfected E. coli with the ability to selectively initiate transcription at the phage T4 late promoters, without participation by E. coli RNA polymerase o- subunit.
Collapse
|
31
|
Jabbar MA, Snyder L. Genetic and physiological studies of an Escherichia coli locus that restricts polynucleotide kinase- and RNA ligase-deficient mutants of bacteriophage T4. J Virol 1984; 51:522-9. [PMID: 6086961 PMCID: PMC254468 DOI: 10.1128/jvi.51.2.522-529.1984] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The RNA ligase and polynucleotide kinase of bacteriophage T4 are nonessential enzymes in most laboratory Escherichia coli strains. However, T4 mutants which do not induce the enzymes are severely restricted in E. coli CTr5X, a strain derived from a clinical E. coli isolate. We have mapped the restricting locus in E. coli CTr5X and have transduced it into other E. coli strains. The restrictive locus seems to be a gene, or genes, unique to CTr5X or to be an altered form of a nonessential gene, since deleting the locus seems to cause loss of the phenotypes. In addition to restricting RNA ligase- and polynucleotide kinase-deficient T4, the locus also restricts bacteriophages lambda and T4 with cytosine DNA. When lambda or T4 with cytosine DNA infect strains with the prr locus, the phage DNA is injected, but phage genes are not expressed and the host cells survive. These phenotypes are unlike anything yet described for a phage-host interaction.
Collapse
|
32
|
Champness WC, Snyder L. Bacteriophage T4 gol site: sequence analysis and effects of the site on plasmid transformation. J Virol 1984; 50:555-62. [PMID: 6323755 PMCID: PMC255670 DOI: 10.1128/jvi.50.2.555-562.1984] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The Escherichia coli lit gene product is required for the multiplication of bacteriophage T4 at temperatures below 34 degrees C. After infection of a lit mutant host, early gene product synthesis is normal, as is T4 DNA replication; however, the late gene products never appear, and early gene product synthesis eventually ceases. Consequently, at late times, there is no protein synthesis of any kind (W. Cooley, K. Sirotkin, R. Green, and L. Snyder, J. Bacteriol. 140:83-91, 1979; W. Champness and L. Snyder, J. Mol. Biol. 155:395-407, 1982), and no phage are produced. We have isolated T4 mutants which can multiply in lit mutant hosts. The responsible T4 mutations (called gol mutations) completely overcome the block to T4 gene expression (Cooley et al., J. Bacteriol. 140:83-91). We have proposed that gol mutations alter a cis-acting regulatory site on T4 DNA rather than a diffusible gene product and that the wild-type form of the gol site (gol+) somehow interferes with gene expression late in infection (Champness and Snyder, J. Mol. Biol. 155:395-409). In this communication, we report the sequence of the gol region of the T4 genome from five different gol mutants. The gol mutations are all single-base-pair transitions within 40 base pairs of DNA. Therefore, the gol site is at least 40 base pairs long. The sequence data confirm that the gol phenotype is not due to an altered protein. We also report that the gol+ site in plasmids prevents transformation of Lit- but not Lit+ E. coli. Thus, the gol site is at least partially active in the absence of the T4 genome.
Collapse
|
33
|
Suhadolnik RJ, Sawada Y, Gabriel J, Reichenbach NL, Henderson EE. Accumulation of low molecular weight DNA and changes in chromatin structure in HeLa cells treated with human fibroblast interferon. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)42912-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
34
|
Gram H, Liebig HD, Hack A, Niggemann E, Rüger W. A physical map of bacteriophage T4 including the positions of strong promoters and terminators recognized in vitro. MOLECULAR & GENERAL GENETICS : MGG 1984; 194:232-40. [PMID: 6328215 DOI: 10.1007/bf00383522] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We present a linearized physical map of the genome of bacteriophage T4. This map contains the cleavage sites for restriction enzymes SmaI, KpnI, SalI, BglII, XhoI, XbaI, ClaI , HaeII, EcoRI, and EcoRV . It also contains about 200 TaqI sites. The promoter sites recognized in vitro and a number of rho independent terminators have also been mapped.
Collapse
|
35
|
Albright LM, Geiduschek EP. Site-specific cleavage of bacteriophage T4 DNA associated with the absence of gene 46 product function. J Virol 1983; 47:77-88. [PMID: 6306283 PMCID: PMC255202 DOI: 10.1128/jvi.47.1.77-88.1983] [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: 01/19/2023] Open
Abstract
A plasmid containing a copy of the late gene 23 was cleaved at two specific locations after bacteriophage T4 infection. Cleavage at the major site, which is at the 3' end of gene 23, was detected only in the absence of gene 46 product function and was independent of the state of modification of cytosine residues. Cutting of plasmid (cytosine-containing) DNA at this site was independent of phage DNA replication and late transcription functions. A second cleavage site, in vector DNA, was also mapped. The minor extent of cutting at this site was independent of gene 46 function. Gene 46 codes for, or controls, an exonuclease involved in T4 DNA recombination and in degradation of cytosine-containing DNA.
Collapse
|
36
|
Abstract
Two physical origins of T4 DNA replication were determined by hybridization of viral DNA prepared 2.5 min after infection to a display of total T4 DNA. This is the earliest time after T4 infection of Escherichia coli at 37 degrees C that labeled and hybridizable DNA can be detected. The two origins, separated by about 25 kilobases, were identified and localized in the early region of the T4 map. One of them is located in a 5.6-kilobase EcoRI fragment containing genes 62-46. The other is located between genes rI and e in a 1.9-kilobase EcoRI fragment. Both of these T4 fragments have been cloned and their interactions with the host cell are discussed.
Collapse
|
37
|
Takahashi H, Saito H. Mechanism of pBR322 transduction mediated by cytosine-substituting T4 bacteriophage. MOLECULAR & GENERAL GENETICS : MGG 1982; 186:497-500. [PMID: 6752658 DOI: 10.1007/bf00337955] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A cytosine-substitution type mutant of bacteriophage T4 (T4dC phage) has been shown to mediate the transfer of plasmid pBR322. The transduction frequency was around 10(-2) per singly infected cell at low multiplicity of infection. The transductants contained either a monomer or multimers of pBR322. The transducing capacity of T4dC phage was resistant to methylmethanesulfonate treatment. The results of Southern blotting experiments have indicated that the pBR322 DNA exists as head-to-tail concatemers in the transducing particles. The mechanism of transfer of pBR322 mediated by T4dC phages is discussed.
Collapse
|
38
|
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]
|
39
|
Herman RE, Snustad DP. Plasmid pR386 renders Escherichia coli cells restrictive to the growth of bacteriophage T4 unf mutants. J Virol 1982; 41:330-3. [PMID: 6177866 PMCID: PMC256756 DOI: 10.1128/jvi.41.1.330-333.1982] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The introduction of the F1 incompatibility group plasmid pR386 Tc into several common laboratory strains of Escherichia coli rendered them restrictive to the growth of bacteriophage T4 unf mutants, which are defective in unfolding the host genome. The growth inhibition was temperature dependent. The single mutant unf39 x 5 exhibited an efficiency of plating of less than 10(-8) at 27 degrees C. However, at 37 degrees C, complete growth inhibition occurred only when host DNA degradation was also absent.
Collapse
|
40
|
|
41
|
Abstract
Mutations in the genes for nuclear disruption (ndd), endonuclease IV (denB), and the D1 region of the T4 genome are essential for converting bacteriophage T4 into a generalized transducing phage. These mutations gave rise to a very low frequency of transduction, about 10(-8) per infected bacterium. The addition of an rII mutation raised the transduction frequency about 20-fold. An additional 100-fold increase in the transduction frequency was observed with mutations in genes 42, 56, and alc. High-frequency generalized transduction by T4 results from the cumulative effect of these mutations.
Collapse
|
42
|
Kutter EM, Bradley D, Schenck R, Guttman BS, Laiken R. Bacteriophage T4 alc gene product: general inhibitor of transcription from cytosine-containing DNA. J Virol 1981; 40:822-9. [PMID: 7321103 PMCID: PMC256693 DOI: 10.1128/jvi.40.3.822-829.1981] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The alc gene of bacteriophage T4 was originally defined on the basis of mutations which allow late protein synthesis directed by T4 DNA containing cytosine rather than hydroxymethylcytosine. The question remained whether the normal alc gene product (gpalc) also blocks the transcription of early genes from cytosine-containing DNA. Complementation experiments were performed between hydroxymethylcytosine-containing phage which direct gpalc synthesis but carry mutations in a given gene(s) and cytosine-containing phage carrying that gene(s). The required protein would then have to be directed by the cytosine-containing DNA: it is looked for directly on polyacrylamide gels or through its physiological effects or both. For all early proteins examined in this way, no synthesis was observed when 95 to 100% of the hydroxymethylcytosine was substituted by cytosine in the infecting DNA, whereas there was significant synthesis with 75% substitution or less. The results indicate that gpalc is carried in with the infecting DNA or is made very early to block transcription of all cytosine-containing DNA.
Collapse
|
43
|
Niggemann E, Green I, Meyer HP, Rüger W. Physical mapping of bacteriophage T4. MOLECULAR & GENERAL GENETICS : MGG 1981; 184:289-99. [PMID: 6276698 DOI: 10.1007/bf00272920] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
44
|
Jacobs KA, Albright LM, Shibata DK, Geiduschek EP. Genetic complementation by cloned bacteriophage T4 late genes. J Virol 1981; 39:31-45. [PMID: 6456362 PMCID: PMC171262 DOI: 10.1128/jvi.39.1.31-45.1981] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Bacteriophage T4 containing nonsense mutations in late genes was found to be genetically complemented by four conjugate T4 genes (7, 11, 23, or 24) located on plasmid or phage vectors. Complementation was at a very low level unless the infecting phage carried a denB mutation (which abolishes T4 DNA endonuclease IV activity). In most experiments, the infecting phage also had a denA mutation, which abolishes T4 DNA endonuclease II activity. Mutations in the alc/unf gene (which allow dCMP-containing T4 late genes to be expressed) further increased complementation efficiency. Most of the alc/unf mutant phage strains used for these experiments were constructed to incorporate a gene 56 mutation, which blocks dCTP breakdown and allows replication to generate dCMP-containing T4 DNA. Effects of the alc/unf:56 mutant combination on complementation efficiency varied among the different T4 late genes. Despite regions of homology, ranging from 2 to 14 kilobase pairs, between cloned T4 genes and infecting genomes, the rate of formation of recombinants after T4 den:alc phage infection was generally low (higher for two mutants in gene 23, lower for mutants in gene 7 and 11). More significantly, when gene 23 complementation had to be preceded by recombination, the complementation efficiency was drastically reduced. We conclude that high complementation efficiency of cloned T4 late genes need not depend on prior complete breakage-reunion events which transpose those genes from the resident plasmid to a late promoter on the infecting T4 genome. The presence of the intact gene 23 on plasmids reduced the yield of T4 phage. The magnitude of this negative complementation effect varied in different plasmids; in the extreme case (plasmid pLA3), an almost 10-fold reduction of yield was observed. The cells can thus be said to have been made partly nonpermissive for this lytic virus by incorporating a part of the viral genome.
Collapse
|
45
|
Abstract
The parameters governing the activity of the cloned T4 gene 23, which codes for the major T4 head protein, were analyzed. Suppressor-negative bacteria carrying wild-type T4 gene 23 cloned into plasmid pCR1 or pBR322 were infected with T4 gene 23 amber phage also carrying mutations in the following genes: (i) denA and denB (to prevent breakdown of plasmid DNA after infection) and (ii) denA, denB, and, in addition, 56 (to generate newly replicated DNA containing dCMP) and alc/unf (because mutations in this last gene allow late genes to be expressed in cytosine-containing T4 DNA). Bacteria infected with these phage were labeled with (14)C-amino acids at various times after infection, and the labeled proteins were separated by one-dimensional gel electrophoresis so that the synthesis of plasmid-coded gp23 could be compared with the synthesis of other, chromosome-coded T4 late proteins. We analyzed the effects of additional mutations that inactivate DNA replication proteins (genes 32 and 43), an RNA polymerase-binding protein (gene 55), type II topoisomerase (gene 52), and an exonuclease function involved in recombination (gene 46) on the synthesis of plasmid-coded gp23 in relation to chromosome-coded T4 late proteins. In the denA:denB:56:alc/unf genetic background, the phage chromosome-borne late genes followed the same regulatory rules (with respect to DNA replication and gp55 action) as in the denA:denB genetic background. The plasmid-carried gene 23 was also under gp55 control, but was less sensitive than the chromosomal late genes to perturbations of DNA replication. Synthesis of plasmid-coded gp23 was greatly inhibited when both the type II T4 topoisomerase and the host's DNA gyrase are inactivated. Synthesis of gp23 was also substantially affected by a mutation in gene 46, but less strongly than in the denA:denB genetic background. These observations are interpreted as follows. The plasmid-borne T4 gene 23 is primarily expressed from a late promoter. Expression of gene 23 from this late promoter responds to an activation event which involves some structural alteration of DNA. In these respects, the requirements for expressing the plasmid-borne gene 23 and chromosomal late genes are very similar (although in the denA:denB:56:alc/unf genetic background, there are significant quantitative differences). For the plasmid-borne gene 23, activation involves the T4 gp46, a protein which is required for DNA recombination. However, for the reasons presented in the accompanying paper (Jacobs et al., J. Virol. 39:31-45, 1981), we conclude that the activation of gene 23 does not require a complete breakage-reunion event which transposes that gene to a later promoter on the phage chromosome. Ways in which gp46 may actually be involved in late promoter activation on the plasmid are discussed.
Collapse
|
46
|
Marsh RC, Hepburn ML. Map of restriction sites on bacteriophage T4 cytosine-containing DNA for endonucleases bamHI, BglII, KpnI, PvuI, SalI, and XbaI. J Virol 1981; 38:104-14. [PMID: 6264096 PMCID: PMC171130 DOI: 10.1128/jvi.38.1.104-114.1981] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A complete map of the cleavage sites of restriction endonucleases BamHI, BglII, KpnI, PvuI, SalI, and XbaI was determined for the cytosine-containing DNA of a bacteriophage T4 alc mutant. The 56 sequence-specific sites were assigned map coordinates based on a least-squares analysis of measured fragment lengths. Altogether, the lengths of 118 fragments from single and double enzyme digestions were measured by electrophoresis of the fragments in agarose gels. DNA fragments of known sequence or DNA fragments calibrated with fragments of known sequence were used as standards. The greatest deviation between an experimentally measured fragment length and its computed map coordinates was 3.0%; the average deviation was 0.8%. The total length of the wild-type T4 genome was calculated to be 166,200 base pairs.
Collapse
|
47
|
Abstract
A restriction map of the bacteriophage T4 genome was aligned with the T4 genetic map. Included were the cleavage sites for BamHI, BglII, KpnI, PvuI, SalI, and XbaI. The alignment utilized the fact that the T4 genetic map had been oriented previously with respect to a T2/T4 heteroduplex map. DNA fragments from a BglII digestion of cytosine-containing DNA from a T4 dCTPase- denA denB(rIIH23B) alc mutant were hybridized with full-length chromosomal strands of bacteriophage T2, and the heteroduplexes were examined by electron microscopy. From their lengths and patterns of substitution and deletion loops, the heteroduplexes formed with 6 of the 13 BglII fragments could be unambiguously identified and positioned on the T2/T4 heteroduplex map. The ends of the T4 DNA strands in the heteroduplexes directly identified the location of 10 BglII cleavage sites. The remaining three BglII cleavage sites could be assigned to the T2/T4 heteroduplex map based on their relative locations on the restriction map. It was also possible to identify the source of the DNA strands (i.e., T2 or T4) in four previously unassigned deletion loops on the T2/T4 heteroduplex. Among the BglII fragments identified in heteroduplexes was the fragment containing the rIIH23B deletion; this deletion was used as the primary point of reference for alignment of the T4 restriction map with the T2/T4 heteroduplex map and, hence, with the T4 genetic map.
Collapse
|
48
|
Liu C, Alberts B. Characterization of RNA primer synthesis in the T4 bacteriophage in vitro DNA replication system. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69688-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
49
|
Carlson K. Correlation between genetic map and map of cleavage sites for sequence-specific endonucleases SalI, KpnI, BglI, and BamHI in bacteriophage T4 cytosine-containing DNA. J Virol 1980; 36:1-17. [PMID: 6255198 PMCID: PMC353611 DOI: 10.1128/jvi.36.1.1-17.1980] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Cleavage sites for SalI, KpnI, BglI, and BamHI in cytosine-containing DNA from T4 alc10(alc) nd28(denA) D2a2(denB) amE51x5(56) amN55x5(42) have been mapped relative to each other, and the positions of deletions sa delta 9 (D1-stp), r1589(rII), del(39-56)12, and tk2(rI-tk) relative to these cleavage sites have been determined. Based on these analyses, a physical map of the T4 genome containing 166 kilobase pairs has been constructed.
Collapse
|
50
|
Mileham AJ, Revel HR, Murray NE. Molecular cloning of the T4 genome; organization and expression of the frd--DNA ligase region. MOLECULAR & GENERAL GENETICS : MGG 1980; 179:227-39. [PMID: 6258011 DOI: 10.1007/bf00425449] [Citation(s) in RCA: 41] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|