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Mulye M, Singh MI, Jain V. From Processivity to Genome Maintenance: The Many Roles of Sliding Clamps. Genes (Basel) 2022; 13:2058. [PMID: 36360296 PMCID: PMC9690074 DOI: 10.3390/genes13112058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 07/30/2023] Open
Abstract
Sliding clamps play a pivotal role in the process of replication by increasing the processivity of the replicative polymerase. They also serve as an interacting platform for a plethora of other proteins, which have an important role in other DNA metabolic processes, including DNA repair. In other words, clamps have evolved, as has been correctly referred to, into a mobile "tool-belt" on the DNA, and provide a platform for several proteins that are involved in maintaining genome integrity. Because of the central role played by the sliding clamp in various processes, its study becomes essential and relevant in understanding these processes and exploring the protein as an important drug target. In this review, we provide an updated report on the functioning, interactions, and moonlighting roles of the sliding clamps in various organisms and its utilization as a drug target.
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Affiliation(s)
- Meenakshi Mulye
- Correspondence: (M.M.); (V.J.); Tel.: +91-755-269-1425 (V.J.); Fax: +91-755-269-2392 (V.J.)
| | | | - Vikas Jain
- Correspondence: (M.M.); (V.J.); Tel.: +91-755-269-1425 (V.J.); Fax: +91-755-269-2392 (V.J.)
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2
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Singh MI, Ganesh B, Jain V. On the domains of T4 phage sliding clamp gp45: An intermolecular crosstalk governs structural stability and biological activity. Biochim Biophys Acta Gen Subj 2016; 1861:3300-3310. [PMID: 27554844 DOI: 10.1016/j.bbagen.2016.08.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/14/2016] [Accepted: 08/18/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND DNA polymerase processivity factors are ubiquitously present in all living organisms. Notwithstanding their high significance, the molecular details of clamps pertaining to the factors contributing to their stability are presently lacking. The bacteriophage T4 sliding clamp gp45 forms a homotrimer that besides being involved in DNA replication, moonlights as a transcription factor. Here we have carried out a detailed characterization of gp45 to understand the role of monomer-monomer interface interactions in stability and functioning of the protein. METHODS We generated several gp45 mutants harboring either Ala or Pro substitutions at the interface residues and performed a detailed investigation using biochemical and biophysical methods including circular dichroism, fluorescence anisotropy and quenching, differential scanning calorimetry, blue-native PAGE, cross-linking, size exclusion chromatography, and dynamic light scattering. We also carried out both transcription and DNA replication to understand the properties of the wild-type and the mutant proteins. RESULTS One specific mutation S88P leads not only to monomerization, but also results in an unstable molecule. Most interestingly, mutating either Q125 or K164 in the gp45 C-terminal domain negatively affects the stability of the N-terminal domain. We also report that these residues upon mutation to alanine make gp45 inactive for late promoter transcription, whereas strand-displacement DNA replication ability remains unaltered. CONCLUSIONS AND GENERAL SIGNIFICANCE The results suggest that the two domains of gp45 demonstrate an "inter-monomer" crosstalk that stabilizes the trimer. We also conclude that the residue-specific interactions at the interface allow the protein to function distinctly as replication and transcription factors.
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Affiliation(s)
- Manika Indrajit Singh
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, India
| | - Bylapudi Ganesh
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, India
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, India.
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3
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Geiduschek EP, Kassavetis GA. Transcription of the T4 late genes. Virol J 2010; 7:288. [PMID: 21029432 PMCID: PMC2988020 DOI: 10.1186/1743-422x-7-288] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 10/28/2010] [Indexed: 11/16/2022] Open
Abstract
This article reviews the current state of understanding of the regulated transcription of the bacteriophage T4 late genes, with a focus on the underlying biochemical mechanisms, which turn out to be unique to the T4-related family of phages or significantly different from other bacterial systems. The activator of T4 late transcription is the gene 45 protein (gp45), the sliding clamp of the T4 replisome. Gp45 becomes topologically linked to DNA through the action of its clamp-loader, but it is not site-specifically DNA-bound, as other transcriptional activators are. Gp45 facilitates RNA polymerase recruitment to late promoters by interacting with two phage-encoded polymerase subunits: gp33, the co-activator of T4 late transcription; and gp55, the T4 late promoter recognition protein. The emphasis of this account is on the sites and mechanisms of actions of these three proteins, and on their roles in the formation of transcription-ready open T4 late promoter complexes.
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Affiliation(s)
- E Peter Geiduschek
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92093-0634, USA.
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4
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Abstract
This is a memoir of circumstances that have shaped my life as a scientist, some of the questions that have excited my interest, and some of the people with whom I have shared that pursuit. I was introduced to transcription soon after the discovery of RNA polymerase and have been fascinated by questions relating to gene regulation since that time. My account touches on early experiments dealing with the ability of RNA polymerase to selectively transcribe its DNA template. Temporal programs of transcription that control the multiplication cycles of viruses (phages) and the precise mechanisms generating this regulation have been a continuing source of fascination and new challenges. A longtime interest in eukaryotic RNA polymerase III has centered on yeast and on the enumeration and properties of its transcription initiation factors, the architecture of its promoter complexes, and the mechanism of transcriptional initiation. These areas of research are widely regarded as separate, but to my thinking they have posed similar questions, and I have been unwilling or unable to abandon either one for the other. An additional interest in archaeal transcription can be seen as stemming naturally from this point of view.
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Affiliation(s)
- E Peter Geiduschek
- Division of Biological Sciences, University of California-San Diego, La Jolla, CA 92093-0634, USA.
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5
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Transcriptional Activation by a Topologically Linkable Protein: Forging a Connection Between Replication and Gene Activity. ACTA ACUST UNITED AC 1997. [DOI: 10.1007/978-3-642-60691-5_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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6
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Bartholomew B, Tinker RL, Kassavetis GA, Geiduschek EP. Photochemical cross-linking assay for DNA tracking by replication proteins. Methods Enzymol 1995; 262:476-94. [PMID: 8594372 DOI: 10.1016/0076-6879(95)62039-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- B Bartholomew
- Department of Medical Biochemistry, Southern Illinois University School of Medicine, Carbondale 62901-6503, USA
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7
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Ouhammouch M, Orsini G, Brody EN. The asiA gene product of bacteriophage T4 is required for middle mode RNA synthesis. J Bacteriol 1994; 176:3956-65. [PMID: 8021178 PMCID: PMC205593 DOI: 10.1128/jb.176.13.3956-3965.1994] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The asiA gene of bacteriophage T4 encodes a 10-kDa peptide which binds strongly in vitro to the sigma 70 subunit of Escherichia coli RNA polymerase, thereby weakening sigma 70-core interactions and inhibiting sigma 70-dependent transcription. To assess the physiological role of this protein, we have introduced an amber mutation into the proximal portion of the asiA gene. On suppressor-deficient hosts, this mutant phage (amS22) produces minute plaques and exhibits a pronounced delay in phage production. During these mutant infections, T4 DNA synthesis is strongly delayed, suggesting that the AsiA protein plays an important role during the prereplicative period of phage T4 development. The kinetics of protein synthesis show clearly that while T4 early proteins are synthesized normally, those expressed primarily via the middle mode exhibit a marked inhibition. In fact, the pattern of protein synthesis after amS22 infection resembles greatly that seen after infection by amG1, an amber mutant in motA, a T4 gene whose product is known to control middle mode RNA synthesis. The amber mutations in the motA and asiA genes complement, both for phage growth and for normal kinetics of middle mode protein synthesis. Furthermore, primer extension analyses show that three different MotA-dependent T4 middle promoters are not recognized after infection by the asiA mutant phage. Thus, in conjunction with the MotA protein, the AsiA protein is required for transcription activation at T4 middle mode promoters.
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Affiliation(s)
- M Ouhammouch
- Department of Biological Sciences, State University of New York at Buffalo 14260
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8
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Geiduschek EP. Two prokaryotic transcriptional enhancer systems. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1992; 43:109-33. [PMID: 1410444 DOI: 10.1016/s0079-6603(08)61046-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- E P Geiduschek
- Department of Biology, University of California, San Diego, La Jolla 92093
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9
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Munn M, Alberts B. DNA footprinting studies of the complex formed by the T4 DNA polymerase holoenzyme at a primer-template junction. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)54888-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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10
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Munn M, Alberts B. The T4 DNA polymerase accessory proteins form an ATP-dependent complex on a primer-template junction. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)54887-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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11
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Herendeen DR, Kassavetis GA, Barry J, Alberts BM, Geiduschek EP. Enhancement of bacteriophage T4 late transcription by components of the T4 DNA replication apparatus. Science 1989; 245:952-8. [PMID: 2672335 DOI: 10.1126/science.2672335] [Citation(s) in RCA: 92] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The expression of the late genes in bacteriophage T4 development is closely connected to viral DNA replication. Three T4-encoded DNA polymerase accessory proteins are shown to stimulate transcription at T4 late promoters in an adenosine triphosphate (ATP) hydrolysis-requiring process. The properties of the activation resemble those found for enhancers of eukaryotic transcription. However, the nature of the enhancer of T4 late transcription is novel in that it is a structure--a break in the nontranscribed DNA stand--to which the three replication proteins bind, rather than a sequence. Since the three DNA polymerase accessory proteins are carried on the moving replication fork as part of the replisome, we postulate that viral DNA replication forks act, in vivo, as the mobile enhancers of T4 late gene transcription. Whereas Escherichia coli RNA polymerase bearing the T4 gene 55 protein can selectively recognize T4 late promoters, it is only capable of responding to the transcription-enhancing activity of the three replication proteins on acquiring an additional T4-specific modification.
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Affiliation(s)
- D R Herendeen
- Department of Biology, Center for Molecular Genetics, University of California, San Diego, La Jolla 92093
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12
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Scarlato V, Storlazzi A, Gargano S, Cascino A. Bacteriophage T4 late gene expression: overlapping promoters direct divergent transcription of the base plate gene cluster. Virology 1989; 171:475-83. [PMID: 2763463 DOI: 10.1016/0042-6822(89)90617-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Eight 5' ends of RNA molecules which encompass the bacteriophage T4 base plate late genes 51 to 26 region have been mapped by S1 nuclease protection and reverse transcription within a 246-bp DNA segment. Two of eight 5' ends are initiated at two absolutely conserved late promoter sites, P51 and P26a, that direct RNA synthesis on opposite strands. These two promoters share four of eight promoter sequence base pairs. A third 5' end arises from another promoter, P26b, which shows one base pair mismatch with respect to the absolutely conserved -10 sequence. All the other 5' ends arise from RNA processing and/or degradation. Since no other late transcription promoter sites were found within the base plate cluster sequence, we propose that the two overlapping late promoters, P51 and P26a, direct the expression of the T4 base plate gene cluster, included between map coordinates 114,000 and 121,038: P51 directs the transcription of genes 51, 27, 28, 29, 48, and 54 on the rDNA strand and P26a the transcription of genes 26 and 25 on the /DNA strand. This peculiar promoter configuration might account for the low level of transcription of these late genes.
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Affiliation(s)
- V Scarlato
- International Institute of Genetics and Biophysics, Naples, Italy
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13
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Rush J, Lin TC, Quinones M, Spicer EK, Douglas I, Williams KR, Konigsberg WH. The 44P Subunit of the T4 DNA Polymerase Accessory Protein Complex Catalyzes ATP Hydrolysis. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)60410-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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14
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Guild N, Gayle M, Sweeney R, Hollingsworth T, Modeer T, Gold L. Transcriptional activation of bacteriophage T4 middle promoters by the motA protein. J Mol Biol 1988; 199:241-58. [PMID: 3280803 DOI: 10.1016/0022-2836(88)90311-7] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Transcriptional activation of middle genes in bacteriophage T4 requires the phage-encoded motA protein. Many middle genes are involved in deoxyribonucleotide biosynthesis and phage DNA replication. In the absence of motA, the gene products that are required for DNA synthesis are transcribed from other, upstream promoters. Using primer extension sequencing on RNA templates isolated from T4 motA+ and motA- infected cells, we have characterized 14 motA-dependent transcripts. The T4 middle promoters have a consensus sequence of nine base-pairs, (a/t)(a/t)TGCTT(t/c)A, spaced 11 to 13 nucleotides away from the Escherichia coli--10 consensus sequence, TAnnnT. The motA protein also can act as a transcriptional repressor for at least one early gene. Furthermore, the phage-encoded motA protein can activate in trans a middle promoter resident on a plasmid.
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Affiliation(s)
- N Guild
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder 80309
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15
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Gauss P, Krassa KB, McPheeters DS, Nelson MA, Gold L. Zinc (II) and the single-stranded DNA binding protein of bacteriophage T4. Proc Natl Acad Sci U S A 1987; 84:8515-9. [PMID: 3120192 PMCID: PMC299575 DOI: 10.1073/pnas.84.23.8515] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The DNA binding domain of the gene 32 protein of the bacteriophage T4 contains a single "zinc-finger" sequence. The gene 32 protein is an extensively studied member of a class of proteins that bind relatively nonspecifically to single-stranded DNA. We have sequenced and characterized mutations in gene 32 whose defective proteins are activated by increasing the Zn(II) concentration in the growth medium. Our results identify a role for the gene 32 protein in activation of T4 late transcription. Several eukaryotic proteins with zinc fingers participate in activation of transcription, and the gene 32 protein of T4 should provide a simple, well-characterized system in which genetics can be utilized to study the role of a zinc finger in nucleic acid binding and gene expression.
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Affiliation(s)
- P Gauss
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder 80309
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16
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Hsu T, Wei RX, Dawson M, Karam JD. Identification of two new bacteriophage T4 genes that may have roles in transcription and DNA replication. J Virol 1987; 61:366-74. [PMID: 3543399 PMCID: PMC253958 DOI: 10.1128/jvi.61.2.366-374.1987] [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: 01/06/2023] Open
Abstract
We have identified two bacteriophage T4 genes, 45.1 and 45.2, that map in the intergenic space between phage replication genes 46 (which encodes a recombination initiation protein) and 45 (which encodes a bifunctional protein required in replication and transcription). The existence of genes 45.1 and 45.2 had not been previously recognized by mutation analysis of the T4 genome. We cloned the T4 gene 45.1/45.2 segment, determined its nucleotide sequence, and expressed its two reading frames at high levels in bacterial plasmids. The results predicted molecular weights of 11,400 (100 amino acids) for gp45.1 and 7,500 (62 amino acids) for gp45.2. We also determined that in T4-infected Escherichia coli, genes 45.1 and 45.2 are cotranscribed with their distal neighbor, gene 45, by at least one mode of transcription. In an accompanying report (K. P. Williams, G. A. Kassavetis, F. S. Esch, and E. P. Geiduschek, J. Virol. 61:600-603, 1987), it is shown that the product of gene 45.1 is the so-called T4-induced 15K protein, an RNA polymerase-binding protein of unknown role in phage development. Possibly, T4 genes 45.2, 45.1, and 45 constitute an operon for host RNA polymerase-binding phage proteins. Jointly with Williams et al., we propose the term rpb (RNA polymerase-binding) to refer to T4 genes whose products bind to the host RNA polymerase and have adopted the name rpbA for T4 gene 45.1.
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17
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Malik S, Goldfarb A. The effect of a bacteriophage T4-induced polypeptide on host RNA polymerase interaction with promoters. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(18)90692-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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18
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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.
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19
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Costanzo M, Hannett N, Brzustowicz L, Pero J. Bacteriophage SPO1 gene 27: location and nucleotide sequence. J Virol 1983; 48:555-60. [PMID: 6413701 PMCID: PMC255381 DOI: 10.1128/jvi.48.2.555-560.1983] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Bacteriophage SPO1 gene 27, whose product is required for late gene transcription and DNA replication, has been cloned in Escherichia coli, and its complete nucleotide sequence has been determined. We infer that the product of gene 27 is a highly basic 17,518-dalton protein of 155 amino acids. The gene for this regulatory protein is transcribed from two promoters: an early promoter situated before the adjacent upstream gene 28 and a middle promoter located between genes 28 and 27.
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20
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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.
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21
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Westin G, Djurhuus R, Skreslett U. In vitro transcription of phage T4 late genes on purified DNA by partially purified RNA polymerase from T4-infected Escherichia coli b cells. BIOCHIMICA ET BIOPHYSICA ACTA 1982; 699:28-39. [PMID: 6756478 DOI: 10.1016/0167-4781(82)90168-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
RNA polymerase was purified from 'late' phage T4-infected Escherichia coli B cells by DNA-cellulose affinity chromatography and high salt agarose filtration. The DNA-cellulose-purified RNA polymerase preparation contained T4-coded DNA endonuclease activity and several proteins, some with sizes comparable with the known T4 maturation factors, essential for late RNA synthesis. Some of these proteins, and the DNA endonuclease utilizing native, parental T4 DNA and supercoiled phi X 174 DNA as substrates, were partially separated from the RNA polymerase as a complex during agarose filtration. In vitro RNA was made by the DNA-cellulose-purified RNA polymerase using native, parental T4 DNA as template. About 26% of the in vitro RNA was transcribed from the DNA r-strand; 75% from the same r-strand region as in vivo late after infection. Both the abundancy and specificity of the in vitro r-strand transcription were markedly reduced after agarose filtration of the enzyme. Addition of the proteins separated from the RNA polymerase during agarose filtration caused a restoration of in vitro r-strand transcription abundance, but not its specificity. These results show that partially purified RNA polymerase from T4-infected E. coli B cells was able to transcribe late T4 genes in vitro with some abundancy and specificity on purified, parental T4 DNA, but further purification of the enzyme caused an irreversible reduction of this ability.
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22
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Abstract
Bacteriophage T4 late transcription is unusual, among prokaryotes, in its complexity. Late transcription requires the host RNA polymerase, the products of T4 genes, 33, 45 and 55, and other small polypeptides, the genes of which have not been identified. In addition the DNA template must be "competent' for late transcription. First the DNA must contain the substituted base 5-hydroxymethyl cytosine in place of cytosine (this requirement is eliminated by a mutation in the T4 alc gene). Second, the DNA must be replicating, although late transcription can be uncoupled from DNA replication by mutations in the T4 genes coding for DNA ligase (gene 30) and DNA exonuclease (gene 46). We report here the location of the initiation sites of the messenger RNAs (mRNAs) synthesized in vivo from four late genes (genes 21, 22, 23 and 36) by S1 nuclease mapping and we have determined the DNA sequences at these sites. We have found strong homology to the sequence TATAAATACTATT immediately upstream from the 5' ends of the late messages and we suggest that this sequence is specifically recognized by the complex responsible for late transcription. Also, we have examine gene 23 mRNA synthetized in the absence of DNA replication using the 30- 46- mutant described above and find that it is identical to the true late transcript synthesized in normal infections.
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23
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24
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Heintz N, Shub DA. Transcriptional regulation of bacteriophage SPO1 protein synthesis in vivo and in vitro. J Virol 1982; 42:951-62. [PMID: 6808157 PMCID: PMC256928 DOI: 10.1128/jvi.42.3.951-962.1982] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
There are six classes of SPO1 transcripts which are, at least partially, regulated independently of each other. Analysis of proteins made in infections by phage mutants defective in DNA synthesis, or in genes which positively control transcription, permitted each protein to be assigned to one transcription class. Most of the late proteins belong to transcription class m2l. There seem to be few, if any, phage proteins in the l class whose mRNA synthesis depends absolutely on phage DNA synthesis, UV irradiation of host cells allowed the detection of many additional early proteins. The early proteins detected in vivo were compared with proteins synthesized in vitro, using bacterial or gp28 phage-modified RNA polymerase in an Escherichia coli cell-free system. Proteins characterized in vivo as belonging to the e transcription class could be made efficiently in vitro only when transcription was performed by bacterial RNA polymerase. em proteins could be elicited through the use of either bacterial or gp28 polymerase, indicating that their genes can be transcribed in either the early or the middle mode.
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Abstract
The SP01 mutant sus HA20 (gene 27) was found to be defective for synthesis of viral late RNA. It is known that gene 27 is also required for viral DNA replication. The SP01 gene 27 product resembles the T4 gene 45 product, which also has a dual role in viral DNA replication and late transcription.
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26
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Bacteriophage T4 infection mechanisms. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/b978-0-444-80400-6.50013-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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27
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Zograff YN. On the role of the Escherichia coli RNA polymerase sigma factor in T4 phage development. MOLECULAR & GENERAL GENETICS : MGG 1981; 183:557-8. [PMID: 7038380 DOI: 10.1007/bf00268782] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The rpoD800 mutation causing the temperature sensitivity of Escherichia coli RNA polymerase sigma factor has been used to demonstrate that the bacterial sigma factor is necessary throughout T4 phage development. In T4-infected RpoD800 mutant cells RNA synthesis is equally depressed at restrictive temperature at early and late stages of infection. The results show the bacterial sigma factor to be necessary for the synthesis of all RNA types in infected cells.
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28
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Haarr L, Nygaard AP. DNA-RNA polymerase complexes associated with the membrane from bacteriophage T2- or T4-infected Escherichia coli. I. General properties. BIOCHIMICA ET BIOPHYSICA ACTA 1980; 610:248-60. [PMID: 7011383 DOI: 10.1016/0005-2787(80)90007-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Properties of DNA-RNA polymerase complexes, apparently bound to a fraction of the cell membrane of bacteriophage T2- or T4-infected Escherichia coli, are described. Evidence is presented to show that the complexes initiate the asymmetric synthesis of RNA, and release the finished product. The transcription capacity per unit of beta' + beta was 10 times higher at 6 min than at 30 min after infection.
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29
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Zograff YN, Gintsburg AL. Transcription termination factor rho and T-even phage development. MOLECULAR & GENERAL GENETICS : MGG 1980; 177:699-705. [PMID: 6991874 DOI: 10.1007/bf00272682] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A functional factor rho is necessary for T-even phage development; phages T2 and T4 require different degrees of rho activity. The rho inactivation by ts-mutations in E. coli causes a reduction of some early protein synthesis and an early formation of some proteins normally typical of a later stage. Besides, it weakens the synthesis of some late proteins, impairs the capsid proteins maturation and sharply inhibits phage DNA replication in infected cells. However, in the absence of a functional rho all the proteins required for phage DNA synthesis the formed, indicating that this factor is directly involved in the process of T-even phage DNA replication. A number of rifampicin-resistant mutations supressing the rho 15 mutation and restoring the ability of cells to grow at high temperature were isolated. However these RNA polymerase mutations do not or only partially suppress the effect of rho mutations on T-even phage development and the phage DNA synthesis. The role of rho in DNA transcription and replication during bacteriophage development is discussed.
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30
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Velten J, Abelson J. The generation and analysis of clones containing bacteriophage T4 DNA fragments. J Mol Biol 1980; 137:235-48. [PMID: 6246245 DOI: 10.1016/0022-2836(80)90327-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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31
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Rabussay D, Geiduschek EP. Relation between bacteriophage T4 DNA replication and late transcription in vitro and in vivo. Virology 1979; 99:286-301. [PMID: 160129 DOI: 10.1016/0042-6822(79)90008-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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32
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Macchiato MF, Grossi GF, Cascino A. Roles of gene 45 product into T4 DNA replication and late gene expression of: temperature reversibility effect. FEBS Lett 1979; 104:187-92. [PMID: 383506 DOI: 10.1016/0014-5793(79)81112-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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33
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DNA replication with bacteriophage T4 proteins. Purification of the proteins encoded by T4 genes 41, 45, 44, and 62 using a complementation assay. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(18)50514-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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34
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Dharmalingam K, Goldberg EB. Restriction in vivo. III. General effects of glucosylation and restriction on phage T4 gene expression and replication. Virology 1979; 96:393-403. [PMID: 380145 DOI: 10.1016/0042-6822(79)90097-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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35
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Morris CF, Hama-Inaba H, Mace D, Sinha NK, Alberts B. Purification of the gene 43, 44, 45, and 62 proteins of the bacteriophage T4 DNA replication apparatus. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(18)50437-3] [Citation(s) in RCA: 101] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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36
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Karam J, Bowles M, Leach M. Expression of bacteriophage T4 genes 45, 44, and 62. I. Discoordinate synthesis of the T4 45- and 44-proteins. Virology 1979; 94:192-203. [PMID: 442532 DOI: 10.1016/0042-6822(79)90449-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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37
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Abstract
The use of a computer-coupled film scanner to measure and analyze autoradiograms of gel electropherograms is described. A program has been written which fits Gaussian curves to the complex band pattern that constitutes a density profile without the need for estimated parameters in the input. The great majority of the fits are satisfactory. This program, which is written in FORTRAN, runs on a small, inexpensive computer. Another program which approximates a Gaussian least squares fit has been run for comparison; this procedure can also be used to refine occasional unsatisfactory fits. Finally, a program has been written which sums the density profile within specified limits, so that the integrated intensities of bands due to isolated protein components may be found.
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Affiliation(s)
- M F Schumaker
- Department of Biology, University of California at San Diego, La Jolla 92093, USA
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38
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Rüger W. Transcription of bacteriophage T4 DNA in vitro: selective initiation with dinucleotides. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 88:109-17. [PMID: 668702 DOI: 10.1111/j.1432-1033.1978.tb12427.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The transcription products of phage T4 DNA in vitro are separated on polyacrylamide gels. The influence of salt, polymerase, triphosphate concentration and glucosylation on the RNA synthesis are shown. Individual transcripts are initiated selectively with dinucleotides and a single triphosphate. This technique allows the prediction of the initiation sequences of several T4 transcripts.
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39
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REMINGTON JA, FLICKINGER RA. TIMING OF INCORPORATION OF TRITIATED NUCLEOSIDES INTO DNA AND RNA OF EMBRYONIC CELLS OF RANA PIPIENS. Dev Growth Differ 1978. [DOI: 10.1111/j.1440-169x.1978.00011.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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40
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Talkington C, Pero J. Restriction fragment analysis of the temporal program of bacteriophage SPO1 transcription and its control by phage-modified RNA polymerases. Virology 1977; 83:365-79. [PMID: 412317 DOI: 10.1016/0042-6822(77)90181-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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41
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Shah DB, DeLorenzo L. Suppression of gene 49 mutations of bacteriophage T4 by a second mutation in gene X: structure of pseudorevertant DNA. J Virol 1977; 24:794-804. [PMID: 592466 PMCID: PMC516001 DOI: 10.1128/jvi.24.3.794-804.1977] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Mutations in gene 49 of bacteriophage T4 were suppressed by a second mutation in gene X. Mapping studies located gene X between genes 41 and 42. Complementation results indicated that mutations in FdsA gene (a suppressor of gene 49 mutants) were in gene X. The intracellular pseudorevertant DNA was examined for unusual properties which could explain its successful encapsidation. After the in vivo inactivation of a temperature-sensitive gene 32 (DNA unwinding) protein, the intracellular pseudorevertant DNA was converted into DNA pieces of approximately genome size. A similar conversion was observed after in vitro digestion of pseudorevertant DNA with single-strand-specific S1 endonuclease. Appreciable quantities of oligomeric intermediates were not produced during this conversion process. These data indicate that pseudorevertant DNA contains sizable single-stranded gaps and has a conformation similar to that of wild-type DNA. The results further suggest that the suppression of gene 49 mutant abnormal DNA phenotype and the encapsidation defect by a second mutation in gene X is associated with the formation of sizable single-stranded gaps. These studies raise the possibility that single-stranded gaps may be involved directly in the DNA encapsidation process, or may act indirectly as a consequence of their effect on the organization of intracellular DNA.
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42
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Wu R, Geiduschek EP. Distinctive protein requirements of replication-dependent and -uncoupled bacteriophage T4 late gene expression. J Virol 1977; 24:436-43. [PMID: 916023 PMCID: PMC515952 DOI: 10.1128/jvi.24.2.436-443.1977] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
This paper further explores the relationship of viral DNA replication to bacteriophage T4 late gene expression. It is shown that replication coupled and -independent late transcription make different qualitative or quantitative demands on phage protein synthesis. In further analysis of these different protein synthesis requirements, experiments were performed with a temperature-sensitive mutant in T4 gene 55 (ts553). It is known that the gene 55 product regulates T4 late gene expression and binds to RNA polymerase. In the experiments presented here, it is shown that the temperature sensitivity of the ts553 gene 55 protein depends on whether it is involved in replication-coupled or -independent T4 late transcription. This is evidence that the proteins constituting the transcription apparatus interact differently with late transcription units in T4 DNA, depending on whether late transcription is replication coupled or independent.
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43
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Grossi G, Macchiato M, Gialanella G, Cascino A. Endonucleolytic cleavage of parental DNA and T4 late-gene expression: distribution analysis of single-strand and double-strand breaks. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 80:73-7. [PMID: 336368 DOI: 10.1111/j.1432-1033.1977.tb11857.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In order to investigate the dependency of late transcription on concurrent DNA replication during bacteriophage T4 development, we analyzed the endonucleolytic cleavage kinetics of the DNA of a T4 mutant lacking DNA polymerase, DNA ligase and exonuclease by using the sucrose gradient sedimentation technique. Our results can be summarized as follows. 1. The single-strand endonucleolytic cleavage of the T4 mutant DNA is not a random process. 2. The number of single-strand nicks reaches a plateau level of 10--12 nicks/molecule. 3. The occurrence of a double-strand break is delayed and their number is at any time lower than the number of single-strand nicks. 4. The circular permutation T4 genome, as computer-simulated by the Monte Carlo method, produces a smoothing of the discrete distribution which would be expected if nicks were localized in the promoter sites of late transcription units. We conclude that our findings support the model which relates single-strand DNA nicks to the late transcription initiation sites.
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44
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Frederick RJ, Snyder L. [Regulation of anti-late RNA synthesis in bacteriophage T4: a delayed early control]. J Mol Biol 1977; 114:461-76. [PMID: 335074 DOI: 10.1016/0022-2836(77)90172-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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45
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46
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Snyder L, Gold L, Kutter E. A gene of bacteriophage T4 whose product prevents true late transcription on cytosine-containing T4 DNA. Proc Natl Acad Sci U S A 1976; 73:3098-102. [PMID: 1067605 PMCID: PMC430943 DOI: 10.1073/pnas.73.9.3098] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
T-even coliphages have 5-hydroxymethylcytosine in their DNA instead of cytosine. In some T4 mutants, the replicated DNA contains cytosine, but then no late gene products are made. We show that the inability to make late gene products with cytosine-containing T4 DNA is due to a T4 gene products. This gene product, while probably nonessential under normal conditions, interacts with an essential part of the transcription apparatus. Mutations in this gene allow viable T4 particles to be made whose DNA has been substituted almost 100% with cytosine.
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47
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Duffy JJ, Geiduschek EP. The virus-specified subunits of a modified B. subtilis RNA polymerase are determinants of DNA binding and RNA chain initiation. Cell 1976; 8:595-604. [PMID: 821619 DOI: 10.1016/0092-8674(76)90227-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The phage SPO1-modified RNA polymerase B-P can form rapidly initiating complexes with SPO1 DNA but not with heterologous phi1 DNA. The B-P enzyme binds only weakly to heterologous phi29 DNA: preincubation with phi29 DNA does not substantially slow the formation of rapidly initiating complexes between polymerase B-P and subsequently added SPO1 DNA. In contrast, B. subtilis holoenzyme and core polymerase are substantially sequestered by preincubation with phi29 DNA. The results show that at least one of the phage SPO1-coded subunits of the polymerase B-P determines selective transcription at the level of DNA binding and RNA chain initiation, weakens the binding of RNA polymerase core to heterologous DNA, and discriminates against promoter complex formation at certain promoters that are utilized by the B. subtilis holoenzyme.
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48
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Wu R, Geiduschek EP. The role of replication proteins in the regulation of bacteriophage T4 transcription. I. Gene 45 and hydroxymethyl-C-containing DNA. J Mol Biol 1975; 96:513-38. [PMID: 1104860 DOI: 10.1016/0022-2836(75)90137-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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49
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Coppo A, Manzi A, Pulitzer JF. Host mutant (tabD)-induced inhibition of bacteriophage T4 late transcription. II. Genetic characterization of mutants. J Mol Biol 1975; 96:601-24. [PMID: 1104862 DOI: 10.1016/0022-2836(75)90141-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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50
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Coppo A, Manzi A, Pulitzer JF, Takahashi H. Host mutant (tabD)-induced inhibition of bacteriophage T4 late transcription. I. Isolation and phenotypic characterization of the mutants. J Mol Biol 1975; 96:579-600. [PMID: 1195367 DOI: 10.1016/0022-2836(75)90140-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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