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King RA, Babbs M, Baugh K, Hamilton C. Isolation and Characterization of Phages That Bypass the Requirement for RNA-Mediated Antitermination. PHAGE (NEW ROCHELLE, N.Y.) 2023; 4:82-89. [PMID: 37350996 PMCID: PMC10282786 DOI: 10.1089/phage.2023.0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
Abstract
Introduction The rpoCY75N mutation in the zinc-binding domain of the β' subunit of Escherichia coli RNA polymerase blocks the RNA-based mechanism of transcription antitermination utilized by bacteriophage HK022. Materials and Methods Mutant phages that overcome the block imposed by the rpoCY75N mutation are described. These phages, designated "orc" (overcomes rpoC), carry mutations that create new promoters. Promoter activity was assessed by cloning the respective regions from the wild-type and orc phages into a promoterless lacZ reporter vector. Results Reporter assays showed that the sequence originating from orc phages had significant promoter activity when compared with the equivalent sequence cloned from the parental phage. Conclusions The newly created promoters facilitate the expression of phage genes that are essential for growth on the rpoCY75N strain by bypassing transcription terminators. The small plaque phenotype of orc phages, when grown on the mutant host, suggests that suppression of the rpoCY75N mutation is incomplete.
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Affiliation(s)
- Rodney A. King
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, USA
| | - Millicent Babbs
- Owensboro Family Medicine, University of Louisville, Owensboro, Kentucky, USA
| | - Kimberly Baugh
- Department of Pharmacy, Franciscan Health Lafayette East, Lafayette, Indiana, USA
| | - Courtney Hamilton
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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2
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Thomason LC, Morrill K, Murray G, Court C, Shafer B, Schneider TD, Court DL. Elements in the λ immunity region regulate phage development: beyond the 'Genetic Switch'. Mol Microbiol 2019; 112:1798-1813. [PMID: 31545538 PMCID: PMC8103288 DOI: 10.1111/mmi.14394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2019] [Indexed: 01/16/2023]
Abstract
Genetic elements in the bacteriophage λ immunity region contribute to stable maintenance and synchronous induction of the integrated Escherichia coli prophage. There is a bistable switch between lysogenic and lytic growth that is orchestrated by the CI and Cro repressors acting on the lytic (PL and PR ) and lysogenic (PRM ) promoters, referred to as the Genetic Switch. Other less well-characterized elements in the phage immunity region include the PLIT promoter and the immunity terminator, TIMM . The PLIT promoter is repressed by the bacterial LexA protein in λ lysogens. LexA repressor, like the λ CI repressor, is inactivated during the SOS response to DNA damage, and this regulation ensures that the PLIT promoter and the lytic PL and PR promoters are synchronously activated. Proper RexA and RexB protein levels are critical for the switch from lysogeny to lytic growth. Mutation of PLIT reduces RexB levels relative to RexA, compromising cellular energetics and causing a 10-fold reduction in lytic phage yield. The RexA and RexB proteins interact with themselves and each other in a bacterial two-hybrid system. We also find that the transcription terminator, TIMM , is a Rho-independent, intrinsic terminator. Inactivation of TIMM has minimal effect on λ lysogenization or prophage induction.
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Affiliation(s)
- Lynn C Thomason
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Kathleen Morrill
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Gillian Murray
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Carolyn Court
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Brenda Shafer
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Thomas D Schneider
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Donald L Court
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
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Zhou Y, Shi T, Mozola MA, Olson ER, Henthorn K, Brown S, Gussin GN, Friedman DI. Evidence that the promoter can influence assembly of antitermination complexes at downstream RNA sites. J Bacteriol 2006; 188:2222-32. [PMID: 16513752 PMCID: PMC1428141 DOI: 10.1128/jb.188.6.2222-2232.2006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The N protein of phage lambda acts with Escherichia coli Nus proteins at RNA sites, NUT, to modify RNA polymerase (RNAP) to a form that overrides transcription terminators. These interactions have been thought to be the primary determinants of the effectiveness of N-mediated antitermination. We present evidence that the associated promoter, in this case the lambda early P(R) promoter, can influence N-mediated modification of RNAP even though modification occurs at a site (NUTR) located downstream of the intervening cro gene. As predicted by genetic analysis and confirmed by in vivo transcription studies, a combination of two mutations in P(R), at positions -14 and -45 (yielding P(R-GA)), reduces effectiveness of N modification, while an additional mutation at position -30 (yielding P(R-GCA)) suppresses this effect. In vivo, the level of P(R-GA)-directed transcription was twice as great as the wild-type level, while transcription directed by P(R-GCA) was the same as that directed by the wild-type promoter. However, the rate of open complex formation at P(R-GA) in vitro was roughly one-third the rate for wild-type P(R). We ascribe this apparent discrepancy to an effect of the mutations in P(R-GCA) on promoter clearance. Based on the in vivo experiments, one plausible explanation for our results is that increased transcription can lead to a failure to form active antitermination complexes with NUT RNA, which, in turn, causes failure to read through downstream termination sites. By blocking antitermination and thus expression of late functions, the effect of increased transcription through nut sites could be physiologically important in maintaining proper regulation of gene expression early in phage development.
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Affiliation(s)
- Ying Zhou
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
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4
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Strauch E, Schaudinn C, Beutin L. First-time isolation and characterization of a bacteriophage encoding the Shiga toxin 2c variant, which is globally spread in strains of Escherichia coli O157. Infect Immun 2004; 72:7030-9. [PMID: 15557626 PMCID: PMC529153 DOI: 10.1128/iai.72.12.7030-7039.2004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A bacteriophage encoding the Shiga toxin 2c variant (Stx2c) was isolated from the human Escherichia coli O157 strain CB2851 and shown to form lysogens on the E. coli K-12 laboratory strains C600 and MG1655. Production of Stx2c was found in the wild-type E. coli O157 strain and the K-12 lysogens and was inducible by growing bacteria in the presence of ciprofloxacin. Phage 2851 is the first reported viable bacteriophage which carries an stx(2c) gene. Electron micrographs of phage 2851 showed particles with elongated hexagonal heads and long flexible tails resembling phage lambda. Sequence analysis of an 8.4-kb region flanking the stx(2c) gene and other genetic elements revealed a mosaic gene structure, as found in other Stx phages. Phage 2851 showed lysis of E. coli K-12 strains lysogenic for Stx phages encoding Stx1 (H19), Stx2 (933W), Stx (7888), and Stx1c (6220) but showed superinfection immunity with phage lambda, presumably originating from the similarity of the cI repressor proteins of both phages. Apparently, phage 2851 integrates at a different chromosomal locus than Stx2 phage 933W and Stx1 phage H19 in E. coli, explaining why Stx2c is often found in combination with Stx1 or Stx2 in E. coli O157 strains. Diagnostic PCR was performed to determine gene sequences specific for phage 2851 in wild-type E. coli O157 strains producing Stx2c. The phage 2851 q and o genes were frequently detected in Stx2c-producing E. coli O157 strains, indicating that phages related to 2851 are associated with Stx2c production in strains of E. coli O157 that were isolated in different locations and time periods.
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Affiliation(s)
- Eckhard Strauch
- Division of Microbial Toxins, Department of Biological Safety, Robert Koch Institute, Nordufer 20, D-13353 Berlin, Germany
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5
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Neely MN, Friedman DI. Arrangement and functional identification of genes in the regulatory region of lambdoid phage H-19B, a carrier of a Shiga-like toxin. Gene 1998; 223:105-13. [PMID: 9858702 DOI: 10.1016/s0378-1119(98)00236-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
H-19B is a lambdoid phage that carries the genes (stx-I) encoding the two toxin subunits of a Shiga-like toxin; Escherichia coli lysogens of H-19B are converted to toxin producers. Based on the determination of a 17-kb region of the H-19B genome and functional studies, we have identified the early regulatory region and associated genes of H-19B, as well as the location of the late regulatory region and the toxin and lysis genes. A comparative analysis of the sequence of the H-19B genome reveals the presence of ORFs and genes found in analogous positions on the genomes of a number of other lambdoid phages. A cloned genomic fragment that confers immunity to an infecting H-19B phage contains an ORF of an analogous size and genomic location for a repressor gene, adjacent to a putative operator region. The lambda replication genes, O and P, are conserved in H-19B except for a 39-bp insert in the O gene creating two new O protein-binding sites in the origin of replication (ori), giving H-19B six binding sites as opposed to the four sites found in lambda. We identify ORFs and sequences involved in transcriptional regulation encoding N-like antitermination systems like those found in other lambdoid phages and nearly identical to sequences found in phage HK97. Our functional studies show that these sequences support antitermination even though they contain significant differences from those of other lambdoid phages. We also identify ORFs and sequences analogous to the Q-p'R late antiterminators-promoters found in other lambdoid phages. The Shiga-like stx-I genes are located directly downstream of the promoter, p'R, for the late genes, and upstream of the lysis genes.
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Affiliation(s)
- M N Neely
- University of Michigan, Department of Microbiology and Immunology, Ann Arbor, MI 48109-0620, USA
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6
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Cheng SW, Court DL, Friedman DI. Transcription termination signals in the nin region of bacteriophage lambda: identification of Rho-dependent termination regions. Genetics 1995; 140:875-87. [PMID: 7672588 PMCID: PMC1206672 DOI: 10.1093/genetics/140.3.875] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The approximately 3-kb nin region of bacteriophage lambda, located between genes P and Q contains transcription termination signals as well as 10 open reading frames. Deletions in the nin region frees phage growth from dependence on the lambda-encoded N-transcription antitermination system, conferring a Nin phenotype (N-independence). A subregion of nin, roc, is defined by a 1.9-kb deletion (delta roc) which partially frees lambda growth from the requirement for N antitermination. The roc region has strong transcription termination activity as assayed by a plasmid-based terminator testing system. We report the following features of the roc region: the biologically significant terminators in the roc region are Rho dependent, deletion analysis located the biologically significant termination signals to a 1.2 kb-segment of roc, and analysis of other deletions and point mutations in the roc region suggested at least two biologically significant regions of termination, tR3 (extending from bp 42020 to 42231) and tR4 (extending from bp 42630 to 42825).
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Affiliation(s)
- S W Cheng
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109-0620, USA
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8
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Abstract
Certain lambda-P22 hybrids, providing that they express the P22 C1 protein, fail to grow in Escherichia coli with the sipB391 mutation. We show that sipB391, previously located to the 57-min region of the E. coli chromosome, is a large deletion that extends into the 3' end of ssrA, a gene encoding the small stable 10Sa RNA. This deletion, apparently created by the excision of a cryptic prophage, CP4-57 (identified by Kirby et al. [J. E. Kirby, J. E. Trempy, and S. Gottesman, J. Bacteriol. 176:2068-2081]), leaves most of ssrA intact but removes the sequence encoding the 3' end of the precursor form of 10Sa RNA. The lack of functional 10Sa RNA, resulting from either the excision of CP4-57 or insertional inactivation of ssrA, appears to be responsible for the inhibition of lambda-P22 growth in E. coli with the sipB391 mutation. We propose that 10Sa RNA acts either directly or indirectly to facilitate removal of C1 protein from its DNA target site.
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Affiliation(s)
- D M Retallack
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109
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9
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Craven MG, Granston AE, Schauer AT, Zheng C, Gray TA, Friedman DI. Escherichia coli-Salmonella typhimurium hybrid nusA genes: identification of a short motif required for action of the lambda N transcription antitermination protein. J Bacteriol 1994; 176:1394-404. [PMID: 8113180 PMCID: PMC205205 DOI: 10.1128/jb.176.5.1394-1404.1994] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The Escherichia coli nusA gene, nusAEc, encodes an essential protein that influences transcription elongation. Derivatives of E. coli in which the Salmonella typhimurium nusA gene, nusASt, has replaced nusAEc are viable. Thus, NusASt can substitute for NusAEc in supporting essential bacterial activities. However, hybrid E. coli strains with the nusASt substitution do not effectively support transcription antitermination mediated by the N gene product of phage lambda. We report the DNA sequence of nusASt, showing that the derived amino acid sequence is 95% identical to the derived amino acid sequence of nusAEc. The alignment of the amino acid sequences reveals scattered single amino acid differences and one region of significant heterogeneity. In this region, called 449, NusAEc has four amino acids and NusASt has nine amino acids. Functional studies of hybrid nusA genes, constructed from nusAEc and nusASt, show that the 449 region of the NusAEc protein is important for lambda N-mediated transcription antitermination. A hybrid that has a substitution of the four E. coli codons for the nine S. typhimurium codons, but is otherwise nusASt, supports the action of the N antitermination protein. The 449 region and, presumably, adjacent sequences appear to compose a functional domain of NusAEc important for the action of the N transcription antitermination protein of phage lambda.
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Affiliation(s)
- M G Craven
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109
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10
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Mason S, Li J, Greenblatt J. Host factor requirements for processive antitermination of transcription and suppression of pausing by the N protein of bacteriophage lambda. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)41792-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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11
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Cheng SW, Lynch EC, Leason KR, Court DL, Shapiro BA, Friedman DI. Functional importance of sequence in the stem-loop of a transcription terminator. Science 1991; 254:1205-7. [PMID: 1835546 DOI: 10.1126/science.1835546] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Intrinsic transcription terminators of prokaryotes are distinguished by a common RNA motif: a stem-loop structure high in guanine and cytosine content, followed by multiple uridine residues. Models explaining intrinsic terminators postulate that the stem-loop sequence is necessary only to form structure. In the tR2 terminator of coliphage lambda, single-nucleotide changes reducing potential RNA stem stability eliminated tR2 activity, and a compensatory change that restored the stem structure restored terminator activity. However, multiple changes in the stem sequence that should have either maintained or increased stability reduced terminator activity. These results suggest that the ability of the stem-loop structure to signal transcription termination depends on sequence specificity and secondary structure.
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Affiliation(s)
- S W Cheng
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109
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12
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Robledo R, Atkinson BL, Gottesman ME. Escherichia coli mutations that block transcription termination by phage HK022 Nun protein. J Mol Biol 1991; 220:613-9. [PMID: 1831236 DOI: 10.1016/0022-2836(91)90104-e] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The nun gene product of the lambdoid coliphage HK022 provokes premature transcription termination at, or near, the phage lambda nut sites. Termination by Nun and antitermination by lambda N protein both require the nut sites and Escherichia coli NusA, NusB and NusE proteins. To characterize further the host requirements for Nun termination, we selected host mutations that blocked termination at lambda nutR. In addition to mutations in nusA, nusB and nusE, we obtained mutations in rpoC, encoding the RNA polymerase beta' subunit. The nusA and rpoC mutations suppressed Nun termination but not antitermination by lambda N function. The mutations antagonized Nun only at lambda nutR; termination at lambda nutL occurred in all the mutant strains. Thus, nutL is not functionally equivalent to nutR. We conclude that the host requirements for Nun termination overlap but are not identical with those for N antitermination, and, in particular, that the beta' subunit of RNP may be Nun-specific.
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Affiliation(s)
- R Robledo
- Institute of Cancer Research, Columbia University College of Physicians and Surgeons, New York, NY 10032
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Costantino N, Zuber M, Court D. Analysis of mutations in the ninR region of bacteriophage lambda that bypass a requirement for lambda N antitermination. J Bacteriol 1990; 172:4610-5. [PMID: 2142940 PMCID: PMC213295 DOI: 10.1128/jb.172.8.4610-4615.1990] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Two mutations in the ninR region of bacteriophage lambda that bypass a requirement for antitermination have been studied. One mutation, byp, has been cloned and mapped by marker rescue to a 417-base-pair segment in the ninR region of the genome. Analysis of the byp mutation by using promoter detection vectors, DNA sequencing, and S1 nuclease analysis showed that the byp mutation created a new promoter that transcribed gene Q. The second mutation analyzed was the deletion nin3. Sequence analysis revealed that 2,485 base pairs of the ninR region were removed, beginning within the ren gene and ending in an open reading frame termed ninG. The tR2 and tR3 terminators, and probably others, were removed by the nin3 deletion, thereby allowing the phage to be N independent and to grow in hosts defective for Nus antitermination factors.
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Affiliation(s)
- N Costantino
- Laboratory of Chromosome Biology, National Cancer Institute-Frederick Cancer Research Facility, Maryland 21702-1201
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Robledo R, Gottesman ME, Weisberg RA. Lambda nutR mutations convert HK022 Nun protein from a transcription termination factor to a suppressor of termination. J Mol Biol 1990; 212:635-43. [PMID: 2139472 DOI: 10.1016/0022-2836(90)90226-c] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The Nun protein of the lambdoid phage HK022 blocks lambda growth by terminating transcription at (or near) the lambda nut sites. An HK022 lysogen carrying a fusion of the lambda pR promoter and nutR site to a gal operon that lacks its own promoter is, therefore, Gal-. To characterize the target of Nun action, spontaneous Gal+ revertants of this strain were isolated and characterized. Two cis-acting mutations are located in the fusion and represent transversions of conserved nucleotides within the boxA sequence (CGCTCTTA) of nutR. One mutation, (CTCTCTTA), is identical with boxA5. The second, boxA16 (CGCTATTA), has not been reported previously. In the absence of Nun, both boxA mutants reduce gal expression. Analysis of in vivo fusion RNA indicates that the mutations increase termination at or near tR1, a rho-dependent lambda terminator located upstream from the fusion point. In contrast to the nutR+ fusion, Nun stimulates gal expression in the boxA mutants by suppressing transcription termination in the tR1 region. Nun antitermination, however, does not extend to distal terminators. The lambda N-function also suppresses termination at or near tR1 in the mutant fusions. N fails to suppress terminators distal to tR1 in the boxA5 fusion, but displays persistent antitermination activity in the boxA16 fusion. A similar reversal of Nun activity occurs when wild-type fusions are introduced into nusA1, nusB5 or nusE71 hosts. We therefore suggest that Nun and N can interact with RNA polymerase in the absence of wild-type boxA, nusA, nusB or nusE, but that the complex formed with mutant components differs functionally from wild-type.
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Affiliation(s)
- R Robledo
- Institute of Cancer Research, Columbia University College of Physicians & Surgeons, New York, NY 10032
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