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Affiliation(s)
- Ronald Micura
- University of Innsbruck, Institute of Organic Chemistry, Innrain 52a, Innsbruck, Austria.
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52
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Haug I, Weissenborn A, Brolle D, Bentley S, Kieser T, Altenbuchner J. Streptomyces coelicolor A3(2) plasmid SCP2*: deductions from the complete sequence. MICROBIOLOGY (READING, ENGLAND) 2003; 149:505-513. [PMID: 12624212 DOI: 10.1099/mic.0.25751-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Plasmid SCP2* is a 31 kb, circular, low-copy-number plasmid originally identified in Streptomyces coelicolor A3(2) as a fertility factor. The plasmid was completely sequenced. The analysis of the 31 317 bp sequence revealed 34 ORFs encoding putative proteins from 31 to 710 aa long, most of them lacking similarity to known proteins. Three functional regions had been identified previously: the replication region, the transfer and spreading region, and the stability region. Three genes were identified in the stability region which contribute to the stability of SCP2 as shown by plasmid stability testing. The first gene, mrpA, encodes a new member of the lambda integrase family of site-specific recombinases. The two genes downstream of mrpA were called parA and parB. The gene product, ParA, shows similarity to a family of ATPases involved in plasmid partition. An increase of plasmid stability could be seen only when both genes were present. By deletion analysis, the replication region could be narrowed down to a 1.6 kb region, consisting of a 650 bp non-coding region and two genes, repI and repII, encoding proteins of 161 and 131 aa. Only RepI exhibits similarities to DNA binding elements and contains a putative helix-turn-helix motif. The traA gene that is essential for DNA transfer and pock formation was identified previously. Upstream of traA, 10 ORFs were found in the same orientation as traA which might be involved in conjugation and DNA spreading, together with one gene in the opposite orientation with similarities to transcriptional regulators of DNA transfer. Two transposable elements were found on SCP2*. IS1648 belongs to the IS3 family of insertion sequences. The second element, Tn5417, shows the highest similarity to the Tn4811 element located in the terminal inverted repeats of the Streptomyces lividans chromosome.
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Affiliation(s)
- Iris Haug
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Anke Weissenborn
- Mikrobiologie/Biotechnologie, Eberhard-Karls-Unversität Tübingen, 72076 Tübingen, Germany
| | - Dirk Brolle
- Team Leader Marketing Urology, Pfizer GmbH, PO Box 4949, 76032 Karlsruhe, Germany
| | - Stephen Bentley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Tobias Kieser
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Josef Altenbuchner
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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53
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Møller-Jensen J, Franch T, Gerdes K. Temporal translational control by a metastable RNA structure. J Biol Chem 2001; 276:35707-13. [PMID: 11461923 DOI: 10.1074/jbc.m105347200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Programmed cell death by the hok/sok locus of plasmid R1 relies on a complex translational control mechanism. The highly stable hok mRNA is activated by 3'-end exonucleolytical processing. Removal of the mRNA 3' end releases a 5'-end sequence that triggers refolding of the mRNA. The refolded hok mRNA is translatable but can also bind the inhibitory Sok antisense RNA. Binding of Sok RNA leads to irreversible mRNA inactivation by an RNase III-dependent mechanism. A coherent model predicts that during transcription hok mRNA must be refractory to translation and antisense RNA binding. Here we provide genetic evidence for the existence of a 5' metastable structure in hok mRNA that locks the nascent transcript in an inactive configuration in vivo. Consistently, the metastable structure reduces the rate of Sok RNA binding and completely blocks hok translation in vitro. Structural analyses of native RNAs strongly support that the 5' metastable structure exists in the nascent transcript. Further structural analyses reveal that the mRNA 3' end triggers refolding of the mRNA 5' end into the more stable tac-stem conformation. These results provide a profound understanding of an unusual and intricate post-transcriptional control mechanism.
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Affiliation(s)
- J Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense University, DK-5230 Odense M, Denmark
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54
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Martinussen J, Schallert J, Andersen B, Hammer K. The pyrimidine operon pyrRPB-carA from Lactococcus lactis. J Bacteriol 2001; 183:2785-94. [PMID: 11292797 PMCID: PMC99494 DOI: 10.1128/jb.183.9.2785-2794.2001] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The four genes pyrR, pyrP, pyrB, and carA were found to constitute an operon in Lactococcus lactis subsp. lactis MG1363. The functions of the different genes were established by mutational analysis. The first gene in the operon is the pyrimidine regulatory gene, pyrR, which is responsible for the regulation of the expression of the pyrimidine biosynthetic genes leading to UMP formation. The second gene encodes a membrane-bound high-affinity uracil permease, required for utilization of exogenous uracil. The last two genes in the operon, pyrB and carA, encode pyrimidine biosynthetic enzymes; aspartate transcarbamoylase (pyrB) is the second enzyme in the pathway, whereas carbamoyl-phosphate synthetase subunit A (carA) is the small subunit of a heterodimeric enzyme, catalyzing the formation of carbamoyl phosphate. The carA gene product is shown to be required for both pyrimidine and arginine biosynthesis. The expression of the pyrimidine biosynthetic genes including the pyrRPB-carA operon is subject to control at the transcriptional level, most probably by an attenuator mechanism in which PyrR acts as the regulatory protein.
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Affiliation(s)
- J Martinussen
- Department of Microbiology, The Technical University of Denmark, DK-2800 Lyngby, Denmark.
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55
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Greenfield TJ, Ehli E, Kirshenmann T, Franch T, Gerdes K, Weaver KE. The antisense RNA of the par locus of pAD1 regulates the expression of a 33-amino-acid toxic peptide by an unusual mechanism. Mol Microbiol 2000; 37:652-60. [PMID: 10931358 DOI: 10.1046/j.1365-2958.2000.02035.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The par stability determinant of the Enterococcus faecalis plasmid pAD1 is the first antisense RNA-regulated post-segregational killing system (PSK) identified in a Gram-positive organism. Par encodes two small, convergently transcribed RNAs, designated RNA I and RNA II, which are the toxin and antidote of the par PSK system respectively. RNA I encodes an open reading frame of 33 codons designated fst. The results presented here demonstrate that the peptide encoded by fst is the par toxin. The fst sequence was shown to be sufficient for cell killing, and removal of the final codon inactivated the toxin. In vitro translation reactions of purified RNA I transcript produced a product of the expected size for the fst-encoded peptide. This product was not produced when purified RNA II transcript was added to the translation reaction. Toeprint analysis demonstrated that purified RNA II was able to inhibit ribosome binding to RNA I. These data suggest that fst expression is regulated by RNA II via an antisense RNA mechanism. In vitro translation studies and toeprint analyses also indicated that fst expression is internally regulated by a stem-loop structure at the 5' end of RNA I. Removal of this structure resulted in better ribosome binding to RNA I and a 300-fold increase in production of the fst-encoded peptide. Finally, RNA II was shown to be less stable than RNA I in vivo, providing a basis for the selective expression of fst in plasmid-free cells.
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Affiliation(s)
- T J Greenfield
- Division of Basic Biomedical Sciences, School of Medicine, University of South Dakota, Vermillion, SD 57069, USA
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56
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Greenfield TJ, Weaver KE. Antisense RNA regulation of the pAD1 par post-segregational killing system requires interaction at the 5' and 3' ends of the RNAs. Mol Microbiol 2000; 37:661-70. [PMID: 10931359 DOI: 10.1046/j.1365-2958.2000.02034.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The par stability determinant of the Enterococcus faecalis plasmid pAD1 is the first antisense RNA-regulated post-segregational killing system (PSK) identified in a Gram-positive organism. Par encodes two small, convergently transcribed RNAs, designated RNA I and RNA II, which are the toxin and antidote of the par PSK system respectively. RNA I encodes an open reading frame for a 33-amino-acid toxin called Fst. Expression of fst is regulated post-transcriptionally by RNA II. In this paper, RNA II is shown to interact with RNA I by a unique antisense RNA mechanism. RNA I and RNA II contain complementary direct repeats at their 5' ends and a complementary transcriptional terminator stem-loop at their 3' ends. Deletion of the terminator or mutations within the terminator loop of RNA II severely reduced the rate of interaction in vitro. Mutations in the 5' direct repeats of RNA II prevented the RNAs from interacting in vitro. For these mutations in RNA II, complementary mutations in RNA I were shown to restore interaction. The reduced binding efficiency of the RNA II mutants was paralleled by the failure of these mutants to suppress par-mediated killing in vivo. These results indicate that regions at both the 5' and the 3' ends of the par transcripts are important for RNA I-RNA II interaction.
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Affiliation(s)
- T J Greenfield
- Division of Basic Biomedical Sciences, School of Medicine, University of South Dakota, Vermillion, SD 57069, USA
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57
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Ravin V, Ravin N, Casjens S, Ford ME, Hatfull GF, Hendrix RW. Genomic sequence and analysis of the atypical temperate bacteriophage N15. J Mol Biol 2000; 299:53-73. [PMID: 10860722 DOI: 10.1006/jmbi.2000.3731] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
N15 is a temperate bacteriophage that forms stable lysogens in Escherichia coli. While its virion is morphologically very similar to phage lambda and its close relatives, it is unusual in that the prophage form replicates autonomously as a linear DNA molecule with closed hairpin telomeres. Here, we describe the genomic architecture of N15, and its global pattern of gene expression, which reveal that N15 contains several plasmid-derived genes that are expressed in N15 lysogens. The tel site, at which processing occurs to form the prophage ends is close to the center of the genome in a similar location to that occupied by the attachment site, attP, in lambda and its relatives and defines the boundary between the left and right arms. The left arm contains a long cluster of structural genes that are closely related to those of the lambda-like phages, but also includes homologs of umuD', which encodes a DNA polymerase accessory protein, and the plasmid partition genes, sopA and sopB. The right arm likewise contains a mixture of apparently phage- and plasmid-derived genes including genes encoding plasmid replication functions, a phage repressor, a transcription antitermination system, as well as phage host cell lysis genes and two putative DNA methylases. The unique structure of the N15 genome suggests that the large global population of bacteriophages may exhibit a much greater diversity of genomic architectures than was previously recognized.
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MESH Headings
- Bacteriolysis
- Bacteriophage lambda/genetics
- Bacteriophages/enzymology
- Bacteriophages/genetics
- Bacteriophages/ultrastructure
- Base Composition
- Base Sequence
- Escherichia coli/physiology
- Escherichia coli/virology
- Gene Expression Regulation, Bacterial
- Genes, Viral/genetics
- Genome, Viral
- Lysogeny/genetics
- Microscopy, Electron
- Plasmids/genetics
- Promoter Regions, Genetic/genetics
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Viral/biosynthesis
- RNA, Viral/genetics
- Response Elements/genetics
- Sequence Analysis, DNA
- Terminator Regions, Genetic/genetics
- Transcription, Genetic/genetics
- Viral Proteins/genetics
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Affiliation(s)
- V Ravin
- Center for Bioengineering, Russian Academy of Science, Moscow, Russia
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58
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Abstract
The hok/sok locus of plasmid R1 mediates plasmid stabilization by the killing of plasmid-free cells. Many bacterial plasmids carry similar loci. For example, the F plasmid carries two hok homologues, flm and srnB, that mediate plasmid stabilization by this specialized type of programmed cell death. Here, we show that the chromosome of E. coli K-12 codes for five hok homologous loci, all of which specify Hok-like toxins. Three of the loci appear to be inactivated by the insertion elements IS150 or IS186 located close to but not in the toxin-encoding reading frames (i.e. hokA, hokC and hokE), one system is probably inactivated by point mutation (hokB), whereas the fifth system is inactivated by a major genetic rearrangement (hokD). In the ECOR collection of wild-type E. coli strains, we identified hokA and hokC loci without IS elements. A molecular and a genetic analysis show that the hokA and hokC loci specify unstable antisense RNAs and stable toxin-encoding mRNAs that are processed at their 3' ends. An alignment of the mRNA sequences reveals all the regulatory elements known to be required for correct folding and refolding of the plasmid-encoded mRNAs. The conserved elements include fbi that ensure a long-range interaction in the full-length mRNAs, and tac and antisense RNA target stem-loops that are required for translation and rapid antisense RNA binding of the processed mRNAs. Consistently, we find that the chromosome-encoded mRNAs are processed at their 3' ends, resulting in the presumed translationally active mRNAs. Despite the presence of all of the regulatory elements, the chromosome-encoded loci do not mediate plasmid stabilization by killing of plasmid-free cells. The chromosome-encoded mRNAs are poorly translated in vitro, thus yielding an explanation for the lacking phenotype. These observations suggest that the chromosomal hok-like genes may be induced by an as yet unknown signal.
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Affiliation(s)
- K Pedersen
- Department of Molecular Biology, Odense University, Campusvej 55, DK-5230 Odense M, Denmark
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59
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Thomsen LE, Pedersen M, Nørregaard-Madsen M, Valentin-Hansen P, Kallipolitis BH. Protein-ligand interaction: grafting of the uridine-specific determinants from the CytR regulator of Salmonella typhimurium to Escherichia coli CytR. J Mol Biol 1999; 288:165-75. [PMID: 10329134 DOI: 10.1006/jmbi.1999.2668] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Members of the LacI family of transcriptional repressors respond to the presence of small effector molecules. The binding of the ligands affect the proteins ability to repress transcription by stabilizing a conformation that, in most cases, is unfavorable for high-affinity DNA binding. The CytR anti-activator diverges from the other family members by relying on the cooperative DNA binding with the global regulator CRP. The inducers of CytR do not affect CytR-DNA binding per se, but alleviate repression by interrupting protein-protein interactions between the two regulators. Here, we have studied of the CytR-inducer interaction by exploring a discrepancy in the inducer response observed for the homologous CytR regulators of Escherichia coli and Salmonella typhimurium. CytR of S. typhimurium (CytRSt) appears to respond to the presence of both uridine and cytidine nucleosides, whereas E. coli CytR (CytREc) responds to cytidine only. We have used a combination of genetic and structural modeling studies to provide detailed information regarding the nature of this discrepancy. By analysis of hybrid CytR proteins followed by site-directed mutagenesis, we have successfully transferred the specificity determinants for uridine from CytRSt to CytREc, revealing that serine substitutions of only two residues (G131 and A152) in CytREc is required to make CytREc sensitive to uridine. In addition, by employing a genetic screen for induction of defective mutants, we have identified four amino acid residues in CytRSt that appear to be important for the response to uridine. The implications of these findings for the understanding of the ligand binding and induction of CytR are discussed in the context of the structural knowledge of CytR and homologous protein-ligand complexes.
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Affiliation(s)
- L E Thomsen
- Department of Molecular Biology, Odense University, Campusvej 55, Odense M, DK-5230, Denmark
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60
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Martinussen J, Hammer K. The carB gene encoding the large subunit of carbamoylphosphate synthetase from Lactococcus lactis is transcribed monocistronically. J Bacteriol 1998; 180:4380-6. [PMID: 9721272 PMCID: PMC107444 DOI: 10.1128/jb.180.17.4380-4386.1998] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The biosynthesis of carbamoylphosphate is catalyzed by the heterodimeric enzyme carbamoylphosphate synthetase. The genes encoding the two subunits of this enzyme in procaryotes are normally transcribed as an operon, but the gene encoding the large subunit (carB) in Lactococcus lactis is shown to be transcribed as an isolated unit. Carbamoylphosphate is a precursor in the biosynthesis of both pyrimidine nucleotides and arginine. By mutant analysis, L. lactis is shown to possess only one carB gene; the same gene product is thus required for both biosynthetic pathways. Furthermore, arginine may satisfy the requirement for carbamoylphosphate in pyrimidine biosynthesis through degradation by means of the arginine deiminase pathway. The expression of the carB gene is subject to regulation at the level of transcription by pyrimidines, most probably by an attenuator mechanism. Upstream of the carB gene, an open reading frame showing a high degree of similarity to those of glutathione peroxidases from other organisms was identified.
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Affiliation(s)
- J Martinussen
- Department of Microbiology, The Technical University of Denmark, DK-2800 Lyngby, Denmark. jm@un,dty,dk
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61
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Kallipolitis BH, Valentin-Hansen P. Transcription of rpoH, encoding the Escherichia coli heat-shock regulator sigma32, is negatively controlled by the cAMP-CRP/CytR nucleoprotein complex. Mol Microbiol 1998; 29:1091-9. [PMID: 9767576 DOI: 10.1046/j.1365-2958.1998.00999.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In Escherichia coli, the rpoH gene encoding the essential heat-shock regulator sigma32, is expressed in a complex manner. Transcription occurs from four promoters (P1, P3, P4 and P5) and is modulated by several factors including (i) two sigma factors (sigma70 and sigmaE); (ii) the global regulator CRP; and (iii) the DnaA protein. Here, a further dissection of the rpoH regulatory region has revealed that an additional transcription control exists that appears to link rpoH expression to nucleoside metabolism. The cAMP-CRP complex and the CytR anti-activator bind co-operatively to the promoter region forming a repression complex that overlaps the sigmaE-dependent P3 promoter and the sigma70-dependent P4 and P5 promoters. During steady-state growth conditions with glycerol as the carbon and energy source, transcription from P3, P4 and P5 is reduced approximately threefold by CytR, whereas transcription from the upstream promoter, P1, appears to be unaffected. Furthermore, in strains that slightly overproduce CytR, transcription from P3, P4 and P5 is reduced even further (approximately 10-fold), and repression can be fully neutralized by the addition of the inducer cytidine to the growth medium. In the induced state, P4 is the strongest promoter and, together with P3 and P5, it is responsible for most rpoH transcription (65-70%). At present, CytR has been shown to 'fine tune' transcription of two genes (rpoH and ppiA) that are connected with protein-folding activities. These findings suggest that additional assistance in protein folding is required under conditions in which CytR is induced (i.e. in the presence of nucleosides).
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62
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Gerdes K, Gultyaev AP, Franch T, Pedersen K, Mikkelsen ND. Antisense RNA-regulated programmed cell death. Annu Rev Genet 1998; 31:1-31. [PMID: 9442888 DOI: 10.1146/annurev.genet.31.1.1] [Citation(s) in RCA: 171] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Eubacterial plasmids and chromosomes encode multiple killer genes belonging to the hok gene family. The plasmid-encoded killer genes mediate plasmid stabilization by killing plasmid-free cells. This review describes the genetics, molecular biology, and evolution of the hok gene family. The complicated antisense RNA-regulated control-loop that regulates posttranscriptional and postsegregational activation of killer mRNA translation in plasmid-free cells is described in detail. Nucleotide covariations in the mRNAs reveal metastable stem-loop structures that are formed at the mRNA 5' ends in the nascent transcripts. The metastable structures prevent translation and antisense RNA binding during transcription. Coupled nucleotide covariations provide evidence for a phylogenetically conserved mRNA folding pathway that involves sequential dynamic RNA rearrangements. Our analyses have elucidated an intricate mechanism by which translation of an antisense RNA-regulated mRNA can be conditionally activated. The complex phylogenetic relationships of the plasmid- and chromosome-encoded systems are also presented and discussed.
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Affiliation(s)
- K Gerdes
- Department of Molecular Biology, Odense University, Denmark.
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63
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Holčík M, Iyer VM. Conditionally lethal genes associated with bacterial plasmids. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 11):3403-3416. [PMID: 9387219 DOI: 10.1099/00221287-143-11-3403] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Martin Holčík
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa Ontario Canada K1S5B6
| | - V M Iyer
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa Ontario Canada K1S5B6
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64
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Franch T, Gultyaev AP, Gerdes K. Programmed cell death by hok/sok of plasmid R1: processing at the hok mRNA 3'-end triggers structural rearrangements that allow translation and antisense RNA binding. J Mol Biol 1997; 273:38-51. [PMID: 9367744 DOI: 10.1006/jmbi.1997.1294] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The hok/sok locus of plasmid R1 mediates plasmid stabilization by killing of plasmid-free cells. The locus specifies two RNAs, hok mRNA and Sok antisense RNA. The post-segregational killing mediated by hok/sok is governed by a complicated control mechanism that involves both post-transcriptional inhibition of translation by Sok-RNA and activation of hok translation by mRNA 3' processing. Sok-RNA inhibits translation of a reading frame (mok) that overlaps with hok, and translation of hok is coupled to translation of mok. In the inactive full-length hok mRNA, the translational activator element at the mRNA 5'-end (tac) is sequestered by the fold-back-inhibitory element located at the mRNA 3'-end (fbi). The 5' to 3' pairing locks the RNA in an inert configuration in which the SDmok and Sok-RNA target regions are sequestered. Here we show that the 3' processing leads to major structural rearrangements in the mRNA 5'-end. The structure of the refolded RNA explains activation of translation and antisense RNA binding. The refolded RNA contains an antisense RNA target stem-loop that presents the target nucleotides in a single-stranded conformation. The stem of the target hairpin contains SDmok and AUGmok in a paired configuration. Using toeprinting analysis, we show that this pairing keeps SDmok in an accessible configuration. Furthermore, a mutational analysis shows that an internal loop in the target stem is prerequisite for efficient translation and antisense RNA binding.
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MESH Headings
- Apoptosis/genetics
- Bacterial Proteins/genetics
- Bacterial Toxins
- Base Sequence
- Blotting, Northern
- Electrophoresis, Polyacrylamide Gel
- Escherichia coli Proteins
- Gene Expression Regulation
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Nucleic Acid Conformation
- Nucleic Acid Hybridization
- Plasmids/genetics
- Protein Biosynthesis
- RNA
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Ribonuclease H/metabolism
- Sequence Deletion
- Transcription, Genetic
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Affiliation(s)
- T Franch
- Department of Molecular Biology, Odense University, Denmark
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65
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Gultyaev AP, Franch T, Gerdes K. Programmed cell death by hok/sok of plasmid R1: coupled nucleotide covariations reveal a phylogenetically conserved folding pathway in the hok family of mRNAs. J Mol Biol 1997; 273:26-37. [PMID: 9367743 DOI: 10.1006/jmbi.1997.1295] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The hok/sok system of plasmid R1 mediates plasmid maintenance by killing of plasmid-free cells. Translation of the stable toxin-encoding hok mRNA is repressed by the unstable Sok antisense RNA. Using genetic algorithm simulations and phylogenetic comparisons, we analyse five plasmid-encoded and two chromosome-encoded hok-homologous mRNAs. A similar folding pathway was found for all mRNAs. Metastable hairpins at the very 5'-ends of the mRNAs were predicted to prevent the formation of structures required for translation and antisense RNA binding. Thus the folding of the mRNA 5'-ends appears to explain the apparent inactivity of the nascent transcripts. In the full-length mRNAs, long-range 5' to 3' interactions were predicted in all cases. The 5' to 3' interactions lock the mRNAs in inactive configurations. Translation of the mRNAs is activated by 3' exonucleolytic processing. Simulation of the 3' processing predicted that it triggers rearrangements of the mRNA 5'-ends with the formation of translational activator and antisense RNA target hairpins. Alignment of the mRNA sequences revealed a large number of nucleotide covariations that support the existence of the proposed secondary structures. Furthermore, coupled covariations support the folding pathway and provide evidence that the mRNA 5'-ends pair with three different partners during the proposed series of dynamic RNA rearrangements.
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Affiliation(s)
- A P Gultyaev
- Leiden Institute of Chemistry, Leiden University, The Netherlands
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66
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Gerdes K, Jacobsen JS, Franch T. Plasmid stabilization by post-segregational killing. GENETIC ENGINEERING 1997; 19:49-61. [PMID: 9193102 DOI: 10.1007/978-1-4615-5925-2_3] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- K Gerdes
- Department of Molecular Biology, Odense University, Denmark
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67
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Andersen PS, Martinussen J, Hammer K. Sequence analysis and identification of the pyrKDbF operon from Lactococcus lactis including a novel gene, pyrK, involved in pyrimidine biosynthesis. J Bacteriol 1996; 178:5005-12. [PMID: 8759867 PMCID: PMC178286 DOI: 10.1128/jb.178.16.5005-5012.1996] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Three genes encoding enzymes involved in the biosynthesis of pyrimidines have been found to constitute an operon in Lactococcus lactis. Two of the genes are the well-known pyr genes pyrDb and pyrF, encoding dihydroorotate dehydrogenase and orotidine monophosphate decarboxylase, respectively. The third gene encodes a protein which was shown to be necessary for the activity of the pyrDb-encoded dihydroorotate dehydrogenase; we propose to name the gene pyrK. The pyrK-encoded protein is homologous to a number of proteins which are involved in electron transfer. The lactococcal pyrKDbF operon is highly homologous to the corresponding part of the much-larger pyr operon of Bacillus subtilis. orf2, the pyrK homolog in B. subtilis, has also been shown to be necessary for pyrimidine biosynthesis (A. E. Kahler and R. L. Switzer, J. Bacteriol. 178:5013-5016, 1996). Four genes adjacent to the operon, i.e., orfE, orfA, orfC, and gidB, were also sequenced. Three of these were excluded as members of the pyr operon by insertional analysis (orfA) or by their opposite direction of transcription (orfE and gidB). orfC, however, seems to be the distal gene in the pyrKDbF-orfC operon.
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Affiliation(s)
- P S Andersen
- Department of Microbiology, Technical University of Denmark, Lyngby, Denmark
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68
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Weaver KE, Jensen KD, Colwell A, Sriram SI. Functional analysis of the Enterococcus faecalis plasmid pAD1-encoded stability determinant par. Mol Microbiol 1996; 20:53-63. [PMID: 8861204 DOI: 10.1111/j.1365-2958.1996.tb02488.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The molecular organization and functional characteristics of the PAD1 replicon-encoded par stability determinant were examined. par encodes two convergently transcribed RNAS of approximately 210 and 65 nucleotides designated RNA I and RNA II, respectively. The sequence of RNA II is largely complementary to RNA I, suggesting that RNA II could regulate RNA I function as an anti-sense RNA. Results of functional studies are consistent with a role for par as a post-segregational killing system, the first to be identified in Gram-positive bacteria, with RNA I encoding the toxin and RNA II the antidote. These results include: (i) destabilization of par-containing replicons in the presence of a second complete par or the RNA II coding sequence in the same cell; (ii) par-dependent stabilization of a highly unstable vector at the expense of host-cell growth rate; and (iii) protection of cells from the toxic effects of overexpression of RNA I by RNA II supplied in trans.
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Affiliation(s)
- K E Weaver
- Department of Microbiology, School of Medicine, University of South Dakota, Vermillion 57069, USA
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69
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Sobecky PA, Easter CL, Bear PD, Helinski DR. Characterization of the stable maintenance properties of the par region of broad-host-range plasmid RK2. J Bacteriol 1996; 178:2086-93. [PMID: 8606188 PMCID: PMC177909 DOI: 10.1128/jb.178.7.2086-2093.1996] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A 3.2-kb fragment encoding five genes, parCBA/DE, in two divergently transcribed operons promotes stable maintenance of the replicon of the broad-host-range plasmid RK2 in a vector-independent manner in Escherichia coli. The parDE operon has been shown to contribute to stabilization through the postsegregational killing of plasmid-free daughter cells, while the parCBA operon encodes a resolvase, ParA, that mediates the resolution of plasmid multimers through site-specific recombination. To date, evidence indicates that multimer resolution alone does not play a significant role in RK2 stable maintenance by the parCBA operon in E. coli. It has been proposed, instead, that the parCBA region encodes an additional stability mechanism, a partition system, that ensures that each daughter cell receives a plasmid copy at cell division. However, studies carried out to date have not directly determined the plasmid stabilization activity of the parCBA operon alone. An assessment was made of the relative contributions of postsegregational killing (parDE) and the putative partitioning system (parCBA) to the stabilization of mini-RK2 replicons in E. coli. Mini-RK2 replicons carrying either the entire 3.2-kb (parCBA/DE) fragment or the 2.3-kb parCBA region alone were found to be stably maintained in two E. coli strains tested. The stabilization found is not due to resolution of multimers. The stabilizing effectiveness of parCBA was substantially reduced when the plasmid copy number was lowered, as in the case of E. coli cells carrying a temperature-sensitive mini-RK2 replicon grown at a nonpermissive temperature. The presence of the entire 3.2-kb region effectively stabilized the replicon, however, under both low- and high-copy-number-conditions. In those instances of decreased plasmid copy number, the postsegregational killing activity, encoded by parDE, either as part of the 3.2-kb fragment or alone played the major role in the stabilization of mini-RK2 replicons within the growing bacterial population. Our findings indicate that the parCBA operon functions to stabilize by a mechanism other than cell killing and resolution of plasmid multimers, while the parDE operon functions solely to stabilize plasmids by cell killing. The relative contribution of each system to stabilization depends on plasmid copy number and the particular E. coli host.
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Affiliation(s)
- P A Sobecky
- Department of Biology and Center for Molecular Genetics, University of California, San Diego, La Jolla, California 92093-0634, USA
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70
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Abstract
The hok (host killing) and sok (suppressor of killing) genes (hok/sok) efficiently maintain the low-copy-number plasmid R1. To investigate whether the hok/sok locus evolved as a phage-exclusion mechanism, Escherichia coli cells that contain hok/sok on a pBR322-based plasmid were challenged with T1, T4, T5, T7, and lambda phage. Upon infection with T4, the optical density of cells containing hok/sok on a high-copy-number plasmid continued to increase whereas the optical density for those lacking hok/sok rapidly declined. The presence of hok/sok reduced the efficiency of plating of T4 by 42% and decreased the plaque size by approximately 85%. Single-step growth experiments demonstrated that hok/sok decreased the T4 burst size by 40%, increased the time to form mature phage (eclipse time) from 22 to 30 min, and increased the time to cell lysis (latent period) from 30 to 60 min. These results further suggest that single cells exhibit altruistic behavior.
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Affiliation(s)
- D C Pecota
- Department of Chemical and Biochemical Engineering, University of California, Irvine, 92717-2575, USA
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71
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Johnson EP, Strom AR, Helinski DR. Plasmid RK2 toxin protein ParE: purification and interaction with the ParD antitoxin protein. J Bacteriol 1996; 178:1420-9. [PMID: 8631720 PMCID: PMC177817 DOI: 10.1128/jb.178.5.1420-1429.1996] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The parDE operon, located within the 3.2-kb stabilization region of plasmid RK2, encodes antitoxin (ParD) and toxin (ParE) proteins that stabilize the maintenance of this broad-host-range plasmid via a postsegregational killing mechanism. A ParE protein derivative, designated ParE', was purified by construction of a fusion protein, GST-ParE, followed by glutathione-agarose binding and cleavage of the fusion protein. ParE' has three additional amino acids on the N terminus and a methionine residue in place of the native leucine residue. The results of glutathione-agarose affinity binding and glutaraldehyde cross-linking indicate that ParE' exists as a dimer in solution and that it binds to the dimeric form of ParD to form a tetrameric complex. The formation of this complex is presumably responsible for the ability of ParD to neutralize ParE toxin activity. Previous studies demonstrated that the parDE operon is autoregulated as a result of the binding of the ParD protein to the parDE promoter. ParE' also binds to the parDE promoter but only in the presence of the autoregulatory ParD protein. ParE', in the presence or absence of the ParD protein, does not bind to any other part of the 3.2-kb stabilization region. The binding of the ParE' protein to ParD did not alter the DNase I footprint pattern obtained as a result of ParD binding to the parDE promoter. The role of ParE in binding along with ParD to the promoter, if any, remains unclear.
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Affiliation(s)
- E P Johnson
- Department of Biology, University of California at San Diego, La Jolla 92037-0634, USA
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72
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Taghavi S, Provoost A, Mergeay M, van der Lelie D. Identification of a partition and replication region in the Alcaligenes eutrophus megaplasmid pMOL28. MOLECULAR & GENERAL GENETICS : MGG 1996; 250:169-79. [PMID: 8628216 DOI: 10.1007/bf02174176] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A 4.64 kb region of the 180 kb heavy metal resistance plasmid pMOL28 of Alcaligenes eutrophus CH34, previously shown to be able to replicate autonomously, was sequenced and analyzed. Three genes involved in plasmid maintenance were identified: parA28 and parB28 are involved in plasmid partitioning and stability, while repA28 encodes a protein required for replication. In addition to the par AB28 genes, a third locus, parS28, required in cis active partitioning was identified. The parABS28 locus of pMOL28 shows strong similarity in organization to the sop, par and rep regions, respectively, of the Escherichia coli F-factor, the E.coli P1 and P7 prophages and the Agrobacterium pTiB6S3 and pRiA4b plasmids. The ParAB28 proteins of pMOL28 also show similarity to the proteins encoded by two conserved open reading frames present in the replication regions of the Pseudomonas putida and Bacillus subtilis chromosomes. The functionality of the pMOL28 par region was examined by performing stability and incompatibility tests between pMOL28 and pMOL846 or pMOL850 which contain the 4.64 EcoRI replicon fragment of pMOL28, cloned in opposite orientations into pSUP202, which is itself unable to replicate in A. eutrophus. The RepA2 8 replication protein showed similarity to the RepL protein of P1, which is required for lytic replication of this E. coli phage. The replication origin of pMOL28, oriV28, seems to be located within the repA28 coding region, and pMOL28 replication may depend on transcriptional activation of oriV28.
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Affiliation(s)
- S Taghavi
- Environmental Technology, Flemish Institute for Technological Research (VITO), Belgium
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73
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Nørregaard-Madsen M, McFall E, Valentin-Hansen P. Organization and transcriptional regulation of the Escherichia coli K-12 D-serine tolerance locus. J Bacteriol 1995; 177:6456-61. [PMID: 7592420 PMCID: PMC177495 DOI: 10.1128/jb.177.22.6456-6461.1995] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We have reinvestigated the genetic organization and the transcription regulation of the dsd operon of Escherichia coli. By combining genetic and biochemical studies, it is demonstrated that the regulatory region of the operon and the gene encoding the specific regulator of D-serine tolerance (dsdC) had been misplaced in previous work on the dsd system. Also, the previous erroneous DNA sequence of the dsdC gene has been corrected. It turned out that an additional gene (dsdX) is present immediately upstream of dsdA (encoding D-serine deaminase) and that dsdC is located adjacent to dsdX. The dsdXA genes are cotranscribed from a common promoter region present in the dsdX-dsdC intercistronic region. The DsdC activator belongs to the LysR-type of transcriptional regulators and is absolutely required for dsdA expression. Additionally, the activity of the dsdXA promoter depends on the cyclic AMP receptor protein, and the two activators act in concert to synergistically activate transcription.
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74
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Nielsen AK, Gerdes K. Mechanism of post-segregational killing by hok-homologue pnd of plasmid R483: two translational control elements in the pnd mRNA. J Mol Biol 1995; 249:270-82. [PMID: 7783193 DOI: 10.1006/jmbi.1995.0296] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The pnd system of plasmid R483 mediates plasmid stabilization by killing of plasmid-free cells. The pnd mRNA is very stable and can be translated into PndA protein, a cell toxin which kills the cells from within by damaging the cell membrane. Translation of the pnd mRNA is inhibited by the PndB antisense, a small labile RNA of 63 nt. The rapid decay of the PndB antidote leads to onset of PndA synthesis in plasmid-free segregants or after addition of rifampicin. Surprisingly however, the full-length pnd mRNA was found to be translationally inactive whereas a 3'-end truncated version of it was found to be active. We have therefore suggested previously, that the 3'-end of the full-length pnd mRNA encodes a fold-back inhibitory sequence (fbi), which prevents its translation. Here we present an analysis of the metabolism of the pnd mRNAs. A mutational analysis shows that single point mutations in the fbi motif results in more rapid truncation. The fbi mutations could not be complemented by second-site mutations in either of the pndA or pndC Shine-Dalgarno (SD) elements. Surprisingly, mutations in the pndC SD element also lead to a more rapid truncation. The effect of these latter mutations was, however, complemented by mutations in a proposed anti-SD element upstream of the pndC SD. Mutations in the anti-SD element were lethal. These results show, that the pnd mRNA contains two negative control elements, one located in its very 3'-end (fbi), and one located just upstream of the pndC SD region (the anti-SD element). These observations add to the complexity of the induction scheme previously proposed to explain activation of pndA expression in plasmid-free cells: In addition to its negative effect of translation, the fbi structure also maintains a reduced processing rate in the 3'-end of the mRNA. This permits the accumulation of a reservoir of pnd mRNA, which can be activated by 3'-end processing in plasmid-free cells. The anti-SD may prevent translation of the pnd mRNA during transcription, thus preventing detrimental synthesis of toxin.
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Affiliation(s)
- A K Nielsen
- Department of Molecular Biology, Odense University, Denmark
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75
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Nørregaard-Madsen M, Mygind B, Pedersen R, Valentin-Hansen P, Søgaard-Andersen L. The gene encoding the periplasmic cyclophilin homologue, PPIase A, in Escherichia coli, is expressed from four promoters, three of which are activated by the cAMP-CRP complex and negatively regulated by the CytR repressor. Mol Microbiol 1994; 14:989-97. [PMID: 7715459 DOI: 10.1111/j.1365-2958.1994.tb01333.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The rot gene in Escherichia coli encodes PPIase A, a periplasmic peptidyl-prolyl cis-trans isomerase with homology to the cyclophilin family of proteins. Here it is demonstrated that rot is expressed in a complex manner from four overlapping promoters and that the rot regulatory region is unusually compact, containing a close array of sites for DNA-binding proteins. The three most upstream rot promoters are activated by the global gene regulatory cAMP-CRP complex and negatively regulated by the CytR repressor protein. Activation of these three promoters occurs by binding of cAMP-CRP to two sites separated by 53 bp. Moreover, one of the cAMP-CRP complexes is involved in the activation of both a Class I and a Class II promoter. Repression takes place by the formation of a CytR/cAMP-CRP/DNA nucleoprotein complex consisting of the two cAMP-CRP molecules and CytR bound in between. The two regulators bind co-operatively to the DNA overlapping the three upstream promoters, simultaneously quenching the cAMP-CRP activator function. These results expand the CytR regulon to include a gene whose product has no known function in ribo- and deoxyribonucleoside catabolism or transport.
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76
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Martinussen J, Hammer K. Cloning and characterization of upp, a gene encoding uracil phosphoribosyltransferase from Lactococcus lactis. J Bacteriol 1994; 176:6457-63. [PMID: 7961396 PMCID: PMC196998 DOI: 10.1128/jb.176.21.6457-6463.1994] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Uracil phosphoribosyltransferase catalyzes the key reaction in the salvage of uracil in many microorganisms. The gene encoding uracil phosphoribosyltransferase (upp) was cloned from Lactococcus lactis subsp. cremoris MG1363 by complementation of an Escherichia coli mutant. The gene was sequenced, and the putative amino acid sequence was deduced. The promoter was mapped by both primer extension and analysis of beta-galactosidase expressed from strains carrying fusion between upp promoter fragments and the lacLM gene. The results showed that the upp gene was expressed from its own promoter. After in vitro construction of an internal deletion, a upp mutant was constructed by a double-crossover event. This implicated the utilization of a plasmid with a thermosensitive origin of replication and a new and easy way to screen for double crossover events in both gram-positive and gram-negative bacterial strains. The phenotype of the uracil phosphoribosyltransferase-deficient strain was established. Surprisingly, the upp strain is resistant only to very low concentrations of 5-fluorouracil. Secondary mutants in thymidine phosphorylase and thymidine kinase were isolated by selection for resistance to high concentrations of 5-fluorouracil.
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Affiliation(s)
- J Martinussen
- Center for Lactic Acid Bacteria, Laboratory of Microbiology, Technical University of Denmark, Lyngby
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77
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Frost LS, Ippen-Ihler K, Skurray RA. Analysis of the sequence and gene products of the transfer region of the F sex factor. Microbiol Rev 1994; 58:162-210. [PMID: 7915817 PMCID: PMC372961 DOI: 10.1128/mr.58.2.162-210.1994] [Citation(s) in RCA: 274] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Bacterial conjugation results in the transfer of DNA of either plasmid or chromosomal origin between microorganisms. Transfer begins at a defined point in the DNA sequence, usually called the origin of transfer (oriT). The capacity of conjugative DNA transfer is a property of self-transmissible plasmids and conjugative transposons, which will mobilize other plasmids and DNA sequences that include a compatible oriT locus. This review will concentrate on the genes required for bacterial conjugation that are encoded within the transfer region (or regions) of conjugative plasmids. One of the best-defined conjugation systems is that of the F plasmid, which has been the paradigm for conjugation systems since it was discovered nearly 50 years ago. The F transfer region (over 33 kb) contains about 40 genes, arranged contiguously. These are involved in the synthesis of pili, extracellular filaments which establish contact between donor and recipient cells; mating-pair stabilization; prevention of mating between similar donor cells in a process termed surface exclusions; DNA nicking and transfer during conjugation; and the regulation of expression of these functions. This review is a compendium of the products and other features found in the F transfer region as well as a discussion of their role in conjugation. While the genetics of F transfer have been described extensively, the mechanism of conjugation has proved elusive, in large part because of the low levels of expression of the pilus and the numerous envelope components essential for F plasmid transfer. The advent of molecular genetic techniques has, however, resulted in considerable recent progress. This summary of the known properties of the F transfer region is provided in the hope that it will form a useful basis for future comparison with other conjugation systems.
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Affiliation(s)
- L S Frost
- Department of Microbiology, University of Alberta, Edmonton, Canada
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78
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Jensen RB, Dam M, Gerdes K. Partitioning of plasmid R1. The parA operon is autoregulated by ParR and its transcription is highly stimulated by a downstream activating element. J Mol Biol 1994; 236:1299-309. [PMID: 8126721 DOI: 10.1016/0022-2836(94)90059-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The parA partitioning system of plasmid R1 mediates efficient stabilization of R1 and F-derived replicons. The parA system is encoded by a continuous DNA segment of approximately 1600 base-pairs and consists of three components. Two adjacent genes, parM and parR, coding for the trans-acting proteins ParM and ParR, and the cis-acting parC site. The centromere-like parC site is located upstream of parM and parR and contains the parA promoter. The parM and parR genes are co-transcribed as an operon from the parA promoter. The 5' end of the parA encoded transcript was mapped to the center of the parC region at +115. The -10 and -35 core promoter sequences are flanked by the two sets of five direct repeats in parC (the ParR boxes). The parA promoter was found to be negatively regulated by the parR gene product, whereas the parM gene product seemingly was not involved in the regulation. Surprisingly, a region downstream of the parA promoter enhanced transcription from the promoter many-fold (30 to 50-fold). The parC site titrated the ParR protein, suggesting that the ParR protein interacts directly with the parC site. Using an engineered parA system we found that the parC site could be complemented in cis by the parM and parR genes. Furthermore, the proper function of the parC site was highly dependent on the expression level of ParM and ParR. The incompatibility associated with the parC site could not be suppressed by overexpression of the ParM and ParR proteins. Based on these results we suggest a novel partition model involving pairing of newly replicated plasmid molecules.
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Affiliation(s)
- R B Jensen
- Department of Molecular Biology, Odense University, Denmark
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79
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Gerdes K, Nielsen A, Thorsted P, Wagner EG. Mechanism of killer gene activation. Antisense RNA-dependent RNase III cleavage ensures rapid turn-over of the stable hok, srnB and pndA effector messenger RNAs. J Mol Biol 1992; 226:637-49. [PMID: 1380562 DOI: 10.1016/0022-2836(92)90621-p] [Citation(s) in RCA: 93] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The hok/sok, srnB and pnd systems of plasmids R1, F and R438 mediate plasmid maintenance by killing plasmid-free segregants. The systems encode exceptionally stable full-length mRNAs that code for potent cell toxins that kill the cells from within. The systems also produce truncated mRNAs whose appearance is correlated with killing activity. The truncated mRNAs are shortened by 35 to 70 nucleotides in the 3' ends, but have the same 5' ends as the full-length transcripts. Translation of the stable killer mRNAs is regulated by unstable antisense RNAs that are complementary to the leader regions of the full-length and truncated mRNAs. We show here, that both the presence of the antisense RNA and of the host enzyme RNase III is required for rapid cleavage of the truncated mRNAs, and we map the cleavage point in the Hok mRNA in vitro and in vivo to be located between nucleotides +245 and +246. The RNase III cleavage products of the Hok mRNA were found to be very unstable in vivo. Thus, RNase III cleavage seems to be the initial event leading to decay of the killer mRNAs. In an rnc- strain, the truncated mRNA species were found in steady-state cells. This observation indicates that the truncated mRNAs are formed constitutively and independently of the presence of the antisense RNAs. Thus, the antisense RNAs prevent the accumulation of the truncated mRNAs solely by mediating their rapid hydrolysis by RNase III. Furthermore, the generation of the truncated killer mRNAs in the rnc- host indicate that RNase III is dispensable for induction of the killer gene systems. Based on these and on observations obtained previously, we present a molecular model that explains the activation of the killer mRNAs in plasmid-free segregants and after addition of rifampicin.
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MESH Headings
- Base Sequence
- Blotting, Northern
- Endoribonucleases/metabolism
- Escherichia coli/genetics
- Escherichia coli Proteins
- Gene Expression Regulation, Bacterial
- Genes, Bacterial
- Genes, Lethal
- Kinetics
- Models, Genetic
- Molecular Sequence Data
- Plasmids
- Protein Biosynthesis
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Bacterial/genetics
- RNA, Bacterial/isolation & purification
- RNA, Bacterial/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/isolation & purification
- RNA, Messenger/metabolism
- Ribonuclease III
- Transcriptional Activation
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Affiliation(s)
- K Gerdes
- Department of Molecular Biology, Odense University, Denmark
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80
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Abstract
The hok/sok locus of plasmid R1, which mediates plasmid stabilization by killing of plasmid-free segregants, codes for two RNAs, Hok mRNA and Sok antisense RNA. Hok mRNA encodes the Hok killer protein of 52 amino acid residues. Expression of hok is regulated post-transcriptionally by Sok antisense RNA. Killing of plasmid-free daughter-cells by the hok/sok system is accomplished through differential decay of the Hok and Sok-RNAs: Hok mRNA is very stable while Sok-RNA decays rapidly, thus leading to derepression of Hok mRNA translation in plasmid-free segregants, ensuring a rapid and selective killing of these cells. Sok antisense RNA is complementary to the leader region of the Hok mRNA. However, the region of complementarity does not overlap with the hok Shine-Dalgarno sequence. Thus, Sok-RNA regulates hok translation indirectly by an as yet unknown mechanism. We show here that Sok antisense RNA regulates the translation of another reading frame located in the hok/sok locus. This new reading frame, which overlaps with almost the entire hok gene, was denoted mok (mediation of killing). Point-mutations that prevent mok translation through the hok translational initiation region abolish efficient expression of hok. Furthermore, these mutations abolish the Sok-RNA-mediated control of hok gene expression. Hence, the antisense-RNA-mediated regulation of the hok gene seems to occur via translational coupling between the hok and mok reading-frames.
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Affiliation(s)
- T Thisted
- Department of Molecular Biology, Odense University, Denmark
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81
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Nielsen AK, Thorsted P, Thisted T, Wagner EG, Gerdes K. The rifampicin-inducible genes srnB from F and pnd from R483 are regulated by antisense RNAs and mediate plasmid maintenance by killing of plasmid-free segregants. Mol Microbiol 1991; 5:1961-73. [PMID: 1722558 DOI: 10.1111/j.1365-2958.1991.tb00818.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The gene systems srnB of plasmid F and pnd of plasmid R483 were discovered because of their induction by rifampicin. Induction caused membrane damage, RNase I influx, degradation of stable RNA and, consequently, cell killing. We show here that the srnB and pnd systems mediate efficient stabilization of a mini-R1 test-plasmid. We also show that the killer genes srnB' and pndA are regulated by antisense RNAs, and that the srnC- and pndB-encoded antisense RNAs, denoted SrnC- and PndB-RNAs, are unstable molecules of approximately 60 nucleotides. The srnB and pndA mRNAs were found to be very stable. The differential decay rates of the inhibitory antisense RNAs and the killer-gene-encoding mRNAs explain the induction of these gene systems by rifampicin. Furthermore, the observed plasmid-stabilization phenotype associated with the srnB and pnd systems is a consequence of this differential RNA decay: the newborn plasmid-free cells inherit the stable mRNAs, which, after decay of the unstable antisense RNAs, are translated into killer proteins, thus leading to selective killing of the plasmid-free segregants. Thus our observations lead us to conclude that the F srnB and R483 pnd systems are phenotypically indistinguishable from the R1 hok/sok system, despite a 50% dissimilarity at the level of DNA sequence.
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Affiliation(s)
- A K Nielsen
- Department of Molecular Biology, Odense University, Denmark
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