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Eckstein S, Brehm J, Seidel M, Lechtenfeld M, Heermann R. Two novel XRE-like transcriptional regulators control phenotypic heterogeneity in Photorhabdus luminescens cell populations. BMC Microbiol 2021; 21:63. [PMID: 33627070 PMCID: PMC7905540 DOI: 10.1186/s12866-021-02116-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/25/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The insect pathogenic bacterium Photorhabdus luminescens exists in two phenotypically different forms, designated as primary (1°) and secondary (2°) cells. Upon yet unknown environmental stimuli up to 50% of the 1° cells convert to 2° cells. Among others, one important difference between the phenotypic forms is that 2° cells are unable to live in symbiosis with their partner nematodes, and therefore are not able to re-associate with them. As 100% switching of 1° to 2° cells of the population would lead to a break-down of the bacteria's life cycle the switching process must be tightly controlled. However, the regulation mechanism of phenotypic switching is still puzzling. RESULTS Here we describe two novel XRE family transcriptional regulators, XreR1 and XreR2, that play a major role in the phenotypic switching process of P. luminescens. Deletion of xreR1 in 1° or xreR2 in 2° cells as well as insertion of extra copies of xreR1 into 2° or xreR2 into 1° cells, respectively, induced the opposite phenotype in either 1° or 2° cells. Furthermore, both regulators specifically bind to different promoter regions putatively fulfilling a positive autoregulation. We found initial evidence that XreR1 and XreR2 constitute an epigenetic switch, whereby XreR1 represses xreR2 expression and XreR2 self-reinforces its own gene by binding to XreR1. CONCLUSION Regulation of gene expression by the two novel XRE-type regulators XreR1 and XreR2 as well as their interplay represents a major regulatory process in phenotypic switching of P. luminescens. A fine-tuning balance between both regulators might therefore define the fate of single cells to convert from the 1° to the 2° phenotype.
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Affiliation(s)
- Simone Eckstein
- Johannes-Gutenberg-Universität Mainz, Institut für Molekulare Physiologie, Biozentrum II, Mikrobiologie und Weinforschung, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany.,Ludwig-Maximilians-Universität München, Biozentrum, Bereich Mikrobiologie, Martinsried, Germany
| | - Jannis Brehm
- Johannes-Gutenberg-Universität Mainz, Institut für Molekulare Physiologie, Biozentrum II, Mikrobiologie und Weinforschung, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Michael Seidel
- Ludwig-Maximilians-Universität München, Biozentrum, Bereich Mikrobiologie, Martinsried, Germany
| | - Mats Lechtenfeld
- Johannes-Gutenberg-Universität Mainz, Institut für Molekulare Physiologie, Biozentrum II, Mikrobiologie und Weinforschung, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Ralf Heermann
- Johannes-Gutenberg-Universität Mainz, Institut für Molekulare Physiologie, Biozentrum II, Mikrobiologie und Weinforschung, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany.
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2
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Bourdichon F, Patrone V, Fontana A, Milani G, Morelli L. Safety demonstration of a microbial species for use in the food chain: Weissella confusa. Int J Food Microbiol 2020; 339:109028. [PMID: 33352462 DOI: 10.1016/j.ijfoodmicro.2020.109028] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 12/01/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023]
Abstract
Due to their traditional use in food fermentation process for centuries, microbial food cultures are considered to have a safe history of use. A specific microbial risk assessment is therefore rarely conducted for fermented foods and their food cultures, inoculated or naturally present. Some of those food cultures have been also considered for their potential health effect as probiotic strain candidates, for which a specific safety demonstration process has been proposed by a joint expert report of FAO and WHO. The European Food Safety Authority (EFSA) Biohazard panel also provides an approach for evaluating the safety of a strain to be added in the food chain, the Qualified Presumption of Safety (QPS). Weissella confusa, former taxon Lactobacillus confusus, is a food culture characterized in the fermentation process of sourdough. Some strains have been recently proposed for their probiotic potential. The species is also documented in recent infection case reports. It is considered nevertheless to be opportunistic as underlying factors have been suggested to explain the infection. We report here the microbial risk assessment of the species, by studying a collection of 26 food and 17 clinical isolates of Weissella confusa. The phenotypic study, genomic characterization and bibliographical survey will allow us to conclude about the safety of the species and confirm its use for food fermentation and consider specific strains for demonstration of their respective health effects as probiotic candidates.
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Affiliation(s)
- François Bourdichon
- Food Safety, Microbiology, Hygiene, 74 Boulevard Blossac, 86100 Châtellerault, France; Facoltà di Scienze Agrarie, Alimentarie Ambientali, Università Cattolica del Sacro Cuore, Piacenza-Cremona, Italy.
| | - Vania Patrone
- Facoltà di Scienze Agrarie, Alimentarie Ambientali, Università Cattolica del Sacro Cuore, Piacenza-Cremona, Italy
| | - Alessandra Fontana
- Facoltà di Scienze Agrarie, Alimentarie Ambientali, Università Cattolica del Sacro Cuore, Piacenza-Cremona, Italy
| | - Giovanni Milani
- Facoltà di Scienze Agrarie, Alimentarie Ambientali, Università Cattolica del Sacro Cuore, Piacenza-Cremona, Italy
| | - Lorenzo Morelli
- Facoltà di Scienze Agrarie, Alimentarie Ambientali, Università Cattolica del Sacro Cuore, Piacenza-Cremona, Italy
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3
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Durante-Rodríguez G, Mancheño JM, Díaz E, Carmona M. Refactoring the λ phage lytic/lysogenic decision with a synthetic regulator. Microbiologyopen 2016; 5:575-81. [PMID: 26987659 PMCID: PMC4985591 DOI: 10.1002/mbo3.352] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/15/2016] [Accepted: 02/18/2016] [Indexed: 11/11/2022] Open
Abstract
In this work, we explore the refactoring of the circuitry of λ phage by engineering a new-to-nature regulator that responds to an ad hoc input signal that behaves orthogonal with respect to the host cell. We tailored a chimeric regulator, termed Qλ, between the CI protein of the λ phage and the BzdR repressor from Azoarcus sp. strain CIB that responds to benzoyl-CoA. When the Qλ was expressed in the appropriate Escherichia coli cells, it was able to reprogram the lytic/lysogenic λ phage decision according to the intracellular production of benzoyl-CoA. Our results are also an example of how generating new artificial regulators that respond to effectors of choice may be useful to control different cellular processes.
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Affiliation(s)
- Gonzalo Durante-Rodríguez
- Environmental Biology Department, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - José Miguel Mancheño
- Institute of Physical Chemistry Rocasolano-CSIC, Serrano 119, 28006, Madrid, Spain
| | - Eduardo Díaz
- Environmental Biology Department, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Manuel Carmona
- Environmental Biology Department, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
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4
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Durante-Rodríguez G, Valderrama JA, Mancheño JM, Rivas G, Alfonso C, Arias-Palomo E, Llorca O, García JL, Díaz E, Carmona M. Biochemical characterization of the transcriptional regulator BzdR from Azoarcus sp. CIB. J Biol Chem 2010; 285:35694-705. [PMID: 20826820 DOI: 10.1074/jbc.m110.143503] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The BzdR transcriptional regulator that controls the P(N) promoter responsible for the anaerobic catabolism of benzoate in Azoarcus sp. CIB constitutes the prototype of a new subfamily of transcriptional regulators. Here, we provide some insights about the functional-structural relationships of the BzdR protein. Analytical ultracentrifugation studies revealed that BzdR is homodimeric in solution. An electron microscopy three-dimensional reconstruction of the BzdR dimer has been obtained, and the predicted structures of the respective N- and C-terminal domains of each BzdR monomer could be fitted into such a reconstruction. Gel retardation and ultracentrifugation experiments have shown that the binding of BzdR to its cognate promoter is cooperative. Different biochemical approaches revealed that the effector molecule benzoyl-CoA induces conformational changes in BzdR without affecting its oligomeric state. The BzdR-dependent inhibition of the P(N) promoter and its activation in the presence of benzoyl-CoA have been established by in vitro transcription assays. The monomeric BzdR4 and BzdR5 mutant regulators revealed that dimerization of BzdR is essential for DNA binding. Remarkably, a BzdRΔL protein lacking the linker region connecting the N- and C-terminal domains of BzdR is also dimeric and behaves as a super-repressor of the P(N) promoter. These data suggest that the linker region of BzdR is not essential for protein dimerization, but rather it is required to transfer the conformational changes induced by the benzoyl-CoA to the DNA binding domain leading to the release of the repressor. A model of action of the BzdR regulator has been proposed.
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Affiliation(s)
- Gonzalo Durante-Rodríguez
- Department of Environmental Biology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
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5
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Miyakoshi M, Shintani M, Terabayashi T, Kai S, Yamane H, Nojiri H. Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1. J Bacteriol 2007; 189:6849-60. [PMID: 17675379 PMCID: PMC2045235 DOI: 10.1128/jb.00684-07] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Accepted: 07/19/2007] [Indexed: 11/20/2022] Open
Abstract
The IncP-7 plasmid pCAR1 of Pseudomonas resinovorans CA10 confers the ability to degrade carbazole upon transfer to the recipient strain P. putida KT2440. We designed a customized whole-genome oligonucleotide microarray to study the coordinated expression of pCAR1 and the chromosome in the transconjugant strain KT2440(pCAR1). First, the transcriptome of KT2440(pCAR1) during growth with carbazole as the sole carbon source was compared to that during growth with succinate. The carbazole catabolic car and ant operons were induced, along with the chromosomal cat and pca genes involved in the catechol branch of the beta-ketoadipate pathway. Additionally, the regulatory gene antR encoding the AraC/XylS family transcriptional activator specific for car and ant operons was upregulated. The characterization of the antR promoter revealed that antR is transcribed from an RpoN-dependent promoter, suggesting that the successful expression of the carbazole catabolic operons depends on whether the chromosome contains the specific RpoN-dependent activator. Next, to analyze whether the horizontal transfer of a plasmid alters the transcription network of its host chromosome, we compared the chromosomal transcriptomes of KT2440(pCAR1) and KT2440 under the same growth conditions. Only subtle changes were caused by the transfer of pCAR1, except for the significant induction of the hypothetical gene PP3700, designated parI, which encodes a putative ParA-like ATPase with an N-terminal Xre-type DNA-binding motif. Further transcriptional analyses showed that the parI promoter was positively regulated by ParI itself and the pCAR1-encoded protein ParA.
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Affiliation(s)
- Masatoshi Miyakoshi
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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6
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Barragán MJL, Blázquez B, Zamarro MT, Mancheño JM, García JL, Díaz E, Carmona M. BzdR, a repressor that controls the anaerobic catabolism of benzoate in Azoarcus sp. CIB, is the first member of a new subfamily of transcriptional regulators. J Biol Chem 2005; 280:10683-94. [PMID: 15634675 DOI: 10.1074/jbc.m412259200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this work, we have studied the transcriptional regulation of the bzd operon involved in the anaerobic catabolism of benzoate in the denitrifying Azoarcus sp. strain CIB. The transcription start site of the P(N) promoter running the expression of the bzd catabolic genes was identified. Gel retardation assays and P(N)::lacZ translational fusion experiments performed both in Azoarcus sp. CIB and Escherichia coli cells have shown that bzdR encodes a specific repressor that controls the inducible expression of the adjacent bzd catabolic operon, being the first intermediate of the catabolic pathway (i.e. benzoyl-CoA, the actual inducer molecule). This is the first report of a transcriptional repressor and a CoA-derived aromatic inducer controlling gene expression in the anaerobic catabolism of aromatic compounds. DNase I footprinting experiments revealed that BzdR protected three regions (operators) at the P(N) promoter. The three operators contain direct repetitions of a TGCA sequence that forms part of longer palindromic structures. In agreement with the repressor role of BzdR, operator region I spans the transcription initiation site as well as the -10 sequence for recognition of the RNA polymerase. Primary sequence analyses of BzdR showed an unusual modular organization with an N-terminal region homologous to members of the HTH-XRE family of transcriptional regulators and a C-terminal region similar to shikimate kinases. A three-dimensional model of the N-terminal and C-terminal regions of BzdR, generated by comparison with the crystal structures of the SinR regulator from Bacillus subtilis and the shikimate kinase I protein from E. coli, strongly suggests that they contain the helix-turn-helix DNA-binding motif and the benzoyl-CoA binding groove, respectively. The BzdR protein constitutes, therefore, the prototype of a new subfamily of transcriptional regulators.
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Affiliation(s)
- María J L Barragán
- Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, Madrid 28040, Spain
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7
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Skaliter R, Eichenbaum Z, Shwartz H, Ascarelli-Goell R, Livneh Z. Spontaneous transposition in the bacteriophage lambda cro gene residing on a plasmid. Mutat Res 1992; 267:139-51. [PMID: 1373849 DOI: 10.1016/0027-5107(92)90118-l] [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: 12/26/2022]
Abstract
A new mutagenesis assay system based on the phage lambda cro repressor gene residing on a plasmid was developed. The assay detects mutations in cro that decrease the binding of the repressor to the OR operator in an OR PR-lacZ fusion present in a lambda prophage. Mutations arose spontaneously during growth of E. coli cells harboring cro plasmids at a frequency of 3-6 x 10(-6). Analysis of some 200 cro mutants from several 'wild-type' strains revealed a substantial fraction of 25-70% insertion events caused by transposition of IS elements. Most of the insertions were caused by IS1, but IS5 insertions were observed too. In strains harboring Tn10, IS10 was responsible for most insertions. Restriction nuclease digestion analysis revealed a preference for insertion of IS10 into the C-terminal half of cro, despite the absence of sequences which are known hot spots for Tn10 insertions. The frequency of IS1 insertions into cro decreased 25-60-fold and that of IS10 insertions decreased 200-fold in cells carrying the recA56 mutation, suggesting that RecA is involved in transposition of these elements. During the logarithmic phase of growth, the mutation frequency was constant for at least 22 generations; however, upon continuous incubation at the stationary phase, the mutation frequency gradually increased, yielding a 3-fold increase in the frequency of insertion and a 4-5-fold increase in point mutation. Genomic Southern analysis of chromosomal IS elements in cells which underwent a transposition from the chromosome into the cro plasmid revealed that the number and distribution of IS1 and IS5 were usually unaltered compared to cells which did not undergo a transposition event. In contrast, essentially each IS10 transposition was accompanied by multiple events which led to changes in the number and distribution of chromosomal IS10 elements.
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Affiliation(s)
- R Skaliter
- Department of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
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8
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Abstract
The TyrR protein regulates the expression of eight transcriptional units that comprise the TyrR regulon. In all but one case, regulation is by repression, while in two cases activation of expression can occur. Notwithstanding the fact that the TyrR protein contains an ATP-binding domain and a helix-turn-helix DNA-binding domain which are structurally homologous to domains of similar functions in proteins such as NifA, NtrC, DctD and XylR, it differs from them in a number of respects. It is not a part of a two-protein component system and it lacks the amino-terminal domain that is present on NtrC and DctD. It activates transcription from 'E sigma 70, promoters but not from 'E sigma 54, promoters. ATP binding seems to be essential for tyrosine-mediated repression but not for activation. In addition, the activity of the TyrR protein is modulated by the binding of one or more of the aromatic amino acids. The consensus sequence for TyrR-binding sites in DNA, referred to as TyrR boxes, is TGTAAAN6TTTACA. Tyrosine-mediated repression occurs at operators containing a pair of adjacent boxes. These have unequal affinities for the TyrR protein. The box that overlaps the RNA polymerase binding site is only bound by TyrR in the presence of both ATP and tyrosine, and binding appears to involve co-operativity between two TyrR protein dimers. In contrast, activation of expression by TyrR appears to require phenylalanine but not ATP.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- A J Pittard
- Microbiology Department, University of Melbourne, Parkville, Victoria, Australia
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9
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Benson N, Youderian P. Phage lambda Cro protein and cI repressor use two different patterns of specific protein-DNA interactions to achieve sequence specificity in vivo. Genetics 1989; 121:5-12. [PMID: 2521838 PMCID: PMC1203605 DOI: 10.1093/genetics/121.1.5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
By assaying the binding of wild-type Cro to a set of 40 mutant lambda operators in vivo, we have determined that the 14 outermost base pairs of the 17 base pair, consensus lambda operator are critical for Cro binding. Cro protein recognizes 4 base pairs in a lambda operator half-site in different ways than cI repressor. The sequence determinants of Cro binding at these critical positions in vivo are nearly perfectly consistent with the model proposed by W. F. ANDERSON, D. H. OHLENDORF, Y. TAKEDA and B. W. MATTHEWS and modified by Y. TAKEDA, A. SARAI and V. M. RIVERA for the specific interactions between Cro and its operator, and explain the relative order of affinities of the six natural lambda operators for Cro. Our data call into question the idea that lambda repressor and Cro protein recognize the consensus lambda operator by nearly identical patterns of specific interactions.
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Affiliation(s)
- N Benson
- Department of Biological Sciences, University of Southern California, Los Angeles 90089-1481
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10
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Lehming N, Sartorius J, Oehler S, von Wilcken-Bergmann B, Müller-Hill B. Recognition helices of lac and lambda repressor are oriented in opposite directions and recognize similar DNA sequences. Proc Natl Acad Sci U S A 1988; 85:7947-51. [PMID: 3186699 PMCID: PMC282330 DOI: 10.1073/pnas.85.21.7947] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Exchanges in positions 1 and 2 of the putative recognition helix allow lac repressor to bind to ideal lac operator variants in which base pair 4 has been replaced. We show here that an Arg-22----Asn exchange in position 6 of the putative recognition helix of lac repressor abolishes lac repressor binding to ideal lac operator. This lac repressor variant, however, binds to a variant of the ideal lac operator 5' TTTGAGCGCTCAAA 3' in which the original G.C of position 6 has been replaced by T.A. This result and our previous data confirm our suggestion that the N terminus of the recognition helix of lac repressor enters the major groove close to the center of symmetry of lac operator and that its C terminus leaves the major groove further away from the center of symmetry. The consequences of this model are discussed in regard to various phage and bacterial repressor operator systems.
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Affiliation(s)
- N Lehming
- Institut für Genetik, Universität zu Köln, Federal Republic of Germany
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11
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Abstract
The c4 gene of phage P1 has been localized to 335 bp of the P1EcoRI-9 fragment, within 50 bp of the EcoRI-9/14 junction. DNA sequence analysis of this fragment reveals a single open reading frame of 66 amino acids. The location of two c4 mutations, both of which produce changes in the predicted amino acid sequence in this reading frame, suggests that the reading frame codes for the c4 repressor. A region with high homology to the E. coli promoter consensus sequence is located approximately 50 bp upstream from the reading frame. Deletion of this potential promoter region abolishes expression of c4, as indicated by the loss of complementation of c4 mutants for lysogeny. Complementation is restored by the introduction of a heterologous promoter (the T7 phi 10 promoter), indicating that c4 expression is absolutely dependent on transcription of the 66-amino acid reading frame.
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12
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Frigerio G, Burri M, Bopp D, Baumgartner S, Noll M. Structure of the segmentation gene paired and the Drosophila PRD gene set as part of a gene network. Cell 1986; 47:735-46. [PMID: 2877746 DOI: 10.1016/0092-8674(86)90516-7] [Citation(s) in RCA: 354] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The sequence of paired, a pair-rule gene required for segmentation in Drosophila, is presented. A search for genes with domains homologous to the paired gene was initiated and three homologues from a set of 12 were characterized with respect to temporal or spatial expression and sequence homologies. All four are transcribed in early development, one in the oocyte and during cleavage stages in the form of a gradient. In addition to the prd-specific his-pro repeat, some of the 12 genes contain M-repeats and two new types of homeo boxes not detectable by hybridization with the two known classes of homeo boxes. The observed linking of gene sets through combinations of homologies coding for protein domains is consistent with a general network concept of gene action.
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13
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Pakula AA, Young VB, Sauer RT. Bacteriophage lambda cro mutations: effects on activity and intracellular degradation. Proc Natl Acad Sci U S A 1986; 83:8829-33. [PMID: 2947238 PMCID: PMC387026 DOI: 10.1073/pnas.83.23.8829] [Citation(s) in RCA: 102] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Following random mutagenesis of the bacteriophage lambda cro gene, we have isolated missense mutations that affect approximately half of the 66 residue positions of Cro. About two-thirds of the mutations change residues involved in the maintenance of Cro structure and stability. The corresponding mutant proteins are severely degraded in the cell but often have specific activities near that of wild-type Cro. The remaining mutations affect residues involved in DNA binding. These mutant proteins are present at moderately reduced intracellular levels, but their specific activities are much lower than that of wild type.
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14
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Antonucci TK, Wagner LM, Oxender DL. Cloning, expression, and nucleotide sequence of livR, the repressor for high-affinity branched-chain amino acid transport in Escherichia coli. Proteins 1986; 1:125-33. [PMID: 3329726 DOI: 10.1002/prot.340010204] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The livR gene encoding the repressor for high-affinity branched-chain amino acid transport in Escherichia coli has been cloned from a library prepared from the episome F106. The inserted DNA fragment from the initial cloned plasmid, pANT1, complemented two independent, spontaneously derived, regulatory mutations. Subcloning as well as the creation of deletions with Bal31 exonuclease revealed that the entire regulatory region is contained within a 1.1-kb RsaI-SalI fragment. Expression of the pANT plasmids in E. coli minicells showed that the regulatory region encodes one detectable protein with an apparent molecular weight of 21,000. DNA sequencing revealed one open reading frame of 501 bp encoding a protein with a calculated MW of 19,155. The potential secondary structure of the regulatory protein has been predicted and it suggests that the carboxy terminus may fold into three consecutive alpha helices. These results suggest that the livR gene encodes a repressor which plays a role in the regulation of expression of the livJ and the livK transport genes.
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Affiliation(s)
- T K Antonucci
- Department of Biological Chemistry, University of Michigan, Ann Arbor 48109-0606
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15
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Metzler WJ, Arndt K, Tecza E, Wasilewski J, Lu P. Lambda phage cro repressor interaction with its operator DNA: 2'-deoxy-5-fluorouracil OR3 analogues. Biochemistry 1985; 24:1418-24. [PMID: 3157402 DOI: 10.1021/bi00327a020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The experiments here show that chemically synthesized DNA containing fluorine at selected sites can be used to test specific predictions of a model for cro repressor--operator interaction. This is done by observation of the perturbation to the fluorine-19 NMR spectra of analogues of OR3 synthesized with 2'-deoxy-5-fluorouracil at specific positions in the DNA helix. Although the three-dimensional structure of the cro repressor from phage lambda has been determined by Matthews and co-workers [Anderson, W., Ohlendorf, D., Takeda, Y., & Matthews, B. (1981) Nature (London) 290, 754-758], direct structural observations on the complex of the protein with its specific DNA recognition sequence, OR3, are limited. From that structure of the protein, alone, a model of its complex to DNA was built by fitting B-form DNA, with some distortion [Ohlendorf, D., Anderson, W., Fisher, R., Takeda, Y., & Matthews, B. (1982) Nature (London) 298, 718-723]. That model proposes that the cro repressor contacts only one side of this DNA double helix and a number of specific protein--DNA contacts. To test the model, 2'-deoxy-5-fluorouracil was used to place the fluorine-19 nuclear spin-label on the side of the DNA contacting the cro repressor and on the opposite side facing away from the cro repressor. The results presented here are consistent with the prediction that lambda phage cro repressor contacts only one side of the DNA double helix.
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16
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Ginsberg AM, King BO, Roeder RG. Xenopus 5S gene transcription factor, TFIIIA: characterization of a cDNA clone and measurement of RNA levels throughout development. Cell 1984; 39:479-89. [PMID: 6210149 DOI: 10.1016/0092-8674(84)90455-0] [Citation(s) in RCA: 274] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Initiation of 5S RNA gene transcription in Xenopus oocytes requires a 38,500 dalton polypeptide, TFIIIA. The levels of both 5S RNA and TFIIIA are regulated throughout oogenesis and embryonic development. To delineate the mechanisms by which the corresponding genes are regulated, as well as to determine the primary structure of TFIIIA, we have isolated a cDNA clone that encodes TFIIIA. Using the cDNA clone, we have determined that there is (are) one or a small number of TFIIIA gene(s) per Xenopus haploid genome, and we have estimated the size and levels of TFIIIA RNA throughout Xenopus development. We report sequence homologies between TFIIIA cDNA and regulatory regions of the Xenopus tmet and 5S RNA genes. Implications of these data for developmental regulation of the TFIIIA and 5S RNA genes are discussed.
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17
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Ljungquist E, Kockum K, Bertani LE. DNA sequences of the repressor gene and operator region of bacteriophage P2. Proc Natl Acad Sci U S A 1984; 81:3988-92. [PMID: 6330728 PMCID: PMC345353 DOI: 10.1073/pnas.81.13.3988] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The nucleotide sequence of the repressor gene C of the temperate phage P2 has been determined. It codes for a nonbasic polypeptide, 99 amino acids long. Twelve repressor-defective mutants have been mapped. All but one are located within the presumed coding part of the gene. There is a strong promoter sequence and an 8-base-pair inverted repeat preceding the gene. The P2 repressor protein shows structural similarity to other DNA-binding proteins. The operator region for the early replication functions was located by sequencing the DNA of three virulent mutants. The sequence indicates that there are two repressor-binding sites. In addition, one of the sites shows sequence homology with part of the operator region of the biotin operon of Escherichia coli.
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Abstract
The GAL4 gene encodes a positive regulator of the galactose-inducible genes in Saccharomyces cerevisiae. Recently, GAL4 has been cloned and its 2.8-kilobase mRNA has been identified. We report here the DNA sequence of GAL4 and the mapping of the 5' and 3' ends of its transcripts. The region sequenced contains a single open reading frame, 881 codons long, which could encode a 99,350-dalton protein. The 5' ends of the GAL4 transcripts fall into two clusters. Transcripts which begin at the upstream cluster would encode the 99,350-dalton protein, whereas those starting at the downstream cluster may result in the synthesis of a shorter, 91,600-dalton protein. The putative GAL4 proteins contain an amino acid sequence near their amino termini which resembles a DNA-binding motif found in bacterial and phage repressors and gene activator proteins.
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19
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Abstract
The GAL4 gene encodes a positive regulator of the galactose-inducible genes in Saccharomyces cerevisiae. Recently, GAL4 has been cloned and its 2.8-kilobase mRNA has been identified. We report here the DNA sequence of GAL4 and the mapping of the 5' and 3' ends of its transcripts. The region sequenced contains a single open reading frame, 881 codons long, which could encode a 99,350-dalton protein. The 5' ends of the GAL4 transcripts fall into two clusters. Transcripts which begin at the upstream cluster would encode the 99,350-dalton protein, whereas those starting at the downstream cluster may result in the synthesis of a shorter, 91,600-dalton protein. The putative GAL4 proteins contain an amino acid sequence near their amino termini which resembles a DNA-binding motif found in bacterial and phage repressors and gene activator proteins.
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20
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Ohlendorf DH, Anderson WF, Lewis M, Pabo CO, Matthews BW. Comparison of the structures of cro and lambda repressor proteins from bacteriophage lambda. J Mol Biol 1983; 169:757-69. [PMID: 6226802 DOI: 10.1016/s0022-2836(83)80169-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The three-dimensional structures of cro repressor protein and of the amino-terminal domain of lambda repressor protein, both from bacteriophage lambda, are compared. The second and third alpha-helices, alpha 2 and alpha 3, are shown to have essentially identical conformations in the two proteins, confirming the significance of the amino acid sequence homology previously noted between these and other DNA binding proteins in the region corresponding to these helices. The correspondence between the two-helical units in cro and lambda repressor protein is better than the striking agreement noted previously between two-helical units in cro and catabolite gene-activator protein. Parts of the first alpha-helices of repressor and cro show a structural correspondence that suggests a revised sequence homology between the two proteins in their extreme amino-terminal regions. In particular, there is a short loop between the alpha 1 and alpha 2 helices of lambda repressor that is missing from cro. This structural difference may account for the observed differences found with different cros and repressors in the pattern of phosphates whose ethylation prevents the binding of these proteins to their specific recognition sites. Although the two proteins have strikingly similar alpha 2-alpha 3 helical units that are presumed to bind to DNA in an essentially similar manner, stereochemical restrictions prevent the alpha 2-alpha 3 units of the respective proteins aligning on the DNA in exactly the same way.
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21
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Abstract
The structures of three proteins that regulate gene expression have been determined recently and suggest how these proteins may bind to their specific recognition sites on the DNA. One protein (Cro) is a repressor of gene expression, the second (CAP) usually stimulates gene expression, and the third (lambda repressor) can act as either a repressor or an activator. The three proteins contain a substructure consisting of two consecutive alpha helices that is virtually identical in each case. Structural and amino acid sequence comparisons suggest that this bihelical fold occurs in a number of proteins that regulate gene expression, and is an intrinsic part of the DNA-protein recognition event. The modes of repression and activation by Cro and lambda repressor are understood reasonably well, but the mode of action of CAP is still unclear.
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22
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Abstract
The gene for histone H3 from the yeast Saccharomyces cerevisiae was placed under the control of the lac promoter of Escherichia coli by fusing the H3 coding sequence to that of beta-galactosidase. The gene was shown to be transcribed in vivo, but its product was not detected in cell extracts. However, synthesis of the fused polypeptide was detected in an in vitro transcription-translation system derived from E. coli. Proteolytic degradation of the newly synthesized polypeptides may be the cause of their apparent absence in the in vivo experiment.
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23
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Bolotina IA, Kurochkin AV, Kirpichnikov MP. Studies of the structure of bacteriophage lambda cro protein in solution. Analysis of the circular dichroism data. FEBS Lett 1983; 155:291-4. [PMID: 6221942 DOI: 10.1016/0014-5793(82)80623-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The secondary and tertiary structures of bacteriophage cro protein were studied by circular dichroism. The pH dependence of this structure was investigated: cro protein is stable over pH 4.5-10.5. At these pH-values cro protein contains approximately 35% alpha-helix, approximately 20% antiparallel beta-structure and approximately 15% beta-turn, while the remaining part of the protein molecule is in the irregular state. The secondary and tertiary structures of the protein are modified abruptly at more acid and more alkaline pH-values. The curves characterizing the secondary and tertiary structures of the protein are symbatic. The effect of Gu-HCl on the secondary and tertiary structures of cro protein at 22 degrees C and pH 7.2 was studied also. The conformational transition occurs within 0.6-1.9 M Gu-HCl. The changes in the secondary and tertiary structures of the protein have a symbatic character. Thermal denaturation of cro protein was examined. A possible mechanism of the protein denaturation is discussed.
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24
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Arndt KT, Boschelli F, Cook J, Takeda Y, Tecza E, Lu P. lambda Phage cro repressor interaction with DNA. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(18)32602-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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25
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Ohlendorf DH, Anderson WF, Matthews BW. Many gene-regulatory proteins appear to have a similar alpha-helical fold that binds DNA and evolved from a common precursor. J Mol Evol 1983; 19:109-14. [PMID: 6571216 DOI: 10.1007/bf02300748] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Amino acid and DNA sequence comparisons suggest that many sequence-specific DNA-binding proteins have in common an homologous region of about 22 amino acids. This region corresponds to two consecutive alpha-helices that occur in both Cro and cI repressor proteins of bacteriophage lambda and in catabolite gene activator protein of Escherichia coli and are presumed to interact with DNA. The results obtained here suggest that this alpha-helical DNA-binding fold occurs in many proteins that regulate gene expression. It also appears that this DNA-binding unit evolved from a common evolutionary precursor.
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26
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Sanger F, Coulson AR, Hong GF, Hill DF, Petersen GB. Nucleotide sequence of bacteriophage lambda DNA. J Mol Biol 1982; 162:729-73. [PMID: 6221115 DOI: 10.1016/0022-2836(82)90546-0] [Citation(s) in RCA: 851] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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27
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Boschelli F, Arndt K, Nick H, Zhang Q, Lu P, Takeda Y. Lambda phage cro repressor. DNA sequence-dependent interactions seen by tyrosine fluorescence. J Mol Biol 1982; 162:251-66. [PMID: 6219228 DOI: 10.1016/0022-2836(82)90525-3] [Citation(s) in RCA: 15] [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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28
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29
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Ptitsyn OB, Finkelstein AV, Kirpichnikov MP, Skryabin KG. cI and lexA repressors consist of three cro-like domains. FEBS Lett 1982; 147:11-5. [PMID: 6216121 DOI: 10.1016/0014-5793(82)81001-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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30
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Anderson WF. Proposed alpha-helical super-secondary structure associated with protein-dna recognition. J Mol Biol 1982; 159:745-51. [PMID: 6897265 DOI: 10.1016/0022-2836(82)90111-5] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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31
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Ho Y, Lewis M, Rosenberg M. Purification and properties of a transcriptional activator. The cII protein of phage lambda. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34252-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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32
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Sauer RT, Yocum RR, Doolittle RF, Lewis M, Pabo CO. Homology among DNA-binding proteins suggests use of a conserved super-secondary structure. Nature 1982; 298:447-51. [PMID: 6896364 DOI: 10.1038/298447a0] [Citation(s) in RCA: 379] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The amino acid sequences of the repressor and cro proteins of phages lambda, 434 and P22 are homologous, especially in a region in which repressor and lambda cro have a similar alpha-helix-turn-alpha-helix secondary structure. Model-building studies indicate that this structure is important in DNA binding, and we suggest it may be a common feature of many DNa-binding proteins.
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Daniels DL, Blattner FR. Nucleotide sequence of the Q gene and the Q to S intergenic region of bacteriophage lambda. Virology 1982; 117:81-92. [PMID: 6461127 DOI: 10.1016/0042-6822(82)90509-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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34
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35
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Greenblatt J, McLimont M, Hanly S. Termination of transcription by nusA gene protein of Escherichia coli. Nature 1981; 292:215-20. [PMID: 6265785 DOI: 10.1038/292215a0] [Citation(s) in RCA: 113] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The nusA gene protein of Escherichia coli and N gene protein of bacteriophage lambda interact in vitro and cooperate in vivo to prevent transcription termination. In vitro the nusA gene protein causes RNA polymerase to pause in the tR2 terminator region of lambda DNA. A completed termination event at tR2 requires both the nusA gene protein and the previously described E. coli termination factor rho. The nusA gene protein is therefore both a transcription termination factor and a protein which couples antitermination factors to the elongating transcription complex.
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36
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Simatake H, Rosenberg M. Purified lambda regulatory protein cII positively activates promoters for lysogenic development. Nature 1981; 292:128-32. [PMID: 6264321 DOI: 10.1038/292128a0] [Citation(s) in RCA: 216] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The bacteriophage lambda regulatory protein, cII, has been purified and shown to activate positively RNA transcription from the two phage promoters which coordinately regulate phage lysogenic development. To obtain this protein, the cII gene was cloned into a plasmid vector carrying the strong, regulatable lambda phage promoter PL such that it was overproduced to levels approaching 5% of cellular protein.
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37
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Anderson WF, Ohlendorf DH, Takeda Y, Matthews BW. Structure of the cro repressor from bacteriophage lambda and its interaction with DNA. Nature 1981; 290:754-8. [PMID: 6452580 DOI: 10.1038/290754a0] [Citation(s) in RCA: 475] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The three-dimensional structure of the 66-amino acid cro repressor protein of bacteriophage lambda suggests how it binds to its operator DNA. We propose that a dimer of cro protein is bound to the B-form of DNA with the 2-fold axis of the dimer coincident with the 2-fold axis of DNA. A pair of 2-fold-related alpha-helices of the repressor, lying within successive major grooves of the DNA, seem to be a major determinant in recognition and binding. In addition, the C-terminal residues of the protein, some of which are disordered in the absence of DNA, appear to contribute to the binding.
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38
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Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol 1981; 146:1-21. [PMID: 6167728 DOI: 10.1016/0022-2836(81)90363-6] [Citation(s) in RCA: 629] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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39
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40
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Calva E, Burgess R. Characterization of a rho-dependent termination site within the cro gene of bacteriophage lambda. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)70409-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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41
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Murotsu T, Matsubara K. Role of an autorepression system in the control of lambda dv plasmid copy number and incompatibility. MOLECULAR & GENERAL GENETICS : MGG 1980; 179:509-19. [PMID: 6449651 DOI: 10.1007/bf00271740] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The lambda dv plasmid genome is composed of two regions: (1) the autorepressor region which consists of promoter-operator (pRoR) and autorepressor (tof) and (2) the origin region which consists of the origin of replication (ori) and two initiator genes (O and P) (Matsubara 1976). Replication of this plasmid is directly connected with transcription from pRoR. Using lambda dvs having various mutations in pRoR, the transcription ability was examined in detail in connection with the control mechanism of replication. The transcription ability of the autorepressor region is controlled by the binding affinity of the tof protein and pRoR. Thus, at steady-state, lambda dvs carrying a highly-constitutive ('strong') pRoR produced the autorepressor at high levels, whereas those carrying a low-constitutive ('weak') pRoR produced the autorepressor at low levels. This relationship did not change even when a fragment of lambda dv genome covering the autorepressor region was cloned into the plasmids pBR322 and pSC138, which could be maintained in a fixed amount within a cell. It was also shown that the autorepressor level at steady-state is a function of copy number of the DNA carrying the region for autorepression. These observations fit the autorepression model of Sompayrac and Maaløe (1973), which predicts that a decreased level of autorepressor activates pRoR and initiates transcription which leads to the production of tof protein until a new steady-state is established. By the same token, if the affinity of autorepressor and pRoR is decreased, pRoR remains active until a higher level of autorepressor is produced. Transcription of the autorepressor region directly affects the level of transcription of the origin region which is located distal to the promoter. Thus, the ability to replicate is connected with an ability to produce autorepressor. The lambda dv plasmids with 'strong' or 'weak' pRoR were maintained at a high or low copy number, respectively. The phenomenon of incompatibility of lambda dv was also examined using pBR322 and pSC138 plasmids carrying the cloned autorepressor region of lambda dv. The chimeric plasmids with 'strong' pRoR exhibited strong incompatibility with lambda dv, whereas those with 'weak' pRoR showed weak incompatibility. This indicates that interaction of the autorepressor and pRoR is related to the incompatibility of lambda dv plasmids.
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Gutte B, Schindler S, Standar F, Wittschieber E. Interaction of synthetic NH2-terminal fragments of bacteriophage lambda cro protein with nucleic acids. Biochem Biophys Res Commun 1980; 95:1071-9. [PMID: 6448050 DOI: 10.1016/0006-291x(80)91582-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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43
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44
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Schmeissner U, Court D, Shimatake H, Rosenberg M. Promoter for the establishment of repressor synthesis in bacteriophage lambda. Proc Natl Acad Sci U S A 1980; 77:3191-5. [PMID: 6447872 PMCID: PMC349580 DOI: 10.1073/pnas.77.6.3191] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Transcription of the lambda repressor gene (cI) is positively regulated by the phage-encoded proteins cII and cIII. We have isolated and characterized the 5'-terminal region of this RNA and shown that it originates at a promoter (pE) located between genes cro and cII. The DNA sequence of this promoter shows little homology to other known promoters. Initiation of transcription from PE is abolished by the cis-dominant mutations cY; these mutations alter the "-10" and "-35" regions of the promoter. We propose that the "-35" region is the site of activation of PE, possibly via the direct interaction of protein cII.
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45
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Meyer BJ, Maurer R, Ptashne M. Gene regulation at the right operator (OR) of bacteriophage lambda. II. OR1, OR2, and OR3: their roles in mediating the effects of repressor and cro. J Mol Biol 1980; 139:163-94. [PMID: 6447795 DOI: 10.1016/0022-2836(80)90303-4] [Citation(s) in RCA: 209] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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46
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Singleton CK, Roeder WD, Bogosian G, Somerville RL, Weith HL. DNA sequence of the E. coli trpR gene and prediction of the amino acid sequence of Trp repressor. Nucleic Acids Res 1980; 8:1551-60. [PMID: 7001368 PMCID: PMC324016 DOI: 10.1093/nar/8.7.1551] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A DNA sequence of 1041 base pairs from a BamHI fragment containing the E. coli trpR gene has been determined. With this sequence and other experimental evidence, the primary structure (88 amino acids) of the Trp repressor can be predicted. Additional features of the DNA sequences include a 22 base pair region upstream from the proposed structural gene which exhibits striking homology with the trp operator, thus implying that expression of the trpR gene may be under autogenous regulation.
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47
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Court D, Brady C, Rosenberg M, Wulff DL, Behr M, Mahoney M, Izumi SU. Control of transcription termination: a rho-dependent termination site in bacteriophage lambda. J Mol Biol 1980; 138:231-54. [PMID: 6447791 DOI: 10.1016/0022-2836(80)90285-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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48
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Abstract
The synthesis of RNA catalysed by RNA polymerase from Escherichia coli is terminated at specific sites on DNA templates through the action of a multimeric basic protein known as rho (refs 1, 2). Three lines of evidence suggest that an interactions of rho with the nascent RNA is important for this termination. First, rho binds strongly to RNA; second, rho expresses an RNA-dependent ATPase activity which is essential for termination; third, RNA polymerase does not terminate RNA synthesis at rho-dependent sites when the nascent RNA is digested by ribonuclease during transcription. From the fact that certain RNAs, particularly single-stranded, pyrimidine-rich polymers containing at least 10% cytidylate residues, are more effective than other RNAs at promoting rho-ATPase, it has been proposed that rho recognises specific sites oion on a mRNA transcribed from bacteriophage lambda DNA.
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49
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Hughes SG, Murray K. The nucleotide sequences recognized by endonucleases AvaI and AvaII from Anabaena variabilis. Biochem J 1980; 185:65-75. [PMID: 6246881 PMCID: PMC1161270 DOI: 10.1042/bj1850065] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Determination of the 5'-terminal sequences flanking all the individual cleavage sites for endonuclease AvaI in bacteriophage-lambda DNA has shown that this enzyme recognizes the hexanucleotide sequences: (Formula: see text), This sequence is cut as shown by the arrows to give single-stranded 5'-tetranucleotide protrusions (cohesive ends). Endonucleases SmaI, XhoI and XmaI recognize different symmetrical subsets of this sequence and provide independent evidence for the occurrence of these subsets at particular endonuclease-AvaI cleavage sites in the bacteriophage-lambda genome. Further evidence for this structure came from the demonstration that DNA fragments generated by endonuclease AvaI can be ligated to form a discrete set of larger molecules and from nearest-neighbor analysis which showed that cytosine residues occurred at the 3'-side of cleavage points. The observation that endonuclease AvaII recognized a subset of the sites recognized by AsuI [Hughes, Bruce & Murray (1979) Biochem. J. 185, 59-63[ led to the deduction that AvaII recognize the pentanucleotide sequence: (Formula: see text), and breaks internucleotide bonds at the positions indicated by the arrows.
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50
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Johnson AD, Pabo CO, Sauer RT. Bacteriophage lambda repressor and cro protein: interactions with operator DNA. Methods Enzymol 1980; 65:839-56. [PMID: 6445470 DOI: 10.1016/s0076-6879(80)65078-2] [Citation(s) in RCA: 132] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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