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Del Duca S, Vassallo A, Semenzato G, Fani R. Mimicking the last step of gene elongation: hints from the bacterial hisF gene. Gene 2023:147533. [PMID: 37279865 DOI: 10.1016/j.gene.2023.147533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/05/2023] [Accepted: 05/31/2023] [Indexed: 06/08/2023]
Abstract
Gene elongation consists in an in-tandem duplication of a gene and divergence and fusion of the two copies, resulting in a gene constituted by two divergent paralogous modules. Many present-day proteins show internal repeats of amino acid sequences, generated by gene elongation events; however, gene elongation is still a poorly studied evolutionary molecular mechanism. The most documented case is that of the histidine biosynthetic genes hisA and hisF, which derive from the gene elongation of an ancestral gene half the size of the extant ones. The aim of this work was to experimentally simulate the possible last step of the gene elongation event occurred during hisF gene evolution under selective pressure conditions. Azospirillum brasilense hisF gene, carrying a single nucleotide mutation that generates a stop codon between the two halves of the gene, was used to transform the histidine-auxotrophic Escherichia coli strain FB182 (hisF892). The transformed strain was subjected to selective pressure (i.e., low concentration/absence of histidine in the growth medium) and the obtained mutants were characterized. The restoration of prototrophy was strongly dependent on the time of incubation and on the strength of the selective pressure. The mutations involved the introduced stop codon with a single base substitution and none of the mutants restored the wild-type codon. Possible correlations between the different mutations and i) E. coli codon usage, ii) three-dimensional structures of the mutated HisF proteins, and iii) growth ability of the mutants were investigated. On the contrary, when the experiment was repeated by mutating a more conserved codon, only a synonymous substitution was obtained. Thus, experiments performed in this study allowed to mimic a possible gene elongation event occurred during the evolution of hisF gene, evidencing the ability of bacterial cells to modify their genome in short times under selective conditions.
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Affiliation(s)
- Sara Del Duca
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino (FI), Italy; Research Centre for Agriculture and Environment, Council for Agricultural Research and Economics (CREA-AA), Via di Lanciola 12/A, 50125, Cascine del Riccio (FI), Italy
| | - Alberto Vassallo
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III Da Varano 1, 62032, Camerino (MC) Italy
| | - Giulia Semenzato
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino (FI), Italy
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino (FI), Italy.
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2
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Romeo L, Esposito A, Bernacchi A, Colazzo D, Vassallo A, Zaccaroni M, Fani R, Del Duca S. Application of Cloning-Free Genome Engineering to Escherichia coli. Microorganisms 2023; 11:microorganisms11010215. [PMID: 36677507 PMCID: PMC9866961 DOI: 10.3390/microorganisms11010215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/06/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
The propagation of foreign DNA in Escherichia coli is central to molecular biology. Recent advances have dramatically expanded the ability to engineer (bacterial) cells; however, most of these techniques remain time-consuming. The aim of the present work was to explore the possibility to use the cloning-free genome editing (CFGE) approach, proposed by Döhlemann and coworkers (2016), for E. coli genetics, and to deepen the knowledge about the homologous recombination mechanism. The E. coli auxotrophic mutant strains FB182 (hisF892) and FB181 (hisI903) were transformed with the circularized wild-type E. coli (i) hisF gene and hisF gene fragments of decreasing length, and (ii) hisIE gene, respectively. His+ clones were selected based on their ability to grow in the absence of histidine, and their hisF/hisIE gene sequences were characterized. CFGE method allowed the recombination of wild-type his genes (or fragments of them) within the mutated chromosomal copy, with a different recombination frequency based on the fragment length, and the generation of clones with a variable number of in tandem his genes copies. Data obtained pave the way to further evolutionary studies concerning the homologous recombination mechanism and the fate of in tandem duplicated genes.
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Affiliation(s)
- Lucia Romeo
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Antonia Esposito
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Alberto Bernacchi
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Daniele Colazzo
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Alberto Vassallo
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy
| | - Marco Zaccaroni
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Renato Fani
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
- Correspondence: (R.F.); (S.D.D.)
| | - Sara Del Duca
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
- Correspondence: (R.F.); (S.D.D.)
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3
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Del Duca S, Puglia AM, Calderone V, Bazzicalupo M, Fani R. Effect of Non-Lethal Selection on Spontaneous Revertants of Frameshift Mutations: The Escherichia coli hisF Case. Microorganisms 2022; 10:692. [PMID: 35456744 PMCID: PMC9032791 DOI: 10.3390/microorganisms10040692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/10/2022] [Accepted: 03/18/2022] [Indexed: 01/25/2023] Open
Abstract
Microorganisms possess the potential to adapt to fluctuations in environmental parameters, and their evolution is driven by the continuous generation of mutations. The reversion of auxotrophic mutations has been widely studied; however, little is known about the reversion of frameshift mutations resulting in amino acid auxotrophy and on the structure and functioning of the protein encoded by the revertant mutated gene. The aims of this work were to analyze the appearance of reverse mutations over time and under different selective pressures and to investigate revertant enzymes' three-dimensional structures and their correlation with a different growth ability. Escherichia coli FB182 strain, carrying the hisF892 single nucleotide deletion resulting in histidine auxotrophy, was subjected to different selective pressures, and revertant mutants were isolated and characterized. The obtained results allowed us to identify different indels of different lengths located in different positions in the hisF gene, and relations with the incubation time and the selective pressure applied were observed. Moreover, the structure of the different mutant proteins was consistent with the respective revertant ability to grow in absence of histidine, highlighting a correlation between the mutations and the catalytic activity of the mutated HisF enzyme.
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Affiliation(s)
- Sara Del Duca
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy; (S.D.D.); (M.B.)
| | - Anna Maria Puglia
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, Viale delle Scienze Ed. 16, 90128 Palermo, Italy;
| | - Vito Calderone
- Magnetic Resonance Center (CERM)/Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy;
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Marco Bazzicalupo
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy; (S.D.D.); (M.B.)
| | - Renato Fani
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy; (S.D.D.); (M.B.)
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4
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Chioccioli S, Bogani P, Del Duca S, Castronovo LM, Vassallo A, Puglia AM, Fani R. In vivo evaluation of the interaction between the Escherichia coli IGP synthase subunits using the Bacterial Two-Hybrid system. FEMS Microbiol Lett 2021; 367:5866475. [PMID: 32614412 DOI: 10.1093/femsle/fnaa112] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/30/2020] [Indexed: 12/18/2022] Open
Abstract
Histidine biosynthesis is one of the most characterized metabolic routes for its antiquity and its central role in cellular metabolism; indeed, it represents a cross-road between nitrogen metabolism and de novo synthesis of purines. This interconnection is due to the activity of imidazole glycerol phosphate synthase, a heterodimeric enzyme constituted by the products of two his genes, hisH and hisF, encoding a glutamine amidotransferase and a cyclase, respectively. Despite their interaction was suggested by several in vitro experiments, their in vivo complex formation has not been demonstrated. On the contrary, the analysis of the entire Escherichia coli interactome performed using the yeast two hybrid system did not suggest the in vivo interaction of the two IGP synthase subunits. The aim of this study was to demonstrate the interaction of the two proteins using the Bacterial Adenylate Cyclase Two-Hybrid (BACTH) system. Data obtained demonstrated the in vivo interaction occurring between the proteins encoded by the E. coli hisH and hisF genes; this finding might also open the way to pharmaceutical applications through the design of selective drugs toward this enzyme.
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Affiliation(s)
- Sofia Chioccioli
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
| | - Patrizia Bogani
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
| | - Sara Del Duca
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
| | - Lara Mitia Castronovo
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
| | - Alberto Vassallo
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
| | - Anna Maria Puglia
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, Viale delle Scienze Ed. 16, 90128 Palermo (PA), Italy
| | - Renato Fani
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
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5
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Papaleo MC, Russo E, Fondi M, Emiliani G, Frandi A, Brilli M, Pastorelli R, Fani R. Structural, evolutionary and genetic analysis of the histidine biosynthetic “core” in the genus Burkholderia. Gene 2009; 448:16-28. [DOI: 10.1016/j.gene.2009.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 07/25/2009] [Accepted: 08/05/2009] [Indexed: 11/28/2022]
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Affiliation(s)
- Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA. kevin.hms.harvard.edu
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7
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Eichler JF, Cramer JC, Kirk KL, Bann JG. Biosynthetic incorporation of fluorohistidine into proteins in E. coli: a new probe of macromolecular structure. Chembiochem 2006; 6:2170-3. [PMID: 16261552 DOI: 10.1002/cbic.200500249] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jack F Eichler
- Department of Chemistry, Wichita State University, Wichita, KS 67226, USA
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8
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Abstract
Operons are clusters of genes that are transcribed as a single message, and regulated by the same gene expression machinery. They are found primarily in prokaryotic genomes. Because genes in the same operon are likely to have related functions, identification of the operon structure is potentially useful for assigning gene function. We report the development and benchmarking of two different methods for detecting operons, based on an analysis of 42 fully sequenced prokaryotic organisms. The Gene Neighbor method (GNM) utilizes the relatively high conservation of gene order in operons, compared with genes in general. The Gene Gap Method (GGM) makes use of the relatively short gap between genes in operons compared with that otherwise found between adjacent genes. The methods have been benchmarked using KEGG pathway data and RegulonDB Escherichia coli operon data. With optimum parameters, the specificity of the GNM is 93% and the sensitivity is 70%. For the GGM, the specificity is 95% and the sensitivity is 68%. Together, the two methods have a sensitivity of 87.2%, while joint predictions have a sensitivity of 50% and a specificity of 98%. The methods are used to infer possible functions for some hypothetical genes in prokaryotic genomes. The methods have proven a useful addition to structure information in deriving protein function in a structural genomics project.
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Affiliation(s)
- Yongpan Yan
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA
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9
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Dabizzi S, Ammannato S, Fani R. Expression of horizontally transferred gene clusters: activation by promoter-generating mutations. Res Microbiol 2001; 152:539-49. [PMID: 11501672 DOI: 10.1016/s0923-2508(01)01228-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The occurrence of promoter-generating mutations allowing the transcription of heterologous genes has been studied in a system based on the plasmid-mediated conjugal transfer of histidine biosynthetic genes from a donor bacterium (Azospirillum brasilense) into a heterologous Escherichia coli mutant population lacking histidine biosynthetic ability and initially unable to recognize the transcriptional signal of the introgressed gene(s). Under selective stressful conditions, His+ revertants accumulated in the E. coli His- culture. The number of His+ colonies was dependent on the time of incubation under selective conditions, the strength of selective pressure, and on the crowding of cells plated; moreover, it was independent of the physiological status of the cell (i.e. the growth phase). Sequence analysis of plasmid DNA extracted from E. coli His+ revertants revealed that single base substitutions in the region upstream of the A. brasilense his operon resulted in an adjustment of the pre-existing sequence that was rendered similar to the E. coli -10 promoter sequence and transcriptable by the host RNA-polymerase. One particular transition (C --> T) was predominant in the His+ revertants. Data presented here indicated that the barriers to the expression of horizontally transferred heterologous genes or operons may be overcome in a short time scale and at high frequency, and supported the selfish operon model on the origin and evolution of gene clusters.
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Affiliation(s)
- S Dabizzi
- Dipartimento di Biologia Animale e Genetica, Università di Firenze, Florence, Italy
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10
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Beismann-Driemeyer S, Sterner R. Imidazole glycerol phosphate synthase from Thermotoga maritima. Quaternary structure, steady-state kinetics, and reaction mechanism of the bienzyme complex. J Biol Chem 2001; 276:20387-96. [PMID: 11264293 DOI: 10.1074/jbc.m102012200] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Imidazole glycerol phosphate synthase, which links histidine and de novo purine biosynthesis, is a member of the glutamine amidotransferase family. In bacteria, imidazole glycerol phosphate synthase constitutes a bienzyme complex of the glutaminase subunit HisH and the synthase subunit HisF. Nascent ammonia produced by HisH reacts at the active site of HisF with N'-((5'-phosphoribulosyl)formimino)-5-aminoimidazole-4-carboxamide-ribonucleotide to yield the products imidazole glycerol phosphate and 5-aminoimidazole-4-carboxamide ribotide. In order to elucidate the interactions between HisH and HisF and the catalytic mechanism of the HisF reaction, the enzymes tHisH and tHisF from Thermotoga maritima were produced in Escherichia coli, purified, and characterized. Isolated tHisH showed no detectable glutaminase activity but was stimulated by complex formation with tHisF to which either the product imidazole glycerol phosphate or a substrate analogue were bound. Eight conserved amino acids at the putative active site of tHisF were exchanged by site-directed mutagenesis, and the purified variants were investigated by steady-state kinetics. Aspartate 11 appeared to be essential for the synthase activity both in vitro and in vivo, and aspartate 130 could be partially replaced only by glutamate. The carboxylate groups of these residues could provide general acid/base catalysis in the proposed catalytic mechanism of the synthase reaction.
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Affiliation(s)
- S Beismann-Driemeyer
- Universität zu Köln, Institut für Biochemie, Otto-Fischer-Str. 12-14, D-50674 Köln, Germany
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11
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Smulski DR, Huang LL, McCluskey MP, Reeve MJ, Vollmer AC, Van Dyk TK, LaRossa RA. Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12. J Bacteriol 2001; 183:3353-64. [PMID: 11344143 PMCID: PMC99633 DOI: 10.1128/jb.183.11.3353-3364.2001] [Citation(s) in RCA: 28] [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
Acivicin, a modified amino acid natural product, is a glutamine analog. Thus, it might interfere with metabolism by hindering glutamine transport, formation, or usage in processes such as transamidation and translation. This molecule prevented the growth of Escherichia coli in minimal medium unless the medium was supplemented with a purine or histidine, suggesting that the HisHF enzyme, a glutamine amidotransferase, was the target of acivicin action. This enzyme, purified from E. coli, was inhibited by low concentrations of acivicin. Acivicin inhibition was overcome by the presence of three distinct genetic regions when harbored on multicopy plasmids. Comprehensive transcript profiling using DNA microarrays indicated that histidine biosynthesis was the predominant process blocked by acivicin. The response to acivicin, however, was quite complex, suggesting that acivicin inhibition resonated through more than a single cellular process.
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Affiliation(s)
- D R Smulski
- Biochemical Science and Engineering, Central Research and Development, DuPont Company, Wilmington, DE 19880-0173, USA
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12
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Valerius O, Draht O, Kübler E, Adler K, Hoffmann B, Braus GH. Regulation of hisHF transcription of Aspergillus nidulans by adenine and amino acid limitation. Fungal Genet Biol 2001; 32:21-31. [PMID: 11277623 DOI: 10.1006/fgbi.2000.1244] [Citation(s) in RCA: 10] [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
The hisHF gene of Aspergillus nidulans encodes imidazole-glycerole-phosphate (IGP) synthase, consisting of a glutamine amidotransferase and a cyclase domain. The enzyme catalyzes the fifth and sixth steps of histidine biosynthesis, which results in an intermediate of the amino acid and an additional intermediate of purine biosynthesis. An A. nidulans hisHF cDNA complemented a Saccharomyces cerevisiae his7Delta strain and Escherichia coli hisH and hisF mutant strains. The genomic DNA encoding the hisHF gene was cloned and its sequence revealed two introns within the 1659-bp-long open reading frame. The transcription of the hisHF gene of A. nidulans is activated upon amino acid starvation, suggesting that hisHF is a target gene of cross pathway control. Adenine but not histidine, both end products of the biosynthetic pathways connected by the IGP synthase, represses hisHF transcription. In contrast to other organisms HISHF overproduction did not result in any developmental phenotype of the fungus in hyphal growth or the asexual life cycle. hisHF overexpression caused a significantly reduced osmotic tolerance and the inability to undergo the sexual life cycle leading to acleistothecial colonies.
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Affiliation(s)
- O Valerius
- Institute of Microbiology & Genetics, Georg-August University, Grisebachstrasse 8, Göttingen, D-37077, Germany
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13
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Abstract
This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.
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Affiliation(s)
- M K Berlyn
- Department of Biology and School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut 06520-8104, USA.
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14
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El Malki F, Frankard V, Jacobs M. Molecular cloning and expression of a cDNA sequence encoding histidinol phosphate aminotransferase from Nicotiana tabacum. PLANT MOLECULAR BIOLOGY 1998; 37:1013-22. [PMID: 9700073 DOI: 10.1023/a:1006007125448] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A Nicotiana tabacum cDNA sequence encoding histidinol phosphate aminotransferase (HPA) was isolated by functional complementation of an Escherichia coli histidine auxotroph (UTH780). The enzymatic assay has confirmed that the isolated cDNA encodes a functional HPA protein. Amino acid sequence alignment of the HPA protein from N. tabacum, Saccharomyces cerevisiae and E. coli revealed that, despite the low degree of identity, some residues were found to be highly conserved. The predicted protein contains a transit peptide sequence at the amino-terminal end, suggesting a chloroplastic localization of the HPA enzyme. Western blot analysis demonstrated that the deduced HPA protein and the mature HPA protein have an apparent molecular mass of about 45 kDa and 40 kDa respectively. Gene copy number estimation by Southern analysis indicates the presence of at least two genes per haploid genome coding for this protein in Nicotiana sp. From northern analysis results, the gene seems to be highly expressed in green tissues and the detected transcript showed a single band of expected molecular size.
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Affiliation(s)
- F El Malki
- Laboratory for Plant Genetics, Vrije Universiteit Brussel, Sint-Genesius Rode, Belgium
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15
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Fani R, Tamburini E, Mori E, Lazcano A, Liò P, Barberio C, Casalone E, Cavalieri D, Perito B, Polsinelli M. Paralogous histidine biosynthetic genes: evolutionary analysis of the Saccharomyces cerevisiae HIS6 and HIS7 genes. Gene X 1997; 197:9-17. [PMID: 9332345 DOI: 10.1016/s0378-1119(97)00146-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The HIS6 gene from Saccharomyces cerevisiae strain YNN282 is able to complement both the S. cerevisiae his6 and the Escherichia coli hisA mutations. The cloning and the nucleotide sequence indicated that this gene encodes a putative phosphoribosyl-5-amino-1-phosphoribosyl-4-imidazolecarboxiamide isomerase (5' Pro-FAR isomerase, EC 5.3.1.16) of 261 amino acids, with a molecular weight of 29,554. The HIS6 gene product shares a significant degree of sequence similarity with the prokaryotic HisA proteins and HisF proteins, and with the C-terminal domain of the S. cerevisiae HIS7 protein (homologous to HisF), indicating that the yeast HIS6 and HIS7 genes are paralogous. Moreover, the HIS6 gene is organized into two homologous modules half the size of the entire gene, typical of all the known prokaryotic hisA and hisF genes. The structure of the yeast HIS6 gene supports the two-step evolutionary model suggested by Fani et al. (J. Mol. Evol. 1994; 38: 489-495) to explain the present-day hisA and hisF genes. According to this idea, the hisF gene originated from the duplication of an ancestral hisA gene which, in turn, was the result of an earlier gene elongation event involving an ancestral module half the size of the extant gene. Results reported in this paper also suggest that these two successive paralogous gene duplications took probably place in the early steps of molecular evolution of the histidine pathway, well before the diversification of the three domains, and that this pathway was one of the metabolic activities of the last common ancestor. The molecular evolution of the yeast HIS6 and HIS7 genes is also discussed.
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Affiliation(s)
- R Fani
- Dipartimento di Biologia Animale e Genetica, Università degli Studi di Firenze, Italy.
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16
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Vinella D, D'Ari R. Thermoinducible filamentation in Escherichia coli due to an altered RNA polymerase beta subunit is suppressed by high levels of ppGpp. J Bacteriol 1994; 176:966-72. [PMID: 8106339 PMCID: PMC205146 DOI: 10.1128/jb.176.4.966-972.1994] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The Escherichia coli strain known as GC2553, FB8, UTH1038, or K12S (Luria), considered an F- lambda- wild-type strain, is shown here to carry a cryptic mutation, ftsR1, causing nonlethal filamentation during exponential growth in Luria-Bertani (LB) broth at 42 degrees C and the inability to grow in salt-free LB broth at 42 degrees C. The ftsR1 mutation is completely suppressed in genetic backgrounds which increase RelA-dependent synthesis of the nucleotide ppGpp, i.e., argS201 (Mecr) and alaS21 (Mecr) mutations, affecting aminoacyl-tRNA synthetases, or the presence of a plac-relA' plasmid. These backgrounds also confer resistance in LB broth to the beta-lactam mecillinam, an antibiotic which specifically inhibits penicillin-binding protein 2 and, in wild-type cells, causes an indirect block in cell division. Furthermore, the ftsR1 mutant (but not an isogenic ftsR+ strain) is sensitive to mecillinam in minimal glucose medium at 37 degrees C. Since the division block caused by mecillinam can be overcome by overproduction of the cell division protein FtsZ, we tested the effect of plasmid pZAQ (carrying the ftsZ, ftsA, and ftsQ genes) on the ftsR1 mutant; it suppressed the filamentation in LB broth and the mecillinam sensitivity on minimal glucose medium at 37 degrees C but not the growth defect in salt-free LB broth at 42 degrees C. Genetic analysis indicated that the full phenotype of the ftsR1 mutant is due to a single mutation in the rpoB gene (90 min), coding for the beta subunit of RNA polymerase; we call this allele rpoB369(Fts). We propose that the rpoB369(Fts) mutation alters the specificity of the polymerase and that the mutant enzyme can recover normal activity in the presence of high salt concentrations or via interaction with the nucleotide ppGpp.
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Affiliation(s)
- D Vinella
- Institut Jacques Monod (Centre National de la Recherche Scientifique, Université Paris 7), France
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17
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Apolinario E, Nocero M, Jin M, Hoffman CS. Cloning and manipulation of the Schizosaccharomyces pombe his7+ gene as a new selectable marker for molecular genetic studies. Curr Genet 1993; 24:491-5. [PMID: 8299169 PMCID: PMC4417482 DOI: 10.1007/bf00351711] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have cloned the his7+ gene of the fission yeast Schizosaccharomyces pombe by complementation of the recessive mutant allele his7-366. The his7+ gene is able to complement a mutation of the Escherichia coli hisI gene, suggesting that his7+ encodes a phosphoribosyl-AMP cyclohydrase. Subcloning experiments localize the gene to a 1.9-kb XbaI-BglII fragment. We describe the construction of plasmids to facilitate the use of his7+ as a selectable marker in S. pombe studies. Plasmid pEA2 carries his7+ cloned into the pUC18 polylinker. From either pEA2 or the original his7+ clone, pMN1, fragments carrying his7+ can be isolated using a variety of restriction enzymes for the construction of gene disruptions. Plasmid pEA500 is a cloning vector that carries his7+ and ars1, yet retains the ability to use the blue/white color screen to identify recombinants.
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Affiliation(s)
- E Apolinario
- Department of Biology, Boston College, Chestnut Hill, MA 02167
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18
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Abstract
A list of currently identified gene products of Escherichia coli is given, together with a bibliography that provides pointers to the literature on each gene product. A scheme to categorize cellular functions is used to classify the gene products of E. coli so far identified. A count shows that the numbers of genes concerned with small-molecule metabolism are on the same order as the numbers concerned with macromolecule biosynthesis and degradation. One large category is the category of tRNAs and their synthetases. Another is the category of transport elements. The categories of cell structure and cellular processes other than metabolism are smaller. Other subjects discussed are the occurrence in the E. coli genome of redundant pairs and groups of genes of identical or closely similar function, as well as variation in the degree of density of genetic information in different parts of the genome.
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Affiliation(s)
- M Riley
- Marine Biological Laboratory, Woods Hole, Massachusetts 02543
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19
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Johnson MS, Taylor BL. Comparison of methods for specific depletion of ATP in Salmonella typhimurium. Appl Environ Microbiol 1993; 59:3509-12. [PMID: 8250574 PMCID: PMC182486 DOI: 10.1128/aem.59.10.3509-3512.1993] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Three methods of ATP depletion in Salmonella typhimurium were compared. ATP concentrations were lowest after arsenate treatment. Arsenate or alpha-methylglucoside-plus-azide treatment nonspecifically lowered all nucleotide triphosphate levels. Histidine starvation in a hisF mutant was relatively specific for ATP depletion and therefore has potential in distinguishing ATP-dependent processes from processes dependent on other nucleotides.
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Affiliation(s)
- M S Johnson
- Department of Microbiology, Loma Linda University School of Medicine, California 92350
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20
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Bouloc P, Vinella D, D'Ari R. Leucine and serine induce mecillinam resistance in Escherichia coli. MOLECULAR & GENERAL GENETICS : MGG 1992; 235:242-6. [PMID: 1465098 DOI: 10.1007/bf00279366] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have previously shown that resistance to the beta-lactam mecillinam in Escherichia coli can be brought about by a high ppGpp pool, as observed under conditions of partial amino acid starvation and RelA-dependent induction of the stringent response. We show here that our E. coli wild-type strain, which is sensitive to mecillinam on minimal glucose plates, becomes resistant in the presence of L-leucine or L-serine (or cysteine, which inactivates the antibiotic). The resistance, which is not a transient effect and does not depend on the physiological state of the cells when plated, is specific for mecillinam and is reversed by the presence of isoleucine and valine in the medium. At least in the case of serine, the resistance is RelA-dependent. We conclude that the presence of leucine and serine in the growth medium cause partial starvation for isoleucine/valine, leading to induction of the stringent response and concomitant resistance to mecillinam.
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Affiliation(s)
- P Bouloc
- Institut Jacques Monod, CNRS, Université Paris, France
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21
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Abstract
The genes of Lactococcus lactis subsp. lactis involved in histidine biosynthesis were cloned and characterized by complementation of Escherichia coli and Bacillus subtilis mutants and DNA sequencing. Complementation of E. coli hisA, hisB, hisC, hisD, hisF, hisG, and hisIE genes and the B. subtilis hisH gene (the E. coli hisC equivalent) allowed localization of the corresponding lactococcal genes. Nucleotide sequence analysis of the 11.5-kb lactococcal region revealed 14 open reading frames (ORFs), 12 of which might form an operon. The putative operon includes eight ORFs which encode proteins homologous to enzymes involved in histidine biosynthesis. The operon also contains (i) an ORF encoding a protein homologous to the histidyl-tRNA synthetases but lacking a motif implicated in synthetase activity, which suggests that it has a role different from tRNA aminoacylation, and (ii) an ORF encoding a protein that is homologous to the 3'-aminoglycoside phosphotransferases but does not confer antibiotic resistance. The remaining ORFs specify products which have no homology with proteins in the EMBL and GenBank data bases.
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Affiliation(s)
- C Delorme
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
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22
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Fani R, Bazzicalupo M, Damiani G, Bianchi A, Schipani C, Sgaramella V, Polsinelli M. Cloning of histidine genes of Azospirillum brasilense: organization of the ABFH gene cluster and nucleotide sequence of the hisB gene. MOLECULAR & GENERAL GENETICS : MGG 1989; 216:224-9. [PMID: 2664449 DOI: 10.1007/bf00334360] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A cluster of four Azospirillum brasilense histidine biosynthetic genes, hisA, hisB, hisF and hisH, was identified on a 4.5 kb DNA fragment and its organization studied by complementation analysis of Escherichia coli mutations and nucleotide sequence. The nucleotide sequence of a 1.3 kb fragment that complemented the E. coli hisB mutation was determined and an ORF of 624 nucleotides which can code for a protein of 207 amino acids was identified. A significant base sequence homology with the carboxy-terminal moiety of the E. coli hisB gene (0.53) and the Saccharomyces cerevisiae HIS3 gene (0.44), coding for an imidazole glycerolphosphate dehydratase activity was found. The amino acid sequence and composition, the hydropathic profile and the predicted secondary structures of the yeast, E. coli and A. brasilense proteins were compared. The significance of the data presented is discussed.
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Affiliation(s)
- R Fani
- Dipartimento di Biologia Animale e Genetica, Università di Firenze, Italy
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23
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Carlomagno MS, Chiariotti L, Alifano P, Nappo AG, Bruni CB. Structure and function of the Salmonella typhimurium and Escherichia coli K-12 histidine operons. J Mol Biol 1988; 203:585-606. [PMID: 3062174 DOI: 10.1016/0022-2836(88)90194-5] [Citation(s) in RCA: 123] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We have determined the complete nucleotide sequence of the histidine operons of Escherichia coli and of Salmonella typhimurium. This structural information enabled us to investigate the expression and organization of the histidine operon. The proteins coded by each of the putative histidine cistrons were identified by subcloning appropriate DNA fragments and by analyzing the polypeptides synthesized in minicells. A structural comparison of the gene products was performed. The histidine messenger RNA molecules produced in vivo and the internal transcription initiation sites were identified by Northern blot analysis and S1 nuclease mapping. A comparative analysis of the different transcriptional and translational control elements within the two operons reveals a remarkable preservation for most of them except for the intercistronic region between the first (hisG) and second (hisD) structural genes and for the rho-independent terminator of transcription at the end of the operon. Overall, the operon structure is very compact and its expression appears to be regulated at several levels.
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Affiliation(s)
- M S Carlomagno
- Centro di Endocrinologia ed Oncologia, Sperimentale del Consiglio, Nazionale delle Ricerche, University of Naples, Napoli, Italy
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24
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Tsygankov YD, Kazakova SM. Development of gene transfer systems in Methylobacillus flagellatum KT: Isolation of auxotrophic mutants. Arch Microbiol 1987. [DOI: 10.1007/bf00425075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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25
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Cloning of the histidine, pyrimidine and cysteine genes of Azospirillum brasilense: Expression of pyrimidine and three clustered histidine genes in Escherichia coli. ACTA ACUST UNITED AC 1987. [DOI: 10.1007/bf00326539] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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26
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Shillitoe EJ, Matney TS, Conley AJ. Induction of mutations in bacteria by a fragment of DNA from herpes simplex virus type 1. Virus Res 1986; 6:181-91. [PMID: 3026115 DOI: 10.1016/0168-1702(86)90049-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A bacterial assay was developed for the study of mutagenesis by DNA of herpes simplex viruses. The histidine mutations from two of the Ames mutagenesis tester strains were recombined into the Salmonella histidine operon of the F'8 plasmid and each was transferred to a derivative strain of E. coli C from which the resident histidine operon had been deleted. One tester strain could be reverted by a chemical mutagen which induces frameshift mutations and the other could be reverted by a mutagen which induces base-pair substitution mutations. The BamHI G fragment of herpes simplex virus type 1 was cloned in each orientation into the BamHI site of the expression vectors pUC7, pUC8 and pUC9 and were introduced into the new strains of E. coli. The pUC9 plasmid carrying the BamHI G fragment of herpes simplex virus type 1 with the G-E' site closest to the lac promoter showed a higher rate of reversion in the frameshift strain, which varied up to 39-fold greater than the background rate. Since many mutagens are carcinogenic these data suggest the existence of a mutagenic peptide of herpes simplex virus type 1 which might be involved in cell transformation.
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27
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Beckler GS, Reeve JN. Conservation of primary structure in the hisI gene of the archaebacterium, Methanococcus vannielii, the eubacterium Escherichia coli, and the eucaryote Saccharomyces cerevisiae. MOLECULAR & GENERAL GENETICS : MGG 1986; 204:133-40. [PMID: 3018439 DOI: 10.1007/bf00330200] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A 2.7 kilobase pair (Kb) fragment of DNA, which complements mutations in the hisI locus of Escherichia coli, has been cloned and sequenced from the genome of the methanogenic archaebacterium Methanococcus vannielii. The cloned DNA directs the synthesis of three polypeptides, with molecular weights of 71,000, 29,000 and 15,600 in minicells of E. coli. Subcloning and mutagenesis demonstrates that hisI complementation results from the activity of the 15,600 molecular weight polypeptide. The primary structure of this archaebacterial gene and its gene product have been compared with the functionally equivalent gene and protein from the eubacterium E. coli (hisI) (Chiariotti et al. 1986) and from the eucaryote Saccharomyces cerevisiae (his4A) (Donahue et al. 1982). The DNA sequences of the archaebacterial and eubacterial genes are 40% homologous, the archaebacterial and eucaryotic DNA sequences are 47% homologous and, as previously reported (Bruni et al. 1986) the eubacterial and eucaryotic DNA sequences are 45% homologous. In E. coli the hisI locus is part of a bifunctional gene (hisI/E) within the single his operon. In S. cerevisiae the his4A locus is part of a multifunctional gene (his4) which encodes a protein with at least four enzymatic activities. The his genes of S. cerevisiae do not form an operon and are not physically linked. The M. vannielii hisI gene does not appear to be part of a multifunctional DNA sequence and, although it does appear to be within an operon, the open reading frames (ORFs) 5' and 3' to the M. vannielii hisI gene are not related to any published his sequences.(ABSTRACT TRUNCATED AT 250 WORDS)
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28
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Chiariotti L, Nappo AG, Carlomagno MS, Bruni CB. Gene structure in the histidine operon of Escherichia coli. Identification and nucleotide sequence of the hisB gene. MOLECULAR & GENERAL GENETICS : MGG 1986; 202:42-7. [PMID: 3007936 DOI: 10.1007/bf00330514] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The bifunctional enzyme imidazoleglycerolphosphate dehydratase and histidinolphosphate phosphatase is encoded by the hisB gene. The fourth gene of the histidine operon, hisB, was cloned and mapped on a 2,300 base pair DNA fragment. In the present study we report the complete nucleotide sequence of the hisB gene of Escherichia coli. The gene is 1,068 nucleotides long and codes for a protein of 355 amino acids with an apparent molecular weight of 39,998 daltons. The protein product(s) of the hisB region of both Salmonella typhimurium and E. coli were identified by subcloning and expression in an in vitro translation system. In both organisms the hisB gene directed the synthesis of a single protein with an apparent molecular weight of 40,500 daltons, consistent with the data derived from the nucleotide sequence analysis.
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29
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Hutchinson F, Wood RD. Mechanisms of mutagenesis of E. coli by ultraviolet light. BASIC LIFE SCIENCES 1986; 38:377-83. [PMID: 2943265 DOI: 10.1007/978-1-4615-9462-8_41] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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30
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Grisolia V, Riccio A, Bruni CB. Structure and function of the internal promoter (hisBp) of the Escherichia coli K-12 histidine operon. J Bacteriol 1983; 155:1288-96. [PMID: 6309747 PMCID: PMC217827 DOI: 10.1128/jb.155.3.1288-1296.1983] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The entire histidine operon of Escherichia coli K-12 was cloned in the vector plasmid pBR313, and a complete restriction map of the operon was determined. By using subclones, complementation tests, and enzyme assays, we were able to make a correlation between the physical map and the genetic map of the operon. We determined the sequence of a fragment of DNA 665 base pairs long, comprising the distal portion of the hisC gene, the proximal portion of the hisB gene, and the internal transcription initiation site hisBp. The efficiency of this promoter was assessed under different physiological conditions by cloning the DNA fragment in a recombinant vector system used to study transcriptional regulatory signals. The precise point at which transcription initiates was determined by S1 nuclease mapping.
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31
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Carlomagno MS, Blasi F, Bruni CB. Gene organization in the distal part of the Salmonella typhimurium histidine operon and determination and sequence of the operon transcription terminator. MOLECULAR & GENERAL GENETICS : MGG 1983; 191:413-20. [PMID: 6314092 DOI: 10.1007/bf00425756] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Several transducing phages, carrying different deletions of the Salmonella typhimurium histidine operon were constructed and mapped. These phages were used to obtain fragments of DNA comprising different regions of the operon, which were subcloned in plasmid vectors. The recombinant plasmids allowed the construction of a physical and restriction map of the histidine operon. The presence of the different genes on individual fragments was confirmed by complementation tests. The transcription termination site of the histidine operon has been established by S1 mapping and sequence analysis. The entire operon measures about 7100 base pairs and the last six structural genes are contained in 3450 bases of genetic materials.
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32
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Grisolia V, Carlomagno MS, Bruni CB. Cloning and expression of the distal portion of the histidine operon of Escherichia coli K-12. J Bacteriol 1982; 151:692-700. [PMID: 6284708 PMCID: PMC220310 DOI: 10.1128/jb.151.2.692-700.1982] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The operator-distal genes hisBHAFI(E) of the Escherichia coli K-12 histidine operon were mapped on a DNA fragment 4,500 base pairs long. This fragment, originally present in a lambda transducing phage, was cloned in the vector plasmid pBR313. A restriction map was determined, allowing identification of the orientation of the genes in the fragment. The cloned genes were expressed in appropriate hosts, independent of the orientation of the DNA fragment, as shown by transformation tests and by enzyme assays of one of the gene products, hisB, histidinol phosphatase. An internal transcription initiation site was identified by isolation of the cellular RNA, hybridization to specific DNA probes, and mapping by S1 nuclease.
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33
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Verde P, Frunzio R, di Nocera PP, Blasi F, Bruni CB. Identification, nucleotide sequence and expression of the regulatory region of the histidine operon of Escherichia coli K-12. Nucleic Acids Res 1981; 9:2075-86. [PMID: 6170941 PMCID: PMC326827 DOI: 10.1093/nar/9.9.2075] [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: 01/18/2023] Open
Abstract
A restriction fragment has been isolated and its nucleotide sequence determined. This fragment contains sites for RNA polymerase binding, initiation and termination of transcription of the Escherichia coli histidine operon. In vitro transcription of plasmids containing this region generates one single histidine-specific, attenuated, small RNA: the leader RNA. This RNA is more efficiently transcribed when the template DNA is supercoiled. Another promoter was identified on the same fragment of deoxyribonucleic acid by in vitro transcription, DNA sequencing and RNA polymerase binding. Both promoters, transcribing in opposite direction, are very A-T rich and are separated by a G-C rich region containing a palyndromic structure.
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34
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Jensen RA, Calhoun DH. Intracellular roles of microbial aminotransferases: overlap enzymes across different biochemical pathways. Crit Rev Microbiol 1981; 8:229-66. [PMID: 7009061 DOI: 10.3109/10408418109085080] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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35
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Blasi F, Bruni CB. Regulation of the histidine operon: translation-controlled transcription termination (a mechanism common to several biosynthetic operons). CURRENT TOPICS IN CELLULAR REGULATION 1981; 19:1-45. [PMID: 6277571 DOI: 10.1016/b978-0-12-152819-5.50018-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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36
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Bruni CB, Musti AM, Frunzio R, Blasi F. Structural and physiological studies of the Escherichia coli histidine operon inserted into plasmid vectors. J Bacteriol 1980; 142:32-42. [PMID: 6246067 PMCID: PMC293896 DOI: 10.1128/jb.142.1.32-42.1980] [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] Open
Abstract
A fragment of deoxyribonucleic acid 5,300 base paris long and containing the promoter-proximal portion of the histidine operon of Escherichia coli K-12, has been cloned in plasmid pBR313 (plasmids pCB2 and pCB3). Restriction mapping, partial nucleotide sequencing, and studies on functional expression in vivo and on protein synthesis in minicells have shown that the fragment contains the regulatory region of the operon, the hisG, hisD genes, and part of the hisC gene. Another plasmid (pCB5) contained the hisG gene and part of the hisD gene. Expression of the hisG gene in the latter plasmid was under control of the tetracycline promoter of the pBR313 plasmid. The in vivo expression of the two groups of plasmids described above, as well as their effect on the expression of the histidine genes not carried by the plasmids but present on the host chromosome, has been studied. The presence of multiple copies of pCB2 or pCB3, but not of pCB5, prevented derepression of the chromosomal histidine operon. Possible interpretations of this phenomenon are discussed.
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37
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Abstract
DMS and DES are monofunctional alkylating agents that have been shown to induce mutations, chromosomal aberrations, and other genetic alterations in a diversity of organisms. They have also been shown to be carcinogenic in animals. As an alkylating agent, DMS is a typical SN2 agent, attacking predominantly nitrogen sites in nucleic acids. DES is capable of SN1 alkylations as well as SN2 and thereby causes some alkylation on oxygen sites including the O6-position of guanine which is thought to be significant in mutagenesis by direct mispairing. The mutagenicity of DMS is better explained in terms of indirect, repair-dependent processes. With respect to both alkylating activity and genetic effects, striking similarities are found between DMS and MMS and between DES and EMS. In most systems where they have been tested, both DMS and DES are mutagenic. Results of many of the mutagenesis studies involving these compounds and other alkylating sulfuric acid esters are summarized in Tables 6, 7, 8, 9 and 10 of this review. Most data are consistent with these agents acting primarily as base-pair substitution mutagens. In the case of DES, strong specificity for G.C to A.T transitions has been reported in some systems but has not been clearly supported in some others. Low levels of frameshift mutations of the deletion type are also likely. In addition to the induction of mutations, recombinogenic and clastogenic effects have been described.
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38
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Norin AJ, Goldschmidt EP. Effect of mutagens, chemotherapeutic agents and defects in DNA repair genes on recombination in F' partial diploid Escherichia coli. Mutat Res 1979; 59:15-26. [PMID: 372790 DOI: 10.1016/0027-5107(79)90191-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The ability of mutagenic agents, nonmutagenic substances and defects in DNA repair to alter the genotype of F' partial diploid (F30) Escherichia coli was determined. The frequency of auxotrophic mutants and histidine requiring (His-) haploid colonies was increased by mutagen treatment but Hfr colonies were not detected in F30 E. coli even with specific selection techniques. Genotype changes due to nonreciprocal recombination were determined by measuring the frequency of His- homogenotes, eg. F' hisC780, hisI+/hisC780, hisI+, arising from a His+ heterogenote, F' hisC780 hisI+/hisC+, his1903. At least 75% of the recombinants were homozygous for histidine alleles which were present on the F' plasmid (exogenote) of the parental hetergenote rather than for histidine alleles on the chromosome. Mutagens, chemotherapeutic agents which histidine alleles on the chromosome. Mutagens, chemotherapeutic agents which block DNA synthesis and a defective DNA polymerase I gene, polA1, were found to increase the frequency of nonreciprocal recombination. A defect in the ability to excise thymine dimers, uvrC34, did not increase spontaneous nonreciprocal recombination. However, UV irradiation but not methyl methanesulfonate (MMS) induced greater recombination in this excision-repair defective mutant than in DNA-repair-proficient strains. Mutagenic agents, with the exception of ethyl methanesulfonate (EMS), induced greater increases in recombination than the chemotherapeutic agents or the polA1 mutation. EMS, which causes relatively little degradation of DNA, was more mutagenic but less recombinogenic than MMS, a homologous compound ths that inhibition of DNA occurring single-stranded regions in replicative intermediates of the DNA. Mutagens which cause the rapid breakdown of DNA may, in addition, introduce lesions into the genome that increase the number of single-stranded regions thus inducing even higher frequencies of recombination.
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39
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Di Nocera PP, Blasi F, Di Lauro R, Frunzio R, Bruni CB. Nucleotide sequence of the attenuator region of the histidine operon of Escherichia coli K-12. Proc Natl Acad Sci U S A 1978; 75:4276-80. [PMID: 360215 PMCID: PMC336096 DOI: 10.1073/pnas.75.9.4276] [Citation(s) in RCA: 84] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The attenuator region of the histidine operon of Escherichia coli K-12 has a potential coding capacity for two peptides, one of 16 amino acids and another of 30 amino acids. This region is followed by a perfect palindrome of 14 base pairs separated by five nucleotides. A G+C-rich region precedes and follows a possible transcription termination sequence. These features are compatible with a model in which active translation of a leader mRNA interferes with transcription termination, thus causing derepression of the histidine operon. The sequence of the region coding for the hypothetical 16-amino acid peptide is of particular relevance because it indicates the site and a possible mechanism of action of histidyl-tRNAhis in regulating histidine gene expression. Seven contiguous histidine codons are present within this sequence: : formula: (see text)
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40
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Cannon FC, Riedel GE, Ausubel FM. Recombinant plasmid that carries part of the nitrogen fixation (nif) gene cluster of Klebsiella pneumoniae. Proc Natl Acad Sci U S A 1977; 74:2963-7. [PMID: 331321 PMCID: PMC431364 DOI: 10.1073/pnas.74.7.2963] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We have cloned fragments of the Klebsiella pneumoniae genome that carry part of the his operon and part of the nitrogen fixation (nif) gene cluster on the amplifiable plasmid pMB9. One particular plasmid, pCRA37, complements mutations in the hisD, nifB, and nifF loci. The physical map of pCRA37 as determined by restriction enzyme analysis correlates with the genetic map of the his-nif region as determined previously by phage P1-mediated cotransductional analysis.
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41
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Bruni CB, Colantuoni V, Sbordone L, Cortese R, Blasi F. Biochemical and regulatory properties of Escherichia coli K-12 hisT mutants. J Bacteriol 1977; 130:4-10. [PMID: 323237 PMCID: PMC235167 DOI: 10.1128/jb.130.1.4-10.1977] [Citation(s) in RCA: 76] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Escherichia coli K-12 hisT mutants were isolated, and their properties were studied. These mutants are derepressed for the histidine operon, map close to the purF locus at about 49.5 min on the E. coli linkage map, and lack pseudouridylate synthetase activity. The defect in this enzyme leads to the absence of pseudouridines in the anticodon loop of several transfer ribonucleic acid species, as evidenced by the altered elution profile on reversed-phase chromatography and resistance to amino acid analogues. Finally, the hisT mutants studied have a reduced growth rate that appears to be linked to hisT, although it is not known whether it is due to the same mutation. The normal generation time can be restored by supplementing the medium with adenine, uracil, and isoleucine.
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Borck K, Beggs JD, Brammar WJ, Hopkins AS, Murray NE. The construction in vitro of transducing derivatives of phage lambda. MOLECULAR & GENERAL GENETICS : MGG 1976; 146:199-207. [PMID: 785220 DOI: 10.1007/bf00268089] [Citation(s) in RCA: 254] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Methods are described for the construction of plaque-forming, transducing derivatives of phage lambda, using appropirate receptor genomes and fragments of DNA generated by the restriction enzymes endo R.EcoRI and endo R.HindIII. The general properties of the transducing derivatives are described and discussed. Plaque-forming phages carrying the E. coli trp, his, cysB, thyA, supD, supE, sup F, hsd, tna and lig genes have been isolated.
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Bachmann BJ, Low KB, Taylor AL. Recalibrated linkage map of Escherichia coli K-12. BACTERIOLOGICAL REVIEWS 1976; 40:116-67. [PMID: 773363 PMCID: PMC413944 DOI: 10.1128/br.40.1.116-167.1976] [Citation(s) in RCA: 845] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Avitabile A, Bruni CB, Covelli A, Di Nocera PP, Sbordone L, Blasi F. In vitro transcription of the Escherichia coli histidine operon. MOLECULAR & GENERAL GENETICS : MGG 1974; 132:1-12. [PMID: 4608432 DOI: 10.1007/bf00268225] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Kang SS. A new type of suppression of temperature sensitive gene activity in Escherichia coli. MOLECULAR & GENERAL GENETICS : MGG 1974; 128:87-92. [PMID: 4595782 DOI: 10.1007/bf00267296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Tebar AR, Fernandez VM, Martin Del Rio R, Ballesteros AO. Studies on the quaternary structure of the first enzyme for histidine biosynthesis. EXPERIENTIA 1973; 29:1477-9. [PMID: 4358959 DOI: 10.1007/bf01943865] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Mosteller RD, Mandula BB. Kinetics of derepression of the tryptophan operon of Escherichia coli and Salmonella typhimurium under different culture conditions. J Mol Biol 1973; 80:801-23. [PMID: 4589650 DOI: 10.1016/0022-2836(73)90211-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Avitabile A, Bruni CB, Carlomagno-Cerillo MS, Meyers M, Vigliar G, Blasi F. Deletion mapping and orientation of the histidine operon of Escherichia coli on a transducing bacteriophage. J Bacteriol 1973; 116:656-62. [PMID: 4583246 PMCID: PMC285430 DOI: 10.1128/jb.116.2.656-662.1973] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The defective prophage phi80ilambdac(I)857dhis has been mapped through both marker rescue and deletion analysis. Deletions have been isolated which put residual his genes close to trp genes. Analysis of these deletions shows that the histidine operon on the prophage is oriented clockwise as on the bacterial chromosome, thus opposite to the orientation of the trp operon. The presence of the his promoter-operator region is inferred by the ability of the prophage-carrying strain to derepress sequentially under conditions in which the histidine concentration is limiting. In addition to his, the gnd gene is also present on the prophage and is located between his and trp operons. The bacterial genes are inserted in the right arm of the prophage and substitute for all of the late function genes, except for the first three. These data indicate that the "sense" strand for transcription of the his operon in vivo must be the "R" strand.
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Abstract
The approximate genetic map locations of auxotrophic and conditional lethal mutations of Escherichia coli can be rapidly determined with replica plating techniques. A set of patches of 15 streptomycin-sensitive (Str(S)) Hfr strains with points of origin distributed around the map is replica plated onto a recombinant-selective plate with a lawn of Str(R) cells which carry an unmapped mutation. The map interval defined by the Hfr points of origin which are closest to the mutant locus is seen by the presence or absence of heavy patches of recombinants produced by transfer of early wild-type genes from the Hfrs. An alternative method is to replicate patches of different mutant strains (100 per plate) onto Hfr lawns; in this case more than 1,000 different mutants can be mapped in a single experiment in a few days. In this way, many types of mutations with similar phenotypes can be grouped as to approximate location on the genetic map. For ordering mutations within groups, the same replica plating methods can be used to cross F-prime derivatives of mutants with other mutants of the same group. Relative merits of these and other mapping methods of E. coli are discussed.
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Avitabile A, Carlomagno-Cerillo S, Favvre R, Blasi F. Isolation of transducing bacteriophages for the histidine and isoleucine-valine operons in Escherichia coli K-12. J Bacteriol 1972; 112:40-7. [PMID: 4562404 PMCID: PMC251378 DOI: 10.1128/jb.112.1.40-47.1972] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
In vitro studies have been of great value in elucidating the mechanism of the regulation of several bacterial operons. To obtain a deoxyribonucleic acid preparation enriched for the histidine (his) and for the isoleucine-valine (ilv) operons, we have isolated bacteriophages carrying the his and the ilv regions of the Escherichia coli chromosome. Transposition of the his operon to a site close to the att80 region of the E. coli chromosome has been carried out selecting for integration of a temperature-sensitive F'his(+) in the tonB locus. This transposed strain has been lysogenized with phi80i(lambda). Upon induction of the lysogen, His(+) transductants have been isolated, which, on further induction give rise to HFT (high frequency of transduction) lysates. Preliminary characterization of the transducing phage is reported. The ilv operon, carried on an F' particle, has been fused to an episome carrying the att80 region. The fused episome has been lysogenized with phi80i lambdat68. Upon induction of the lysogen, Ilv(+) transductants have been isolated which on further induction give rise to HFT lysates.
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