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Grigaitis P, Olivier BG, Fiedler T, Teusink B, Kummer U, Veith N. Protein cost allocation explains metabolic strategies in Escherichia coli. J Biotechnol 2020; 327:54-63. [PMID: 33309962 DOI: 10.1016/j.jbiotec.2020.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/15/2020] [Accepted: 11/01/2020] [Indexed: 12/14/2022]
Abstract
In-depth understanding of microbial growth is crucial for the development of new advances in biotechnology and for combating microbial pathogens. Condition-specific proteome expression is central to microbial physiology and growth. A multitude of processes are dependent on the protein expression, thus, whole-cell analysis of microbial metabolism using genome-scale metabolic models is an attractive toolset to investigate the behaviour of microorganisms and their communities. However, genome-scale models that incorporate macromolecular expression are still inhibitory complex: the conceptual and computational complexity of these models severely limits their potential applications. In the need for alternatives, here we revisit some of the previous attempts to create genome-scale models of metabolism and macromolecular expression to develop a novel framework for integrating protein abundance and turnover costs to conventional genome-scale models. We show that such a model of Escherichia coli successfully reproduces experimentally determined adaptations of metabolism in a growth condition-dependent manner. Moreover, the model can be used as means of investigating underutilization of the protein machinery among different growth settings. Notably, we obtained strongly improved predictions of flux distributions, considering the costs of protein translation explicitly. This finding in turn suggests protein translation being the main regulation hub for cellular growth.
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Affiliation(s)
- Pranas Grigaitis
- Modeling of Biological Processes, BioQuant/Center for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany; Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU Amsterdam, De Boelelaan 1085, NL-1081HZ Amsterdam, The Netherlands
| | - Brett G Olivier
- Modeling of Biological Processes, BioQuant/Center for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany; Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU Amsterdam, De Boelelaan 1085, NL-1081HZ Amsterdam, The Netherlands
| | - Tomas Fiedler
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical Center, Schillingallee 70, D-18055 Rostock, Germany
| | - Bas Teusink
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU Amsterdam, De Boelelaan 1085, NL-1081HZ Amsterdam, The Netherlands
| | - Ursula Kummer
- Modeling of Biological Processes, BioQuant/Center for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany
| | - Nadine Veith
- Modeling of Biological Processes, BioQuant/Center for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany.
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Chen JW, Bennett DC, Umbarger HE. Specificity of attenuation control in the ilvGMEDA operon of Escherichia coli K-12. J Bacteriol 1991; 173:2328-40. [PMID: 1706705 PMCID: PMC207786 DOI: 10.1128/jb.173.7.2328-2340.1991] [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: 12/28/2022] Open
Abstract
Three different approaches were used to examine the regulatory effects of the amino acids specified by the peptide-coding region of the leader transcript of the ilvGMEDA operon of Escherichia coli K-12. Gene expression was examined in strains carrying an ilvGMED'-lac operon fusion. In one approach, auxotrophic derivatives were starved of single amino acids for brief periods, and the burst of beta-galactosidase synthesis upon adding the missing amino acid was determined. Auxotrophic derivatives were also grown for brief periods with a limited supply of one amino acid (derepression experiments). Finally, prototrophic strains were grown in minimal medium supplemented with single and multiple supplements of the chosen amino acids. Although codons for arginine, serine, and proline are interspersed among the codons for the three branched-chain (regulatory) amino acids, they appeared to have no effect when added in excess to prototrophs or when supplied in restricted amounts to auxotrophs. Deletions removing the terminator stem from the leader removed all ilv-specific control, indicating that the attenuation mechanism is the sole mechanism for ilv-specific control.
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Affiliation(s)
- J W Chen
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
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3
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Lawther RP, Calhoun DH, Adams CW, Hauser CA, Gray J, Hatfield GW. Molecular basis of valine resistance in Escherichia coli K-12. Proc Natl Acad Sci U S A 1981; 78:922-5. [PMID: 7015336 PMCID: PMC319916 DOI: 10.1073/pnas.78.2.922] [Citation(s) in RCA: 141] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The relationship of valine resistance to the expression of the ilvGEDA operon of Escherichia coli K-12 has been determined. DNA sequence and in vivo protein analyses indicate that in wild-type E. coli K-12 there is a frameshift site within the gene (ilvG) for valine resistance. The ilvG+2096 (formerly designated ilv02096) mutation displaces this frameshift site, resulting in the expression of ilvG and the relief of transcriptional polarity on the distal genes of this operon. Thus, the "ilv0" mutation, which concomitantly confers valine resistance and increased expression of the ilvEDA genes, is, in fact, the "reversion" of a polar site within the first structural gene of the ilvGEDA operon.
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4
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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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5
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Daniel J, Danchin A. Involvement of cyclic AMP and its receptor protein in the sensitivity of Escherichia coli K 12 toward serine: excretion of 2-ketobutyrate, a precursor of isoleucine. MOLECULAR & GENERAL GENETICS : MGG 1979; 176:343-50. [PMID: 230407 DOI: 10.1007/bf00333096] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A relationship between serine-induced growth sensitivity and the cAMP-CAP complex is established. Mutants of Escherichia coli K 12 deficient either in the cya or crp gene function exhibit a resistant phenotype on serine media although they harbor a relA allele normally leading to sensitivity toward serine. The presence of a crp allele in a cya delta relA background restores the sensitivity phenotype, while the analysis of serine resistant mutants selected from a crp cya delta relA strain shows that the mutation leading to resistance is located at, or very near, the crp gene, giving a more or less Crp- phenotype. In addition crp cya delta relA strains excrete large quantities of 2-ketobutyrate when grown on glucose M63 medium. This excretion is unambiguously linked to the presence of the crp allele and is correlated with an enhanced threonine deaminase activity. Besides, the complex regulation exerted on the acetolactate synthase activities is discussed.
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6
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De Felice M, Levinthal M, Iaccarino M, Guardiola J. Growth inhibition as a consequence of antagonism between related amino acids: effect of valine in Escherichia coli K-12. Microbiol Rev 1979; 43:42-58. [PMID: 379577 PMCID: PMC281461 DOI: 10.1128/mr.43.1.42-58.1979] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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7
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Lawther RP, Hatfield GW. Effects of altered rho gene product on the expression of the Escherichia coli histidine operon. J Bacteriol 1978; 136:1201-4. [PMID: 214421 PMCID: PMC218560 DOI: 10.1128/jb.136.3.1201-1204.1978] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
An altered rho gene product affects expression of the his operon of Escherichia coli. The effect is greater for the operator proximal portion of the his operon than for the operator distal portion. This "rho effect" appears to be independent of the site of action of hisT-altered histidyl-tRNA.
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8
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Lawther RP, Hatfield GW. A site of action for tRNA mediated regulation of the ilvOEDA operon of Escherichia coli K12. MOLECULAR & GENERAL GENETICS : MGG 1978; 167:227-34. [PMID: 366386 DOI: 10.1007/bf00266916] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Transfer RNA (tRNA), rho factor threonine deaminase and the ilvO locus are molecular participants in the regulation of isoleucine-valine (ilv) biosynthesis. Isogenic strains have been constructed with the hisT76 mutation in pairwise combination with ilvO mutations, the rho221 mutation and the ilvDAC115 deletion mutation. The role of the altered tRNA of the hisT76 mutation was found to be independent of the sites of action of the ilvO- mutation, rho factor, and threonine deaminase. The expression of the ilvOEDA operon is stimulated 2-fold when the hisT76 mutation is present in strains containing either ilvO- or rho221 mutations. The expression of the ilvOEDA operon remains nonrepressed in a hisT76 strain deleted for threonine deaminase. These results indicate that the hisT76 undermodified tRNAs are influencing the initiation of transcription of the ilvOEDA operon.
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Abstract
Expression of the Escherichia coli histidine operon was measured in four independently isolated sets of strains carrying ten different rho mutations. Rho factor does not act as a major regulatory element of histidine operon attenuation.
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10
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Iaccarino M, Guardiola J, De Felice M, Favre R. Regulation of isoleucine and valine biosynthesis. CURRENT TOPICS IN CELLULAR REGULATION 1978; 14:29-73. [PMID: 365469 DOI: 10.1016/b978-0-12-152814-0.50006-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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12
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Davis MG, Calvo JM. Relationship between messenger ribonucleic acid and enzyme levels specified by the leucine operon of Escherichia coli K-12. J Bacteriol 1977; 131:997-1007. [PMID: 330509 PMCID: PMC235558 DOI: 10.1128/jb.131.3.997-1007.1977] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The levels of leucine-forming enzymes in Escherichia coli K-12 varied over a several thousand-fold range, depending upon conditions of growth. The highest levels were achieved by growing auxotrophs in a chemostat under conditions of leucine limitation. Under such conditions, enzyme levels were increased 45- to 90-fold relative to cells grown in minimal medium containing leucine (the latter values arbitrarily called 1). Leucine operon-specific messenger ribonucleic acid levels were elevated to about the same extent as enzyme levels in cells grown in a chemostat. Growth in media of greater complexity resulted in progressively lower levels of leucine-forming enzymes, reaching a value of less than 0.02 for growth in a medium containing tryptone broth and yeast extract. The levels of leucine operon-specified enzymes and messenger ribonucleic acid were also measured in strains containing about 25 copies of plasmid pCV1(ColE1-leu) per chromosome. For such strains grown in minimal medium, enzyme levels were proportional to the number of plasmids per cell. Furthermore, they followed the same trends as those described above upon derepression in a chemostat or upon repression following growth in rich media. Leucine messenger ribonucleic acid, measured both by pulse-labeling and hybridization-competition experiments, was roughly proportional to enzyme levels over this entire range. For a plasmid-containing strain grown in a chemostat under conditions of leucine limitation (about 100 plasmids per chromosome), about 27% of pulse-labeled ribonucleic acid was coded for by genes in or adjacent to the leucine operon, and 10% of the total protein was beta-isopropylmalate dehydrogenase.
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13
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Doi RH. Role of ribonucleic acid polymerase in gene selection in procaryotes. BACTERIOLOGICAL REVIEWS 1977; 41:568-94. [PMID: 410404 PMCID: PMC414017 DOI: 10.1128/br.41.3.568-594.1977] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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14
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Quay SC, Oxender DL. Regulation of amino acid transport in Escherichia coli by transcription termination factor rho. J Bacteriol 1977; 130:1024-9. [PMID: 324970 PMCID: PMC235323 DOI: 10.1128/jb.130.3.1024-1029.1977] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Amino acid transport rates and amino acid binding proteins were examined in a strain containing the rho-120 mutation (formerly SuA), which has been shown to lower the rho-dependent, ribonucleic acid-activated adenosine triphosphatase activity to 9% of the rho activity in the isogenic wild-type strain. Tryptophan and proline transport, which occur by membrane-bound systems, were not altered. On the other hand, arginine, histidine, leucine, isoleucine, and valine transport were variably increased by a factor of 1.4 to 5.0. Kinetics of leucine transport showed that the LIV (leucine, isoleucine, and valine)-I (binding protein-associated) transport system is increased 8.5-fold, whereas the LIV-II (membrane-bound) system is increased 1.5-fold in the rho mutant under leucine-limited growth conditions. The leucine binding protein is increased fourfold under the same growth conditions. The difference in leucine transport in these strains was greatest during leucine-limited growth; growth on complex media repressed both strains to the same transport activity. We propose that rho-dependent transcriptional termination is important for leucine-specific repression of branched-chain amino acid transport, although rho-independent regulation, presumably by a corepressor-aporepressor-type mechanism, must also occur.
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15
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Oxender DL, Quay SC. Regulation of leucine transport and binding proteins in Escherichia coli. J Cell Physiol 1976; 89:517-21. [PMID: 795811 DOI: 10.1002/jcp.1040890405] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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16
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Smith JM, Smolin DE, Umbarger HE. Polarity and the regulation of the ilv gene cluster in Escherichia coli strain K-12. MOLECULAR & GENERAL GENETICS : MGG 1976; 148:111-24. [PMID: 790150 DOI: 10.1007/bf00268374] [Citation(s) in RCA: 67] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A series of Mu-1 induced isoleucine and valine auxotrophs derived from the wild type K-12 strain of Escherichia coli and from a valine resistant (ilvO-) mutant were examined. It was concluded that the genes ilvE, ilvD and ilvA constitute a single operon and are transcribed from E to A. Furthermore, the ilvG gene, expressed only in ilvO- strains, does not lie between ilvE and ilvD as previously assumed. A mutation in rho was examined for its effect on the ilvEDA operon. One effect of the rho- mutation was a mimicking of an isoleucine limitation signal. A model for the regulation of the ilvEDA operon is discussed. The model involves multiple attentuation sites and a possible role for the ilvO locus which lies at the distal end of the ilvEDA operon (but is not part of it). Supportive evidence for the proposed direction of transcription was obtained by examination of a series of gammailv transducing phages.
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17
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Korn LJ, Yanofsky C. Polarity suppressors defective in transcription termination at the attenuator of the tryptophan operon of Escherichia coli have altered rho factor. J Mol Biol 1976; 106:231-41. [PMID: 135845 DOI: 10.1016/0022-2836(76)90082-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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18
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Subrahmanyam CS, Das HK. Amino acid starvation in Escherichia coli K-12: characteristics of the translation process. J Bacteriol 1976; 126:1042-51. [PMID: 780337 PMCID: PMC233124 DOI: 10.1128/jb.126.3.1042-1051.1976] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Some characteristics of the translation process during amino acid starvation in Escherichia coli have been examined. Once starvation has been established, premature termination of polypeptides is negligible and complete proteins are formed. There is some preference for the synthesis of shorter proteins. The number of ribosomes involved in protein synthesis appears to decline to about half during amino acid-starvation. The assembly time of proteins during amino acid starvation is increased to only about fourfold, though protein synthesis maintained by turnover is reduced to 10%. To explain these observations, a model has been proposed for the course of events that possibly take place from the onset of starvation.
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19
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Korn LJ, Yanofsky C. Polarity suppressors increase expression of the wild-type tryptophan operon of Escherichia coli. J Mol Biol 1976; 103:395-409. [PMID: 781273 DOI: 10.1016/0022-2836(76)90319-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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20
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Levinthal M, Levinthal M, Williams LS. The regulation of the ilv ADGE operon: evidence for positive control by threonine deaminase. J Mol Biol 1976; 102:453-65. [PMID: 775108 DOI: 10.1016/0022-2836(76)90327-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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21
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Ratner D. Evidence that mutations in the suA polarity suppressing gene directly affect termination factor rho. Nature 1976; 259:151-3. [PMID: 1107855 DOI: 10.1038/259151a0] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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22
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Bertrand K, Korn L, Lee F, Platt T, Squires CL, Squires C, Yanofsky C. New features of the regulation of the tryptophan operon. Science 1975; 189:22-6. [PMID: 1094538 DOI: 10.1126/science.1094538] [Citation(s) in RCA: 205] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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23
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Childs GJ, Freundlich M. Transcriptional control of the isoleucine-valine messenger RNA's in E. coli K-12. MOLECULAR & GENERAL GENETICS : MGG 1975; 138:257-68. [PMID: 1102933 DOI: 10.1007/bf00269352] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Hybridization of messenger ribonucleic acid (mRNA) isolated from Escherichia Coli K-12 to deoxyribonucleic acid (DNA) from lambdaCI857st68h80dilv was used to detect isoleucine-valine (ilv) specific mRNA. A number of strains partially constitutive for the isoleucine-valine enzymes had levels of ilv mRNA 2 to 3-fold higher than the parent strain. Starvation for any of the branched-chain amino acids resulted in a 20 to 23-fold increase in ilv mRNA as compared to repressed levels. These differences were not due to altered growth rates or to changes in the stability of ilv mRNA. These data indicate that regulation of the isoleucine-valine enzymes by multivalent repression occurs mainly at the level of transcription. Kinetics of elongation of ilv mRNA after repression are consistent with the assumption that the mechanism of multivalent repression involves the prevention of further initiations by RNA polymerase.
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Quay SC, Oxender DL, Tsuyumu S, Umbarger HE. Separate regulation of transport and biosynthesis of leucine, isoleucine, and valine in bacteria. J Bacteriol 1975; 122:994-1000. [PMID: 1097409 PMCID: PMC246151 DOI: 10.1128/jb.122.3.994-1000.1975] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Since both transport activity and the leucine biosynthetic enzymes are repressed by growth on leucine, the regulation of leucine, isoleucine, and valine biosynthetic enzymes was examined in Escherichia coli K-12 strain EO312, a constitutively derepressed branched-chain amino acid transport mutant, to determine if the transport derepression affected the biosynthetic enzymes. Neither the iluB gene product, acetohydroxy acid synthetase (acetolactate synthetase, EC 4.1.3.18), NOR THE LEUB gene product, 3-isopropylmalate dehydrogenase (2-hydroxy-4-methyl-3-carboxyvalerate-nicotinamide adenine dinucleotide oxido-reductase, EC 1.1.1.85), were significantly affected in their level of derepression or repression compared to the parental strain. A number of strains with alterations in the regulation of the branched-chain amino acid biosynthetic enzymes were examined for the regulation of the shock-sensitive transport system for these amino acids (LIV-I). When transport activity was examined in strains with mutations leading to derepression of the iluB, iluADE, and leuABCD gene clusters, the regulation of the LIV-I transport system was found to be normal. The regulation of transport in an E. coli strain B/r with a deletion of the entire leucine biosynthetic operon was normal, indicating none of the gene products of this operon are required for regulation of transport. Salmonella typhimurium LT2 strain leu-500, a single-site mutation affecting both promotor-like and operator-like function of the leuABCD gene cluster, also had normal regulation of the LIV-I transport system. All of the strains contained leucine-specific transport activity, which was also repressed by growth in media containing leucine, isoleucine and valine. The concentrated shock fluids from these strains grown in minimal medium or with excess leucine, isoleucine, and valine were examined for proteins with leucine-binding activity, and the levels of these proteins were found to be regulated normally. It appears that the branched-chain amino acid transport systems and biosynthetic enzymes in E. coli strains K-12 and B/r and in S. typhimurium strain LT2 are not regulated together by a cis-dominate type of mechanism, although both systems may have components in common.
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Vonder Haar RA, Umbarger HE. Isoleucine and valine metabolism in Escherichia coli K-12: detection and measurement of ilv-specific messenger ribonucleic acid. J Bacteriol 1974; 120:687-96. [PMID: 4616946 PMCID: PMC245828 DOI: 10.1128/jb.120.2.687-696.1974] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Ribonucleic acid-deoxyribonucleic acid (RNA-DNA) hybridization was employed for the determination of messenger RNA transcribed from the ilv gene cluster of Escherichia coli K-12. Strains with derepressed levels of the isoleucine and valine biosynthetic enzymes owing to linked or unlinked genetic lesions were found to exhibit ilv messenger RNA levels from 1.5- to 4-fold higher than did their isogenic parents. When grown under conditions that specifically repressed the synthesis of isoleucine- and valine-forming enzymes, most strains exhibited drastically reduced ilv messenger RNA levels. Hybridization performed with the separated strands of ilv DNA showed that all the ilv genes are transcribed from the same strand, the "l strand" of lambdaphi80CI857St68dilv DNA. Sucrose gradient analyses of RNA extracted from cells starved for isoleucine, valine, or leucine resulted in the detection of at least two distinct types of ilv messenger RNA.
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Wasmuth JJ, Umbarger HE. Role for free isoleucine of glycyl-leucine in the repression of threonine deaminase in Escherichia coli. J Bacteriol 1974; 117:29-39. [PMID: 4587610 PMCID: PMC246521 DOI: 10.1128/jb.117.1.29-39.1974] [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: 01/11/2023] Open
Abstract
In Escherichia coli, the three branched-chain amino acid activating enzymes appear to be essential for multivalent repression of the isoleucine- and valine-forming enzymes. The results of experiments with a mutant, strain CU18, having an altered threonine deaminase, indicate that free isoleucine and some form of threonine deaminase (the product of the ilvA gene) are also involved in multivalent repression. This strain exhibits abnormally high derepressibility but normal repressibility of its ilv gene products, and its threonine deaminase is inhibited only by high concentrations of isoleucine. In strain CU18, the isoleucine analogue, thiaisoleucine, is incapable of replacing isoleucine in the multivalent repression of the ilv genes, whereas the analogue can fully replace the natural amino acid in repression in other strains examined. The dipeptide, glycyl-leucine, which, like isoleucine, is a heterotropic negative effector of threonine deaminase but is not a substrate for isoleucyl-transfer ribonucleic acid synthetase, can completely prevent the accumulation of threonine deaminase-forming potential during isoleucine starvation in strains with normal threonine deaminases. It can not, however, prevent such accumulation in strain CU18 or in other strains in which threonine deaminase is insensitive to any concentration of isoleucine.
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27
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Wasmuth JJ, Umbarger HE. Participation of branched-chain amino acid analogues in multivalent repression. J Bacteriol 1973; 116:562-70. [PMID: 4583240 PMCID: PMC285418 DOI: 10.1128/jb.116.2.562-570.1973] [Citation(s) in RCA: 6] [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
Two isoleucine analogues and two leucine analogues were examined for their ability to replace the natural amino acid preventing the accumulation of threonine deaminase-forming potential. The procedure used to study repression by the analogues distinguishes between true repression and the formation of inactive enzyme by the analogue in question. The leucine analogue 4-azaleucine was found to replace leucine in multivalent repression of threonine deaminase-forming potential in Escherichia coli but not in Salmonella typhimurium. Another leucine analogue, trifluoroleucine, was only partially effective in causing repression in either organism. The isoleucine analogue 4-azaisoleucine was ineffective in replacing isoleucine in repression. In contrast, 4-thiaisoleucine effectively replaced isoleucine in the repression of threonine deaminase-forming potential in S. typhimurium and E. coli.
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