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Purohit A, Pawar L, Yadav SK. Fermenter scale production of recombinant beta-mannanase by E. coli BL21 cells under microaerobic environment. Carbohydr Res 2024; 541:109150. [PMID: 38788560 DOI: 10.1016/j.carres.2024.109150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 04/29/2024] [Accepted: 05/18/2024] [Indexed: 05/26/2024]
Abstract
Aim of the study was to optimize and produce beta-mannanase at fermenter scale by using cheaper minimal media. Increased production of beta-mannanase from Microbacterium camelliasinensis CIAB417 was achieved by heterologous expression in E. coli BL21 (DE3). The scale-up production of beta-mannanase was optimized from shake flask to 5-L fermenter. The cost-effective minimal media (M9+e) without any vitamins was found to be most effective and optimized for culturing the cells. The same media displayed no significant fluctuation in the pH while culturing the cells for the production of beta-mannanase both at shake flask and fermenter level. Additionally, E. coli cells were able to produce similar amount of dry cell weight and recombinant beta-mannanase both in the presence of micro and macro-oxygen environment. The optimized media was demonstrated to show no significant drop in pH throughout the recombinant protein production process. In one litre medium, 2.0314 g dry weight of E. coli cells yielded 1.8 g of purified recombinant beta-mannanase. The purified enzyme was lyophilized and demonstrated to hydrolyse locust bean gum to release mannooligosaccharides.
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Affiliation(s)
- Anjali Purohit
- Center of Innovative and Applied Bioprocessing (CIAB), Sector-81, Knowledge City, Mohali, 140306, India
| | - Lata Pawar
- Center of Innovative and Applied Bioprocessing (CIAB), Sector-81, Knowledge City, Mohali, 140306, India
| | - Sudesh Kumar Yadav
- Center of Innovative and Applied Bioprocessing (CIAB), Sector-81, Knowledge City, Mohali, 140306, India; CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, (HP), India.
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Observation of universal ageing dynamics in antibiotic persistence. Nature 2021; 600:290-294. [PMID: 34789881 DOI: 10.1038/s41586-021-04114-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/08/2021] [Indexed: 11/08/2022]
Abstract
Stress responses allow cells to adapt to changes in external conditions by activating specific pathways1. Here we investigate the dynamics of single cells that were subjected to acute stress that is too strong for a regulated response but not lethal. We show that when the growth of bacteria is arrested by acute transient exposure to strong inhibitors, the statistics of their regrowth dynamics can be predicted by a model for the cellular network that ignores most of the details of the underlying molecular interactions. We observed that the same stress, applied either abruptly or gradually, can lead to totally different recovery dynamics. By measuring the regrowth dynamics after stress exposure on thousands of cells, we show that the model can predict the outcome of antibiotic persistence measurements. Our results may account for the ubiquitous antibiotic persistence phenotype2, as well as for the difficulty in attempts to link it to specific genes3. More generally, our approach suggests that two different cellular states can be observed under stress: a regulated state, which prepares cells for fast recovery, and a disrupted cellular state due to acute stress, with slow and heterogeneous recovery dynamics. The disrupted state may be described by general properties of large random networks rather than by specific pathway activation. Better understanding of the disrupted state could shed new light on the survival and evolution of cells under stress.
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Yeom J, Groisman EA. Reduced ATP-dependent proteolysis of functional proteins during nutrient limitation speeds the return of microbes to a growth state. Sci Signal 2021; 14:14/667/eabc4235. [PMID: 33500334 DOI: 10.1126/scisignal.abc4235] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
When cells run out of nutrients, the growth rate greatly decreases. Here, we report that microorganisms, such as the bacterium Salmonella enterica serovar Typhimurium, speed up the return to a rapid growth state by preventing the proteolysis of functional proteins by ATP-dependent proteases while in the slow-growth state or stationary phase. This reduction in functional protein degradation resulted from a decrease in the intracellular concentration of ATP that was nonetheless sufficient to allow the continued degradation of nonfunctional proteins by the same proteases. Protein preservation occurred under limiting magnesium, carbon, or nitrogen conditions, indicating that this response was not specific to low availability of a particular nutrient. Nevertheless, the return to rapid growth required proteins that mediate responses to the specific nutrient limitation conditions, because the transcriptional regulator PhoP was necessary for rapid recovery only after magnesium starvation. Reductions in intracellular ATP and in ATP-dependent proteolysis also enabled the yeast Saccharomyces cerevisiae to recover faster from stationary phase. Our findings suggest that protein preservation during a slow-growth state is a conserved microbial strategy that facilitates the return to a growth state once nutrients become available.
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Affiliation(s)
- Jinki Yeom
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA.,Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore.,Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, Korea.,Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA. .,Yale Microbial Sciences Institute, P.O. Box 27389, West Haven, CT 06516, USA
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Arumugaperumal A, Paul S, Lathakumari S, Balasubramani R, Sivasubramaniam S. The draft genome of a new Verminephrobacter eiseniae strain: a nephridial symbiont of earthworms. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01549-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Abstract
Purpose
Verminephrobacter is a genus of symbiotic bacteria that live in the nephridia of earthworms. The bacteria are recruited during the embryonic stage of the worm and transferred from generation to generation in the same manner. The worm provides shelter and food for the bacteria. The bacteria deliver micronutrients to the worm. The present study reports the genome sequence assembly and annotation of a new strain of Verminephrobacter called Verminephrobacter eiseniae msu.
Methods
We separated the sequences of a new Verminephrobacter strain from the whole genome of Eisenia fetida using the sequence of V. eiseniae EF01-2, and the bacterial genome was assembled using the CLC Workbench. The de novo-assembled genome was annotated and analyzed for the protein domains, functions, and metabolic pathways. Besides, the multigenome comparison was performed to interpret the phylogenomic relationship of the strain with other proteobacteria.
Result
The FastqSifter sifted a total of 593,130 Verminephrobacter genomic reads. The de novo assembly of the reads generated 1832 contigs with a total genome size of 4.4 Mb. The Average Nucleotide Identity denoted the bacterium belongs to the species V. eiseniae, and the 16S rRNA analysis confirmed it as a new strain of V. eiseniae. The AUGUSTUS genome annotation predicted a total of 3809 protein-coding genes; of them, 3805 genes were identified from the homology search.
Conclusion
The bioinformatics analysis confirmed the bacterium is an isolate of V. eiseniae, and it was named Verminephrobacter eiseniae msu. The whole genome of the bacteria can be utilized as a useful resource to explore the area of symbiosis further.
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Mahaseth T, Kuzminov A. Prompt repair of hydrogen peroxide-induced DNA lesions prevents catastrophic chromosomal fragmentation. DNA Repair (Amst) 2016; 41:42-53. [PMID: 27078578 PMCID: PMC4851570 DOI: 10.1016/j.dnarep.2016.03.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 03/25/2016] [Indexed: 12/13/2022]
Abstract
Iron-dependent oxidative DNA damage in vivo by hydrogen peroxide (H2O2, HP) induces copious single-strand(ss)-breaks and base modifications. HP also causes infrequent double-strand DNA breaks, whose relationship to the cell killing is unclear. Since hydrogen peroxide only fragments chromosomes in growing cells, these double-strand breaks were thought to represent replication forks collapsed at direct or excision ss-breaks and to be fully reparable. We have recently reported that hydrogen peroxide kills Escherichia coli by inducing catastrophic chromosome fragmentation, while cyanide (CN) potentiates both the killing and fragmentation. Remarkably, the extreme density of CN+HP-induced chromosomal double-strand breaks makes involvement of replication forks unlikely. Here we show that this massive fragmentation is further amplified by inactivation of ss-break repair or base-excision repair, suggesting that unrepaired primary DNA lesions are directly converted into double-strand breaks. Indeed, blocking DNA replication lowers CN+HP-induced fragmentation only ∼2-fold, without affecting the survival. Once cyanide is removed, recombinational repair in E. coli can mend several double-strand breaks, but cannot mend ∼100 breaks spread over the entire chromosome. Therefore, double-strand breaks induced by oxidative damage happen at the sites of unrepaired primary one-strand DNA lesions, are independent of replication and are highly lethal, supporting the model of clustered ss-breaks at the sites of stable DNA-iron complexes.
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Affiliation(s)
- Tulip Mahaseth
- Department of Microbiology, University of Illinois at Urbana-Champaign, USA
| | - Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, USA.
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Continued protein synthesis at low [ATP] and [GTP] enables cell adaptation during energy limitation. J Bacteriol 2008; 191:1083-91. [PMID: 19028899 DOI: 10.1128/jb.00852-08] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One of biology's critical ironies is the need to adapt to periods of energy limitation by using the energy-intensive process of protein synthesis. Although previous work has identified the individual energy-requiring steps in protein synthesis, we still lack an understanding of the dependence of protein biosynthesis rates on [ATP] and [GTP]. Here, we used an integrated Escherichia coli cell-free platform that mimics the intracellular, energy-limited environment to show that protein synthesis rates are governed by simple Michaelis-Menten dependence on [ATP] and [GTP] (K(m)(ATP), 27 +/- 4 microM; K(m)(GTP), 14 +/- 2 microM). Although the system-level GTP affinity agrees well with the individual affinities of the GTP-dependent translation factors, the system-level K(m)(ATP) is unexpectedly low. Especially under starvation conditions, when energy sources are limited, cells need to replace catalysts that become inactive and to produce new catalysts in order to effectively adapt. Our results show how this crucial survival priority for synthesizing new proteins can be enforced after rapidly growing cells encounter energy limitation. A diminished energy supply can be rationed based on the relative ATP and GTP affinities, and, since these affinities for protein synthesis are high, the cells can adapt with substantial changes in protein composition. Furthermore, our work suggests that characterization of individual enzymes may not always predict the performance of multicomponent systems with complex interdependencies. We anticipate that cell-free studies in which complex metabolic systems are activated will be valuable tools for elucidating the behavior of such systems.
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Mayer RJ, Russell SM, Burgess RJ, Wilde CJ, Paskin N. Coordination of protein synthesis and degradation. CIBA FOUNDATION SYMPOSIUM 2008:253-72. [PMID: 399891 DOI: 10.1002/9780470720585.ch16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The degree of coordination between protein synthesis and protein degradation in developing and mature cels is considered. Studies on specific enzyme and general protein turnover in developing liver and differentiating mammary gland are presented. In the mature liver mitochondrion average protein degradation rates are higher for outer membrane and intermembrane space proteins than for matrix and inner membrane proteins. Significant heterogeneity of protein degradation rates was observed only in the outer mitochondrial membrane. During postnatal development the rates of degradation of proteins in many liver cellular fractions are increased. In the mitochondrion only the average rates of degradation of proteins in the outer membrane and intermembrane space fractions increase during development. Evidence for hormonally regulated changes in both protein synthesis and degradation during mammary cell differentiation is given. The data indicate that a transitory decrease in protein degradation accompanies the increase in protein synthesis on hormonal stimulation of the tissue. The results from the two model systems are collated and used to formulate a phenomenological hypothesis of protein degradation and its integration with protein synthesis in steady-state and non-steady-state conditions.
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Goldberg AL, Strnad NP, Swamy KH. Studies of the ATP dependence of protein degradation in cells and cell extracts. CIBA FOUNDATION SYMPOSIUM 2008:227-51. [PMID: 399890 DOI: 10.1002/9780470720585.ch15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Experiments with metabolic inhibitors in vivo indicate that intracellular protein degradation requires the continuous production of ATP. We have established soluble cell-free preparations from rabbit reticulocytes, rat liver, and Escherichia coli that degrade abnormal protein in an ATP-dependent fashion. These enzymes appear to be responsible for the selective breakdown of abnormal protein that may result from mutations, biosynthetic errors or intracellular denaturation. Experiments with inhibitors indicate that this process and the degradation of many short-lived normal proteins does not occur in the lysosome. The cell-free extracts prepared from these crude extracts hydrolyse [14C] globin by a process stimulated 2--3-fold by ATP and to a lesser extent by GTP, CTP or UTP. These activities degrade globin to large peptides which are then cleaved by soluble peptidases. The ATP-stimulated protease that partially purified from rat liver cytoplasm is also stimulated by pyrophosphate. This protease has an apparent molecular weight of 480,000. In contrast, the E. coli enzyme has an apparent molecular weight of 115,000 and is completely dependent on ATP, after partial purification by ion exchange and gel chromatography. This enzyme can be distinguished from six other proteolytic enzymes from E. coli active at pH 7.8. E. coli contains, in addition, four proteases that are not stimulated by ATP and degrade globin to acid-soluble material. We have also demonstrated in E. coli and reticulocytes other proteases that appear specific for small protein substrates and may play a role in the later steps in protein breakdown. The ATP-stimulated endoproteases appear to catalyse the rate-limiting steps in intracellular protein breakdown. However, the actual role of ATP in the degradative process is not known.
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10
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Kuroda A, Tanaka S, Ikeda T, Kato J, Takiguchi N, Ohtake H. Inorganic polyphosphate kinase is required to stimulate protein degradation and for adaptation to amino acid starvation in Escherichia coli. Proc Natl Acad Sci U S A 1999; 96:14264-9. [PMID: 10588694 PMCID: PMC24425 DOI: 10.1073/pnas.96.25.14264] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inorganic polyphosphate (polyP) kinase was studied for its roles in physiological responses to nutritional deprivation in Escherichia coli. A mutant lacking polyP kinase exhibited an extended lag phase of growth, when shifted from a rich to a minimal medium (nutritional downshift). Supplementation of amino acids to the minimal medium abolished the extended growth lag of the mutant. Levels of the stringent response factor, guanosine 5'-diphosphate 3'-diphosphate, increased in response to the nutritional downshift, but, unlike in the wild type, the levels were sustained in the mutant. These results suggested that the mutant was impaired in the induction of amino acid biosynthetic enzymes. The expression of an amino acid biosynthetic gene, hisG, was examined by using a transcriptional lacZ fusion. Although the mutant did not express the fusion in response to the nutritional downshift, Northern blot analysis revealed a significant increase of hisG-lacZ mRNA. Amino acids generated by intracellular protein degradation are very important for the synthesis of enzymes at the onset of starvation. In the wild type, the rate of protein degradation increased in response to the nutritional downshift whereas it did not in the mutant. Supplementation of amino acids at low concentrations to the minimal medium enabled the mutant to express the hisG-lacZ fusion. Thus, the impaired regulation of protein degradation results in the adaptation defect, suggesting that polyP kinase is required to stimulate protein degradation.
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Affiliation(s)
- A Kuroda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan.
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11
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Goldberg AL, Moerschell RP, Chung CH, Maurizi MR. ATP-dependent protease La (lon) from Escherichia coli. Methods Enzymol 1994; 244:350-75. [PMID: 7845219 DOI: 10.1016/0076-6879(94)44027-1] [Citation(s) in RCA: 155] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- A L Goldberg
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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12
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Abstract
In E. coli, protein degradation plays important roles in regulating the levels of specific proteins and in eliminating damaged or abnormal proteins. E. coli possess a very large number of proteolytic enzymes distributed in the cytoplasm, the inner membrane, and the periplasm, but, with few exceptions, the physiological functions of these proteases are not known. More than 90% of the protein degradation occurring in the cytoplasm is energy-dependent, but the activities of most E. coli proteases in vitro are not energy-dependent. Two ATP-dependent proteases, Lon and Clp, are responsible for 70-80% of the energy-dependent degradation of proteins in vivo. In vitro studies with Lon and Clp indicate that both proteases directly interact with substrates for degradation. ATP functions as an allosteric effector promoting an active conformation of the proteases, and ATP hydrolysis is required for rapid catalytic turnover of peptide bond cleavage in proteins. Lon and Clp show virtually no homology at the amino acid level, and thus it appears that at least two families of ATP-dependent proteases have evolved independently.
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Affiliation(s)
- M R Maurizi
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, Maryland 20892
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13
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Protein degradation during sporulation ofBacillus megaterium: Effect of actinomycin D. Curr Microbiol 1990. [DOI: 10.1007/bf02092093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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O'Hara MB, Hageman JH. Energy and calcium ion dependence of proteolysis during sporulation of Bacillus subtilis cells. J Bacteriol 1990; 172:4161-70. [PMID: 2115863 PMCID: PMC213238 DOI: 10.1128/jb.172.8.4161-4170.1990] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Bacterial cells degrade intracellular proteins at elevated rates during starvation and can selectively degrade proteins by energy-dependent processes. Sporulating bacteria can degrade protein with apparent first-order rate constants of over 0.20 h-1. We have shown, with an optimized [14C]leucine-labeling and chasing procedure, in a chemically defined sporulation medium, that intracellular protein degradation in sporulating cells of Bacillus subtilis 168 (trpC2) is apparently energy dependent. Sodium arsenate, sodium azide, carbonyl cyanide m-chlorophenylhydrozone, and N,N'-dicyclohexylcarbodiimide, at levels which did not induce appreciable lysis (less than or equal to 10%) over 10-h periods of sporulation, inhibited intracellular proteolysis by 13 to 93%. Exponentially growing cells acquired arsenate resistance. In contrast to earlier reports, we found that chloramphenicol (100 micrograms/ml) strongly inhibited proteolysis (68%) even when added 6 h into the sporulation process. Restricting the calcium ion concentration (less than 2 microM) in the medium had no effect on rates or extent of vegetative growth, strongly inhibited sporulation (98%), and inhibited rates of proteolysis by 60% or more. Inhibitors of energy metabolism, at the same levels which inhibited proteolysis, did not affect the rate or degree of uptake of Ca2+ by cells, which suggested that the Ca2+ and metabolic energy requirements of proteolysis were independent. Restricting the Ca2+ concentration in the medium reduced by threefold the specific activity in cells of the major intracellular serine proteinase after 12 h of sporulation. Finally, cells of a mutant of B. subtilis bearing an insertionally inactivated gene for the Ca2(+)-dependent intracellular proteinase-1 degraded protein in chemically defined sporulation medium at a rate indistinguishable from that of the wild-type cells for periods of 8 h.
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Affiliation(s)
- M B O'Hara
- Department of Chemistry, New Mexico State University, Las Cruces 88003
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15
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MacDonald HL, Neway JO. Effects of medium quality on the expression of human interleukin-2 at high cell density in fermentor cultures of Escherichia coli K-12. Appl Environ Microbiol 1990; 56:640-5. [PMID: 2180368 PMCID: PMC183398 DOI: 10.1128/aem.56.3.640-645.1990] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We examined the ability of transformed Escherichia coli cells in fermentor cultures to accumulate interleukin-2 (IL-2) intracellularly under temperature-regulated control of the phage lambda pL promoter. Induction of expression was undertaken at different culture optical densities, and specific IL-2 accumulation was found to decrease with increasing cell density at induction. Induction at higher culture optical densities was also accompanied by decreased growth during induction and increased acetate accumulation in the culture medium. Experiments were undertaken to study the effect of replacing spent medium by perfusion with fresh medium both before induction and during IL-2 expression at high cell density. Improved IL-2 expression was seen only when perfusion was continued past 1.6 h after the start of induction, and it was accompanied by a significant reduction in acetate buildup. Further improvements were not seen when perfusion was continued beyond hour 3 of induction. Replenishing medium components and decreasing the concentration of diffusible inhibitors before induction did not alleviate acetate buildup, growth limitation, or limitation of IL-2 synthesis. These results suggested that accumulation of diffusible inhibitors such as acetate during induction may be a significant factor limiting IL-2 expression in high-density cultures, but other factors intrinsic to the organism or the protein also played a major role.
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Affiliation(s)
- H L MacDonald
- Department of Fermentation Research and Development, Cetus Corporation, Emeryville, California 94608
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16
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Cherrington CA, Hinton M, Chopra I. Effect of short-chain organic acids on macromolecular synthesis in Escherichia coli. THE JOURNAL OF APPLIED BACTERIOLOGY 1990; 68:69-74. [PMID: 1690200 DOI: 10.1111/j.1365-2672.1990.tb02550.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Incubating cultures of Escherichia coli with propionic acid (5 mmol/l) or formic acid (10 mmol/l) at pH 5.0 produced bacteriostasis lasting 30 and 120 min respectively. During this time rates of RNA, DNA, protein, lipid and cell wall synthesis were reduced. Growth resumed after continued incubation in the presence of acid, but cells from acid-treated cultures were larger than controls. DNA synthesis was particularly sensitive to the presence of the propionic or formic acid.
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Affiliation(s)
- C A Cherrington
- Department of Microbiology, Medical School, University of Bristol, UK
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17
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Grau PP, Heredia CF. Diguanosine 5',5'''-P1,P4-tetraphosphate and other purine nucleotides inhibit endoribonuclease VI from Artemia. FEBS Lett 1988; 236:291-4. [PMID: 3410043 DOI: 10.1016/0014-5793(88)80040-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The activity of the endoribonuclease VI from Artemia is sensitive to several purine nucleotides. The enzyme is non-competitively inhibited by diguanosine tetraphosphate (Ki = 75 microM), a nucleotide abundant in Artemia encysted gastrulae and located in the same particulate fraction as the gastrular ribonuclease. Diguanosine triphosphate and diadenosine tetraphosphate are less efficient inhibitors (Ki congruent to 200 microM). The ribonuclease is non-competitively inhibited by 5'-AMP (Ki = 10 microM) and 5'-GMP (Ki = 50 microM) but is insensitive to the corresponding 5'-phosphates of cytosine and uridine. Other purine mononucleotides inhibit the enzyme activity less efficiently. The modulation of the enzyme activity by these nucleotides is discussed in relation with the changes in ribonuclease activity during early development of Artemia.
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Affiliation(s)
- P P Grau
- Instituto de Investigaciones Biomédicas del CSIC, Facultad de Medicina, UAM, Madrid, Spain
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18
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Hwang BJ, Woo KM, Goldberg AL, Chung CH. Protease Ti, a new ATP-dependent protease in Escherichia coli, contains protein-activated ATPase and proteolytic functions in distinct subunits. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68366-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Parkhouse WS. Regulation of skeletal muscle myofibrillar protein degradation: relationships to fatigue and exercise. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1988; 20:769-75. [PMID: 3049180 DOI: 10.1016/0020-711x(88)90062-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
1. Exercise results in large alterations in cellular metabolic homeostasis and protein turnovers. Exhaustive exercise (as well as starvation, dystrophy, motor nerve disease) results in myofibrillar degradation and has been associated with the decreased force generating capabilities of muscle at fatigue. 2. Complete protein degradation is accomplished by the combined actions of non-lysosomal and lysosomal proteases and the initial breakdown of myofibrillar protein appears to be non-lysosomal mediated. 3. Current evidence suggests that covalent modification (mixed-function oxidation, formation of mixed disulfides, oxidation of methionine residues and phosphorylation) of proteins may mark them for degradation by rendering them more susceptible to proteolytic attack. 4. The rate of covalent modification can be controlled by the level of stabilizing and destabilizing ligands and by factors affecting the activity of the marking reaction. 5. The activities of individual proteases may be controlled by activators and inhibitors. 6. It is suggested that the large alterations in metabolism (hormonal profiles, energy status, redox status and Ca2+ levels) which accompany exercise serve to activate specific proteases and/or induce covalent modifications which mark specific myofibrillar proteins for subsequent proteolytic attack.
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Affiliation(s)
- W S Parkhouse
- School of Physical Education and Recreation, University of British Columbia, Vancouver, Canada
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20
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Klemes Y, Godinger D, Aronovitch J. Temporary exposure to hydrogen peroxide increases intracellular protein degradation inE. coli. FEMS Microbiol Lett 1987. [DOI: 10.1111/j.1574-6968.1987.tb02282.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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21
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Goff S, Goldberg A. An increased content of protease La, the lon gene product, increases protein degradation and blocks growth in Escherichia coli. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)61221-9] [Citation(s) in RCA: 96] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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22
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Peretti SW, Bailey JE. Mechanistically detailed model of cellular metabolism for glucose-limited growth ofEscherichia coli B/r-A. Biotechnol Bioeng 1986; 28:1672-89. [DOI: 10.1002/bit.260281111] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Rivett AJ. Regulation of intracellular protein turnover: covalent modification as a mechanism of marking proteins for degradation. CURRENT TOPICS IN CELLULAR REGULATION 1986; 28:291-337. [PMID: 2878793 DOI: 10.1016/b978-0-12-152828-7.50010-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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24
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The ATP dependence of the degradation of short- and long-lived proteins in growing fibroblasts. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(19)83626-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Thiam K, Favre A. Role of the stringent response in the expression and mechanism of near-ultraviolet induced growth delay. EUROPEAN JOURNAL OF BIOCHEMISTRY 1984; 145:137-42. [PMID: 6208028 DOI: 10.1111/j.1432-1033.1984.tb08532.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The near-ultraviolet (300-400 nm) induced growth delay of Escherichia coli cells was compared in isogenic relA+ and relA- cells illuminated either in the stationary or the exponential phase. In the latter case: (a) the relA- strains of K12 and B/r exhibited similar maximal growth lags (65 min and 55 min respectively); (b) the maximal lags were 1.5-fold and 4-fold longer, respectively, in the isogenic relA+ strains; (c) the rate of the relA- -dependent guanosine 3',5'-bis(diphosphate) (ppGpp) accumulation was three-times lower in the K12 relA+ strain as compared to the B/r relA- strain: (d) a K12 spoT mutant having an impaired rate of ppGpp degradation had a 2-fold longer lag. On the other hand, when illumination is performed in the stationary phase, isogenic relA+ and relA- cells (B/r or K12) exhibited similar growth lags at any fluences, indicating little if any involvement of the stringent response. These data extend previous observations of T.V. Ramabhadran an J. Jagger [(1976) Proc. Natl Acad. Sci. USA, 73, 59-63] but do not support their conclusion that the stringent response is the main factor responsible for growth delay. By monitoring the intracellular level of ppGpp in relA+ spoT- and relA+ spoT+ growing cells during illumination and the subsequent growth lag we observed that the initial burst of ppGpp decreases slowly all along the lag; in all relA+ strains checked the return of ppGpp to its basal level coincides with the recovery of normal growth. We conclude that it is the accumulation of ppGpp over the basal level due either to the stringent response or to prevention of ppGpp degradation that is responsible for an amplification of the growth lag.
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Ruppen ME, Switzer RL. Degradation of Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase in vivo. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(18)32794-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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27
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Williams DE, Jackson JM, Chaney SG. Characterization of RNA synthesis in an Escherichia coli mutant with a temperature-sensitive lesion in stable RNA synthesis. J Bacteriol 1983; 153:616-26. [PMID: 6185464 PMCID: PMC221677 DOI: 10.1128/jb.153.2.616-626.1983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Previous experiments with Escherichia coli strain 2S142 have shown that the synthesis of stable RNA is preferentially blocked at the restrictive temperature. In this paper, we have examined the capacity of this mutant strain to synthesize RNA in vitro. Growth of the strain for as short a period as 10 min at 42 degrees C resulted in a 40 to 60% loss of RNA synthetic capacity and a fourfold decrease in percent rRNA synthesized in toluenized cell preparations. The time course for the loss and recovery of this RNA synthetic capacity correlated very well with the changes in RNA synthesis observed in vivo. We found no difference in temperature sensitivity of the purified RNA polymerase from the mutant and the parental strains. Moreover, there was no detectable alteration in the amount of enzyme, specific activity of the enzyme, or electrophoretic mobility of the subunits when the mutant strain was grown at 42 degrees C. The capacity for rRNA synthesis was also measured with the Zubay in vitro system (Reiness et al., Proc. Natl. Acad. Sci. 72:2881-2885, 1975). Supernatant fractions (S-30) prepared from cells grown at 30 degrees C were capable of up to 31.2% rRNA synthesis, using phi 80d3 DNA as template. S-30 fractions from cells grown at 42 degrees C synthesized 8.6% rRNA. The bottom one-third of the S-100 fraction and the ribosomal salt wash from 30 degrees C cells contained one or more factors which partially restored preferential rRNA synthesis in S-30 fractions from cells grown at 42 degrees C. Preliminary evidence suggests that the factor(s) is protein in nature.
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28
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Mosteller RD, Nishimoto KR, Bush PR, Golstein RV. Energy-dependent inactivation and modification of a tryptophan biosynthetic enzyme in Escherichia coli. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34002-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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29
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Larimore FS, Waxman L, Goldberg AL. Studies of the ATP-dependent proteolytic enzyme, protease La, from Escherichia coli. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34704-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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30
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Gancedo JM, López S, Ballesteros F. Calculation of half-lives of proteins in vivo. Heterogeneity in the rate of degradation of yeast proteins. Mol Cell Biochem 1982; 43:89-95. [PMID: 6283331 DOI: 10.1007/bf00423096] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A method is given for the calculation of half-lives of proteins in vivo from the measurement of the decrease of radioactivity in pulse-labelled proteins with time. This method could be particularly useful for the study of the degradation of proteins in cells that have a low growth rate. The method applied to growing yeast indicates that there are two major classes of protein. The class with low turnover constitutes the bulk of yeast protein and has a half-life of 160 h in a medium with glucose or galactose and of 50 h in a medium with ethanol. The class of proteins with high turnover (half-life between 0.8 and 2.4 hours) represents from 1% of total protein in yeast growing on glucose to 7% in yeast growing on ethanol. It is shown that some proteins which are depressed during growth on ethanol or induced during growth on galactose are particularly susceptible to degradation in a medium which contains glucose. It is proposed that protein degradation is regulated by a coarse control at the level of protease activity and a fine control on the susceptibility of individual proteins to proteases.
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31
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Tischler M, Desautels M, Goldberg A. Does leucine, leucyl-tRNA, or some metabolite of leucine regulate protein synthesis and degradation in skeletal and cardiac muscle? J Biol Chem 1982. [DOI: 10.1016/s0021-9258(19)68081-6] [Citation(s) in RCA: 129] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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32
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Voellmy RW, Goldberg AL. ATP-stimulated endoprotease is associated with the cell membrane of E. coli. Nature 1981; 290:419-21. [PMID: 7012639 DOI: 10.1038/290419a0] [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: 01/23/2023]
Abstract
Despite knowledge of the physiological significance and regulation of protein degradation in bacteria, the pathway of proteolysis and the responsible enzymes are still not known. Degradation of cell proteins in bacterial and animal cells requires continuous ATP production, inhibition of which in Escherichia coli prevents the degradation of normal proteins in growing cells, accelerated breakdown of such proteins in starving cultures and the very rapid breakdown of abnormal proteins. Intracellular proteolysis proceeds by repeated endoproteolytic steps and ATP is required for the initial cleavages of the substrate. We have recently demonstrated ATP stimulation of proteolysis in extracts of bacterial and animal cells. These ATP-stimulated systems seem to be responsible for the rapid degradation of abnormal proteins in vivo, but they may also be involved in the catabolism of normal cell proteins, limited proteolysis, such as the processing of precursors for secreted or membrane proteins, and the selective inactivation of specific proteins, as occurs in the ATP-dependent cleavage of the lambda repressor by the recA protein. We report here that membrane fragments contain an ATP-stimulated protease that degrades cell proteins to large peptides (of molecular weight (MW) 71,500) which are then rapidly hydrolysed to amino acids by soluble ATP-independent enzymes.
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Alberghina L, Sturani E. Control of growth and of the nuclear division cycle in Neurospora crassa. Microbiol Rev 1981; 45:99-122. [PMID: 6452573 PMCID: PMC281500 DOI: 10.1128/mr.45.1.99-122.1981] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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35
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Photoaffinity labeling of the cell surface adenosine 3‘:5‘-monophosphate receptor of Dictyostelium discoideum and its modification in down-regulated cells. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)70017-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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36
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Yen C, Green L, Miller CG. Degradation of intracellular protein in Salmonella typhimurium peptidase mutants. J Mol Biol 1980; 143:21-33. [PMID: 7003162 DOI: 10.1016/0022-2836(80)90122-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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37
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St John AC, Goldberg AL. Effects of starvation for potassium and other inorganic ions on protein degradation and ribonucleic acid synthesis in Escherichia coli. J Bacteriol 1980; 143:1223-33. [PMID: 6157670 PMCID: PMC294483 DOI: 10.1128/jb.143.3.1223-1233.1980] [Citation(s) in RCA: 31] [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
Starvation of Escherichia coli for potassium, phosphate, or magnesium ions leads to a reversible increase in the rate of protein degradation and an inhibition of ribonucleic acid (RNA) synthesis. In cells deprived of potassium, the breakdown of the more stable cell proteins increased two- to threefold, whereas the hydrolysis of short-lived proteins, both normal ones and analog-containing polypeptides, did not change. The mechanisms initiating the enhancement of proteolysis during starvation for these ions were examined. Upon starvation for amino acids or amino acyl-transfer RNA (tRNA), protein breakdown increases in relA+ (but not relA) cells as a result of the rapid synthesis of guanosine-5'-diphosphate-3'-diphosphate (ppGpp). However, a lack of amino acyl-tRNA does not appear to be responsible for the increased protein breakdown in cells starved for inorganic ions, since protein breakdown increased in the absence of these ions in both relA+ and relA cultures, and since a large excess of amino acids did not affect this response. In bacteria in which energy production is restricted, ppGpp levels also rise, and protein breakdown increases. The ion-deprived cultures did show a 40 to 75% reduction in adenosine-5'-triphosphate levels,l similar to that seen upon glucose starvation. However, this decrease in ATP content does not appear to cause the increase in protein breakdown or lead to an accumulation of ppGpp. No consistent change in intracellular ppGpp levels was found in relA+ or relA cells starved for these ions. In addition, in relX mutants, removal of these ions led to accelerated protein degradation even though relX cells are unable to increase ppGpp levels or proteolysis when deprived of a carbon source. In the potassium-, phosphate-, and magnesium-deprived cultures, the addition of choramphenicol or tetracycline caused a reduction in protein breakdown toward basal levels. Such findings, however, do not indicate that protein synthesis is essential for the enhancement of protein degradation, since blockage of protein synthesis by inactivation of a temperature-sensitive valyl-tRNA synthetase did not restore protein catabolism to basal levels. These various results and related studies suggest that the mechanism for increased protein catabolism on starvation for inorganic ions differs from that occurring upon amino acid or arbon deprivation and probably involves an enhanced susceptibility of various cell proteins (especially ribosomal proteins) to proteolysis.
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38
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Mitchell J, Lucas-Lenard J. The effect of alcohols on guanosine 5‘-diphosphate-3‘-diphosphate metabolism in stringent and relaxed Escherichia coli. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(18)43738-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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39
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Wood NB, Haselkorn R. Control of phycobiliprotein proteolysis and heterocyst differentiation in Anabaena. J Bacteriol 1980; 141:1375-85. [PMID: 6767709 PMCID: PMC293836 DOI: 10.1128/jb.141.3.1375-1385.1980] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Phycobiliprotein degradation can be initiated in cultures of the cyanobacterium Anabaena by removal of combined nitrogen from the medium. Certain strains of Anabaena differentiate cells specialized for aerobic nitrogen fixation (heterocysts) under such conditions. We describe here a procedure for the preparation of extracts from heterocysts or vegetative cells that contain an activity capable of degrading only the phycobiliproteins in a mixture of soluble Anabaena proteins in vitro. This activity increased under nitrogen starvation conditions or in ammonia-replete cultures treated with the glutamine synthetase inhibitor methionine sulfoximine. The increase in activity induced by nitrogen starvation was prevented by chloramphenicol or by carbon starvation. Under all these conditions, phycobiliprotein degradative activity assayed in vitro was correlated with the loss of phycobiliprotein absorbance in vivo. Finally, starvation of a met auxotroph of Anabaena for methionine (in the presence of ammonia) did not induce phycobiliprotein degradation in vivo or the increase in proteinase activity. Together with direct measurements of ppGpp, these results indicate that proteolysis in Anabaena is not controlled by compounds associated with the stringent response in Escherichia coli. Since the increase in proteinase activity appears to be regulated by the same variables that control heterocyst differentiation, the activity should provide a useful biochemical marker for the early events of differentiation.
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40
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Mosteller R, Goldstein R, Nishimoto K. Metabolism of individual proteins in exponentially growing Escherichia coli. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)85924-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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41
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Guanosine-5‘-diphosphate-3‘-diphosphate (ppGpp) and the regulation of protein breakdown in Escherichia coli. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)86133-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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42
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Dietzler D, Leckie M, Lewis J, Porter S, Taxman T, Lais C. Evidence for new factors in the coordinate regulation of energy metabolism in Escherichia coli. Effects of hypoxia, chloramphenicol succinate, and 2,4-dinitrophenol on glucose utilization, glycogen synthesis, adenylate energy charge, and hexose phosphates during the first two periods of nitrogen starvation. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(19)86889-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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43
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Murakami K, Voellmy R, Goldberg A. Protein degradation is stimulated by ATP in extracts of Escherichia coli. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(19)86875-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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44
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45
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Further evidence for the involvement of charged tRNA and guanosine tetraphosphate in the control of protein degradation in Escherichia coli. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(17)34782-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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