51
|
Abstract
Proteolysis in Escherichia coli serves to rid the cell of abnormal and misfolded proteins and to limit the time and amounts of availability of critical regulatory proteins. Most intracellular proteolysis is initiated by energy-dependent proteases, including Lon, ClpXP, and HflB; HflB is the only essential E. coli protease. The ATPase domains of these proteases mediate substrate recognition. Recognition elements in target are not well defined, but are probably not specific amino acid sequences. Naturally unstable protein substrates include the regulatory sigma factors for heat shock and stationary phase gene expression, sigma 32 and RpoS. Other cellular proteins serve as environmental sensors that modulate the availability of the unstable proteins to the proteases, resulting in rapid changes in sigma factor levels and therefore in gene transcription. Many of the specific proteases found in E. coli are well-conserved in both prokaryotes and eukaryotes, and serve critical functions in developmental systems.
Collapse
Affiliation(s)
- S Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892-4255, USA.
| |
Collapse
|
52
|
Biville F, Laurent-Winter C, Danchin A. In vivo positive effects of exogenous pyrophosphate on Escherichia coli cell growth and stationary phase survival. Res Microbiol 1996; 147:597-608. [PMID: 9157485 DOI: 10.1016/0923-2508(96)84015-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have studied the effect of exogenous pyrophosphate on growing cells of Escherichia coli. In the presence of 10 mM of pyrophosphate, the entry into the stationary phase was delayed and thus a significant increase in the growth yield was observed (25 to 35%) when the bacteria were grown in glucose minimal medium. Furthermore, the synthesis of 52 polypeptides was affected, as demonstrated by two-dimensional electrophoresis. Among the 22 proteins identified by comparison with the E. coli gene-protein index and/or by microsequencing procedures, 15 were involved either in catabolic or anabolic pathways of the intermediary metabolism or in stress responses. Subsequent physiological experiments enabled us to conclude that pyrophosphate exerted a direct or indirect effect on bacterial growth by (1) conferring upon cells a better capacity to use carbon sources and (2) inducing biosynthetic processes. Finally, we show that exogeneous pyrophosphate enhanced the stationary phase survival of E. coli cells.
Collapse
Affiliation(s)
- F Biville
- Départment de Biochimie et Génétique moléculaire, Institut Pasteur, Paris
| | | | | |
Collapse
|
53
|
Krüger E, Msadek T, Hecker M. Alternate promoters direct stress-induced transcription of the Bacillus subtilis clpC operon. Mol Microbiol 1996; 20:713-23. [PMID: 8793870 DOI: 10.1111/j.1365-2958.1996.tb02511.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
clpC of Bacillus subtilis is part of an operon containing six genes. Northern blot analysis suggested that all genes are co-transcribed and encode stress-inducible proteins. Two promoters (PA and PB) were mapped upstream of the first gene. PA resembles promoters recognized by the vegetative RNA polymerase E sigma A. The other promoter (PB) was shown to be dependent on sigma B, the general stress sigma factor in B. subtilis, suggesting that clpC, a potential chaperone, is expressed in a sigma B-dependent manner. This is the first evidence that sigma B in B. subtilis is involved in controlling the expression of a gene whose counterpart, clpB, is subject to regulation by sigma 32 in Escherichia coli, indicating a new function of sigma B-dependent general stress proteins. PB deviated from the consensus sequence of sigma B promoters and was only slightly induced by starvation conditions. Nevertheless, strong induction by heat, ethanol, and salt stress occurred at the sigma B-dependent promoter, whereas the vegetative promoter was only weakly induced under these conditions. However, in a sigB mutant, the sigma A-like promoter became inducible by heat and ethanol stress, completely compensating for sigB deficiency. Only the downstream sigma A-like promoter was induced by certain stress conditions such as hydrogen peroxide or puromycin. These results suggest that novel stress-induction mechanisms are acting at a vegetative promoter. Involvement of additional elements in this mode of induction are discussed.
Collapse
Affiliation(s)
- E Krüger
- Institut für Mikrobiologie und Molekularbiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | | | | |
Collapse
|
54
|
Blumenthal RM, Borst DW, Matthews RG. Experimental analysis of global gene regulation in Escherichia coli. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1996; 55:1-86. [PMID: 8787606 DOI: 10.1016/s0079-6603(08)60189-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- R M Blumenthal
- Department of Microbiology, Medical College of Ohio, Toledo 43699, USA
| | | | | |
Collapse
|
55
|
Abstract
The control of rRNA synthesis in response to both extra- and intracellular signals has been a subject of interest to microbial physiologists for nearly four decades, beginning with the observations that Salmonella typhimurium cells grown on rich medium are larger and contain more RNA than those grown on poor medium. This was followed shortly by the discovery of the stringent response in Escherichia coli, which has continued to be the organism of choice for the study of rRNA synthesis. In this review, we summarize four general areas of E. coli rRNA transcription control: stringent control, growth rate regulation, upstream activation, and anti-termination. We also cite similar mechanisms in other bacteria and eukaryotes. The separation of growth rate-dependent control of rRNA synthesis from stringent control continues to be a subject of controversy. One model holds that the nucleotide ppGpp is the key effector for both mechanisms, while another school holds that it is unlikely that ppGpp or any other single effector is solely responsible for growth rate-dependent control. Recent studies on activation of rRNA synthesis by cis-acting upstream sequences has led to the discovery of a new class of promoters that make contact with RNA polymerase at a third position, called the UP element, in addition to the well-known -10 and -35 regions. Lastly, clues as to the role of antitermination in rRNA operons have begun to appear. Transcription complexes modified at the antiterminator site appear to elongate faster and are resistant to the inhibitory effects of ppGpp during the stringent response.
Collapse
Affiliation(s)
- C Condon
- Department of Molecular Biology and Microbiology, Tufts University Health Sciences Campus, Boston, Massachusetts 02111, USA
| | | | | |
Collapse
|
56
|
Abstract
Mu transposition is promoted by an extremely stable complex containing a tetramer of the transposase (MuA) bound to the recombining DNA. Here we purify the Escherichia coli ClpX protein, a member of a family of multimeric ATPases present in prokaryotes and eukaryotes (the Clp family), on the basis of its ability to remove the transposase from the DNA after recombination. Previously, ClpX has been shown to function with the ClpP peptidase in protein turnover. However, neither ClpP nor any other protease is required for disassembly of the transposase. The released MuA is not modified extensively, degraded, or irreversibly denatured, and is able to perform another round of recombination in vitro. We conclude that ClpX catalyzes the ATP-dependent release of MuA by promoting a transient conformational change in the protein and, therefore, can be considered a molecular chaperone. ClpX is important at the transition between the recombination and DNA replication steps of transposition in vitro; this function probably corresponds to the essential contribution of ClpX for Mu growth. Deletion analysis reveals that the sequence at the carboxyl terminus of MuA is important for disassembly by ClpX and can target MuA for degradation by ClpXP in vitro. These data contribute to the emerging picture that members of the Clp family are chaperones specifically suited for disaggregating proteins and are able to function with or without a collaborating protease.
Collapse
Affiliation(s)
- I Levchenko
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge 02139, USA
| | | | | |
Collapse
|
57
|
Visick JE, Clarke S. Repair, refold, recycle: how bacteria can deal with spontaneous and environmental damage to proteins. Mol Microbiol 1995; 16:835-45. [PMID: 7476182 DOI: 10.1111/j.1365-2958.1995.tb02311.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Proteins, like DNA, are subject to various forms of damage that can render them non-functional. Conformational changes and covalent chemical alterations occur spontaneously, and the rates of these reactions can be increased by environmental stresses such as heat, oxidative agents, or changes in pH or osmotic conditions. Although affected proteins can be replaced by de novo biosynthesis, cells--especially those subjected to stress or nutrient limitation--have developed mechanisms which can either restore damaged polypeptides to an active state or remove them. Such mechanisms can spare the biosynthetic capacity of the cell and ensure that the presence of non-functional molecules does not disrupt cell physiology. Three major mechanisms, which operate in bacteria as well as eukaryotic organisms, have been described. First, chaperones not only assist in proper de novo folding of proteins but also provide an important means of restoring activity to conformationally damaged proteins. Second, enzymatic 'repair' systems exist to directly reverse certain forms of protein damage, including proline isomerization, methionine oxidation and the formation of isoaspartyl residues. Finally, proteolysis provides a 'last-resort' means of dealing with abnormal proteins which cannot be repaired. Protein maintenance and repair may be of special importance for bacteria preparing to survive extended periods in stationary phase: both constitutive and induced mechanisms are utilized to permit survival despite greatly reduced protein synthesis.
Collapse
Affiliation(s)
- J E Visick
- Department of Chemistry and Biochemistry, University of California, Los Angeles 90024-1569, USA
| | | |
Collapse
|
58
|
Lehnherr H, Yarmolinsky MB. Addiction protein Phd of plasmid prophage P1 is a substrate of the ClpXP serine protease of Escherichia coli. Proc Natl Acad Sci U S A 1995; 92:3274-7. [PMID: 7724551 PMCID: PMC42148 DOI: 10.1073/pnas.92.8.3274] [Citation(s) in RCA: 145] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Plasmid-encoded addiction genes augment the apparent stability of various low copy number bacterial plasmids by selectively killing plasmid-free (cured) segregants or their progeny. The addiction module of plasmid prophage P1 consists of a pair of genes called phd and doc. Phd serves to prevent host death when the prophage is retained and, should retention mechanisms fail, Doc causes death on curing. Doc acts as a cell toxin to which Phd is an antidote. In this study we show that host mutants with defects in either subunit of the ClpXP protease survive the loss of a plasmid that contains a P1 addiction module. The small antidote protein Phd is fully stable in these two mutant hosts, whereas it is labile in a wild-type host. We conclude that the role of ClpXP in the addiction mechanism of P1 is to degrade the Phd protein. This conclusion situates P1 among plasmids that elicit severe withdrawal symptoms and are able to do so because they encode both a cell toxin and an actively degraded macromolecule that blocks the synthesis or function of the toxin.
Collapse
Affiliation(s)
- H Lehnherr
- Laboratory of Biochemistry, National Cancer Institute, Bethesda, MD 20892-4255, USA
| | | |
Collapse
|
59
|
Hübel A, Brandau S, Dresel A, Clos J. A member of the ClpB family of stress proteins is expressed during heat shock in Leishmania spp. Mol Biochem Parasitol 1995; 70:107-18. [PMID: 7637691 DOI: 10.1016/0166-6851(95)00012-p] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We have identified and isolated the Leishmania major homologue to the bacterial ClpB gene and to the yeast Hsp104 gene. ClpB in Leishmania major is a single-copy gene and encodes a low-abundance mRNA which is induced several-fold during a heat stress. We raised antibodies against the product of the recombinant gene and show that the leishmanial ClpB encodes a predominantly cytoplasmic protein of approx. 100 kDa which is detectable in Leishmania promastigotes of various species after exposure to elevated temperatures. We, therefore, term this protein Hsp100.
Collapse
Affiliation(s)
- A Hübel
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | | |
Collapse
|
60
|
Lee YR, Nagao RT, Key JL. A soybean 101-kD heat shock protein complements a yeast HSP104 deletion mutant in acquiring thermotolerance. THE PLANT CELL 1994; 6:1889-97. [PMID: 7866031 PMCID: PMC160569 DOI: 10.1105/tpc.6.12.1889] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
A cDNA clone encoding a 101-kD heat shock protein (HSP101) of soybean was isolated and sequenced. Genomic DNA gel blot analysis indicated that the corresponding gene is a member of a multigene family. The mRNA for HSP101 was not detected in 2-day-old etiolated soybean seedlings grown at 28 degrees C but was induced by elevated temperatures. DNA sequence comparison has shown that the corresponding gene belongs to the Clp (caseinolytic protease) (or Hsp100) gene family, which is evolutionarily conserved and found in both prokaryotes and eukaryotes. On the basis of the spacer length between the two conserved ATP binding regions, this gene has been identified as a member of the ClpB subfamily. Unlike other Clp genes previously isolated from higher plants, the expression of this soybean Hsp101 gene is heat inducible, and it does not have an N-terminal signal peptide for targeting to chloroplasts. Transformation of the soybean Hsp101 gene into a yeast HSP104 deletion mutant complemented restoration of acquired thermotolerance, a process in which cells survive an otherwise lethal heat stress after they are given a permissive heat treatment.
Collapse
Affiliation(s)
- Y R Lee
- Department of Botany, University of Georgia, Athens 30602
| | | | | |
Collapse
|
61
|
Borodovsky M, Rudd KE, Koonin EV. Intrinsic and extrinsic approaches for detecting genes in a bacterial genome. Nucleic Acids Res 1994; 22:4756-67. [PMID: 7984428 PMCID: PMC308528 DOI: 10.1093/nar/22.22.4756] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The unannotated regions of the Escherichia coli genome DNA sequence from the EcoSeq6 database, totaling 1,278 'intergenic' sequences of the combined length of 359,279 basepairs, were analyzed using computer-assisted methods with the aim of identifying putative unknown genes. The proposed strategy for finding new genes includes two key elements: i) prediction of expressed open reading frames (ORFs) using the GeneMark method based on Markov chain models for coding and non-coding regions of Escherichia coli DNA, and ii) search for protein sequence similarities using programs based on the BLAST algorithm and programs for motif identification. A total of 354 putative expressed ORFs were predicted by GeneMark. Using the BLASTX and TBLASTN programs, it was shown that 208 ORFs located in the unannotated regions of the E. coli chromosome are significantly similar to other protein sequences. Identification of 182 ORFs as probable genes was supported by GeneMark and BLAST, comprising 51.4% of the GeneMark 'hits' and 87.5% of the BLAST 'hits'. 73 putative new genes, comprising 20.6% of the GeneMark predictions, belong to ancient conserved protein families that include both eubacterial and eukaryotic members. This value is close to the overall proportion of highly conserved sequences among eubacterial proteins, indicating that the majority of the putative expressed ORFs that are predicted by GeneMark, but have no significant BLAST hits, nevertheless are likely to be real genes. The majority of the putative genes identified by BLAST search have been described since the release of the EcoSeq6 database, but about 70 genes have not been detected so far. Among these new identifications are genes encoding proteins with a variety of predicted functions including dehydrogenases, kinases, several other metabolic enzymes, ATPases, rRNA methyltransferases, membrane proteins, and different types of regulatory proteins.
Collapse
Affiliation(s)
- M Borodovsky
- School of Biology, Georgia Institute of Technology, Atlanta 30332-0230
| | | | | |
Collapse
|
62
|
Seol JH, Yoo SJ, Kim KI, Kang MS, Ha DB, Chung CH. The 65-kDa protein derived from the internal translational initiation site of the clpA gene inhibits the ATP-dependent protease Ti in Escherichia coli. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)43903-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
63
|
Myler PJ, Venkataraman GM, Lodes MJ, Stuart KD. A frequently amplified region in Leishmania contains a gene conserved in prokaryotes and eukaryotes. Gene 1994; 148:187-93. [PMID: 7958944 DOI: 10.1016/0378-1119(94)90688-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A 27.5-kb sequence that is present in an approx. 2-Mb chromosome in Leishmania also occurs as an inverted dimer in a multicopy, 55-kb circular molecule (LD1) in Leishmania infantum ITMAP263. Sequence analysis of a 7100-bp cloned segment from the circular molecule revealed three open reading frames (ORFs). The ORFs are likely to have protein coding function by a number of criteria, including Northern blot analyses. The amino acid (aa) sequences deduced from two ORFs showed no similarity to other sequences in the databases. The C-terminal aa sequence from the third ORF is related (22-29% identity, 57-71% similarity) to a family of genes conserved in bacteria and humans. One member (sfhB) of the gene family in Escherichia coli appears to have a role in regulation of cell growth.
Collapse
Affiliation(s)
- P J Myler
- Seattle Biomedical Research Institute, WA 98109-1651
| | | | | | | |
Collapse
|
64
|
Dharmatilake AJ, Kendrick KE. Expression of the division-controlling gene ftsZ during growth and sporulation of the filamentous bacterium Streptomyces griseus. Gene 1994; 147:21-8. [PMID: 8088545 DOI: 10.1016/0378-1119(94)90034-5] [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]
Abstract
The branched, filamentous cells of Streptomyces form two different types of septum: those found infrequently in vegetative mycelia and those that form the boundaries of developing spores. To begin to understand the role of cell septation events in the Streptomyces life cycle, we have isolated the ftsZ locus from Streptomyces griseus, an organism that undergoes sporulation on solid surfaces and in liquid culture. The nucleotide sequence of the cloned DNA indicates that ftsZ in S. griseus lies within a region containing other genes likely to be involved in cell division and cell wall biogenesis. A gene (ORF1) showing significant similarity to ftsQ maps a short distance upstream from ftsZ, but there is no evidence for an ftsA homologue between ftsZ and ORF1. Transcription analysis suggests that ftsZ is expressed during both vegetative growth and sporulation. Immunoblots of soluble protein preparations from vegetative and sporulating mycelia indicate that FtsZ is present at similar levels during growth and differentiation. There appears to be only one ftsZ gene in S. griseus. We interpret these results to indicate that any temporal regulation of FtsZ that may be necessary for the enhanced synthesis of septa during sporulation of S. griseus is likely to occur predominantly at the level of activity rather than synthesis.
Collapse
Affiliation(s)
- A J Dharmatilake
- Department of Microbiology, Ohio State University, Columbus 43210
| | | |
Collapse
|
65
|
Msadek T, Kunst F, Rapoport G. MecB of Bacillus subtilis, a member of the ClpC ATPase family, is a pleiotropic regulator controlling competence gene expression and growth at high temperature. Proc Natl Acad Sci U S A 1994; 91:5788-92. [PMID: 8016066 PMCID: PMC44082 DOI: 10.1073/pnas.91.13.5788] [Citation(s) in RCA: 125] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The Bacillus subtilis DegS-DegU histidine kinase-response regulator pair controls the expression of genes encoding degradative enzymes such as levansucrase (sacB) and of genes involved in genetic competence. The mecA and mecB mutations were previously isolated as allowing competence gene expression in complex media. We have shown that the mec mutations also lead to overexpression of sacB, bypassing the DegS-DegU requirement. This expression was shown to be entirely dependent upon ComK, a positive regulator of competence gene expression. The mecB gene was cloned and its nucleotide sequence was determined. The predicted MecB protein show very high similarity over its entire length with members of the ClpC family of ATPases (60% identity). MecB is essential for growth of B. subtilis at high temperature. MecB also acts as a negative regulator of ComK synthesis, thus preventing late competence gene expression. We suggest that under these conditions MecB may interact with MecA to sequester or otherwise inactivate ComK. In response to an unknown signal, active ComK would accumulate through a positive feedback loop, leading to expression of competence genes allowing DNA uptake.
Collapse
Affiliation(s)
- T Msadek
- Unité de Recherche Associée 1300 du Centre National de la Recherche Scientifique, Institut Pasteur, Département des Biotechnologies, Paris, France
| | | | | |
Collapse
|
66
|
Abstract
With the discovery of molecular chaperones and the development of heterologous gene expression techniques, protein folding in bacteria has come into focus as a potentially limiting factor in expression and as a topic of interest in its own right. Many proteins of importance in biotechnology contain disulphide bonds, which form in the Escherichia coli periplasm, but most work on protein folding in the periplasm of E. coli is very recent and is often speculative. This MicroReview gives a short overview of the possible fates of a periplasmic protein from the moment it is translocated, as well as of the E. coli proteins involved in this process. After an introduction to the specific physiological situation in the periplasm of E. coli, we discuss the proteins that might help other proteins to obtain their correctly folded conformation--disulphide isomerase, rotamase, parts of the translocation apparatus and putative periplasmic chaperones--and briefly cover the guided assembly of multi-subunit structures. Finally, our MicroReview turns to the fate of misfolded proteins: degradation by periplasmic proteases and aggregation phenomena.
Collapse
Affiliation(s)
- C Wülfing
- Biochemisches Institut, Universität Zurich, Switzerland
| | | |
Collapse
|
67
|
Mhammedi-Alaoui A, Pato M, Gama MJ, Toussaint A. A new component of bacteriophage Mu replicative transposition machinery: the Escherichia coli ClpX protein. Mol Microbiol 1994; 11:1109-16. [PMID: 8022280 DOI: 10.1111/j.1365-2958.1994.tb00387.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have shown previously that some particular mutations in bacteriophage Mu repressor, the frameshift vir mutations, made the protein very sensitive to the Escherichia coli ATP-dependent Clp protease. This enzyme is formed by the association between a protease subunit (ClpP) and an ATPase subunit. ClpA, the best characterized of these ATPases, is not required for the degradation of the mutant Mu repressors. Recently, a new potential ClpP associated ATPase, ClpX, has been described. We show here that this new subunit is required for Mu vir repressor degradation. Moreover, ClpX (but not ClpP) was found to be required for normal Mu replication. Thus ClpX has activities that do not require its association with ClpP. In the pathway of Mu replicative transposition, the block resides beyond the strand transfer reaction, i.e. after the transposition reaction per se is completed, suggesting that ClpX is required for the transition to the formation of the active replication complex at one Mu end. This is a new clear-cut case of the versatile activity of polypeptides that form multi-component ATP-dependent proteases.
Collapse
Affiliation(s)
- A Mhammedi-Alaoui
- Unité Transposition Bactérienne, Université Libre de Bruxelles, Rhode St Genèse, Belgium
| | | | | | | |
Collapse
|
68
|
HSP78 encodes a yeast mitochondrial heat shock protein in the Clp family of ATP-dependent proteases. Mol Cell Biol 1993. [PMID: 8413229 DOI: 10.1128/mcb.13.10.6304] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Saccharomyces cerevisiae nuclear gene for a 78-kDa mitochondrial heat shock protein (hsp78) was identified in a lambda gt11 expression library through immunological screening with an hsp78-specific monoclonal antibody. Sequencing of HSP78 revealed a long open reading frame capable of encoding an 811-amino-acid, 91.3-kDa basic protein with a putative mitochondrial leader sequence and two potential nucleotide-binding sites. Sequence comparisons revealed that hsp78 is a member of the highly conserved family of Clp proteins and is most closely related to the Escherichia coli ClpB protein, which is thought to be an ATPase subunit of an intracellular ATP-dependent protease. The steady-state levels of HSP78 transcripts and protein varied in response to both thermal stress and carbon source with an approximately 30-fold difference between repressed levels in cells growing fermentatively on glucose at 30 degrees C and derepressed levels in heat-shocked cells growing on a nonfermentable carbon source. The response to heat shock is consistent with the presence of a characteristic heat shock regulatory element in the 5'-flanking DNA. Submitochondrial fractionation showed that hsp78 is a soluble protein located in the mitochondrial matrix. Cells carrying disrupted copies of HSP78 lacked hsp78 but were not impaired in respiratory growth at normal and elevated temperatures or in the ability to survive and retain mitochondrial function after thermal stress. The absence of a strong mitochondrial phenotype in hsp78 mutants is comparable to the nonlethal phenotypes of mutations in other Clp genes in bacteria and yeast. HSP78 is the third gene, with SSC1 and HSP60, known to encode a yeast mitochondrial heat shock protein and the second gene, with HSP104, for a yeast ClpB homolog.
Collapse
|
69
|
Affiliation(s)
- C H Chung
- Department of Molecular Biology, College of Natural Sciences, Seoul National University, Korea
| |
Collapse
|
70
|
Leonhardt SA, Fearson K, Danese PN, Mason TL. HSP78 encodes a yeast mitochondrial heat shock protein in the Clp family of ATP-dependent proteases. Mol Cell Biol 1993; 13:6304-13. [PMID: 8413229 PMCID: PMC364689 DOI: 10.1128/mcb.13.10.6304-6313.1993] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The Saccharomyces cerevisiae nuclear gene for a 78-kDa mitochondrial heat shock protein (hsp78) was identified in a lambda gt11 expression library through immunological screening with an hsp78-specific monoclonal antibody. Sequencing of HSP78 revealed a long open reading frame capable of encoding an 811-amino-acid, 91.3-kDa basic protein with a putative mitochondrial leader sequence and two potential nucleotide-binding sites. Sequence comparisons revealed that hsp78 is a member of the highly conserved family of Clp proteins and is most closely related to the Escherichia coli ClpB protein, which is thought to be an ATPase subunit of an intracellular ATP-dependent protease. The steady-state levels of HSP78 transcripts and protein varied in response to both thermal stress and carbon source with an approximately 30-fold difference between repressed levels in cells growing fermentatively on glucose at 30 degrees C and derepressed levels in heat-shocked cells growing on a nonfermentable carbon source. The response to heat shock is consistent with the presence of a characteristic heat shock regulatory element in the 5'-flanking DNA. Submitochondrial fractionation showed that hsp78 is a soluble protein located in the mitochondrial matrix. Cells carrying disrupted copies of HSP78 lacked hsp78 but were not impaired in respiratory growth at normal and elevated temperatures or in the ability to survive and retain mitochondrial function after thermal stress. The absence of a strong mitochondrial phenotype in hsp78 mutants is comparable to the nonlethal phenotypes of mutations in other Clp genes in bacteria and yeast. HSP78 is the third gene, with SSC1 and HSP60, known to encode a yeast mitochondrial heat shock protein and the second gene, with HSP104, for a yeast ClpB homolog.
Collapse
Affiliation(s)
- S A Leonhardt
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst 01003
| | | | | | | |
Collapse
|
71
|
Wojtkowiak D, Georgopoulos C, Zylicz M. Isolation and characterization of ClpX, a new ATP-dependent specificity component of the Clp protease of Escherichia coli. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)41572-4] [Citation(s) in RCA: 194] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
72
|
Gottesman S, Clark W, de Crecy-Lagard V, Maurizi M. ClpX, an alternative subunit for the ATP-dependent Clp protease of Escherichia coli. Sequence and in vivo activities. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)41573-6] [Citation(s) in RCA: 240] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
73
|
Hobbs M, Mattick JS. Common components in the assembly of type 4 fimbriae, DNA transfer systems, filamentous phage and protein-secretion apparatus: a general system for the formation of surface-associated protein complexes. Mol Microbiol 1993; 10:233-43. [PMID: 7934814 DOI: 10.1111/j.1365-2958.1993.tb01949.x] [Citation(s) in RCA: 312] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The Pseudomonas aeruginosa genes pilB-D and pilQ are necessary for the assembly of type 4 fimbriae. Homologues of these genes and of the subunit (pilin) gene have been described in various different bacterial species, but not always in association with type 4 fimbrial biosynthesis and function. Pil-like proteins are also involved in protein secretion, DNA transfer by conjugation and transformation, and morphogensis of filamentous bacteriophages. It seems likely that the Pil homologues function in the processing and export of proteins resembling type 4 fimbrial subunits, and in their organization into fimbrial-like structures. These may either be true type 4 fimbriae, or components of protein complexes which act in the transport of macromolecules (DNA or protein) into or out of the cell. Some PilB-like and PilQ-like proteins are apparently also involved in the assembly of non-type 4 polymeric structures (filamentous phage virions and conjugative pili). The diverse studies summarized in this review are providing insight into an extensive infrastructural system which appears to be utilized in the formation of a variety of cell surface-associated complexes.
Collapse
Affiliation(s)
- M Hobbs
- Centre for Molecular Biology and Biotechnology, University of Queensland, Brisbane, Australia
| | | |
Collapse
|
74
|
Park S, Kim K, Woo K, Seol J, Tanaka K, Ichihara A, Ha D, Chung C. Site-directed mutagenesis of the dual translational initiation sites of the clpB gene of Escherichia coli and characterization of its gene products. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(20)80709-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
75
|
Abstract
An updated compilation of 300 E. coli mRNA promoter sequences is presented. For each sequence the most recent relevant paper was checked, to verify the location of the transcriptional start position as identified experimentally. We comment on the reliability of the sequence databanks and analyze the conservation of known promoter features in the current compilation. This database is available by E-mail.
Collapse
Affiliation(s)
- S Lisser
- Department of Molecular Genetics, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | | |
Collapse
|
76
|
Gage DJ, Neidhardt FC. Modulation of the heat shock response by one-carbon metabolism in Escherichia coli. J Bacteriol 1993; 175:1961-70. [PMID: 8458838 PMCID: PMC204276 DOI: 10.1128/jb.175.7.1961-1970.1993] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
A genetic screen designed to isolate mutants of Escherichia coli W3110 altered in the ability to induce the heat shock response identified a strain unable to induce the heat shock proteins in a rich, defined medium lacking methionine after exposure to 2,4-dinitrophenol. This strain also grew slowly at 28 degrees C and linearly at 42 degrees C in this medium. The abnormal induction of the heat shock proteins and abnormal growth at both high and low temperatures were reversed when methionine was included in the growth medium. The mutation responsible for these phenotypes mapped to the glyA gene, a biosynthetic gene encoding the enzyme that converts serine and tetrahydrofolate to glycine and 5,10-methylenetetrahydrofolate. This reaction is the major source of glycine and one-carbon units in the cell. Because fixed one-carbon units, in the form of methionine, allowed mutant cells to induce the heat shock response after exposure to 2,4-dinitrophenol, a one-carbon restriction may be responsible for the phenotypes described above.
Collapse
Affiliation(s)
- D J Gage
- Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor 48109-0620
| | | |
Collapse
|
77
|
Abstract
Dinucleotide AppppA (5',5'''-P1,P4-diadenosine tetraphosphate) is rapidly synthesized in Escherichia coli cells during heat shock. apaH mutants lack AppppN hydrolase activity and, therefore, contain constitutively levels of AppppA, which affect several cellular processes. However, the precise role of AppppA remains undetermined. Photo-crosslinking experiments with radioactively labelled azido-AppppA have shown that a number of proteins, including heat shock proteins DnaK and GroEL, specifically bind to AppppA. Several other unidentified proteins (C40, C45, and E89) also bind strongly to AppppA. In this work, we have identified the AppppA-binding protein E89 as heat shock protein ClpB. In addition, since ClpB belongs to a family of proteins implicated in proteolysis, we have examined the effects of apaH mutants on protein degradation. Constitutively elevated levels of AppppA stimulate lon-independent proteolysis only in heat-shocked cells. We also show that overproduction of ClpB from a plasmid rescues apaH mutants from sensitivity to killing by heat.
Collapse
Affiliation(s)
- E K Fuge
- Department of Molecular and Cellular Toxicology, Harvard School of Public Health, Boston, Massachusetts 02115
| | | |
Collapse
|
78
|
Parsell DA, Taulien J, Lindquist S. The role of heat-shock proteins in thermotolerance. Philos Trans R Soc Lond B Biol Sci 1993; 339:279-85; discussion 285-6. [PMID: 8098532 DOI: 10.1098/rstb.1993.0026] [Citation(s) in RCA: 127] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The role of heat-shock proteins (hsps) in thermotolerance was examined in the budding yeast Saccharomyces cerevisiae and in the fruit fly Drosophila melanogaster. In yeast cells, the major protein responsible for thermotolerance is hsp 100. In cells carrying mutations in the hsp 100 gene, HSP 104, growth is normal at both high and low temperatures, but the ability of cells to survive extreme temperatures is severely impaired. The loss of thermotolerance is apparently due to the absence of the hsp 104 protein itself because, with the exception of the hsp 104 protein, no differences in protein profiles were observed between mutant and wild-type cells. Aggregates found in mutant cells at high temperatures suggest that the cause of death may be the accumulation of denatured proteins. No differences in the rates of protein degradation were observed between mutant and wild-type cells. This, and genetic analysis of cells carrying multiple hsp 70 and hsp 104 mutations, suggests that the primary function of hsp 104 is to rescue proteins from denaturation rather than to degrade them once they have been denatured. Drosophila cells do not produce a protein in the hsp 100 class in response to high temperatures. In this organism, hsp 70 appears to be the primary protein involved in thermotolerance. Thus, the relative importance of different hsps in thermotolerance changes from organism to organism.
Collapse
Affiliation(s)
- D A Parsell
- Howard Hughes Medical Institute, University of Chicago, Illinois 60637
| | | | | |
Collapse
|
79
|
Damerau K, St John AC. Role of Clp protease subunits in degradation of carbon starvation proteins in Escherichia coli. J Bacteriol 1993; 175:53-63. [PMID: 8416909 PMCID: PMC196096 DOI: 10.1128/jb.175.1.53-63.1993] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
When deprived of a carbon source, Escherichia coli induces the synthesis of a group of carbon starvation proteins. The degradation of proteins labeled during starvation was found to be an energy-dependent process which was inhibited by the addition of KCN and accelerated when cells were resupplied with a carbon source. The degradation of the starvation proteins did not require the ATP-dependent Lon protease or the energy-independent proteases protease I, protease IV, OmpT, and DegP. During starvation, mutants lacking either the ClpA or ClpP subunit of the ATP-dependent Clp protease showed a partial reduction in the degradation of starvation proteins. Strains lacking ClpP failed to increase degradation of starvation proteins when glucose was added to starving cells. The clpP mutants showed a competitive disadvantage compared with wild-type cells when exposed to repeated cycles of carbon starvation and growth. Surprisingly, the glucose-stimulated, ClpP-dependent degradation of starvation proteins did not require either the ClpA or ClpB protein. The patterns of synthesis of starvation proteins were similar in clpP+ and clpP cells. The clpP mutants had reduced rates of degradation of certain starvation proteins in the membrane fraction when a carbon source was resupplied to the starved cells.
Collapse
Affiliation(s)
- K Damerau
- Nelson Biology Laboratories, Department of Biological Sciences, Rutgers University, Piscataway, New Jersey 08855-1059
| | | |
Collapse
|
80
|
Abstract
A number of critical regulatory proteins in both prokaryotic and eukaryotic cells are subject to rapid, energy-dependent proteolysis. Rapid degradation combined with control over biosynthesis provides a mechanism by which the availability of a protein can be limited both temporally and spatially. Highly unstable regulatory proteins are involved in numerous biological functions, particularly at the commitment steps in developmental pathways and in emergency responses. The proteases involved in energy-dependent proteolysis are large proteins with the ability to use ATP to scan for appropriate targets and degrade complete proteins in a processive manner. These cytoplasmic proteases are also able to degrade many abnormal proteins in the cell.
Collapse
Affiliation(s)
- S Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892
| | | |
Collapse
|
81
|
Woo K, Kim K, Goldberg A, Ha D, Chung C. The heat-shock protein ClpB in Escherichia coli is a protein-activated ATPase. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)88720-3] [Citation(s) in RCA: 138] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
82
|
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.
Collapse
Affiliation(s)
- M R Maurizi
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, Maryland 20892
| |
Collapse
|
83
|
Affiliation(s)
- C Squires
- Department of Biological Sciences, Columbia University, New York, New York 10027
| | | |
Collapse
|
84
|
Goldberg AL. The mechanism and functions of ATP-dependent proteases in bacterial and animal cells. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 203:9-23. [PMID: 1730246 DOI: 10.1111/j.1432-1033.1992.tb19822.x] [Citation(s) in RCA: 375] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- A L Goldberg
- Department of Cellular and Molecular Physiology, Harvard Medical School, Boston, MA 02115
| |
Collapse
|
85
|
Ang D, Liberek K, Skowyra D, Zylicz M, Georgopoulos C. Biological role and regulation of the universally conserved heat shock proteins. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)54216-2] [Citation(s) in RCA: 221] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
|
86
|
Pontis E, Sun XY, Jörnvall H, Krook M, Reichard P. ClpB proteins copurify with the anaerobic Escherichia coli reductase. Biochem Biophys Res Commun 1991; 180:1222-6. [PMID: 1953774 DOI: 10.1016/s0006-291x(05)81326-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Two proteins, called alpha and beta 3, copurify with the anaerobic ribonucleotide reductase from Escherichia coli (Eliasson et al. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 3314-3318). Both are now identified as products of the clpB gene that is presumed to code for a subunit of an ATP dependent protease. The tight associations suggest the possibility that the ClpB proteins are involved in the regulation of the anaerobic reductase.
Collapse
Affiliation(s)
- E Pontis
- Department of Biochemistry I, Karolinska Institute, Stockholm, Sweden
| | | | | | | | | |
Collapse
|
87
|
New nucleotide sequence data on the EMBL File Server. Nucleic Acids Res 1991; 19:6063-79. [PMID: 1945897 PMCID: PMC329084 DOI: 10.1093/nar/19.21.6063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
|
88
|
Parsell DA, Sanchez Y, Stitzel JD, Lindquist S. Hsp104 is a highly conserved protein with two essential nucleotide-binding sites. Nature 1991; 353:270-3. [PMID: 1896074 DOI: 10.1038/353270a0] [Citation(s) in RCA: 221] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Most eukaryotic cells produce proteins with relative molecular masses in the range of 100,000 to 110,000 after exposure to high temperatures. These proteins have been studied only in yeast and mammalian cells. In Saccharomyces cerevisiae, heat-shock protein hsp104 is vital for tolerance to heat, ethanol and other stresses. The mammalian hsp110 protein is nucleolar and redistributes with growth state, nutritional conditions and heat shock. The relationships between hsp110, hsp104 and the high molecular mass heat-shock proteins of other organisms were unknown. We report here that hsp104 is a member of the highly conserved ClpA/ClpB protein family first identified in Escherichia coli and that additional heat-inducible members of this family are present in Schizosaccharomyces pombe and in mammals. Mutagenesis of two putative nucleotide-binding sites in hsp104 indicates that both are essential for function in thermotolerance.
Collapse
Affiliation(s)
- D A Parsell
- Howard Hughes Medical Institute, University of Chicago, Illinois 60637
| | | | | | | |
Collapse
|
89
|
Abstract
ClpB is thought to be involved in proteolysis because of its sequence similarity to the ClpA subunit of the ClpA-ClpP protease. It has recently been shown that ClpP is a heat shock protein. Here we show that ClpB is the Escherichia coli heat shock protein F84.1. The F84.1 protein was overproduced in strains containing the clpB gene on a plasmid and was absent from two-dimensional gels from a clpB null mutation. Besides possessing a slower growth rate at 44 degrees C, the null mutant strain had a higher rate of death at 50 degrees C. We used reverse transcription of in vivo mRNA to show that the clpB gene was expressed from a sigma 32-specific promoter consensus sequence at both 37 and 42 degrees C. We noted that the clpB+ gene also caused the appearance of a second protein spot, F68.5, on two-dimensional gels. This spot was approximately 147 amino acids smaller than F84.1 and most probably is the result of a second translational start on the clpB mRNA. F68.5 can be observed on many published two-dimensional gels of heat-induced E. coli proteins, but the original catalog of 17 heat shock proteins did not include this spot.
Collapse
Affiliation(s)
- C L Squires
- Department of Biological Sciences, Columbia University, New York, New York 10027
| | | | | | | |
Collapse
|