Starvation promoters of Escherichia coli. Their function, regulation, and use in bioprocessing and bioremediation.
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Bacterial Proteins↗
Biomedical subjects
A Matin
Publications and source records attributed to A Matin.
Characterization of the sigma 38-dependent expression of a core Escherichia coli starvation gene, pexB.
A reverse genetics approach was used to clone a pex starvation gene that codes for an 18-kDa polypeptide, designated PexB. Single-copy pexB-lacZ operon fusions were constructed to study transcriptional regulation and the promoter region of this gene. The induction by carbon starvation or osmotic stress was transcriptional and controlled by sigma 38 but was independent of this sigma factor by the oxidative stress; presumably, it was sigma 70 mediated under the latter stress. During nitrogen starvation, the induction was controlled at the posttranscriptional level. The pexB upstream region contained 245 nucleotides within which sequences approximating the consensus for cyclic AMP receptor protein and integration host factor binding sites were discernible. Deletion of 164 bp of the upstream region, which included these consensus sequences, did not affect starvation-or osmotic stress-mediated induction of pexB but abolished its induction by oxidative stress. The same start site was used in transcription during carbon starvation, osmotic stress, or oxidative stress, suggesting that the pexB promoter can be recognized in vivo by both sigma 38 and sigma 70, depending, presumably, on the presence of appropriate transcriptional factors. The -10 and -35 regions of pexB resembled those of some but not all genes known to be controlled by sigma 38.
Adaptation, Physiological↗
The retinoblastoma gene product, Rb, represses neu expression through two regions within the neu regulatory sequence.
The neu oncogene is frequently overexpressed in breast, ovarian and lung cancers, and its overexpression correlates with poor disease prognosis. The exact mechanism of deregulation of neu expression is not well understood. Our previous studies indicate that the tumor suppressor retinoblastoma gene product, Rb, represses transcription of neu through the GTG enhancer (-243 to -234 relative to initiation of translation site of rat neu). We carried out further deletion analysis of the regulatory sequences of neu and found that Rb also represses neu close to transcription initiation sites (-172 to -79). Bal 31 deletions downstream of nucleotide -172 show that the sequence TCGAGGAA (-172 to -165) is important for efficient transcription from the neu promoter and also for repression by Rb. Rb mutants with mutations in the large T/E1a binding domain repress transcription from transcription initiation sites but not the GTG enhancer, suggesting that Rb modulates different regions of the regulatory sequence of neu by different pathways. The net effect of the Rb mutants is to repress not only transcription but also the transforming activity of activated neu in focus-forming assays. Thus, one mechanism whereby Rb may act as a tumor suppressor is to repress transcription of the strongly transforming neu oncogene.
3T3 Cells↗
Transcriptional regulation of neu by RB and E1A in rat-1 cells.
Functional inactivation of the tumor-suppressing retinoblastoma gene (Rb) is involved in the etiology of many types of human cancers, including hereditary retinoblastomas. The neu gene is a dominant transforming oncogene, and we previously found that the Rb-encoded protein (RB) suppresses neu-induced transformation in NIH3T3 cells by repressing transcription of the neu oncogene. We report here that RB was unable to repress neu oncogene transcription in Rat-1 cells but could functionally antagonize transcriptional repression of neu by the adenovirus E1A. Mutant forms of RB that have mutations in either the E1A-binding or carboxy-terminal regions had less or no antagonizing effects on E1A-mediated repression of neu in Rat-1 cells. Results of focus-formation assays showed that the transformation activity of the neu oncogene in Rat-1 cells could be regulated by E1A and RB in accordance with their transcriptional regulation activities. The data demonstrate that RB can regulate transcription of neu in a negative or positive manner depending on the cell type. Carboxy terminus of RB as well as the E1A-binding region can mediate transcriptional regulation. Based on these results, we propose a model for the complex transcriptional regulation of neu by RB and E1A.
Adenoviridae↗
Significant dispersed recurrent DNA sequences in the Escherichia coli genome. Several new groups.
New computer and statistical methods were used to determine significant direct and inverted repeats in the Escherichia coli contig sequence collection of aggregate 1.6 x 10(6) base-pairs. Eight groups of mostly new structural repeat identities were uncovered. Apart from the high statistical significance of these repeat sequences, there are suggestive relationships of the group matches in terms of neighboring genes, of genomic distributions, of their texts, and of their potentials for secondary structure. Four of these groups are relatively numerous, 11 to 26 members, one is in coding sequences and three are in non-coding. The coding group consists of the ATP-activated transmembrane component of a typical high-affinity protein-binding transport system. One of the non-coding groups consists of a special rho-independent transcription termination signal closely following an operon. The gene neighbors of this group often appear to be involved in some way in processing RNA or DNA. A second non-coding group has, for one or both neighboring genes, a component of a system responding to stress or starvation for some nutrient.
Algorithms↗
Repression of neu-induced clonogenicity by dimethylsulfoxide correlates with decreased levels of neu-encoded cell-surface p185 and changes in phosphotyrosine content of endogenous proteins.
Treatment of neu-transformed fibroblasts with dimethylsulfoxide (DMSO), results in change in morphology and loss of clonogenicity. Although the total amount of neu-encoded p185 protein and mRNA remained constant after DMSO treatment, cell-surface p185 decreased by 60%, indicating that transmembrane p185 protein is not located in its physiological position. The aberrant location of p185 induced by DMSO resulted in increased tyrosine phosphorylation of p185 and concomitant decreased tyrosine phosphorylation of potential substrate proteins of p185 in the cell. However, the autophosphorylation activity of p185 in vitro was unaffected by DMSO. Thus, DMSO-induced loss of clonogenicity may be due to inappropriate location of p185, which prevents interaction between p185 and its substrates and therefore inhibits p185-mediated signal transduction pathway.
Animals↗
The putative sigma factor KatF is regulated posttranscriptionally during carbon starvation.
Transcriptional and translational 'lacZ reporter fusions were constructed to the katF gene, which encodes a putative sigma factor centrally involved in starvation-mediated general resistance in Escherichia coli. Transcription of katF was found to increase ca. twofold after carbon starvation in minimal medium. The protein fusion containing the longest fragment of katF induced ca. eightfold under the same conditions, whereas fusions to shorter segments showed only a twofold increase in expression. The protein fusion was expressed at higher levels in a strain containing a katF::Tn10 mutation, indicating katF autoregulation. The posttranscriptional regulation of katF by starvation did not require a component of the spent minimal medium. katF was also posttranscriptionally regulated during entry into late log phase in complex medium. This induction was coincident with an increase in katE transcription, suggesting that the cellular concentration of KatF directly followed the induction of the katF protein fusion.
Bacterial Proteins↗
Negative regulation of the neu promoter by the SV40 large T antigen.
The neu gene is amplified and its protein product is overexpressed in certain human tumors. The adenovirus 5 E1a gene product and c-myc repress neu transcription. Moreover, expression of E1a in neu-transformed cells leads to decrease in transformation phenotype and metastatic potential. The simian virus 40 large T antigen (LT) shares structural and functional homology with E1a and c-myc, and all three proteins bind to the retinoblastoma gene product, Rb. We found that LT also represses neu expression at the transcriptional level. However, LT represses neu promoter by a different mechanism compared to E1a and c-myc, because the region of the neu promoter mediating repression by LT (-172 to -79) is downstream from the region responding to E1a and c-myc (-312 to -172). In addition, a LT mutant (K1) unable to complex Rb still represses neu promoter activity, indicating that the Rb binding domain of LT is not required for repression of neu. Since K1, unlike LT, does not transform Rat-1 cells but, like LT, represses the neu promoter, we tested whether K1 functions as a transformation suppressor of activated neu oncogene. Focus-forming assays showed that K1 indeed suppresses the strong cell-transforming activity of activated neu.
Animals↗
Genetics of bacterial stress response and its applications.
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Bacteria↗
The retinoblastoma gene product suppresses neu oncogene-induced transformation via transcriptional repression of neu.
The retinoblastoma susceptibility gene (Rb) is a tumor suppressor gene involved in the etiology of many types of human cancers. However, the molecular mechanisms involved in tumor suppression by Rb are largely unknown. The neu gene is a dominant transforming oncogene and a member of the growth factor receptor tyrosine kinase gene family. Both inactivation of the Rb gene and overexpression of the neu gene are involved in human breast and lung cancers. Therefore, it is of interest and importance to investigate the potential interactions between Rb and neu. Here we show that Rb suppresses neu-induced transformation by focus formation assays. This transformation suppression by Rb was further shown to be due to transcriptional repression of neu using Rb expressing effector plasmid and neu promoter-chloramphenicol acetyltransferase reporter gene. The cis-acting element conferring Rb-mediated repression was mapped to a recently identified novel enhancer in the neu promoter. The data indicate that the growth factor receptor neu is a target for the Rb gene product and transcriptional repression of a dominant oncogene expression may be one of the molecular mechanisms of Rb-mediated tumor suppression.
3T3 Cells↗
DnaK-mediated alterations in human growth hormone protein inclusion bodies.
Protein overproduction in microbes frequently results in protein misfolding and aggregation though the molecular basis for this process is unclear. The HSP70 chaperonin, DnaK, was identified as an important factor controlling heterologous protein aggregation in Escherichia coli. Co-overproduction of DnaK significantly reduced human growth hormone (HGH) protein inclusion body formation and the extent of HGH aggregation.
Bacterial Proteins↗
Physiology, molecular biology and applications of the bacterial starvation response.
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Bacteria↗
Unique and overlapping pollutant stress proteins of Escherichia coli.
Exposure of growing batch cultures of Escherichia coli to nine different "model micropollutants" (benzene, cadmium chloride, chlorpyrivos, 2,4-dichloroaniline, dioctylphtalate, hexachlorobenzene, pentachlorophenol, trichloroethylene, and tetrapropylbenzosulfonate) led to the induction of 13 to 39 proteins, as analyzed by two-dimensional gel electrophoresis. Some of these proteins overlapped with heat shock and carbon starvation proteins, but at least 50% were unique to a given chemical. The stress protein induction showed a temporal pattern, indicating sequential gene expression. Chemical stress protein synthesis occurred even at concentrations that had no effect on growth. Thus, the synthesis of these proteins can be a sensitive index of stress and the nature of environmental pollution.
Bacterial Proteins↗
Molecular and functional characterization of a carbon starvation gene of Escherichia coli.
Escherichia coli induces the synthesis of at least 30 proteins at the onset of carbon starvation, two-thirds of which are positively regulated by the cyclic AMP (cAMP) and cAMP receptor protein (CRP) complex. Two of the cAMP-CRP-dependent genes mapped to 14 and 93 minutes of the chromosome and are designated cstA and cstB, respectively. The cstA promoter region was cloned and localized to a 600 base-pair fragment downstream from the iron-regulated entCEBA-P15 operon. Carbon starvation-inducible transcription initiated at three sites spaced one turn of the DNA helix apart. All had--10 sequences similar to consensus E sigma 70 promoters and poor--35 sequences. Deletion of a putative CRP binding site abolished carbon starvation-mediated induction. Sequence analysis of the cstA coding region revealed the presence of three sequential open reading frames potentially encoding two hydrophobic proteins of 60,223 Da and 15,201 Da and a hydrophilic protein of 7467 Da. Overexpression of the cstA region produced starvation-inducible proteins of the expected sizes. Suggestive evidence was obtained that cstA is involved in peptide utilization.
Amino Acid Sequence↗
The molecular basis of carbon-starvation-induced general resistance in Escherichia coli.
At the onset of starvation Escherichia coli undergoes a temporally ordered program of starvation gene expression involving 40-80 genes which some four hours later yields cells possessing an enhanced general resistance. Two classes of genes are induced upon carbon starvation: the cst genes, requiring cyclic AMP, and the pex genes, not requiring this nucleotide for induction. The cst genes are not involved in the development of the resistant state and are concerned with escape from starvation, while the pex gene induction appears to be associated with resistance. Many of the latter are induced in response to a variety of starvation conditions. They include heat shock and oxidation resistance genes, and some utilize minor, stationary-phase-specific sigma factors for induction during starvation. The protective role of stress proteins may be due to their ability to rescue misfolded macromolecules. The starvation promoters can be potentially useful for selective expression of desired genes in metabolically sluggish populations, e.g. in high-density industrial fermentations and in situ bioremediation.
Bacterial Proteins↗
The putative sigma factor KatF has a central role in development of starvation-mediated general resistance in Escherichia coli.
KatF is required for the expression of some 32 carbon starvation proteins in Escherichia coli including 6 previously identified as Pex. Mutants with the katF gene survive carbon and nitrogen starvation poorly. Many of the KatF-regulated starvation proteins are common to those induced by other stresses, and the mutant failed to develop starvation-mediated cross protection to osmotic, oxidative, and heat stresses. Furthermore, thermal resistance was not induced in the mutant by heat preadaptation, and it exhibited an altered pattern of protein synthesis at elevated temperature. Thus, KatF is a major switch that controls the starvation-mediated resistant state in E. coli.
Bacterial Proteins↗
Role of RpoH, a heat shock regulator protein, in Escherichia coli carbon starvation protein synthesis and survival.
Escherichia coli starvation proteins include several heat shock proteins whose induction by heat is controlled by the minor sigma factor, sigma 32. The level of sigma 32 increased in wild-type E. coli upon starvation, and three sigma 32-controlled heat shock proteins (DnaK, GroEL, and HtpG) were not induced during starvation in an isogenic delta rpoH strain, which is unable to synthesize sigma 32. Thus, sigma 32 plays a role in the induction of these proteins during both heat shock and starvation. The delta rpoH strain was more sensitive to starvation but could develop starvation-mediated cross protection against heat and oxidation.
Bacterial Proteins↗
Chloride transport pathways and their bioenergetic implications in the obligate acidophile Bacillus coagulans.
The protonophore-mediated collapse of the large delta pH that acidophiles maintain across their cytoplasmic membranes was augmented by the presence of Cl-, and Cl- influx into the cells occurred evidently in response to the protonophore-induced increase in the inside-positive membrane potential (+ delta psi). In respiring cells, the addition of Cl- but not SO4(2-) salts caused a rapid and precipitous decrease in the + delta psi. A Nernstian relationship between the imposed transmembrane K+ gradient and the valinomycin-induced K+ diffusion potentials was observed when everted membrane vesicles were loaded with K2SO4 or KH2PO4 but not when loaded with KCl or KNO3. Thus, electrogenic Cl- transport occurred in Bacillus coagulans. In addition, a nonelectrogenic temperature-sensitive Cl- transport mechanism, with the net Cl- efflux coefficient (PCl-) ranging from 1.5 x 10(-4) to 6.1 x 10(-6) cm/s, accounted for the massive Cl- efflux from Cl(-)-loaded cells. Thus, B. coagulans, despite its dependence on the + delta psi and therefore the need to exclude anions, apparently possesses specific mechanisms for Cl- permeation. Active cells of B. coagulans prevented Cl- accumulation from attaining an electrochemical equilibrium, maintaining a delta micro Cl- of ca. -63 mV. B. coagulans therefore also possesses an energy-dependent mechanism for Cl- exclusion from the cells.
Anions↗