Irvin N. Hirshfield

Folding in vivo of bacterial cytoplasmic proteins: Role of GroEL

A general role for chaperonin ring structures in mediating folding of newly translated proteins has been suggested. Here we have directly examined the role of the E. coli chaperonin GroEL in the bacterial cytoplasm by production of temperature-sensitive lethal mutations in this essential gene. After shift to nonpermissive temperature, the rate of general translation in the mutant cells was reduced, but, more specifically, a defined group of cytoplasmic proteins--including citrate synthase, ketoglutarate dehydrogenase, and polynucleotide phosphorylase--were translated but failed to reach native form. Similarly, a monomeric test protein, maltose-binding protein, devoid of its signal domain, was translated but failed to fold to its native conformation. We conclude that GroEL indeed is a machine at the distal end of the pathway of transfer of genetic information, assisting a large and specific set of newly translated cytoplasmic proteins to reach their native tertiary structures.

Two-dimensional gel electrophoretic resolution of the polypeptides of rat liver mitochondria and the outer membrane

The proteins of highly purified rat liver mitochondria were resolved by two-dimensional polyacrylamide gel electrophoresis, and detected by staining with either Coomassie blue or silver. Approximately 250 polypeptides were detected with silver staining which is 2- to 3-times that observed with Coomassie blue. Silver staining was especially more effective than Coomassie blue for detecting polypeptides of less than 50 000 daltons. A two-dimensional gel pattern of rat liver microsomes was distinct from that of the mitochondria. The mitochondrial outer membrane was prepared from purified mitochondria either with digitonin or by swelling in a hypotonic medium. As assessed by marker enzymes, the latter method yielded a considerably purer outer membrane preparation (20-fold purification) than the former (2.6-fold purification). Approximately 50 polypeptides were observed in a two-dimensional gel (pH 3-10) of the highly purified outer membrane fraction. Three isoelectric forms of the pore (VDAC) protein were observed with pI values of 8.2, 7.8 and 7.1. Monoamine oxidase was identified as a polypeptide of Mr 60 000. About 50 polypeptides were also resolved in a reverse polarity non-equilibrium pH gradient electrophoresis gel of the outer membrane, pH 3-10, with at least six isoelectric forms of the VDAC protein observed under these conditions. The six isoforms of the VDAC protein were also observed in a non-equilibrium gel with 2 micrograms of the purified protein.

The effect of acid treatment on survival and protein expression of a laboratory K-12 strain Escherichia coli

Pre-exposure of log phase enteric bacteria to nonlethal acidic pH induces phenotypic changes that protect the organisms against subsequent lethal acidity. Studies have revealed that when Salmonella typhimurium is grown in minimal medium at pH 5.5 and 4.3 the organism develops a biphasic acid tolerance. This two-stage response has not been reported at present in Escherichia coli; rather it is thought that when this organism is grown in rich medium there is a single stress response throughout the pH range of 4 to 6. We believe that the evidence for such a report is lacking; therefore, in this study the acid response of log phase E. coli was examined in rich medium (LB). The pH 3.0 acid survival assays of a laboratory strain of E. coli K-12 MG1655, after cultures had been exposed to LB acidified to pH 5.5 or pH 4.3 indicate that like S. typhimurium, E. coli shows both an acid tolerance and an acid-shock response to pH 5.5 and 4.3 exposure, respectively. It was consistently found, however, that longer pre-exposure (60 min rather than 15 min) at either pH afforded better protection against the lethal pH 3.0 challenge. Analysis of polypeptide induction at pH 5.5 and 4.3 by two-dimensional gel electrophoresis clearly shows different profiles. Together the results show that in E. coli, pre-treatment between pH 4 and 6 does not result in a flat protective response.

Rapid approach to identify an unrecognized viral agent.

Abstract For epidemic control, rapid identification and characterization of the responsible unknown agent are crucial. To address this critical question, a method was developed for virus discovery based on a flexible nested-PCR subtraction hybridization. As a positive control, we used hepatitis C virus as a hypothetical unrecognized virus and “discover” it in the sample. Using template-switching universal long-PCR to produce large quantities of cDNA, our nested-PCR-based subtractive hybridization coupled with a single-strand deletion technology removed most of the common cDNA. Following subtraction hybridization, a cDNA library was constructed and displayed by differential reverse dot blot hybridization. This new genomic subtraction hybridization method will be ideally suited to identify rapidly any previously unrecognized viral agent.

The Physiological and Molecular Characterization of a Small Colony Variant of Escherichia coli and Its Phenotypic Rescue

Small colony variants (SCVs) can be defined as a naturally occurring sub-population of bacteria characterized by their reduced colony size and distinct biochemical properties. SCVs of Staphylococcus aureus have been studied extensively over the past two decades due to their role in recurrent human infections. However, little work has been done on SCVs of Escherichia coli, and this work has focused on the physiology and morphology that define these colonies of E. coli, such as small size and slow growth. E. coli strain JW0623, has a null lipA mutation in the lipoic acid synthase gene (lipA), and is a lipoic acid auxotroph. When the mutant was grown in LB medium to log phase, it showed remarkable resistance to acid (pH 3), hydrogen peroxide, heat and osmotic stress compared to its parent BW25113. Using RT-PCR and real time RT-PCR, the expression of certain genes was compared in the two strains in an attempt to create a molecular profile of Escherichia coli SCVs. These include genes involved in glycolysis, TCA cycle, electron transport, iron acquisition, biofilm formation and cyclopropane fatty acid synthesis. It was also demonstrated that the addition of 5 μg/ml of lipoic acid to LB medium allows for the phenotypic rescue of the mutant; reversing its slow growth, its resistance characteristics, and elevated gene expression. These results indicate that the mutation in lipA leads to an E. coli SCV that resembles an electron transport defective SCV of S. aureus These strains are typically auxotrophs, and are phenotypically rescued by adding the missing metabolite to rich medium. There are global shifts in gene expression which are reversible and depend on whether the auxotrophic molecule is absent or present. Looking at the E. coli SCV from an evolutionary point of view, it becomes evident that its path to survival is to express genes that confer stress resistance.

Differential Gene Expression Analysis of a Small Colony Variant of Escherichia coli K-12

As persistent residents of planktonic bacterial cultures, small colony variants (SCVs) constitute a slow-growing subpopulation with atypical colony morphology and unusual biochemical characteristics that, in the case of clinical isolates, cause latent and recurrent infections. We propose a novel blueprint for the formation of E. coli SCVs through DNA microarray analysis, coupled with complete genome sequencing and verification by qRT-PCR. While others have used DNA microarrays to study quorum sensing in E. coli SCVs, our work represents the first proposal for a combination of novel mutations, amplified by a differential shift in expression of select gene groups that work in concert to establish and maintain the SCV phenotype. This combination of genetic and expression events fall under selective pressure, leading to unequal fitness in our strain, SCV IH9 versus its parental strain, BW7261 (a MG1655 descendant). We hypothesize that this combination of events would ordinarily be lethal for bacteria, but instead confers a survival advantage to SCV IH9 due to its slow growth and resistance to acidic and oxidative stress challenges.