Analysis of products of the Escherichia coli genomic genes and regulation of their expressions: an applicable procedure for genomic analysis of other microorganisms

Molecular basis and functional development of membrane-based microbial metabolism

My research interest has so far been focused on metabolisms related to the "membrane" of microorganisms, such as the respiratory chain, membrane proteins, sugar uptake, membrane stress and cell lysis, and fermentation. These basic metabolisms are important for the growth and survival of cell, and their knowledge can be used for efficient production of useful materials. Notable achievements in research on metabolisms are elucidation of the structure and function of membrane-bound glucose dehydrogenase as a primary enzyme in the respiratory chain, elucidation of ingenious expression regulation of several operons or by divergent promoters, elucidation of stress-induced programed-cell lysis and its requirement for survival during a long-term stationary phase, elucidation of molecular mechanism of survival at a critical high temperature, elucidation of thermal adaptation and its limit, isolation of thermotolerant fermenting yeast strains, and development of high-temperature fermentation and green energy production technologies. These achievements are described together in this review.

Analysis of reading frame and expressional regulation of randomly selected promoter-proximal genes in Escherichia coli

The expression of seventy-seven randomly cloned genes of Escherichia coli was examined following a variety of treatments including heat shock, glucose starvation, phosphate starvation, ammonium starvation or osmotic shock, with the aid of lacZ reporter gene protein fusions on multicopy plasmids. Two of 77 genes (amr and yigL) had not previously been identified as protein encoding open-reading frames (ORFs) in annotations of the E. coli genome database. Thirteen genes exhibited significant changes in expression in response to at least one of the treatments, and six of them appeared to be controlled by more than one sigma (sigma) factor of RNA polymerase. This study thus allows us not only to identify the reading frame of the genomic genes but also to support the hypothesis earlier proposed that a significant proportion of genes in E. coli are involved in adaptations to various stresses to which the organism is likely to be exposed in the environment.

Characterization of the ssnA gene, which is involved in the decline of cell viability at the beginning of stationary phase in Escherichia coli

When grown in rich medium, Escherichia coli exhibits a drastic reduction of the number of viable cells at the beginning of stationary phase. The decline of cell viability was retarded by disruption of the ssnA gene, which was identified as a gene subject to RpoS-dependent negative regulation. Moreover, ssnA expression was induced at the time of decline of cell viability at early stationary phase. The viability decline was augmented in the rpoS background, and this augmentation was suppressed by ssnA mutation. Cloning of the ssnA gene in a multicopy plasmid, pBR322, caused small colony formation and slow growth in liquid medium. Cells harboring the ssnA clone showed aberrant morphology that included enlarged and filamentous shapes. The gene product was identified as a 44-kDa soluble protein, but its function could not be deduced by homology searching. From these results, we conclude that ssnA is expressed in response to a phase-specific signal(s) and that its expression level is controlled by RpoS, by a mechanism which may contribute to determination of cell number in the stationary phase.

Characterization of TreR, the major regulator of the Escherichia coli trehalose system

The pathway of trehalose utilization in Escherichia coli is different at low and high osmolarity. The low osmolarity system takes up trehalose as trehalose 6-phosphate which is hydrolyzed to glucose and glucose 6-phosphate. treB and treC, the genes for the enzymes involved, form an operon that is controlled by TreR (encoded by treR), the repressor of the system, for which trehalose 6-phosphate is the inducer. We have cloned and sequenced treR. The protein contains 315 amino acids with a molecular weight of 34,508. TreR was purified and shown to bind as a dimer trehalose 6-phosphate and trehalose with a Kd of 10 and 280 microM, respectively. The conformations of the protein differ from each other with either one or the other substrate-bound. Protease treatment removed the DNA-binding domain from the intact protein leaving the dimerization domain (a 29-kDa carboxyl-terminal fragment) intact. Nuclease protection experiments revealed a palindromic sequence located directly upstream of the -35 promoter sequence of treB that functions as the operator of the system.

A new periplasmic protein of Escherichia coli which is synthesized in spheroplasts but not in intact cells

The gene spy from Escherichia coli has been cloned and sequenced. It encodes a precursor of a so far unknown 139-residue, rather basic periplasmic protein. It was not detectable immunologically in intact cells but was produced abundantly in spheroplasts. It could be a stress protein specific for spheroplasting.

RpoS-dependent regulation of genes expressed at late stationary phase in Escherichia coli

We have identified 6 Escherichia coli genomic genes, including 4 new genes, responsive to the stationary phase. One of them was regulated positively by RpoS at the stationary phase, and the remaining 5 negatively at a late stationary phase, all of them responding to multiple environmental stresses. Nucleotide sequences as well as such multiple responses revealed that those genes may have more than one overlapping-promoter recognized by different sigma-factors which regulate gene expressions during their cell growth.

Sequence and characterization of the Escherichia coli genome between the ndk and gcpE genes

The region of the chromosome immediately upstream of the Escherichia coli gene gcpE has been cloned and sequenced. This region contains two functional open reading frames, orf 384 and orf 337, encoding proteins of 43,082 and 36,189 Da, respectively. Sequencing analysis (this paper) and the isolation of a DNA fragment containing a functional promoter (Talukder, A.A., Yanai, S., and Yamada, M. (1994) Biosci. Biotech. Biochem. 58, 117-120) indicate that orf 337 is in an operon with gcpE. The gene orf 384 is immediately downstream of the gene ndk, which encodes nucleoside diphosphate kinase.