Jyotirmoy Das

Stress response in pathogenic bacteria

Bacterial pathogens survive under two entirely different conditions, namely, their natural environment and in their hosts. Response of these pathogens to stresses encountered during transition from the natural environment to human hosts has been described. The virulence determinants of pathogenic bacteria are under the control of transcriptional activators which respond to fluctuations in growth temperature, osmolarity, metal ion concentration and oxygen tension of the environment. The regulation of stress induced genes may occur at the level of transcription or translation or by post-translational modifications. Under certain stress conditions local changes in the superhelicity of DNA induce or repress genes. In addition to their role in survival of bacteria under stressful situations, the stress induced proteins are also implicated in the manifestation of pathogenicity of bacterial pathogensin vivo.

Chaos game representation of proteins

The present report proposes a new method for the chaos game representation (CGR) of different families of proteins. Using concatenated amino acid sequences of proteins belonging to a particular family and a 12-sided regular polygon, each vertex of which represents a group of amino acid residues leading to conservative substitutions, the method can generate the CGR of the family and allows pictorial representation of the pattern characterizing the family. An estimation of the percentages of points plotted in different segments of the CGR (grid points) allows quantification of the nonrandomness of the CGR patterns generated. The CGRs of different protein families exhibited distinct visually identifiable patterns. This implies that different functional classes of proteins follow specific statistical biases in the distribution of different mono-, di-, tri-, or higher order peptides along their primary sequences. The potential of grid counts as the discriminative and diagnostic signature of a family of proteins is discussed.

Cholera toxin (CTX) genetic element in Vibrio cholerae O139.

PFGE analysis of the NotI- and SfiI-digested genome of Vibrio cholerae O139 strains isolated from different epidemic regions of India showed that all the strains are of clonal origin and the genome size is about 2.2 Mb. An analysis of the electrophoretic profiles of the genome of O139 strains, the RFLP of the cholera toxin (ctx) gene and Southern blot hybridization of NotI-digested genomes of classical, El Tor and O139 with a NotI-linking clone of classical strain 569B, suggest that these strains closely resemble V. cholerae O1 biotype El Tor, but are widely different from the classical O1 vibrios. Using restriction enzymes which cleave a single site in either the core region or in the direct repeat sequence (RS) of the CTX genetic element, it has been shown that the genome of most of the O139 strains has two copies of the ctx gene in tandem connected by two RSs. The chromosomal location of the CTX genetic element in the O139 strain is the same as that reported for El Tor vibrios. The organization of the virulence gene cassettes in different O139 strains shows genetic heterogeneity in the population. Whilst most of the epidemic strains have two copies of the CTX genetic element, in some strains the number of elements has been amplified and in at least one strain a single copy of the element has been deleted.

Mathematical characterization of Chaos Game Representation: New algorithms for nucleotide sequence analysis

Chaos Game Representation (CGR) can recognize patterns in the nucleotide sequences, obtained from databases, of a class of genes using the techniques of fractal structures and by considering DNA sequences as strings composed of four units, G, A, T and C. Such recognition of patterns relies only on visual identification and no mathematical characterization of CGR is known. The present report describes two algorithms that can predict the presence or absence of a stretch of nucleotides in any gene family. The first algorithm can be used to generate DNA sequences represented by any point in the CGR. The second algorithm can simulate known CGR patterns for different gene families by setting the probabilities of occurrence of different di- or trinucleotides by a trial and error process using some guidelines and approximate rules-of-thumb. The validity of the second algorithm has been tested by simulating sequences that can mimic the CGRs of vertebrate non-oncogenes, proto-oncogenes and oncogenes. These algorithms can provide a mathematical basis of the CGR patterns obtained using nucleotide sequences from databases.

Lysis of Vibrio cholerae cells: direct isolation of the outer membrane from whole cells by treatment with urea.

Cells of Vibrio cholerae underwent rapid autolysis when suspended in media of low osmolarity under non-growing conditions. Chaotropes like urea and guanidine. HCl which are potent protein denaturants caused complete and immediate lysis of whole cells. This unique sensitivity of V. cholerae to protein denaturants led to the development of a rapid method for the selective isolation of the outer membrane upon treatment of whole cells with urea. The composition of the outer membrane isolated from both whole cells and crude envelopes by treatment with urea was comparable with that of the outer membrane isolated by other conventional methods.

Enterotoxin production, DNA repair and alkaline phosphatase of Vibrio cholerae before and after animal passage.

Summary: Three strains of Vibrio cholerae differing in biotype, serotype and/or toxinogenicity were studied. The capability for dark repair of DNA and stability of alkaline phosphatase decreased concomitantly with toxinogenicity on laboratory passage of highly enterotoxinogenic strain 569B. These properties could be restored by passaging strain 569B once through a guinea-pig.

Rearrangements in the genomes of Vibrio cholerae strains belonging to different serovars and biovars

The intron-encoded enzyme I-CeuI provides an excellent tool for rapidly examining the organization of genomes of related species of bacteria. Vibrio cholerae strains belonging to serovars O1 and O139 have 9 I-ceuI sites in their genomes, and V. cholerae strains belonging to serovars non-O1 and non-O139 have 10 I-ceuI sites in their genomes. This information can be used as a criterion to differentiate O1 strains from non-O1 and non-O139 strains. To our knowledge, intraspecies variation in the number of rrn operons has not been reported in any other organism. Our data revealed extensive restriction fragment length polymorphism based on a comparison of the I-ceuI digestion profiles of strains belonging to different serovars and biovars. From the analysis of partial digestion products, I-CeuI macrorestriction maps of several classical, El Tor, and O139 strains were constructed. While the linkage maps are conserved within biovars, linkage maps vary substantially between biovars.

Repair of ultraviolet-light-induced DNA damage in Vibrio cholerae

Repair of ultraviolet-light-induced DNA damage in a highly pathogenic Gram-negative bacterium, Vibrio cholerae, has been examined. All three strains of V. cholerae belonging to two serotypes, Inaba and Ogawa, are very sensitive to ultraviolet irradiation, having inactivation cross-sections ranging from 0.18 to 0.24 m2/J. Although these cells are proficient in repairing the DNA damage by a photoreactivation mechanism, they do not possess efficient dark repair systems. The mild toxinogenic strain 154 of classical Vibrios presumably lacks any excision repair mechanism and studies of irradiated cell DNA indicate that the ultraviolet-induced pyrimidine dimers may not be excised. Ultraviolet-irradiated cells after saturation of dark repair can be further photoreactivated.

Presence of exposed phospholipids in the outer membrane of Vibrio cholerae

Vibrio cholerae 569B was found to be highly sensitive to a wide range of chemicals, particularly hydrophobic compounds and neutral and anionic detergents. The phospholipid profile of the outer membrane was similar to that reported for other Gram-negative bacteria. The lipopolysaccharide (LPS) contained O-antigenic sugars and exhibited heterogeneity. In addition, the LPS moiety was characterized by a relatively low negative charge. Analysis by topological probes revealed the presence of a significant amount of exposed phospholipids in the outer membrane. The reduced negative charge of LPS molecules and the exposed phospholipids present in the outer membrane could be important in the increased permeation of exogenous compounds in V. cholerae.

The DNA adenine methyltransferase-encoding gene (dam) of Vibrio cholerae

The DNA adenine methyltransferase (MTase)-encoding gene (dam) of Vibrio cholerae, an organism belonging to the family Vibrionaceae, has been cloned and the complete nucleotide (nt) sequence determined. V. cholerae dam encodes a 21.5-kDa protein and is directly involved in methyl-directed DNA mismatch repair. It can substitute for the Escherichia coli enzyme and can suppress the phenotypic traits associated with E. coli dam mutants. Overproduction of V. cholerae Dam MTase does not result in hypermutability in either V. cholerae or E. coli cells. Overproduction of V. cholerae Dam in a pUC plasmid, however, fails to suppress the 2-aminopurine (2-AP)-sensitive phenotype of E. coli dam mutants. Homology between the nt and deduced amino acid (aa) sequences of the E. coli and V. cholerae dam genes is only 30-35%.