- transposases-Transposase is an enzyme that binds to the ends of a transposon and catalyzes the movement of the transposon to another part of the genome by a cut and paste mechanism or a replicative transposition mechanism. en.wikipedia.org/wiki/Transposases
- chemontaxis-movement by a cell or organism in reaction to a chemical stimulus. wordnetweb.princeton.edu/perl/webwn
- prophage-A prophage is a phage genome inserted as part of the linear structure of the DNA chromosome of a bacterium. en.wikipedia.org/wiki/Prophage
- integron-A genetic unit that, among others, encodes proteins that splice gene cassettes into chromosomes, where the cassettes can become functional. www.nature.com/nrg/journal/v5/n3/glossary/nrg1292_glossary.html
- aetiological- the cause of a disease. wordnetweb.princeton.edu/perl/webwn
- heterotrophic- obtaining nourishment from organic substances, not from food produced within the organism.wordnetweb.princeton.edu/perl/webwn
- Transposon- a segment of DNA that can become integrated at many different sites along a chromosome (especially a segment of bacterial DNA that can be translocated as a whole).wordnetweb.princeton.edu/perl/webwn
- pathogenesis- the origination and development of a disease. wordnetweb.princeton.edu/perl/webwn
- Permease - The permeases are membrane transport proteins, a class of multipass transmembrane proteins that facilitate the diffusion of a specific molecule in or out of the cell.en.wikipedia.org/wiki/Permease
- Rho-Independent terminator- The rho-independent signal is found on the DNA template strand and consists of a region that contains a section that is then repeated a few base pairs away in the inverted sequence. http://www.sparknotes.com/biology/molecular/dnatranscription/section2.rhtml
What is Vibrio Cholerae
- the aetiological agent of cholera
- includes pathognenic and non pathognenic strains that vary in gene content
- contains a wide variety of strains and biotypes
- receives and transfers genes for toxins
- has colonization factors
- is resistant to antibiotics
- has capsular polysaccharides that provide resistance to chlorine and new surface antigens
- it represents a significant portion of the culturable heterotrophic bacteria of oceans, coastal waters and estuaries
- these bacteria strongly influence nutrient cycling in the marine environment
Purpose of the Work
- To determine and analyze the genome sequence of Vibrio Cholerae.
- It is an important step toward the complete molecular description of how this free-living environmental organism became a human pathogen by horizontal gene transfer.
Genome Analysis & Comparative Genome Analysis
- Sequenced by the whole genome random sequencing method.
- Two circular chromosomes make up this genome
- 3,885 predicted open reading frames (ORFs) and 792 predicted Rho-independent terminators
- Most genes required for growth and viability are located on chromosome 1
- two-chromosome structure of V. cholerae allows for comparisons
- There is pronounced asymmetry in the distribution of genes known to be essential for growth and virulence between the two chromosomes
- Chromosome 2 contains a larger fraction (59%) of hypothetical genes and genes of unknown function, compared with chromosome
- Most genes known to be essential in bacterial pathogenicityare located on chromosome 1
Linear representation of the V. cholerae chromosomes
- Shows the location of the predicted coding regions, colour-coded by biological role, RNA genes, tRNAs, other RNAs, Rho-independent terminators and Vibrio cholerae repeats.
- Arrows represent the direction of transcription for each predicted coding region
Circular representation of the V. cholerae genome
- 2 chromosomes
- the first and second circles show predicted protein-coding regions on the plus and minus strand
- The third circle shows recently duplicated genes on the same chromosome and on different chromosomes
- The fourth circle shows transposon-related (black), phage-related (blue), VCRs (pink) and pathogenesis genes (red
- The fifth circle shows regions with significant values for trinucleotide composition in a 2,000-bp window
- The sixth circle shows percentage G+C in relation to mean G+C for the chromosome.
- The seventh and eighth circles are tRNAs and rRNAs, respectively.
- Pathways for energy production and the metabolism of organic compounds, acids and aldehydes are shown.
- Transporters are grouped by substrate specificity.
- Question marks associated with transporters indicate a putative gene, uncertainty in substrate specificity, or direction of transport
- Export or import of solutes is designated by the direction of the arrow through the transporter
- Gene location on the two chromosomes, for both transporters and metabolic steps, is indicated by arrow color.
General features of the Vibrio cholerae genome.
- self explanatory
- the size, number of ORF, the number of tRNA, the number rRNA, the number of significant and unsignificant proteins and other things are listed.
Percentage of total Vibrio cholerae open reading frames (ORFs) in biological roles compared with other -Proteobacteria
- V. cholerae, chromosome 1 (blue)
- V. cholerae, chromosome 2 (red)
- Escherichia coli (yellow)
- Haemophilus influenzae (pale blue)
Comparison of the V. cholerae ORFs with those of other completely sequenced genomes
- All V. cholerae ORFs (large chromosome, blue; small chromosome, red) were searched against all other genomes with FASTA
Phylogenetic tree of methyl-accepting chemotactic proteins (MCP) homologues in completed genomes
- Amino-acid sequences of the proteins were aligned using CLUSTALW
- Neighbor-joining phylogenetic tree was generated from the alignment using the PAUP program
- Grown from a single isolated colony
- Cloning, sequencing and assembly were as described for genomes sequenced by TIGR
- Sequences from both ends of served as a genome make up to show the orientation, order and integrity of the contigs
- Sequence gaps were closed by editing the end sequences and/or primer
- The initial set of ORFs was identified with GLIMMER and those shorter than 30 codons were eliminated
- ORFs were searched against a non-redundant protein database
- Frameshifts and point mutations were detected and corrected when needed
- Paralogous gene families were made by searching the ORFs against themselves using the program BLASTX
- Probability values for this analysis are based on the assumption that the DNA composition is relatively uniform throughout the genome
- Homologues of the genes of interest were identified using the BLASTP and FASTA3 search programs
- All homologues were then aligned to each other using the CLUSTALW program with default settings
- Phylogenetic trees were generated from the alignments using the neighbour-joining algorithm
- New starting point for the study of V. Cholerae environmental and pathobiological characteristics
- The genomic sequence of V. cholerae should facilitate the study of this model multi-chromosomal prokaryotic organism
- Might provide important clues to understanding the metabolic and regulatory networks that link genes on the two chromosomes
- Represents a promising genetic system for studying how several horizontally acquired loci located on separate chromosomes can still efficiently interact at the regulatory, cell biology and biochemical levels
Jennifer Okonta 13:32, 17 October 2010 (EDT)