Bacterial Genomics

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Bacterial Genomics
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Bacterial Genomics Bacterial Genomics a study of
the molecular organization of genomes, their
information content and the gene products they
encode Structural genomics physical nature
of the genome i.e., DNA sequence Functional
genomics an examination of the transcripts and
the proteins encoded Comparative genomics
an examination of the genomes of different
organisms
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Structural genomics physical nature of the
genome i.e., DNA sequence Sequencing the
genome Dideoxy sequencing
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Dideoxy sequencing
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(No Transcript)
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Shotgun sequencing 1. fragment the genome
and purify fragments 2. insert fragment into
plasmid and clone 3. sequence fragments
(automated sequencer) 4. fragment nucleotide
sequences compared (by computer)
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Shotgun sequencing 1. fragment the genome
and purify fragments 2. insert fragment into
plasmid and clone 3. sequence fragments
(automated sequencer) 4. fragment nucleotide
sequences compared (by computer) 5. edit
to resolve any ambiguities in the sequence
6. annotation locate specific genes locate
Open Reading Frame (ORF) greater than 100
codons ORF nucleotide sequence not
interrupted by a stop codon compare to known
nucleotide amino acid sequences
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Bioinformatics management and analysis of
data using computer focus is on DNA and
protein sequences develop phylogenetic
relationships family tree
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Characteristics of microbial genomes genes
are clustered in functional groups many
genes have no known function Haemophilus
influenzae 40 unknown E. coli 2,500 of
4,288 (predicted) genes unknown
Archaebacteria are different Methanococcus
jannaschii more similar to eukaryotes
Rickettsia resemble mitochondria protein coding
sections resemble those of mitochondria
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Characteristics of microbial genomes
Chlamydia genome similar to other
bacteria called energy parasite but it can
make some has genes for mucopeptide, but none in
the wall may hint at penicillin
sensitivity has 20 genes that may be of
eukaryotic origin Treponema pallidum not
cultivated in the lab 40 of genes have no known
function lacks TCA cycle and oxidative
phosphorylation lacks many biosynthetic
pathways many transport proteins (5) family of
surface proteins, with many repetitive
sequences
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Characteristics of microbial genomes
Mycobacterium tuberculosis large genome, 4.4
Mb 4,000 genes 40 have assigned function 16
resemble no known proteins 250 genes for lipid
metabolism Mycobacterium leprae different
from M. tuberculosis 2/3 the size of M.
tuberculosis 50 junk DNA, degraded,
nonfunctional genes