Genomics 4-6 Flashcards
What is the central dogma who designed it ?
DNA>RNA>Protein
Francis crick
What are the 4 model bacteria ?
Eschericha coli -
Neisseria meningitidis -
Heliobacter pylori -
Bacillus subtilis +
Name the 6 strains of E.coli
EPEC- Enteropathogenic e.coli EHEC- Enterohaemorrhagic e.coli ETEC- Enterotoxigenic e.coli EAEC- Enteroaggregative e.coli EIEC- Enteroinvasive e.coli DAEC- Diffusely adherent e.coli
What is a pathogencity island ?
a series of contiguous genes including one or more that determines virulence, acquired by horizontal gene transfer. It is transposable.
What type of E.coli attacks the colon and secretes Shigatoxin ?
EHEC- Enterohaemorrhagic e.coli
What type of E.coli is taken up by cytosis and forms an actin tale ?
EIEC- Enteroinvasive e.coli
What is unique about DAEC- Diffusely adherent e.coli ?
Uses villi for protection
What does EAEC- Enteroaggregative e.coli form ?
Biofilm
What E.coli secretes a temperature sensitive toxin ?
Enterotoxigenic e.coli- Stable and labile enterotoxins
What does enteropathogenic e.coli do to the villi ?
Changes physiological structure and secretes type 3 effective molecules into the cell that take over actin cytoskeleton.
What is natural competence ?
The ability to take up DNA from the environment
What model bacteria use the pseudo type IV pilus system ?
Bacillus subtilis
Neisseria meningitidis
What allows heliobacter pylori to be naturally competent ?
Type IV secretion system
What do optical tweezers measure in terms of DNA uptake ?
Measures the force that DNA is being pulled into the cell
What allows nerisseria meningitidis to take up DNA that is specific to nerisseria genus ?
Uses a minor pilin (ComP) combined with a major pilin (PiLE)
What do all of the DNA uptake systems have in common ?
All require ATP dependent stripping of the dsDNA to ssDNA.
What is the pathogenecity island in heliobacter pylori ?
Cag- Continually takes up DNA and alters genome.
What allows DNA to pass through the outer membrane of neisseria meningitidis ?
A secreton
What is the pilus made up of in bacillus subtilis and what are the bonds holding the proteins together ?
ComGC protein and disulphide bonds
What are the minimum standards provided by genomic consortium ?
A table dedicated to classification.
A table dedicated to project info.
A table dedicated to genome statistics
A table dedicated to COG database
What is special about the genome of borrellia burgdoferi ?
Contains linear chromosomes and linear and circular plasmids.
What is a replicon ?
A region of DNA that replicates from a single origin of replication.
What limits 16s rRNA sequences from being a good determining factor for phylogentic relationships ?
There tends to be more than 1 copy of genes
16s rRNA sequences can vary alot even within the same genome
What is a biosynthetic cluster ?
A physical cluster of of 2 or more genes in a genome that together encode for a pathway which produces a metabolite
What do CRISPR molecules do ?
Play a role in bacteria defence against phage attack
Allows uptake of exogenous genetic material
What are the families of bioactive secondary metabolites ?
PKs
NRPs
RiPPs
isoprenoids
What is the benefit of whole genome sequencing ?
Allows whole genome comp
What is the problem with identifying genomes by similarity ?
A third of genes have insufficient similarity
Similarity based on function is often wrong
How can microarrays be used for the identification of gene function ?
By knocking out the gene being identified for function and growing the bacteria in different growth conditions and then comparing to reference strain
What is a cryptic prophage ?
A phage that integrates in the genome but have lost function.
Why are cryptic phages retained ?
Essential for growth under stressful conditions
What are the limitations of random barcode transposon site sequencing ?
Cannot recreate natural environment
Knock out gene may not show in phenotype due to synthetic lethality (other proteins producing the knock out gene product)
What has random barcode transposon site sequencing allowed for ?
Allows genes of unknown function to be given a putative function as it allows comparison of multiple genomes at once
Higher throughput than microarrays
What has transposon directed insertion site sequencing allowed for ?
Allows core genes for infection and colonisation to be found as bacteria are injected into real life environments
During random barcode transposon site sequencing what allows for the identification of the unique knockouts ?
PCR using primers that are specific to the adapters that have been added and the barcoded transposon.
During random barcode transposon site sequencing what allows for multiple species to be studied at once ?
A second primer added into the PCR
What sort of dye do microarrays contain ?
Tetrazolium
What does random barcode transposon site sequencing do ?
Creates library of knock outs all over the genome with an associated barcode to each unique knock out.
What are the limitations of phenotypic microarray analysis ?
Low through put as a compromise of high number of mutants or high number of environmental conditions has to be made
In B. subtilis, what does the inactivation of comEC (large polytopic transmembrane protein) prevent ?
prevents not only uptake of DNA, but also the degradation of the nontransforming strand
In Bacillus subtilis what does ComFA do and what does it contain to allow this ?
Helicase and translocase motifs
Allows stripping of dsDNA and movement of ssDNA
What do the binding proteins in Bacillus subtilis allow and do ?
Cover the DNA allowing it to be replicated and transferred into the chromosome
What is the only DNA sequence Neisseria meningitidis recognises ?
GCCGTCTGAA
Known as DNA uptake sequence
What is the major protein on heliobacter pylori’s uptake system ?
ComB9
