L5- bacterial genomes and genomics

Examples of bacteria shapes (4)

• round/coccus

• Rod

• Spirillum

• Spirochete

Examples of environemtns bacteria live in (3) and why

• human micro biome

• Soyabean roots

  • Soyabean fixes nitrogen tat is used by bacteria

• Extremen environemtns

  • Salt plains

  • Thermal springs

• They can adapt to environemtns

Genome

The complete set of genetic material in a bacterial cell

How long is unwound E. coli genome

1.56mm

How long is one E. coli cell

3 micro meter

What is the genome wound into

Nucleoide

Is the nucleoid membrane bound or noto

Not

Features of the E. coli genome (5)

• circular

• Has single origin of replication

• Genes are densely packed

• Average distance between E. coli genes is only 118BP

• Has clusters of genes with related función transcribed in a single mRNA= an operon

How many genes does E. coli have

4,300

Examples of common mobile genetic elements (4)

• plasmids

• Bacteriophage

• Transposons and insertion sequences

• Integrons

Plasmids

Small extrachromosomal circular dna

Bacteriophage

• bacterial virus

• Use lysocigen cycle

• Can trasnfer genes via transduction

Lysogenic cycle with bacteriophages (3)

• stable insertion in host chromosomes

• DNA inserted into the chromomse of bacteria

• Cell undergoes division and passes on bacteriophage dan

Transposons and insertion sequence (4)

• jump in and out of chromomse es and plasmids

• Often carry resistant genes so can be helpful

• Can cause problems I f disrupts a key gene

• Transposase gene help with jumping in and out

Integrons

Integrate useful genes at specific sites

Useful genes in plasmids (3)

• tra

  • Plasmid trasnfers from cell to cell by conjugation

• Mer, sul, str, cat

  • Antibiotic resistant genes

• Has gene which allow replciation and stable inheritance

Shigella

A relation of E. coli that causes gastroenteritis and dysentry

Prevalence of gastroenteritis in the us

450,000 infections / year

What causes the high virulence of shigella

• pINV gene encodes key virulence

• Has a pathogenicity island which encodes fro type 3 secretion system that has a long needle which can poke through the next memrbaen and relase toxins into the next cell

Pathogenicity islands

clusters of genes of foreign appeared eg altered GC content, present in certain strains and correlated with virulence

Core genome t

The key ‘housekeepong’ genes possess by all strains of a species

Accessory genome

Includes ‘mobile elements’ of different origins and can vary between strains of species

Pangeome

Totality of genes found Ñ across different isolates of a species

E. coli pangeome (3)

• 5000 genes

• 2000 core genes

• Pangeoms of 15000 genes

First kind of sequencing

Sanger

Pros and cons of Sanger sequencing (3)

+accurate

-slow

-expensive

Step of Sanger sequencing (5)

• detangle fragment of interese

• Run PCR with modified nucleotides to amply dna

• Produces different fragments each of which ends with a nucleotide I that has a dye

• Run an agarose gel

• Can tell which base is at the end due to the colour

Second method of sequenc in g

Illumina

Pros and cons of illumina sequencing (2)

+much faster

-relies on shorter fragments so have to break dna more

Steps of illumina sequencing (4)

• Break dna into smal sequences

• Fragment, denatured nd lígate adapter onto strains

• Add T o flow cell and undergo cluster amplifaication

• Will be sequenced with fluorescety labelled nucleotides

What happens to sequences from illumination

• sequences overlap

• Have to work out where they overlap

• Repetitive sequences interfere with assbely of genes

Pros of oxford nanopore (4)

• Very long reads

• 10-39kbp genomiclibraries in common

• Fast

• small devices so sequencing can be done in the field

Negatives of oxford nanopore

• generally less accurate

How does the oxford nanopore work (2)

• adapter sequence brings dna to specific pore in the membrane

• Motor protein unwinds the dan and pushes it through T he pore which has ionic current so the base pairs can be read as they have a different current

benefits of bioinformatics In infectious disease and epidemiology (3)

• pre screen patients for problem organism to prevent hospitalisation

• Identify all virulence factors and antibiotic resistance in patient sample to prescribe appropriate treatments and identify new threats and respond quickly

• Sequenc isolates from multiple patients to determine whether epidemics are clónale, track the spread of disease, and trance origin of new variants

How to interpret phenotype (4)

• isolate mutan with interesting phenotype

• Obtain complete genome sequenc of mutant

• Compare with parent sequenc and identifwsy base changes

• Interpret phenotype in terms of the alteration in a specific gene

Why are bacteria hard to isolate and unculturable

Live in extreme environemtns

Metagenomics

The study of genetic material recovered directly from envronemtnal samples

How many different strains of mycetoma are there

70

Why is mycetoma difficult to treat

Various antibiotic resistance

What is the micro biome

The community of microorganisms in a particular environemtns