4. Diversity of bacterial genomes Flashcards
What is a bacterial species?
Phylogenetic species concept - a group which members are descendants from a common ancestor + who all possess a combination of certain traits
- genomically coherent compared to other strains
ex: (in)ability to fermet lactose
What is the level of DNA relatedness required for bacteria to be considered same species?
>70% DNA-DNA relatedness - defined by hibridisation (at what temp DNA re-anneals)
or
~94% average nucleotide identity (ANI) of all orthologous genes shared between two genomes - alignment of two genomes
What drives microbial evolution?
Pan-genome (core+accessory genes) - large gene pool + gene change (HGT, gene acquisition, genome reduction)
Explain closed and open pan-genomes
Closed pan-genome: acquired/lost genes are on plasmids - pan-genome (chromosome) size doesn’t change
Open pan-genome: new genes are acquired onto the chromosome - dispensable (accessory genes) - pan-genome size changes - increases because of increasing number of genes
What are the main mechanisms of acquiring new genes in bacterial genomes?
Via bacteriophages and transposable elements - both HGT
Would most bacteria be still pathogenic of pathogenticity islandes were removed?
No, usually core genome is non-pathogenic - toxins + host-specific factors that make bacteria pathogenic encoded in pathogenicity islands (PAIs) - acquired through HGT
What can be determined from GC skew data?
GC skew data can tell:
- the site of origin of replication
- regions that have recently inverted
Do all bacteria have one circular chromosome?
No, can have several circular chromosomes + plasmids
ec: Vibrio cholerea has 2 circular chromosomes
How can a second chromosome evolve?
Second chromosome could evolve from a plasmid - in Burkholderia pseudomallei second chromosome contains plasmid replication gene homologs
What determines plasmid vs chromosome?
Plasmid vs chromosome: plasmid contains the origin of replication and therefore it is self-replicative - while chromosomal DNA replicates with the genome
Chromosomes usually have core genes - can’t lose - won’t survive - but both chromosome and plasmid important for pathogenicity
Explain what is genome reduction
Genome reduction - process by which a genome shrinks relative to its ancestor
How can genome reduction happen in bacterial genomes?
Genome reduction - multiple insertion sequences - very similar - indirect repeats at sequence ends -> HR -> sequence excision
Compare Burkholderia pseudomallei vs mallei
Burkholderia mallei - smaller genome than pseudomallei - mallei evolved from pseudomallei via genome reduction -> now needs a mammalian host, can’t survive in th env - pseudomallei can - independence genes deleted in genome reduction
- further antigenic variation on surface + virulence proteins in mallei caused by frameshift - because of simple di-, tri- sequence repeats
What is the likely mechanism how Vibrio cholerae virulence evolved?
Cholera toxin in bacterial genome is encoded by integrated bacteriophage CTXϕ (if this bacteriophage removed - bacteria would not be pathogenic) - PAI
How bacteriophages integrate into bacterial genomes?
Bacteriophages inetgrate via site-specific recombination using integrases in lysogenic cycles
Compare Streptococcus equi subspecies: equi and zooepidemicus
S. equi - only in horses - horizontally acquired genes + genome reduction made it host restricted
S. zooepidemicus - infects wide range of animals and humans
96% ANI but have differences to be considered different subspecies
Describe Streptococcus equi pathogenicity
Streptococcus equi causes strangles in horses: infects horses - inflammation of lymph nodes - swell - difficulty breathing + swallowing - can crush trachea
How did S. equi evolved to become a pathogen?
- point mutations
- HGT (genome acquisition)
- genome reduction
Lecture summary
What are paralogous groups of genes?
Paralogous groups of genes - sets of genes in a genome that share common ancestry through gene duplication events - duplicated genes = paralogs - homologous sequences evolved in the same genome
ex: human histone 1 and 2 sequences - homologs
