Prokaryotic Genomes II

lateral/horizontal gene transfer

the movement of genetic material between different species in a manner other than traditional reproduction (to be contrasted with vertical transfer of genes from parent to offspring via sexual or clonal reproduction)

key steps in lateral gene transfer

divergence of genomes of different lineages

movement of DNA from one lineage to another

maintenance and replication of the foreign DNA

possible positive selection for the foreign DNA

spread into the new species’ population

amelioration

how do we detect foreign genes in a genome and determine where they come from?

gene presence/absence

compositional anomalies/genomic landscape

phylogenetic incongruence

mechanisms of gene transfer in prokaryotes

bacterial transformation, transduction, conjugation

bacterial transformation

simpler, low specificity

donor cell dies, undergoes lysis

DNA is released, containing antibiotic-resistance gene

recipient cell takes up foreign DNA, incorporates it into genome

• some prokaryotes are more competent at taking up DNA than others

bacterial transduction

can be general (can transfer any DNA) or specialized (limited to specific genes)

phage-infected donor cell releases phage, it attaches to recipient cell and inserts DNA

bacterial conjugation

complex, higher specificity process

can involve chromosomal integration of plasmid, in part or in whole

donor cell contains transposon, recipient cell becomes connected with donor cell (both cells alive and in contact)

plasmid from donor is received by recipient cell

integrative and conjugative elements (ICEs)

bacterial mobile genetic elements that primarily reside in the host chromosome, but can excuse and be transferred to other cells by conjugation

highly mosaic: contain a variety of different genes associated with conjugation and mobility

integrade and excisionase proteins in ICEs

integration/excision mediated by them, mediate DNA recombination at ‘att’ sites in bacterial chromosome and ICE sequences

where does integration of ICEs often occur?

at tRNA genes

how does conjugative transfer typically occur?

via assembly of a type IV secretion system, through which DNA passes by rolling circle replication

rolling circle replication

nuclease cuts one strand, nucleotides added to 3’ end, displacing other end while chromosome rolls in direction opposite of replication, other strand copied discontinuously

ICEs example

SXT family found in Vibrio cholerae and related bacteria, 52 genes in total

confer multi-drug resistance and other adaptive features to their bacterial hosts

where do genomic islands come from?

many are ICEs that have lost the ability to mediate excision and/or conjugation, see similar mobility genes present in both these and ICEs

deciding between gene gain or gene loss often involves

parsimony, need to have a reasonably good understanding of relationships between the organisms under consideration

synteny

gene order conservation

over time, genomes evolve characteristic compositional features, such as

G+C content and codon usage patterns, as a result of natural selection, drift, and mutation pressure

if the donor genome differs from the recipient genome in characteristic compositional features,

then the transferred gene may appear anomalous in these characteristics

amelioration

over time, the selective and mutational pressures that operate on the recipient will make the transferred gene come to resemble (in composition) the genome in which it now resides

a change in the nucleotide composition of a LGT towards that of its current genomic context, acquired genes resemble their donor genomes in G+C content and codon bias at the time of transfer; over time they come to resemble their recipient genome

the compositional signal of LGT goes not last very long

phylogenetic incongruence

if you know the relationships between organisms of interest, you can make an alignment of the DNA and/or protein and build a phylogenetic tree

if the resulting topology is different with known/predicted relationships, LGT can be reasonably inferred

factors influencing frequency of successful transfer between organisms

physical proximity, gene-transfer mechanisms, metabolic compatability, gene expression systems

physical proximity

do organisms share the same environment?

gene-transfer mechanisms

do processes exist to move genetic material from one cell to another and how effective are they? (NOTE—sometimes we are very confident that LGT has occurred but have no idea about the mechanism)

metabolic compatibility

is the gene product of a transferred gene compatible with the recipient cell?

gene expression systems

is the structure of a transferred gene compatible with it being expressed in its new location?

pan-genome

the collection of genes shared among members of the same ‘species’

E coli and its two genome

pan-genome is growing by 30-50 genes with each additional strain sequenced

core-genome is unexpectedly small and getting smaller with each new genome

prokaryotic genomes are highly dynamic entities comprised of

a relatively stable (albeit unexpectedly small) core of genes and variable accessory genes which come and go via LGT, facilitating rapid adaptation of the organism to new environments