Prokaryotic Genomes III

factors influencing frequency of successful transfer between organisms

physical proximity, gene-transfer mechanisms, metabolic compatibility, gene expression systems, genome size and number of genes

physical proximity

do organisms share the same environment?

sharing habitats increases probability of successful LGT events

environment matters, with soil rich in nutrients increasing LGT events and hot geysers decreasing them due to inability to support much life

rates of LGT were found to be higher for genes encoding

peripheral metabolism and transport proteins

and proteins with more interactions

rates of LGT were found to be lowest for

informational genes

complexity hypothesis

the role of proteins that depend on many interactions is most likely a limitation for the gene to be kept when transferred to a different organism

rates of LGT were found to be higher in species with

more genes and larger genomes

they can have a larger fraction of their genomes more susceptible to rapid evolution and gene exchange

species with reduced genome sizes have fewer

LGT genes

reduced opportunities for the uptake of new genes by LGT and strong selection for fast replication and a small genome

pangenomes

the collection of genes shared among members of the same species

the genetic repertoire of a bacterial species is much larger than the gene content of an individual strain

closed pangenomes

characterized by large core genomes and small accessory genomes

size tend to be asymptotic despite adding more genomes (because of this, complete size can be predicted)

open pangenomes

tend to have small core genomes and large accessory genomes

size tend to increase with every added genome

pangenome of E coli

growing by 30-50 or more genes with each additional strain sequenced

core genome of E coli

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

free-living prokaryotes tend to

have increased levels of LGT so as to adapt to different environments, want to take up new genetic material for this purpose, i.e. tend to have larger accessory genes

obligate intracellular prokaryotes (endosymbionts) tend to

have less LGT given that they want to stay within their host, have no need to take up new genetic material to adapt to new environments