How bacteria undergo genome evolution

Genome A new study examines how bacterial and archaeal genomic repertoires evolve to face new challenges by acquiring genes from other individuals. Microbes live and thrive in incredibly diverse and harsh conditions, from boiling or freezing water to the human immune system. This remarkable adaptability results from their ability to quickly modify their repertoire of protein functions by gaining, losing and modifying their genes. Microbes were known to modify genes to expand their repertoire of protein families in two ways: via duplication processes followed by slow functional specialization, in the same way as large multicellular organisms like us, and by acquiring different genes directly from other microbes. The latter process, known as horizontal gene transfer (HGT), is notoriously conspicuous in the spread of antibiotic resistance, turning some bacteria into drug-resistant ‘superbugs’ such as MRSA (methicillin-resistant Staphylococcus aureus), a serious public health concern.

The researchers examined a large database of microbial genomes, including some of the most virulent human pathogens, to discover whether duplication or HGT was the most common expansion method. They show that gene family expansion can indeed follow both routes, but unlike large multicellular organisms, it predominantly takes place by horizontal transfer. Thus, quick diversification of microbial functions results from the recruitment by microbes of pre-existing adaptations from other microbes. The study concludes with the observation that, since microbes invented the majority of life’s biochemical diversity, from respiration to photosynthesis, we should recognize the predominant role of HGT in the diversification of all protein families.

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes. (2011) PLoS Genet 7(1): e1001284. doi:10.1371/journal.pgen.1001284
Gene duplication followed by neo- or sub-functionalization deeply impacts the evolution of protein families and is regarded as the main source of adaptive functional novelty in eukaryotes. While there is ample evidence of adaptive gene duplication in prokaryotes, it is not clear whether duplication outweighs the contribution of horizontal gene transfer in the expansion of protein families. We analyzed closely related prokaryote strains or species with small genomes (Helicobacter, Neisseria, Streptococcus, Sulfolobus), average-sized genomes (Bacillus, Enterobacteriaceae), and large genomes (Pseudomonas, Bradyrhizobiaceae) to untangle the effects of duplication and horizontal transfer. After removing the effects of transposable elements and phages, we show that the vast majority of expansions of protein families are due to transfer, even among large genomes. Transferred genes — xenologs — persist longer in prokaryotic lineages possibly due to a higher/longer adaptive role. On the other hand, duplicated genes — paralogs — are expressed more, and, when persistent, they evolve slower. This suggests that gene transfer and gene duplication have very different roles in shaping the evolution of biological systems: transfer allows the acquisition of new functions and duplication leads to higher gene dosage. Accordingly, we show that paralogs share most protein–protein interactions and genetic regulators, whereas xenologs share very few of them. Prokaryotes invented most of life’s biochemical diversity. Therefore, the study of the evolution of biology systems should explicitly account for the predominant role of horizontal gene transfer in the diversification of protein families.

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