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CURATOR
A pinboard by
Eva Garmendia

PhD candidate, Uppsala University

PINBOARD SUMMARY

Bacteria are many and varied - I study why some chromosomal characteristics seem unchanged.

Although bacterial species have been evolving in planet earth for many millions of years and they have all the life-styles ever imagined (from extreme cold, to extreme hot, passing by living in natural environments or specialized hosts!), certain characteristics of their chromosome (cell component formed by their DNA) and genome content (the DNA sequences) seem to not have changed much. For example: they seem to really like having circular chromosomes with equal arm sizes, or locating genes that make a lot of the cellular content near the beginning of the chromosome.

Why are those characteristics important? Can we experimentally assess the significances of those organizational traits? What happens if we change those traits and mess around with them? Can we get bacteria to experimentally evolve and overcome the challenges we put them through in the lab? If so, how does it happen?

My research focuses on all these questions and tackles them by experimentally modifying those conserved traits and observing their effect. On a follow up, I experimentally evolve the modified bacteria to understand how evolution works around those changes. My results so far indicate that there are selective forces constraining the evolution of the chromosome and genome content. These forces are shaping the evolution of the bacterial species and can explain the biases we see in the nature for those characteristics.

11 ITEMS PINNED

Functional Constraints on Replacing an Essential Gene with Its Ancient and Modern Homologs.

Abstract: Genes encoding proteins that carry out essential informational tasks in the cell, in particular where multiple interaction partners are involved, are less likely to be transferable to a foreign organism. Here, we investigated the constraints on transfer of a gene encoding a highly conserved informational protein, translation elongation factor Tu (EF-Tu), by systematically replacing the endogenous tufA gene in the Escherichia coli genome with its extant and ancestral homologs. The extant homologs represented tuf variants from both near and distant homologous organisms. The ancestral homologs represented phylogenetically resurrected tuf sequences dating from 0.7 to 3.6 billion years ago (bya). Our results demonstrate that all of the foreign tuf genes are transferable to the E. coli genome, provided that an additional copy of the EF-Tu gene, tufB, remains present in the E. coli genome. However, when the tufB gene was removed, only the variants obtained from the gammaproteobacterial family (extant and ancestral) supported growth which demonstrates the limited functional interchangeability of E. coli tuf with its homologs. Relative bacterial fitness correlated with the evolutionary distance of the extant tuf homologs inserted into the E. coli genome. This reduced fitness was associated with reduced levels of EF-Tu and reduced rates of protein synthesis. Increasing the expression of tuf partially ameliorated these fitness costs. In summary, our analysis suggests that the functional conservation of protein activity, the amount of protein expressed, and its network connectivity act to constrain the successful transfer of this essential gene into foreign bacteria.IMPORTANCE Horizontal gene transfer (HGT) is a fundamental driving force in bacterial evolution. However, whether essential genes can be acquired by HGT and whether they can be acquired from distant organisms are very poorly understood. By systematically replacing tuf with ancestral homologs and homologs from distantly related organisms, we investigated the constraints on HGT of a highly conserved gene with multiple interaction partners. The ancestral homologs represented phylogenetically resurrected tuf sequences dating from 0.7 to 3.6 bya. Only variants obtained from the gammaproteobacterial family (extant and ancestral) supported growth, demonstrating the limited functional interchangeability of E. coli tuf with its homologs. Our analysis suggests that the functional conservation of protein activity, the amount of protein expressed, and its network connectivity act to constrain the successful transfer of this essential gene into foreign bacteria.

Pub.: 31 Aug '17, Pinned: 14 Oct '17