Horizontal gene transfer studied (Introduction)

by David Turell , Sunday, June 18, 2023, 18:59 (524 days ago) @ David Turell

Looking at ease of transfer:

https://phys.org/news/2023-06-complexity-barrier-horizontal-gene.html

"This process is a major contributor to microbial evolution, accounting for 10–20% of the protein-coding genes in most bacterial genomes, while HGT is less prevalent among eukaryotes. Through HGT, bacteria and archaea can acquire new traits, ranging from antibiotic resistance to metabolic capabilities, which enhances their ability to adapt to changing environments.

"In a new study from Genome Biology and Evolution titled "Empirical evidence that complexity limits horizontal gene transfer," researchers from the University of North Carolina, led by Christina Burch and Corbin Jones, investigated the factors that influence the ability of individual genes to be transferred into a new recipient bacterial strain via HGT.

"Their study reveals that a gene's transferability is affected by several factors, including its sequence divergence from the recipient and how many interaction partners the resulting protein has (i.e., its connectivity). Moreover, a gene's divergence and connectivity interact to further influence its transferability.

"While previous studies have observed a relationship between gene transferability and protein connectivity, scientists have puzzled over the mechanism underlying this link. Two potential hypotheses have been suggested: the Balance Hypothesis and the Complexity Hypothesis.

"The Balance Hypothesis suggests that newly transferred genes may result in gene dysregulation by upsetting the balance between expressed proteins, while the Complexity Hypothesis proposes that newly transferred genes may fail to engage in normal protein-protein interactions. Importantly, while the divergence between the donor and recipient strains should not affect the former process, it is expected to impact the latter, as more divergent proteins are more likely to experience protein-protein interaction failure.

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"After correcting for biases related to bacterial physiology (i.e., frequent initiation of replication in actively growing cells), the authors investigated the relationship between gene transferability (as estimated by sequencing coverage) and several factors that may affect HGT, including gene function, protein connectivity, the divergence between the donor species and E. coli, and the expression level of the native gene in E. coli.

"Importantly, they found a significant interaction between divergence and connectivity, supporting the Complexity Hypothesis and suggesting that the ability of a transferred gene to engage in normal protein-protein interactions plays a key role in the success or failure of HGT.

"In addition to these findings, an important contribution of this study was the development of a statistical test capable of evaluating the Complexity Hypothesis. Burch notes, "Prior to this work, the Complexity Hypothesis had been described only using verbal arguments. I think it was an important step forward to translate the hypothesis into a specific statistical test. The fact that we could then conduct the statistical test on existing genomic data was icing on the cake. We are grateful to the Sorek team for leading the way."

"One caveat of this analysis is that all the genes studied were on the plasmids (i.e., extrachromosomal DNA) used to transfer them into the recipient cell. Different dynamics may be observed when genes are transferred directly onto bacterial or archaeal chromosomes.

"Ultimately, we would like to understand better the consequences of incorporating transferred genes into recipient genomes," says Burch. "Modern genome sequencing technology makes it possible to investigate that question using microbial evolution experiments, and a few have been done, but a lot more data are needed."

"Moreover, the current analysis was necessarily limited to genes that were already present in the E. coli genome. "We would also like to understand better the horizontal transfer of new or accessory genes that are not already present in recipient cells," continues Burch. "Those genes are not relevant to the Complexity Hypothesis, so that investigation remains for future work.."

Comment: it is not surprising that complexity limits horizontal gene transfer. As organisms become very complex through evolution the process disappears. In humans viral infections have added to our DNA without making us something different. It is not a significant event.