Fundamentals of Bioinformatics - Ogurtsov A.N. 2013

Information Principles in Biotechnology
Genome Analysis
Horizontal Gene Transfer

One of the most striking Examples of interspecies, or horizontal, Gene transfer is The Structure of Trypsin in the bacterium Streptomyces griseus (a bacterium that acquired the gene from the substrate on which it grew, which in turn was formed by The activity of another species). Upon discovering that the trypsin in S. griseus is more closely related to bovine trypsin than to microbial proteinases, Brian Hartley wrote in 1970 that "...the bacterium must have been infected by a cow."

Earlier examples of horizontal gene transfer were the classic pneumococcal transformation experiments conducted by Oswald Avery, Colin MacLeod, and Maclyn McCarty, which established that DNA is the genetic material.

In general terms, horizontal gene transfer is the acquisition of genetic material by one Organism from another (usually by natural means, but occasionally through laboratory Procedures) by mechanisms other than Replication or duplication.

Several mechanisms of horizontal gene transfer are known, such as direct uptake (as in the pneumococcal transformation experiments) or via viral vectors.

Sequence analysis has shown that horizontal gene transfer is not such a rare phenomenon, although it occurs predominantly in microbial genomes. It requires us to move away from conventional, vertical models of inheritance in our thinking. Evidence supporting horizontal gene transfer includes, first, discrepancies among phylogenetic trees constructed from different genes and, second, direct comparisons of gene sequences across different species.

Thus, in E. coli, 755 open reading frames (totaling 547,8 kbp, or about 18% of The Genome) originated via horizontal gene transfer following divergence from the descendants of Salmonella 100 million years ago.

In microbial evolution, horizontal gene transfer is more prevalent among operational genes than among informational genes.

For example, Bradyrhizobium japonicum, a nitrogen-fixing bacterium that forms a Symbiosis with higher plants, possesses two Glutamine Synthetase genes. One is identical to those found in other related Bacteria; the other shares 50% identity with the homologous gene in higher plants.

The enzyme RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase), which is primarily responsible for carbon dioxide fixation in The Calvin Cycle (see [6], sec. 11.1), also arose through Gene Duplication.

Many bacteriophage-derived genes found in the E. coli genome not only provide further examples of horizontal gene transfer but also shed light on its mechanism. However, horizontal gene transfer is not restricted to prokaryotes and is also known to occur in eukaryotes.

Eukaryotes acquired their informational genes primarily from a Methanococcus-related organism, and their operational genes mainly from proteobacteria, with minor "contributions" from cyanobacteria and methanogenic archaea. Conversely, almost all informational genes in Methanococcus are homologous to those of Yeast.

However, horizontal gene transfer was not confined to distant evolutionary history. It has been suggested (though the claim is currently disputed) that numerous bacterial genes have integrated into The Human Genome. Furthermore, at least eight human genes have been identified in the genome of Mycobacterium tuberculosis.

These findings led to the hypothesis of a "global organism," suggesting that a shared genetic "marketplace" exists across the Earth's biosphere—a veritable "World Wide DNA-Web" from which organisms can download genes as needed.

This immediately raises the question of how the existence of such a "public gene library" can be reconciled with actual biodiversity, which is not erased by this kind of "globalization."

The traditional explanation is that the biosphere contains ecological "niches" to which individual species adapt. Diversity of niches gives rise to biodiversity. However, this explanation relies On the Stability of vertical inheritance, which is essential for maintaining the "health" and integrity of species.

Why doesn't the "global organism" dissolve species boundaries in the same way that global access to pop culture threatens to erase national and ethnic cultural boundaries? A possible answer lies in informational genes, which are inherently less susceptible to horizontal gene transfer and therefore define species uniqueness.

Interestingly, although The Significance of horizontal gene transfer is now clear and undeniable, the mechanism was long regarded as rare and negligible. This oversight stemmed from the fact that vertical gene transfer from parents to offspring forms the foundation of the Darwinian model of biological evolution through Selection (differential reproduction) of parental phenotypes, which alters gene frequencies in the next generation.

Conversely, the acquisition of genes by offspring from sources other than their parents was associated with Lamarckian models and other alternatives unfavorably received by proponents of Darwinian theory.

The notion that the evolutionary tree is the organizing principle of biological relatedness is so deeply rooted in scientific thinking that researchers display almost "ecological" zeal in their commitment to genealogical trees, even when tree-like models are ill-suited for inferring relationships.

It is worth recalling that Darwin knew nothing about genes; the mechanism generating trait variation during selection remained a mystery to him. It is quite possible that he would have been more receptive to horizontal gene transfer as an evolutionary mechanism than his later followers.