Horizontal Gene Transfer

[CitrusHigh]

I want to start a thread on this very relevant topic. Especially among bacteria which exchange genetic material with others in their environment so readily as to be labeled promiscuous. I'll kick it off with this abstract on the myth of bacterial species. I posted this in off topic even though it is highly pertinent to what we're all about here, just to save time a fuss. Enjoy!

http://rd.springer.com/article/10.1007/s10539-010-9215-5

"The Tree of Life hypothesis frames the evolutionary process as a series of events whereby lineages diverge from one another, thus creating the diversity of life as descendent lineages modify properties from their ancestors. This hypothesis is under scrutiny due to the strong evidence for lateral gene transfer between distantly related bacterial taxa, thereby providing extant taxa with more than one parent. As a result, one argues, the Tree of Life becomes confounded as the original branching structure is gradually superseded by reticulation, ultimately losing its ability to serve as a model for bacterial evolution. Here we address a more fundamental issue: is there a Tree of Life that results from bacterial evolution without considering such lateral gene transfers? Unlike eukaryotic speciation events, lineage separation in bacteria is a gradual process that occurs over tens of millions of years, whereby genetic isolation is established on a gene-by-gene basis. As a result, groups of closely related bacteria, while showing robust genetic isolation as extant lineages, were not created by an unambiguous series of lineage-splitting events. Rather, a temporal fragmentation of the speciation process results in cognate genes showing different genetic relationships. We argue that lineage divergence in bacteria does not produce a tree-like framework, and inferences drawn from such a framework have the potential to be incorrect and misleading. Therefore, the Tree of Life is an inappropriate paradigm for bacterial evolution regardless of the extent of gene transfer between distantly related taxa."

[CitrusHigh]

"The Bacteria and Archaea are the most genetically diverse superkingdoms of life, and techniques for exploring that diversity are only just becoming widespread. Taxonomists classify these organisms into species in much the same way as they classify eukaryotes, but differences in their biology—including horizontal gene transfer between distantly related taxa and variable rates of homologous recombination—mean that we still do not understand what a bacterial species is. This is not merely a semantic question; evolutionary theory should be able to explain why species exist at all levels of the tree of life, and we need to be able to define species for practical applications in industry, agriculture, and medicine. Recent studies have emphasized the need to combine genetic diversity and distinct ecology in an attempt to define species in a coherent and convincing fashion. The resulting data may help to discriminate among the many theories of prokaryotic species that have been produced to date. "

http://www.sciencemag.org/content/323/5915/741.short

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The genome itself is embedded within the epigenetic net, and is far from stable or insulated from environmental exigencies. A large number of processes appear to be designed especially to destablize genomes during the life-time of all organisms, so much so that molecular geneticists have been inspired to coin the descriptive phrase, "the fluid genome". Mutations, insertions, deletions, amplifications, rearrangements, recombinations, gene-jumpings, and gene-conversions keep genomes in a constant state of flux in evolutionary time. Genes are found to jump between species that do not interbreed, being carried by mobile genetic elements, viruses or microorganisms, which can exchange genes at a prolific rate, as witnessed by the rapid horizontal spread of antiobiotic resistance in bacteria. Parasites that infect more than one species are also vectors for horizontal gene transfer. A particular genetic element - the P-element - has spread to all species of fruitflies in the wild within the span of less than 50 years, probably carried by a parasitic mite. These 'fluid genome' processes are by no means entirely stochastic or meaningless, but are subject to physiological and cellular control. Gene jumping, recombination and other alterations of the genome are frequent responses to stress or starvation in non-dividing cells that enable them to adapt or adjust to new situations. Similarly, cellular processes regularly inactivate whole batteries of genes by chemically marking them during normal development, or imprint them with binding proteins that alter the expression of the genes. Some of these marks and imprints are created early in development and may be passed on to the next generation via the germ cells. These instances of 'epigenetic inheritance' already constitute a substantial body of literature.

http://www.epigenetics.ch/gpage1.html

"Since the emergence of horizontal gene transfer as a way of explaining phylogenetic incongruence using different gene trees, a considerable number of studies have been published about genes that have been acquired by horizontal gene transfer (Gogarten et al. 2002; Lerat et al. 2005), both in Bacteria (Saunders et al. 1999; Ochman et al. 2000) and Archaea (Doolittle & Logsdon 1998; Faguy & Doolittle 1999), as well as in eukaryotes (Andersson 2005). These studies show that the transfer can occur not only among but also between domains in all possible directions: from Bacteria to Archaea (Rest & Mindell 2003), from Archaea to Bacteria (Gophna et al. 2004), from Archaea to Eukarya (Andersson et al. 2003), from Bacteria to Eukarya (Watkins & Gray 2006), from Eukarya to Bacteria (Guljamow et al. 2007) and even within Eukarya (Nedelcu et al. 2008). However, it is in bacterial and archaeal evolution that horizontal gene transfer has been more widely documented and accepted."

http://rspb.royalsocietypublishing.org/content/277/1683/819.full

[CitrusHigh]

"The acquisition and incorporation of genetic material between nonmating species, or horizontal gene transfer (HGT), has been frequently described for phylogenetically related organisms, but far less evidence exists for HGT between highly divergent organisms. Here we report the identification and characterization of a horizontally transferred fragment of the human long interspersed nuclear element L1 to the genome of the strictly human pathogen Neisseria gonorrhoeae. A 685-bp sequence exhibiting 98 to 100% identity to copies of the human L1 element was identified adjacent to the irg4 gene in some N. gonorrhoeae genomes. The L1 fragment was observed in ~11% of the N. gonorrhoeae population sampled but was not detected in Neisseria meningitidis or commensal Neisseria isolates. In addition, N. gonorrhoeae transcripts containing the L1 sequence were detected by reverse transcription-PCR, indicating that an L1-derived gene product may be produced. The high degree of identity between human and gonococcal L1 sequences, together with the absence of L1 sequences from related Neisseria species, indicates that this HGT event occurred relatively recently in evolutionary history. The identification of L1 sequences in N. gonorrhoeae demonstrates that HGT can occur between a mammalian host and a resident bacterium, which has important implications for the coevolution of both humans and their associated microorganisms. "

"IMPORTANCE The interactions between microbes and their hosts are relevant to several aspects of biology, including evolution, development, immunity, and disease. Neisseria gonorrhoeae serves as a particularly informative model for this interaction because it has exclusively coevolved with humans and is not known to be found in any other environment."

http://mbio.asm.org/content/2/1/e00005-11.abstract

[CitrusHigh]

Genetic Transfer - part 1

[CitrusHigh]

"The use of broad spectrum antibiotics creates a selective pressure on the bacterial flora, thus increasing the emergence of multiresistant bacteria, which results in a vicious circle of treatments and emergence of new antibiotic resistant bacteria. The human gastrointestinal tract is a massive reservoir of bacteria with a potential for both receiving and transferring antibiotic resistance genes. The increased use of fermented food products and probiotics, as food supplements and health promoting products containing massive amounts of bacteria acting as either donors and/or recipients of antibiotic resistance genes in the human GI tract, also contributes to the emergence of antibiotic resistant strains. This paper deals with the assessment of antibiotic resistance gene transfer occurring in the gut.'

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3034945/


"The fact that genes can move between distant branches of the tree of life even at low probabilities raises challenges to scientists trying to reconstruct evolution by studying genes and gene sequences in different organisms. Horizontal gene transfer (HGT) effectively scrambles the information on which biologists rely to reconstruct the phylogeny of organisms.

Furthermore, HGT poses challenges for the ambitious reconstruction of the earliest events in evolution. Because the early branches of the tree of life spanned long time intervals and involved large numbers of organisms, many low-probability HGT events are certain to have occurred."

http://en.wikipedia.org/wiki/Horizontal_gene_transfer_in_evolution