Abstract
Horizontal gene transfer (HGT) has a great role as a driving force in the evolution of prokaryotes and eukaryotes and has occupied a major role in evolutionary thinking. Many studies have shown how prokaryotic evolution has been manipulated by HGT such as the spread of antibiotic resistance in bacteria. The importance of HGT in eukaryotes has long been eclipsed due to variety of reasons. In the last decade, the study of interest now seems to focus more on eukaryotes and with the availability of more public databases and more advanced analytical tools, the reported incidence of eukaryotic HGT seems to increase. As scientific knowledge about HGT continues to grow, it changes our current understanding of evolution and phylogenetic analysis of tree of life.
Introduction
Horizontal gene transfer is the transfer of the genetic materials from one organism to another and its stable integration within the genome of the host organism. HGT is also known as lateral gene transfer (LGT) and is quite different from vertical gene transfer which involves the transfer of genetic information from parents to offspring (Fitzpatrick, 2012). The discovery of HGT dates to late 1920s when Frederick Griffith first demonstrated that non-virulent Streptococcus pneumoniae was able to become pathogenic through the transfer of unknown factor from the heat-killed virulent S. pneumoniae. It was in 1944 when Avery, MacLeod, and McCarty illustrated that DNA was the unknown factor that was transformed from the heat-killed virulent strain to the non-virulent one (Sieber et al., 2017). The role of HGT in prokaryotic evolution has been widely studied for many years and is considered as an important factor in creating genetic diversity among the prokaryotes. However, its role in eukaryotic evolution has been less established. In recent years, more studies have indicated that HGT has a significant role in the evolution of multicellular eukaryotes too (Huang et al., 2017).
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Mechanism of Horizontal Gene Transfer
The mechanism underlying the transmission of genetic materials is well understood and described in the case of prokaryotes. But the mechanism by which HGT takes place in case of eukaryotes is not fully understood. However, a few possible mechanisms in Saccharomyces cerevisiae has been reported by Heinemann & Sprague in 1989 to describe the exchange of bacterial plasmid through conjugation and by Bundock et al. in 1995 to describe the Agrobacterium tumefaciens-mediated transformation (reviewed by Fitzpatrick, 2012).
Three of the well-documented mechanism of HGT are conjugation, transformation and transduction. Conjugation is the transfer of genetic materials from a donor cell to the recipient cell and requires cell-cell contact (sex-pilus). Transformation is the uptake of foreign DNA by the recipient cell from outside of the cells, typically from dead organisms. Lastly, transduction occurs when a virus carries the bacterial genome and transfects it into another bacterium.
DNA, once integrated into the cytoplasm of the host cells, can have many fates. It can undergo degradation by host’s restriction enzymes, DNAse or may remain in the cell and replicate on its own such as plasmids. Also, the genome may be integrated into the host chromosome that may or may not provide a novel trait to the recipient organism (Daubin and Szöllősi, 2016).
Role of HGT in prokaryotic evolution
The role of horizontal gene transfer is widely studied and accepted among prokaryotes because of the availability of numerous prokaryotic genomes for comparative analysis (Koonin et al., 2001). Koonin et al. described that each microbe might have gained around 1.6 to 32.6 percent of the genes through HGT. Dagan et al. in 2008 performed a network analysis of shared genes in 181 sequenced prokaryotic genomes and showed that it increases dramatically to 81±15 per cent. Transfer of gene seems to take place at a greater extent between archaea and bacteria and it shows the role of HGT in the evolution of prokaryotes over the evolutionary periods. A study was performed by Kanhere & Vingron in 2009 to find ancient transfer events in prokaryotic genomes. They found that 118 of the 171 gene transfer events were between Archaea and Bacteria and those transferred genes were related mainly to metabolism (reviewed by Boto, 2010).
While HGT between prokaryotes seem prominent, transfer of genetic materials from eukaryotes to prokaryotes has also been reported and most of them are contributed mainly through the symbiotic relationship between the organisms (Keeling and Palmer, 2008). A study was conducted to find out probable HGT events in 1,059 reference microbial genome isolated from six major body sites of healthy humans and sampled by the NIH Human Microbiome Project (Jeong et al., 2019). They found out that more than 50% of the genes in those pathogens were transferred through HGT.
One interesting example of eukaryote-prokaryote LGT includes the transfer of eukaryotic aminoacyl-tRNA synthetases (aaRS) to bacteria. Phylogenetic analysis of the aaRS done in 20 specificities showed that gain of eukaryotic aaRS is most common in Spirochetes and Chlamydia(Koonin et al., 2001).
Few other examples of genetic transfer from eukaryote to prokaryote have been reported such as in case of Legionella pneumophila (reviewed by Dunning Hotopp, 2011). Phylogenetic analysis showed that it encodes about 29 of the proteins that have eukaryotic ancestry.
HGT as a key player in the evolution of antibiotic-resistant bacteria
HGT is the prime reason because of which bacteria have evolved to acquire resistance and thrive even in the presence of antibiotics. One such example as studied by Paterson and Bonomo is the acquisition of plasmid-mediated Extended-spectrum β-lactamases (ESBLs) and carbapenemase gene by bacteria through conjugation. It provides them the ability to hydrolyse β-lactam antibiotics and carbapenems (reviewed by Lerminiaux and Cameron, 2019). Bacteriophage is another important mediator in driving the resistant gene from one bacterium to another. Several cases of transduction in various bacterial species have been documented: Fard et al. documented transfer of tetracycline resistant gene in enterococci; plasmid encoding antibiotics transfer in Methicillin-resistant Staphylococcus aureus by Varga et al. (reviewed by von Wintersdorff et al., 2016)
In the same way, HGT has a role in the evolution and transmission of virulence in bacteria. Mobile genetic elements play a major role in the transmission of virulence such as plasmids and bacteriophage(Keen, 2012). According to Brussow et al., non-virulent strains of Escherichia coli, Staphylococcus aureus, Vibrio cholera can become highly virulent by acquiring external virulent genes from the bacteriophages (reviewed by Keen, 2012).
Role of HGT in eukaryotic evolution
The importance of HGT in eukaryotic evolution has largely been a subject of debate considering the fact in difficulty to prove it exclusively and barriers enforced by germline in the spread of horizontally transferred genes (Boto, 2014; Koonin et al., 2001). But the rapid progress in bioinformatics tools and sequencing has led to the detection of more number of LGT in eukaryotes and to the conclusion that it has an important role in its evolution (Sieber et al., 2017).
Prokaryote to eukaryote transfer is very important and widely studied when talking about the HGT in eukaryotic evolution. Very few eukaryotic to eukaryotic HGT has been documented because of the complexity of genomes in a higher organism and erroneous report comprising the evidence of HGT in higher animals(reviewed by Keeling and Palmer, 2008). Mainly studied and accepted prokaryote to eukaryotic transfer is the organellar transfer of genes from mitochondria and plastid ancestors. These organelles originally originated from α-proteobacteria and Cyanobacteria respectively and transferred to eukaryotes through endosymbiosis (Sieber et al., 2017).
Apart from organelle transfer, several other events of HGT has been described in a wide range of the eukaryotes including unicellular fungi and several metazoans. Due to the relatively less complex genome of the fungi, complete genome sequencing of over 100 fungal species has been done which allows the comparative study of HGT in evolution of fungi(Fitzpatrick, 2012). Comparative genome analysis of fungi for detection of HGT has shown that the majority of donor groups are bacteria and few of those events also contain fungi to fungi transfer.
Garcia-Vallve et al. have described the gain of glycosyl hydrolase from the prokaryote by rumen fungi that allows them to utilise cellulose and hemicellulose. HGT of entire metabolic pathways gene has been described by Slot and Rokas in which sterigmatocystin pathway (~57-kb genomic region containing all 23 genes) has been transferred from Aspergillus nidulans to Podospora anserina (reviewed by (Fitzpatrick, 2012).
Not only fungi, but multicellular metazoans and higher organisms also acquire novel traits by means of LGT indicating its significance(Boto, 2014). In his review paper, he has described the events of LGT in a wide range of animals such as sponges, cnidarians, nematodes, arthropods as well as chordates. One interesting study describes that one of the cnidarians, Hydra magnipapillata genome has a homology in its seventy-one genes with bacterial genes. Moreover, it also lacks homologues with other metazoans in about 51 of those genes suggesting that H. magnipapillata has acquired those genes from bacteria through HGT(Chapman et al., 2010). Another example of HGT in metazoans includes the study done by Acuna et al. in a beetle Hypothenemus hampei. The beetle gained a bacterial hnMAN1 gene through LGT which makes it fit to adapt to a new environment (Sieber et al., 2017).
Controversial case of HGT in the tardigrade
Despite all the studies indicating the role of HGT in eukaryotes, it is still seen as a matter of controversy. It may be considered due to the fact that transcriptional and translation control of the prokaryotic genes are quite different as compared to the eukaryotes. Therefore, the functional understanding of those genes will still be difficult even if those genes are integrated into the eukaryotic genome (Danchin, 2016). One such controversial case about the prokaryote-eukaryote HGT can be seen in the tardigrade case (Arakawa, 2016). Initially, it was suggested that the tardigrade genome contains up to 17% of the gene acquired through HGT representing it as highest proportion in animals. Later it was reported that only 1-2% of those genes are acquired through HGT and the exaggerated rate of HGT is probably due to wrong interpretation of bacterial contamination as horizontally acquired genes.
The conclusion that can be drawn from this controversial case is that more care and thorough study should be done before claiming LGT. However, one such incidence cannot rule out all the possibility of the HGT between prokaryotes and eukaryotes and HGT is an important driving force in the evolution of eukaryotes.
HGT in human genome
The occurrence and role of HGT in humans have always been a controversy. A first comparative and analytical study of the human genome in 2001 by Lander et al. suggested that 223 human proteins were derived from bacteria through LGT. However, this finding was invalidated by scientists suggesting alternative explanations such as gene loss or other evolutionary changes(reviewed by Sieber et al., 2017). These explanation makes sense because humans do not usually favour the addition of new functions in our genome and the germ line usually prevent the spread of horizontally transferred genes(Robinson and Hotopp, 2016).
Regardless of the sceptical attitude from some of the scientific community, several studies involving HGT in the human genome has been presented. Recent pair-wise alignment analysis by Huang et al. between the human reference genome and other vertebrates indicated that HGT is more common in human than what was thought before (Huang et al., 2017). In my opinion, as viral genomes and mitochondrial genome frequently integrate into the human genome, there is a high possibility that bacterial DNA can also integrate into the human genome. There is a widespread of microbes in our body and therefore it provides a large source of DNA that could possibly be integrated into our genome.
Looking forward
The increasing reports of HGT in eukaryotes including humans is the result of availability of public database that has been fast growing due to the advancement in sequencing technologies(Fitzpatrick, 2012; Sieber et al., 2017). The earlier report of LGT in humans by Lander et al. was solely based on so-called surrogate methods (Fitzpatrick, 2012). The surrogate approach is attractive and uses atypical GC content of the genome, unusual codon usage and BLAST searches in detecting the incidence of HGT but it does prove insufficient(Daubin and Szöllősi, 2016; Keeling and Palmer, 2008). Fitzpatrick has suggested in his review paper that combining surrogate methods with a more robust method such as phylogenetic analysis (for validation) could provide accurate data when investigating HGT(2012).
As sequencing data becomes more easily available and the technology for LGT detection advances, more studies about LGT will be available. The true importance of HGT in driving our complex genome and its role in the evolution of higher organisms will be clearer.
HGT challenge the tree of life
The tree of life has undergone many reconstructions since the early evolution of biological science (Boto, 2015). Fox and Woese in the late 1970s established a systematic phylogenetic classification of the organisms which was most generally accepted as a tree of life (Daubin and Szöllősi, 2016). Fox and Woese established a phylogenetic relationship based on a sequence of ribosomal RNA termed 16S in prokaryotes and 18S in eukaryotes and since then three main domains of life was classified: Archaea, Bacteria and Eukaryotes.
James et al. proposed a complexity hypothesis in 1999 that assumes that these genes (ribosomal RNA) are not transferred through HGT and evolutionary relationship derived from it should be correct (reviewed by Fitzpatrick, 2012). However, there is a report that tells the evidence of HGT in these universally distributed genes suggesting the need for re-evaluation of the phylogenetic tree based on these genes. (Creevey et al., 2011). While some scientists suggest that alternative methods should be used to reconstruct phylogenetic tree, some believe that tree of life can still be recovered using the analysis of a number of universally distributed genes (reviewed by Boto, 2015). As we all are familiar with the complexity of gene evolution, future development of more upstanding methodologies may allow the correct reconstruction of the tree of life.
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