Mechanisms of gene transfer between bacteria include which of the following?

Abstract

Horizontal gene transfer (HGT) is recognized as a process of acquiring new gene in both prokaryotes and eukaryotes. It becomes a major driving force leading to genomic variability that possibly contribute to its evolution via adaptation and survivability with the newly transferred gene(s). Previously, the detection of HGT event is solely on molecular hybridization practice and not applicable to whole genome sequences. Advent in next generation sequencing technologies allow the occurrence of HGT events in inter- or intra- species and even kingdom to be detected comprehensively. Here, we discuss several computational approaches in the discovery of HGT events in bacteria and plant using pan-genome data and transcriptome profiling. The illustrative case studies give an insight into the HGT effect in increasing the capabilities of organism to evolve and adapt in different environments.

5 The impact of horizontal gene transfer on oomycete evolution

Horizontal gene transfer (HGT), or lateral gene transfer (LGT), is the nonvertical transfer of genetic material between different species (Savory, Leonard, & Richards, 2015). HGT can have significant evolutionary consequences, such as facilitating recipient species to adapt to different ecosystems or exploit new hosts. Before oomycete genomes were first sequenced, it was known that HGT played an important role in the evolution of oomycetes. Phylogenetic analysis of Ph. infestans EST sequences identified an endopolygalacturonase gene (pipg1), encoding an enzyme involved in pectin breakdown, that's most closely related homologs belonged to fungi suggesting a possible HGT event from fungi to Phytophthora (Torto, Rauser, & Kamoun, 2002). Sequencing of the Ph. ramorum and Ph. sojae genome (Tyler et al., 2006) facilitated more in-depth analyses of HGT which led to the identification of four HGT events from ascomycete fungi to Phytophthora with strong phylogenetic evidence (Richards et al., 2006). Interestingly, each of the four genes are likely to be involved in osmotrophy-related functions, implying that HGT may have played a role in the convergent evolution of osmotrophy and filamentous growth between fungi and oomycetes. There is also evidence of HGT events from bacteria to oomycetes, including secreted cutinases (important virulence factors involved in the breakdown of the plant cuticle) that appear to have been transferred from Actinobacteria to oomycetes and later duplicated, with 16 copies being found in the Ph. sojae genome (Belbahri, Calmin, Mauch, & Andersson, 2008). Another analysis that examined metabolic enzymes from eukaryotic genomes showed that 2% of metabolic enzymes in the genomes of Ph. ramorum and Ph. sojae potentially originated via HGT (Whitaker, McConkey, & Westhead, 2009).

The availability of more oomycete genomes has allowed for more comprehensive, whole-genome scans to identify genes that may have been gained via HGT. Similarly, the availability of more non-oomycete genomes has led to increased taxon sampling in databases adding further support for the validity of HGT events. Phylogenetic analysis of four oomycetes genomes (Hy. arabidopsidis, Ph. infestans, Ph. ramorum and Ph. sojae) using a database of 795 (173 eukaryotic and 622 prokaryotic) genomes identified 34 gene transfers between fungi and oomycetes (Richards et al., 2011). Interestingly, 62%–76% of genes identified as originating via HGT from fungi in the four analyzed species possess a predicted secretion signal, representing between 2.7% and 7.6% of the total predicted secretomes of these species. Many of the identified genes have functions associated with the breakdown of plant cell walls and the uptake of nitrogen, nucleic acids, phosphate and sugars from the environment (Richards et al., 2011). This adds further support to the hypothesis that HGT events from fungi have played a part in the convergent evolution of osmotrophy and filamentous growth between fungi and oomycetes. Genome analysis of Sa. parasitica led to the identification of five gene families (four of which are secreted) that appear to have been gained by Sa. parasitica via HGT from bacteria or animals (Jiang et al., 2013). An additional six HGT events were reported from the genome sequences of Ac. hypogyna and Th. clavata, all of which are predicted to be secreted and involved in pathogenicity or carbohydrate metabolism (Misner et al., 2015).

Reanalysis of 48 HGT gene families based on the 23 oomycetes genomes that were available in 2015 highlighted several important findings (Savory et al., 2015). For example, 33 (69%) of the 48 HGT families are predicted to be secreted and 40 (83%) of the 48 HGT families appear to have a fungal origin. Only seven cases of HGT could be mapped back to the ancestor of the four crown oomycete orders, suggesting that HGT played a limited role in early oomycete evolution. HGT appears to have had a greater impact on plant pathogenic oomycetes, with 33 HGT events identified within the Phytophthora, Hy. arabidopsidis and Pythium clade, compared to only five in the branch leading to the Saprolegniales order (Savory et al., 2015). Interestingly, many of the HGT derived genes have not only become fixed in the recipient genomes but have been duplicated, sometimes multiple times. For example, Pythium and Phytopythium species have a mean of 2.1 copies of each HGT derived gene, whereas Phytophthora species have a mean of 4.4 (Savory et al., 2015). Acquisition of genes via HGT can potentially change the phenotype of the recipient and also provide genetic material that has the potential to evolve novel or expanded functions. Detailed functional analyses of transporter proteins that were transferred to oomycetes before the divergence of Peronosporales and Saprolegniales revealed an HGT derived paralogue belonging to Py. aphanidermatum that has evolved an expanded substrate range enabling it to uptake not only dicarboxylic acid (the ancestral function) but also tricarboxylic acid (Savory, Milner, Miles, & Richards, 2018).

Analysis of EST sequences from Py. oligandrum identified a homolog of a type 2 NLP from bacteria (Horner, Grenville-Briggs, & van West, 2012). Type 2 NLPs were previously thought to be absent in oomycetes and only found in fungi and bacteria. A follow-up analysis of effector proteins in 37 oomycete genomes using network and phylogenetic methods identified type 2 NLPs in three oomycete species—Py. oligandrum, Pilasporangium apinafurcum and Pp. vexans (McGowan & Fitzpatrick, 2017). Phylogenetic analysis suggested that the genes were likely gained via HGT from a Proteobacterial source and later duplicated with 2 copies in Pp. vexans, 6 copies in Pi. apinafurcum and 17 copies present in Py. oligandrum. An additional five instances of HGT from bacteria to oomycetes were reported in another study focusing on 14 plant pathogenic oomycete genomes including a putative secreted protein, a class II fumarase, an oxidoreductase, an alcohol dehydrogenase, and a hydrolase (McCarthy & Fitzpatrick, 2016).

Based on the genome analyses conducted to date, it is clear that HGT has played a significant role in oomycete genome evolution. In particular, HGT has had a major impact on the secretomes of plant pathogenic oomycetes such as Phytophthora. Furthermore, convergent evolution between fungi and oomycetes was likely driven, in part, by HGT. As more genome sequences become available it will be possible to more accurately place the timing of putative HGT events, e.g., in an oomycete ancestor or specific to particular oomycete lineages, and also to rule out possible effects of poor taxon sampling.

2.3.4.1.D Horizontal Gene Transfer

Horizontal gene transfer, also known as lateral gene transfer, refers to nonsexual transmission of genetic material between unrelated genomes; hence, horizontal gene transfer involves gene transfer across species boundaries. The phenomenon of horizontal gene transfer throws a wrench in the concepts of last common ancestor, syntenic relationship between genomes, phylogeny and the evolution of discrete species units, taxonomic nomenclature, etc.m The majority of examples of horizontal gene transfer are known in prokaryotes. In bacteria, three principal mechanisms can mediate horizontal gene transfer: transformation (uptake of free DNA), conjugation (plasmid-mediated transfer), and transduction (phage-mediated transfer). In plants, introgression can mediate horizontal gene transfer; this means gene flow from one gene pool to another gene pool—that is, from one species to another species by repeated backcrossing between an interspecific hybrid and one of its parent species. Therefore, introgression depends on the extent of reproductive isolation between the two species. Introgression has also been reported between duck species, between butterfly species involved in mimicry, and between human and Neanderthal.41

Horizontal gene transfer in animals is not common, but there are some reports. For example, Acuña et al.42 identified the gene HhMAN1 from the coffee berry borer beetle, Hypothenemus hampei, which shows clear evidence of horizontal gene transfer from bacteria. HhMAN1 encodes the enzyme mannanase, which hydrolyzes galactomannan. Phylogenetic analyses of the mannanase from both prokaryotes and eukaryotes revealed that mannanases from plants, fungi, and animals formed a distinct eukaryotic clade, but HhMAN1 was most closely related to prokaryotic mannanases, grouping with the Bacillus clade. HhMAN1 was not detected in the closely related species H. obscurus, which does not colonize coffee beans. The authors hypothesized that the acquisition of the HhMAN1 gene from bacteria was likely an adaptation in response to need in a specific ecological niche.

There are also some examples of horizontal gene transfer from fungi to arthropods, such as aphids (insects) and mites (arachnids). Phylogenetic analysis revealed the evidence of horizontal transfer of genes encoding carotenoid desaturase and carotenoid cyclase–carotenoid synthase from fungi to pea aphid,43 and to spider mite.44 Notably, the fused carotenoid cyclase–carotenoid synthase gene is characteristic of fungi but not of plants or bacteria. The authors discussed the possible mechanism of such gene transfer. Gene transfer into a single arthropod ancestor of both spider mites and aphids is not likely because it would require subsequent loss of these genes in most other living arthropod taxa. The most likely scenario is the transfer of these genes through symbiosis, which probably occurred independently in both aphids and spider mites. It has been suggested that the frequent association of mites with viruses makes them ideal horizontal gene transfer vectors, including incorporation of mobile genes into their own genomes.

32.4.2 Role of Horizontal Gene Transfer

HGT is also known as lateral gene transfer in which one adult bacterium transfers its genes to another either through conjugation, transformation, or transduction. Conjugation is direct transfer of genes between bacteria through conjugation tube. Transduction is the transfer of genes between two bacteria through bacteriophage. Transformation is the transfer of DNA from extracellular environment into bacterial cells directly. In not more than recent time, the role of HGT was considered very significant in terms of evolution (Juhas, 2015).

Horizontal transfer of pathogenic genes or pathogenicity islands is very common in Gram-positive bacteria (Novick et al., 2010). Bacteria are known to use Type IV secretion system for the conjugation to transfer their genes to the adjacent organism (Juhas et al., 2008). HGT is not nonspecific at all; some “smart” bacteria like Neisseria and Helicobacter use host-specific sequences to integrate the foreign DNA into their genome (Ambur et al., 2007, 2009; Treangen et al., 2008).

Horizontal transfer of gene is not a screening free process when a cell receives the DNA it screens, and if the DNA is found to be fit, then only it gets expressed or integrated into the genome or else it’s digested by nucleases. However, there are some factors which also affects HGT of genes; the main factors known till now are surface exclusion as it happens in case of F plasmid in E. coli. Restriction digestion is another barrier to the HGT as it digests the foreign DNA. Restriction to the replication of the newly imported DNA is another factor which affects the horizontal transfer of genes (Thomas and Nielsen, 2005).

HGT essentially provides the organism with various functional genes without undergoing mutation. It provides genes that provide resistance toward antibiotic or they provide pathogenicity to organism so the organism can infect the host as well; they can be resistant to various antibiotics. Apart from bacteria, eukaryotes are also involved in HGT and they have acquired some important functional genes (Soucy et al., 2015).

Horizontal Gene Transfer

Horizontal gene transfer (HGT) is also known as the exchange and stable integration of genetic material between different strains or species, and has been reported in plants, animals, and fungi. HGT of individual genes, gene clusters, or entire chromosomes can affect colonization of new environments (niche specifications) or fitness (disease emergence or shift in metabolic capabilities) (Fitzpatrick, 2011). Fungi have gained genes by HGT and this gene movement could have different origins. After whole-genome evaluation of Aspergillus fumigates, it was found that HGT in this microorganism emerged from bacteria (40%), fungi (25%), and viruses (22%) (Mallet et al., 2010). The fungal HGT is very interesting because fungi are recalcitrant to gene transfer because they have robust cell walls and have lost phagotrophic capacities. However they possess mechanisms that favor HGT such as anastomosis, conjugation-like transfer, and exchange of supernumerary chromosomes (Richards et al., 2011).

Aspergillus produces a large number of secondary metabolites during morphological and chemical differentiation. The secondary metabolite gene clusters of fungi are some of the largest functionally related genes. HGT is episodic and acts in a category-or-lineage-specific manner and had a great impact on clustered genes, which suggests that metabolic gene clusters are hotspots for generation of Aspergillus metabolic diversity (Wisecaver et al., 2014). One of these clusters codifies for fumonisin and evidence indicates that it was horizontally transferred into A. niger, most probably from a Sordariomycete species (Khaldi and Wolfe, 2011). There are reports indicating that biosynthetic genes of several mycotoxins such as AFs, ochratoxin A (OA), and patulin are clustered, suggesting that these clusters could be horizontally transferred (Varga et al., 2003).

On the other hand, HGT have added diversity to the core nutrient-processing metabolism of many fungi (Richards et al., 2011). For example, some antibiotics (v.g. hydrophilic cephalosporins) are produced by both fungi and bacteria species. The evidence indicates that the genes codifying for these antibiotics passed by HGT from bacteria to Aspergillus because of the absence of introns and that genes are located in clusters (García-Estrada et al., 2010). Gene transfer can also be from Aspergillus to an unrelated organism. It has been reported that a cluster composed of 23 genes jumped from Aspergillus to Podospora (Slot and Rokas, 2011). Based on this observation, producing abilities of Aspergillus were lost (or gained) several times during the evolution of the genus (Varga et al., 2003). The phylogenetic analyses are the best approaches to find and test potential examples of HGT (Richards et al., 2011). Coelho et al. (2013) indicated that interspecies HGT may have contributed much more substantially to shape fungal genomes than heretofore assumed.

8.7.1 Horizontal Gene Transfer in Human Pathogens

Horizontal gene transfer has a tremendous impact on the genome plasticity, adaptation, and evolution of bacteria. Horizontally transferred mobile genetic elements are involved in the dissemination of antibiotic resistance and virulence genes, thus contributing to the emergence of novel “superbugs.” Horizontal gene transfer plays in pathogenicity of the emerging human pathogens: hypervirulent Clostridium difficile and Escherichia coli (including the most recent haemolytic uraemic syndrome outbreak strain) and methicillin-resistant S. aureus (MRSA), which have been associated with largest outbreaks of infection recently.

Pathogenic bacteria remain among the major worldwide causes of morbidity and mortality. Sequence and functional genome analyses revealed that a number of genes augmenting virulence of the major human pathogens have been acquired in the course of evolution by horizontal gene transfer. Several novel multiresistant and/or hypervirulent “superbugs” emerged over the last years as a result of horizontal acquisition of antibiotic resistance and virulence genes, causing serious outbreaks not only in hospital, but also in communal settings among otherwise healthy individuals. Recent advances have gained attention in the investigation of horizontal gene transfer and its role in the evolution of pathogenic bacteria with particular emphasis on horizontal gene transfer in C. difficile. E. coli, and S. aureus. These three bacterial species seem to resonate most among general public and academic community nowadays. They have caused large infection outbreaks and currently represent a major threat to public health.

Horizontal Gene Transfer

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Horizontal (or lateral) gene transfer occurs when genetic information is passed “sideways” to a relatively unrelated organism (as opposed to a direct descendent).

The extent of horizontal gene transfer is difficult to measure accurately and has often been over-estimated.

Transmission of genetic information from parent to offspring is termed vertical gene transfer. Lateral movement, or movement of genetic information from a donor to an unrelated recipient, is called horizontal gene transfer.

The transfer of genetic material horizontally usually involves the use of viruses, plasmids, or mobile elements such as transposons. Horizontal gene transfer occurs not only for unrelated species, but for related species as well. Estimates from DNA sequences suggest that 5–6% of the genes in a bacterial genome are derived from horizontal gene transfer.

Instances of horizontal gene transfer are difficult to measure. Therefore, horizontal gene transfer is often over-estimated. Several reasons for this exist. First, only a few eukaryotic genomes have been sequenced, but hundreds of prokaryotic genomes have been sequenced. This results in sampling bias. Second, homologs for genes may be lost in some lineages. Third, gene duplication followed by divergence gives rise to novel genes. Fourth, laboratory transfer of genes is easier than the real life scenarios. And finally, during laboratory experiments, it is difficult to completely purify away all of the eukaryotic DNA from bacterial and viral genetic information.

Dunning Hotopp JC (2011) Horizontal gene transfer between bacteria and animals. Trends in Genetics 27:157–163.

Focus on Relevant Research

Horizontal gene transfer among bacteria or related eukaryotes is well-documented. Eukaryote to eukaryote gene transfer is rare, but instances have been documented, such as for some Drosophila genes. However, a more intriguing phenomenon is the horizontal gene transfer across the domains of life. Archaeal genes have been discovered in bacteria. Additionally, some plants received DNA from Agrobacterium species for the formation of tumors. Evidence even exists for the transfer of some trypanosome genes into human germ cell lines.

In horizontal gene transfer involving bacteria-to-animals, the source of the bacteria remains the dividing line. For endosymbionts, the transfer is more frequent because of the close association with the host. Horizontal gene transfer is crucial in the transition of endosymbionts to cellular organelles.

Examples of horizontal gene transfer for this scenario include genes transferred from the endosymbiont Wolbachia to the host arthropod genome. Wolbachia is also an endosymbiont of some nematodes and evidence also suggests that horizontal gene transfer has occurred between these two organisms as well.

In addition to horizontal gene transfers between Wolbachia and its hosts, other examples of transfer between bacteria and animals exist. Endosymbionts of pea aphids are also able to exchange genetic information with their hosts. Additionally, evidence in Hydra, a freshwater animal, suggests that the origins of DNA for horizontal transfer does not have to come from an endosymbiont, as they have genes derived from bacteria, but do not have any known endosymbionts.

Finally, eukaryotes are also able to transfer genes to bacteria, although these are not well-described but are expected to occur quite often. Legionella pneumophila encodes over 100 eukaryotic-derived proteins. Additionally, a cyanobacterium has acquired eukaryotic actin and actin-binding proteins, and used these to generate a shell-like structure to protect it against changes in osmolarity.

Many horizontal gene transfers are difficult to identify due to the lack of sequence data. Additionally, reports tend to be skewed towards arthropod- and nematode-involved transfers due to their abundance on Earth.

What are the 3 ways bacteria transfer genes?

What are the 3 mechanisms of gene transfer in prokaryotes?

What are the methods of gene transfer between bacteria and describe each?