User:Meengis/sandbox

= PLANT FUNGI HORIZONTAL GENE TRANSFER =

Introduction
Transmission of genetic material nonsexually between distant species is less frequent than gene transmission from parent to offspring. Horizontal Gene Transfer (HGT) is a universal phenomenon observed in fungi, viruses, bacteria, and other eukaryotes. HGT research highlights prokaryotic organisms because of the abundant sequence data from diverse prokaryotic lineages. HGT is assumed not to play a significant role in eukaryotes.

Most Plant-Fungi HGT events are ancient and rare but possibly provided valuable gene functions like wider substrate use and habitat spread for plants and fungal species. Since these events are rare and ancient, they have been difficult to detect. Plant-Fungi HGT events and mechanism are relatively unknown. Plant-Fungi interactions could also play one part in a multi HGT pathway between many other organisms.

Mechanisms
In HGT, foreign DNA needs to enter the cell. The gene can be naked or harbored within a cell. The gene must be incorporated into the host nucleus and be expressed by proteins. Although there are instances a gene can be incorporated into the nucleus and still not be expressed, natural selection pressures will often maintain the incorporated gene as long as it can be useful.

Unsuccessful incorporation of DNA could produce pseudogenes. Genes not under purifying selection could accumulate deleterious mutations. When a gene transfer is successful, it can be maintained in the population. When the same gene is present in other related eukaryotes, pattern sequence variation could show the specific amino acid sequences are under purifying selection. Genetic elements like plasmids, mycoviruses, introns, and transposons provide possible methods for transferring DNA.

HGT in eukaryotes can transfer genes from organelles. This transfer moves genes from the endosymbiotic origin in mitochondrion and plastids to the nucleus of eukaryotic cell. Other gene transfers could take place between unrelated species.

Often phagotrophic mechanisms are attributed to HGT events. Phagotrophic microbial eukaryotes show a regular pattern of gene transfer into eukaryotic genomes and act as a driving force for HGT. Fungi-plant mediated HGT show similar phagotropic mechanisms as well as nonphagotropic mechanisms. Nonphagotrophic mechanisms have been seen in transmission of transposable elements, plastid-derived endosymbiotic gene transfer, prokaryote-derived gene transfer, Agrobacterium tumerfaciens mediated DNA transfer, cross-species hybridization events, and gene transfer between mitochondrial genes. HGT could bypass Eukaryotic barrier features like linear chromatin-based chromosomes, intron-exon gene structures, and the nuclear envelope.

HGT events occur between microorganisms sharing overlapping ecological niches and associations like parasitism or symbiosis. Ecological association can facilitate HGT in plants and fungi and is an unstudied factor in shared evolutionary histories.

Most HGT events from fungi into plants predate the rise of land plants. Still, a greater genomic inventory of gene family and taxon sampling is needed to find Plant-Fungi HGT events.

Found In Unusual Genetic Elements
Evidence for Fungi and Eukaryotic gene transfer is discovered indirectly. Evidence is found in the unusual features of genetic elements. These features include: inconsistency between phylogeny across genetic elements, high DNA or amino acid similarity from phylogenetically distant organisms, irregular distribution of genetic elements in variety of species, similar genes shared among species within a specific habitat or geography independent of phylogenetic relationship, and genes characteristics inconsistent with resident genome such as high G+C content, codon usage, and introns.

Alternative Hypotheses For Present Evidence
Other alternative hypotheses and explanations include: erroneous species phylogenies, inappropriate comparison of paralogous sequences, sporadic retention of shared ancestral characteristics, uneven rates of character change in other lineages, and introgressive hybridization.

Horizontal Gene Transfer as a Multi-Vector Pathway
Plant-Fungi HGT could take place during plant infection. There are many possible vectors for HGT to take place such as plant-fungus-insect interactions. The ability for fungi to infect other organisms provides this possible pathway for HGT.

In Rice (Oryza sativa)
Rice (Oryza sativa) have demonstrated a “Fungi–plant” pathway through ancestral lineages. In Richards, 'Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi," a phylogeny was constructed from all 1689 genes identified and all homologs available from rice (Oryza sativa) genome from 3177 gene families. 14 candidate plant-fungi HGT events were defined. Further phylogenetic analyses revealed nine HGT showed infrequent pattern of HGT between plants and fungi. From the phylogenetic analysis, HGT events could have contributed to: L-Fucose permease sugar transporter, zinc binding alcohol dehydrogenase, membrane transporter, phospholipase/ carboxylesterase, iucA/ iucC family protein in siderophore biosynthesis, DUF239 domain protein, Phosphate-response 1 family protein, a hypothetical protein similar to zinc finger (C2H2-type) protein, and another conserver hypothetical protein.

Ancestral Shikimate Pathway
Some plants obtained shikimate pathway though symbiotic fungi though ancestral origins.

Plant shikimate pathway enzymes share similarities to prokaryote homologues and could have ancestry from a plastid progenitor genome. It is possible the shikimate pathway and the pentrafunctional arom has its ancient origins in eukaryotes or was conveyed by eukaryote-eukaryote HGT. The evolutionary history of shikimate pathway could have been influenced by a prokaryote-to-eukaryote gene transfer event. Ascomycete fungi along with zygomycete, basidiomycete, apicomplexa, ciliates, and oomycetes retained elements of a ancestral pathway given through the bikont/unikont eukaryote root.

Ancestral Land Plants
Fungi and bacteria could have contributed to the phenylpropanoid pathway in ancestral land plants for synthesis of flavonoids and lignin through HGT. Phenylalanine ammonia lyase (PAL) is known to be present in fungi. An example is Basidomicietes yeast like Rhodotorula and Ascomycetes such as Aspergillus and Neurospora. These fungi participate in catabolism of phenylalanine for carbon and nitrogen. PAL in some plants and fungi also have a tyrosine ammonia lyase (TAL) for synthesis of p-coumaric acid into p-coumaroyl-CoA. PAL likely emerged from bacteria as an antimicrobial role. HGT took place through an pre-Dikarya divergent fungal lineage and a Nostocale or soil-sediment bacterium through symbiosis. The fungal PAL was then transferred to an ancestor of a land plant by an ancient AM symbiosis that later developed in the phenylpropanoid pathway and land plant colonization. PAL enzymes in early bacteria and fungi could have contributed to protection against UV radiation, acted as light capturing pigment, or in antimicrobial defense.

Gene Transfer For Enhanced Intermediate & Secondary Metabolism Abilities
Sterigmatocystin gene transfer has been observed with Podospora anserina and Aspergiullus. HGT in Aspergillus and Podospora contributed to fungal metabolic diversity in secondary metabolism. Aspergillus nidulans produces of sterigmatocystin (ST)–a precursor to aflatoxins (AF). Asperigullis was found to be horizontal transferred to Podospora anserina. Podospora and Aspergillus show high conservation and microsynteny SF/AF clusters along with intergenic regions containing 14 binding sites for AfIR, a transcription factor for activation of ST/AF biosynthetic genes. Aspergillus to Podospora represents a large metabolic gene transfer which could have contributed to fungal metabolic diversity. Transposable elements and other mobile genetic elements like plasmids and viruses could allow for chromosomal rearrangement and integration of foreign genetic material. HGT could have significantly contribute to fungal genome remodeling and metabolic diversity.

Acquired Pathogenic Capabilities
In Stagonospora and Pyrenophora as well as Fusarium and Alternaria, HGT provides powerful mechanism for enabling fungi to acquire pathogenic capabilities to infect a new host plant. HGT and interspecific hybridization between pathogenic species allows for hybrid offspring that have expanded host range. HGT in these events can cause disease outbreaks on new crops when a encoded protein is able to cause pathogenicity. Interspecific transfer of virulence factors in fungal pathogens between Stagonospora modorum and Pyrenophora tritici-repentis. Host selective toxin (ToxA) from S. nodorum conferred virulence to P. tritici-repentis on wheat and caused virulent identifying tan spot on wheat around 1941.

In Fusarium, experimentally have converted a nonpathogenic strain into a pathogen and could have contributed to pathogen adaption in large genome portions. Fusarium graminearum, Fusarium verticilliodes, and Fusarium oxysprorum are maize and tomato pathogens and produce fumonisin mycotoxins to contaminate grain. These examples highlight the apparent polyphyletic origins of host specialization and the emergence of new pathogenic lineages distinct from genetic backgrounds. The ability to transfer genetic material could increase disease in susceptible plant populations.