Nuclear Gene Transfer Research Articles

Chloroplast acquisition without the gene transfer in kleptoplastic sea slugs, Plakobranchus ocellatus.

Some sea slugs sequester chloroplasts from algal food in their intestinal cells and photosynthesize for months. This phenomenon, kleptoplasty, poses a question of how the chloroplast retains its activity without the algal nucleus. There have been debates on the horizontal transfer of algal genes to the animal nucleus. To settle the arguments, this study reported the genome of a kleptoplastic sea slug, Plakobranchus ocellatus, and found no evidence of photosynthetic genes encoded on the nucleus. Nevertheless, it was confirmed that light illumination prolongs the life of mollusk under starvation. These data presented a paradigm that a complex adaptive trait, as typified by photosynthesis, can be transferred between eukaryotic kingdoms by a unique organelle transmission without nuclear gene transfer. Our phylogenomic analysis showed that genes for proteolysis and immunity undergo gene expansion and are up-regulated in chloroplast-enriched tissue, suggesting that these molluskan genes are involved in the phenotype acquisition without horizontal gene transfer.

The Transfer of the Ferredoxin Gene From the Chloroplast to the Nuclear Genome Is Ancient Within the Paraphyletic Genus Thalassiosira.

Ferredoxins are iron–sulfur proteins essential for a wide range of organisms because they are an electron transfer mediator involved in multiple metabolic pathways. In phytoplankton, these proteins are active in the mature chloroplasts, but the petF gene, encoding for ferredoxin, has been found either to be in the chloroplast genome or transferred to the nuclear genome as observed in the green algae and higher plant lineage. We experimentally determined the location of the petF gene in 12 strains of Thalassiosira covering three species using DNA sequencing and qPCR assays. The results showed that petF gene is located in the nuclear genome of all confirmed Thalassiosira oceanica strains (CCMP0999, 1001, 1005, and 1006) tested. In contrast, all Thalassiosira pseudonana (CCMP1012, 1013, 1014, and 1335) and Thalassiosira weissflogii (CCMP1010, 1049, and 1052) strains studied retained the gene in the chloroplast genome, as generally observed for Bacillariophyceae. Our evolutionary analyses further extend the dataset on the localization of the petF gene in the Thalassiosirales. The realization that the petF gene is nuclear-encoded in the Skeletonema genus allowed us to trace the petF gene transfer back to a single event that occurred within the paraphyletic genus Thalassiosira. Phylogenetic analyses revealed the need to reassess the taxonomic assignment of the Thalassiosira strain CCMP1616, since the genes used in our study did not cluster within the T. oceanica lineage. Our results suggest that this strains’ diversification occurred prior to the ferredoxin gene transfer event. The functional transfer of petF genes provides insight into the evolutionary processes leading to chloroplast genome reduction and suggests ecological adaptation as a driving force for such chloroplast to nuclear gene transfer.

Medusavirus Ancestor in a Proto-Eukaryotic Cell: Updating the Hypothesis for the Viral Origin of the Nucleus.

The mechanistic evolutionary origin of the eukaryotic cell nucleus remains unknown. Among several plausible hypotheses, the most controversial is that large DNA viruses, such as poxviruses, led to the emergence of the eukaryotic cell nucleus. Several recent findings, including the discovery of a nucleus-like structure in prokaryotic viruses and prokaryotes possessing nucleus-like inner membranes, suggest genomic DNA compartmentalization not only in eukaryotes but also in prokaryotes. The sophisticated viral machinery of mimiviruses is thought to resemble the eukaryotic nucleus: DNA replicates both inside the viral factory and nucleus, which is at least partially surrounded by membranes and is devoid of ribosomes. Furthermore, several features of the recently identified Acanthamoeba castellanii medusavirus suggest that the evolutionary relationship between ancestral viral factory and eukaryotic nucleus. Notably, Ran, DNA polymerase, and histones show molecular fossils of lateral transfer of nuclear genes between the virus and host. These results suggest viral innovation in the emergence of the eukaryotic nucleus. According to these results, a new scenario explaining the origin of the eukaryotic nucleus from the perspective of viral participation is proposed. This new scenario could substantially impact the study of eukaryogenesis and stimulate further discussion about viral contributions to the evolution of the eukaryotic nucleus.

On the evolutionary significance of horizontal gene transfers in plants.

Horizontal gene transfer (HGT) has long been seen as a crucial process in the evolution of prokaryotic species, but until recently it was thought to have little, if any, effect on the evolution of eukaryotic life forms. Detecting and describing HGT events in eukaryotes is difficult, making this phenomenon at times controversial. However, modern advances in genomics and bioinformatics have radically altered our view of HGT in eukaryotes, especially in plants. It now appears that HGT to and from plant lineages is more common than previously suspected. Importantly, the transfer of functional nuclear genes with adaptive significance has been reported in numerous taxa. Here we review several recent studies that have found evidence of the horizontal transfer of nuclear genes, and argue that HGT has undoubtedly had profound impacts on plant evolution as a whole.

Horizontal transfer of a \xdf-1,6-glucanase gene from an ancestral species of fungal endophyte to a cool-season grass host

Molecular characterisation has convincingly demonstrated some types of horizontal gene transfer in eukaryotes, but nuclear gene transfer between distantly related eukaryotic groups appears to have been rare. For angiosperms (flowering plants), nuclear gene transfer events identified to date have been confined to genes originating from prokaryotes or other plant species. In this report, evidence for ancient horizontal transfer of a fungal nuclear gene, encoding a ß-1,6-glucanase enzyme for fungal cell wall degradation, into an angiosperm lineage is presented for the first time. The gene was identified from de novo sequencing and assembly of the genome and transcriptome of perennial ryegrass, a cool-season grass species. Molecular analysis confirmed the presence of the complete gene in the genome of perennial ryegrass. No corresponding sequence was found in other plant species, apart from members of the Poeae sub-tribes Loliinae and Dactylidinae. Evidence suggests that a common ancestor of the two sub-tribes acquired the gene from a species ancestral to contemporary grass-associated fungal endophytes around 9–13 million years ago. This first report of horizontal transfer of a nuclear gene from a taxonomically distant eukaryote to modern flowering plants provides evidence for a novel adaptation mechanism in angiosperms.

Recent introgressive hybridization revealed by exclusive mtDNA transfer from Oreochromis leucostictus (Trewavas, 1933) to Oreochromis niloticus (Linnaeus, 1758) in Lake Baringo, Kenya

Nuclear DNA and mtDNA polymorphisms were surveyed in various species of East African Oreochromis. In Lake Baringo, where only Oreochromis niloticus baringoensis is present, alien mtDNA haplotypes were observed, apparently the result of introgressive hybridization with Oreochromis leucostictus. This introgression is not accompanied by any substantial or recorded transfer of nuclear genes into O. n. baringoensis.

Natural transfer of nuclear genes in hybrid populations of green frogs Rana esculenta L., 1758 complex: space?time analysis of the phenomenon

Natural transfer of nuclear genes in hybrid populations of green frogs Rana esculenta L., 1758 complex: space?time analysis of the phenomenon

Inducible Expression, Enzymatic Activity, and Origin of Higher Plant Homologues of Bacterial RelA/SpoT Stress Proteins in Nicotiana tabacum

All living cells possess adaptive responses to environmental stress that are essential to ensuring cell survival. For motile organisms, this can culminate in avoidance or attractile behavior, but for sessile organisms such as plants, stress adaptation is a process of success or failure within the confines of a given environment. Nearly all bacterial species possess a highly evolved system for stress adaptation, known as the "stringent response." This ancient and ubiquitous regulatory response is mediated by production of a second messenger of general stress, the nucleotide guanosine-3',5'-(bis)pyrophosphate (ppGpp), which mediates reprogramming of the global transcriptional output of the cell. Accumulation of ppGpp is stress-induced through the enzymatic activation of the well known bacterial ppGpp synthetases, RelA and SpoT. We have recently discovered homologues of bacterial relA/spoT genes in the model plant Nicotiana tabacum. We hypothesize that these homologues (designated RSH genes for RelA/SpoT homologues) serve a stress-adaptive function in plants analogous with their function in bacteria. In support of this hypothesis, we find 1) inducibility of tobacco RSH gene expression following treatment with jasmonic acid; 2) bona fide ppGpp synthesis activity of purified recombinant Nt-RSH2 protein, and 3) a wide spread distribution of RSH gene expression in the plant kingdom. Phylogenetic analyses identifies a distinct phylogenetic branch for the plant RSH proteins with two subgroups and supports ancient symbiosis and nuclear gene transfer as a possible origin for these stress response genes in plants. In addition, we find that Nt-RSH2 protein co-purifies with chloroplasts in subcellular fractionation experiments. Taken together, our findings implicate a direct mode of action of these ppGpp synthetases with regard to plant physiology, namely regulation of chloroplast gene expression in response to plant defense signals.

Rapid and highly efficient gene transfer into natural killer cells by nucleofection

Natural killer (NK) cells are important mediators of virus- and tumor-specific immune responses. The transfection of genes into NK cells has been proven difficult and so far requires infection with virus-based vectors. Here, the application of a novel nonviral, electroporation-based gene transfer method is described for the rapid and highly efficient transient transfection of NK cell lines as well as freshly isolated NK cells. In contrast to conventional methods, this technique, termed nucleofection, leads to direct transfer of DNA into the nucleus. Using reporter proteins H-2K k, luciferase+, and enhanced yellow green fluorescent protein (EYFP) as independent read-out systems, transfection efficiencies of well over 50% were achieved in transient transfection assays. The highest luciferase activity could be measured only 4 h after transfection, whereas EYFP, when analyzed by flow cytometry, showed expression peaks after 28 h. Interestingly, best transfection efficiencies were achieved with non-dividing NK cells. The novel nuclear gene transfer method presented here is highly useful for the analysis of NK cell-specific gene regulation and should facilitate the development of NK cell-based gene therapy approaches.

Intergeneric nuclear gene transfer between somatically and sexually incompatible plants through asymmetric protoplast fusion

A stable intergeneric transfer of nuclear genes from Physalis minima into the genome of Datura innoxia has been achieved through asymmetric protoplast fusion. No hybrid plants could be obtained from these species either by traditional methods of sexual breeding or by somatic hybridization via fusion of protoplasts containing complete nuclear genomes. The incompatibility barriers were bypassed by the fusion of highly X-irradiated (LD100) wild-type Physalis with nuclear albino mutant Datura protoplasts. In this intergeneric reconstruction, 1.15% of the total heterokaryons restored the chlorophyll synthesis in their regenerants. Two representative transformed lines, TRL-A and TRL-D, were further characterized, showing 0.43–0.78 pg. additional nuclear DNA (4.45–8.07% nuclear DNA of P. minima). Since chromosomes of the species of Datura and Physalis were distinguishable, the mitotic complement of the transformed regenerants showed only 3 and 1 chromosomes of the donor in tetraploid (2n=48) and octoploid (2n=96) genomes of the recipient, respectively. The introduction and expression of limited genes of Physalis in Datura have also been confirmed by the allelic expression of various isoenzymes. Such stable gene transfer via asymmetric fusion of protoplasts has been discussed in relation to its application in the genetic manipulation of plants.

Transfer of mitochondria by protoplast fusion in Saccharomyces cerevisiae

INTRASPECIFIC and interspecific transfer of nuclear genes of fungi has recently been achieved by fusion of protoplasts1–5. We describe here the transfer of mitochondrial genome using the protoplast fusion technique. The experiments were carried out with strains of identical mating-type, so we also report successful complementation of auxotrophic yeast cells of the same mating-type after protoplast fusion.