Chromosomal gene transfer of human cytosol thymidine kinase into mouse cells: integration or association of the transferred gene with a non-homologous mouse chromosome.
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Animals↗
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Chromosome-mediated gene transfer with resultant expression and integration of the transferred genes in eukaryotic cells.
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Animals↗
Algae-to-host horizontal gene transfer in Paramecium bursaria is associated with host adaptation during endosymbiosis.
Paramecium bursaria maintains a stable endosymbiosis with green algae, yet the evolutionary consequences of this association remain unclear. Here, we screened the host genome for algal-derived horizontally transferred genes (HTGs) using a lineage-aware workflow designed to detect horizontal gene transfer (HGT) between two defined lineages. We identified 16 candidate HTGs, including four putative newly transferred genes and 12 homologous transferred genes, most of which were functionally associated with redox homeostasis and metabolism. Five HTGs showed symbiosis-dependent expression. RNAi knockdown of GH32s and SATs reduced host proliferation, total cell area, and motility, while GH32s knockdown also reduced endosymbiont load. Duplication patterns suggest that most transfers may have occurred after the P. bursaria lineage diverged from the sampled Paramecium species but before its lineage-specific whole-genome duplication (WGD). The HTGs also showed host-associated shifts in GC content and gene length, while representative HTGs retained conserved domains and functional motifs. Together, our results support algae-to-host HGT in P. bursaria and suggest that some transferred genes may contribute to metabolic integration during endosymbiosis.
Gene Transfer, Horizontal↗
Genetic construction by chromosomal gene transfer of mouse cell clones which harbor a transferred selected gene firmly associated with a nonhomologous chromosome.
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Animals↗
Bacteriophage-associated gene transfer in pneumococcus: transduction or pseudotransduction?
Lysates of pneumococcal phage PG24 transferred genes from one host to another in a process with many of the properties of generalized transduction, in that the host genes were packaged in DNase-resistant particles that closely resembled infectious phage in physical properties, adsorbed to the recipient cells like phage, and were inhibited by antisera to the phage and by trypsin. However, phage processes did not complete the transfer of host DNA as they did phage DNA. Instead, gene transfer required development of competence and entry of the host DNA by the endonuclease-dependent pathway used for transforming and transfecting DNA. This process often occurred on the assay plate hours after adsorption of the particles to the cells, and the transfer was DNase sensitive if challenged at this time. Phenotypic expression was therefore also delayed. The product of entry was like that in transformation, a single strand of DNA that integrates by formation of a hex-sensitive donor-recipient heteroduplex. Whether this gene transfer process is unique to this system or is only the first one described is not clear. The term "pseudotransduction" may be useful in calling attention to its unexpected features. The DNA of PG24 phage has anomalous physical properties reflecting unusual bases.
Bacteriophages↗
Cotransfer of thymidine kinase and galactokinase genes by chromosome-mediated gene transfer.
The Chinese hamster genes for thymidine kinase (ATP:thymidine 5'-phosphotransferase, EC 2.7.1.75) and galactokinase (ATP:D-galactose 1-phosphotransferase, EC 2.7.1.6) have been cotransferred to mouse cells by chromosome-mediated gene transfer. Hamster metaphase chromosomes were incubated with mouse B82 cells and 22 independent colonies were isolated in a selective medium. All of the 12 colonies analyzed expressed the donor form of thymidine kinase; the hamster form of galactokinase was also expressed in 2 of these colonies, indicating cotransfer with a frequency of about 20%. There was coordinate loss of both transferred genes from each colony when selection was applied for the loss of thymidine kinase alone. Comparison of the regional localization of these two linked genes with the frequency of cotransfer suggests that the transgenome is probably not larger than about 0.25% of the donor genome.
Cells, Cultured↗
Serial transfer of a human gene to rodent cells by sequential chromosome-mediated gene transfer.
The human hypoxanthine phosphoribosyl-transferase (IMP:pyrophosphate phosphoribosyltransferase, EC 2.4.2.8) gene (hprt) has been serially transferred to mouse cells and then to Chinese hamster fibroblasts by two cycles of metaphase chromosome isolation and incubation with recipient cells. Human metaphase chromosomes were incubated with mouse A9 cells deficient in hypoxanthine phosphoribosyltransferase, and independent colonies expressing the human species form of this gene were isolated in a selective medium. Metaphase chromosomes isolated from two of these clonal lines were incubated with Chinese hamster fibroblasts deficient in hypoxanthine phosphoribosyltransferase; five resulting independent colonies again expressed the human species of this gene. The transfer frequencies in the two cycles of chromosome-mediated gene transfer were similar (about 10(-7)). These results indicate that the transferred human chromosome fragment is closely associated with the chromosomes of the mouse A9 cells and it is probably integrated into the chromosomal DNA of the recipient cell.
Animals↗
Entrapment of metaphase chromosomes into phospholipid vesicles (lipochromosomes): carrier potential in gene transfer.
Transfer of genes from one type of cultured mammalian cell to another by using isolated metaphase chromosomes has been reported with a frequency of one per 10(6)-10(8) cells. Very recently a rate of 16/10(6) has been reported with Chinese hamster ovary cells [Spandidos, D. A. & Siminovitch, L. (1977) Proc. Natl. Acad. Sci. USA 74, 3480-3484]. To increase the frequency of gene transfer, we isolated metaphase chromosomes from hypoxanthine guanine phosphoribosyltransferase (HGPRT) positive cells, entrapped them in liposomes, and fused the lipochromosomes with HGPRT-negative cells. Lipochromosomes were prepared with cholesterol and egg lecithin, using isolated metaphase chromosomes from a mouse-human somatic hybrid cell line (A9/HRBC2); the entire X chromosome, including the HGPRT, glucose-6-phosphate dehydrogenase, and phosphoglycerate kinase genes, is the only recognizable human genetic material retained by the hybrids. Enclosure of the chromosomes in the lipid envelope was confirmed by electron and fluorescence microscopy and differential centrifugation. These lipochromosomes were fused with HGPRT(-) mouse cells (A9) in the presence or absence of polyethylene glycol and transferents were selected in hypoxanthine/aminopterin/thymidine (HAT) medium. The frequency of transfer was at least once per 10(5) cells, a minimum 10-fold improvement over previous methods. The selected cells contained HGPRT activity similar to the amount found in the A9/HRBC2 cells. Starch gel electrophoresis verified that the observed HGPRT activity in the transferents is due to the human enzyme. Human glucose-6-phosphate dehydrogenase and phosphoglycerate kinase were also identified electrophoretically in the transferents. Karyotyping with C and Q banding did not reveal the presence of the whole human X chromosome or a visible extra fragment of a human chromosome associated with the mouse genome. The biochemical data strongly suggest, however, that transfer of a portion of the human X chromosome has occurred in these transferents. Thus, at least three X-linked genes have been transferred from one cell to another with high frequency, using metaphase chromosomes.
Cell Line↗
Hurdles to horizontal gene transfer: species-specific effects of synonymous variation and plasmid copy number determine antibiotic resistance phenotype.
Could codon composition condition the immediate success and the orientation of horizontal gene transfer? Horizontal gene transfer represents a change in the genome of expression of the transferred gene, and experimental evidence has accumulated indicating that the codon composition of a sequence is an important determinant of its compatibility with the translation machinery of the genome in which it is expressed. This suggests that codon composition influences the phenotype and the fitness conferred by a transferred gene and thus the immediate success of the transfer. To directly test this hypothesis, we characterized the resistance conferred by synonymous variants of a gentamicin resistance gene in three bacterial species: Escherichia coli, Acinetobacter baylyi and Pseudomonas aeruginosa. The strongest determinant of the resistance level conferred was the species in which the resistance gene was transferred, very likely because of important differences in the copy number of the plasmid carrying the gene. Significant differences in resistance were also found between synonymous variants within each of the three species, but more importantly, there was a strong interaction between species and variant: variants conferring high resistance in one species confer low resistance in another. However, the similarity in codon usage between the synonymous variants and the host genome only explained part of the phenotypic differences between variants in one species, P. aeruginosa. Further investigation of alternative explanations did not reveal common universal mechanisms across our three bacterial species. We conclude that codon composition can be a determinant of post-horizontal gene transfer success. However, there are multiple paths leading from synonymous sequence to phenotype, and sensitivity to these different paths is species-specific.
Gene Transfer, Horizontal↗
Gene transfer agents: The ambiguous role of selfless viruses in genetic exchange and bacterial evolution.
Gene transfer agents (GTAs) are genetic elements derived from ancestral bacteriophages that have become domesticated by the host. GTAs are present in diverse prokaryotic organisms, where they can facilitate horizontal gene transfer under certain conditions. Unlike typical bacteriophages, GTAs do not exhibit any preference for the replication or transfer of the genes encoding them; instead, they exhibit a remarkable capacity to package chromosomal, and sometimes extrachromosomal, DNA into virus-like capsids and disseminate it to neighboring cells. Because GTAs resemble defective prophages, identification of novel GTAs is not trivial. The detection of candidates relies on the genetic similarity to known GTAs, which has been fruitful in α-proteobacterial lineages but challenging in more distant bacteria. Here we consider several fundamental questions: What is the true prevalence of GTAs in prokaryote genomes? Given there are high costs for GTA production, what advantage do GTAs provide to the bacterial host to justify their maintenance? How is the bacterial chromosome recognized and processed for inclusion in GTA particles? This article highlights the challenges in comprehensively understanding GTAs' prevalence, function and DNA packaging method. Going forward, broad study of atypical GTAs and use of ecologically relevant conditions are required to uncover their true impact on bacterial chromosome evolution.
Gene Transfer, Horizontal↗
Transfer gene expression during fertility inhibition of the Escherichia coli K12 sex factor F by the I-like plasmid R62.
Further understanding of how the FinQ fertility inhibition system of the I-like plasmid R62 inhibits transfer of the sex factor F has been gained by the use of a genetic assay for individual transfer gene products. The technique involved construction of a series of Flac plasmids carrying suppressible mutations in individual transfer genes together with a FinQ inhibitor-insensitive traQ mutation. The transfer of the Flac double mutants from a strain carrying wild-type Fhis and R62 then indicated the effect of R62-encoded transfer inhibition on the expression of individual F transfer genes. During such inhibition the products of genes traJ, traA, traE, traB and traC were present in quantities sufficient to permit efficient F transfer, whereas the levels of the traF, traH, traG and traD gene products were so reduced as to limit F transfer. These findings and a failure to obtain recombination between traC and traQ mutations suggest that the R62 fertility inhibition system terminates transcription of the transfer operon between traC and traF.
Coliphages↗
Genetic analysis of mutations in the transfer genes of pDU202 tra::Tn10 plasmids, caused by the excision of Tn10.
Transfer-deficient derivatives of pDU202 (a Tcs deletion mutant of R100-1) caused by the insertion of Tn10 into the R factor's transfer genes have been described previously. Tetracyline-sensitive mutants of four of these were selected. In the majority of cases the Tcs mutation was caused by a deletion of the Tcr genes which was often accompanied either by a deletion of some of the flanking transfer genes or by a secondary mutation which was probably an inversion. A number of preferred end points for the deletions and inversions occur in the transfer operon of pDU202. Analysis of the mutants by complementation tests with Flac tra elements confirmed that the order of genes in the promoter distal part of the tra region of pDU202 is traKBCFHGSD and traI.
Escherichia coli↗
Gene transfer to human cells: transducing phage lambda plac gene expression in GMI-gangliosidosis fibroblasts.
Genetic information from the bacterium Escherichia coli was transferred to human cells by means of the specialized transducing phage lambda plac carrying the bacterial z gene for the enzyme beta-galactosidase (geta-D-galactoside galactohydrolase, EC 3.2.1.23). As recipient cells, cultured skin fibroblasts from a patient with generalized gangliosidosis (GMI-gangliosidosis Type I) characterized by a severe deficiency of beta-galactosidase activity were used. The deficient human cells were incubated with the bacteriophage lambda plac or lambda plac DNA and beta-galactosidase activity was measured in order to detect gene transfer and acceptance of the prokaryotic information in the mammalian system for transcription and translation. The expression of the phage genome in the deficient fibroblasts could be demonstrated by detection of higher beta-galactosidase activity after incubation with phage lambda plac in three out of 19 experiments and in four out of 16 experiments after treatment with lambda plac DNA. Lambda plac DNA induced much higher enzyme activities than infective phage particles. Immunochemical and physicochemical assays could not distinguish the induced beta-galactosidase activity from that of the z-gene product of E. coli.
Cell Line↗
A compendium of horizontal gene transfers in Metazoa.
With more eukaryotic genomes available for study researchers have been able to identify a growing number of horizontal gene transfer (HGT) candidates. We compiled 9,495 protein coding genes that were identified as horizontally transferred to metazoan hosts in the published literature. This dataset contains gene transfers from bacteria, fungi, archaea and protists to metazoans. We assigned a confidence score to each gene based on the methods used in the scientific paper reporting HGT. All the coding sequences and protein sequences for the HGT genes are stored in a fig share repository. This dataset can be used to identify trends in genome and protein evolution and provide a foundation for creating a centralized HGT database for eukaryotes.
Gene Transfer, Horizontal↗
Phenotype stabilisation and integration of transferred material in chromosome-mediated gene transfer.
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Animals↗
AAV6 vectors provide superior gene transfer compared to AAV9 vectors following intramyocardial administration.
Cardiac gene therapy using adeno-associated viral (AAV) vectors holds great promise for treating heart diseases but would benefit from more potent AAV vectors. Vectors based on the AAV serotypes 6 and 9 have been used in pre-clinical gene therapy studies, yet the therapeutic outcomes varied depending on the experimental model and delivery route used. Here, we evaluated the transduction efficiency of AAV6, AAV9, and AAV9-derived MyoAAVs for local cardiac delivery. Vectors were tested in neonatal rat ventricular myocytes, and subsequently in mouse hearts by direct intramyocardial injection. Vector genome levels, mRNA expression levels, and fluorescence were measured. The AAV6 and AAV9 vectors were further validated in porcine hearts, human-induced pluripotent stem-cell-derived cardiomyocytes, and human atrial myocardial slices. In both rat cardiomyocytes and mouse hearts, AAV6 exhibited the highest transduction efficiency. Direct comparison of the AAV6 and AAV9 vectors in porcine and human models confirmed that AAV6 is more potent. In conclusion, AAV6 vectors are superior to AAV9 and its derivative vectors for cardiac transduction by direct intramyocardial injection. In addition, the in vivo transduction efficiency correlates with in vitro and ex vivo assays, thereby facilitating the development of more potent AAV variants for cardio-selective delivery methods.
AAV vector↗
Transposon 10 promoted deletions and inversions in the transfer genes of R100-1.
Spontaneous tetracycline-sensitive, transfer-deficient mutants of R100-1 were selected and analysed by genetic complementation tests and with the restriction endonuclease EcoR1. While some of the Tets Tra- mutants were caused by a single deletion event which removed the Tetr genes and extended into the neighbouring transfer genes, other mutants were the result of the deletion of the Tetr genes within Tn10 which was accompanied by an inversion of adjacent DNA sequences. A clustering of deletion and inversion endpoints occurred in the traA gene. Some of the transfer genes of R100-1 were assigned to EcoR1 fragments.
Chromosome Deletion↗
Naturally competent bacteria and their genetic parasites-a battle for control over horizontal gene transfer?
Host-mediated natural competence for transformation of DNA and mobile genetic element (MGE)-driven conjugation and transduction are key modes of horizontal gene transfer. While these mechanisms are traditionally believed to shape bacterial evolution by enabling the acquisition of new genetic traits, numerous studies have elucidated an antagonistic relationship between natural transformation and MGEs. A new role of natural transformation as a chromosome-curing mechanism has now been proposed. Experimental data, along with mathematical models, suggest that transformation can eliminate deleterious MGEs. Supporting this hypothesis, MGEs have been shown to use various mechanisms to decrease or block transformability, such as disrupting competence genes, regulating the development of competence, hindering DNA uptake machinery, producing DNases that target the exogenous (transforming) DNA, and causing lysis of competent cells. A few examples of synergistic relationships between natural transformation and MGEs have also been reported, with natural transformation facilitating MGE transfer and phages enhancing transformation by supplying extracellular DNA through lysis and promoting competence via kin discrimination. Given the complexity of the relationships between natural transformation and MGEs, the balance between antagonism and synergy likely depends on specific selection pressures in a given context. The evidence collected here indicates a continuous conflict over horizontal gene transfer in bacteria, with semiautonomous MGEs attempting to disrupt host-controlled DNA acquisition, while host competence mechanisms work to resist MGE interference.
Gene Transfer, Horizontal↗