Trans-kingdom Conjugation Research Articles

Isolation and Analysis of Donor Chromosomal Genes Whose Deficiency Is Responsible for Accelerating Bacterial and Trans-Kingdom Conjugations by IncP1 T4SS Machinery

Conjugal transfer is a major driving force of genetic exchange in eubacteria, and the system in IncP1-type broad-host-range plasmids transfers DNA even to eukaryotes and archaea in a process known as trans-kingdom conjugation (TKC). Although conjugation factors encoded on plasmids have been extensively analyzed, those on the donor chromosome have not. To identify the potential conjugation factor(s), a genome-wide survey on a comprehensive collection of Escherichia coli gene knockout mutants (Keio collection) as donors to Saccharomyces cerevisiae recipients was performed using a conjugal transfer system mediated by the type IV secretion system (T4SS) of the IncP1α plasmid. Out of 3,884 mutants, three mutants (ΔfrmR, ΔsufA, and ΔiscA) were isolated, which showed an increase by one order of magnitude in both E. coli–E. coli and E. coli–yeast conjugations without an increase in the mRNA accumulation level for the conjugation related genes examined. The double-knockout mutants for these genes (ΔfrmRΔsufA and ΔiscAΔfrmR) did not show synergistic effects on the conjugation efficiency, suggesting that these factors affect a common step in the conjugation machinery. The three mutants demonstrated increased conjugation efficiency in IncP1β-type but not in IncN- and IncW-type broad-host-range plasmid transfers, and the homologous gene knockout mutants against the three genes in Agrobacterium tumefaciens also showed increased TKC efficiency. These results suggest the existence of a specific regulatory system in IncP1 plasmids that enables the control of conjugation efficiency in different hosts, which could be utilized for the development of donor strains as gene introduction tools into bacteria, eukaryotes, and archaea.

Transfer of plasmid into the pentose-fermenting yeast Pachysolen tannophilus

The pentose-fermenting yeast Pachysolen tannophilus can convert glucose and xylose in lignocellulosic hydrolysates to ethanol. However, it performs poorly in industrially relevant lignocellulosic hydrolysates containing mixed sugars and inhibitors. Efforts have been directed at improving the performance of this yeast to enable efficient lignocellulosic biomass conversion. While some successes have been reported using random mutagenesis and/or hybridization-based approaches, further genetic improvement of this yeast is hampered by the lack of efficient gene transfer methods as well as limited genetic information to guide further construction of robust strains of P. tannophilus. In this study, we aimed to address this short-coming by establishing the optimal conditions needed for efficient gene transfer into P. tannophilus. We ascertained that plasmids can be transferred into P. tannophilus through trans-kingdom conjugation or lithium acetate (LiAc) transformation. The efficiency of plasmid YEp13 (2-micron, LEU2) transferred into a P. tannophilus leucine auxotroph (Leu−) reached as high as 1.93 × 10−2 transconjugants per input recipient and 3.25 × 104 transformants per μg plasmid DNA through trans-kingdom conjugation and transformation, respectively. In trans-kingdom conjugation, the number of recipient P. tannophilus cells played an important role, while the ratio of donor (Escherichia coli) to recipient cells was less important. For efficient transformation in P. tannophilus, the use of PEG 3350 was essential, as no transformants were obtained in its absence. The transformation efficiency increased with the addition of single-stranded carrier DNA and incubation at 30 °C for >60 min. Plasmids with different replication origins or 2-micron plasmids with different CUG codon-optimized antibiotic resistance markers were unable to transform P. tannophilus under our experimental conditions. The results are of interest in the genetic manipulation and improvement of P. tannophilus.

A Fast and Practical Yeast Transformation Method Mediated by Escherichia coli Based on a Trans-Kingdom Conjugal Transfer System: Just Mix Two Cultures and Wait One Hour

Trans-kingdom conjugation is a phenomenon by which DNA is transferred into a eukaryotic cell by a bacterial conjugal transfer system. Improvement in this method to facilitate the rapid co-cultivation of donor bacterial and recipient eukaryotic cell cultures could make it the simplest transformation method, requiring neither isolation of vector DNA nor preparation of competent recipient cells. To evaluate this potential advantage of trans-kingdom conjugation, we examined this simple transformation method using vector combinations, helper plasmids, and recipient Saccharomyces cerevisiae strains. Mixing donor Escherichia coli and recipient S. cerevisiae overnight cultures (50 μL each) consistently yielded on the order of 101 transformants using the popular experimental strain BY4742 derived from S288c and a shuttle vector for trans-kingdom conjugation. Transformation efficiency increased to the order of 102 using a high receptivity trans-kingdom conjugation strain. In addition, either increasing the amount of donor cells or pretreating the recipient cells with thiols such as dithiothreitol improved the transformation efficiency by one order of magnitude. This simple trans-kingdom conjugation-mediated transformation method could be used as a practical yeast transformation method upon enrichment of available vectors and donor E. coli strains.

Trans-Kingdom Horizontal DNA Transfer from Bacteria to Yeast Is Highly Plastic Due to Natural Polymorphisms in Auxiliary Nonessential Recipient Genes

With the rapid accumulation of genomic information from various eukaryotes in the last decade, genes proposed to have been derived from recent horizontal gene transfer (HGT) events have been reported even in non-phagotrophic unicellular and multicellular organisms, but the molecular pathways underlying HGT remain to be explained. The development of in vitro HGT detection systems, which permit the molecular and genetic analyses of donor and recipient organisms and quantify HGT, are helpful in order to gain insight into mechanisms that may contribute to contemporary HGT events or may have contributed to past HGT events. We applied a horizontal DNA transfer system model based on conjugal gene transfer called trans-kingdom conjugation (TKC) from the prokaryote Escherichia coli to the eukaryote Saccharomyces cerevisiae, and assessed whether and to what extent genetic variations in the eukaryotic recipient affect its receptivity to TKC. Strains from a collection of 4,823 knock-out mutants of S. cerevisiae MAT-α haploids were tested for their individual TKC receptivity. Two types of mutants, an ssd1 mutant and respiratory mutants, which are also found in experimental strains and in nature widely, were identified as highly receptive mutants. The TKC efficiency for spontaneously accrued petite (rho −/0) mutants of the functional allele (SSD1-V) strain showed increased receptivity. The TKC efficiency of the ssd1Δ mutant was 36% for bacterial conjugation, while that of the petite/ssd1Δ double mutants was even higher (220% in average) compared to bacterial conjugation. This increased TKC receptivity was also observed when other conjugal transfer systems were applied and the donor bacterium was changed to Agrobacterium tumefaciens. These results support the idea that the genomes of certain eukaryotes have been exposed to exogenous DNA more frequently and continuously than previously thought.

Transkingdom Genetic Transfer from Escherichia coli to Saccharomyces cerevisiae as a Simple Gene Introduction Tool

Transkingdom conjugation (TKC) permits transfer of DNA from bacteria to eukaryotic cells using a bacterial conjugal transfer system. However, it is not clear whether the process of DNA acceptance in a recipient eukaryote is homologous to the process of conjugation between bacteria. TKC transfer requires mobilizable shuttle vectors that are capable of conjugal transfer and replication in the donor and recipient strains. Here, we developed TKC vectors derived from plasmids belonging to the IncP and IncQ groups. We also investigated forms of transfer of these vectors from Escherichia coli into Saccharomyces cerevisiae to develop TKC as a simple gene introduction method. Both types of vectors were transferred precisely, conserving the origin of transfer (oriT) sequences, but IncP-based vectors appeared to be more efficient than an IncQ-based vector. Interestingly, unlike in agrobacterial T-DNA (transfer DNA) transfer, the efficiency of TKC transfer was similar between a wild-type yeast strain and DNA repair mutants defective in homologous recombination (rad51Δ and rad52Δ) or nonhomologous end joining (rad50Δ, yku70Δ, and lig4Δ). Lastly, a shuttle vector with two repeats of IncP-type oriT (oriT(P)) sequences flanking a marker gene was constructed. TKC transfer of this vector resulted in precise excision of both the oriT(P) loci as well as the marker gene, albeit at a low frequency of 17% of all transconjugants. This feature would be attractive in biotechnological applications of TKC. Taken together, these results strongly suggest that in contrast to agrobacterial T-DNA transfer, the circularization of vector single-stranded DNA occurs either before or after transfer but requires a factor(s) from the donor. TKC is a simple method of gene transfer with possible applications in yeast genetics and biotechnology.

Screening for yeast mutants defective in recipient ability for transkingdom conjugation with Escherichia coli revealed importance of vacuolar ATPase activity in the horizontal DNA transfer phenomenon

Proteobacterium Escherichia coli strains harboring wide-transfer-range conjugative plasmids are able to transfer these plasmids to several yeast species. Whole plasmid DNA is mobilizable in the transkingdom conjugation phenomenon. Owing to the availability of various conjugative plasmids in bacteria, the horizontal DNA transfer has potential to occur between various bacteria and eukaryotes. In order to know host factor genes involved in such conjugation, we systematically tested the conjugability of strains among a yeast library comprising single-gene-knockout mutants in this study. This genome-wide screen identified 26 host chromosomal genes whose absence reduced the efficiency of the transkingdom conjugation. Among the 26 genes, 20 are responsible for vacuolar ATPase activity, while 5 genes (SHP1, CSG2, CCR4, NOT5, and HOF1) seem to play a role in maintaining the cell surface. Lack of either ZUO1 gene or SSZ1 gene, each of which encodes a component of the ribosome-associated cytoplasmic molecular chaperone, also strongly affected transkingdom conjugation.

Localization of the plasmid-encoded proteins TraI and MobA in eukaryotic cells

Conjugation mediates gene transfer not only between bacterial species but also from bacteria to yeast, plant, and animal cells. DNA transferred by conjugative plasmids from bacteria to eukaryotes must traverse subcellular membranes in the recipient before the transferred genes can be expressed and inherited. This process is most likely facilitated by putative DNA pilot proteins such as VirD2 of the Agrobacterium tumefaciens Ti plasmid. Here, we test this model as a general feature of trans-kingdom conjugation using the DNA-relaxases TraI and MobA of the IncP and IncQ groups. TraI localized unambiguously and uniformly to the nuclei of both yeast and human cells, whereas MobA displayed a range of subcellular localization patterns. The tendency to localize to the nucleus was not correlated with predicted nuclear localization sequence motifs in either protein, suggesting a lack of stringent requirements for nuclear localizing potential in pilot proteins mediating conjugative DNA transfer to eukaryotes. Further, our results indicate that nuclear localization ability may be more commonly associated with conjugative pilot proteins than previously recognized.

Trans-kingdom conjugation in vitro by using toluenized cells.

To establish in vitro trans-kingdom conjugation, we developed a novel direct cell PCR by using toluenized cells which permeate enzymes, primers and substrates. The cells was shown to be successful recipients in conjugation.

Transformation Systems of non-Saccharomyces Yeasts

ABSTRACT: This review describes the transformation systems including vectors, replicons, genetic markers, transformation methods, vector stability, and copy numbers of 13 genera and 31 species of non-Saccharomyces yeasts. Schizosaccharomyces pombe was the first non-Saccharomyces yeast studied for transformation and genetics. The replicons of non-Saccharomyces yeast vectors are from native plasmids, chromosomal DNA, and mitochondrial DNA of Saccharomyces cerevisiae, non-Saccharomyces yeasts, protozoan, plant, and animal. Vectors such as YAC, YCp, YEp, YIp, and YRp were developed for non-Saccharomyces yeasts. Forty-two types of genes from bacteria, yeasts, fungi, and plant were used as genetic markers that could be classified into biosynthetic, dominant, and colored groups to construct non-Saccharomyces yeasts vectors. The LEU2 gene and G418 resistance gene are the two most popular markers used in the yeast transformation. All known transformation methods such as spheroplast-mediating method, alkaline ion treatment method, electroporation, trans-kingdom conjugation, and biolistics have been developed successfully for non-Saccharomyces yeasts, among which the first three are most widely used. The highest copy number detected from non-Saccharomyces yeasts is 60 copies in Kluyveromyces lactis. No general rule is known to illustrate the transformation efficiency, vector stability, and copy number, although factors such as vector composition, host strain, transformation method, and selective pressure might influence them.

Trans-kingdom conjugation between bacterial chromosome-less mini-cells and yeasts.

We introduced a novel convenient method to prepare chromosome-less mini-cells from cell mixture of Escherichia coli P678-54 by using penicillin. The mini-cells prepared by this method could successfully transferred their harboring conjugative plasmids into eukaryotic yeast cells by trans-kingdom conjugation.

Trans-kingdom conjugation offers a powerful gene targeting: tool in yeast

Gene targeting is one of the powerful techniques used to investigate eukaryotic genes. In a typical eukaryotic microbe, Saccharomyces cerevisiae yeast, we examined trans-kingdom conjugation between Escherichia coli bacterium and yeast as a gene targeting tool. Here, it is shown that trans-kingdom conjugation effectively induced gene replacement even on yeast's target loci (e.g. ura3-52 allele) which is never targeted by conventional transformation. This clearly indicates that trans-kingdom conjugation offers a very powerful gene targeting tool in yeasts. In fact, Southern hybridization analysis of transconjugants distinctly verified the accuracy in the conjugative gene replacement. The efficiency of gene replacement was about 0.4×10 −7 per recipient yeast. This is enough to sustain gene targeting with gene replacement by trans-kingdom conjugation. We also discuss the mechanism of conjugative gene replacement.

The construction of novel mobilizable YAC plasmids and their behavior during tranks-kingdom conjugation between bacteria and yeasts

Trans-kingdom conjugation is an easy and efficient method for gene transfer from prokaryotes to eukaryotes since it does not require DNA extraction and purification. We constructed novel mobilizable plasmids pAY-YAC-B and pAY-YAC-E. The origin of conjugal transfer ( oriT) was inserted at two different positions, pAY-YAC-B contains oriT region in between two telomeres whereas pAY-YAC-E has oriT at the cloning site of pYAC4. By conjugation, both plasmids were successfully transferred from E. coli to S. cerevisiae and S. kluyveri yeasts with the aid of helper plasmid pRH220 which harbors mob and tra genes. The plasmids were transferred more efficiently in S. cerevisiae compared to S. kluyveri. The analyses by restriction enzyme digestion and Southern hybridization indicated that both plasmids maintained their original structure and size in transconjugant yeasts, therefore, reflecting the faithful nicking and subsequent resealing of plasmids during conjugation. The comparison between conjugative transfer and transformation has also been performed and discussed.

Trans-kingdom conjugation between Agrobacterium tumefaciens and Saccharomyces cerevisiae, a bacterium and a yeast.

For conjugation between prokaryotic Agrobacterium tumefaciens and eukaryotic Saccharomyces cerevisiae, we constructed two novel conjugative plasmids. A. tumefaciens transmitted the plasmids to S. cerevisiae with the aid of tra genes on a helper plasmid. The transmitted plasmids retained their original structure and function in transconjugant yeasts. The presence of Ti plasmid barely affected the trans-kingdom conjugation.

The yeast Saccharomyces kluyveri as a recipient eukaryote in transkingdom conjugation: behavior of transmitted plasmids in transconjugants

The prokaryote Escherichia coli successfully conjugated with the eukaryote Saccharomyces kluyveri, which is relatively distant from the species S. cerevisiae. To achieve this transkingdom conjugation, we constructed three types of conjugative plasmids, namely integrative, replicative, and centromere vectors, for S. cerevisiae. By transfer of any of the three plasmids from E. coli, an S. kluyveri Ura- mutant was converted to the Ura+ phenotype. This phenotype was easily lost under nonselective conditions. Southern analysis of the transconjugants clearly indicated the presence of the plasmids in many different structures and sizes.

Movement of Shuttle Plasmids from Escherichia coli into Yeasts Other Than Saccharomyces cerevisiae Using Trans-kingdom Conjugation

Transfer of bacteria/yeast shuttle plasmids from Escherichia coli into the yeast species Kluyveromyces lactis, Pichia angusta ( Hansenula polymorpha), and Pachysolen tannophilus has been accomplished, presumably through inter-kingdom conjugal transfer. Plasmid pEK2 was transferred into a K. lactis mutant to complement trp auxotrophy, while plasmid YEp13 was mobilized into and complemented P. angusta and P. tannophilus Leu - auxotrophs. Plasmid DNA in the recipient strains was detected by transformation of E. coli with crude yeast cell extracts. Freely replicating plasmids without detectable alterations as well as plasmids with rearrangements were recovered from yeast transconjugants.

DNA integration into recipient yeast chromosomes by trans-kingdom conjugation between Escherichia coli and Saccharomyces cerevisiae.

IncQ-derived conjugative shuttle vectors, which carried the yeast gene URA3 and/or the yeast autonomously replicating sequence (ARS1), were constructed. Both the ars-plus plasmid pAY205 and the ars-less plasmid pAY201 were successfully transmitted from E. coli to S. cerevisiae by the action of mob and tra. In this trans-kingdom conjugation, plasmid pAY205 could replicate and be retained in transconjugants. Plasmid pAY201 caused the formation of "micro-colonies" of abortive transconjugants due to its transient expression and rapid disappearance. Nevertheless, one per about 10(3) colonies caused by transmitted pAY201 plasmids were uncurable by integration into the homologous region of a yeast chromosome. Analyses by restriction enzyme mapping and Southern hybridization indicate that this integration is primarily caused by a double crossover during conjugation and not by a single reciprocal recombination.

Genetic exchange between kingdoms

Bacterial conjugation with two evolutionarily divergent yeasts has been observed in the laboratory. Whether such trans-kingdom conjugation events, other than the well known Agrobacterium-plant cell interaction, actually occur in nature is not known. However, a few putative events have recently been uncovered by gene (or protein) sequence analysis, suggesting that horizontal gene transfer between phylogenetic kingdoms may be a real phenomenon.