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Mechanisms of gene flow in Archaea.pptx
- 1. Mechanisms of gene flow in Archaea Wagner A, Whitaker RJ, Krause DJ, Heilers JH, van Wolferen M, van der Does C, & Albers SV
- 2. Definition of terms Multilocus sequence typing Mesophilic archaea Type IV secretion Hyperthermophile Nanopods Proviruses
- 3. Definition of terms Episomes Temperate viruses Gene transfer agents Partitioning system Type IV Pilus Polytopic membrane protein
- 4. Introduction
- 5. Introduction Archaea -Single-celled, anucleate -found nearly in all habitats -highly diverse -observes gene flow Horizontal gene transfer - a major driving force for evolution
- 6. Introduction Footprints of recombination in natural populations Population genomics and whole-genome sequencing enable the identification of gene transfer events with greater precision and even infer donor–recipient patterns of DNA transfer in isolates. Sulfalobus islandicus (MLST) & Halorubrum spp. (MLST)
- 7. Introduction DNA transfer mechanisms in archaea
- 8. Introduction Objective of the study: Discuss the knowledge of archaeal mechanisms of DNA transfer and its role in archaeal evolution. Barriers of DNA transfer is also discussed.
- 9. Discussion Signatures of HGT in Archaea Horizontally transferred genes in archaea originate from bacteria. The genes are involved in the metabolism, cell envelope biogenesis, and adaptation. 1. Haloarchaea originated from methanogens 2. Interdomain HGT in marine Thaumarchaeota and Euyarcheota 3. Mesophilic archaea • DNA Gyrase - contributed to the adaptation of archaea to lower temperature • Bacterial chaperones 4. Rapid inter-genera HGT in haloarchaea (Halobacterium/Halorubrum) 5. Interspecies homologous chromosome in Sulfolobus spp. - diverse CRISPR immune profiles and genome architecture
- 10. Discussion Experimental observations of gene flow: • Laboratory mating experiments of cultured archaea have demonstrated DNA transfer, homologous recombination and HGT (Euyarchaeota & Crenarchaeota) • Selection of recombinants using markers and DNA transfer between Haloferax spp., parasitic inteins change the rate of homologous recombination between strains • DNA transfer and homologous recombination were observed using auxotrophic marker pyrEF in Sulfolobus acidocaldarius. • DNA transfer has a role in DNA repair in the same species
- 11. Discussion Mechanisms of Archaeal DNA Transfer: • Natural transformation -DNA is obtained from the environment • Transduction -Contact-independent transfer of DNA via phages • Conjugation -Contact-dependent transfer of DNA via conjugative pilus • Exchange plasmid DNA through vesicles (Thermococcales) • Chromosomal DNA exchange through cell fusions (haloarchaea) • Crenarchaeal exchange of DNA (Ced) system (Sulfolobales, Crenarchaeota)
- 12. Discussion Natural competence Methanococcus voltae PS and Methanothermobacter thermautotrophicus Marburg have low frequencies of DNA uptake Thermococcus kodakarensis can be naturally transformed with linear or circular DNA Pyrococcus furiosus can take up linear or circular DNA which its efficiency is similar to competent bacteria However, competence systems of these species are unknown.
- 13. Discussion Membrane Vesicles Hypothetically foundation of cellular compartmentalization and eukaryogenesis Thermococcales – vesicles are resistant to high temperature and DNase contain chromosomal and plasmid DNA Thermococcus onnurineus NA1 – vesicles with linear fragments of chromosomal DNA Thermococcus nautilus – pTN1 (transformed into T. kodakarensis) Thermococcus gammatolerans and T. kodakarensis – vesicles through nanopods Crenarchaeal species – endosomal sorting complex required for transport III (ESCRT-III) homologues mediates vesicle transfer (no DNA observed; sulfolobicins)
- 14. Discussion Transduction and chromosomally encoded mobile genetic elements Integrase Sulfolobus spindle-shaped virus 1 (SSV1) – persist as episome Temperate viruses integrate chromosomes in Euryarchaeota Gene transfer agents (M. voltae) Intron exchange (Desulfurococcus mobilis -> S. acidocaldarius)
- 15. Discussion Conjugative plasmids Little information is known Sulfolobaceae has conjugative plasmids (e.g.: pNOB8) which have three distinct regions: • 1st region: putative origin of replication • 2nd region: protein-coding genes for plasmid replication and integrase • 3rd region: ORFs for protein for conjugation: • AAA+ ATPase (homologous to ATPase VirB4 • VirD4 of bacterial T4 Secretion Systems • Protein for translocation pore for DNA transfer Once introduced to foreign host, the conjugative plasmids become unstable due to recombination or CRISPR-Cas system. Example: pNOB8 -> pNOB8-33, cuts gene for plasmid partitioning system
- 16. Discussion Cell fusion hybrids in haloarchaea DNA Transfer through cell fusion or cytoplasmic bridges is bidirectional (H. volcanii in biofilms) Both chromosomal and plasmid DNA is transported via the bridges Plasmids in the hetero-diploid cells can be divided unequally leading to novel genotype
- 17. Discussion The Ups and Ced systems (Sulfolobales) Ups operon encodes type VI pilus assembly system for DNA transfer. Ups operon can be induced in biofilm. Ced genes: • CedA (polytopic membrane protein) resembles ComEC or VirB6 • CedB is a homologue of VirB4 and HerA The connection between the two systems is still not clear
- 18. Discussion Barriers to DNA transfer: • Decreasing similarity of S-layers • Surface exclusion is relevant barrier for conjugation • CRISPR-Cas systems • Restriction-modification systems • Methytransferase • Toxin-antitoxin modules • DNA divergence
- 19. Conclusion Genomic and metagenomic studies can uncover HGT among archaea and interdomains as well Many proteins involve in the archaeal gene transfer are still unknown The archaeal DNA transfer mechanisms is based only on work with Sulfolobus spp. and haloarchaea Future structural and biochemical work will provide new insights into the archaeal DNA transfer mechanisms.
Editor's Notes
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- . In regions of the genome in which rates of recombination are high, positive selection can act on a single locus and decrease polymorphism at that locus within a population through a selective sweep and increase divergence between independent populations (see the figure, part a). In regions in which rates of recombination are low, the same selection can decrease polymorphism and increase divergence at a locus and all of the linked neutral loci around it (see the figure, part b Despite the effect of recombination on the chromosome of Sulfolobus spp., such events do not occur rapidly enough in this archaeon to enable genomic loci to evolve independently. This results in large linked ‘continents’ in the genome and impedes the identification of single loci that are under selection in different populations36. Recent ongoing work suggests that regions of high recombination are under strong selection and are associated with selection for combinations of alleles.
- For example, haloarchaea, which are oxygen-respiring heterotrophs, originated from methanogens, which are strictly anaerobic hydrogendependent autotrophs. Many of the acquired genes were transferred as functional units, which, for example, are involved in the terminal oxidation of oxygen, membrane transport of reduced carbon compounds and the synthesis of menaquinone interdomain HGT in marine Thaumarchaeota and Euryarchaeota, which acquired 24% and 30% of their genes from bacteria, respectively22,23. Similarly to what was found for methanogens, most of the genes transferred to these archaea are involved in metabolism and membrane biogenesis. The acquisition of these genes probably provided an advantage for life in the cold oligotrophic ocean23. Moreover, it was shown that both lineages recently acquired foreign genes from distant donors, which suggests that HGT is still ongoing23. Several studies provide evidence that mesophilic archaea have obtained more genes from bacteria than hyperthermophilic archaea (Crenarchaeota, Korarchaeota, Thermococcales, non-methanogenic Archaeoglobales and Thermoplasmatales, and most DPANN species)11,15,23. This is in agreement with the hypothesis that the adaptation of archaea to mesophilic environments was the result of the massive acquisition of bacterial genes24. This assumption is further supported by the finding that haloarchaea, marine Euryarchaeota and their sister groups independently acquired a DNA gyrase from bacteria Unlike reverse gyrase, which is found in hyperthermophilic archaea and introduces positive supercoils into DNA, DNA gyrase introduces negative supercoils to relax supercoils that are produced through transcription and replication mesophilic archaea contain some bacterial chaperones that assist in correct protein folding and that seem to be absent in hyperthermophilic archaea11,23,30. With the increasing availability of archaeal genomes, it needs to be shown whether archaea indeed adapted to the mesophilic lifestyle by obtaining bacterial genes or whether there are archaea that have adapted to lower temperatures without acquiring bacterial genes.
- . In archaea, little information about conjugation is available. In 1995, the first archaeal conjugative plasmid (pNOB8) was isolated from the hyperthermophilic Crenarchaeon Sulfolobus sp. NOB8H2 (REF. 18). In the following years, several conjugative plasmids were isolated exclusively in members of the family Sulfolobaceae, which suggests that conjugative plasmids might be limited to this family18,100–104 (FIG. 1d). Sequence comparison of six conjugative plasmids revealed three distinct regions of genes102. The first region contains a putative origin of replication. The second region consists of genes that encode proteins that are probably involved in plasmid replication and a gene that encodes an integrase102. The integrase enables site-specific integration of the plasmid into the host chromosome105. The third region comprises several ORFs that are suggested to be involved in conjugation102. Highly conserved in the latter cluster are two ORFs encoding AAA+ ATPases that exhibit homology to the ubiquitous ATPase VirB4 and the coupling protein VirD4 of bacterial type IV secretion systems (T4SSs) Another conserved ORF encodes a protein with 10–12 transmembrane helices that possibly forms the translocation pore for DNA transfer102. This protein has no homology to bacterial T4SS proteins. Although archaeal conjugative plasmids are self-transmissible, no clear homologues of known conjugative relaxases or other DNA transfer and replication proteins, except VirB4 and VirD4, were identified102. The absence of a known relaxase homologue suggests a novel mechanism of DNA transfer
- The observation that cell fusion and interspecies recombination indeed occur is in agreement with phylogenetic data that suggest high levels of interspecies DNA transfer between haloarchaea11,19,31,32. Haloarchaeal genomes often contain a high density of insertion elements and transposons32. Therefore, it would be interesting to study their role in gene shuffling during cell fusion32.
- In Sulfolobus spp., DNA damage triggers the expression of Ups pili and the Ced system (FIG. 2d). In the first step, Ups pili mediate species-specific cellular aggregation. Through an unknown mechanism, DNA is exported from the donor cell after cell-to-cell contact is initiated. DNA is then actively imported by the Ced system. Although it is unknown whether single-stranded DNA or double-stranded DNA is transported, incoming DNA can be used as a template for homologous recombination to repair damaged DNA. A contact-dependent DNA import system has thus far not been observed in other archaea, or in bacteria or eukaryotes21. It is currently unknown whether conjugative plasmids of members of the Sulfolobaceae might use Ups pili or the Ced system for transfer. Further studies should reveal the mechanisms of DNA transport by conjugation and through the Ups and Ced systems, and whether any connections exist between these two processes.
- Barriers to horizontal gene transfer (HGT) have a fundamental role in the establishment and maintenance of species by preventing DNA transfer and the incorporation of foreign DNA. Physical barriers prevent random gene flux and lead to the geographical isolation of microorganisms121. Environmental factors, such as pH, ion strength or temperature, can destabilize or degrade external DNA, and thereby prevent DNA transfer122,123. Foreign DNA, including plasmid, virus and chromosomal DNA (red), has to cross the species-specific surface layer (S-layer) and the membrane of a recipient cell. DNA transport proteins, which are encoded on a plasmid and are anchored in the membrane, reduce the import of other plasmid DNA in a process that is known as surface exclusion124. In the cytoplasm, foreign DNA can be recognized and degraded by the Cas proteins of the CRISPR–Cas immune system or through a restriction–modification system.126–128. In restriction–modification, a restriction endonuclease (REase) only cuts non-modified DNA, whereas the chromosomal DNA is protected (blue dots) by a respective modification enzyme (MTase). Furthermore, the spread of viral and plasmid DNA can be prevented by chromosomally encoded toxin–antitoxin modules (T–A)130. The homologous recombination machinery will only incorporate foreign DNA that is homologous to chromosomal DNA135–137. Dashed arrows indicate the genetic source of the respective system.