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Benutzer:LunMa4/Gene transfer agent

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Vorlage:Short description

Comparison of typical phage (bacteriophage) infection and transduction (A) with typical GTA (gene transfer agent) production and transduction (B).

Gene transfer agents (GTA) sind DNA-haltige Virus-ähnliche Partikel, welche von einigen Bakterien und Archaeenfür den horizontalen Gentransfer produziert werden. Im Laufe der Zeit haben sich verschiedene GTA Typen unabhängig von Viren in verschiedenen Bakterien- und Archaeenstämmen entwickelt. Die von der Zellen produzierten GTAs enthalten kurze, zufällige Abschnitten der Zell-DNA. Nachdem die GTAs von der Erzeugerzelle freigesetzt werden, können sie sich an verwandte Zellen anlagen und die DNA in das Cytoplasma injizieren. Die DNA kann jetzt in das Genom der Empfängerzellen eingebaut werden.[1][2][3][4]

GTAs are classified as viriforms in the ICTV taxonomy. Among the GTAs mentioned by the article, RcGTA and DsGTA are now in the family Rhodogtaviriformidae, BaGTA in Bartogtaviriformidae, and VSH-1 in Brachygtaviriformidae.[5] Dd1 and VTA do not yet have a classification.

Entdeckung

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Methods for detecting gene transfer agents. (A) Method used by Marrs in 1974. (B) Cell-free extract method.

Das erste GTA-System wurde 1974 entdeckt, als Mischkulturen von Rhodobacter capsulatus-Stämmen eine hohe Häufigkeit von Zellen mit neuen Genkombinationen hervorbrachten.[6] Der verantwortliche Faktor unterschied sich von den bekannten Gentransfermechanismen dadurch, dass er unabhängig vom Zellkontakt war, unempfindlich gegen Desoxyribonuklease und nicht mit der Phagenproduktion verbunden. Aufgrund seiner vermuteten Funktion wurde er als Gentransfer-Agent (GTA, jetzt RcGTA) bezeichnet. In jüngster Zeit wurden weitere Gentransfer-Agent-Systeme entdeckt, indem gefiltertes (zellfreies) Kulturmedium mit einem genetisch unterschiedlichen Stamm inkubiert wurde[3]

GTA-Gene und Evolution

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Typical prophage and GTA gene clusters.
 
Schematic diagram of phylogenetic relationships between known bacterial gene transfer agents.
 
The evolutionary forces that act on bacterial gene transfer agent and the cells that produce it.

Die Gene, die GTAs spezifizieren, stammen von der DNA eines Bakteriophagen (Phagen), der sich in ein Wirtschromosom integriert hat. Solche Prophagen weisen häufig Mutationen auf, die sie defekt und unfähig machen, Phagenpartikel zu produzieren. Viele bakteriellen Genome enthalten einen oder mehrere defekte Prophagen, die mehr oder weniger stark mutiert und gelöscht wurden. Gentransfer-Agenten entstehen wie auch defekte Prophagen durch Mutationen von Prophagenen, wobei sie aber funktionelle Gene für die Kopf- und Schwanzkomponenten des Phagenpartikels (Strukturgene) und die Gene für die DNA-Verpackung behalten. The phage genes specifying its regulation and DNA replication have typically been deleted, and expression of the cluster of structural genes is under the control of cellular regulatory systems. Additional genes that contribute to GTA production or uptake are usually present at other chromosome locations. Some of these have regulatory functions, and others contribute directly to GTA production (e.g. the phage-derived lysis genes) or uptake and recombination (e.g. production of cell-surface capsule and DNA transport proteins) These GTA-associated genes are often under coordinated regulation with the main GTA gene cluster.[7]  Phage-derived cell-lysis proteins (holin and endolysin) then weaken the cell wall and membrane, allowing the cell to burst and release the GTA particles. The number of GTA particles produced by each cell is not known.

Some GTA systems appear to be recent additions to their host genomes, but others have been maintained for many millions of years. Where studies of sequence divergence have been done (dN/dS analysis), they indicate that the genes are being maintained by natural selection for protein function (i.e. defective versions are being eliminated).[8][9]

However, the nature of this selection is not clear. Although the discoverers of GTA assumed that gene transfer was the function of the particles, the presumed benefits of gene transfer come at a substantial cost to the population. Most of this cost arises because GTA-producing cells must lyse (burst open) to release their GTA particles, but there are also genetic costs associated with making new combinations of genes because most new combinations will usually be less fit than the original combination.[10]   One alternative explanation is that GTA genes persist because GTAs are genetic parasites that spread infectiously to new cells. However this is ruled out because GTA particles are typically too small to contain the genes that encode them. For example, the main RcGTA cluster (see below) is 14 kb long, but RcGTA particles can contain only 4–5 kb of DNA.   

Most bacteria have not been screened for the presence of GTAs, and many more GTA systems may await discovery. Although DNA-based surveys for GTA-related genes have found homologs in many genomes, but interpretation is hindered by the difficulty of distinguishing genes that encode GTAs from ordinary prophage genes.[8] [9]

GTA production

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Typical steps in the production of bacterial gene transfer agents. (1) Transcription and translation of the GTA genes. (2) Assembly of GTA structural proteins into empty heads and unattached tails. (3) Packaging of 'headful' segments of DNA into heads and attachment of tails. (4) Lysis of the cell.

In laboratory cultures, production of GTAs is typically maximized by particular growth conditions that induce transcription of the GTA genes; most GTAs are not induced by the DNA-damaging treatments that induce many prophages.  Even under maximally inducing conditions only a small fraction of the culture produces GTAs, typically less than 1%.[11][12]

The steps in GTA production are derived from those of phage infection. The structural genes are first transcribed and translated, and the proteins assembled into empty heads and unattached tails.  The DNA packaging machinery then packs DNA into each head, cutting the DNA when the head is full, attaching a tail to the head, and then moving the newly-created DNA end on to a new empty head. Unlike prophage genes, the genes encoding GTAs are not excised from the genome and replicated for packaging in GTA particles.  The two best studied GTAs (RcGTA and BaGTA) randomly package all of the DNA in the cell, with no overrepresentation of GTA-encoding genes.[11][13] The number of GTA particles produced by each cell is not known.

GTA-mediated transduction

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Genetic transduction by bacterial gene transfer agents. (1) GTA particles encounter a suitable recipient cell. (2) Particles attach to cell and inject their DNA, and cellular proteins translocate the DNA across the inner membrane. (3) DNA is degraded if it cannot recombine with the recipient genome. (4) DNA with similar sequences to the recipient genome undergoes recombination.

Whether release of GTA particles leads to transfer of DNA to new genomes depends on several factors.   First, the particles must survive in the environment – little is known about this, although particles are reported to be quite unstable under laboratory conditions.[14] Second, particles must encounter and attach to suitable recipient cells, usually members of the same or a closely related species.  Like phages, GTAs attach to specific protein or carbohydrate structures on the recipient cell surface before injecting their DNA.  Unlike phage, the well-studied GTAs appear to inject their DNA only across the first of the two membranes surrounding the recipient cytoplasm, and they use a different system, competence-derived rather than phage-derived, to transport one strand of the double-stranded DNA across the inner membrane into the cytoplasm.[15][16]

If the cell's recombinational repair machinery finds a chromosomal sequence very similar to the incoming DNA, it replaces the former with the latter by homologous recombination, mediated by the cell's RecA protein. If the sequences are not identical this will produce a cell with a new genetic combination.  However, if the incoming DNA is not closely related to DNA sequences in the cell it will be degraded, and the cell will reuse its nucleotides for DNA replication.

Specific GTA systems

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RcGTA/Rhodobactegtaviriform (Rhodobacter capsulatus)

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Regulation diagram for RcGTA, the Rhodobacter capsulatus gene transfer agent

The GTA produced by the alphaproteobacterium Rhodobacter capsulatus, named R. capsulatus GTA (RcGTA), is currently the best studied GTA. When laboratory cultures of R. capsulatus enter stationary phase, a subset of the bacterial population induces production of RcGTA, and the particles are subsequently released from the cells through cell lysis.[12] Most of the RcGTA structural genes are encoded in a ~ 15 kb genetic cluster on the bacterial chromosome. However, other genes required for RcGTA function, such as the genes required for cell lysis, are located separately.[2][17] RcGTA particles contain 4.5 kb DNA fragments, with even representation of the whole chromosome except for a 2-fold dip at the site of the RcGTA gene cluster. 

Regulation of GTA production and transduction has been best studied in R. capsulatus, where a quorum-sensing system and a CtrA-phosphorelay control expression of not only the main RcGTA gene cluster, but also a holin/endolysin cell lysis system, particle head spikes, an attachment protein (possibly tail fibers), and the capsule and DNA processing genes needed for RcGTA recipient function. An uncharacterized stochastic process further limits expression of the gene cluster is to only 0.1-3% of the cells.  

RcGTA-like clusters are found in a large subclade of the alphaproteobacteria, although the genes also appear to be frequently lost by deletion. Recently, several members of the order Rhodobacterales have been demonstrated to produce functional RcGTA-like particles. Groups of genes with homology to the RcGTA are present in the chromosomes of various types of alphaproteobacteria.[8]

DsGTA/Dinogtaviriform (Dinoroseobacter shibae)

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D. shibae, like R. capsulatus, is a member of the Order Rhodobacterales, and its GTA shares a common ancestor and many features with RcGTA, including gene organization, packaging of short DNA fragments (4.2 kb) and regulation by quorum sensing and a CtrA phosphorelay.[18]  However, its DNA packaging machinery has much more specificity, with sharp peaks and valleys of coverage suggestion that it may preferentially initiate packaging at specific sites in the genome.  The DNA of the major DsGTA gene cluster is packaged very poorly.   

BaGTA/Bartonegtaviriform (Bartonella species)

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Bartonella species are members of the Alphaproteobacteria like R. capsulatus and D. shibae, but BaGTA is not related to RcGTA and DsGTA.[19]  BaGTA particles are larger than RcGTA and contain 14 kb DNA fragments.  Although this capacity could in principle allow BaGTA to package and transmit its 14 kb GTA cluster, measurements of DNA coverage show reduced coverage of the cluster. An adjacent region of high coverage is thought to be due to local DNA replication.[13]

VSH-1 (Brachyspira hyodysenteriae)

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Brachyspira is a genus of spirochete; several species have been shown to carry homologous GTA gene clusters.  Particles contain 7.5 kb DNA fragments.  Production of VSH-1 is stimulated by the DNA-damaging agent mitomycin C and by some antibiotics.  It is also associated with detectable cell lysis, indicating that a substantial fraction of the culture may be producing VSH-1.[20]

Dd1 (Desulfovibriondesulfuricans)

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D. desulfuricans is a soil bacterium in the deltaproteobacteria; Dd1 packages 13.6 kb of DNA fragments. It is unclear which genes encode for this GTA: there is one 17.8 kb area with phage-like structural genes in the bacterial genome, but their link to GTA production is not yet experimentally proven.[21]

VTA (Methanococcus voltae)

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M. voltae is an archaean; its GTA is known to transfer 4.4 kb DNA fragments but has not been otherwise characterized,[22] although a defective provirus related to Methanococcus head-tailed viruses (Caudoviricetes) in M. voltae A3 genome has been suggested to represent the GTA locus.[23] A possible terL terminase (UniProt D7DSG2) was again identified in 2019.[24]

See also

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References

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Vorlage:Reflist

Category:Genetics Category:Microbial population biology

  1. ↑ Lang AS, Westbye AB, Beatty JT: The Distribution, Evolution, and Roles of Gene Transfer Agents in Prokaryotic Genetic Exchange. In: Annual Review of Virology. 4. Jahrgang, Nr. 1, September 2017, S. 87–104, doi:10.1146/annurev-virology-101416-041624, PMID 28784044.
  2. ↑ a b Lang AS, Zhaxybayeva O, Beatty JT: Gene transfer agents: phage-like elements of genetic exchange. In: Nature Reviews. Microbiology. 10. Jahrgang, Nr. 7, Juni 2012, S. 472–82, doi:10.1038/nrmicro2802, PMID 22683880, PMC 3626599 (freier Volltext).
  3. ↑ a b Stanton TB: Prophage-like gene transfer agents-novel mechanisms of gene exchange for Methanococcus, Desulfovibrio, Brachyspira, and Rhodobacter species. In: Anaerobe. 13. Jahrgang, Nr. 2, April 2007, S. 43–9, doi:10.1016/j.anaerobe.2007.03.004, PMID 17513139.
  4. ↑ Grüll MP, Mulligan ME, Lang AS: Small extracellular particles with big potential for horizontal gene transfer: membrane vesicles and gene transfer agents. In: FEMS Microbiology Letters. 365. Jahrgang, Nr. 19, Oktober 2018, doi:10.1093/femsle/fny192, PMID 30085064.
  5. ↑ R Kogay, S Koppenhöfer, JT Beatty, JH Kuhn, AS Lang, O Zhaxybayeva: Formal recognition and classification of gene transfer agents as viriforms. In: Virus Evolution. 8. Jahrgang, Nr. 2, 2022, S. veac100, doi:10.1093/ve/veac100, PMID 36381234, PMC 9662315 (freier Volltext).
  6. ↑ Marrs B: Genetic recombination in Rhodopseudomonas capsulata. In: Proceedings of the National Academy of Sciences of the United States of America. 71. Jahrgang, Nr. 3, März 1974, S. 971–3, doi:10.1073/pnas.71.3.971, PMID 4522805, PMC 388139 (freier Volltext), bibcode:1974PNAS...71..971M.
  7. ↑ Westbye AB, Beatty JT, Lang AS: Guaranteeing a captive audience: coordinated regulation of gene transfer agent (GTA) production and recipient capability by cellular regulators. In: Current Opinion in Microbiology. 38. Jahrgang, August 2017, S. 122–129, doi:10.1016/j.mib.2017.05.003, PMID 28599143.
  8. ↑ a b c Shakya M, Soucy SM, Zhaxybayeva O: Insights into origin and evolution of α-proteobacterial gene transfer agents. In: Virus Evolution. 3. Jahrgang, Nr. 2, Juli 2017, S. vex036, doi:10.1093/ve/vex036, PMID 29250433, PMC 5721377 (freier Volltext).
  9. ↑ a b Tamarit D, Neuvonen MM, Engel P, Guy L, Andersson SG: Origin and Evolution of the Bartonella Gene Transfer Agent. In: Molecular Biology and Evolution. 35. Jahrgang, Nr. 2, Februar 2018, S. 451–464, doi:10.1093/molbev/msx299, PMID 29161442.
  10. ↑ Redfield RJ, Soucy SM: Evolution of Bacterial Gene Transfer Agents. In: Frontiers in Microbiology. 9. Jahrgang, 2018, S. 2527, doi:10.3389/fmicb.2018.02527, PMID 30410473, PMC 6209664 (freier Volltext) – (englisch).
  11. ↑ a b Hynes AP, Mercer RG, Watton DE, Buckley CB, Lang AS: DNA packaging bias and differential expression of gene transfer agent genes within a population during production and release of the Rhodobacter capsulatus gene transfer agent, RcGTA. In: Molecular Microbiology. 85. Jahrgang, Nr. 2, Juli 2012, S. 314–25, doi:10.1111/j.1365-2958.2012.08113.x, PMID 22640804.
  12. ↑ a b Fogg PC, Westbye AB, Beatty JT: One for all or all for one: heterogeneous expression and host cell lysis are key to gene transfer agent activity in Rhodobacter capsulatus. In: PLOS ONE. 7. Jahrgang, Nr. 8, 2012, S. e43772, doi:10.1371/journal.pone.0043772, PMID 22916305, PMC 3423380 (freier Volltext), bibcode:2012PLoSO...743772F.
  13. ↑ a b Berglund EC, Frank AC, Calteau A, Vinnere Pettersson O, Granberg F, Eriksson AS, Näslund K, Holmberg M, Lindroos H, Andersson SG: Run-off replication of host-adaptability genes is associated with gene transfer agents in the genome of mouse-infecting Bartonella grahamii. In: PLOS Genetics. 5. Jahrgang, Nr. 7, Juli 2009, S. e1000546, doi:10.1371/journal.pgen.1000546, PMID 19578403, PMC 2697382 (freier Volltext).
  14. ↑ B. Marrs, H. C. Yen, M. Solioz: Release and uptake of gene transfer agent by Rhodopseudomonas capsulata. In: Journal of Bacteriology. 123. Jahrgang, Nr. 2, 1. August 1975, ISSN 1098-5530, S. 651–657, doi:10.1128/jb.123.2.651-657.1975, PMID 1150627, PMC 235772 (freier Volltext) – (englisch).
  15. ↑ Brimacombe CA, Stevens A, Jun D, Mercer R, Lang AS, Beatty JT: Quorum-sensing regulation of a capsular polysaccharide receptor for the Rhodobacter capsulatus gene transfer agent (RcGTA). In: Molecular Microbiology. 87. Jahrgang, Nr. 4, Februar 2013, S. 802–17, doi:10.1111/mmi.12132, PMID 23279213, PMC 3641046 (freier Volltext).
  16. ↑ Brimacombe CA, Ding H, Johnson JA, Beatty JT: Homologues of Genetic Transformation DNA Import Genes Are Required for Rhodobacter capsulatus Gene Transfer Agent Recipient Capability Regulated by the Response Regulator CtrA. In: Journal of Bacteriology. 197. Jahrgang, Nr. 16, August 2015, S. 2653–63, doi:10.1128/JB.00332-15, PMID 26031909, PMC 4507343 (freier Volltext).
  17. ↑ Westbye AB, Leung MM, Florizone SM, Taylor TA, Johnson JA, Fogg PC, Beatty JT: Phosphate concentration and the putative sensor kinase protein CckA modulate cell lysis and release of the Rhodobacter capsulatus gene transfer agent. In: Journal of Bacteriology. 195. Jahrgang, Nr. 22, November 2013, S. 5025–40, doi:10.1128/JB.00669-13, PMID 23995641, PMC 3811591 (freier Volltext).
  18. ↑ Tomasch J, Wang H, Hall AT, Patzelt D, Preusse M, Petersen J, Brinkmann H, Bunk B, Bhuju S, Jarek M, Geffers R, Lang AS, Wagner-Döbler I: Packaging of Dinoroseobacter shibae DNA into Gene Transfer Agent Particles Is Not Random. In: Genome Biology and Evolution. 10. Jahrgang, Nr. 1, Januar 2018, S. 359–369, doi:10.1093/gbe/evy005, PMID 29325123, PMC 5786225 (freier Volltext).
  19. ↑ Québatte M, Christen M, Harms A, Körner J, Christen B, Dehio C: Gene Transfer Agent Promotes Evolvability within the Fittest Subpopulation of a Bacterial Pathogen. In: Cell Systems. 4. Jahrgang, Nr. 6, Juni 2017, S. 611–621.e6, doi:10.1016/j.cels.2017.05.011, PMID 28624614, PMC 5496983 (freier Volltext).
  20. ↑ Motro Y, La T, Bellgard MI, Dunn DS, Phillips ND, Hampson DJ: Identification of genes associated with prophage-like gene transfer agents in the pathogenic intestinal spirochaetes Brachyspira hyodysenteriae, Brachyspira pilosicoli and Brachyspira intermedia. In: Veterinary Microbiology. 134. Jahrgang, Nr. 3–4, März 2009, S. 340–5, doi:10.1016/j.vetmic.2008.09.051, PMID 18950961 (edu.au).
  21. ↑ AS Lang, O Zhaxybayeva, JT Beatty: Gene transfer agents: phage-like elements of genetic exchange. In: Nature Reviews. Microbiology. 10. Jahrgang, Nr. 7, 11. Juni 2012, S. 472–82, doi:10.1038/nrmicro2802, PMID 22683880, PMC 3626599 (freier Volltext).
  22. ↑ Bertani G: Transduction-like gene transfer in the methanogen Methanococcus voltae. In: Journal of Bacteriology. 181. Jahrgang, Nr. 10, Mai 1999, S. 2992–3002, doi:10.1128/JB.181.10.2992-3002.1999, PMID 10321998, PMC 93752 (freier Volltext).
  23. ↑ M Krupovic, P Forterre, DH Bamford: Comparative analysis of the mosaic genomes of tailed archaeal viruses and proviruses suggests common themes for virion architecture and assembly with tailed viruses of bacteria. In: Journal of Molecular Biology. 397. Jahrgang, Nr. 1, 2010, S. 144–60, doi:10.1016/j.jmb.2010.01.037, PMID 20109464.
  24. ↑ D Sherlock, JX Leong, PCM Fogg: Identification of the First Gene Transfer Agent (GTA) Small Terminase in Rhodobacter capsulatus and Its Role in GTA Production and Packaging of DNA. In: Journal of Virology. 93. Jahrgang, Nr. 23, 1. Dezember 2019, doi:10.1128/JVI.01328-19, PMID 31534034, PMC 6854486 (freier Volltext).
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