Gene transfer agents (GTAs) are phage-like particles that transfer pieces of cellular genomic DNA to other cells. Homologues of the Rhodobacter capsulatus GTA (RcGTA) structural genes are widely distributed in the Alphaproteobacteria and particularly well conserved in the order Rhodobacterales. Possible reasons for their widespread conservation are still being discussed. It has been suggested that these alphaproteobacterial elements originate from a prophage that was present in an ancestral bacterium and subsequently evolved into a GTA that is now widely maintained in extant descendant lineages. Here, we analysed genomic properties that might relate to the conservation of these alphaproteobacterial GTAs. This revealed that the chromosomal locations of the GTA gene clusters are biased. They primarily occur on the leading strand of DNA replication, at large distances from long repetitive elements, and thus are in regions of lower plasticity, and in areas of extreme GC skew, which also accumulate core genes. These extreme GC skew regions arise from the preferential use of codons with an excess of G over C, a distinct phenomenon from the elevated GC content that has previously been found to be associated with GTA genes. The observed properties, along with their high level of conservation, show that GTA genes share multiple features with core genes in the examined lineages of the Alphaproteobacteria.

Department of Biology Memorial University of Newfoundland St John's Newfoundland and Labrador Canada

Laboratory of Anoxygenic Phototrophs Institute of Microbiology of the Czech Academy of Science Centre Algatech Třeboň Czech Republic

Zobrazit více v PubMed

Lang AS, Westbye AB, Beatty JT. The distribution, evolution, and roles of gene transfer agents in prokaryotic genetic exchange. Annu Rev Virol. 2017;4:87–104. doi: 10.1146/annurev-virology-101416-041624. PubMed DOI

Lang AS, Beatty JT. Importance of widespread gene transfer agent genes in α-proteobacteria. Trends Microbiol. 2007;15:54–62. doi: 10.1016/j.tim.2006.12.001. PubMed DOI

Shakya M, Soucy SM, Zhaxybayeva O. Insights into origin and evolution of α-proteobacterial gene transfer agents. Virus Evol. 2017;3:vex036. doi: 10.1093/ve/vex036. PubMed DOI PMC

Tomasch J, Wang H, Hall ATK, Patzelt D, Preusse M, et al. Packaging of Dinoroseobacter shibae DNA into gene transfer agent particles is not random. Genome Biol Evol. 2018;10:359–369. doi: 10.1093/gbe/evy005. PubMed DOI PMC

Biers EJ, Wang K, Pennington C, Belas R, Chen F, et al. Occurrence and expression of gene transfer agent genes in marine bacterioplankton. Appl Environ Microbiol. 2008;74:2933–2939. doi: 10.1128/AEM.02129-07. PubMed DOI PMC

Nagao N, Yamamoto J, Komatsu H, Suzuki H, Hirose Y, et al. The gene transfer agent-like particle of the marine phototrophic bacterium Rhodovulum sulfidophilum . Biochem Biophys Rep. 2015;4:369–374. doi: 10.1016/j.bbrep.2015.11.002. PubMed DOI PMC

Lang AS, Beatty JT. Genetic analysis of a bacterial genetic exchange element: the gene transfer agent of Rhodobacter capsulatus . Proc Natl Acad Sci. 2000;97:859–864. doi: 10.1073/pnas.97.2.859. PubMed DOI PMC

Redfield RJ. Do bacteria have sex? Microbes Evol. 2014;2:139–144. doi: 10.1128/9781555818470. DOI

Marrs B, Wall JD, Gest H. Emergence of the biochemical genetics and molecular biology of photosynthetic bacteria. Trends in Biochemical Sciences. 1977;2:105–108. doi: 10.1016/0968-0004(77)90173-6. DOI

Québatte M, Christen M, Harms A, Körner J, Christen B, et al. Gene transfer agent promotes evolvability within the fittest subpopulation of a bacterial pathogen. Cell Syst. 2017;4:611–621. doi: 10.1016/j.cels.2017.05.011. PubMed DOI PMC

Redfield RJ, Soucy SM. Evolution of bacterial gene transfer agents. Front Microbiol. 2018;9:2527. doi: 10.3389/fmicb.2018.02527. PubMed DOI PMC

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. Mol Microbiol. 2012;85:314–325. doi: 10.1111/j.1365-2958.2012.08113.x. PubMed DOI

Fogg PCM, 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 . PLoS One. 2012;7:e43772. doi: 10.1371/journal.pone.0043772. PubMed DOI PMC

Lang AS, Zhaxybayeva O, Beatty JT. Gene transfer agents: phage-like elements of genetic exchange. Nat Rev Microbiol. 2012;10:472–482. doi: 10.1038/nrmicro2802. PubMed DOI PMC

Westbye AB, Beatty JT, Lang AS. Guaranteeing a captive audience: coordinated regulation of gene transfer agent (GTA) production and recipient capability by cellular regulators. Curr Opin Microbiol. 2017;38:122–129. doi: 10.1016/j.mib.2017.05.003. PubMed DOI

Kogay R, Wolf YI, Koonin EV, Zhaxybayeva O. Selection for reducing energy cost of protein production drives the GC content and amino acid composition bias in gene transfer agents. mBio. 2020;11:e01206-20. doi: 10.1128/mBio.01206-20. PubMed DOI PMC

Westbye AB, O’Neill Z, Schellenberg-Beaver T, Beatty JT. The Rhodobacter capsulatus gene transfer agent is induced by nutrient depletion and the RNAP omega subunit. Microbiology. 2017;163:1355–1363. doi: 10.1099/mic.0.000519. PubMed DOI

Koppenhöfer S, Wang H, Scharfe M, Kaever V, Wagner-Döbler I, et al. Integrated transcriptional regulatory network of quorum sensing, replication control, and SOS response in Dinoroseobacter shibae . Front Microbiol. 2019;10:803. doi: 10.3389/fmicb.2019.00803. PubMed DOI PMC

Lobry JR. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol. 1996;13:660–665. doi: 10.1093/oxfordjournals.molbev.a025626. PubMed DOI

Freeman JM, Plasterer TN, Smith TF, Mohr SC. Patterns of genome organization in bacteria. Science. 1998;279:1827. doi: 10.1126/science.279.5358.1827a. DOI

Rocha EPC. Order and disorder in bacterial genomes. Curr Opin Microbiol. 2004;7:519–527. doi: 10.1016/j.mib.2004.08.006. PubMed DOI

Rocha EPC. The replication-related organization of bacterial genomes. Microbiology. 2004;150:1609–1627. doi: 10.1099/mic.0.26974-0. PubMed DOI

Bhagwat AS, Hao W, Townes JP, Lee H, Tang H, et al. Strand-biased cytosine deamination at the replication fork causes cytosine to thymine mutations in Escherichia coli . Proc Natl Acad Sci. 2016;113:2176–2181. doi: 10.1073/pnas.1522325113. PubMed DOI PMC

Kono N, Tomita M, Arakawa K. Accelerated laboratory evolution reveals the influence of replication on the GC skew in Escherichia coli . Genome Biol Evol. 2018;10:3110–3117. doi: 10.1093/gbe/evy237. PubMed DOI PMC

Zhao HL, Xia ZK, Zhang FZ, Ye YN, Guo FB. Multiple factors drive replicating strand composition bias in bacterial genomes. Int J Mol Sci. 2015;16:23111–23126. doi: 10.3390/ijms160923111. PubMed DOI PMC

Achaz G, Coissac E, Netter P, Rocha EPC. Associations between inverted repeats and the structural evolution of bacterial genomes. Genetics. 2003;164:1279–1289. doi: 10.1093/genetics/164.4.1279. PubMed DOI PMC

Vandecraen J, Chandler M, Aertsen A, Van Houdt R. The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit Rev Microbiol. 2017;43:709–730. doi: 10.1080/1040841X.2017.1303661. PubMed DOI

Sela I, Wolf YI, Koonin EV. Selection and genome plasticity as the key factors in the evolution of bacteria. Phys Rev X. 2019;9 doi: 10.1103/PhysRevX.9.031018. DOI

Rocha EPC, Blanchard A. Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution. Nucleic Acids Res. 2002;30:2031–2042. doi: 10.1093/nar/30.9.2031. PubMed DOI PMC

Gao F, Zhang C-T. Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes. BMC Bioinformatics. 2008;9:79. doi: 10.1186/1471-2105-9-79. PubMed DOI PMC

Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF, et al. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics. 2011;12:124. doi: 10.1186/1471-2105-12-124. PubMed DOI PMC

Arndt D, Grant JR, Marcu A, Sajed T, Pon A, et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016;44:W16–21. doi: 10.1093/nar/gkw387. PubMed DOI PMC

Achaz G, Boyer F, Rocha EPC, Viari A, Coissac E. Repseek, a tool to retrieve approximate repeats from large DNA sequences. Bioinformatics. 2007;23:119–121. doi: 10.1093/bioinformatics/btl519. PubMed DOI

Kung SH, Retchless AC, Kwan JY, Almeida RPP. Effects of DNA size on transformation and recombination efficiencies in Xylella fastidiosa . Appl Environ Microbiol. 2013;79:1712–1717. doi: 10.1128/AEM.03525-12. PubMed DOI PMC

Darling ACE, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004;14:1394–1403. doi: 10.1101/gr.2289704. PubMed DOI PMC

Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol. 2018;35:1547–1549. doi: 10.1093/molbev/msy096. PubMed DOI PMC

Hawkey J, Hamidian M, Wick RR, Edwards DJ, Billman-Jacobe H, et al. ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data. BMC Genomics. 2015;16:667. doi: 10.1186/s12864-015-1860-2. PubMed DOI PMC

Mangiameli SM, Merrikh CN, Wiggins PA, Merrikh H. Transcription leads to pervasive replisome instability in bacteria. Elife. 2017;6:1–27. doi: 10.7554/eLife.19848. PubMed DOI PMC

Lin Y-L, Pasero P. Interference between DNA replication and transcription as a cause of genomic instability. Curr Genomics. 2012;13:65–73. doi: 10.2174/138920212799034767. PubMed DOI PMC

Rocha EPC, Danchin A. Gene essentiality determines chromosome organisation in bacteria. Nucleic Acids Res. 2003;31:6570–6577. doi: 10.1093/nar/gkg859. PubMed DOI PMC

Merrikh CN, Merrikh H. Gene inversion potentiates bacterial evolvability and virulence. Nat Commun. 2018;9:4662. doi: 10.1038/s41467-018-07110-3. PubMed DOI PMC

Lu J, Salzberg SL. SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes. PLoS Comput Biol. 2020;16:1–16. doi: 10.1371/journal.pcbi.1008439. PubMed DOI PMC

Liu H, Zhang J. Testing the adaptive hypothesis of lagging-strand encoding in bacterial genomes. Nat Commun. 2022;13:2628. doi: 10.1038/s41467-022-30000-8. PubMed DOI PMC

Dewey CN, Pachter L. Evolution at the nucleotide level: the problem of multiple whole-genome alignment. Hum Mol Genet. 2006;15 Spec No 1:R51–6. doi: 10.1093/hmg/ddl056. PubMed DOI

Bobay LM, Rocha EPC, Touchon M. The adaptation of temperate bacteriophages to their host genomes. Mol Biol Evol. 2013;30:737–751. doi: 10.1093/molbev/mss279. PubMed DOI PMC

Duncan BK, Miller JH. Mutagenic deamination of cytosine residues in DNA. Nature. 1980;287:560–561. doi: 10.1038/287560a0. PubMed DOI

Daubin V, Gouy M, Perrière G. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res. 2002;12:1080–1090. doi: 10.1101/gr.187002. PubMed DOI PMC

Hartono SR, Korf IF, Chédin F. GC skew is a conserved property of unmethylated CpG island promoters across vertebrates. Nucleic Acids Res. 2015;43:9729–9741. doi: 10.1093/nar/gkv811. PubMed DOI PMC

Ginno PA, Lim YW, Lott PL, Korf I, Chédin F. GC skew at the 5’ and 3’ ends of human genes links R-loop formation to epigenetic regulation and transcription termination. Genome Res. 2013;23:1590–1600. doi: 10.1101/gr.158436.113. PubMed DOI PMC

Dai Y, Holland PWH. The interaction of natural selection and GC skew may drive the fast evolution of a sand rat homeobox gene. Mol Biol Evol. 2019;36:1473–1480. doi: 10.1093/molbev/msz080. PubMed DOI PMC

Fischer W, Windhager L, Rohrer S, Zeiller M, Karnholz A, et al. Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer. Nucleic Acids Res. 2010;38:6089–6101. doi: 10.1093/nar/gkq378. PubMed DOI PMC

Han H, Wong H-C, Kan B, Guo Z, Zeng X, et al. Genome plasticity of Vibrio parahaemolyticus: microevolution of the “pandemic group.”. BMC Genomics. 2008;9:1–12. doi: 10.1186/1471-2164-9-570. PubMed DOI PMC

Brilli M, Fondi M, Fani R, Mengoni A, Ferri L, et al. The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis. BMC Syst Biol. 2010;4:52. doi: 10.1186/1752-0509-4-52. PubMed DOI PMC

Fioravanti A, Fumeaux C, Mohapatra SS, Bompard C, Brilli M, et al. DNA binding of the cell cycle transcriptional regulator GcrA depends on N6-adenosine methylation in Caulobacter crescentus and other Alphaproteobacteria. PLoS Genet. 2013;9:e1003541. doi: 10.1371/journal.pgen.1003541. PubMed DOI PMC

Haakonsen DL, Yuan AH, Laub MT. The bacterial cell cycle regulator GcrA is a σ70 cofactor that drives gene expression from a subset of methylated promoters. Genes Dev. 2015;29:2272–2286. doi: 10.1101/gad.270660.115. PubMed DOI PMC

Tomasch J, Koppenhöfer S, Lang AS. Connection between chromosomal location and function of CtrA phosphorelay genes in Alphaproteobacteria. Front Microbiol. 2021;12:1–8. doi: 10.3389/fmicb.2021.662907. PubMed DOI PMC

Mohapatra SS, Fioravanti A, Vandame P, Spriet C, Pini F, et al. Methylation-dependent transcriptional regulation of crescentin gene (creS) by GcrA in Caulobacter crescentus . Mol Microbiol. 2020;114:127–139. doi: 10.1111/mmi.14500. PubMed DOI

Samson JE, Magadán AH, Sabri M, Moineau S. Revenge of the phages: defeating bacterial defences. Nat Rev Microbiol. 2013;11:675–687. doi: 10.1038/nrmicro3096. PubMed DOI

Yin T, Cook D, Lawrence M. ggbio: an R package for extending the grammar of graphics for genomic data. Genome Biol. 2012;13:R77. doi: 10.1186/gb-2012-13-8-r77. PubMed DOI PMC

Toedling J, Skylar O, Sklyar O, Krueger T, Fischer JJ, et al. Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics. 2007;8:1–4. doi: 10.1186/1471-2105-8-221. PubMed DOI PMC

Elek A, Kuzman M, Vlahovicek K. CoRdon: codon usage analysis and prediction of gene expressivity. R package version 140. 2019

On the evolution of chromosomal regions with high gene strand bias in bacteria