Abstract
Wolbachia is an obligate intracellular bacterium that has undergone extensive genomic streamlining in its arthropod and nematode hosts. Because the gene encoding the bacterial DNA recombination/repair protein RecA is not essential in Escherichia coli, abundant expression of this protein in a mosquito cell line persistently infected with Wolbachia strain wStri was unexpected. However, RecA’s role in the lytic cycle of bacteriophage lambda provides an explanation for retention of recA in strains known to encode lambda-like WO prophages. To examine DNA recombination/repair capacities in Wolbachia, a systematic examination of RecA and related proteins in complete or nearly complete Wolbachia genomes from supergroups A, B, C, D, E, F, J and S was undertaken. Genes encoding proteins including RecA, RecF, RecO, RecR, RecG and Holliday junction resolvases RuvA, RuvB and RuvC are uniformly absent from Wolbachia in supergroup C and have reduced representation in supergroups D and J, suggesting that recombination and repair activities are compromised in nematode-associated Wolbachia, relative to strains that infect arthropods. An exception is filarial Wolbachia strain wMhie, assigned to supergroup F, which occurs in a nematode host from a poikilothermic lizard. Genes encoding LexA and error-prone polymerases are absent from all Wolbachia genomes, suggesting that the SOS functions induced by RecA-mediated activation of LexA do not occur, despite retention of genes encoding a few proteins that respond to LexA induction in E. coli. Three independent E. coli accessions converge on a single Wolbachia UvrD helicase, which interacts with mismatch repair proteins MutS and MutL, encoded in nearly all Wolbachia genomes. With the exception of MutL, which has been mapped to a eukaryotic association module in Phage WO, proteins involved in recombination/repair are uniformly represented by single protein annotations. Putative phage-encoded MutL proteins are restricted to Wolbachia supergroups A and B and show higher amino acid identity than chromosomally encoded MutL orthologs. This analysis underscores differences between nematode and arthropod-associated Wolbachia and describes aspects of DNA metabolism that potentially impact development of procedures for transformation and genetic manipulation of Wolbachia.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
There are no large-scale data.
References
Anisimova M, Gascuel O (2006) Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst Biol 55(4):539–552. https://doi.org/10.1080/10635150600755453
Badawi M, Giraud I, Vavre F, Greve P, Cordaux R (2014) Signs of neutralization in a redundant gene involved in homologous recombination in Wolbachia endosymbionts. Genome Biol Evol 6(10):2654–2664. https://doi.org/10.1093/gbe/evu207
Baldridge GD, Witthuhn BA, Higgins L, Markowski TW, Fallon AM (2014) Proteomic analysis of a robust Wolbachia infection in an Aedes albopictus cell line. Mol Microbiol 94:537–556. https://doi.org/10.1111/mmi.1768
Baldridge GD, Markowski TW, Witthuhn BA, Higgins LA, Baldridge AS, Fallon AM (2016) The Wolbachia WO bacteriophage proteome in the Aedes albopictus C/wStr1 cell line: evidence for lytic activity? In Vitro Cell Dev Biol Anim 5:77–88
Ballard JWO (2003) Sequential evolution of a symbiont inferred from the Host: wolbachia and drosophila simulans. Molec Biol Evol 21(3):428–442
Bordenstein SR, Bordenstein SR (2016) Eukaryotic association module in phage WO genomes from Wolbachia. Nature Communications 7(1)
Brown AMV, Wasala SK, Howe DK, Peetz AB, Zasada IA, Denver DR (2016) Genomic evidence for plant-parasitic nematodes as the earliest Wolbachia hosts. Sci Rep 6:34955. https://doi.org/10.1038/srep34955
Comandatore F, Cordaux R, Bandi C, Blaxter M, Darby A, Makepeace BL, Montagna M, Sassera D (2015) Supergroup C. Wolbachia, mutualist symbionts of filarial nematodes, have a distinct genome structure. Open Bio 5(12):150099
Cox MM (2007) Regulation of bacterial RecA protein. Crit Rev Biochem Mol Biol 42:41–63. https://doi.org/10.1080/10409230701260258
Csonka LN, Clark AJ (1979) Deletions generated by the transposon Tn10 in the srl recA region of the Escherichia coli K-12 chromosome. Genetics 93:321–343
De Henestrosa ARF, Ogi T, Aoyagi S, Chafin D, Hayes JJ, Ohmori H, Woodgate R (2000) Identification of additional genes belonging to the LexA regulon in Escherichia coli. Mol Microbiol 35:1560–1572
Del Val E, Nasser W, Abaibou H, Reverchon S (2019) RecA and DNA recombination: a review of molecular mechanisms. Biochem Soc Trans 47:1511–1531. https://doi.org/10.1042/BST20190558
Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 36 (Web Server issue): W465–W469. https://doi.org/10.1093/nar/gkn180.36
Dereeper A, Audic S, Claverie JM, Blanc G (2010) BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BMC Evol Biol 10:8. https://doi.org/10.1186/1471-2148-10-8
Dillingham MS, Kowalczykowski SC (2008) RecBCD enzyme and the repair of double-stranded DNA breaks. Micro Mol Biol Rev 72:642–671. https://doi.org/10.1128/MMBR.00020-08
Driscoll TP, Verhoeve VI, Gillespie JJ, Johnston JS, Guillotte ML, Rennoll-Bankert KE, Rahman MS, Hagen D, Elsik CG, Macaluso KR, Azad AF (2020) A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity. BMC Biol 18:70. https://doi.org/10.1186/s12915-020-00802-7
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797
Ellegaard KM, Klasson L, Naslund K, Bourtzis K, Andersson SGE (2013) Comparative genomics of Wolbachia and the bacterial species concept. PLoS Genet 9(4):e1003381. https://doi.org/10.1371/journal.pgen.1003381
Fallon AM (2020) Computational evidence for antitoxins associated with RelE/ParE, RatA, Fic, and AbiEii-family toxins in Wolbachia genomes. Mol Genet Genomics 295:891–909. https://doi.org/10.1007/s00438-020-01662-0
Fallon AM, Baldridge GD, Higgins LA, Witthuhn BA (2013) Wolbachia from the planthopper Laodelphax striatellus establishes a robust, persistent, streptomycin-resistant infection in clonal mosquito cells. In Vitro Cell Dev Biol Anim 49:66–73
Fenn K, Conlon C, Jones M, Quail MA, Holroyd NE, Parkhill BM (2006) Phylogenetic relationships of the Wolbachia of nematodes and arthropods. PLoS Pathog 2(9):e94. https://doi.org/10.1371/journal.ppat.0020094
Fornelos N, Browning DF, Butala M (2016) The use and abuse of LexA by mobile genetic elements. Trends Microbiol 24(5):391–401. https://doi.org/10.1016/j.tim.2016.02.009
Fraser JE, De Bruyne SL, Iturbe-Ormaetxe I, Stepnell J, Burns RL, Flores HA, O’Neill SL (2017) Novel Wolbachia-transinfected Aedes aegypti mosquitoes possess diverse fitness and vector competence phenotypes. PLoS Pathog 13(12):e1006751. https://doi.org/10.1371/journal.ppat.1006751
Gerth M, Gansauge MT, Weigert A, Bleidorn C (2014) Phylogenomic analyses uncover origin and spread of the Wolbachia pandemic. Nat Commun. 5(1):5117. https://doi.org/10.1038/ncomms6117
Ghilarov D, Serebryakova M, Stevenson CEM, Heamshaw SJ, Volkov DS, Maxwell A, Lawson DM, Severinov K (2017) The origins of specificity in the microcin-processing protease TldD/E. Structure 25:1549–1561. https://doi.org/10.1016/j.str.2017.08.006
Graber L, Fallon AM (2019) Tetracycline reduces feeding and reproduction of the parthenogenetic springtail Folsomia candida. Symbiosis 77:257–264. https://doi.org/10.1007/s13199-018-00593-0
Hastings PJ, Hersh MN, Thornton PC, Fonville NC, Slack A, Frisch RL, Ray MP, Harris RS, Leal SM, Rosenberg SM (2010) Competition of Escherichia coli DNA polymerases I, II and III with DNA Pol IV in stressed cells. PLoS ONE 5(5):e10862. https://doi.org/10.1371/journal.pone.0010862
Hegde SP, Qin M-H, Li X-H, Atkinson MA, Clark A, Rajagopalan M, Madiraju MVVS (1996) Interactions of RecF protein with RecO, RecR, and single-stranded DNA binding proteins reveal roles for the RecF–RecO–RecR complex in DNA repair and recombination. Proc Natl Acad Sci USA 93:14468–14473. https://doi.org/10.1073/pnas.93.25.14468
Hellemans S, Kaczmarek N, Marynowska M, Calusinska M, Roisin Y, Fournier D (2019) Bacteriome-associated Wolbachiaof the parthenogenetic termite Cavitermes tuberosus. FEMS Micro Ecol 95:fiy235. https://doi.org/10.1093/femsec/fiy235
Hoffmann AA, Ross PA, Rasic G (2015) Wolbachia strains for disease control: ecological and evolutionary considerations. Evol Appl 8:751–768. https://doi.org/10.1111/eva.12286
Ihara M, Oda Y, Yamamoto K (1985) Convenient construction of strains useful for transducing recA mutations with bacteriophage P1. FEMS Micro Lett 30:33–35
Johnston KL, Ford L, Umareddy I, Townson S, Specht S, Pfarr K, Hoerauf A, Altmeyer R, Taylor MJ (2014) Repurposing of approved drugs from the human pharmacopoeia to target Wolbachia endosymbionts of onchocerciasis and lymphatic filariasis. Int J Parasitol Drugs Drug Resist 4:278–286. https://doi.org/10.1016/j.ijpddr.2014.09.001
Kampfraath AA, Klasson L, Anvar SY, Vossen RHAM, Roelofs D, Kraaijeveld K, Ellers J (2019) Genome expansion of an obligate parthenogenesis associated Wolbachia poses an exception to the symbiont reduction model. BMC Genomics 20:106. https://doi.org/10.1186/s12864-019-5492-9
Karoui ME, Biaudet V, Schbath S, Gruss A (1999) Characteristics of Chi distribution on different bacterial genomes. Res Microbiol 150:579–587
Kent BN, Bordenstein SR (2010) Phage WO of Wolbachia: lambda of the endosymbiont world. Trends Microbiol 18(4):173–181. https://doi.org/10.1016/j.tim.2009.12.011
Kent BN, Funkhouser LJ, Setia S, Bordenstein SR (2011) Evolutionary genetics of a temperate bacteriophage in an obligate intracellular bacteria (Wolbachia). PLoS One 6(9):e24984. https://doi.org/10.1371/journal.pone.0024984
Kowalczykowski SC (1991) Biochemical and biological function of Escherichia coli RecA protein: behavior of mutant RecA proteins. Biochimie 73:289–304
Kowalczykowski SC, Dixon DA, Eggleston AK, Lauder SD, Rehrauer WM (1994) Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev 58:401–465
Kreuzer KN (2013) DNA damage responses in procaryotes: Regulating gene expression, modulating growth patterns, and manipulating replication forks. Cold Spring Harb Perspect Biol 5(11):a012674
Lee EH, Kornberg A (1991) Replication deficiencies in priA mutants of Escherichia coli lacking the primosomal replication N’ protein. Proc Natl Acad Sci USA 88:3029–3032
Lee CM, Wang G, Pertsinidis A, Marians KJ (2019) Topoisomerase III acts at the replication fork to remove precatenanes. J Bacteriol 201(7):e00563-e618. https://doi.org/10.1128/JB.00563-18
Lefoulon E, Clark T, Borveto F, Perriat-Sanguinet M, Moulia C, Slatko BE, Gavote L (2020a) Pseudoscorpion Wolbachia symbionts: diversity and evidence for a new supergroup S. BMC Microbiol 20:188. https://doi.org/10.1186/s12866-020-01863-y
Lefoulon E, Clark T, Guerrero R, Canizales I, Cardenas-Callirgos JM, Junker K, Vallarino-Lhermitte N, Makepeace BL, Darby AC, Foster JM, Martin C, Slatko, BE (2020b) Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm. Microb Genom 6(12). https://doi.org/10.1101/2020.06.18.160200
Little JW (1991) Mechanism of specific LexA cleavage and the role of RecA coprotease. Biochimie 73:411–422
Lovett ST, Kolodner RD (1989) Identification and purification of a single-stranded-DNA-specific exonuclease encoded by the recJ gene of Escherichia coli. Proc Natl Acad Sci USA 86:2627–2631
Marceau AH, Bahng S, Massoni SC, George NP, Sandler SJ, Marians KJ, Keck JL (2011) Structure of the SSB-DNA polymerase III interface and its role in DNA replication. EMBO J 30:4236–4247
Marsic N, Salaj-Smic E, Stojiljkovic I, Trgovcevic Z (1991) Interaction of lambda Gam protein with the RecD subunit of RecBCD enzyme increases radioresistance of the wild type Escherichia coli. Biochimie 73:501–503. https://doi.org/10.1016/0300-9084(91)90119-L
Maslowska KH, Makiela-Dzbenska K, Fijalkowska IJ (2019) The SOS system: a complex and tightly regulated response to DNA damage. Environ Mol Mutagen 60:368–384. https://doi.org/10.1002/em22267
Meeske AJ, Jia N, Cassel AK, Kozlova A, Liao J, Wiedmann M, Patel DJ, Marraffini LA (2020) A phage encoded anti-CRISPR enables complete evasion of typeVI-A CRISPR-cas immunity. Science 369:54–59. https://doi.org/10.1126/Science.abb6151
Mercot H, Charlat S (2004) Wolbachia infections in Drosophila melanogaster and D. simulans: polymorphism and levels of cytoplasmic incompatibility. Genetica 120(1–3):51–59
Moore T, McGlynn P, Ngo HP, Sharples GJ, Lloyd RG (2003) The RdgC protein of Escherichia coli binds DNA and counters a toxic effect of RecFOR in strains lacking the replication restart protein PriA. EMBO J 22:735–745
Morimatsu K, Kowalczykowski SC (2003) RecFOR proteins load RecA protein on to gapped DNA to accelerate DNA strand exchange: a universal step of recombinational repair. Mol Cell 11:1337–1347
Murphy KC (2012) Phage recombinases and their applications. Adv Virus Res 83:367–414. https://doi.org/10.1016/B978-0-12-394438-2.00008-6
Nakamura Y, Yukuhiro F, Matsumura M, Noda H (2012) Cytoplasmic incompatibility involving Cardinium and Wolbachia in the white-backed planthopper Sogatella furcifera (Hemiptera: Delphaciadae). Appl Entomol Zool 47:273–283. https://doi.org/10.1007/s13355-012-0120-z
Noda H, Koizumi Y, Zhang Q, Deng K (2001) Infection density of Wolbachia and incompatibility level in two planthopper species, Laodelphax striatellus and Sogatella furcifera. Insect Biochem Mol Biol 31:727–737
Noda H, Miyoshi T, Koizumi Y (2002) In vitro cultivation of Wolbachia in insect and mammalian cell lines. In Vitro Cell Dev Biol Anim 38:423–427
Nurse P, DiGate R, Zavitz KH, Marians KJ (1990) Molecular cloning and DNA sequence analysis of Escherichia coli priA, the gene encoding the primosomal protein replication factor Y. Proc Natl Acad Sci USA 87:4615–4619. https://doi.org/10.1073/pnas.87.12.4615
Ordabayev YA, Nguyen B, Koslov AG, Jia H, Lohman TM (2019) UvrD helicase activation by MutL involves rotation of its 2B domain. Proc Natl Acad Sci USA 116:16320–16325. https://doi.org/10.1073/pnas.1905513166
Reece RJ, Maxwell A (1991) DNA gyrase: structure and function. Crit Rev Biochem Mol Biol 26(3–4):335–375. https://doi.org/10.3109/10409239109114072
Refardt D, Rainey PB (2010) Tuning a genetic switch: experimental evolution and natural variation of prophage induction. Evolution 64(4):1086–1097. https://doi.org/10.1111/j.1558-5646.2009.00882.x
Roberts JW, Roberts CW, Craig NL (1978) Escherichia coli recA gene product inactivates phage l repressor. Proc Natl Acad Sci USA 75:4714–4718
Sandler SJ, Marians KJ (2000) Role of PriA in replication fork reactivation in Escherichia coli. J Bacteriol 182:9–13. https://doi.org/10.1128/JB.182.1.9-13.2000
Sexton JZ, Wigle TJ, He Q, Hughes MA, Smith GR, Singleton SF, Williams AL, Yeh L-A (2010) Novel inhibitors of E. coli RecA ATPase activity. Curr Chem Genom 4:34–42
Shaver AC, Sniegowski PD (2003) Spontaneously arising MutL mutants in evolving Escherichia coli populations are the result of changes in repeat length. J Bacteriol 185:6076–6082. https://doi.org/10.1128/JB.185.20.6076-6082.2003
Slupska MM, Chiang J-H, Luther WM, Stewart JL, Amii L, Conrad A, Miller JH (2000) Genes involved in the determination of the rate of inversions at short inverted repeats. Genes Cells 5:425–437
Stockum A, Lloyd RG, Rudolph CJ (2012) On the viability of Escherichia coli cells lacking DNA topoisomerase I. BMC Microbiol 12:26. https://doi.org/10.1186/1471-2180-12-26
Sun Z, Hashemi M, Warren G, Bianco PR, Lyubshenko YL (2018) Dynamics of the interaction of RecG protein with stalled replication forks. Biochemistry 57:1967–1976. https://doi.org/10.1021/acs.biochem.7b01235
Taylor MJ, Bandi C, Hoerauf A (2005) Wolbachia bacterial endosymbionts of filarial nematodes. Adv Parasitol 60:245–284
Taylor AF, Amundsen SK, Smith GR (2016) Unexpected DNA-context-dependence identifies a new determinant of Chi recombination hotspots. Nucl Acids Res 44:8216–8228. https://doi.org/10.1093/nar/gkw541
Tham K-C, Hermans N, Winterwerp HHK, Cox MM, Wyman C, Kanaar R, Lebbink JHG (2013) Mismatch repair inhibits homeologous recombination via coordinated directional unwinding of trapped DNA structures. Mol Cell 51:326–337. https://doi.org/10.1016/j.molcel.2013.07.008
Verhoeven EE, van Kesteren M, Moolenaar GF, Visse R, Goosen N (2000) Catalytic sites for 3’ and 5’ incision of Escherichia coli nucleotide excision repair are both located in UvrC*. Biol Chem 275(7):5120–5123
Verhoeven EE, Wyman C, Moolenaar GF, Goosen N (2002) The presence of two UvrB subunits in the UvrA complex ensures damage detection in both DNA strands. EMBO J 21:4196–4205
Wang L, Lutkenhaus J (1998) FtsK is an essential cell division protein that is localized to the septum and induced as part of the SOS response. Mol Microbiol 29(3):731–740. https://doi.org/10.1046/j.1365-2958.1998.00958x
Webb BL, Cox MM, Inman RB (1997) Recombinational DNA repair: the RecF and RecR proteins limit the extension of RecA filaments beyond single-strand DNA gaps. Cell 91:347–356
Wegrzyn G, Licznerska K, Wegrzyn A (2012) Phage lambda—new insights into regulatory circuits. Adv Virus Res 82:155. https://doi.org/10.1016/B978-0-12-394621-8.00016-9
Werren JH, Baldo L, Clark ME (2008) Wolbachia: master manipulators of invertebrate biology. Nat Rev Microbiol 6(10):741–751. https://doi.org/10.1038/nrmicro1969
Windgassen TA, Leroux M, Satyshur KA, Sandler SJ, Keck JL (2018) Structure-specific DNA replication-fork recognition directs helicase and replication restart activities of the PriA helicase. Proc Natl Acad Sci USA 115:E9075–E9084
Worth L Jr, Clark S, Radman M, Modrich P (1994) Mismatch repair proteins MutS and MutL inhibit RecA-catalyzed strand transfer between diverged DNAs. Proc Natl Acad Sci USA 91:3238–3241
Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C, Ahmadinejad N, Wiegand C, Madupu R, Beanan MJ, Brinkac LM, Daugherty SC, Durkin AS, Kolonay JF, Nelson WC, Mohamoud Y, Lee P, Berry K, Young MB, Utterback T, Weidman J, Nierman WC, Paulsen IT, Nelson KE, Tettelin H, O’Neill SL, Eisen JA (2004) Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol 2:e69. https://doi.org/10.1371/journal.pbio.0020069
Zahradka D, Zahradka K, Petranovic M, Dermic D, Brcic-Kostic K (2002) The RuvABC resolvase is indispensable for recombinational repair in sbcB15 mutants of Escherichia coli. J Bacteriol 184:4141–4147. https://doi.org/10.1128/JB.184.15.4141-4147.2002
Zhou W, Rousset F, O’Neill S (1998) Phylogeny and PCR-based classification of Wolbachia strains using wsp gene sequences. Proc Biol Sci 265:509–515. https://doi.org/10.1098/rspb.1998.0324
Acknowledgement
This work was supported by the University of Minnesota Agricultural Experiment Station, St. Paul, MN.
Funding
This work was supported by the University of Minnesota Agricultural Experiment Station, St. Paul, MN, which provided salary to the author. There were no external grants.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The author declares that she has no conflicts of interest.
Ethical approval
This article does not contain any studies with human participants or animals performed by the author.
Additional information
Communicated by Stefan Hohmann.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Below is the link to the electronic supplementary material.
Below is the link to the electronic supplementary material.
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Fallon, A.M. DNA recombination and repair in Wolbachia: RecA and related proteins. Mol Genet Genomics 296, 437–456 (2021). https://doi.org/10.1007/s00438-020-01760-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00438-020-01760-z