(C) PLOS One
This story was originally published by PLOS One and is unaltered.
. . . . . . . . . .



Intra-lineage microevolution of Wolbachia leads to the emergence of new cytoplasmic incompatibility patterns [1]

['Alice Namias', 'Isem', 'Université De Montpellier', 'Cnrs', 'Ird', 'Ephe', 'Montpellier', 'Annais Ngaku', 'Patrick Makoundou', 'Sandra Unal']

Date: 2024-02

Mosquitoes of the Culex pipiens complex are worldwide vectors of arbovirus, filarial nematodes, and avian malaria agents. In these hosts, the endosymbiotic bacteria Wolbachia induce cytoplasmic incompatibility (CI), i.e., reduced embryo viability in so-called incompatible crosses. Wolbachia infecting Culex pipiens (wPip) cause CI patterns of unparalleled complexity, associated with the amplification and diversification of cidA and cidB genes, with up to 6 different gene copies described in a single wPip genome. In wPip, CI is thought to function as a toxin-antidote (TA) system where compatibility relies on having the right antidotes (CidA) in the female to bind and neutralize the male’s toxins (CidB). By repeating crosses between Culex isofemale lines over a 17 years period, we documented the emergence of a new compatibility type in real time and linked it to a change in cid genes genotype. We showed that loss of specific cidA gene copies in some wPip genomes results in a loss of compatibility. More precisely, we found that this lost antidote had an original sequence at its binding interface, corresponding to the original sequence at the toxin’s binding interface. We showed that these original cid variants are recombinant, supporting a role for recombination rather than point mutations in rapid CI evolution. These results strongly support the TA model in natura, adding to all previous data acquired with transgenes expression.

Funding: This work was funded by the French MUSE project from the Université de Montpellier (reference ANR-16-IDEX-0006)(granted to MW). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Copyright: © 2024 Namias et al. This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Introduction

Wolbachia are maternally transmitted endosymbiotic bacteria that infect up to 50% of arthropod species [1–3]. These bacteria are well known for their wide range of reproductive manipulations in arthropods. Their most common manipulation is cytoplasmic incompatibility (CI), i.e., in its simplest form, a reduction in embryo hatching rates (HRs) in crosses between infected males and uninfected females. CI results from a Wolbachia-induced modification that perturbs the first division of embryos, which infected females are able to rescue [4,5]. CI is thus formalized in a modification-rescue framework.

CI can also occur between 2 infected individuals if they are infected with genetically different and incompatible Wolbachia strains. In Culex pipiens mosquitoes, in which Wolbachia infection is fixed [6], the Wolbachia infecting Culex pipiens (wPip) strains are responsible for a unique (to date) complexity of CI patterns based on multiple uni- and bidirectional incompatibilities [7–10].

In 2013, putative CI genes were identified using a combination of proteomic and genetic approaches [11]. Then, in 2017, two functional studies based on transgenic expression confirmed that these genes were key for CI, naming them cif for “CI factors” [12,13]. The cif genes were described in cifA-cifB tandems, playing a central role in CI, although the precise molecular mechanisms of CI are still to be determined. Although other models exist [14,15], in a growing range of Wolbachia, including wPip, CI is thought to function as a toxin-antidote (TA) model [4,16–22]. In this model, a cross will be compatible if binding occurs between the cidA(s) (antidotes) present in the egg and the cidB(s) (toxins) present in the sperm, neutralizing cidB(s) toxicity [16,18,23,24].

Sequencing of Wolbachia genomes from different host species revealed several different pairs of cif genes, with distinct functional domains that categorized them into 5 clades [25–27]. All wPip genomes sequenced so far have cif genes from 2 of these clades: clade I cif, in which the cifB gene has a deubiquitinase domain (the tandem is thus called cid, with d denoting the deubiquitinase domain), and clade IV cif, in which cifB bears a nuclease domain (thus called cin) [12,13]. Here, we use this functional-based nomenclature [28].

Before the discovery of the cif genes, models based on Culex-crossing experiments predicted that several factors or pairs of genes were required to encode the complex crossing patterns induced by wPip [9,29]. Studies on cif (cid and cin) genes present in wPip genomes highlighted that cin genes were always monomorphic, whereas cid genes were amplified and diversified in all sequenced wPip genomes [21], with up to 6 different copies of each gene in a single Wolbachia wPip genome. The different cidA/cidB copies in a given wPip genome are known as “variants” and the full set of all copies constitutes the “cid repertoire.” In wPip genomes, the polymorphism of both cidA and cidB genes are located in 2 specific regions, which were named “upstream” and “downstream” regions and predicted to be involved in CidA-CidB interactions [21]. This has been confirmed by the recently obtained structure of a CidA-CidB cocrystal: out of the 3 interaction regions identified, 2 perfectly match the previously identified upstream and downstream regions for both CidA and CidB [23,24]. In addition to showing that CidA and CidB from wPip bind together, this recent study also showed that the different CidA-CidB variants have different binding properties, thus lending further support to the TA model for explaining wPip CI complexity [24].

Evolutionary changes of Wolbachia genomes on long time scales have been widely documented in different host species. The comparison of cif genes in Wolbachia strains from different arthropod hosts showed that they are quite divergent, and highly subject to lateral gene transfers [30,31] so that the congruence between Wolbachia and cif phylogenies is totally disrupted [25,26]. Such lateral transfers may be phage-linked, as cif genes are located in WO prophage regions [13,25], with lateral transfers of genes in prophage WO regions being previously documented [32–35]. Transposon-dependent transfers of cif genes have also been described [30]. By contrast, although the ability of Wolbachia to rapidly adapt to new environmental conditions has been suggested [36], very few studies have explored the short-term evolution of Wolbachia. To our knowledge, the only studies linking rapid changes in phenotypes (in a few host generations) to underlying genomic variations in Wolbachia were reported for the “Octomom region” in wMel and wMelPop, showing that variations in the amplification level of this region were responsible for variations in both Wolbachia virulence and antiviral protection conferred by wMel [37–39].

CI patterns in Culex were previously shown to change over a few host generations [40]. Yet, these changes were described before the discovery of cif genes. Here, we observed a change in the CI pattern between 2 isofemale lines kept in our laboratory since 2005: Slab (wPip III) and Istanbul (Ist, wPip IV) [10]. While crosses between Slab females and Ist males were compatible from 2005 to 2017 [10,41], we observed fully incompatible crosses for the first time in 2021 (the reverse cross remaining incompatible). No changes in patterns were observed in the reverse cross (Slab males and Ist females), fully incompatible since 2005. This shift in CI patterns presented an opportunity to study the underlying genetic basis of CI evolution in laboratory-controlled isofemale lines.

The emergence of a new CI phenotype may have resulted from (i) contamination; (ii) the acquisition of a new toxin in some Ist Wolbachia; or (iii) the loss of antidotes in some Slab Wolbachia. We took advantage of a recent methodological development that enables the rapid and extensive acquisition of cidA and cidB repertoires using Nanopore Technologies sequencing [42] to address these 3 hypotheses. We were able to rule out the contamination hypothesis and show that no less than 3 distinct Wolbachia sublineages with different cidA repertoires evolved and now coexist in the Slab isofemale line (but do not appear to coinfect the same individuals). We also found, in accordance with TA model, that the loss of cidA variants (i.e., antidotes) in Slab females perfectly matches variations in their rescuing ability. The cidA variant whose presence/absence explains the change in compatibility has original amino acid combinations at its interaction interface with CidB, probably resulting from a recombination.

[END]
---
[1] Url: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002493

Published and (C) by PLOS One
Content appears here under this condition or license: Creative Commons - Attribution BY 4.0.

via Magical.Fish Gopher News Feeds:
gopher://magical.fish/1/feeds/news/plosone/

You are viewing proxied material from magical.fish. The copyright of proxied material belongs to its original authors. Any comments or complaints in relation to proxied material should be directed to the original authors of the content concerned. Please see the disclaimer for more details.