Transposons to toxins: the provenance, architecture and diversification of a widespread class of eukaryotic effectors

Abstract

Enzymatic effectors targeting nucleic acids, proteins and other cellular components are the mainstay of conflicts across life forms. Using comparative genomics we identify a large class of eukaryotic proteins, which include effectors from oomycetes, fungi and other parasites. The majority of these proteins have a characteristic domain architecture with one of several N-terminal ‘Header’ domains, which are predicted to play a role in trafficking of these effectors, including a novel version of the Ubiquitin fold. The Headers are followed by one or more diverse C-terminal domains, such as restriction endonuclease (REase), protein kinase, HNH endonuclease, LK-nuclease (a RNase) and multiple distinct peptidase domains, which are predicted to carry their toxicity determinants. The most common types of these proteins appear to have originated from prokaryotic transposases (e.g. TN7 and Mu) and combine a CDC6/ORC1-STAND clade NTPase domain with a C-terminal REase domain. Other than the so-called Crinkler effectors of oomycetes and fungi, these effectors are encoded by other eukaryotic parasites such as trypanosomatids (the RHS proteins) and the rhizarian Plasmodiophora, and symbionts like Capsaspora. Remarkably, we also find these proteins in free-living eukaryotes, including several viridiplantae, fungi, amoebozoans and animals. These versions might either still be transposons or function in other poorly understood eukaryote-specific inter-organismal and inter-genomic conflicts. These include the Medea1 selfish element of Tribolium that spreads via post-zygotic killing. We present a unified mechanism for the recombination-dependent diversification and action of this widespread class of molecular weaponry deployed across diverse conflicts ranging from parasitic to free-living forms.

Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi

“…However, incubation of Bd zoospores with Tw tissue for 2 h showed an increased expression of CRN genes, whereas Bsal zoospores were associated with decreased expression, indicating that CRN genes are of interest in the early infection stage of Bd , but not Bsal ; the notable expansion of CRN-like genes in Bd suggests that they are of importance, however their function remains unknown. These data corroborate recent findings showing that the CRN-like family occur broadly though patchily throughout microbial eukaryotes as effectors in inter-organismal conflicts18.…”

Random mutagenesis screen shows that Phytophthora capsici CRN83_152‐mediated cell death is not required for its virulence function(s)

“…Recently, two CRN effectors have been shown to directly bind DNA to achieve their virulence functions (Ramirez‐Garcés et al ., ; Song et al ., ). In addition, the targeting of DNA‐related processes has been predicted to be a conserved feature of CRN effectors (Zhang et al ., ), making further investigation into the mechanisms involved in PcCRN83_152‐mediated chromatin re‐localization of upmost importance.…”

“…In the case of CRN effectors, an N‐terminal LXLFLAK motif has been shown to be required for CRN effector translocation (Schornack et al ., ). The LXLFLAX motif sits between strands 2 and 3 of a ubiquitin‐like domain which is believed to be important in CRN translocation processes, but does not appear to be present in all CRN N‐termini (Zhang et al ., ). Although detailed functional studies have provided great insights into RXLR protein function (Anderson et al ., ), the CRN protein family has thus far been understudied (Amaro et al ., ).…”

“…These results were further substantiated in experiments with transgenic P. capsici lines in which PcCRN83_152 expression was suppressed (silencing), showing reduced growth in both Arabidopsis and N. benthamiana leaves (Mafurah et al ., ). In contrast with the RXLR family, members of the CRN protein family can be found in a wide range of eukaryotic organisms (Zhang et al ., ). Virulence functions for CRN effectors from outside the Phytophthora genus have also been demonstrated.…”

“…Subsequent studies then led to the identification of additional family members in P. infestans and other Phytophthora species initially, followed by their discovery in distantly related organisms. These results have led to the suggestion that, collectively, the CRNs form an ancient protein family, emerging before the RXLR effectors (Amaro et al, 2017;Haas et al, 2009;Stam et al, 2013b;Zhang et al, 2016).…”