The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Oomycete secretory protein processing motif permissive variant
Functional site description:
Oomycetes are fungus-like organisms that are not true fungi but are often susceptible to many fungicides and plants. Some are free living but many species are parasitic and often invade the host cell and modulate the regulation of the host immune system and suppress their defence mechanisms, resulting in a modified host physiology. The RxLR motif is found in secreted proteins which can be cleaved at the site and was shown to play a role in targeting the host cell (Dou,2008), while RxLR motif-containing proteins were associated with functions perturbing host cell processes.
ELM Description:
Oomycete effector proteins localizing into the host cell cytoplasm often contain an RxLR motif after their signal peptide(Dou,2008). The so-called RxLR effectors share a number of structural features and have modular architectures: an N-terminal signal peptide, followed by the RxLR motif and then often (but not always) associated with a downstream dEER sequence in a disordered region. The C-terminal region carries characteristic structural segments (termed as W, Y, and L) that are part of an alpha helical folded domain (Ye,2015). Considering the first part of the RxLR dEER dipartite motif, in oomycetes the 3rd and 4th positions seem to be the most conserved (Leu-Arg), while some level of amino acid substitution is allowed at the 2nd position (typically Phe-Gln-Ser-Leu). In most of the cases 1st position is Arg, with 2 outlier cases where there is no Arg, however a Lys residue is present at the -1st position. It was proposed that the RxLR motif gets cleaved before secretion (Wawra,2017), however, there is no information on which enzyme is responsible for the processing, therefore it is hard to find a molecular explanation for the conserved and less conserved positions. Even less information is known about dEER, but it appears in most of the RxLR motif-containing proteins: two acidic residues followed by a positively charged Arg or Lys, or in some instances three acidic residues.
For searching the stricter version of the motif, which includes the downstream dEER motif, SLiMSearch (Krystkowiak,2017) could be used with the following regular expression: ((R)|(K.)).LR.{1,40}(([DE][DE][RK])|(D[DE][DE]))
Pattern: ((R)|(K.)).LR
Pattern Probability: 0.0005828
Present in taxon: Oomycetes
o See 5 Instances for TRG_Oom_RxLR_1
o Abstract
Oomycetes belong to Stramenopiles within the SAR supergroup, and they include a diverse range of eukaryotic microorganisms, including obligate parasites such as Phytophthora infestans, the world’s most economically destructive agricultural pathogen, responsible for the Irish potato blight in the 1870s, and still causing billions of euros loss yearly just in the EU. Phytophthora species are filamentous and spore-forming eukaryotic microorganisms, belonging to the class Oomycota; fungus-like organisms that are not true fungi, but are susceptible to many fungicides. It is an obligate parasite, adapted for infecting plants of the Solanaceae family, including potato, tomato, aubergine, and chili peppers (Potato late blight and tuber blight).

The conserved Arg-X-Leu-Arg (RxLR) sequence motif was shown to play an essential role in transporting the secreted pathogen proteins across the plant membrane (Dou,2008). Interestingly, the processing of the motif shows similarities to the PEXEL motif in Plasmodium falciparum. Both PEXEL and RxLR motif containing proteins have a preceding signal peptide and they get N-terminally acetylated after cleavage. However, while the PEXEL motif is partially retained in P. falciparum, the RxLR version seems to be completely cleaved in P. infestans (Wawra,2017). In AVR3a (D0NPN8) the acetylation occurs right after the RxLR motif is cleaved at Lys-48, the first amino acid downstream of the RxLR(Wawra,2017). It was proposed that fungal RxLR motif enables binding the phospholipid, phosphatidylinositol-3-phosphate (PI3P) and pathogen entry might involve lipid raft-mediated endocytosis. As PI3P is abundant at the plant cell surface, it may mediate entry of some effectors to the host cell cytoplasm (Kale,2010). This observation was challenged in general as this mechanism could not be reproduced(Wawra,2012) at least not in the case of AVR3a (D0NPN8). Considering all evidence, the RxLR motif is involved in secretion rather than working as an uptake motif; however, the exact mechanism of action is still elusive.

RxLR dEER motif containing proteins were associated with functions perturbing host cell processes: Avh241 (E0W4Y2) localizes to the plasma membrane and induces cell death (Yu,2012); PexRD2 (G3KFL3) interacts with MAPKKKε, perturbs the signaling pathway and blocks cell death (King,2014). The AIM motif of the effector protein PexRD54 (D0NBE6) binds to ATG8 and perturbs host-selective autophagy (Maqbool,2016). AVRblb2 (D0P1A8) is also an RxLR motif containing protein without a recognizable downstream dEER motif, that prevents the secretion of C14 protease to the haustorial interface (Bozkurt,2011).

Notably, RxLR-like segments with similar functions seem to be present in more distant organisms too, such as the pathogenic fungi Puccinia striiformis (Gu,2011) (KRLT) and Melampsora lini (Rafiqi,2010) (KFLK, RFYR). However, slight changes in the sequence make it hard to unambiguously correlate these motifs with the Oomycete version of the motif.

The RxLR motif is reminiscent of the metazoan golgi-based furin processing motif R.[RK]R (see entry CLV_PCSK_FUR_1).
o 4 selected references:

o 9 GO-Terms:

o 5 Instances for TRG_Oom_RxLR_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
51 55 DPVRHDTKQLLRTSDTAVTK TP 3 Pseudoperonospora cubensis
E2DWQ7 Avr3a
44 47 YIHDSAGRRLLRKNEENEET TP 7 Phytophthora infestans (Potato late blight agent)
E0W4Q8 Avh
51 55 ASEDITVKSSLRYGDALAAD TP 3 Phytophthora sojae
E0W547 Avh5
43 46 VQTVTRSRRFLRTADTDIVY TP 4 Phytophthora sojae
50 53 TVQDDNYDRQLRGFYATENT TP 4 Phytophthora infestans T30-4
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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