Evolutionary history exposes radical diversification among classes of interaction partners of the MLLE domain of plant poly(A)-binding proteins

Abstract

BackgroundPoly(A)-binding proteins (PABPs) are evolutionarily conserved proteins that have important functions in the regulation of translation and the control of mRNA stability in eukaryotes. Most PABPs encode a C-terminal domain known as the MLLE domain (previously PABC or CTC), which can mediate protein interactions. In earlier work we identified and predicted that four classes of MLLE-interacting proteins were present in Arabidopsis thaliana, which we named CID A, B, C, and D. These proteins encode transcription-activating domains (CID A), the Lsm and LsmAD domains of ataxin-2 (CID B), the CUE and small MutS-related domains (CID C), and two RNA recognition domains (CID D). We recently found that a novel class that lacks the LsmAD domain is present in CID B proteins.ResultsWe extended our analysis to other classes of CIDs present in the viridiplantae. We found that novel variants also evolved in classes CID A and CID C. A specific transcription factor domain is present in a distinct lineage in class A, and a variant that lacks at least two distinct domains was also identified in a divergent lineage in class C. We did not detect any variants in Class D CIDs. This class often consists of four to six highly conserved RNA-binding proteins, which suggests that major redundancy is present in this class.ConclusionsCIDs are likely to operate as components of posttranscriptional regulatory assemblies. The evident diversification of CIDs may be neutral or may be important for plant adaptation to the environment and for acquisition of specific traits during evolution. The fact that CIDs subclasses are maintained in early lineages suggest that a presumed interference between duplicates was resolved, and a defined function for each subclass was achieved.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0475-1) contains supplementary material, which is available to authorized users.

Investigating the effect of target of rapamycin kinase inhibition on the Chlamydomonas reinhardtii phosphoproteome: from known homologs to new targets

“…These include sites on a translation‐related protein (Cre17.g696250.t1.1) and RNA‐binding proteins (Cre10.g441200.t1.2, Cre10.g466450.t1.1, Cre16.g659150.t1.1, Cre16.g662702.t1.1 Cre17.g729150.t1.2). One of the most downmodulated proteins annotated as CTC‐interacting domain 4 (CID4, Cre01.g063997.t1.1), has been shown to have an important function in regulation of translation and mRNA stability in eukaryotes (Bravo et al ., ; Jiménez‐López et al ., ). CID4 had two sites, Ser441 (FC = 0.2 AZD8055 , FC = 0.14 TORIN1 ) and Ser439/Ser441/Ser446:NL (FC = 0.03 AZD8055 , FC = 0.05 TORIN1 ) with a large decrease in phosphorylation upon inhibitor treatment.…”

Phosphorylation and interactions associated with the control of theLeishmaniaPoly-A Binding Protein 1 (PABP1) function during translation initiation

“…The characterization of this interaction highlights even further the diversity observed in PABP interacting proteins which bind through the PAM2/MLLE interaction. This has been more recently discussed in plants, where the large number of PABP homologues is probably associated with multiple processes involved in different aspects of mRNA metabolism and which might have major impacts on regulation of gene expression and translation [34,70].…”

“…In mammals, the PABP linker region seems to be involved in the multimerization process where multiple PABP molecules associate with each other attached to the poly-A tail [30,31]. As for the C-terminal MLLE domain, it mediates the interaction of PABP with other polypeptides having a conserved peptide motif named PAM2 [32][33][34].…”

Ataxin-2: From RNA Control to Human Health and Disease

“…These are thought to be important, as the ATXN2 gene is evolutionarily conserved from yeast to RNA-binding domains mediate physical interactions between LSm proteins and their target RNAs [ 9 ]. In addition to these domains, ATXN2 contains conserved proline-rich domains as well as a C-terminal PAM2 domain, which mediates interactions with the poly(A)-binding protein (PABP1) [ 10 , 11 , 12 , 13 ]. ATXN2 functions mammals ( Figure 1 ).…”