title: Evolutionary history exposes radical diversification among classes of interaction partners of the MLLE domain of plant poly(A)-binding proteins.
abstract: BACKGROUND
  Poly(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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  CIDs 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.
authors.affiliation: Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Unidad Irapuato, Apartado Postal 629, Irapuato, Gto., 36821, Mexico.
authors.forename: Domingo
authors.initials: D
authors.lastname: Jiménez-López
authors.affiliation: Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Unidad Irapuato, Apartado Postal 629, Irapuato, Gto., 36821, Mexico.|Present address: Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
authors.forename: Jaime
authors.initials: J
authors.lastname: Bravo
authors.affiliation: Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Unidad Irapuato, Apartado Postal 629, Irapuato, Gto., 36821, Mexico. pguzman@ira.cinvestav.mx.
authors.forename: Plinio
authors.initials: P
authors.lastname: Guzmán
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D019143:Evolution, Molecular; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D010944:Plants / Q000145:classification* / Q000235:genetics*; D039102:Poly(A)-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D020871:RNA Stability; D057948:Viridiplantae / Q000235:genetics
chemical_list: D010940:Plant Proteins; D039102:Poly(A)-Binding Proteins