Identification and phylogenetic analysis of RNA binding domain abundant in apicomplexans or RAP proteins

The RNA binding domain abundant in apicomplexans (RAP) is a protein domain identified in a diverse group of proteins, called RAP proteins, many of which have been shown to be involved in RNA binding. To understand the expansion and potential function of the RAP proteins, we conducted a hidden Markov model based screen among the proteomes of 54 eukaryotes, 17 bacteria and 12 archaea. We demonstrated that the domain is present in closely and distantly related organisms with particular expansions in Alveolata and Chlorophyta, and are not unique to Apicomplexa as previously believed. All RAP proteins identified can be decomposed into two parts. In the N-terminal region, the presence of variable helical repeats seems to participate in the specific targeting of diverse RNAs, while the RAP domain is mostly identified in the C-terminal region and is highly conserved across the different phylogenetic groups studied. Several conserved residues defining the signature motif could be crucial to ensure the function(s) of the RAP proteins. Modelling of RAP domains in apicomplexan parasites confirmed an ⍺/β structure of a restriction endonuclease-like fold. The phylogenetic trees generated from multiple alignment of RAP domains and full-length proteins from various distantly related eukaryotes indicated a complex evolutionary history of this family. We further discuss these results to assess the potential function of this protein family in apicomplexan parasites.

Download Full-text

Gene overlap results in a viral protein having an RNA binding domain and a major coat protein domain

Cell ◽

10.1016/0092-8674(88)90225-5 ◽

1988 ◽

Vol 55 (4) ◽

pp. 663-671 ◽

Cited By ~ 58

Author(s):

Tsutomu Fujimura ◽

Reed B. Wickner

Keyword(s):

Coat Protein ◽

Viral Protein ◽

Rna Binding ◽

Binding Domain ◽

Protein Domain ◽

Major Coat Protein ◽

Rna Binding Domain ◽

Gene Overlap

Download Full-text

Characterization of Functional Domains of Equine Infectious Anemia Virus Rev Suggests a Bipartite RNA-Binding Domain

Journal of Virology ◽

10.1128/jvi.80.8.3844-3852.2006 ◽

2006 ◽

Vol 80 (8) ◽

pp. 3844-3852 ◽

Cited By ~ 16

Author(s):

Jae-Hyung Lee ◽

Sean C. Murphy ◽

Michael Belshan ◽

Wendy O. Sparks ◽

Yvonne Wannemuehler ◽

...

Keyword(s):

Genetic Variation ◽

Central Region ◽

Equine Infectious Anemia Virus ◽

Rna Binding ◽

Binding Domain ◽

Terminal Region ◽

Functional Domains ◽

Equine Infectious Anemia ◽

Rna Binding Domain ◽

Anemia Virus

ABSTRACT Equine infectious anemia virus (EIAV) Rev is an essential regulatory protein that facilitates expression of viral mRNAs encoding structural proteins and genomic RNA and regulates alternative splicing of the bicistronic tat/rev mRNA. EIAV Rev is characterized by a high rate of genetic variation in vivo, and changes in Rev genotype and phenotype have been shown to coincide with changes in clinical disease. To better understand how genetic variation alters Rev phenotype, we undertook deletion and mutational analyses to map functional domains and to identify specific motifs that are essential for EIAV Rev activity. All functional domains are contained within the second exon of EIAV Rev. The overall organization of domains within Rev exon 2 includes a nuclear export signal, a large central region required for RNA binding, a nonessential region, and a C-terminal region required for both nuclear localization and RNA binding. Subcellular localization of green fluorescent protein-Rev mutants indicated that basic residues within the KRRRK motif in the C-terminal region of Rev are necessary for targeting of Rev to the nucleus. Two separate regions of Rev were necessary for RNA binding: a central region encompassing residues 57 to 130 and a C-terminal region spanning residues 144 to 165. Within these regions were two distinct, short arginine-rich motifs essential for RNA binding, including an RRDRW motif in the central region and the KRRRK motif near the C terminus. These findings suggest that EIAV Rev utilizes a bipartite RNA-binding domain.

Download Full-text