A case of convergent evolution of nucleic acid binding modules

@article{Graumann1996ACO,
  title={A case of convergent evolution of nucleic acid binding modules},
  author={Peter L. Graumann and Mohamed A. Marahiel},
  journal={BioEssays},
  year={1996},
  volume={18}
}
Divergent evolution can explain how many proteins containing structurally similar domains, which perform a variety of related functions, have evolved from a relatively small number of modules or protein domains. However, it cannot explain how protein domains with similar, but distinguishable, functions and similar, but distinguishable, structures have evolved. Examples of this are the RNA‐binding proteins containing the RNA‐binding domain (RBD), and a newly established protein group, the cold… 
RNA-binding strategies common to cold-shock domain- and RNA recognition motif-containing proteins.
TLDR
This model of the CSD(FRG)-RNA complex constitutes the first prediction of the three-dimensional structure of a CSD-RNA complex and is consistent with the hypothesis of a convergent evolution of CSD and RRM towards a related single-stranded RNA-binding surface.
Composition, conservation, evolution, and function of the cold shock domain proteins in plants
TLDR
The overall objective of this study was to understand the evolution and function of the cold shock domain in plant model systems and build a foundation of knowledge of its functional importance in higher plants of agronomic importance.
Complex Evolutionary Relationships Among Four Classes of Modular RNA-Binding Splicing Regulators in Eukaryotes: The hnRNP, SR, ELAV-Like and CELF Proteins
TLDR
It is proposed that these proteins were derived independently rather than through the expansion of a single protein family to create genes of mixed evolutionary origin, and highlighted inconsistencies in the current classification system for these regulators.
The poly(C)-binding proteins: a multiplicity of functions and a search for mechanisms.
TLDR
The roles of these proteins in mRNA stabilization, translational activation, and translational silencing suggest a complex and diverse set of post-transcriptional control pathways.
Comparison of structure, function and regulation of plant cold shock domain proteins to bacterial and animal cold shock domain proteins.
TLDR
In this review, the structure, function and regulation of plant CSPs are compared and contrasted to the characteristics of bacterial and animal C SPs.
RNA binding specificity of Unr, a protein with five cold shock domains.
TLDR
The SELEX-generated consensus motifs for Unr differ from the AACAUC motif selected by the Xenopus Y-box factor FRGY2, indicating that a diversity of RNA sequences could be recognized by CSD-containing proteins.
Resilience of biochemical activity in protein domains in the face of structural divergence.
The pleiotropic functions of the Y-box-binding protein, YB-1.
TLDR
This review will begin by briefly describing the characteristics of YB-1 and will then summarize the pleiotropic functions brought about via DNA-RNA transaction and protein-protein interactions, which will discuss the diverse range of potential physiological and pathological functions of YBs.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 45 REFERENCES
Structural and functional properties of the evolutionarily ancient Y‐box family of nucleic acid binding proteins
  • A. Wolffe
  • Biology
    BioEssays : news and reviews in molecular, cellular and developmental biology
  • 1994
TLDR
The Y‐box proteins are the most evolutionarily conserved nucleic acid binding proteins yet defined in bacteria, plants and animals and range from the control of the E. coli cold‐shock stress response to the translational masking of messenger RNA in vertebrate gametes.
Multiple RNA binding domains (RBDs) just don't add up.
TLDR
A clearer understanding of multi-RBD binding is essential to critically evaluating the role of these proteins in RNA splicing, packaging and transport, and it is found that individual RBDs are separated by 'linker' sequences of highly variable length.
Crystal structure of prokaryotic ribosomal protein L9: a bi‐lobed RNA‐binding protein.
TLDR
Comparisons with other prokaryotic L9 sequences show that while the length of the connecting alpha‐helix is invariant, the sequence within the exposed central region is not conserved, which suggests that the alpha-helix has an architectural role and serves to fix the relative separation and orientation of the N‐ and C‐terminal domains within the ribosome.
Ribosomal protein L6: structural evidence of gene duplication from a primitive RNA binding protein.
TLDR
The crystal structure of ribosomal protein L6 from the thermophilic bacterium Bacillus stearothermophilus solved at 2.6 A resolution is presented, implying that it was created by an ancient gene duplication event.
RNP-1, an RNA-binding motif is conserved in the DNA-binding cold shock domain.
  • D. Landsman
  • Biology, Chemistry
    Nucleic acids research
  • 1992
TLDR
The cold shock domain (CSD) family of proteins, which includes several transcription factors which have been shown to bind to DNA, has now been identified to contain a motif similar to RNP-1, which is common to two families of apparently unrelated proteins.
Mutational analysis of the putative nucleic acid‐binding surface of the cold‐shock domain, CspB, revealed an essential role of aromatic and basic residues in binding of single‐stranded DNA containing the Y‐box motif
TLDR
The potential role of conserved aromatic and basic residues in nucleic acid binding by site‐directed mutagenesis is analysed and single substitutions including the conserved basic residues Lys‐7, Lys‐13 and Arg‐56 as well as the aromatic residues Trp‐8 and Phe‐30 strongly suggest that CspB uses the sidechains of these amino acids for specific interaction with nucleic acids.
Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein
TLDR
As a prototype of the cold-shock domain, the structure of CspB has been determined here from two crystal forms and is present as an antiparallel five-stranded β-barrel that is presumably involved in nucleic acid binding.
OB(oligonucleotide/oligosaccharide binding)‐fold: common structural and functional solution for non‐homologous sequences.
TLDR
The determinants of the OB‐fold are described and a reinterpretation of the controversial structure of gene 5 ssDNA binding protein is suggested, which exhibits some topological and functional similarities with the OB•fold proteins.
Nucleic acid binding and intracellular localization of unr, a protein with five cold shock domains
TLDR
It is reported that unr is a novel single-stranded nucleic acid binding protein which is likely to be associated with cytoplasmic mRNA in vivo and characterized by its low affinity for double-Stranded and structured RNAs.
The determinants of RNA-binding specificity of the heterogeneous nuclear ribonucleoprotein C proteins.
TLDR
It is proposed that the highly conserved beta alpha beta beta alpha alpha beta core structure of the RNP motif RBD confers a general RNA binding activity to RNP logo RBDs and that the determinants of RNA-binding specificity reside in the most variable regions, the loops connecting the beta-strands and/or the contiguous NH2 and COOH termini of theRBD.
...
1
2
3
4
5
...