PSEUDOKNOTS IN HUMAN SNRNPS

SAYAK GANGULI¹*, SANJAY KUMAR DEY², PAUSHALI ROY³, PROTIP BASU⁴, HIRAK JYOTI CHAKRABORTY⁵, ABHIJIT DATTA^6
1DBT-Centre for Bioinformatics, Presidency University, Kolkata
²DBT-Centre for Bioinformatics, Presidency University, Kolkata
³DBT-Centre for Bioinformatics, Presidency University, Kolkata
⁴DBT-Centre for Bioinformatics, Presidency University, Kolkata
⁵DBT-Centre for Bioinformatics, Presidency University, Kolkata
⁶Post Graduate Department of Botany, Bethune College, Kolkata
* Corresponding Author : sayakbif@yahoo.com

Received : 05-04-2011     Accepted : 20-05-2011     Published : 21-06-2011
Volume : 3     Issue : 1       Pages : 194 - 199
Int J Bioinformatics Res 3.1 (2011):194-199
DOI : http://dx.doi.org/10.9735/0975-3087.3.1.194-199

Conflict of Interest : None declared

Snurps or small nuclear ribonucleoproteins (snRNPs), are RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a Spliceosome, comprising of five small nuclear RNAs (snRNAs)-U1, U2, U4, U5, and U6 snRNA-as well as many protein factors, upon which splicing of pre-mRNA occurs. While, RNA pseudoknots play crucial role in protein synthesis by helping in internal ribosome entry, frameshifting, stop codon readthrough in many viral species and the 3’NCR pseudoknots helps viral RNAs to replicate, has been reported by a number of investigators, its presence in human snurps has not yet been done. The present in silico study reveals the presence of pseudoknots in the mRNAs of the proteins associated with human Spliceosome. It not only emphasizes their significance as catalytic RNA world relics but also opens the scope of research in the functional and structural associations of RNA pseudoknots in eukaryotic gene regulation.

snRNP, splicing, pseudoknot, gene regulation, catalytic RNA world.

Small nuclear ribonucleoproteins (snRNPs) are known to assemble in a stepwise manner onto the pre-mRNA to form the spliceosome. The spliceosome is comprised of five small nuclear RNAs (snRNAs)— U1, U2, U4, U5, and U6 snRNA and many protein factors [1,2] . The coding regions (exons) of the gene are separated by non-coding DNA (introns) that are not involved in gene expression. These introns are removed by the process known as splicing, resulting in the finally processed mRNA. An RNA pseudoknot is a tertiary structural element formed when bases of a single- stranded loop pair interact with complementary bases outside the loop within the RNA molecule [3,4] . Though the presences of 14 topologically possible distinct types of pseudoknots have been hypothesized, most commonly occurring pseudoknots are of the H-type, where H signifies a hairpin loop [3] . The other important types are HH type, LL type, HLOUT type and HLIN type etc. [3] . In the case of H-type pseudoknots, bases in a hairpin loop pair with complementary bases outside the loop [Fig-1] . HH-type pseudoknot is formed by base pairing of a hairpin loop with another hairpin loop and HL type pseudoknot is formed due to base pairing of a hairpin loop with a single stranded part of a bulge or of an internal or multiple loops [Fig-1] . Base pairing of single stranded bulge (B), interior (I) and multibranched (M) loops with complementary regions elsewhere in the RNA also makes pseudoknots. The B, M and I nomenclatures as well as H-H type are not used extensively; rather most structures are referred to as H-type pseudoknots [4] .
In eukaryotes, the pseudoknots in 80S ribosomal complex correspond to an L shaped density located at the mRNA exit channel of ribosomal proteins S5 (rsS5). These pseudoknots are important for the formation of the ribosomal A (amino-acyl), P (peptidyl) and E (exit) sites by the interaction of the IRES (internal ribosome entry site) with many key protein component and the 80S complex during protein synthesis [4] .
Programmed-ribosomal Frameshifting is a translational mechanism used by many viruses to coordinately express proteins from an mRNA [5] . RNA pseudoknots within the coding regions are mainly responsible for this frame shifting activity. Another important function of the pseudoknot is to facilitate read through of the stop codon, in this regard H-type pseudoknot present at eight nucleotides downstream of the stop codon has been reported to enhance the process [6] . Pseudoknots are also used as binding sites for proteins or single stranded loops of RNA. Indeed pseudoknotted RNAs are often generated during in vitro selection of RNA aptamers that bind various biomolecules [4] . Pseudoknotting is also being the most efficient way of folding RNAs in an active conformation (for example- ribozymes) [4] .
The role of RNA pseudoknots in translation has been reported in detail, but its presence in human snurps has yet not been revealed. Thus identification of RNA pseudoknots in the mRNAs of the protein part of the human snRNPs will be of excellent biological significance to establish the structural and functional relationship between the RNA pseudoknots and gene expression strategies in eukaryotes.

• The DNA sequences for the human snRNPs were downloaded from the Genbank of NCBI website. The sequences used in this study are listed in [Table-1] .
• The DNA sequences were then converted into RNA sequences using an in house tool.
• The RNAs were then analyzed by Pseudoviewer package.

The results of the pseudoknot analysis showed four types of pseudoknots, namely, HLOUT, LL, classical H and HLIN types. The HLOUT type pseudoknot was found to be the most predominant type occurring in 41 of the cases. While LL, classical H and HLIN types of pseudoknots were found 21, 14 and 12 times respectively [Table-2] , [Fig-1] .

As is evident from the results, several pseudoknot motifs were identified in the human snurps [Table-2] , [Fig-1] . The presence of this important structural element is a significant finding in RNA biology as it has been known over the years that pseudoknots are important ubiquitous structures in the mRNA which guides the process of translation through its twists and turns. Furthermore Cech [7] has emphasized that pseudoknot and associated structures formed the core of RNA based gene regulation in the ancient RNA world before the adaptive radiation of proteins in their diverse biological functions. The basics of RNA based gene regulation that exists in the modern RNA world comprises of the riboswitches and the various attenuator and repressor systems found in bacteria and few eukaryotes. The identification and characterization of pseudoknots in the proteins associated with the spliceosome provides further evidences that these pseudoknots are RNA world relics and probably originate from an ancestral stock of RNA regulons. It is important to note that the identification of RNA based regulation of important mammalian gene regulatory systems promotes the fact that we are still under the control of RNA, though there has been the evolution of DNA based genomes.

The authors acknowledge the support from Department of Biotechnology, Govt. of India for this work.

[1] Kruger K., Grabowski P.J., Zaug A.J., Sands J., Gottschling D.E. and Cech T.R. (1982) Cell, 31(1), 147-57.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[2] Guerrier-Takada C., Gardiner K., Marsh T., Pace N. and Altman S. (1983) Cell, 35, 849−857.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[3] Brierley I., Pennell S. and Gilbert R. J. C. (2007) Nature Reviews Microbiology, 5, 598-610.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[4] Namy O., Moran S. J., Stuart D. I., Gilbert R. J. C. and Brierley I. (2006) Nature, 44, 244-247.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[5] Gluick T. C., Wills N. M, Gesteland R. F. and Draper D. E. (1997) Biochemistry, 36 (51), 16173–16186.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[6] Gesteland R.F., Cech T.R., Atkins J.F. (eds). (2006) The RNA world (Cold Spring Harbor Laboratory, Cold Spring Harbor) 3rd edition, 309.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

	Fig. 1- (a-d): Four major types of pseudoknots found in Human snRNPs.
	Table 1- The accession numbers for DNA sequences of the human snRNPs mRNA under study
	Table 2- Accession numbers and description of predominant types of Pseudoknots found in Human snurps