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In silico characterization of a RNA binding protein of cattle filarial parasite Setaria digitata

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In silico characterization of a RNA binding protein of cattle filarial parasite Setaria digitata

Auteurs : Nirupa Nagaratnam ; Eric Hamilton Karunanayake ; Kamani Hemamala Tennekoon ; Sameera Ranganath Samarakoon ; Karthika Mayan

Source :

Bioinformation [ 0973-8894 ] ; 2014.

RBID : PMC:4166771

Abstract

Human lymphatic filariasis (HLF) is a neglected tropical disease which threatens nearly 1.4 billion people in 73 countries worldwide. Wuchereria bancrofti is the major causative agent of HLF and it closely resembles cattle filarial parasite Setaria digitata. Due to difficulties in procuring W. bancrofti parasite material, S. digitata cDNA library has been constructed to identify novel drug targets against HLF and many of the cDNA sequences are yet to be assigned structure and function. In this study, a 549 bp long cDNA (sdrbp) has been sequenced and characterized in silico. The shortest ORF of 249 bp from the isolated cDNA encodes a polypeptide of 82 amino acids and shows an amino acid identity of 54% with the RRM domain of human cleavage stimulation factor-64 kDa subunit (CstF-64). Structure of the protein (sdRBP) obtained by homology modelling using RRM of CstF-64 as template adopts classical RRM topology (β1α1β2β3α2β4). sdRBP model built was validated by superimposition tools and Ramachandran plot analysis. CstF-64 plays an important role in pre-mRNA polyadenylation by interacting with specific GU-rich downstream sequence element. Molecular docking studies of sdRBP with different RNA molecules revealed that sdRBP has greater binding affinity to GU-rich RNA and comparable results were obtained upon similar docking of RRM of CstF-64 with the same RNA molecules. Therefore, sdRBP is likely to perform homologous function in S. digitata. This study brings new dimensions to the functional analysis of RNA binding proteins of S. digitata and their evaluation as new drug targets against HLF.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166771

DOI: 10.6026/97320630010512
PubMed: 25258487
PubMed Central: 4166771

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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en"><italic>In silico</italic>
 characterization of a RNA binding protein of cattle filarial parasite <italic>Setaria digitata</italic>
</title>
<author><name sortKey="Nagaratnam, Nirupa" sort="Nagaratnam, Nirupa" uniqKey="Nagaratnam N" first="Nirupa" last="Nagaratnam">Nirupa Nagaratnam</name>
</author>
<author><name sortKey="Karunanayake, Eric Hamilton" sort="Karunanayake, Eric Hamilton" uniqKey="Karunanayake E" first="Eric Hamilton" last="Karunanayake">Eric Hamilton Karunanayake</name>
</author>
<author><name sortKey="Tennekoon, Kamani Hemamala" sort="Tennekoon, Kamani Hemamala" uniqKey="Tennekoon K" first="Kamani Hemamala" last="Tennekoon">Kamani Hemamala Tennekoon</name>
</author>
<author><name sortKey="Samarakoon, Sameera Ranganath" sort="Samarakoon, Sameera Ranganath" uniqKey="Samarakoon S" first="Sameera Ranganath" last="Samarakoon">Sameera Ranganath Samarakoon</name>
</author>
<author><name sortKey="Mayan, Karthika" sort="Mayan, Karthika" uniqKey="Mayan K" first="Karthika" last="Mayan">Karthika Mayan</name>
</author>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><italic>In silico</italic>
 characterization of a RNA binding protein of cattle filarial parasite <italic>Setaria digitata</italic>
</title>
<author><name sortKey="Nagaratnam, Nirupa" sort="Nagaratnam, Nirupa" uniqKey="Nagaratnam N" first="Nirupa" last="Nagaratnam">Nirupa Nagaratnam</name>
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<author><name sortKey="Karunanayake, Eric Hamilton" sort="Karunanayake, Eric Hamilton" uniqKey="Karunanayake E" first="Eric Hamilton" last="Karunanayake">Eric Hamilton Karunanayake</name>
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<author><name sortKey="Tennekoon, Kamani Hemamala" sort="Tennekoon, Kamani Hemamala" uniqKey="Tennekoon K" first="Kamani Hemamala" last="Tennekoon">Kamani Hemamala Tennekoon</name>
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<author><name sortKey="Samarakoon, Sameera Ranganath" sort="Samarakoon, Sameera Ranganath" uniqKey="Samarakoon S" first="Sameera Ranganath" last="Samarakoon">Sameera Ranganath Samarakoon</name>
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<author><name sortKey="Mayan, Karthika" sort="Mayan, Karthika" uniqKey="Mayan K" first="Karthika" last="Mayan">Karthika Mayan</name>
</author>
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<series><title level="j">Bioinformation</title>
<idno type="ISSN">0973-8894</idno>
<idno type="eISSN">0973-2063</idno>
<imprint><date when="2014">2014</date>
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<front><div type="abstract" xml:lang="en"><p>Human lymphatic filariasis (HLF) is a neglected tropical disease which threatens nearly 1.4 billion people in 73 countries
worldwide. <italic>Wuchereria bancrofti</italic>
 is the major causative agent of HLF and it closely resembles cattle filarial parasite <italic>Setaria digitata</italic>.
Due to difficulties in procuring <italic>W. bancrofti</italic>
 parasite material, <italic>S. digitata</italic> cDNA library has been constructed to identify novel drug
targets against HLF and many of the cDNA sequences are yet to be assigned structure and function. In this study, a 549 bp long
cDNA (<italic>sdrbp</italic>
) has been sequenced and characterized <italic>in silico</italic>. The shortest ORF of 249 bp from the isolated cDNA encodes a
polypeptide of 82 amino acids and shows an amino acid identity of 54% with the RRM domain of human cleavage stimulation
factor-64 kDa subunit (CstF-64). Structure of the protein (sdRBP) obtained by homology modelling using RRM of CstF-64 as
template adopts classical RRM topology (β1α1β2β3α2β4). sdRBP model built was validated by superimposition tools and
Ramachandran plot analysis. CstF-64 plays an important role in pre-mRNA polyadenylation by interacting with specific GU-rich
downstream sequence element. Molecular docking studies of sdRBP with different RNA molecules revealed that sdRBP has greater
binding affinity to GU-rich RNA and comparable results were obtained upon similar docking of RRM of CstF-64 with the same
RNA molecules. Therefore, sdRBP is likely to perform homologous function in <italic>S. digitata</italic>. This study brings new dimensions to the
functional analysis of RNA binding proteins of <italic>S. digitata</italic>
 and their evaluation as new drug targets against HLF.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Sharma, Op" uniqKey="Sharma O">OP Sharma</name>
</author>
</analytic>
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<biblStruct><analytic><author><name sortKey="Schwab, Ae" uniqKey="Schwab A">AE Schwab</name>
</author>
</analytic>
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<biblStruct><analytic><author><name sortKey="Perez Ca Adillas, Jm" uniqKey="Perez Ca Adillas J">JM Pérez Cañadillas</name>
</author>
<author><name sortKey="Varani, G" uniqKey="Varani G">G Varani</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Clery, A" uniqKey="Clery A">A Cléry</name>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
  <front><journal-meta><journal-id journal-id-type="nlm-ta">Bioinformation</journal-id>
<journal-id journal-id-type="iso-abbrev">Bioinformation</journal-id>
<journal-id journal-id-type="publisher-id">Bioinformation</journal-id>
<journal-title-group><journal-title>Bioinformation</journal-title>
</journal-title-group>
<issn pub-type="ppub">0973-8894</issn>
<issn pub-type="epub">0973-2063</issn>
<publisher><publisher-name>Biomedical Informatics</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">25258487</article-id>
<article-id pub-id-type="pmc">4166771</article-id>
<article-id pub-id-type="publisher-id">97320630010512</article-id>
<article-id pub-id-type="doi">10.6026/97320630010512</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Hypothesis</subject>
</subj-group>
</article-categories>
<title-group><article-title><italic>In silico</italic>
 characterization of a RNA binding protein of cattle filarial parasite <italic>Setaria digitata</italic>
</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Nagaratnam</surname>
<given-names>Nirupa</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Karunanayake</surname>
<given-names>Eric Hamilton</given-names>
</name>
<xref ref-type="corresp" rid="COR1">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Tennekoon</surname>
<given-names>Kamani Hemamala</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Samarakoon</surname>
<given-names>Sameera Ranganath</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Mayan</surname>
<given-names>Karthika</given-names>
</name>
</contrib>
<aff>Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo 90, Cumaratunga Munidasa Mawatha, Colombo 03, Sri Lanka</aff>
</contrib-group>
<author-notes><corresp id="COR1"><label>*</label>
Eric Hamilton Karunanayake: <email>erick@ibmbb.cmb.ac.lk</email>
</corresp>
</author-notes>
<pub-date pub-type="collection"><year>2014</year>
</pub-date>
<pub-date pub-type="epub"><day>30</day>
<month>8</month>
<year>2014</year>
</pub-date>
<volume>10</volume>
<issue>8</issue>
<fpage>512</fpage>
<lpage>517</lpage>
<history><date date-type="received"><day>08</day>
<month>7</month>
<year>2014</year>
</date>
<date date-type="accepted"><day>11</day>
<month>7</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-statement>© 2014 Biomedical Informatics</copyright-statement>
<copyright-year>2014</copyright-year>
<license license-type="open-access"><license-p>This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium,
for non-commercial purposes, provided the original author and source are credited.</license-p>
</license>
</permissions>
<abstract><p>Human lymphatic filariasis (HLF) is a neglected tropical disease which threatens nearly 1.4 billion people in 73 countries
worldwide. <italic>Wuchereria bancrofti</italic>
 is the major causative agent of HLF and it closely resembles cattle filarial parasite <italic>Setaria digitata</italic>.
Due to difficulties in procuring <italic>W. bancrofti</italic>
 parasite material, <italic>S. digitata</italic> cDNA library has been constructed to identify novel drug
targets against HLF and many of the cDNA sequences are yet to be assigned structure and function. In this study, a 549 bp long
cDNA (<italic>sdrbp</italic>
) has been sequenced and characterized <italic>in silico</italic>. The shortest ORF of 249 bp from the isolated cDNA encodes a
polypeptide of 82 amino acids and shows an amino acid identity of 54% with the RRM domain of human cleavage stimulation
factor-64 kDa subunit (CstF-64). Structure of the protein (sdRBP) obtained by homology modelling using RRM of CstF-64 as
template adopts classical RRM topology (β1α1β2β3α2β4). sdRBP model built was validated by superimposition tools and
Ramachandran plot analysis. CstF-64 plays an important role in pre-mRNA polyadenylation by interacting with specific GU-rich
downstream sequence element. Molecular docking studies of sdRBP with different RNA molecules revealed that sdRBP has greater
binding affinity to GU-rich RNA and comparable results were obtained upon similar docking of RRM of CstF-64 with the same
RNA molecules. Therefore, sdRBP is likely to perform homologous function in <italic>S. digitata</italic>. This study brings new dimensions to the
functional analysis of RNA binding proteins of <italic>S. digitata</italic>
 and their evaluation as new drug targets against HLF.</p>
</abstract>
<kwd-group><kwd>Cleavage stimulation factor</kwd>
<kwd>RRM domain</kwd>
<kwd>superimposition</kwd>
<kwd>Ramachandran plot</kwd>
<kwd>pre-mRNA polyadenylation</kwd>
<kwd>GU-rich downstream sequence element</kwd>
<kwd>Molecular docking</kwd>
</kwd-group>
</article-meta>
</front>
<floats-group><fig id="F1" position="float"><label>Figure 1</label>
<caption><p>(a) Homology model of the hypothetical protein,
sdRBP built by SWISS-MODEL Workspace. (b) NMR structure
of the N-terminal RRM domain of human CstF-64 (PDB ID:
1P1T_A). (c) NMR structure of human CstF-64 (PDB ID: 1P1T)
retrieved from RCSB-PDB (d) Superposition of sdRBP (blue)
with the RRM of CstF-64 (pink) showing how similar these
proteins are even in the orientation of the loops, with one
significant exception at two N- and C-terminal helices of the
RRM of CstF-64 which are not found in sdRBP. (e) Proposed
RNP1 (RGFGFCEF) and RNP2 (VFVGNL) sequences of sdRBP
are located in the two central β‑strands, β3 and β1 respectively</p>
</caption>
<graphic xlink:href="97320630010512F1"></graphic>
</fig>
<fig id="F2" position="float"><label>Figure 2</label>
<caption><p>(a) 82 amino acid polypeptide (sdRBP) derived by the conceptual translation of the shortest ORF (249 bp) showing the
locations and sequences of four β strands (green) and two α helices (yellow). (b) Multiple alignment of sdRBP with CstF-64 using
UCSF chimera results in 54% amino acid identity and the four key amino acids of the RRM of CstF-64 (S10, F12, R39, and F54)
reported to be essential for RNA binding activity are conserved in sdRBP (conserved positions are indicated in the alignment by
red spots).</p>
</caption>
<graphic xlink:href="97320630010512F2"></graphic>
</fig>
<fig id="F3" position="float"><label>Figure 3</label>
<caption><p>(a) Automated molecular docking of sdRBP with three types of RNA octamers shown in pink (1: 5'GUGUUUAC-3'
[472D_A], 2: 5'GUAGGCAC-3' [472D_B], 3: 5'- GGCGAGCC)-3' [1SA9]) using Hex 8.0.0 Cuda software (viewed by UCSF Chimera)
showing sdRBP has greater binding affinity to GU-rich RNA which comprises of consecutive Us (a.1). (b) Automated molecular
docking of RRM of CstF-64 with the same three types of RNA octamers results in comparable results as obtained for sdRBP
revealing the fact that sdRBP has significant functional similarity with human CstF-64.</p>
</caption>
<graphic xlink:href="97320630010512F3"></graphic>
</fig>
</floats-group>
</pmc>
</record>

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In silico characterization of a RNA binding protein of cattle filarial parasite Setaria digitata

In silico characterization of a RNA binding protein of cattle filarial parasite Setaria digitata

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