Analysis of beta-carotene hydroxylase gene cDNA isolated from the American oil-palm (Elaeis oleifera) mesocarp tissue cDNA library
Identifieur interne : 000D04 ( Ncbi/Merge ); précédent : 000D03; suivant : 000D05Analysis of beta-carotene hydroxylase gene cDNA isolated from the American oil-palm (Elaeis oleifera) mesocarp tissue cDNA library
Auteurs : Subhash J. Bhore [Malaisie] ; Amelia Kassim [Malaisie] ; Chye Ying Loh [Malaisie] ; Farida H. Shah [Malaisie]Source :
- Bioinformation [ 0973-2063 ] ; 2010.
Abstract
It is well known that the nutritional quality of the American oil-palm (
ESTs - expressed sequence tags,
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PubMed: 21364789
PubMed Central: 3040485
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Analysis of beta-carotene hydroxylase gene cDNA isolated from the American oil-palm (Elaeis oleifera) mesocarp tissue cDNA library</title><author><name sortKey="Bhore, Subhash J" sort="Bhore, Subhash J" uniqKey="Bhore S" first="Subhash J" last="Bhore">Subhash J. Bhore</name><affiliation wicri:level="1"><nlm:aff id="A1">1Molecular Biology Division, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka, Malaysia;</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>1Molecular Biology Division, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka</wicri:regionArea><wicri:noRegion>Melaka</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A2">Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Bedong, 08100, Kedah Darul Aman, Malaysia;</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Bedong, 08100, Kedah Darul Aman</wicri:regionArea><wicri:noRegion>Kedah Darul Aman</wicri:noRegion></affiliation></author><author><name sortKey="Kassim, Amelia" sort="Kassim, Amelia" uniqKey="Kassim A" first="Amelia" last="Kassim">Amelia Kassim</name><affiliation wicri:level="1"><nlm:aff id="A1">1Molecular Biology Division, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka, Malaysia;</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>1Molecular Biology Division, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka</wicri:regionArea><wicri:noRegion>Melaka</wicri:noRegion></affiliation></author><author><name sortKey="Loh, Chye Ying" sort="Loh, Chye Ying" uniqKey="Loh C" first="Chye Ying" last="Loh">Chye Ying Loh</name><affiliation wicri:level="1"><nlm:aff id="A2">Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Bedong, 08100, Kedah Darul Aman, Malaysia;</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Bedong, 08100, Kedah Darul Aman</wicri:regionArea><wicri:noRegion>Kedah Darul Aman</wicri:noRegion></affiliation></author><author><name sortKey="Shah, Farida H" sort="Shah, Farida H" uniqKey="Shah F" first="Farida H" last="Shah">Farida H. Shah</name><affiliation wicri:level="1"><nlm:aff id="A1">1Molecular Biology Division, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka, Malaysia;</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>1Molecular Biology Division, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka</wicri:regionArea><wicri:noRegion>Melaka</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21364789</idno><idno type="pmc">3040485</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040485</idno><idno type="RBID">PMC:3040485</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">000E41</idno><idno type="wicri:Area/Pmc/Curation">000E40</idno><idno type="wicri:Area/Pmc/Checkpoint">000F75</idno><idno type="wicri:Area/Ncbi/Merge">000D04</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Analysis of beta-carotene hydroxylase gene cDNA isolated from the American oil-palm (Elaeis oleifera) mesocarp tissue cDNA library</title><author><name sortKey="Bhore, Subhash J" sort="Bhore, Subhash J" uniqKey="Bhore S" first="Subhash J" last="Bhore">Subhash J. Bhore</name><affiliation wicri:level="1"><nlm:aff id="A1">1Molecular Biology Division, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka, Malaysia;</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>1Molecular Biology Division, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka</wicri:regionArea><wicri:noRegion>Melaka</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A2">Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Bedong, 08100, Kedah Darul Aman, Malaysia;</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Bedong, 08100, Kedah Darul Aman</wicri:regionArea><wicri:noRegion>Kedah Darul Aman</wicri:noRegion></affiliation></author><author><name sortKey="Kassim, Amelia" sort="Kassim, Amelia" uniqKey="Kassim A" first="Amelia" last="Kassim">Amelia Kassim</name><affiliation wicri:level="1"><nlm:aff id="A1">1Molecular Biology Division, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka, Malaysia;</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>1Molecular Biology Division, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka</wicri:regionArea><wicri:noRegion>Melaka</wicri:noRegion></affiliation></author><author><name sortKey="Loh, Chye Ying" sort="Loh, Chye Ying" uniqKey="Loh C" first="Chye Ying" last="Loh">Chye Ying Loh</name><affiliation wicri:level="1"><nlm:aff id="A2">Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Bedong, 08100, Kedah Darul Aman, Malaysia;</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Bedong, 08100, Kedah Darul Aman</wicri:regionArea><wicri:noRegion>Kedah Darul Aman</wicri:noRegion></affiliation></author><author><name sortKey="Shah, Farida H" sort="Shah, Farida H" uniqKey="Shah F" first="Farida H" last="Shah">Farida H. Shah</name><affiliation wicri:level="1"><nlm:aff id="A1">1Molecular Biology Division, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka, Malaysia;</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>1Molecular Biology Division, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka</wicri:regionArea><wicri:noRegion>Melaka</wicri:noRegion></affiliation></author></analytic><series><title level="j">Bioinformation</title><idno type="eISSN">0973-2063</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>It is well known that the nutritional quality of the American oil-palm (<italic>Elaeis oleifera</italic>) mesocarp oil is superior to that of African oil-palm (<italic>Elaeis
guineensis</italic> Jacq. Tenera) mesocarp oil. Therefore, it is of important to identify the genetic features for its superior value. This could be achieved through
the genome sequencing of the oil-palm. However, the genome sequence is not available in the public domain due to commercial secrecy. Hence, we
constructed a cDNA library and generated expressed sequence tags (3,205) from the mesocarp tissue of the American oil-palm. We continued to annotate
each of these cDNAs after submitting to GenBank/DDBJ/EMBL. A rough analysis turned our attention to the beta-carotene hydroxylase (<italic>Chyb</italic>) enzyme
encoding cDNA. Then, we completed the full sequencing of cDNA clone for its both strands using M13 forward and reverse primers. The full nucleotide
and protein sequence was further analyzed and annotated using various Bioinformatics tools. The analysis results showed the presence of fatty acid
hydroxylase superfamily domain in the protein sequence. The multiple sequence alignment of selected <italic>Chyb</italic> amino acid sequences from other plant
species and algal members with <italic>E. oleifera Chyb</italic> using ClustalW and its phylogenetic analysis suggest that <italic>Chyb</italic> from monocotyledonous plant species,
<italic>Lilium hubrid</italic>, <italic>Crocus sativus</italic> and <italic>Zea mays</italic> are the most evolutionary related with <italic>E. oleifera Chyb</italic>. This study reports the annotation of <italic>E. oleifera Chyb</italic>.</p><sec id="ABB"><title>Abbreviations</title><p>ESTs - expressed sequence tags,
<italic>EoChyb</italic> - <italic>Elaeis oleifera beta-carotene hydroxylase</italic>,
MC - main cluster</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Muniran, F" uniqKey="Muniran F">F Muniran</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Asemota, O" uniqKey="Asemota O">O Asemota</name></author><author><name sortKey="Shah, Fh" uniqKey="Shah F">FH Shah</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lange, Bm" uniqKey="Lange B">BM Lange</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ohlrogge, J" uniqKey="Ohlrogge J">J Ohlrogge</name></author><author><name sortKey="Benning, C" uniqKey="Benning C">C Benning</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ronning, Cm" uniqKey="Ronning C">CM Ronning</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sreenivasulu, N" uniqKey="Sreenivasulu N">N Sreenivasulu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, J" uniqKey="Liu J">J Liu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Keith, Cs" uniqKey="Keith C">CS Keith</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Park, Ys" uniqKey="Park Y">YS Park</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hofte, H" uniqKey="Hofte H">H Hofte</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Umeda, M" uniqKey="Umeda M">M Umeda</name></author><author><name sortKey="Uchimiya, H" uniqKey="Uchimiya H">H Uchimiya</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marchler Bauer, A" uniqKey="Marchler Bauer A">A Marchler-Bauer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Martin, Jf" uniqKey="Martin J">JF Martin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Baroli, I" uniqKey="Baroli I">I Baroli</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vallabhaneni, R" uniqKey="Vallabhaneni R">R Vallabhaneni</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Shah, Fh" uniqKey="Shah F">FH Shah</name></author><author><name sortKey="Cha, Ts" uniqKey="Cha T">TS Cha</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Singh, R" uniqKey="Singh R">R Singh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Arthington, Ba" uniqKey="Arthington B">BA Arthington</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><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="publisher-id">Bioinformation</journal-id><journal-title-group><journal-title>Bioinformation</journal-title></journal-title-group><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">21364789</article-id><article-id pub-id-type="pmc">3040485</article-id><article-id pub-id-type="publisher-id">002500052010</article-id><article-categories><subj-group subj-group-type="heading"><subject>Hypothesis</subject></subj-group></article-categories><title-group><article-title>Analysis of beta-carotene hydroxylase gene cDNA isolated from the American oil-palm (Elaeis oleifera) mesocarp tissue cDNA library</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Bhore</surname><given-names>Subhash J</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="aff" rid="A2">2</xref><xref ref-type="corresp" rid="COR1">*</xref></contrib><contrib contrib-type="author"><name><surname>Kassim</surname><given-names>Amelia</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Loh</surname><given-names>Chye Ying</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Shah</surname><given-names>Farida H</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><aff id="A1"><label>1</label>1Molecular Biology Division, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka, Malaysia;</aff><aff id="A2"><label>2</label>Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Bedong, 08100, Kedah Darul Aman, Malaysia;</aff></contrib-group><author-notes><corresp id="COR1"><label>*</label>Subhash J Bhore: <email>subhashbhore@gmail.com</email>Phone: +60-4-429 8176; Fax: +60-4-429 8109</corresp></author-notes><pub-date pub-type="collection"><year>2010</year></pub-date><pub-date pub-type="epub"><day>20</day><month>9</month><year>2010</year></pub-date><volume>5</volume><issue>3</issue><fpage>104</fpage><lpage>112</lpage><history><date date-type="received"><day>19</day><month>8</month><year>2010</year></date><date date-type="accepted"><day>26</day><month>8</month><year>2010</year></date></history><permissions><copyright-statement>© 2010 Biomedical Informatics</copyright-statement><copyright-year>2010</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>It is well known that the nutritional quality of the American oil-palm (<italic>Elaeis oleifera</italic>) mesocarp oil is superior to that of African oil-palm (<italic>Elaeis
guineensis</italic> Jacq. Tenera) mesocarp oil. Therefore, it is of important to identify the genetic features for its superior value. This could be achieved through
the genome sequencing of the oil-palm. However, the genome sequence is not available in the public domain due to commercial secrecy. Hence, we
constructed a cDNA library and generated expressed sequence tags (3,205) from the mesocarp tissue of the American oil-palm. We continued to annotate
each of these cDNAs after submitting to GenBank/DDBJ/EMBL. A rough analysis turned our attention to the beta-carotene hydroxylase (<italic>Chyb</italic>) enzyme
encoding cDNA. Then, we completed the full sequencing of cDNA clone for its both strands using M13 forward and reverse primers. The full nucleotide
and protein sequence was further analyzed and annotated using various Bioinformatics tools. The analysis results showed the presence of fatty acid
hydroxylase superfamily domain in the protein sequence. The multiple sequence alignment of selected <italic>Chyb</italic> amino acid sequences from other plant
species and algal members with <italic>E. oleifera Chyb</italic> using ClustalW and its phylogenetic analysis suggest that <italic>Chyb</italic> from monocotyledonous plant species,
<italic>Lilium hubrid</italic>, <italic>Crocus sativus</italic> and <italic>Zea mays</italic> are the most evolutionary related with <italic>E. oleifera Chyb</italic>. This study reports the annotation of <italic>E. oleifera Chyb</italic>.</p><sec id="ABB"><title>Abbreviations</title><p>ESTs - expressed sequence tags,
<italic>EoChyb</italic> - <italic>Elaeis oleifera beta-carotene hydroxylase</italic>,
MC - main cluster</p></sec></abstract><kwd-group><kwd>African oil-palm</kwd><kwd>American oil-palm</kwd><kwd>fatty acids</kwd><kwd>fatty acid hydroxylase</kwd><kwd>oleic acid</kwd><kwd>sterol desaturase</kwd><kwd>zeaxanthin</kwd></kwd-group></article-meta></front><floats-group><fig id="F1" position="float"><label>Figure 1</label><caption><p>Nucleotide and deduced amino acid sequences of <italic>E. oleifera</italic> beta-carotene hydroxylase cDNA clone. An open reading frame and noncoding
regions are shown in capital and small letters, respectively. The deduced amino acid sequence is given below the nucleotide sequence, which is numbered
at the both ends of each sequence line. The open reading frame encodes for a protein of 325 amino acid residues. Amino acid residues are numbered
beginning with the initial methionine till last glycine (G) residue. Initiation and termination codons are shown in bold. The beta-carotene hydroxylase
(fatty acid hydroxylase super family) conserved domain (PLN02601) [<xref ref-type="bibr" rid="R25">25</xref>] residues are shown in green colour. The sterol desaturase [Lipid metabolism]
domain (ERG3) [<xref ref-type="bibr" rid="R26">26</xref>] residues are underlined. *represent the termination codon. This cDNA was isolated by random method of gene isolation from <italic>E.
oleifera</italic> 17 week old mesocarp tissue cDNA library.</p></caption><graphic xlink:href="97320630005104F1"></graphic></fig><fig id="F2" position="float"><label>Figure 2</label><caption><p>Rooted dendrogram showing clustering of beta-carotene hydroxylase (<italic>Chyb</italic>) from <italic>E. oleifera</italic> and other organisms. Amino acid sequences for
different organisms were obtained from NCBI database. Alignment of amino acid sequences and dendrogram construction was carried out using multiple
sequence alignment by ClustalW [<xref ref-type="bibr" rid="R19">19</xref>] program using default parameters. Location of <italic>E. oleifera Chyb</italic> in phylogenetic tree is shown in pink box. The ID
of <italic>Chyb</italic> proteins used in the study is given in Table 2 (see <xref ref-type="supplementary-material" rid="SD1">supplementary material</xref>). MC stands for main cluster.</p></caption><graphic xlink:href="97320630005104F2"></graphic></fig><fig id="F3" position="float"><label>Figure 3</label><caption><p>Similarity comparison of amino acid sequences of the <italic>E. oleifera</italic> beta-carotene hydroxylase (<italic>Chyb</italic>) protein and <italic>Chyb</italic> amino acid sequences
from other organisms. Amino acid sequences are numbered at the end of each sequence row. (*), (:) and (.) denote single fully conserved residues,
residues with conserved strong groups and residues with conserved weak groups in <italic>Chyb</italic>, respectively. Aa, <italic>Adonis aestivalis</italic>; At, <italic>Arabidopsis thaliana</italic>;
Bn, <italic>Brassica napus</italic>; Can, <italic>Capsicum annuum</italic>; Car, <italic>Coffea arabica</italic>; Cr, <italic>Chlamydomonas reinhardtii</italic>; Csi, <italic>Citrus sinensis</italic>; Csa, <italic>Crocus sativus</italic>; Cxm,
<italic>Chrysanthemum x morifolium hybrid</italic>; Dc, <italic>Daucus carota</italic>; Dk, <italic>Diospyros kaki</italic>; Eo, <italic>Elaeis oleifera</italic>; Gl, <italic>Gentiana lutea</italic>; Gm, <italic>Glycine max</italic>; Hp,
<italic>Haematococcus pluvialis</italic>; Lh, <italic>Lilium hybrid</italic>; Mz, <italic>Muriella zofingiensis</italic>; Sl, <italic>Solanum lycopersicum</italic>; Vv, <italic>Vitis vinifera</italic>; Zm, <italic>Zea mays</italic>. This alignment is
produced by clustal 2.0.11 multiple sequence alignment program.</p></caption><graphic xlink:href="97320630005104F3"></graphic></fig></floats-group></pmc><affiliations><list><country><li>Malaisie</li></country></list><tree><country name="Malaisie"><noRegion><name sortKey="Bhore, Subhash J" sort="Bhore, Subhash J" uniqKey="Bhore S" first="Subhash J" last="Bhore">Subhash J. Bhore</name></noRegion><name sortKey="Bhore, Subhash J" sort="Bhore, Subhash J" uniqKey="Bhore S" first="Subhash J" last="Bhore">Subhash J. Bhore</name><name sortKey="Kassim, Amelia" sort="Kassim, Amelia" uniqKey="Kassim A" first="Amelia" last="Kassim">Amelia Kassim</name><name sortKey="Loh, Chye Ying" sort="Loh, Chye Ying" uniqKey="Loh C" first="Chye Ying" last="Loh">Chye Ying Loh</name><name sortKey="Shah, Farida H" sort="Shah, Farida H" uniqKey="Shah F" first="Farida H" last="Shah">Farida H. Shah</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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