Independent modulation of individual genomic component transcription and a cis-acting element related to high transcriptional activity in a multipartite DNA virus.
Identifieur interne : 000108 ( Main/Exploration ); précédent : 000107; suivant : 000109Independent modulation of individual genomic component transcription and a cis-acting element related to high transcriptional activity in a multipartite DNA virus.
Auteurs : Nai-Tong Yu [République populaire de Chine] ; Hui-Min Xie [République populaire de Chine] ; Yu-Liang Zhang [République populaire de Chine] ; Jian-Hua Wang [République populaire de Chine] ; Zhongguo Xiong [États-Unis] ; Zhi-Xin Liu [République populaire de Chine]Source :
- BMC genomics [ 1471-2164 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : RNA, Messenger.
- genetics : Babuvirus, Genome, Viral, Regulatory Elements, Transcriptional.
- Genomics, Sequence Analysis, RNA, Transcription, Genetic.
Abstract
BACKGROUND
The genome of Banana bunchy top virus (BBTV) consists of at least six circular, single-stranded DNA components of ~ 1 kb in length. Some BBTV isolates may also carry satellite DNA molecules that are not essential for BBTV infection. The relation between multipartite DNA virus replication and their transcriptional levels and the underlying mechanism remain unclear.
RESULTS
To understand the coordinated replication and transcription of the multiple genomic components, the absolute amounts of each BBTV DNA component were measured by real-time PCR (qPCR), and their transcriptional levels were determined by RNAseq and reverse transcription-qPCR (qRT-PCR). Significant differences were found in the absolute amounts of individual BBTV genomic components. Transcriptional levels of each BBTV genomic component obtained from the RNAseq data matched closely to those obtained from qRT-PCR, but did not correspond to the absolute amount of each DNA component. The ratio of transcript over DNA copies ranged from 46.21 to 1059.44%, which was possibly regulated by the promoter region in the intergenic region of each component. To further determine this speculation, the promoter region of the DNA-S, -M or -N was constructed to the upstream of green fluorescent protein (GFP) gene for transient expression by agrobacterium-mediated transformation method. The qRT-PCR showed the highest transcriptional activity was promoted by DNA-N promoter, about 386.58% activity comparing with CaMV 35S promoter. Confocal microscopy observation showed that the intensity of green fluorescence was corresponding to that of qRT-PCR.
CONCLUSIONS
Our data clearly showed that BBTV was able to control the transcriptional level of each DNA component independently by through the promoter sequences in the intergenic region. Moreover, a cis-acting element from DNA-N component had a high transcriptional activity.
DOI: 10.1186/s12864-019-5901-0
PubMed: 31296162
PubMed Central: PMC6625112
Affiliations:
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571101</wicri:regionArea><wicri:noRegion>571101</wicri:noRegion></affiliation></author><author><name sortKey="Xie, Hui Min" sort="Xie, Hui Min" uniqKey="Xie H" first="Hui-Min" last="Xie">Hui-Min Xie</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101</wicri:regionArea><wicri:noRegion>571101</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Yu Liang" sort="Zhang, Yu Liang" uniqKey="Zhang Y" first="Yu-Liang" last="Zhang">Yu-Liang Zhang</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101</wicri:regionArea><wicri:noRegion>571101</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Jian Hua" sort="Wang, Jian Hua" uniqKey="Wang J" first="Jian-Hua" last="Wang">Jian-Hua Wang</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural 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Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101</wicri:regionArea><wicri:noRegion>571101</wicri:noRegion></affiliation></author><author><name sortKey="Xie, Hui Min" sort="Xie, Hui Min" uniqKey="Xie H" first="Hui-Min" last="Xie">Hui-Min Xie</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.</nlm:affiliation><country 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Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101</wicri:regionArea><wicri:noRegion>571101</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Jian Hua" sort="Wang, Jian Hua" uniqKey="Wang J" first="Jian-Hua" last="Wang">Jian-Hua Wang</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101</wicri:regionArea><wicri:noRegion>571101</wicri:noRegion></affiliation></author><author><name sortKey="Xiong, Zhongguo" sort="Xiong, Zhongguo" uniqKey="Xiong Z" first="Zhongguo" last="Xiong">Zhongguo Xiong</name><affiliation wicri:level="1"><nlm:affiliation>School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, 85721, USA. zxiong@email.arizona.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, 85721</wicri:regionArea><wicri:noRegion>85721</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Zhi Xin" sort="Liu, Zhi Xin" uniqKey="Liu Z" first="Zhi-Xin" last="Liu">Zhi-Xin Liu</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China. liuzhixin@itbb.org.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101</wicri:regionArea><wicri:noRegion>571101</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Babuvirus (genetics)</term><term>Genome, Viral (genetics)</term><term>Genomics (MeSH)</term><term>RNA, Messenger (genetics)</term><term>Regulatory Elements, Transcriptional (genetics)</term><term>Sequence Analysis, RNA (MeSH)</term><term>Transcription, Genetic (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN messager (génétique)</term><term>Analyse de séquence d'ARN (MeSH)</term><term>Babuvirus (génétique)</term><term>Génome viral (génétique)</term><term>Génomique (MeSH)</term><term>Transcription génétique (MeSH)</term><term>Éléments de régulation transcriptionnelle (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Messenger</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Babuvirus</term><term>Genome, Viral</term><term>Regulatory Elements, Transcriptional</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN messager</term><term>Babuvirus</term><term>Génome viral</term><term>Éléments de régulation transcriptionnelle</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genomics</term><term>Sequence Analysis, RNA</term><term>Transcription, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ARN</term><term>Génomique</term><term>Transcription génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>The genome of Banana bunchy top virus (BBTV) consists of at least six circular, single-stranded DNA components of ~ 1 kb in length. Some BBTV isolates may also carry satellite DNA molecules that are not essential for BBTV infection. The relation between multipartite DNA virus replication and their transcriptional levels and the underlying mechanism remain unclear.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>To understand the coordinated replication and transcription of the multiple genomic components, the absolute amounts of each BBTV DNA component were measured by real-time PCR (qPCR), and their transcriptional levels were determined by RNAseq and reverse transcription-qPCR (qRT-PCR). Significant differences were found in the absolute amounts of individual BBTV genomic components. Transcriptional levels of each BBTV genomic component obtained from the RNAseq data matched closely to those obtained from qRT-PCR, but did not correspond to the absolute amount of each DNA component. The ratio of transcript over DNA copies ranged from 46.21 to 1059.44%, which was possibly regulated by the promoter region in the intergenic region of each component. To further determine this speculation, the promoter region of the DNA-S, -M or -N was constructed to the upstream of green fluorescent protein (GFP) gene for transient expression by agrobacterium-mediated transformation method. The qRT-PCR showed the highest transcriptional activity was promoted by DNA-N promoter, about 386.58% activity comparing with CaMV 35S promoter. Confocal microscopy observation showed that the intensity of green fluorescence was corresponding to that of qRT-PCR.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>Our data clearly showed that BBTV was able to control the transcriptional level of each DNA component independently by through the promoter sequences in the intergenic region. Moreover, a cis-acting element from DNA-N component had a high transcriptional activity.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31296162</PMID><DateCompleted><Year>2019</Year><Month>12</Month><Day>09</Day></DateCompleted><DateRevised><Year>2020</Year><Month>02</Month><Day>25</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>20</Volume><Issue>1</Issue><PubDate><Year>2019</Year><Month>Jul</Month><Day>11</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Independent modulation of individual genomic component transcription and a cis-acting element related to high transcriptional activity in a multipartite DNA virus.</ArticleTitle><Pagination><MedlinePgn>573</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-019-5901-0</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The genome of Banana bunchy top virus (BBTV) consists of at least six circular, single-stranded DNA components of ~ 1 kb in length. Some BBTV isolates may also carry satellite DNA molecules that are not essential for BBTV infection. The relation between multipartite DNA virus replication and their transcriptional levels and the underlying mechanism remain unclear.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">To understand the coordinated replication and transcription of the multiple genomic components, the absolute amounts of each BBTV DNA component were measured by real-time PCR (qPCR), and their transcriptional levels were determined by RNAseq and reverse transcription-qPCR (qRT-PCR). Significant differences were found in the absolute amounts of individual BBTV genomic components. Transcriptional levels of each BBTV genomic component obtained from the RNAseq data matched closely to those obtained from qRT-PCR, but did not correspond to the absolute amount of each DNA component. The ratio of transcript over DNA copies ranged from 46.21 to 1059.44%, which was possibly regulated by the promoter region in the intergenic region of each component. To further determine this speculation, the promoter region of the DNA-S, -M or -N was constructed to the upstream of green fluorescent protein (GFP) gene for transient expression by agrobacterium-mediated transformation method. The qRT-PCR showed the highest transcriptional activity was promoted by DNA-N promoter, about 386.58% activity comparing with CaMV 35S promoter. Confocal microscopy observation showed that the intensity of green fluorescence was corresponding to that of qRT-PCR.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Our data clearly showed that BBTV was able to control the transcriptional level of each DNA component independently by through the promoter sequences in the intergenic region. Moreover, a cis-acting element from DNA-N component had a high transcriptional activity.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yu</LastName><ForeName>Nai-Tong</ForeName><Initials>NT</Initials><AffiliationInfo><Affiliation>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xie</LastName><ForeName>Hui-Min</ForeName><Initials>HM</Initials><AffiliationInfo><Affiliation>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Yu-Liang</ForeName><Initials>YL</Initials><AffiliationInfo><Affiliation>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Jian-Hua</ForeName><Initials>JH</Initials><AffiliationInfo><Affiliation>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xiong</LastName><ForeName>Zhongguo</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, 85721, USA. zxiong@email.arizona.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Zhi-Xin</ForeName><Initials>ZX</Initials><AffiliationInfo><Affiliation>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China. liuzhixin@itbb.org.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>31401709</GrantID><Agency>National Natural Science Foundation of China</Agency><Country></Country></Grant><Grant><GrantID>No. 20153130</GrantID><Agency>Hainan Provincial Natural Science Foundation</Agency><Country></Country></Grant><Grant><GrantID>No.19CXTD-33</GrantID><Agency>Central Public-interest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences</Agency><Country></Country></Grant><Grant><GrantID>CSTC-QN201704</GrantID><Agency>the Young Elite Scientists Sponsorship Program by CSTC</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>07</Month><Day>11</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012333">RNA, Messenger</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D052658" MajorTopicYN="N">Babuvirus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="Y">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012333" MajorTopicYN="N">RNA, Messenger</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D050436" MajorTopicYN="N">Regulatory Elements, Transcriptional</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014158" MajorTopicYN="Y">Transcription, Genetic</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Banana bunchy top virus</Keyword><Keyword MajorTopicYN="N">Cis-acting element</Keyword><Keyword 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sortKey="Yu, Nai Tong" sort="Yu, Nai Tong" uniqKey="Yu N" first="Nai-Tong" last="Yu">Nai-Tong Yu</name></noRegion><name sortKey="Liu, Zhi Xin" sort="Liu, Zhi Xin" uniqKey="Liu Z" first="Zhi-Xin" last="Liu">Zhi-Xin Liu</name><name sortKey="Wang, Jian Hua" sort="Wang, Jian Hua" uniqKey="Wang J" first="Jian-Hua" last="Wang">Jian-Hua Wang</name><name sortKey="Xie, Hui Min" sort="Xie, Hui Min" uniqKey="Xie H" first="Hui-Min" last="Xie">Hui-Min Xie</name><name sortKey="Zhang, Yu Liang" sort="Zhang, Yu Liang" uniqKey="Zhang Y" first="Yu-Liang" last="Zhang">Yu-Liang Zhang</name></country><country name="États-Unis"><noRegion><name sortKey="Xiong, Zhongguo" sort="Xiong, Zhongguo" uniqKey="Xiong Z" first="Zhongguo" last="Xiong">Zhongguo Xiong</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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