Ontology type: schema:ScholarlyArticle
2017-03
AUTHORSWenjing Cui, Jintao Cheng, Shengnan Miao, Li Zhou, Zhongmei Liu, Junling Guo, Zhemin Zhou
ABSTRACTTuneable gene expression controlled by synthetic biological elements is of great importance to biotechnology and synthetic biology. The synthetic riboswitch is a pivotal type of elements that can easily control the heterologous gene expression in diverse bacteria. In this study, the theophylline-dependent synthetic riboswitch and the corresponding variants with varied spacings between Shine-Dalgarno (SD) sequence and start codon were employed to comprehensively characterize the induction and regulation properties through combining a strong promoter aprE in Bacillus subtilis. Amongst the sets of newly constructed expression elements, the expression element with 9-bp spacing exhibited the higher expression level, a superior induction fold performance, and a considerably lower leaky expression than those with longer or shorter spacings. The riboswitch expression element with 9-bp spacing showed an approximately linear dose dependence from 0 to 8 mM of theophylline. Modification of the SD sequence through the insertion of a single A base prior to the native sequence enables the increase of the expression level post induction while decreasing the induction fold as a result of the elevated leaky level. The riboswitch elements with the engineered SD and the optimal 9-bp spacing exhibit an altered dose dependency in which the approximately linear range shifts to 0-4 mM, although it has a similar profile to the induction process. These results not only provide comprehensive data for the induced expression by a theophylline riboswitch combined with a strong native promoter from B. subtilis but also provide the two pivotal features of SD essential to the modular design of other synthetic riboswitches. More... »
PAGES2107-2120
http://scigraph.springernature.com/pub.10.1007/s00253-016-7988-4
DOIhttp://dx.doi.org/10.1007/s00253-016-7988-4
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1028784875
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/27986992
JSON-LD is the canonical representation for SciGraph data.
TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT
[
{
"@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json",
"about": [
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Genetics",
"type": "DefinedTerm"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Biological Sciences",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Bacillus subtilis",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Bacterial Proteins",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Base Sequence",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Codon, Initiator",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Gene Expression Regulation, Bacterial",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Peptide Chain Elongation, Translational",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Promoter Regions, Genetic",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Riboswitch",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Theophylline",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "Jiangnan University",
"id": "https://www.grid.ac/institutes/grid.258151.a",
"name": [
"School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China",
"Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, Jiangsu, China"
],
"type": "Organization"
},
"familyName": "Cui",
"givenName": "Wenjing",
"id": "sg:person.01303557140.44",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01303557140.44"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Jiangnan University",
"id": "https://www.grid.ac/institutes/grid.258151.a",
"name": [
"School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China"
],
"type": "Organization"
},
"familyName": "Cheng",
"givenName": "Jintao",
"id": "sg:person.01305332665.01",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01305332665.01"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Jiangnan University",
"id": "https://www.grid.ac/institutes/grid.258151.a",
"name": [
"School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China"
],
"type": "Organization"
},
"familyName": "Miao",
"givenName": "Shengnan",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Jiangnan University",
"id": "https://www.grid.ac/institutes/grid.258151.a",
"name": [
"School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China",
"Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, Jiangsu, China"
],
"type": "Organization"
},
"familyName": "Zhou",
"givenName": "Li",
"id": "sg:person.01317022424.30",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01317022424.30"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Jiangnan University",
"id": "https://www.grid.ac/institutes/grid.258151.a",
"name": [
"School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China",
"Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, Jiangsu, China"
],
"type": "Organization"
},
"familyName": "Liu",
"givenName": "Zhongmei",
"id": "sg:person.0660472025.99",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0660472025.99"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Jiangnan University",
"id": "https://www.grid.ac/institutes/grid.258151.a",
"name": [
"School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China",
"Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, Jiangsu, China"
],
"type": "Organization"
},
"familyName": "Guo",
"givenName": "Junling",
"id": "sg:person.0630041765.48",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0630041765.48"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Jiangnan University",
"id": "https://www.grid.ac/institutes/grid.258151.a",
"name": [
"School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China",
"Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, Jiangsu, China"
],
"type": "Organization"
},
"familyName": "Zhou",
"givenName": "Zhemin",
"id": "sg:person.0774720425.90",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0774720425.90"
],
"type": "Person"
}
],
"citation": [
{
"id": "https://doi.org/10.1128/jb.01673-09",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1003572223"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/22.23.4953",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1004183838"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gkh321",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1005614544"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/aem.01697-14",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1008941709"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.plasmid.2005.05.001",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1013611181"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/s0378-1119(99)00210-3",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1014159565"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1146/annurev.biochem.78.070507.135656",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1014292039"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0029266",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1022884783"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/aem.67.1.403-410.2001",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1032274862"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.jbiotec.2006.12.007",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1034901016"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.sbi.2005.05.003",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1035260291"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s12934-015-0341-2",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1036655403",
"https://doi.org/10.1186/s12934-015-0341-2"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nrm1403",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1041144702",
"https://doi.org/10.1038/nrm1403"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nrm1403",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1041144702",
"https://doi.org/10.1038/nrm1403"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nrm1403",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1041144702",
"https://doi.org/10.1038/nrm1403"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature01145",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1042040531",
"https://doi.org/10.1038/nature01145"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/aem.01537-10",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1043164164"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/aem.71.12.8818-8824.2005",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1043712429"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/jb.185.18.5372-5379.2003",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1045762293"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/pcp/pct115",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1048630889"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/s0092-8674(03)00391-x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1048727079"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.biotechadv.2011.09.013",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1049255084"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.bbagrm.2014.05.005",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1049285290"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1111/j.1365-2958.1992.tb01548.x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1049499653"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gks989",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1052247808"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/cb9003139",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055227298"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1080/15476286.2015.1017235",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1058402959"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1099/mic.0.067322-0",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1060395549"
],
"type": "CreativeWork"
},
{
"id": "https://app.dimensions.ai/details/publication/pub.1076904140",
"type": "CreativeWork"
}
],
"datePublished": "2017-03",
"datePublishedReg": "2017-03-01",
"description": "Tuneable gene expression controlled by synthetic biological elements is of great importance to biotechnology and synthetic biology. The synthetic riboswitch is a pivotal type of elements that can easily control the heterologous gene expression in diverse bacteria. In this study, the theophylline-dependent synthetic riboswitch and the corresponding variants with varied spacings between Shine-Dalgarno (SD) sequence and start codon were employed to comprehensively characterize the induction and regulation properties through combining a strong promoter aprE in Bacillus subtilis. Amongst the sets of newly constructed expression elements, the expression element with 9-bp spacing exhibited the higher expression level, a superior induction fold performance, and a considerably lower leaky expression than those with longer or shorter spacings. The riboswitch expression element with 9-bp spacing showed an approximately linear dose dependence from 0 to 8\u00a0mM of theophylline. Modification of the SD sequence through the insertion of a single A base prior to the native sequence enables the increase of the expression level post induction while decreasing the induction fold as a result of the elevated leaky level. The riboswitch elements with the engineered SD and the optimal 9-bp spacing exhibit an altered dose dependency in which the approximately linear range shifts to 0-4\u00a0mM, although it has a similar profile to the induction process. These results not only provide comprehensive data for the induced expression by a theophylline riboswitch combined with a strong native promoter from B. subtilis but also provide the two pivotal features of SD essential to the modular design of other synthetic riboswitches.",
"genre": "research_article",
"id": "sg:pub.10.1007/s00253-016-7988-4",
"inLanguage": [
"en"
],
"isAccessibleForFree": false,
"isFundedItemOf": [
{
"id": "sg:grant.7204578",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1083533",
"issn": [
"0175-7598",
"1432-0614"
],
"name": "Applied Microbiology and Biotechnology",
"type": "Periodical"
},
{
"issueNumber": "5",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "101"
}
],
"name": "Comprehensive characterization of a theophylline riboswitch reveals two pivotal features of Shine-Dalgarno influencing activated translation property",
"pagination": "2107-2120",
"productId": [
{
"name": "readcube_id",
"type": "PropertyValue",
"value": [
"891fb17a82c89925e0f320a5ba400b697fdffca5d278713204b70b6153608f86"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"27986992"
]
},
{
"name": "nlm_unique_id",
"type": "PropertyValue",
"value": [
"8406612"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1007/s00253-016-7988-4"
]
},
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1028784875"
]
}
],
"sameAs": [
"https://doi.org/10.1007/s00253-016-7988-4",
"https://app.dimensions.ai/details/publication/pub.1028784875"
],
"sdDataset": "articles",
"sdDatePublished": "2019-04-11T12:40",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000363_0000000363/records_70053_00000001.jsonl",
"type": "ScholarlyArticle",
"url": "https://link.springer.com/10.1007%2Fs00253-016-7988-4"
}
]
Download the RDF metadata as: json-ld nt turtle xml License info
JSON-LD is a popular format for linked data which is fully compatible with JSON.
curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/s00253-016-7988-4'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/s00253-016-7988-4'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s00253-016-7988-4'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s00253-016-7988-4'
This table displays all metadata directly associated to this object as RDF triples.
232 TRIPLES
21 PREDICATES
65 URIs
30 LITERALS
18 BLANK NODES