Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2011-12

AUTHORS

Kang Zhou, Lihan Zhou, Qing 'En Lim, Ruiyang Zou, Gregory Stephanopoulos, Heng-Phon Too

ABSTRACT

BACKGROUND: Accurate interpretation of quantitative PCR (qPCR) data requires normalization using constitutively expressed reference genes. Ribosomal RNA is often used as a reference gene for transcriptional studies in E. coli. However, the choice of reliable reference genes has not been systematically validated. The objective of this study is to identify a set of reliable reference genes for transcription analysis in recombinant protein over-expression studies in E. coli. RESULTS: In this study, the meta-analysis of 240 sets of single-channel Affymetrix microarray data representing over-expressions of 63 distinct recombinant proteins in various E. coli strains identified twenty candidate reference genes that were stably expressed across all conditions. The expression of these twenty genes and two commonly used reference genes, rrsA encoding ribosomal RNA 16S and ihfB, was quantified by qPCR in E. coli cells over-expressing four genes of the 1-Deoxy-D-Xylulose 5-Phosphate pathway. From these results, two independent statistical algorithms identified three novel reference genes cysG, hcaT, and idnT but not rrsA and ihfB as highly invariant in two E. coli strains, across different growth temperatures and induction conditions. Transcriptomic data normalized by the geometric average of these three genes demonstrated that genes of the lycopene synthetic pathway maintained steady expression upon enzyme overexpression. In contrast, the use of rrsA or ihfB as reference genes led to the mis-interpretation that lycopene pathway genes were regulated during enzyme over-expression. CONCLUSION: This study identified cysG/hcaT/idnT to be reliable novel reference genes for transcription analysis in recombinant protein producing E. coli. More... »

PAGES

18

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2199-12-18

DOI

http://dx.doi.org/10.1186/1471-2199-12-18

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1048912473

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/21513543


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

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": "Escherichia coli", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Expression Profiling", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genes, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Metabolic Networks and Pathways", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Polymerase Chain Reaction", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Protein Array Analysis", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Recombinant Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Reference Standards", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Up-Regulation", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Singapore-MIT Alliance for Research and Technology", 
          "id": "https://www.grid.ac/institutes/grid.429485.6", 
          "name": [
            "Chemical and Pharmaceutical Engineering, Singapore-MIT Alliance, 4 Engineering Drive 3, Singapore"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Zhou", 
        "givenName": "Kang", 
        "id": "sg:person.01167116124.68", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01167116124.68"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "National University of Singapore", 
          "id": "https://www.grid.ac/institutes/grid.4280.e", 
          "name": [
            "Chemical and Pharmaceutical Engineering, Singapore-MIT Alliance, 4 Engineering Drive 3, Singapore", 
            "Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Zhou", 
        "givenName": "Lihan", 
        "id": "sg:person.0711144463.63", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0711144463.63"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "National University of Singapore", 
          "id": "https://www.grid.ac/institutes/grid.4280.e", 
          "name": [
            "Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lim", 
        "givenName": "Qing 'En", 
        "id": "sg:person.01315743666.22", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01315743666.22"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Singapore-MIT Alliance for Research and Technology", 
          "id": "https://www.grid.ac/institutes/grid.429485.6", 
          "name": [
            "Chemical and Pharmaceutical Engineering, Singapore-MIT Alliance, 4 Engineering Drive 3, Singapore"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Zou", 
        "givenName": "Ruiyang", 
        "id": "sg:person.01016417510.02", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01016417510.02"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Massachusetts Institute of Technology", 
          "id": "https://www.grid.ac/institutes/grid.116068.8", 
          "name": [
            "Chemical and Pharmaceutical Engineering, Singapore-MIT Alliance, 4 Engineering Drive 3, Singapore", 
            "Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Stephanopoulos", 
        "givenName": "Gregory", 
        "id": "sg:person.014617115137.99", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014617115137.99"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "National University of Singapore", 
          "id": "https://www.grid.ac/institutes/grid.4280.e", 
          "name": [
            "Chemical and Pharmaceutical Engineering, Singapore-MIT Alliance, 4 Engineering Drive 3, Singapore", 
            "Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Too", 
        "givenName": "Heng-Phon", 
        "id": "sg:person.01006722667.07", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01006722667.07"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1093/nar/gkm815", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006532483"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/aem.02750-07", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007384955"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1105/tpc.6.8.1107", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007462489"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/aem.00914-09", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010143760"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/bit.20912", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010675974"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/bit.20912", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010675974"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/1097-0290(20000220)72:4<408::aid-bit1003>3.0.co;2-h", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010803217"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1754-6834-1-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011011803", 
          "https://doi.org/10.1186/1754-6834-1-8"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00395-007-0649-0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011220824", 
          "https://doi.org/10.1007/s00395-007-0649-0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00395-007-0649-0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011220824", 
          "https://doi.org/10.1007/s00395-007-0649-0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/bit.22379", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015228133"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/bit.22379", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015228133"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.ymben.2005.08.005", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016352117"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1475-2859-6-30", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017144984", 
          "https://doi.org/10.1186/1475-2859-6-30"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/bit.22084", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017643650"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1159/000109945", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020794746"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0003-2697(02)00311-1", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024832430"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0003-2697(02)00311-1", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024832430"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1158/0008-5472.can-04-0496", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025731697"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1191652", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030042869"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkm740", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031292231"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/bit.20704", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033172401"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/bit.20704", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033172401"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.ymben.2004.10.002", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033219497"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1038/msb.2009.34", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036105985"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1038/msb.2009.34", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036105985"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-11-75", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036224619", 
          "https://doi.org/10.1186/1471-2164-11-75"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt1029", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038843880", 
          "https://doi.org/10.1038/nbt1029"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt1029", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038843880", 
          "https://doi.org/10.1038/nbt1029"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2002-3-7-research0034", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039751959", 
          "https://doi.org/10.1186/gb-2002-3-7-research0034"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/labinvest.3700208", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044148244", 
          "https://doi.org/10.1038/labinvest.3700208"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/labinvest.3700208", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044148244", 
          "https://doi.org/10.1038/labinvest.3700208"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/labinvest.3700208", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044148244", 
          "https://doi.org/10.1038/labinvest.3700208"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.jbiotec.2008.02.023", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044583537"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1132067", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049271832"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.2307/3869889", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1070467849"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1082972383", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1083288785", 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2011-12", 
    "datePublishedReg": "2011-12-01", 
    "description": "BACKGROUND: Accurate interpretation of quantitative PCR (qPCR) data requires normalization using constitutively expressed reference genes. Ribosomal RNA is often used as a reference gene for transcriptional studies in E. coli. However, the choice of reliable reference genes has not been systematically validated. The objective of this study is to identify a set of reliable reference genes for transcription analysis in recombinant protein over-expression studies in E. coli.\nRESULTS: In this study, the meta-analysis of 240 sets of single-channel Affymetrix microarray data representing over-expressions of 63 distinct recombinant proteins in various E. coli strains identified twenty candidate reference genes that were stably expressed across all conditions. The expression of these twenty genes and two commonly used reference genes, rrsA encoding ribosomal RNA 16S and ihfB, was quantified by qPCR in E. coli cells over-expressing four genes of the 1-Deoxy-D-Xylulose 5-Phosphate pathway. From these results, two independent statistical algorithms identified three novel reference genes cysG, hcaT, and idnT but not rrsA and ihfB as highly invariant in two E. coli strains, across different growth temperatures and induction conditions. Transcriptomic data normalized by the geometric average of these three genes demonstrated that genes of the lycopene synthetic pathway maintained steady expression upon enzyme overexpression. In contrast, the use of rrsA or ihfB as reference genes led to the mis-interpretation that lycopene pathway genes were regulated during enzyme over-expression.\nCONCLUSION: This study identified cysG/hcaT/idnT to be reliable novel reference genes for transcription analysis in recombinant protein producing E. coli.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/1471-2199-12-18", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1356898", 
        "issn": [
          "1471-2199"
        ], 
        "name": "BMC Molecular Biology", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "12"
      }
    ], 
    "name": "Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR", 
    "pagination": "18", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "e9024bfa0e8750275ba815171ef4384ef0a415d115ee272c3e25d1b9d0d51387"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "21513543"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "100966983"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1471-2199-12-18"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1048912473"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1471-2199-12-18", 
      "https://app.dimensions.ai/details/publication/pub.1048912473"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T15:00", 
    "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/v90/0000000001_0000000264/records_8663_00000508.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1186%2F1471-2199-12-18"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

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.10.1186/1471-2199-12-18'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2199-12-18'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2199-12-18'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2199-12-18'


 

This table displays all metadata directly associated to this object as RDF triples.

239 TRIPLES      21 PREDICATES      67 URIs      30 LITERALS      18 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1471-2199-12-18 schema:about N057f5fd0777b46cfaa082ff59d6fd3ab
2 N371b29e2dcac453a986857159dad1ba0
3 N49a5dd6df8194e2d840242fcb46b5c54
4 N5ef4050f9b6747adb1d4fd189b8cbd27
5 N5f43b34bcbd54aa49e5f4a9d34b1271f
6 N78c6e46585b342f5b66a6d419e33a51f
7 N9f68e19427534ddcbeee36bca9891dc6
8 Ndfc2eb2b7aba48cf98642f8ac641ce55
9 Nff64f0d53b654503940b941faf210074
10 anzsrc-for:06
11 anzsrc-for:0604
12 schema:author N67e6cfe4005947f3beb505db885f2836
13 schema:citation sg:pub.10.1007/s00395-007-0649-0
14 sg:pub.10.1038/labinvest.3700208
15 sg:pub.10.1038/nbt1029
16 sg:pub.10.1186/1471-2164-11-75
17 sg:pub.10.1186/1475-2859-6-30
18 sg:pub.10.1186/1754-6834-1-8
19 sg:pub.10.1186/gb-2002-3-7-research0034
20 https://app.dimensions.ai/details/publication/pub.1082972383
21 https://app.dimensions.ai/details/publication/pub.1083288785
22 https://doi.org/10.1002/1097-0290(20000220)72:4<408::aid-bit1003>3.0.co;2-h
23 https://doi.org/10.1002/bit.20704
24 https://doi.org/10.1002/bit.20912
25 https://doi.org/10.1002/bit.22084
26 https://doi.org/10.1002/bit.22379
27 https://doi.org/10.1016/j.jbiotec.2008.02.023
28 https://doi.org/10.1016/j.ymben.2004.10.002
29 https://doi.org/10.1016/j.ymben.2005.08.005
30 https://doi.org/10.1016/s0003-2697(02)00311-1
31 https://doi.org/10.1038/msb.2009.34
32 https://doi.org/10.1093/nar/gkm740
33 https://doi.org/10.1093/nar/gkm815
34 https://doi.org/10.1105/tpc.6.8.1107
35 https://doi.org/10.1126/science.1132067
36 https://doi.org/10.1126/science.1191652
37 https://doi.org/10.1128/aem.00914-09
38 https://doi.org/10.1128/aem.02750-07
39 https://doi.org/10.1158/0008-5472.can-04-0496
40 https://doi.org/10.1159/000109945
41 https://doi.org/10.2307/3869889
42 schema:datePublished 2011-12
43 schema:datePublishedReg 2011-12-01
44 schema:description BACKGROUND: Accurate interpretation of quantitative PCR (qPCR) data requires normalization using constitutively expressed reference genes. Ribosomal RNA is often used as a reference gene for transcriptional studies in E. coli. However, the choice of reliable reference genes has not been systematically validated. The objective of this study is to identify a set of reliable reference genes for transcription analysis in recombinant protein over-expression studies in E. coli. RESULTS: In this study, the meta-analysis of 240 sets of single-channel Affymetrix microarray data representing over-expressions of 63 distinct recombinant proteins in various E. coli strains identified twenty candidate reference genes that were stably expressed across all conditions. The expression of these twenty genes and two commonly used reference genes, rrsA encoding ribosomal RNA 16S and ihfB, was quantified by qPCR in E. coli cells over-expressing four genes of the 1-Deoxy-D-Xylulose 5-Phosphate pathway. From these results, two independent statistical algorithms identified three novel reference genes cysG, hcaT, and idnT but not rrsA and ihfB as highly invariant in two E. coli strains, across different growth temperatures and induction conditions. Transcriptomic data normalized by the geometric average of these three genes demonstrated that genes of the lycopene synthetic pathway maintained steady expression upon enzyme overexpression. In contrast, the use of rrsA or ihfB as reference genes led to the mis-interpretation that lycopene pathway genes were regulated during enzyme over-expression. CONCLUSION: This study identified cysG/hcaT/idnT to be reliable novel reference genes for transcription analysis in recombinant protein producing E. coli.
45 schema:genre research_article
46 schema:inLanguage en
47 schema:isAccessibleForFree true
48 schema:isPartOf N993bf7832f604c099fe895e0f695b9ef
49 Nc02e2b8bebc24fb593d8d45657fc041f
50 sg:journal.1356898
51 schema:name Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR
52 schema:pagination 18
53 schema:productId N41c41605113c42d8983b79167da5310e
54 N8deb05056ee24ab58dded13c43274465
55 N992c11108fe1479da890c02223b785fa
56 Nd421f4971c2f48e397854b437e518d88
57 Ned6c506c676d4a628f3690cfc49db232
58 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048912473
59 https://doi.org/10.1186/1471-2199-12-18
60 schema:sdDatePublished 2019-04-10T15:00
61 schema:sdLicense https://scigraph.springernature.com/explorer/license/
62 schema:sdPublisher N37baefe89abc4a1f9abfa2d19eded5b9
63 schema:url http://link.springer.com/10.1186%2F1471-2199-12-18
64 sgo:license sg:explorer/license/
65 sgo:sdDataset articles
66 rdf:type schema:ScholarlyArticle
67 N057f5fd0777b46cfaa082ff59d6fd3ab schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
68 schema:name Reference Standards
69 rdf:type schema:DefinedTerm
70 N1533c997d54646ac9f1ce87192ddcb6a rdf:first sg:person.01006722667.07
71 rdf:rest rdf:nil
72 N371b29e2dcac453a986857159dad1ba0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
73 schema:name Up-Regulation
74 rdf:type schema:DefinedTerm
75 N37baefe89abc4a1f9abfa2d19eded5b9 schema:name Springer Nature - SN SciGraph project
76 rdf:type schema:Organization
77 N41c41605113c42d8983b79167da5310e schema:name dimensions_id
78 schema:value pub.1048912473
79 rdf:type schema:PropertyValue
80 N49a5dd6df8194e2d840242fcb46b5c54 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
81 schema:name Escherichia coli
82 rdf:type schema:DefinedTerm
83 N5ef4050f9b6747adb1d4fd189b8cbd27 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
84 schema:name Genes, Bacterial
85 rdf:type schema:DefinedTerm
86 N5f43b34bcbd54aa49e5f4a9d34b1271f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
87 schema:name Protein Array Analysis
88 rdf:type schema:DefinedTerm
89 N67e6cfe4005947f3beb505db885f2836 rdf:first sg:person.01167116124.68
90 rdf:rest Nfa51d3a8ea7542b2a2c02f330b13146c
91 N78c6e46585b342f5b66a6d419e33a51f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
92 schema:name Metabolic Networks and Pathways
93 rdf:type schema:DefinedTerm
94 N8deb05056ee24ab58dded13c43274465 schema:name pubmed_id
95 schema:value 21513543
96 rdf:type schema:PropertyValue
97 N8f7a51f1d2c540c38acd9167e41d5197 rdf:first sg:person.01016417510.02
98 rdf:rest Nf4335b2bd1c647148c221814214de465
99 N992c11108fe1479da890c02223b785fa schema:name nlm_unique_id
100 schema:value 100966983
101 rdf:type schema:PropertyValue
102 N993bf7832f604c099fe895e0f695b9ef schema:issueNumber 1
103 rdf:type schema:PublicationIssue
104 N9f68e19427534ddcbeee36bca9891dc6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
105 schema:name Recombinant Proteins
106 rdf:type schema:DefinedTerm
107 Nc02e2b8bebc24fb593d8d45657fc041f schema:volumeNumber 12
108 rdf:type schema:PublicationVolume
109 Nd421f4971c2f48e397854b437e518d88 schema:name readcube_id
110 schema:value e9024bfa0e8750275ba815171ef4384ef0a415d115ee272c3e25d1b9d0d51387
111 rdf:type schema:PropertyValue
112 Nde8fbb51b6974b06a1ee53932e63e4f6 rdf:first sg:person.01315743666.22
113 rdf:rest N8f7a51f1d2c540c38acd9167e41d5197
114 Ndfc2eb2b7aba48cf98642f8ac641ce55 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
115 schema:name Polymerase Chain Reaction
116 rdf:type schema:DefinedTerm
117 Ned6c506c676d4a628f3690cfc49db232 schema:name doi
118 schema:value 10.1186/1471-2199-12-18
119 rdf:type schema:PropertyValue
120 Nf4335b2bd1c647148c221814214de465 rdf:first sg:person.014617115137.99
121 rdf:rest N1533c997d54646ac9f1ce87192ddcb6a
122 Nfa51d3a8ea7542b2a2c02f330b13146c rdf:first sg:person.0711144463.63
123 rdf:rest Nde8fbb51b6974b06a1ee53932e63e4f6
124 Nff64f0d53b654503940b941faf210074 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
125 schema:name Gene Expression Profiling
126 rdf:type schema:DefinedTerm
127 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
128 schema:name Biological Sciences
129 rdf:type schema:DefinedTerm
130 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
131 schema:name Genetics
132 rdf:type schema:DefinedTerm
133 sg:journal.1356898 schema:issn 1471-2199
134 schema:name BMC Molecular Biology
135 rdf:type schema:Periodical
136 sg:person.01006722667.07 schema:affiliation https://www.grid.ac/institutes/grid.4280.e
137 schema:familyName Too
138 schema:givenName Heng-Phon
139 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01006722667.07
140 rdf:type schema:Person
141 sg:person.01016417510.02 schema:affiliation https://www.grid.ac/institutes/grid.429485.6
142 schema:familyName Zou
143 schema:givenName Ruiyang
144 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01016417510.02
145 rdf:type schema:Person
146 sg:person.01167116124.68 schema:affiliation https://www.grid.ac/institutes/grid.429485.6
147 schema:familyName Zhou
148 schema:givenName Kang
149 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01167116124.68
150 rdf:type schema:Person
151 sg:person.01315743666.22 schema:affiliation https://www.grid.ac/institutes/grid.4280.e
152 schema:familyName Lim
153 schema:givenName Qing 'En
154 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01315743666.22
155 rdf:type schema:Person
156 sg:person.014617115137.99 schema:affiliation https://www.grid.ac/institutes/grid.116068.8
157 schema:familyName Stephanopoulos
158 schema:givenName Gregory
159 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014617115137.99
160 rdf:type schema:Person
161 sg:person.0711144463.63 schema:affiliation https://www.grid.ac/institutes/grid.4280.e
162 schema:familyName Zhou
163 schema:givenName Lihan
164 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0711144463.63
165 rdf:type schema:Person
166 sg:pub.10.1007/s00395-007-0649-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011220824
167 https://doi.org/10.1007/s00395-007-0649-0
168 rdf:type schema:CreativeWork
169 sg:pub.10.1038/labinvest.3700208 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044148244
170 https://doi.org/10.1038/labinvest.3700208
171 rdf:type schema:CreativeWork
172 sg:pub.10.1038/nbt1029 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038843880
173 https://doi.org/10.1038/nbt1029
174 rdf:type schema:CreativeWork
175 sg:pub.10.1186/1471-2164-11-75 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036224619
176 https://doi.org/10.1186/1471-2164-11-75
177 rdf:type schema:CreativeWork
178 sg:pub.10.1186/1475-2859-6-30 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017144984
179 https://doi.org/10.1186/1475-2859-6-30
180 rdf:type schema:CreativeWork
181 sg:pub.10.1186/1754-6834-1-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011011803
182 https://doi.org/10.1186/1754-6834-1-8
183 rdf:type schema:CreativeWork
184 sg:pub.10.1186/gb-2002-3-7-research0034 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039751959
185 https://doi.org/10.1186/gb-2002-3-7-research0034
186 rdf:type schema:CreativeWork
187 https://app.dimensions.ai/details/publication/pub.1082972383 schema:CreativeWork
188 https://app.dimensions.ai/details/publication/pub.1083288785 schema:CreativeWork
189 https://doi.org/10.1002/1097-0290(20000220)72:4<408::aid-bit1003>3.0.co;2-h schema:sameAs https://app.dimensions.ai/details/publication/pub.1010803217
190 rdf:type schema:CreativeWork
191 https://doi.org/10.1002/bit.20704 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033172401
192 rdf:type schema:CreativeWork
193 https://doi.org/10.1002/bit.20912 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010675974
194 rdf:type schema:CreativeWork
195 https://doi.org/10.1002/bit.22084 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017643650
196 rdf:type schema:CreativeWork
197 https://doi.org/10.1002/bit.22379 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015228133
198 rdf:type schema:CreativeWork
199 https://doi.org/10.1016/j.jbiotec.2008.02.023 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044583537
200 rdf:type schema:CreativeWork
201 https://doi.org/10.1016/j.ymben.2004.10.002 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033219497
202 rdf:type schema:CreativeWork
203 https://doi.org/10.1016/j.ymben.2005.08.005 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016352117
204 rdf:type schema:CreativeWork
205 https://doi.org/10.1016/s0003-2697(02)00311-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024832430
206 rdf:type schema:CreativeWork
207 https://doi.org/10.1038/msb.2009.34 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036105985
208 rdf:type schema:CreativeWork
209 https://doi.org/10.1093/nar/gkm740 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031292231
210 rdf:type schema:CreativeWork
211 https://doi.org/10.1093/nar/gkm815 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006532483
212 rdf:type schema:CreativeWork
213 https://doi.org/10.1105/tpc.6.8.1107 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007462489
214 rdf:type schema:CreativeWork
215 https://doi.org/10.1126/science.1132067 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049271832
216 rdf:type schema:CreativeWork
217 https://doi.org/10.1126/science.1191652 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030042869
218 rdf:type schema:CreativeWork
219 https://doi.org/10.1128/aem.00914-09 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010143760
220 rdf:type schema:CreativeWork
221 https://doi.org/10.1128/aem.02750-07 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007384955
222 rdf:type schema:CreativeWork
223 https://doi.org/10.1158/0008-5472.can-04-0496 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025731697
224 rdf:type schema:CreativeWork
225 https://doi.org/10.1159/000109945 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020794746
226 rdf:type schema:CreativeWork
227 https://doi.org/10.2307/3869889 schema:sameAs https://app.dimensions.ai/details/publication/pub.1070467849
228 rdf:type schema:CreativeWork
229 https://www.grid.ac/institutes/grid.116068.8 schema:alternateName Massachusetts Institute of Technology
230 schema:name Chemical and Pharmaceutical Engineering, Singapore-MIT Alliance, 4 Engineering Drive 3, Singapore
231 Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, USA
232 rdf:type schema:Organization
233 https://www.grid.ac/institutes/grid.4280.e schema:alternateName National University of Singapore
234 schema:name Chemical and Pharmaceutical Engineering, Singapore-MIT Alliance, 4 Engineering Drive 3, Singapore
235 Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore
236 rdf:type schema:Organization
237 https://www.grid.ac/institutes/grid.429485.6 schema:alternateName Singapore-MIT Alliance for Research and Technology
238 schema:name Chemical and Pharmaceutical Engineering, Singapore-MIT Alliance, 4 Engineering Drive 3, Singapore
239 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...