Real-time PCR determination of rRNA gene copy number: absolute and relative quantification assays with Escherichia coli View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2007-12-11

AUTHORS

Changsoo Lee, Seungyong Lee, Seung Gu Shin, Seokhwan Hwang

ABSTRACT

Real-time polymerase chain reaction (PCR)-based methodology for the determination of rRNA gene (rrn) copy number was introduced and demonstrated. Both absolute and relative quantifications were tested with Escherichia coli. The separate detection of rRNA gene and chromosomal DNA was achieved using two primer sets, specific for 16S rRNA gene and for D-1-deoxyxylulose 5-phosphate synthase gene (dxs), respectively. As dxs is a single-copy gene of E. coli chromosomal DNA, the rrn copy number can be determined as the copy ratio of rrn to dxs. This methodology was successfully applied to determine the rrn copy number in E. coli cells. The results from absolute and relative quantifications were identical and highly reproducible with coefficient of variation (CV) values of 1.8–4.6%. The estimated rrn copy numbers also corresponded to the previously reported value in E. coli (i.e., 7), indicating that the results were reliable. The methodology introduced in this study is faster and cost-effective without safety problems compared to the traditionally used Southern blot analysis. The fundamentals in our methodology would be applicable to any microorganism, as long as having the sequence information of the rRNA gene and another chromosomal gene with a known copy number. More... »

PAGES

371-376

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/s00253-007-1300-6

DOI

http://dx.doi.org/10.1007/s00253-007-1300-6

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1030443497

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/18074129


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/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "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"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Escherichia coli", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Dosage", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genes, rRNA", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Polymerase Chain Reaction", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Reproducibility of Results", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Transferases", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Microbial Ecology Laboratory, Department of Microbiology and Environmental Change Institute (ECI), National University of Ireland, Galway, Republic of Ireland", 
          "id": "http://www.grid.ac/institutes/grid.6142.1", 
          "name": [
            "Microbial Ecology Laboratory, Department of Microbiology and Environmental Change Institute (ECI), National University of Ireland, Galway, Republic of Ireland"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lee", 
        "givenName": "Changsoo", 
        "id": "sg:person.01223414772.50", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01223414772.50"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "School of Environmental Science and Engineering, POSTECH, San 31, Hyoja-dong, Nam-gu, Pohang, 790-784, Gyungbuk, Republic of Korea", 
          "id": "http://www.grid.ac/institutes/grid.49100.3c", 
          "name": [
            "School of Environmental Science and Engineering, POSTECH, San 31, Hyoja-dong, Nam-gu, Pohang, 790-784, Gyungbuk, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lee", 
        "givenName": "Seungyong", 
        "id": "sg:person.01025676763.25", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01025676763.25"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "School of Environmental Science and Engineering, POSTECH, San 31, Hyoja-dong, Nam-gu, Pohang, 790-784, Gyungbuk, Republic of Korea", 
          "id": "http://www.grid.ac/institutes/grid.49100.3c", 
          "name": [
            "School of Environmental Science and Engineering, POSTECH, San 31, Hyoja-dong, Nam-gu, Pohang, 790-784, Gyungbuk, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Shin", 
        "givenName": "Seung Gu", 
        "id": "sg:person.01033143073.36", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01033143073.36"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "School of Environmental Science and Engineering, POSTECH, San 31, Hyoja-dong, Nam-gu, Pohang, 790-784, Gyungbuk, Republic of Korea", 
          "id": "http://www.grid.ac/institutes/grid.49100.3c", 
          "name": [
            "School of Environmental Science and Engineering, POSTECH, San 31, Hyoja-dong, Nam-gu, Pohang, 790-784, Gyungbuk, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hwang", 
        "givenName": "Seokhwan", 
        "id": "sg:person.01263620073.62", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01263620073.62"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1007/978-3-642-59524-0_3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037794192", 
          "https://doi.org/10.1007/978-3-642-59524-0_3"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s002530100760", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049788524", 
          "https://doi.org/10.1007/s002530100760"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2007-12-11", 
    "datePublishedReg": "2007-12-11", 
    "description": "Real-time polymerase chain reaction (PCR)-based methodology for the determination of rRNA gene (rrn) copy number was introduced and demonstrated. Both absolute and relative quantifications were tested with Escherichia coli. The separate detection of rRNA gene and chromosomal DNA was achieved using two primer sets, specific for 16S rRNA gene and for D-1-deoxyxylulose 5-phosphate synthase gene (dxs), respectively. As dxs is a single-copy gene of E. coli chromosomal DNA, the rrn copy number can be determined as the copy ratio of rrn to dxs. This methodology was successfully applied to determine the rrn copy number in E. coli cells. The results from absolute and relative quantifications were identical and highly reproducible with coefficient of variation (CV) values of 1.8\u20134.6%. The estimated rrn copy numbers also corresponded to the previously reported value in E. coli (i.e., 7), indicating that the results were reliable. The methodology introduced in this study is faster and cost-effective without safety problems compared to the traditionally used Southern blot analysis. The fundamentals in our methodology would be applicable to any microorganism, as long as having the sequence information of the rRNA gene and another chromosomal gene with a known copy number.", 
    "genre": "article", 
    "id": "sg:pub.10.1007/s00253-007-1300-6", 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1083533", 
        "issn": [
          "0175-7598", 
          "1432-0614"
        ], 
        "name": "Applied Microbiology and Biotechnology", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "2", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "78"
      }
    ], 
    "keywords": [
      "rrn copy number", 
      "rRNA gene copy numbers", 
      "rRNA gene", 
      "gene copy number", 
      "copy number", 
      "chromosomal DNA", 
      "E. coli chromosomal DNA", 
      "single-copy gene", 
      "Escherichia coli", 
      "relative quantification", 
      "E. coli cells", 
      "Southern blot analysis", 
      "chromosomal genes", 
      "synthase gene", 
      "coli cells", 
      "sequence information", 
      "genes", 
      "primer sets", 
      "blot analysis", 
      "E. coli", 
      "copy ratios", 
      "real-time polymerase chain reaction", 
      "coli", 
      "real-time PCR determination", 
      "DNA", 
      "quantification assays", 
      "polymerase chain reaction", 
      "rrnS", 
      "chain reaction", 
      "PCR determination", 
      "microorganisms", 
      "cells", 
      "assays", 
      "number", 
      "quantification", 
      "variation values", 
      "analysis", 
      "results", 
      "determination", 
      "study", 
      "information", 
      "set", 
      "separate detection", 
      "reaction", 
      "detection", 
      "DX", 
      "ratio", 
      "values", 
      "methodology", 
      "safety problems", 
      "fundamentals", 
      "coefficient", 
      "problem"
    ], 
    "name": "Real-time PCR determination of rRNA gene copy number: absolute and relative quantification assays with Escherichia coli", 
    "pagination": "371-376", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1030443497"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/s00253-007-1300-6"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "18074129"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1007/s00253-007-1300-6", 
      "https://app.dimensions.ai/details/publication/pub.1030443497"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2022-08-04T16:57", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20220804/entities/gbq_results/article/article_433.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1007/s00253-007-1300-6"
  }
]
 

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.10.1007/s00253-007-1300-6'

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/s00253-007-1300-6'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s00253-007-1300-6'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s00253-007-1300-6'


 

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

170 TRIPLES      21 PREDICATES      86 URIs      76 LITERALS      13 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/s00253-007-1300-6 schema:about N04b8a2df3f244c0fbff61282ee659ded
2 N53454aec0b1643d7a31f30af6e5c3465
3 N5ac3d0ca77ba4dd7adc61ba962ae1c74
4 N7fafd7a4242e419a9ab3638131f8e8ab
5 Nb3166e05dc1f45908a61aa635abb5866
6 Ncae40393e4a84a36af52ea4fb04ae3a7
7 anzsrc-for:06
8 anzsrc-for:0604
9 schema:author N0be3bf606afa48739b27791f74cf9035
10 schema:citation sg:pub.10.1007/978-3-642-59524-0_3
11 sg:pub.10.1007/s002530100760
12 schema:datePublished 2007-12-11
13 schema:datePublishedReg 2007-12-11
14 schema:description Real-time polymerase chain reaction (PCR)-based methodology for the determination of rRNA gene (rrn) copy number was introduced and demonstrated. Both absolute and relative quantifications were tested with Escherichia coli. The separate detection of rRNA gene and chromosomal DNA was achieved using two primer sets, specific for 16S rRNA gene and for D-1-deoxyxylulose 5-phosphate synthase gene (dxs), respectively. As dxs is a single-copy gene of E. coli chromosomal DNA, the rrn copy number can be determined as the copy ratio of rrn to dxs. This methodology was successfully applied to determine the rrn copy number in E. coli cells. The results from absolute and relative quantifications were identical and highly reproducible with coefficient of variation (CV) values of 1.8–4.6%. The estimated rrn copy numbers also corresponded to the previously reported value in E. coli (i.e., 7), indicating that the results were reliable. The methodology introduced in this study is faster and cost-effective without safety problems compared to the traditionally used Southern blot analysis. The fundamentals in our methodology would be applicable to any microorganism, as long as having the sequence information of the rRNA gene and another chromosomal gene with a known copy number.
15 schema:genre article
16 schema:isAccessibleForFree false
17 schema:isPartOf N1d016e29163b44a1829be2cec3f01061
18 N8627dadb15174d7fb0868585b023cdd6
19 sg:journal.1083533
20 schema:keywords DNA
21 DX
22 E. coli
23 E. coli cells
24 E. coli chromosomal DNA
25 Escherichia coli
26 PCR determination
27 Southern blot analysis
28 analysis
29 assays
30 blot analysis
31 cells
32 chain reaction
33 chromosomal DNA
34 chromosomal genes
35 coefficient
36 coli
37 coli cells
38 copy number
39 copy ratios
40 detection
41 determination
42 fundamentals
43 gene copy number
44 genes
45 information
46 methodology
47 microorganisms
48 number
49 polymerase chain reaction
50 primer sets
51 problem
52 quantification
53 quantification assays
54 rRNA gene
55 rRNA gene copy numbers
56 ratio
57 reaction
58 real-time PCR determination
59 real-time polymerase chain reaction
60 relative quantification
61 results
62 rrn copy number
63 rrnS
64 safety problems
65 separate detection
66 sequence information
67 set
68 single-copy gene
69 study
70 synthase gene
71 values
72 variation values
73 schema:name Real-time PCR determination of rRNA gene copy number: absolute and relative quantification assays with Escherichia coli
74 schema:pagination 371-376
75 schema:productId N344dd06db8db48b7a266c03e17e15e84
76 N650489b2bf194d258586c4339540fd16
77 Nc496a75083704f1bb86c19dd8dd48569
78 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030443497
79 https://doi.org/10.1007/s00253-007-1300-6
80 schema:sdDatePublished 2022-08-04T16:57
81 schema:sdLicense https://scigraph.springernature.com/explorer/license/
82 schema:sdPublisher Nf4bbffeab4474b85a644350fbbef26b9
83 schema:url https://doi.org/10.1007/s00253-007-1300-6
84 sgo:license sg:explorer/license/
85 sgo:sdDataset articles
86 rdf:type schema:ScholarlyArticle
87 N04b8a2df3f244c0fbff61282ee659ded schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
88 schema:name Transferases
89 rdf:type schema:DefinedTerm
90 N0be3bf606afa48739b27791f74cf9035 rdf:first sg:person.01223414772.50
91 rdf:rest N7181f757d2f4411c96aa727ba5239923
92 N1d016e29163b44a1829be2cec3f01061 schema:volumeNumber 78
93 rdf:type schema:PublicationVolume
94 N25a50ebdacc947a3861c32cd55a147b0 rdf:first sg:person.01033143073.36
95 rdf:rest N3a6ee18bb33c405fa15a5c240ee6483a
96 N344dd06db8db48b7a266c03e17e15e84 schema:name dimensions_id
97 schema:value pub.1030443497
98 rdf:type schema:PropertyValue
99 N3a6ee18bb33c405fa15a5c240ee6483a rdf:first sg:person.01263620073.62
100 rdf:rest rdf:nil
101 N53454aec0b1643d7a31f30af6e5c3465 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
102 schema:name Genes, rRNA
103 rdf:type schema:DefinedTerm
104 N5ac3d0ca77ba4dd7adc61ba962ae1c74 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
105 schema:name Gene Dosage
106 rdf:type schema:DefinedTerm
107 N650489b2bf194d258586c4339540fd16 schema:name doi
108 schema:value 10.1007/s00253-007-1300-6
109 rdf:type schema:PropertyValue
110 N7181f757d2f4411c96aa727ba5239923 rdf:first sg:person.01025676763.25
111 rdf:rest N25a50ebdacc947a3861c32cd55a147b0
112 N7fafd7a4242e419a9ab3638131f8e8ab schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
113 schema:name Reproducibility of Results
114 rdf:type schema:DefinedTerm
115 N8627dadb15174d7fb0868585b023cdd6 schema:issueNumber 2
116 rdf:type schema:PublicationIssue
117 Nb3166e05dc1f45908a61aa635abb5866 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
118 schema:name Polymerase Chain Reaction
119 rdf:type schema:DefinedTerm
120 Nc496a75083704f1bb86c19dd8dd48569 schema:name pubmed_id
121 schema:value 18074129
122 rdf:type schema:PropertyValue
123 Ncae40393e4a84a36af52ea4fb04ae3a7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
124 schema:name Escherichia coli
125 rdf:type schema:DefinedTerm
126 Nf4bbffeab4474b85a644350fbbef26b9 schema:name Springer Nature - SN SciGraph project
127 rdf:type schema:Organization
128 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
129 schema:name Biological Sciences
130 rdf:type schema:DefinedTerm
131 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
132 schema:name Genetics
133 rdf:type schema:DefinedTerm
134 sg:journal.1083533 schema:issn 0175-7598
135 1432-0614
136 schema:name Applied Microbiology and Biotechnology
137 schema:publisher Springer Nature
138 rdf:type schema:Periodical
139 sg:person.01025676763.25 schema:affiliation grid-institutes:grid.49100.3c
140 schema:familyName Lee
141 schema:givenName Seungyong
142 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01025676763.25
143 rdf:type schema:Person
144 sg:person.01033143073.36 schema:affiliation grid-institutes:grid.49100.3c
145 schema:familyName Shin
146 schema:givenName Seung Gu
147 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01033143073.36
148 rdf:type schema:Person
149 sg:person.01223414772.50 schema:affiliation grid-institutes:grid.6142.1
150 schema:familyName Lee
151 schema:givenName Changsoo
152 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01223414772.50
153 rdf:type schema:Person
154 sg:person.01263620073.62 schema:affiliation grid-institutes:grid.49100.3c
155 schema:familyName Hwang
156 schema:givenName Seokhwan
157 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01263620073.62
158 rdf:type schema:Person
159 sg:pub.10.1007/978-3-642-59524-0_3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037794192
160 https://doi.org/10.1007/978-3-642-59524-0_3
161 rdf:type schema:CreativeWork
162 sg:pub.10.1007/s002530100760 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049788524
163 https://doi.org/10.1007/s002530100760
164 rdf:type schema:CreativeWork
165 grid-institutes:grid.49100.3c schema:alternateName School of Environmental Science and Engineering, POSTECH, San 31, Hyoja-dong, Nam-gu, Pohang, 790-784, Gyungbuk, Republic of Korea
166 schema:name School of Environmental Science and Engineering, POSTECH, San 31, Hyoja-dong, Nam-gu, Pohang, 790-784, Gyungbuk, Republic of Korea
167 rdf:type schema:Organization
168 grid-institutes:grid.6142.1 schema:alternateName Microbial Ecology Laboratory, Department of Microbiology and Environmental Change Institute (ECI), National University of Ireland, Galway, Republic of Ireland
169 schema:name Microbial Ecology Laboratory, Department of Microbiology and Environmental Change Institute (ECI), National University of Ireland, Galway, Republic of Ireland
170 rdf:type schema:Organization
 




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


...