Structural features and expression analysis of a linear mitochondrial plasmid in rapeseed (Brassica napus L.) View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2002-08

AUTHORS

H. Handa, K. Itani, H. Sato

ABSTRACT

A linear plasmid molecule about 11 kb in length is present in the mitochondria of some varieties of rapeseed (Brassica napus L.). This plasmid can be inherited from the male parent, through the pollen, as well as by the usual maternal route, although the main mitochondrial genome is maternally inherited in rapeseed. We determined the complete nucleotide sequence of this plasmid DNA and clarified its genetic organization. The length of the linear plasmid is 11,640 bp. At the termini of the plasmid molecule are inverted repeats of 327 bp. The GC content of the plasmid DNA is 30.9%; thus, the plasmid is quite AT-rich compared to the main mitochondrial genome in higher plants. The plasmid has six ORFs, two of which encode a phage-type DNA polymerase and a phage-type RNA polymerase, respectively. RT-PCR analyses revealed that all six ORFs are transcribed, and all four ORFs on the minus strand are probably cotranscribed from a single promoter located in the terminal inverted repeat. We also show here that at least three of the six ORFs are translated into proteins in rapeseed mitochondria, and expressed at relatively high levels in flowers, as shown by Western analysis. These results suggest that this linear DNA molecule is able to replicate as an autonomous replicon and to express the genes it carries in rapeseed mitochondria. More... »

PAGES

797-805

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/s00438-002-0711-4

DOI

http://dx.doi.org/10.1007/s00438-002-0711-4

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1006034884

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/12207227


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": "Amino Acid Sequence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Brassica napus", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA, Mitochondrial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA, Plant", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA-Directed DNA Polymerase", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA-Directed RNA Polymerases", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Electrophoresis, Agar Gel", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Immunoblotting", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Molecular Sequence Data", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Open Reading Frames", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Plasmids", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Reverse Transcriptase Polymerase Chain Reaction", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Alignment", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Analysis, DNA", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "National Agricultural Research Center for Hokkaido Region", 
          "id": "https://www.grid.ac/institutes/grid.419106.b", 
          "name": [
            "Laboratory of Plant Genecology, National Agricultural Research Center for Hokkaido Region, 1, Hitsuji-ga-oka, Toyohira-ku, Sapporo 062-8555, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Handa", 
        "givenName": "H.", 
        "id": "sg:person.0712021774.43", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0712021774.43"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "National Agricultural Research Center for Hokkaido Region", 
          "id": "https://www.grid.ac/institutes/grid.419106.b", 
          "name": [
            "Laboratory of Plant Genecology, National Agricultural Research Center for Hokkaido Region, 1, Hitsuji-ga-oka, Toyohira-ku, Sapporo 062-8555, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Itani", 
        "givenName": "K.", 
        "id": "sg:person.0746313624.11", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0746313624.11"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "National Agricultural Research Center for Hokkaido Region", 
          "id": "https://www.grid.ac/institutes/grid.419106.b", 
          "name": [
            "Laboratory of Plant Genecology, National Agricultural Research Center for Hokkaido Region, 1, Hitsuji-ga-oka, Toyohira-ku, Sapporo 062-8555, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Sato", 
        "givenName": "H.", 
        "id": "sg:person.01322634612.40", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01322634612.40"
        ], 
        "type": "Person"
      }
    ], 
    "datePublished": "2002-08", 
    "datePublishedReg": "2002-08-01", 
    "description": "A linear plasmid molecule about 11 kb in length is present in the mitochondria of some varieties of rapeseed (Brassica napus L.). This plasmid can be inherited from the male parent, through the pollen, as well as by the usual maternal route, although the main mitochondrial genome is maternally inherited in rapeseed. We determined the complete nucleotide sequence of this plasmid DNA and clarified its genetic organization. The length of the linear plasmid is 11,640 bp. At the termini of the plasmid molecule are inverted repeats of 327 bp. The GC content of the plasmid DNA is 30.9%; thus, the plasmid is quite AT-rich compared to the main mitochondrial genome in higher plants. The plasmid has six ORFs, two of which encode a phage-type DNA polymerase and a phage-type RNA polymerase, respectively. RT-PCR analyses revealed that all six ORFs are transcribed, and all four ORFs on the minus strand are probably cotranscribed from a single promoter located in the terminal inverted repeat. We also show here that at least three of the six ORFs are translated into proteins in rapeseed mitochondria, and expressed at relatively high levels in flowers, as shown by Western analysis. These results suggest that this linear DNA molecule is able to replicate as an autonomous replicon and to express the genes it carries in rapeseed mitochondria.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1007/s00438-002-0711-4", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1297380", 
        "issn": [
          "1617-4615", 
          "1432-1874"
        ], 
        "name": "Molecular Genetics and Genomics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "6", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "267"
      }
    ], 
    "name": "Structural features and expression analysis of a linear mitochondrial plasmid in rapeseed (Brassica napus L.)", 
    "pagination": "797-805", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "1cbf4d8e2178abd3c5ec9886545a2f5e3584f5dbc59178320de60975c38680ba"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "12207227"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101093320"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/s00438-002-0711-4"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1006034884"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1007/s00438-002-0711-4", 
      "https://app.dimensions.ai/details/publication/pub.1006034884"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T14:09", 
    "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_8660_00000510.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1007%2Fs00438-002-0711-4"
  }
]
 

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/s00438-002-0711-4'

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/s00438-002-0711-4'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s00438-002-0711-4'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s00438-002-0711-4'


 

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

139 TRIPLES      20 PREDICATES      43 URIs      35 LITERALS      23 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/s00438-002-0711-4 schema:about N0d37d08ab5c840f5af5223d518b4a2ee
2 N1feb3f8dfb824a4ca15d51a5164725d6
3 N5747bf4f2db8423aa1efb800002a97df
4 N5eb3de30249c4a8b8f24733424f02831
5 N69fa80d6e51c488483334f06b824c925
6 N812cdecb4fdb42d98fded2bbf905a359
7 N91d13aea9fb341679deec73f9acfdf8b
8 Na02b8a2ff3144f3dab61a915cd1700e0
9 Na3df62beebd043d9951dfcc3bf848e21
10 Nb24c70806d9f4dd9ba1d4505f9a9fd78
11 Nbe66181ef8c6438bb73df3d6cae55bca
12 Nd86a193fe0e0478f9f0f7356f4ac7fae
13 Ne53a941c2286410dbaead00e54bd3229
14 Nf0a798565e3748b9b6ba71b8ac8c427c
15 anzsrc-for:06
16 anzsrc-for:0604
17 schema:author N999f41d65a2c4cbbaef1e81effb55bf3
18 schema:datePublished 2002-08
19 schema:datePublishedReg 2002-08-01
20 schema:description A linear plasmid molecule about 11 kb in length is present in the mitochondria of some varieties of rapeseed (Brassica napus L.). This plasmid can be inherited from the male parent, through the pollen, as well as by the usual maternal route, although the main mitochondrial genome is maternally inherited in rapeseed. We determined the complete nucleotide sequence of this plasmid DNA and clarified its genetic organization. The length of the linear plasmid is 11,640 bp. At the termini of the plasmid molecule are inverted repeats of 327 bp. The GC content of the plasmid DNA is 30.9%; thus, the plasmid is quite AT-rich compared to the main mitochondrial genome in higher plants. The plasmid has six ORFs, two of which encode a phage-type DNA polymerase and a phage-type RNA polymerase, respectively. RT-PCR analyses revealed that all six ORFs are transcribed, and all four ORFs on the minus strand are probably cotranscribed from a single promoter located in the terminal inverted repeat. We also show here that at least three of the six ORFs are translated into proteins in rapeseed mitochondria, and expressed at relatively high levels in flowers, as shown by Western analysis. These results suggest that this linear DNA molecule is able to replicate as an autonomous replicon and to express the genes it carries in rapeseed mitochondria.
21 schema:genre research_article
22 schema:inLanguage en
23 schema:isAccessibleForFree false
24 schema:isPartOf N0686ab11b7ae43e1bd884ef36a0d3694
25 N5ac0458a471e4d8e99531399d4c744d2
26 sg:journal.1297380
27 schema:name Structural features and expression analysis of a linear mitochondrial plasmid in rapeseed (Brassica napus L.)
28 schema:pagination 797-805
29 schema:productId N2ecdd3683458474ea1c1e8e75e6e7cad
30 N49705f79e97641b39d4c300bd93245e9
31 N80abab97e3844e27860a5cb586befa13
32 N81191f9452e043ad8a145e8ee9fd650f
33 N88e73c2311794cb78309840099d5c922
34 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006034884
35 https://doi.org/10.1007/s00438-002-0711-4
36 schema:sdDatePublished 2019-04-10T14:09
37 schema:sdLicense https://scigraph.springernature.com/explorer/license/
38 schema:sdPublisher N04e626aaaa6e408ca46da5e0cc6d37d3
39 schema:url http://link.springer.com/10.1007%2Fs00438-002-0711-4
40 sgo:license sg:explorer/license/
41 sgo:sdDataset articles
42 rdf:type schema:ScholarlyArticle
43 N04e626aaaa6e408ca46da5e0cc6d37d3 schema:name Springer Nature - SN SciGraph project
44 rdf:type schema:Organization
45 N0686ab11b7ae43e1bd884ef36a0d3694 schema:issueNumber 6
46 rdf:type schema:PublicationIssue
47 N0d37d08ab5c840f5af5223d518b4a2ee schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
48 schema:name DNA, Mitochondrial
49 rdf:type schema:DefinedTerm
50 N1feb3f8dfb824a4ca15d51a5164725d6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
51 schema:name Open Reading Frames
52 rdf:type schema:DefinedTerm
53 N2ecdd3683458474ea1c1e8e75e6e7cad schema:name doi
54 schema:value 10.1007/s00438-002-0711-4
55 rdf:type schema:PropertyValue
56 N49705f79e97641b39d4c300bd93245e9 schema:name readcube_id
57 schema:value 1cbf4d8e2178abd3c5ec9886545a2f5e3584f5dbc59178320de60975c38680ba
58 rdf:type schema:PropertyValue
59 N5747bf4f2db8423aa1efb800002a97df schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
60 schema:name Sequence Analysis, DNA
61 rdf:type schema:DefinedTerm
62 N5ac0458a471e4d8e99531399d4c744d2 schema:volumeNumber 267
63 rdf:type schema:PublicationVolume
64 N5eb3de30249c4a8b8f24733424f02831 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
65 schema:name DNA, Plant
66 rdf:type schema:DefinedTerm
67 N69fa80d6e51c488483334f06b824c925 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
68 schema:name Sequence Alignment
69 rdf:type schema:DefinedTerm
70 N80abab97e3844e27860a5cb586befa13 schema:name nlm_unique_id
71 schema:value 101093320
72 rdf:type schema:PropertyValue
73 N81191f9452e043ad8a145e8ee9fd650f schema:name dimensions_id
74 schema:value pub.1006034884
75 rdf:type schema:PropertyValue
76 N812cdecb4fdb42d98fded2bbf905a359 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
77 schema:name Immunoblotting
78 rdf:type schema:DefinedTerm
79 N88e73c2311794cb78309840099d5c922 schema:name pubmed_id
80 schema:value 12207227
81 rdf:type schema:PropertyValue
82 N91d13aea9fb341679deec73f9acfdf8b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
83 schema:name Brassica napus
84 rdf:type schema:DefinedTerm
85 N999f41d65a2c4cbbaef1e81effb55bf3 rdf:first sg:person.0712021774.43
86 rdf:rest Ncd02e57d2d184a39bf8ba3230bb866a9
87 Na02b8a2ff3144f3dab61a915cd1700e0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
88 schema:name Reverse Transcriptase Polymerase Chain Reaction
89 rdf:type schema:DefinedTerm
90 Na3df62beebd043d9951dfcc3bf848e21 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
91 schema:name Amino Acid Sequence
92 rdf:type schema:DefinedTerm
93 Nb24c70806d9f4dd9ba1d4505f9a9fd78 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
94 schema:name DNA-Directed RNA Polymerases
95 rdf:type schema:DefinedTerm
96 Nbe66181ef8c6438bb73df3d6cae55bca schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
97 schema:name DNA-Directed DNA Polymerase
98 rdf:type schema:DefinedTerm
99 Ncd02e57d2d184a39bf8ba3230bb866a9 rdf:first sg:person.0746313624.11
100 rdf:rest Nd6be8749a3a1484782e0ef1f69f58e33
101 Nd6be8749a3a1484782e0ef1f69f58e33 rdf:first sg:person.01322634612.40
102 rdf:rest rdf:nil
103 Nd86a193fe0e0478f9f0f7356f4ac7fae schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
104 schema:name Plasmids
105 rdf:type schema:DefinedTerm
106 Ne53a941c2286410dbaead00e54bd3229 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
107 schema:name Molecular Sequence Data
108 rdf:type schema:DefinedTerm
109 Nf0a798565e3748b9b6ba71b8ac8c427c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
110 schema:name Electrophoresis, Agar Gel
111 rdf:type schema:DefinedTerm
112 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
113 schema:name Biological Sciences
114 rdf:type schema:DefinedTerm
115 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
116 schema:name Genetics
117 rdf:type schema:DefinedTerm
118 sg:journal.1297380 schema:issn 1432-1874
119 1617-4615
120 schema:name Molecular Genetics and Genomics
121 rdf:type schema:Periodical
122 sg:person.01322634612.40 schema:affiliation https://www.grid.ac/institutes/grid.419106.b
123 schema:familyName Sato
124 schema:givenName H.
125 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01322634612.40
126 rdf:type schema:Person
127 sg:person.0712021774.43 schema:affiliation https://www.grid.ac/institutes/grid.419106.b
128 schema:familyName Handa
129 schema:givenName H.
130 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0712021774.43
131 rdf:type schema:Person
132 sg:person.0746313624.11 schema:affiliation https://www.grid.ac/institutes/grid.419106.b
133 schema:familyName Itani
134 schema:givenName K.
135 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0746313624.11
136 rdf:type schema:Person
137 https://www.grid.ac/institutes/grid.419106.b schema:alternateName National Agricultural Research Center for Hokkaido Region
138 schema:name Laboratory of Plant Genecology, National Agricultural Research Center for Hokkaido Region, 1, Hitsuji-ga-oka, Toyohira-ku, Sapporo 062-8555, Japan
139 rdf:type schema:Organization
 




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


...