An Attempt to Pinpoint the Phylogenetic Introduction of Glutaminyl-tRNA Synthetase Among Bacteria View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

1999-12

AUTHORS

Jacob Handy, Russell F. Doolittle

ABSTRACT

Until recently it was believed that most Bacteria form Gln-tRNA(GLN) by the amidation of Glu-tRNA(GLN), only a few members of the gamma subdivision of Proteobacteria being able to charge tRNA(GLN) directly. We undertook a phylogenetic study in an attempt to determine at what point the changeover to the direct system may have occurred. To this end, we selected a number of representative Proteobacteria to see if we could find a division point. We constructed degenerate primers and conducted PCR analysis to identify which Bacteria had Gln-tRNA synthetase, on the one hand, and which had the amidotransferase system, on the other. At the same time, we surveyed data banks of completely sequenced microbial genomes, as well as those for genomes in the process of being sequenced. These combined efforts revealed four Proteobacteria in a phylogenetically intermediate position which have the genetic potential for both mechanisms. Perplexingly, however, three distantly related bacteria were also found to have both enzymes. More... »

PAGES

709-715

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/pl00006592

DOI

http://dx.doi.org/10.1007/pl00006592

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1024605605

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/10594171


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/2008/0605", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Microbiology", 
        "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": "Amino Acyl-tRNA Synthetases", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Base Sequence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA Primers", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Databases, Factual", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Evolution, Molecular", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gammaproteobacteria", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genes, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Molecular Sequence Data", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Phylogeny", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Polymerase Chain Reaction", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "RNA, Ribosomal, 16S", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Homology, Amino Acid", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Time Factors", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "University of California, San Diego", 
          "id": "https://www.grid.ac/institutes/grid.266100.3", 
          "name": [
            "Department of Biology, Center for Molecular Genetics, University of California, San Diego, La Jolla, CA 92093-0634, USA, US"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Handy", 
        "givenName": "Jacob", 
        "id": "sg:person.01362054202.54", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01362054202.54"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of California, San Diego", 
          "id": "https://www.grid.ac/institutes/grid.266100.3", 
          "name": [
            "Department of Biology, Center for Molecular Genetics, University of California, San Diego, La Jolla, CA 92093-0634, USA, US"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Doolittle", 
        "givenName": "Russell F.", 
        "id": "sg:person.0725046016.27", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0725046016.27"
        ], 
        "type": "Person"
      }
    ], 
    "datePublished": "1999-12", 
    "datePublishedReg": "1999-12-01", 
    "description": "Until recently it was believed that most Bacteria form Gln-tRNA(GLN) by the amidation of Glu-tRNA(GLN), only a few members of the gamma subdivision of Proteobacteria being able to charge tRNA(GLN) directly. We undertook a phylogenetic study in an attempt to determine at what point the changeover to the direct system may have occurred. To this end, we selected a number of representative Proteobacteria to see if we could find a division point. We constructed degenerate primers and conducted PCR analysis to identify which Bacteria had Gln-tRNA synthetase, on the one hand, and which had the amidotransferase system, on the other. At the same time, we surveyed data banks of completely sequenced microbial genomes, as well as those for genomes in the process of being sequenced. These combined efforts revealed four Proteobacteria in a phylogenetically intermediate position which have the genetic potential for both mechanisms. Perplexingly, however, three distantly related bacteria were also found to have both enzymes.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1007/pl00006592", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1016442", 
        "issn": [
          "0022-2844", 
          "1432-1432"
        ], 
        "name": "Journal of Molecular Evolution", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "6", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "49"
      }
    ], 
    "name": "An Attempt to Pinpoint the Phylogenetic Introduction of Glutaminyl-tRNA Synthetase Among Bacteria", 
    "pagination": "709-715", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "7538c06e0d9033aa0aa4e192937989e88dd72fe755bc7d433b2b46cc62b53ddd"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "10594171"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "0360051"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/pl00006592"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1024605605"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1007/pl00006592", 
      "https://app.dimensions.ai/details/publication/pub.1024605605"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T22:32", 
    "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_8690_00000512.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1007%2FPL00006592"
  }
]
 

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/pl00006592'

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/pl00006592'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/pl00006592'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/pl00006592'


 

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

136 TRIPLES      20 PREDICATES      44 URIs      36 LITERALS      24 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/pl00006592 schema:about N197a266b436d4df9a2ead60959327ab1
2 N20a9d4751b0343bc81d4dd779cdb563a
3 N46051fd45819405eb92fe778e6b78d7d
4 N4b9f5ff26bff43adb3f74e4cc546f111
5 N519dbded3052415f9c912d2d873d4830
6 N5ba8c24de9394d67baf0f962acab12f0
7 N69098dee9cb240a98dbea413b5c6dfda
8 N73ac61b46bc54eb3900ab2a5650c3aa7
9 N9ca66eb4f4f34e688ca90b0ea00c0f84
10 Na076546c3bfa47debde85f31fb7bf974
11 Nb816d7e08d52425bbff269aa5e23978c
12 Nca091b7bf9b943389621418ada32592d
13 Ne6e8c0e55ece4297a90ddb70ae0c3b04
14 Nf30175c51e1148d5a70d386868e5fd6d
15 Nf31f96c209034b16938c4c4235635af8
16 anzsrc-for:06
17 anzsrc-for:0605
18 schema:author N656228c090b94aeeb1d1d89929c54ad0
19 schema:datePublished 1999-12
20 schema:datePublishedReg 1999-12-01
21 schema:description Until recently it was believed that most Bacteria form Gln-tRNA(GLN) by the amidation of Glu-tRNA(GLN), only a few members of the gamma subdivision of Proteobacteria being able to charge tRNA(GLN) directly. We undertook a phylogenetic study in an attempt to determine at what point the changeover to the direct system may have occurred. To this end, we selected a number of representative Proteobacteria to see if we could find a division point. We constructed degenerate primers and conducted PCR analysis to identify which Bacteria had Gln-tRNA synthetase, on the one hand, and which had the amidotransferase system, on the other. At the same time, we surveyed data banks of completely sequenced microbial genomes, as well as those for genomes in the process of being sequenced. These combined efforts revealed four Proteobacteria in a phylogenetically intermediate position which have the genetic potential for both mechanisms. Perplexingly, however, three distantly related bacteria were also found to have both enzymes.
22 schema:genre research_article
23 schema:inLanguage en
24 schema:isAccessibleForFree false
25 schema:isPartOf N9af1ffc0812940d38cead0fef3008f26
26 Nccaf228e6f4441759e0d013dfac5101f
27 sg:journal.1016442
28 schema:name An Attempt to Pinpoint the Phylogenetic Introduction of Glutaminyl-tRNA Synthetase Among Bacteria
29 schema:pagination 709-715
30 schema:productId N049e7e9f2a9a48119175133f8307c349
31 N7e355192ca634dbb9867056cbf267ceb
32 Nae0cb3a50da54e36ba3aae1efb17caf4
33 Nd38e0d79de374a01ba77596db0358230
34 Ne156b1a3c2e64c20897f40cf7547dcaf
35 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024605605
36 https://doi.org/10.1007/pl00006592
37 schema:sdDatePublished 2019-04-10T22:32
38 schema:sdLicense https://scigraph.springernature.com/explorer/license/
39 schema:sdPublisher N0797e6f6699940f49f5f8e30b9b24ec9
40 schema:url http://link.springer.com/10.1007%2FPL00006592
41 sgo:license sg:explorer/license/
42 sgo:sdDataset articles
43 rdf:type schema:ScholarlyArticle
44 N049e7e9f2a9a48119175133f8307c349 schema:name readcube_id
45 schema:value 7538c06e0d9033aa0aa4e192937989e88dd72fe755bc7d433b2b46cc62b53ddd
46 rdf:type schema:PropertyValue
47 N0797e6f6699940f49f5f8e30b9b24ec9 schema:name Springer Nature - SN SciGraph project
48 rdf:type schema:Organization
49 N197a266b436d4df9a2ead60959327ab1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
50 schema:name Genes, Bacterial
51 rdf:type schema:DefinedTerm
52 N20a9d4751b0343bc81d4dd779cdb563a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
53 schema:name Gammaproteobacteria
54 rdf:type schema:DefinedTerm
55 N46051fd45819405eb92fe778e6b78d7d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
56 schema:name Sequence Homology, Amino Acid
57 rdf:type schema:DefinedTerm
58 N4b9f5ff26bff43adb3f74e4cc546f111 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
59 schema:name Polymerase Chain Reaction
60 rdf:type schema:DefinedTerm
61 N519dbded3052415f9c912d2d873d4830 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
62 schema:name Evolution, Molecular
63 rdf:type schema:DefinedTerm
64 N5ba8c24de9394d67baf0f962acab12f0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
65 schema:name Databases, Factual
66 rdf:type schema:DefinedTerm
67 N656228c090b94aeeb1d1d89929c54ad0 rdf:first sg:person.01362054202.54
68 rdf:rest Ne7184c3de7af48638238778db75ea789
69 N69098dee9cb240a98dbea413b5c6dfda schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
70 schema:name Amino Acid Sequence
71 rdf:type schema:DefinedTerm
72 N73ac61b46bc54eb3900ab2a5650c3aa7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
73 schema:name Time Factors
74 rdf:type schema:DefinedTerm
75 N7e355192ca634dbb9867056cbf267ceb schema:name doi
76 schema:value 10.1007/pl00006592
77 rdf:type schema:PropertyValue
78 N9af1ffc0812940d38cead0fef3008f26 schema:volumeNumber 49
79 rdf:type schema:PublicationVolume
80 N9ca66eb4f4f34e688ca90b0ea00c0f84 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
81 schema:name Genome, Bacterial
82 rdf:type schema:DefinedTerm
83 Na076546c3bfa47debde85f31fb7bf974 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
84 schema:name Base Sequence
85 rdf:type schema:DefinedTerm
86 Nae0cb3a50da54e36ba3aae1efb17caf4 schema:name nlm_unique_id
87 schema:value 0360051
88 rdf:type schema:PropertyValue
89 Nb816d7e08d52425bbff269aa5e23978c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
90 schema:name DNA Primers
91 rdf:type schema:DefinedTerm
92 Nca091b7bf9b943389621418ada32592d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
93 schema:name RNA, Ribosomal, 16S
94 rdf:type schema:DefinedTerm
95 Nccaf228e6f4441759e0d013dfac5101f schema:issueNumber 6
96 rdf:type schema:PublicationIssue
97 Nd38e0d79de374a01ba77596db0358230 schema:name pubmed_id
98 schema:value 10594171
99 rdf:type schema:PropertyValue
100 Ne156b1a3c2e64c20897f40cf7547dcaf schema:name dimensions_id
101 schema:value pub.1024605605
102 rdf:type schema:PropertyValue
103 Ne6e8c0e55ece4297a90ddb70ae0c3b04 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
104 schema:name Amino Acyl-tRNA Synthetases
105 rdf:type schema:DefinedTerm
106 Ne7184c3de7af48638238778db75ea789 rdf:first sg:person.0725046016.27
107 rdf:rest rdf:nil
108 Nf30175c51e1148d5a70d386868e5fd6d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
109 schema:name Molecular Sequence Data
110 rdf:type schema:DefinedTerm
111 Nf31f96c209034b16938c4c4235635af8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
112 schema:name Phylogeny
113 rdf:type schema:DefinedTerm
114 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
115 schema:name Biological Sciences
116 rdf:type schema:DefinedTerm
117 anzsrc-for:0605 schema:inDefinedTermSet anzsrc-for:
118 schema:name Microbiology
119 rdf:type schema:DefinedTerm
120 sg:journal.1016442 schema:issn 0022-2844
121 1432-1432
122 schema:name Journal of Molecular Evolution
123 rdf:type schema:Periodical
124 sg:person.01362054202.54 schema:affiliation https://www.grid.ac/institutes/grid.266100.3
125 schema:familyName Handy
126 schema:givenName Jacob
127 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01362054202.54
128 rdf:type schema:Person
129 sg:person.0725046016.27 schema:affiliation https://www.grid.ac/institutes/grid.266100.3
130 schema:familyName Doolittle
131 schema:givenName Russell F.
132 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0725046016.27
133 rdf:type schema:Person
134 https://www.grid.ac/institutes/grid.266100.3 schema:alternateName University of California, San Diego
135 schema:name Department of Biology, Center for Molecular Genetics, University of California, San Diego, La Jolla, CA 92093-0634, USA, US
136 rdf:type schema:Organization
 




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


...