Substrate specificity of chlorophenoxyalkanoic acid-degrading bacteria is not dependent upon phylogenetically related tfdA gene types View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2001-06

AUTHORS

Christopher W. Smejkal, Tatiana Vallaeys, Sara K. Burton, Hilary M. Lappin-Scott

ABSTRACT

. The phenoxyalkanoic acid herbicides constitute a group of chemically related molecules that have been widely used for over 50 years. A range of bacteria have been selected from various locations for their ability to degrade these compounds. Previously reported strains able to utilise 2,4-dichlorophenoxyacetic acid (2,4-D) include, Ralstonia eutropha JMP134, Burkholderia sp. RASC and Variovorax paradoxus TV1 and Sphingomonas sp. AW5 able to utilise 2,4,5-trichlorophenoxyacetic acid (2,4,5-T). In addition a novel set of mecoprop-degrading strains including Alcaligenes denitrificans, Alcaligenes sp. CS1 and Ralstonia sp. CS2 are here described. It has been reported recently that TfdA enzymes, initially reported to have a role in 2,4-D catabolism are also involved in the first-step cleavage of related phenoxyalkanoate herbicides. However, a diversity of tfdA gene sequences have been reported. We relate the tfdA gene type to the metabolic ability of these strains. The tfdA-like genes were investigated by polymerase chain reaction amplification using a set of specific tfdA primers. Degradation ability was observed via phenol production from a range of unsubstituted and substituted phenoxyalkanoics including, 2,4-D, 2-methyl 4-chlorophenoxyacetic acid (MCPA), racemic mecoprop, (R)-mecoprop, 2-(2,4-dichlorophenoxy) propionic acid (racemic 2,4-DP), 2,4,5-T, 2,4-dichlorophenoxybutyric acid (2,4-DB), 4-chloro-2-methylphenoxybutyric acid (MCPB) and phenoxyacetate. Mecoprop-degrading strains showed partial tfdA sequences identical to the one described for V. paradoxus TV1 (a strain isolated on 2,4-D). However, substrate specificity was not identical as V. paradoxus exhibited greatest activity towards 2,4-D and MCPA only, whereas the mecoprop-degrading strains showed intense activity towards 2,4-D, MCPA, racemic mecoprop and (R)-mecoprop as substrates. However, Sphingomonas sp. AW5 which has been shown to carry a very different tfdA-like gene was the only strain to utilise the phenoxybutyric acid MCPB as a sole carbon source. In this study, we thus demonstrate that sequence diversity is not related to substrate specificity within the tfdA-like gene family. However, phylogenetically unrelated sequences may govern substrate specific activity. More... »

PAGES

507-513

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/s003740100360

DOI

http://dx.doi.org/10.1007/s003740100360

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1041890836


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"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "School of Biological Sciences, University of Exeter, Hatherly Laboratories, Prince of Wales Road, Exeter EX4 4PS, UK", 
          "id": "http://www.grid.ac/institutes/grid.8391.3", 
          "name": [
            "School of Biological Sciences, University of Exeter, Hatherly Laboratories, Prince of Wales Road, Exeter EX4 4PS, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Smejkal", 
        "givenName": "Christopher W.", 
        "id": "sg:person.01007107071.06", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01007107071.06"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "INRA Microbiologie, Domaine de Vilvert, 78352 Jouy en Josas, France", 
          "id": "http://www.grid.ac/institutes/None", 
          "name": [
            "INRA Microbiologie, Domaine de Vilvert, 78352 Jouy en Josas, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Vallaeys", 
        "givenName": "Tatiana", 
        "id": "sg:person.010726224076.16", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010726224076.16"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "School of Biological Sciences, University of Exeter, Hatherly Laboratories, Prince of Wales Road, Exeter EX4 4PS, UK", 
          "id": "http://www.grid.ac/institutes/grid.8391.3", 
          "name": [
            "School of Biological Sciences, University of Exeter, Hatherly Laboratories, Prince of Wales Road, Exeter EX4 4PS, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Burton", 
        "givenName": "Sara K.", 
        "id": "sg:person.0615077335.37", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0615077335.37"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "School of Biological Sciences, University of Exeter, Hatherly Laboratories, Prince of Wales Road, Exeter EX4 4PS, UK", 
          "id": "http://www.grid.ac/institutes/grid.8391.3", 
          "name": [
            "School of Biological Sciences, University of Exeter, Hatherly Laboratories, Prince of Wales Road, Exeter EX4 4PS, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lappin-Scott", 
        "givenName": "Hilary M.", 
        "id": "sg:person.01234702403.15", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01234702403.15"
        ], 
        "type": "Person"
      }
    ], 
    "datePublished": "2001-06", 
    "datePublishedReg": "2001-06-01", 
    "description": "Abstract. The phenoxyalkanoic acid herbicides constitute a group of chemically related molecules that have been widely used for over 50\u00a0years. A range of bacteria have been selected from various locations for their ability to degrade these compounds. Previously reported strains able to utilise 2,4-dichlorophenoxyacetic acid (2,4-D) include, Ralstonia eutropha JMP134, Burkholderia sp. RASC and Variovorax paradoxus TV1 and Sphingomonas sp. AW5 able to utilise 2,4,5-trichlorophenoxyacetic acid (2,4,5-T). In addition a novel set of mecoprop-degrading strains including Alcaligenes denitrificans, Alcaligenes sp. CS1 and Ralstonia sp. CS2 are here described. It has been reported recently that TfdA enzymes, initially reported to have a role in 2,4-D catabolism are also involved in the first-step cleavage of related phenoxyalkanoate herbicides. However, a diversity of tfdA gene sequences have been reported. We relate the tfdA gene type to the metabolic ability of these strains. The tfdA-like genes were investigated by polymerase chain reaction amplification using a set of specific tfdA primers. Degradation ability was observed via phenol production from a range of unsubstituted and substituted phenoxyalkanoics including, 2,4-D, 2-methyl 4-chlorophenoxyacetic acid (MCPA), racemic mecoprop, (R)-mecoprop, 2-(2,4-dichlorophenoxy) propionic acid (racemic 2,4-DP), 2,4,5-T, 2,4-dichlorophenoxybutyric acid (2,4-DB), 4-chloro-2-methylphenoxybutyric acid (MCPB) and phenoxyacetate. Mecoprop-degrading strains showed partial tfdA sequences identical to the one described for V. paradoxus TV1 (a strain isolated on 2,4-D). However, substrate specificity was not identical as V. paradoxus exhibited greatest activity towards 2,4-D and MCPA only, whereas the mecoprop-degrading strains showed intense activity towards 2,4-D, MCPA, racemic mecoprop and (R)-mecoprop as substrates. However, Sphingomonas sp. AW5 which has been shown to carry a very different tfdA-like gene was the only strain to utilise the phenoxybutyric acid MCPB as a sole carbon source. In this study, we thus demonstrate that sequence diversity is not related to substrate specificity within the tfdA-like gene family. However, phylogenetically unrelated sequences may govern substrate specific activity.", 
    "genre": "article", 
    "id": "sg:pub.10.1007/s003740100360", 
    "inLanguage": "en", 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1031627", 
        "issn": [
          "0178-2762", 
          "1432-0789"
        ], 
        "name": "Biology and Fertility of Soils", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "6", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "33"
      }
    ], 
    "keywords": [
      "tfdA-like genes", 
      "substrate specificity", 
      "racemic mecoprop", 
      "gene types", 
      "Sphingomonas sp", 
      "acid-degrading bacteria", 
      "Ralstonia eutropha JMP134", 
      "sole carbon source", 
      "range of bacteria", 
      "gene family", 
      "gene sequences", 
      "sequence diversity", 
      "Burkholderia sp", 
      "tfdA sequences", 
      "eutropha JMP134", 
      "Ralstonia sp", 
      "unrelated sequences", 
      "metabolic abilities", 
      "sp", 
      "phenoxyalkanoate herbicides", 
      "polymerase chain reaction amplification", 
      "Alcaligenes sp", 
      "carbon source", 
      "chain reaction amplification", 
      "genes", 
      "phenoxyalkanoic acid herbicides", 
      "sequence", 
      "specific activity", 
      "diversity", 
      "bacteria", 
      "reaction amplification", 
      "only strain", 
      "degradation ability", 
      "Alcaligenes denitrificans", 
      "AW5", 
      "strains", 
      "TV1", 
      "novel set", 
      "herbicides", 
      "related molecules", 
      "tfdA", 
      "acid", 
      "JMP134", 
      "specificity", 
      "paradoxus", 
      "denitrificans", 
      "activity", 
      "RASC", 
      "primers", 
      "greater activity", 
      "catabolism", 
      "phenol production", 
      "MCPA", 
      "cleavage", 
      "MCPB", 
      "ability", 
      "family", 
      "amplification", 
      "mecoprop", 
      "molecules", 
      "substrate", 
      "production", 
      "role", 
      "propionic acid", 
      "acid herbicides", 
      "types", 
      "intense activity", 
      "CS1", 
      "addition", 
      "compounds", 
      "range", 
      "location", 
      "set", 
      "source", 
      "study", 
      "group", 
      "one", 
      "years", 
      "CS2", 
      "Variovorax paradoxus TV1", 
      "paradoxus TV1", 
      "mecoprop-degrading strains", 
      "first-step cleavage", 
      "related phenoxyalkanoate herbicides", 
      "tfdA gene sequences", 
      "tfdA gene type", 
      "specific tfdA primers", 
      "tfdA primers", 
      "phenoxyalkanoics", 
      "partial tfdA sequences", 
      "different tfdA-like gene", 
      "phenoxybutyric acid MCPB", 
      "acid MCPB", 
      "tfdA-like gene family", 
      "substrate specific activity", 
      "chlorophenoxyalkanoic acid-degrading bacteria"
    ], 
    "name": "Substrate specificity of chlorophenoxyalkanoic acid-degrading bacteria is not dependent upon phylogenetically related tfdA gene types", 
    "pagination": "507-513", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1041890836"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/s003740100360"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1007/s003740100360", 
      "https://app.dimensions.ai/details/publication/pub.1041890836"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2022-01-01T18:10", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20220101/entities/gbq_results/article/article_314.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1007/s003740100360"
  }
]
 

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/s003740100360'

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/s003740100360'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s003740100360'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s003740100360'


 

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

178 TRIPLES      21 PREDICATES      122 URIs      114 LITERALS      6 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/s003740100360 schema:about anzsrc-for:06
2 anzsrc-for:0604
3 schema:author N05f2b0ce84f24f07ad296c6ea440debd
4 schema:datePublished 2001-06
5 schema:datePublishedReg 2001-06-01
6 schema:description Abstract. The phenoxyalkanoic acid herbicides constitute a group of chemically related molecules that have been widely used for over 50 years. A range of bacteria have been selected from various locations for their ability to degrade these compounds. Previously reported strains able to utilise 2,4-dichlorophenoxyacetic acid (2,4-D) include, Ralstonia eutropha JMP134, Burkholderia sp. RASC and Variovorax paradoxus TV1 and Sphingomonas sp. AW5 able to utilise 2,4,5-trichlorophenoxyacetic acid (2,4,5-T). In addition a novel set of mecoprop-degrading strains including Alcaligenes denitrificans, Alcaligenes sp. CS1 and Ralstonia sp. CS2 are here described. It has been reported recently that TfdA enzymes, initially reported to have a role in 2,4-D catabolism are also involved in the first-step cleavage of related phenoxyalkanoate herbicides. However, a diversity of tfdA gene sequences have been reported. We relate the tfdA gene type to the metabolic ability of these strains. The tfdA-like genes were investigated by polymerase chain reaction amplification using a set of specific tfdA primers. Degradation ability was observed via phenol production from a range of unsubstituted and substituted phenoxyalkanoics including, 2,4-D, 2-methyl 4-chlorophenoxyacetic acid (MCPA), racemic mecoprop, (R)-mecoprop, 2-(2,4-dichlorophenoxy) propionic acid (racemic 2,4-DP), 2,4,5-T, 2,4-dichlorophenoxybutyric acid (2,4-DB), 4-chloro-2-methylphenoxybutyric acid (MCPB) and phenoxyacetate. Mecoprop-degrading strains showed partial tfdA sequences identical to the one described for V. paradoxus TV1 (a strain isolated on 2,4-D). However, substrate specificity was not identical as V. paradoxus exhibited greatest activity towards 2,4-D and MCPA only, whereas the mecoprop-degrading strains showed intense activity towards 2,4-D, MCPA, racemic mecoprop and (R)-mecoprop as substrates. However, Sphingomonas sp. AW5 which has been shown to carry a very different tfdA-like gene was the only strain to utilise the phenoxybutyric acid MCPB as a sole carbon source. In this study, we thus demonstrate that sequence diversity is not related to substrate specificity within the tfdA-like gene family. However, phylogenetically unrelated sequences may govern substrate specific activity.
7 schema:genre article
8 schema:inLanguage en
9 schema:isAccessibleForFree false
10 schema:isPartOf N16a3d399477b4513bd15b5aa54e823b7
11 Nf03e61dff6aa408ead116ddfa51b8dce
12 sg:journal.1031627
13 schema:keywords AW5
14 Alcaligenes denitrificans
15 Alcaligenes sp
16 Burkholderia sp
17 CS1
18 CS2
19 JMP134
20 MCPA
21 MCPB
22 RASC
23 Ralstonia eutropha JMP134
24 Ralstonia sp
25 Sphingomonas sp
26 TV1
27 Variovorax paradoxus TV1
28 ability
29 acid
30 acid MCPB
31 acid herbicides
32 acid-degrading bacteria
33 activity
34 addition
35 amplification
36 bacteria
37 carbon source
38 catabolism
39 chain reaction amplification
40 chlorophenoxyalkanoic acid-degrading bacteria
41 cleavage
42 compounds
43 degradation ability
44 denitrificans
45 different tfdA-like gene
46 diversity
47 eutropha JMP134
48 family
49 first-step cleavage
50 gene family
51 gene sequences
52 gene types
53 genes
54 greater activity
55 group
56 herbicides
57 intense activity
58 location
59 mecoprop
60 mecoprop-degrading strains
61 metabolic abilities
62 molecules
63 novel set
64 one
65 only strain
66 paradoxus
67 paradoxus TV1
68 partial tfdA sequences
69 phenol production
70 phenoxyalkanoate herbicides
71 phenoxyalkanoic acid herbicides
72 phenoxyalkanoics
73 phenoxybutyric acid MCPB
74 polymerase chain reaction amplification
75 primers
76 production
77 propionic acid
78 racemic mecoprop
79 range
80 range of bacteria
81 reaction amplification
82 related molecules
83 related phenoxyalkanoate herbicides
84 role
85 sequence
86 sequence diversity
87 set
88 sole carbon source
89 source
90 sp
91 specific activity
92 specific tfdA primers
93 specificity
94 strains
95 study
96 substrate
97 substrate specific activity
98 substrate specificity
99 tfdA
100 tfdA gene sequences
101 tfdA gene type
102 tfdA primers
103 tfdA sequences
104 tfdA-like gene family
105 tfdA-like genes
106 types
107 unrelated sequences
108 years
109 schema:name Substrate specificity of chlorophenoxyalkanoic acid-degrading bacteria is not dependent upon phylogenetically related tfdA gene types
110 schema:pagination 507-513
111 schema:productId N010a64b83aa34cbdb73011e9a5b00f16
112 Nad7f4bf569b441d0bd8b4ee59840d9a2
113 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041890836
114 https://doi.org/10.1007/s003740100360
115 schema:sdDatePublished 2022-01-01T18:10
116 schema:sdLicense https://scigraph.springernature.com/explorer/license/
117 schema:sdPublisher N3349b35c3ca047e082244fd987153e4d
118 schema:url https://doi.org/10.1007/s003740100360
119 sgo:license sg:explorer/license/
120 sgo:sdDataset articles
121 rdf:type schema:ScholarlyArticle
122 N010a64b83aa34cbdb73011e9a5b00f16 schema:name doi
123 schema:value 10.1007/s003740100360
124 rdf:type schema:PropertyValue
125 N05f2b0ce84f24f07ad296c6ea440debd rdf:first sg:person.01007107071.06
126 rdf:rest N121dd9cfa8c74a9b96ff74b3f773f81a
127 N121dd9cfa8c74a9b96ff74b3f773f81a rdf:first sg:person.010726224076.16
128 rdf:rest Nef1313f274854e33b2c0c9dfc2e3ab0d
129 N16a3d399477b4513bd15b5aa54e823b7 schema:issueNumber 6
130 rdf:type schema:PublicationIssue
131 N3349b35c3ca047e082244fd987153e4d schema:name Springer Nature - SN SciGraph project
132 rdf:type schema:Organization
133 Nad7f4bf569b441d0bd8b4ee59840d9a2 schema:name dimensions_id
134 schema:value pub.1041890836
135 rdf:type schema:PropertyValue
136 Nbe5133c01958493491503e46a1a9e5f5 rdf:first sg:person.01234702403.15
137 rdf:rest rdf:nil
138 Nef1313f274854e33b2c0c9dfc2e3ab0d rdf:first sg:person.0615077335.37
139 rdf:rest Nbe5133c01958493491503e46a1a9e5f5
140 Nf03e61dff6aa408ead116ddfa51b8dce schema:volumeNumber 33
141 rdf:type schema:PublicationVolume
142 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
143 schema:name Biological Sciences
144 rdf:type schema:DefinedTerm
145 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
146 schema:name Genetics
147 rdf:type schema:DefinedTerm
148 sg:journal.1031627 schema:issn 0178-2762
149 1432-0789
150 schema:name Biology and Fertility of Soils
151 schema:publisher Springer Nature
152 rdf:type schema:Periodical
153 sg:person.01007107071.06 schema:affiliation grid-institutes:grid.8391.3
154 schema:familyName Smejkal
155 schema:givenName Christopher W.
156 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01007107071.06
157 rdf:type schema:Person
158 sg:person.010726224076.16 schema:affiliation grid-institutes:None
159 schema:familyName Vallaeys
160 schema:givenName Tatiana
161 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010726224076.16
162 rdf:type schema:Person
163 sg:person.01234702403.15 schema:affiliation grid-institutes:grid.8391.3
164 schema:familyName Lappin-Scott
165 schema:givenName Hilary M.
166 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01234702403.15
167 rdf:type schema:Person
168 sg:person.0615077335.37 schema:affiliation grid-institutes:grid.8391.3
169 schema:familyName Burton
170 schema:givenName Sara K.
171 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0615077335.37
172 rdf:type schema:Person
173 grid-institutes:None schema:alternateName INRA Microbiologie, Domaine de Vilvert, 78352 Jouy en Josas, France
174 schema:name INRA Microbiologie, Domaine de Vilvert, 78352 Jouy en Josas, France
175 rdf:type schema:Organization
176 grid-institutes:grid.8391.3 schema:alternateName School of Biological Sciences, University of Exeter, Hatherly Laboratories, Prince of Wales Road, Exeter EX4 4PS, UK
177 schema:name School of Biological Sciences, University of Exeter, Hatherly Laboratories, Prince of Wales Road, Exeter EX4 4PS, UK
178 rdf:type schema:Organization
 




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


...