Cloning of a Novel 6-Chloronicotinic Acid Chlorohydrolase from the Newly Isolated 6-Chloronicotinic Acid Mineralizing Bradyrhizobiaceae Strain SG-6C
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{"title"=>"Cloning of a Novel 6-Chloronicotinic Acid Chlorohydrolase from the Newly Isolated 6-Chloronicotinic Acid Mineralizing Bradyrhizobiaceae Strain SG-6C", "type"=>"journal", "authors"=>[{"first_name"=>"Madhura", "last_name"=>"Shettigar", "scopus_author_id"=>"55512260500"}, {"first_name"=>"Stephen", "last_name"=>"Pearce", "scopus_author_id"=>"54389798600"}, {"first_name"=>"Rinku", "last_name"=>"Pandey", "scopus_author_id"=>"24171833700"}, {"first_name"=>"Fazlurrahman", "last_name"=>"Khan", "scopus_author_id"=>"41861802400"}, {"first_name"=>"Susan J.", "last_name"=>"Dorrian", "scopus_author_id"=>"6505783311"}, {"first_name"=>"Sahil", "last_name"=>"Balotra", "scopus_author_id"=>"55512783300"}, {"first_name"=>"Robyn J.", "last_name"=>"Russell", "scopus_author_id"=>"7403934393"}, {"first_name"=>"John G.", "last_name"=>"Oakeshott", "scopus_author_id"=>"7005180684"}, {"first_name"=>"Gunjan", "last_name"=>"Pandey", "scopus_author_id"=>"7202575630"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84870593186", "pui"=>"366207355", "doi"=>"10.1371/journal.pone.0051162", "isbn"=>"10.1371/journal.pone.0051162", "sgr"=>"84870593186", "pmid"=>"23226482"}, "id"=>"0357eccf-76f9-3f60-900e-7335b18bf675", "abstract"=>"A 6-chloronicotinic acid mineralizing bacterium was isolated from enrichment cultures originating from imidacloprid-contaminated soil samples. This Bradyrhizobiaceae, designated strain SG-6C, hydrolytically dechlorinated 6-chloronicotinic acid to 6-hydroxynicotinic acid, which was then further metabolised via the nicotinic acid pathway. This metabolic pathway was confirmed by growth and resting cell assays using HPLC and LC-MS studies. A candidate for the gene encoding the initial dechlorination step, named cch2 (for 6-chloronicotinic acid chlorohydrolase), was identified using genome sequencing and its function was confirmed using resting cell assays on E. coli heterologously expressing this gene. The 464 amino acid enzyme was found to be a member of the metal dependent hydrolase superfamily with similarities to the TRZ/ATZ family of chlorohydrolases. We also provide evidence that cch2 was mobilized into this bacterium by an Integrative and Conjugative Element (ICE) that feeds 6-hydroxynicotinic acid into the existing nicotinic acid mineralization pathway.", "link"=>"http://www.mendeley.com/research/cloning-novel-6chloronicotinic-acid-chlorohydrolase-newly-isolated-6chloronicotinic-acid-mineralizin", "reader_count"=>14, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Student > Doctoral Student"=>2, "Researcher"=>2, "Student > Ph. D. Student"=>1, "Student > Postgraduate"=>1, "Student > Master"=>1, "Other"=>1, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Student > Doctoral Student"=>2, "Researcher"=>2, "Student > Ph. D. Student"=>1, "Student > Postgraduate"=>1, "Student > Master"=>1, "Other"=>1, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_subject_area"=>{"Engineering"=>2, "Unspecified"=>1, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>5, "Medicine and Dentistry"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>5}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"Norway"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/289300", "https://ndownloader.figshare.com/files/289357", "https://ndownloader.figshare.com/files/289402"], "description"=>"<div><p>A 6-chloronicotinic acid mineralizing bacterium was isolated from enrichment cultures originating from imidacloprid-contaminated soil samples. This Bradyrhizobiaceae, designated strain SG-6C, hydrolytically dechlorinated 6-chloronicotinic acid to 6-hydroxynicotinic acid, which was then further metabolised via the nicotinic acid pathway. This metabolic pathway was confirmed by growth and resting cell assays using HPLC and LC-MS studies. A candidate for the gene encoding the initial dechlorination step, named <em>cch2</em> (for 6-<u>c</u>hloronicotinic acid <u>c</u>hloro<u>h</u>ydrolase), was identified using genome sequencing and its function was confirmed using resting cell assays on <em>E. coli</em> heterologously expressing this gene. The 464 amino acid enzyme was found to be a member of the metal dependent hydrolase superfamily with similarities to the TRZ/ATZ family of chlorohydrolases. We also provide evidence that <em>cch2</em> was mobilized into this bacterium by an Integrative and Conjugative Element (ICE) that feeds 6-hydroxynicotinic acid into the existing nicotinic acid mineralization pathway.</p> </div>", "links"=>[], "tags"=>["cloning", "6-chloronicotinic", "chlorohydrolase", "mineralizing", "bradyrhizobiaceae", "sg-6c"], "article_id"=>116962, "categories"=>["Biological Sciences", "Genetics", "Microbiology"], "users"=>["Madhura Shettigar", "Stephen Pearce", "Rinku Pandey", "Fazlurrahman Khan", "Susan J. Dorrian", "Sahil Balotra", "Robyn J. Russell", "John G. Oakeshott", "Gunjan Pandey"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0051162.s001", "https://dx.doi.org/10.1371/journal.pone.0051162.s002", "https://dx.doi.org/10.1371/journal.pone.0051162.s003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Cloning_of_a_Novel_6_Chloronicotinic_Acid_Chlorohydrolase_from_the_Newly_Isolated_6_Chloronicotinic_Acid_Mineralizing_Bradyrhizobiaceae_Strain_SG_6C__/116962", "title"=>"Cloning of a Novel 6-Chloronicotinic Acid Chlorohydrolase from the Newly Isolated 6-Chloronicotinic Acid Mineralizing Bradyrhizobiaceae Strain SG-6C", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-11-30 01:56:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/533935"], "description"=>"<p>Four commercial chloropyridinylmethyl (CPM) neonitotinoids (A) and their degradation to 6-chloronicotinic acid via methylene hydroxylation (B).</p>", "links"=>[], "tags"=>["genetics and genomics", "microbiology", "Computational biology"], "article_id"=>204423, "categories"=>["Biological Sciences", "Genetics", "Microbiology"], "users"=>["Madhura Shettigar", "Stephen Pearce", "Rinku Pandey", "Fazlurrahman Khan", "Susan J. Dorrian", "Sahil Balotra", "Robyn J. Russell", "John G. Oakeshott", "Gunjan Pandey"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0051162.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Chloropyridinylmethyl_CPM_neonitotinoids_/204423", "title"=>"Chloropyridinylmethyl (CPM) neonitotinoids.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-30 01:13:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/534057"], "description"=>"<p>Degradation kinetics of NA, 6-CNA, and 6-HNA as sole carbon sources in growth and resting cell studies by strain SG-6C. Values are the means of three replicates with standard deviations, if visible.</p>", "links"=>[], "tags"=>["resting", "cells", "assays"], "article_id"=>204548, "categories"=>["Biological Sciences", "Genetics", "Microbiology"], "users"=>["Madhura Shettigar", "Stephen Pearce", "Rinku Pandey", "Fazlurrahman Khan", "Susan J. Dorrian", "Sahil Balotra", "Robyn J. Russell", "John G. Oakeshott", "Gunjan Pandey"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0051162.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Growth_and_resting_cells_assays_of_SG_6C_/204548", "title"=>"Growth and resting cells assays of SG-6C.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-30 01:15:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/534147"], "description"=>"<p>A) LC-MS TOF Total Ion Chromatogram (TIC) showing appearance of 6-HNA in the supernatant of resting cells cultures supplemented with 6-CNA. Mass spectra of the two compounds are shown underneath the TIC. B) LC-MS TOF TIC showing appearance of 6-HNA in the supernatant of resting cells cultures supplemented with NA. Mass spectra the two compounds are shown underneath the TIC.</p>", "links"=>[], "tags"=>["6-hna", "metabolic", "intermediate", "6-cna", "na", "resting", "cells"], "article_id"=>204627, "categories"=>["Biological Sciences", "Genetics", "Microbiology"], "users"=>["Madhura Shettigar", "Stephen Pearce", "Rinku Pandey", "Fazlurrahman Khan", "Susan J. Dorrian", "Sahil Balotra", "Robyn J. Russell", "John G. Oakeshott", "Gunjan Pandey"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0051162.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Appearance_of_6_HNA_as_a_metabolic_intermediate_of_6_CNA_and_NA_in_resting_cells_of_strain_SG_6C_/204627", "title"=>"Appearance of 6-HNA as a metabolic intermediate of 6-CNA and NA in resting cells of strain SG-6C.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-30 01:17:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/534286"], "description"=>"<p>A) Nicotinate degradation cluster in <i>Azorhizobium caulinodans</i> and selected Bradyrhizobiaceae strains. Genes were identified by Blast searches using the nicotinate degradation cluster of <i>Eubacterium barkeri </i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051162#pone.0051162-Alhapel1\" target=\"_blank\">[23]</a>. Genome accession numbers and locus tags for the displayed genes are as follows: <i>Azorhizobium caulinodans</i> ORS571 – NC_009937 (AZC_2804 to AZC_2790), <i>Bradyrhizobium japonicum</i> USDA110 – NC004463 (blr3818 to blr3830), <i>Rhodopseudomonas palustris</i> HaA2 – NC007778 (RPB_1671 to RPB_1658), Bradyrhizobiaceae bacterium SG-6C – AFOF01000023 (CSIRO_2076 to CSIRO_2090). Genes not conserved in the nicotinate degradation cluster are shown in white. B) Pathway for nicotinate and 6-chloronicotinate degradation in SG-6C. Nicotinate is metabolised via THON by the nicotinate degradation cluster shown above. 6-CNA is also metabolised via THON, after being converted to 6-hydroxynicotinate by Cch2. Pathways for nicotinate degradation in other organisms (not observed in strain SG-6C) are shown in grey.</p>", "links"=>[], "tags"=>["6-chloronicotinic", "degradation"], "article_id"=>204779, "categories"=>["Biological Sciences", "Genetics", "Microbiology"], "users"=>["Madhura Shettigar", "Stephen Pearce", "Rinku Pandey", "Fazlurrahman Khan", "Susan J. Dorrian", "Sahil Balotra", "Robyn J. Russell", "John G. Oakeshott", "Gunjan Pandey"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0051162.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nicotinic_acid_and_6_chloronicotinic_acid_degradation_in_SG_6C_/204779", "title"=>"Nicotinic acid and 6-chloronicotinic acid degradation in SG-6C.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-30 01:19:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/534380"], "description"=>"<p>(A) Comparison of the <i>Mesorhizobium loti</i> symbiosis island (ICE<i>Ml</i>Sym<sup>R7A</sup>) and SG-6C. Blast matches for genes involved in the excision, conjugative transfer and integration of the symbiosis island are all found in SG-6C (indicated by grey shading). The location of <i>cch2</i> in the accessory gene region of the SG-6C ICE is indicated; (B) The two potential forms of the SG-6C ICE, integrated and excised. Binding sites of primers used to confirm the presence of both forms are indicated by half arrows; (C) PCR of strain SG-6C genomic DNA using primer combinations as indicated. L: 1kb+ ladder, 1: CHR1 & ICE1, 2: ICE2 & CHR2, 3: CHR1 & CHR2, 4: ICE1 & ICE2, 5: negative control.</p>", "links"=>[], "tags"=>["containing"], "article_id"=>204870, "categories"=>["Biological Sciences", "Genetics", "Microbiology"], "users"=>["Madhura Shettigar", "Stephen Pearce", "Rinku Pandey", "Fazlurrahman Khan", "Susan J. Dorrian", "Sahil Balotra", "Robyn J. Russell", "John G. Oakeshott", "Gunjan Pandey"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0051162.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identifying_an_ICE_containing_cch2_/204870", "title"=>"Identifying an ICE containing <i>cch2</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-30 01:21:10"}

PMC Usage Stats | Further Information

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Relative Metric

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