Nanopore Long-Read Guided Complete Genome Assembly of Hydrogenophaga intermedia , and Genomic Insights into 4-Aminobenzenesulfonate, p -Aminobenzoic Acid and Hydrogen Metabolism in the Genus Hydrogenophaga
We improved upon the previously reported draft genome of strain PBC, a 4-aminobenzenesulfonate-degrading bacterium, by supplementing the assembly with Nanopore long reads which enabled the reconstruction of the genome as a single contig. From the complete genome, major genes responsible for the cata...
Saved in:
| Published in: | Frontiers in microbiology Vol. 8; p. 1880 |
|---|---|
| Main Authors: | , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
Switzerland
Frontiers Media S.A
04-10-2017
|
| Subjects: | |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| Abstract | We improved upon the previously reported draft genome of
strain PBC, a 4-aminobenzenesulfonate-degrading bacterium, by supplementing the assembly with Nanopore long reads which enabled the reconstruction of the genome as a single contig. From the complete genome, major genes responsible for the catabolism of 4-aminobenzenesulfonate in strain PBC are clustered in two distinct genomic regions. Although the catabolic genes for 4-sulfocatechol, the deaminated product of 4-aminobenzenesulfonate, are only found in
, the
operon responsible for the first deamination step of 4-aminobenzenesulfonate is conserved in various
strains. The absence of
gene in the complete genome of
PBC is consistent with its
-aminobenzoic acid (pABA) auxotrophy but surprisingly comparative genomics analysis of 14
genomes indicate that pABA auxotrophy is not an uncommon feature among members of this genus. Of even more interest, several
strains do not possess the genomic potential for hydrogen oxidation, calling for a revision to the taxonomic description of
as "hydrogen eating bacteria." |
|---|---|
| AbstractList | We improved upon the previously reported draft genome of Hydrogenophaga intermedia strain PBC, a 4-aminobenzenesulfonate-degrading bacterium, by supplementing the assembly with Nanopore long reads which enabled the reconstruction of the genome as a single contig. From the complete genome, major genes responsible for the catabolism of 4-aminobenzenesulfonate in strain PBC are clustered in two distinct genomic regions. Although the catabolic genes for 4-sulfocatechol, the deaminated product of 4-aminobenzenesulfonate, are only found in H. intermedia, the sad operon responsible for the first deamination step of 4-aminobenzenesulfonate is conserved in various Hydrogenophaga strains. The absence of pabB gene in the complete genome of H. intermedia PBC is consistent with its p-aminobenzoic acid (pABA) auxotrophy but surprisingly comparative genomics analysis of 14 Hydrogenophaga genomes indicate that pABA auxotrophy is not an uncommon feature among members of this genus. Of even more interest, several Hydrogenophaga strains do not possess the genomic potential for hydrogen oxidation, calling for a revision to the taxonomic description of Hydrogenophaga as “hydrogen eating bacteria.” We improved upon the previously reported draft genome of strain PBC, a 4-aminobenzenesulfonate-degrading bacterium, by supplementing the assembly with Nanopore long reads which enabled the reconstruction of the genome as a single contig. From the complete genome, major genes responsible for the catabolism of 4-aminobenzenesulfonate in strain PBC are clustered in two distinct genomic regions. Although the catabolic genes for 4-sulfocatechol, the deaminated product of 4-aminobenzenesulfonate, are only found in , the operon responsible for the first deamination step of 4-aminobenzenesulfonate is conserved in various strains. The absence of gene in the complete genome of PBC is consistent with its -aminobenzoic acid (pABA) auxotrophy but surprisingly comparative genomics analysis of 14 genomes indicate that pABA auxotrophy is not an uncommon feature among members of this genus. Of even more interest, several strains do not possess the genomic potential for hydrogen oxidation, calling for a revision to the taxonomic description of as "hydrogen eating bacteria." We improved upon the previously reported draft genome of Hydrogenophaga intermedia strain PBC, a 4-aminobenzenesulfonate-degrading bacterium, by supplementing the assembly with Nanopore long reads which enabled the reconstruction of the genome as a single contig. From the complete genome, major genes responsible for the catabolism of 4-aminobenzenesulfonate in strain PBC are clustered in two distinct genomic regions. Although the catabolic genes for 4-sulfocatechol, the deaminated product of 4-aminobenzenesulfonate, are only found in H. intermedia , the sad operon responsible for the first deamination step of 4-aminobenzenesulfonate is conserved in various Hydrogenophaga strains. The absence of pabB gene in the complete genome of H. intermedia PBC is consistent with its p -aminobenzoic acid (pABA) auxotrophy but surprisingly comparative genomics analysis of 14 Hydrogenophaga genomes indicate that pABA auxotrophy is not an uncommon feature among members of this genus. Of even more interest, several Hydrogenophaga strains do not possess the genomic potential for hydrogen oxidation, calling for a revision to the taxonomic description of Hydrogenophaga as “hydrogen eating bacteria.” |
| Author | Gan, Han M Lee, Yin P Austin, Christopher M |
| AuthorAffiliation | 2 Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia , Bandar Sunway , Malaysia 3 School of Science, Monash University Malaysia , Bandar Sunway , Malaysia 1 Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University , Geelong, VIC , Australia |
| AuthorAffiliation_xml | – name: 1 Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University , Geelong, VIC , Australia – name: 3 School of Science, Monash University Malaysia , Bandar Sunway , Malaysia – name: 2 Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia , Bandar Sunway , Malaysia |
| Author_xml | – sequence: 1 givenname: Han M surname: Gan fullname: Gan, Han M organization: School of Science, Monash University Malaysia, Bandar Sunway, Malaysia – sequence: 2 givenname: Yin P surname: Lee fullname: Lee, Yin P organization: School of Science, Monash University Malaysia, Bandar Sunway, Malaysia – sequence: 3 givenname: Christopher M surname: Austin fullname: Austin, Christopher M organization: School of Science, Monash University Malaysia, Bandar Sunway, Malaysia |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/29046667$$D View this record in MEDLINE/PubMed |
| BookMark | eNpdkk1v1DAQhiNUREvpnRPykUOz2I7jJBek1Qq2Ky0gIZC4Wf6YZF0ldrATpOU_8p_w7ralxQd_zMz7zMh6X2ZnzjvIstcEL4qibt61g9VqQTGpFpjUNX6WXRDOWV5g-uPs0f08u4rxFqfFME37i-ycNphxzquL7M9n6fzoA6Ctd13-FaRB69kaMGjlh7GHCdAanB8ALWOEQfV75Ft0szfBdyk-7mQnkXUThAGMlegaSWdOEqvRxkXb7aZ4qPCI5cvBOq_A_QYHce5b7-QE12hE_zI-yZbamiPnvg_6BJNUvrdxSCg07Y5TzfG_QV5lz1vZR7i6Oy-z7x8_fFvd5Nsv681quc0143TKFWUg24JLVhakYmWtSiMLSdq6KUuTnpoWDHCbUpxAraGFksnGKKYpxYoUl9nmxDVe3oox2EGGvfDSimPAh07IMFndgzBMl1xxzDVuWENUjTHlFeamMkpzDIn1_sQaZ5W-UIObguyfQJ9mnN2Jzv8SJS9ozVgCvL0DBP9zhjiJwUYNfS8d-DkK0pQFbeqKHErxqVQHH2OA9qENweJgKnE0lTiYShxNlSRvHo_3ILi3UPEXXbbPAg |
| CitedBy_id | crossref_primary_10_1007_s11356_023_31063_w crossref_primary_10_1111_1462_2920_15692 crossref_primary_10_1093_gigascience_gix137 crossref_primary_10_1186_s12864_019_5704_3 crossref_primary_10_3389_fmicb_2019_01346 crossref_primary_10_1007_s00203_022_02865_2 crossref_primary_10_1093_jimb_kuad008 crossref_primary_10_1016_j_jgar_2019_07_008 crossref_primary_10_1007_s11356_022_22198_3 crossref_primary_10_3389_fmicb_2019_02011 crossref_primary_10_1016_j_cej_2024_149592 crossref_primary_10_1021_acs_est_7b04152 crossref_primary_10_7717_peerj_6366 crossref_primary_10_1007_s00253_019_10323_1 crossref_primary_10_12688_f1000research_21570_1 crossref_primary_10_1016_j_envpol_2023_122802 crossref_primary_10_1128_MRA_01045_18 crossref_primary_10_1016_j_margen_2019_02_002 crossref_primary_10_1021_acssensors_7b00957 crossref_primary_10_1016_j_ibiod_2020_105140 crossref_primary_10_1016_j_envpol_2021_117003 |
| Cites_doi | 10.1128/JB.00611-07 10.1093/mollus/66.4.573 10.1093/bioinformatics/btr039 10.1093/nar/gkw387 10.1186/s13742-016-0137-2 10.1016/S0723-2020(00)80022-3 10.1093/bioinformatics/btv681 10.7150/jgen.20216 10.1093/bib/bbs017 10.1128/genomeA.01162-16 10.1016/j.chemosphere.2010.10.094 10.1111/j.1574-6968.2011.02245.x 10.1093/nar/gkw569 10.1093/bioinformatics/btp348 10.1099/00207713-39-3-319 10.1093/bioinformatics/btv688 10.1101/gr.223057.117 10.1046/j.1365-2958.2001.02505.x 10.1038/ncomms4900 10.3109/10409230903505596 10.1038/ncomms3304 10.1186/1471-2164-12-402 10.1128/jb.01165-12 10.1016/j.jhazmat.2009.04.002 10.1099/mic.0.29136-0 10.1111/j.1574-6968.2007.00983.x 10.1128/JB.00990-12 10.1371/journal.pcbi.1002195 10.1016/j.nbt.2012.11.019 10.1099/mic.0.059550-0 10.1186/1471-2105-11-119 10.1111/j.1574-6968.2008.01417.x 10.1016/j.jbiotec.2016.11.013 10.1128/jb.01688-14 10.1080/09168451.2016.1176521 10.1093/molbev/mst197 10.1093/bioinformatics/btw569 10.1007/s002530000474 10.1007/BF00058181 10.1099/ijs.0.03041-0 10.1016/j.fm.2016.05.013 10.1093/molbev/msu300 10.1093/molbev/mst010 10.1038/nature16192 10.1093/nar/gkg128 |
| ContentType | Journal Article |
| Copyright | Copyright © 2017 Gan, Lee and Austin. 2017 Gan, Lee and Austin |
| Copyright_xml | – notice: Copyright © 2017 Gan, Lee and Austin. 2017 Gan, Lee and Austin |
| DBID | NPM AAYXX CITATION 7X8 5PM DOA |
| DOI | 10.3389/fmicb.2017.01880 |
| DatabaseName | PubMed CrossRef MEDLINE - Academic PubMed Central (Full Participant titles) Directory of Open Access Journals |
| DatabaseTitle | PubMed CrossRef MEDLINE - Academic |
| DatabaseTitleList | PubMed |
| Database_xml | – sequence: 1 dbid: DOA name: Directory of Open Access Journals url: http://www.doaj.org/ sourceTypes: Open Website |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1664-302X |
| EndPage | 1880 |
| ExternalDocumentID | oai_doaj_org_article_d4c56b606c09491b80026706d7dbc60e 10_3389_fmicb_2017_01880 29046667 |
| Genre | Journal Article |
| GroupedDBID | 53G 5VS 9T4 AAFWJ AAKDD ACGFO ACGFS ACXDI ADBBV ADRAZ AENEX ALMA_UNASSIGNED_HOLDINGS AOIJS BAWUL BCNDV DIK ECGQY GROUPED_DOAJ GX1 HYE IAO IEA IHR IPNFZ KQ8 M48 M~E NPM O5R O5S OK1 PGMZT RIG RNS RPM AAYXX CITATION 7X8 5PM AFPKN |
| ID | FETCH-LOGICAL-c462t-b24eaf36a45317458b5da3a1f8955d58bc234e0f74561e8cefe54a9db4c220b13 |
| IEDL.DBID | RPM |
| ISSN | 1664-302X |
| IngestDate | Tue Oct 22 15:10:12 EDT 2024 Tue Sep 17 21:27:48 EDT 2024 Fri Oct 25 09:11:53 EDT 2024 Thu Nov 21 22:14:21 EST 2024 Wed Oct 16 01:00:26 EDT 2024 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Keywords | Hydrogenophaga phylogeny hydrogen metabolism Nanopore comparative genomics |
| Language | English |
| License | This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c462t-b24eaf36a45317458b5da3a1f8955d58bc234e0f74561e8cefe54a9db4c220b13 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Edited by: John R. Battista, Louisiana State University, United States This article was submitted to Evolutionary and Genomic Microbiology, a section of the journal Frontiers in Microbiology Reviewed by: Nikolai Ravin, Research Center for Biotechnology (RAS), Russia; Rommel Thiago Juca Ramos, Federal University of Pará, Brazil |
| OpenAccessLink | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5632844/ |
| PMID | 29046667 |
| PQID | 1953298714 |
| PQPubID | 23479 |
| PageCount | 1 |
| ParticipantIDs | doaj_primary_oai_doaj_org_article_d4c56b606c09491b80026706d7dbc60e pubmedcentral_primary_oai_pubmedcentral_nih_gov_5632844 proquest_miscellaneous_1953298714 crossref_primary_10_3389_fmicb_2017_01880 pubmed_primary_29046667 |
| PublicationCentury | 2000 |
| PublicationDate | 2017-10-04 |
| PublicationDateYYYYMMDD | 2017-10-04 |
| PublicationDate_xml | – month: 10 year: 2017 text: 2017-10-04 day: 04 |
| PublicationDecade | 2010 |
| PublicationPlace | Switzerland |
| PublicationPlace_xml | – name: Switzerland |
| PublicationTitle | Frontiers in microbiology |
| PublicationTitleAlternate | Front Microbiol |
| PublicationYear | 2017 |
| Publisher | Frontiers Media S.A |
| Publisher_xml | – name: Frontiers Media S.A |
| References | 26576653 - Bioinformatics. 2016 Mar 15;32(6):929-31 25371430 - Mol Biol Evol. 2015 Jan;32(1):268-74 22887664 - J Bacteriol. 2012 Sep;194(17):4759-60 17660282 - J Bacteriol. 2007 Oct;189(19):6998-7006 27614348 - Bioinformatics. 2017 Jan 1;33(1):49-55 11454212 - Mol Microbiol. 2001 Jul;41(1):199-205 12520025 - Nucleic Acids Res. 2003 Jan 1;31(1):371-3 27457073 - Gigascience. 2016 Jul 26;5(1):32 18031533 - FEMS Microbiol Lett. 2008 Jan;278(1):94-100 20067338 - Crit Rev Biochem Mol Biol. 2010 Feb;45(1):50-69 19025569 - FEMS Microbiol Lett. 2009 Jan;290(1):114-20 22039361 - PLoS Comput Biol. 2011 Oct;7(10):e1002195 22609751 - Microbiology. 2012 Aug;158(Pt 8):1933-41 21323982 - FEMS Microbiol Lett. 2011 May;318(2):108-14 24845058 - Nat Commun. 2014 May 21;5:3900 22933765 - J Bacteriol. 2012 Sep;194(18):5139-40 11234949 - Appl Microbiol Biotechnol. 2001 Jan;55(1):101-7 19505945 - Bioinformatics. 2009 Aug 1;25(15):1972-3 27851894 - J Biotechnol. 2017 Jan 10;241:76-80 15653898 - Int J Syst Evol Microbiol. 2005 Jan;55(Pt 1):341-4 21094980 - Chemosphere. 2011 Jan;82(4):507-13 26633631 - Nature. 2015 Dec 17;528(7582):364-9 27342282 - Nucleic Acids Res. 2016 Aug 19;44(14 ):6614-24 8782393 - Biodegradation. 1996 Jun;7(3):223-9 28461322 - Genome Res. 2017 May;27(5):xi-xiii 27141966 - Nucleic Acids Res. 2016 Jul 8;44(W1):W16-21 24706738 - J Bacteriol. 2014 Jun;196(12):2210-5 27108596 - Biosci Biotechnol Biochem. 2016 Aug;80(8):1663-5 22517427 - Brief Bioinform. 2013 Mar;14(2):178-92 24132122 - Mol Biol Evol. 2013 Dec;30(12):2725-9 11249018 - Syst Appl Microbiol. 2000 Dec;23(4):487-93 27811091 - Genome Announc. 2016 Nov 3;4(6) 21278367 - Bioinformatics. 2011 Apr 1;27(7):1009-10 28775791 - J Genomics. 2017 Jul 10;5:77-82 23201074 - N Biotechnol. 2013 Sep 25;30(6):629-34 23942190 - Nat Commun. 2013;4:2304 19423220 - J Hazard Mater. 2009 Sep 30;169(1-3):1163-7 26589280 - Bioinformatics. 2016 Apr 1;32(7):1009-15 21824423 - BMC Genomics. 2011 Aug 08;12:402 17074892 - Microbiology. 2006 Nov;152(Pt 11):3207-16 27375262 - Food Microbiol. 2016 Oct;59:213-23 23329690 - Mol Biol Evol. 2013 Apr;30(4):772-80 20211023 - BMC Bioinformatics. 2010 Mar 08;11:119 Eddy (B11) 2011; 7 Halak (B19) 2006 Dangmann (B9) 1996; 7 Halak (B20) 2007; 189 Povolo (B31) 2013; 30 Segata (B34) 2013; 4 Storari (B36) 2016; 59 Tatusova (B40) 2016; 44 Arndt (B3) 2016; 44 Gan (B14); 194 Yoon (B46) 2008; 278 Thorvaldsdóttir (B41) 2013; 14 Qin (B32) 2014; 196 Willems (B43) 1989; 39 Hegedüs (B22) 2017; 241 Gan (B17) Tamura (B39) 2013; 30 Antipov (B2) 2016; 32 Contzen (B8) 2000; 23 Nguyen (B28) 2015; 32 Yoon (B45) 2009; 290 Richter (B33) 2016; 32 Phillippy (B30) 2017; 27 Hayase (B21) 2016; 80 Hickman (B23) 2010; 45 Cao (B5) 2016; 5 Katoh (B26) 2013; 30 Wang (B42) 2009; 169 Gan (B13); 194 Bai (B4) 2015; 528 Gan (B15); 318 Capella-Gutiérrez (B6) 2009; 25 Suzuki (B38) 2014; 5 Gan (B16); 82 Sullivan (B37) 2011; 27 Yang (B44) 2012 Haft (B18) 2003; 31 Alikhan (B1) 2011; 12 Kampfer (B25) 2005 Kim (B27) 2017; 5 Perei (B29) 2001; 55 Sokolov (B35) 2000; 66 David (B10) 2016; 33 Contzen (B7) 2001; 41 Fixen (B12) 2016; 4 Hyatt (B24) 2010; 11 |
| References_xml | – volume: 189 start-page: 6998 year: 2007 ident: B20 article-title: 4-Sulfomuconolactone hydrolases from Hydrogenophaga intermedia S1 and Agrobacterium radiobacter S2. publication-title: J. Bacteriol. doi: 10.1128/JB.00611-07 contributor: fullname: Halak – volume: 66 start-page: 573 year: 2000 ident: B35 article-title: An improved method for DNA isolation from mucopolysaccharide-rich molluscan tissues. publication-title: J. Molluscan Stud. doi: 10.1093/mollus/66.4.573 contributor: fullname: Sokolov – volume: 27 start-page: 1009 year: 2011 ident: B37 article-title: Easyfig: a genome comparison visualizer. publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr039 contributor: fullname: Sullivan – volume: 44 start-page: W16 year: 2016 ident: B3 article-title: PHASTER: a better, faster version of the PHAST phage search tool. publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkw387 contributor: fullname: Arndt – volume: 5 year: 2016 ident: B5 article-title: Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencing. publication-title: Gigascience doi: 10.1186/s13742-016-0137-2 contributor: fullname: Cao – volume: 23 start-page: 487 year: 2000 ident: B8 article-title: Hydrogenophaga intermedia sp. nov., a 4-aminobenzenesulfonate degrading organism. publication-title: Syst. Appl. Microbiol. doi: 10.1016/S0723-2020(00)80022-3 contributor: fullname: Contzen – volume: 32 start-page: 929 year: 2016 ident: B33 article-title: JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv681 contributor: fullname: Richter – volume: 5 start-page: 77 year: 2017 ident: B27 article-title: A glimpse into the genetic basis of symbiosis between Hydrogenophaga and their helper strains in the biodegradation of 4-aminobenzenesulfonate. publication-title: J. Genomics doi: 10.7150/jgen.20216 contributor: fullname: Kim – volume: 14 start-page: 178 year: 2013 ident: B41 article-title: Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. publication-title: Brief. Bioinform. doi: 10.1093/bib/bbs017 contributor: fullname: Thorvaldsdóttir – volume: 4 year: 2016 ident: B12 article-title: Genome sequences of eight bacterial species found in coculture with the haptophyte Chrysochromulina tobin. publication-title: Genome Announc. doi: 10.1128/genomeA.01162-16 contributor: fullname: Fixen – volume: 82 start-page: 507 ident: B16 article-title: Biodegradation of 4-aminobenzenesulfonate by Ralstonia sp. PBA and Hydrogenophaga sp. PBC isolated from textile wastewater treatment plant. publication-title: Chemosphere doi: 10.1016/j.chemosphere.2010.10.094 contributor: fullname: Gan – volume: 318 start-page: 108 ident: B15 article-title: Identification of genes involved in the 4-aminobenzenesulfonate degradation pathway of Hydrogenophaga sp. PBC via transposon mutagenesis. publication-title: FEMS Microbiol. Lett. doi: 10.1111/j.1574-6968.2011.02245.x contributor: fullname: Gan – volume: 44 start-page: 6614 year: 2016 ident: B40 article-title: NCBI prokaryotic genome annotation pipeline. publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkw569 contributor: fullname: Tatusova – volume: 25 start-page: 1972 year: 2009 ident: B6 article-title: trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp348 contributor: fullname: Capella-Gutiérrez – volume: 39 start-page: 319 year: 1989 ident: B43 article-title: Hydrogenophaga, a new genus of hydrogen-oxidizing bacteria that includes Hydrogenophaga flava comb. nov. (formerly Pseudomonas flava), Hydrogenophaga palleronii (formerly Pseudomonas palleronii), Hydrogenophaga pseudoflava (formerly Pseudomonas pseudoflava and “Pseudomonas carboxydoflava”), and Hydrogenophaga taeniospiralis (formerly Pseudomonas taeniospiralis). publication-title: Int. J. Syst. Evol. Microbiol. doi: 10.1099/00207713-39-3-319 contributor: fullname: Willems – volume: 32 start-page: 1009 year: 2016 ident: B2 article-title: hybridSPAdes: an algorithm for hybrid assembly of short and long reads. publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv688 contributor: fullname: Antipov – volume: 27 year: 2017 ident: B30 article-title: New advances in sequence assembly. publication-title: Genome Res. doi: 10.1101/gr.223057.117 contributor: fullname: Phillippy – volume: 41 start-page: 199 year: 2001 ident: B7 article-title: Cloning of the genes for a 4-sulphocatechol-oxidizing protocatechuate 3,4-dioxygenase from Hydrogenophaga intermedia S1 and identification of the amino acid residues responsible for the ability to convert 4-sulphocatechol. publication-title: Mol. Microbiol. doi: 10.1046/j.1365-2958.2001.02505.x contributor: fullname: Contzen – volume: 5 year: 2014 ident: B38 article-title: Physiological and genomic features of highly alkaliphilic hydrogen-utilizing Betaproteobacteria from a continental serpentinizing site. publication-title: Nat. Commun. doi: 10.1038/ncomms4900 contributor: fullname: Suzuki – volume: 45 start-page: 50 year: 2010 ident: B23 article-title: Integrating prokaryotes and eukaryotes: DNA transposases in light of structure. publication-title: Crit. Rev. Biochem. Mol. Biol. doi: 10.3109/10409230903505596 contributor: fullname: Hickman – volume: 4 year: 2013 ident: B34 article-title: PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. publication-title: Nat. Commun. doi: 10.1038/ncomms3304 contributor: fullname: Segata – volume: 12 year: 2011 ident: B1 article-title: BLAST ring image generator (BRIG): simple prokaryote genome comparisons. publication-title: BMC Genomics doi: 10.1186/1471-2164-12-402 contributor: fullname: Alikhan – volume: 194 start-page: 5139 ident: B13 article-title: Genome sequence of Ralstonia sp. strain PBA, a bacterium involved in the biodegradation of 4-aminobenzenesulfonate. publication-title: J. Bacteriol. doi: 10.1128/jb.01165-12 contributor: fullname: Gan – volume: 169 start-page: 1163 year: 2009 ident: B42 article-title: Biodegradation of 4-aminobenzenesulfonate by a novel Pannonibacter sp. W1 isolated from activated sludge. publication-title: J. Hazard. Mater. doi: 10.1016/j.jhazmat.2009.04.002 contributor: fullname: Wang – start-page: 3207 year: 2006 ident: B19 article-title: Characterization of the genes encoding the 3-carboxy-cis,cis-muconate-lactonizing enzymes from the 4-sulfocatechol degradative pathways of Hydrogenophaga intermedia S1 and Agrobacterium radiobacter S2. publication-title: Microbiology doi: 10.1099/mic.0.29136-0 contributor: fullname: Halak – volume: 278 start-page: 94 year: 2008 ident: B46 article-title: Isolation and characterization of a new facultatively autotrophic hydrogen-oxidizing Betaproteobacterium, Hydrogenophaga sp. AH-24. publication-title: FEMS Microbiol. Lett. doi: 10.1111/j.1574-6968.2007.00983.x contributor: fullname: Yoon – volume: 194 start-page: 4759 ident: B14 article-title: Genome sequence of Hydrogenophaga sp. strain PBC, a 4-aminobenzenesulfonate-degrading bacterium. publication-title: J. Bacteriol. doi: 10.1128/JB.00990-12 contributor: fullname: Gan – volume: 7 year: 2011 ident: B11 article-title: Accelerated profile HMM searches. publication-title: PLOS Comput Biol. doi: 10.1371/journal.pcbi.1002195 contributor: fullname: Eddy – volume: 30 start-page: 629 year: 2013 ident: B31 article-title: Polyhydroxyalkanoate biosynthesis by Hydrogenophaga pseudoflava DSM1034 from structurally unrelated carbon sources. publication-title: New Biotechnol. doi: 10.1016/j.nbt.2012.11.019 contributor: fullname: Povolo – start-page: 1933 ident: B17 article-title: Cloning and functional analysis of the genes coding for 4-aminobenzenesulfonate 3,4-dioxygenase from Hydrogenophaga sp. PBC. publication-title: Microbiology doi: 10.1099/mic.0.059550-0 contributor: fullname: Gan – volume: 11 year: 2010 ident: B24 article-title: Prodigal: prokaryotic gene recognition and translation initiation site identification. publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-11-119 contributor: fullname: Hyatt – volume: 290 start-page: 114 year: 2009 ident: B45 article-title: Purification and biochemical characterization of a membrane-bound [NiFe]-hydrogenase from a hydrogen-oxidizing, lithotrophic bacterium, Hydrogenophaga sp. AH-24. publication-title: FEMS Microbiol. Lett. doi: 10.1111/j.1574-6968.2008.01417.x contributor: fullname: Yoon – volume: 241 start-page: 76 year: 2017 ident: B22 article-title: Complete genome sequence of Novosphingobium resinovorum SA1, a versatile xenobiotic-degrading bacterium capable of utilizing sulfanilic acid. publication-title: J. Biotechnol. doi: 10.1016/j.jbiotec.2016.11.013 contributor: fullname: Hegedüs – volume: 196 start-page: 2210 year: 2014 ident: B32 article-title: A proposed genus boundary for the prokaryotes based on genomic insights. publication-title: J. Bacteriol. doi: 10.1128/jb.01688-14 contributor: fullname: Qin – volume: 80 start-page: 1663 year: 2016 ident: B21 article-title: Isolation and characterization of Bradyrhizobium sp. 224 capable of degrading sulfanilic acid. publication-title: Biosci. Biotechnol. Biochem. doi: 10.1080/09168451.2016.1176521 contributor: fullname: Hayase – start-page: 46 year: 2012 ident: B44 article-title: Isolation and characterization of a sulfanilic acid degrading bacterial strain. publication-title: Appl. Mech. Mater. contributor: fullname: Yang – volume: 30 start-page: 2725 year: 2013 ident: B39 article-title: MEGA6: molecular evolutionary genetics analysis version 6.0. publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/mst197 contributor: fullname: Tamura – volume: 33 start-page: 49 year: 2016 ident: B10 article-title: Nanocall: an open source basecaller for oxford nanopore sequencing data. publication-title: Bioinformatics doi: 10.1093/bioinformatics/btw569 contributor: fullname: David – volume: 55 start-page: 101 year: 2001 ident: B29 article-title: Biodegradation of sulfanilic acid by Pseudomonas paucimobilis. publication-title: Appl. Microbiol. Biotechnol. doi: 10.1007/s002530000474 contributor: fullname: Perei – volume: 7 start-page: 223 year: 1996 ident: B9 article-title: Degradation of 4-aminobenzenesulfonate by a two-species bacterial coculture. Physiological interactions between Hydrogenophaga palleronii S1 and Agrobacterium radiobacter S2. publication-title: Biodegradation doi: 10.1007/BF00058181 contributor: fullname: Dangmann – start-page: 341 year: 2005 ident: B25 article-title: Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov., isolated from activated sludge. publication-title: Int. J. Syst. Evol. Microbiol. doi: 10.1099/ijs.0.03041-0 contributor: fullname: Kampfer – volume: 59 start-page: 213 year: 2016 ident: B36 article-title: Genomic approach to studying nutritional requirements of Clostridium tyrobutyricum and other Clostridia causing late blowing defects. publication-title: Food Microbiol. doi: 10.1016/j.fm.2016.05.013 contributor: fullname: Storari – volume: 32 start-page: 268 year: 2015 ident: B28 article-title: IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msu300 contributor: fullname: Nguyen – volume: 30 start-page: 772 year: 2013 ident: B26 article-title: MAFFT multiple sequence alignment software version 7: improvements in performance and usability. publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/mst010 contributor: fullname: Katoh – volume: 528 start-page: 364 year: 2015 ident: B4 article-title: Functional overlap of the Arabidopsis leaf and root microbiota. publication-title: Nature doi: 10.1038/nature16192 contributor: fullname: Bai – volume: 31 start-page: 371 year: 2003 ident: B18 article-title: The TIGRFAMs database of protein families. publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkg128 contributor: fullname: Haft |
| SSID | ssj0000402000 |
| Score | 2.3315156 |
| Snippet | We improved upon the previously reported draft genome of
strain PBC, a 4-aminobenzenesulfonate-degrading bacterium, by supplementing the assembly with Nanopore... We improved upon the previously reported draft genome of Hydrogenophaga intermedia strain PBC, a 4-aminobenzenesulfonate-degrading bacterium, by supplementing... We improved upon the previously reported draft genome of Hydrogenophaga intermedia strain PBC, a 4-aminobenzenesulfonate-degrading bacterium, by supplementing... |
| SourceID | doaj pubmedcentral proquest crossref pubmed |
| SourceType | Open Website Open Access Repository Aggregation Database Index Database |
| StartPage | 1880 |
| SubjectTerms | comparative genomics hydrogen metabolism Hydrogenophaga Microbiology Nanopore phylogeny |
| SummonAdditionalLinks | – databaseName: Directory of Open Access Journals dbid: DOA link: http://sdu.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV1Lj9MwELZgJSQuiDdZHjISF6QNOIkTN8cCu1sk4AJI3CI_JruRWrtqmkP5i_wpZpy2bFdIXLhESvyUZ2x_kxl_ZuxVVcjWZEanUtGjlDbVUrcpTHLjhBa1zehw8uyr-vJj8uGUaHL2V31RTNhIDzwO3FsnbVkZhNkWDZE6MwRwKiUqp5yxlYC4-orqijEV12Ayi4QY_ZJohdUops4aCuVSbwRxkB3sQ5Gu_28Y83qo5JW95-wuu7MFjXw6dvYeuwH-Prs1XiO5ecB-4RIZEEcD_xT8RUpx8fx86Bw4TtMdJQP8HHxYACcf78LMNzy0fLZxq0AcrctLfaE5EUes4kGSE669G0t0ln_0PRnwPWUIXKbTReeDAf-TVslh3tLvdzjhyz8JAUtNbediNbtW-GdYo8LNu36BNXHEndTC0F_rxkP2_ez02_tZur2kIbWyytepySXotqi0xNmsZDkxpdOFztpJXZYOX21eSBCtIqQGEwstlFLXzkib58JkxSN25IOHJ4wrIxXUqpAWdQaBm850DboyWWalU3mZsNc7kTXLkYujQRuGxNtE8TYk3iaKN2HvSKb7fMSiHT-gbjVb3Wr-pVsJe7nTiAZnHblStIcw9A05H_MajU2ZsMejhuybymsh0ShUCVMHunPQl8MU311GZu-yKhAuyOP_0fmn7DYNRww8lM_Y0Xo1wHN2s3fDizhXfgPDKB2B priority: 102 providerName: Directory of Open Access Journals |
| Title | Nanopore Long-Read Guided Complete Genome Assembly of Hydrogenophaga intermedia , and Genomic Insights into 4-Aminobenzenesulfonate, p -Aminobenzoic Acid and Hydrogen Metabolism in the Genus Hydrogenophaga |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/29046667 https://search.proquest.com/docview/1953298714 https://pubmed.ncbi.nlm.nih.gov/PMC5632844 https://doaj.org/article/d4c56b606c09491b80026706d7dbc60e |
| Volume | 8 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://sdu.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1ba9swFBZLYbCXsfu8S9FgL4M68UW27Mesa5vBOgbbYG9GN6eGWApx_JD9xf2pnSPHbVP2tBeDLckSPp_k80lHnwh5n6eslrEUIeN4yZgKBRN1aIpE6khEpYpxc_LiO__6q_h0hjI52bgXxgftK9lM7aqd2ubKx1auWzUb48Rm3y5PszyFUZXNJmQCvuEtiu6HX2REUTQsSQIBK8FCjZIYxcWnEcqPoQBwCbww94fL3_yNvGj_vzzNuwGTt_5A54_Iw73rSOdDEx-Te8Y-IfeHwyR3T8kfGCgdeNOGfnF2GWJ0PL3oG200xU4P9jH0wljXGoorva1c7air6WKnNw6VWtdXYikoykds_HaSEyqsHko0in62HdL4DjM4ysJ521gnjf2NY2W_qnES3pzQ9U2Cg1Jz1Wj_mrEWemm2ALtV07XwJgreJ9bQd3ea8Yz8PD_7cboI90c1hIrlyTaUCTOiTnPBoE9zlhUy0yIVcV2UWabhViUpM1HN0V8zhTK1yZgotWQqSSIZp8_JkXXWvCSUS8ZNyVOmADngvolYlEbkMo4V0zzJAvJhNFm1HhQ5KmAyaOnKW7pCS1fe0gH5iDa9zoda2v6B2yyrPaIqzVSWSyByCqhuGUt0oXMe5ZprqfLIBOTdiIgK-h4uqAhrXN9VuASZlEA5WUBeDAi5rmpEWED4AXYO2nKYAnD3-t57eL_675KvyQP8Bj7mkL0hR9tNb96SSaf7Yz_ncOx7zF9kdh-u |
| link.rule.ids | 230,315,729,782,786,866,887,2106,27933,27934,53800,53802 |
| linkProvider | National Library of Medicine |
| linkToHtml | http://sdu.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1bb9MwFLbYEIIX7oNwNRIvSEvrJE7cPJaxrRPthMSQeIt8SxepsaumeSh_kT-Fj9Ns68TTXiIlvir-fHyOz_FnhD5nCS1FJHhIGTxSKkNOeRnqUSwU4SSXERxOnvxk579H346BJiftz8L4oH0pqoFZ1ANTXfrYymUth32c2PDH7CjNEidV6XAP3XfzlZAbRroXwGATEdI5JZ0JlrsxqqSAOC42IEBABhTAubMMM3-9_PV65Gn7_6dr3g6ZvLEGnTy5Y--fosdbpROPu-Rn6J42z9GD7hrKzQv014lY6_RwjafWzEOIq8enbaW0wiAu3MhqfKqNrTUGH3EtFhtsSzzZqJUFjtflJZ9zDMQTK38Q5RBzo7oSlcRnpoENgAYyWEzDcV0ZK7T5A1K2XZSwfa8P8fI6wbpSY1kpX03fCp7ptQPsompqVxN2eiu00Da3uvES_To5vjiahNtLHkJJs3gdiphqXiYZp04aMJqORKp4wqNylKepcq8yTqgmJQNNT4-kLnVKea4ElXFMRJQcoH1jjX6NMBOU6ZwlVDrMOcWPRzzXPBNRJKlicRqgL_1QF8uOy6NwNhAgpPAIKQAhhUdIgL4CFq7yAQu3_2BX82I7moWiMs2EMwGlM5LzSIDynTGSKaaEzIgO0KceSYWbteCK4UbbtinAeRnnzlilAXrVIeuqqR6ZAWI7mNvpy26Kg5pnBt9C682dS35EDycXs2kxPTv__hY9gv_hIxfpO7S_XrX6PdprVPvBz7d_c7E0QQ |
| linkToPdf | http://sdu.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV3JbtswECWaFC166b64Kwv0UiCytVCidXSTOA6aBAHaAr0J3OQIsEjDsg7uL_anOkPZThz01F4ESCRFSnwcznCGj4R8yhJWykiKgHG8pEwFgokyMMNY6lCEuYpwc_LkG7_4OTw6Rpqc7VFfPmhfyapvZ3XfVlc-tnJeq8EmTmxweX6YZglIVTaY63KwR-7CmA3jG4a6F8JoF4Vh55gEMyyHfqqUxFgu3g-RhAxpgHOwDjN_xPz1nOSp-_-mb94Om7wxD40f_ccXPCYP18onHXVZnpA7xj4l97rjKFfPyG8QtQ70cUPPnJ0GGF9PT9pKG01RbEAPG3pirKsNRV9xLWcr6ko6WemFQ67X-ZWYCooEFAu_IeWACqu7EpWip7bBhYAGMzjKglFdWSeN_YXStp2VuIxvDuj8OsFBqZGqtH_NphZ6bpYA3FnV1PAmCvor1tA2t5rxnPwYH38_nATrwx4CxbJ4GciYGVEmmWAgFThLhzLVIhFROczTVMOtihNmwpKjxmeGypQmZSLXkqk4DmWUvCD71lnzilAuGTc5T5gC7IECKCKRG5HJKFJM8zjtkc-b7i7mHadHAbYQoqTwKCkQJYVHSY98QTxs8yEbt3_gFtNi3aOFZirNJJiCCozlPJKohGc8zDTXUmWh6ZGPGzQVMHrRJSOscW1ToBMzzsFoZT3yskPXtqoNOnuE7-Bupy27KQA3zxC-htfrfy75gdy_PBoXZ6cXX9-QB_g7fAAje0v2l4vWvCN7jW7f-yH3B_DENsE |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Nanopore+Long-Read+Guided+Complete+Genome+Assembly+of+Hydrogenophaga+intermedia%2C+and+Genomic+Insights+into+4-Aminobenzenesulfonate%2C+p-Aminobenzoic+Acid+and+Hydrogen+Metabolism+in+the+Genus+Hydrogenophaga&rft.jtitle=Frontiers+in+microbiology&rft.au=Gan%2C+Han+M&rft.au=Lee%2C+Yin+P&rft.au=Austin%2C+Christopher+M&rft.date=2017-10-04&rft.issn=1664-302X&rft.eissn=1664-302X&rft.volume=8&rft.spage=1880&rft.epage=1880&rft_id=info:doi/10.3389%2Ffmicb.2017.01880&rft.externalDBID=NO_FULL_TEXT |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1664-302X&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1664-302X&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1664-302X&client=summon |