Transcriptome analysis of Pseudomonas sp. from subarctic tundra soil: pathway description and gene discovery for humic acids degradation
Although humic acids (HA) are involved in many biological processes in soils and thus their ecological importance has received much attention, the degradative pathways and corresponding catalytic genes underlying the HA degradation by bacteria remain unclear. To unveil those uncertainties, we analyz...
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| Veröffentlicht in: | Folia microbiologica 2018-05, Vol.63 (3), p.315-323 |
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| creator | Kim, Dockyu Park, Ha Ju Sul, Woo Jun Park, Hyun |
| description | Although humic acids (HA) are involved in many biological processes in soils and thus their ecological importance has received much attention, the degradative pathways and corresponding catalytic genes underlying the HA degradation by bacteria remain unclear. To unveil those uncertainties, we analyzed transcriptomes extracted from
Pseudomonas
sp. PAMC 26793 cells time-dependently induced in the presence of HA in a lab flask. Out of 6288 genes, 299 (microarray) and 585 (RNA-seq) were up-regulated by > 2.0-fold in HA-induced cells, compared with controls. A significant portion (9.7% in microarray and 24.1% in RNA-seq) of these genes are predicted to function in the transport and metabolism of small molecule compounds, which could result from microbial HA degradation. To further identify lignin (a surrogate for HA)-degradative genes, 6288 protein sequences were analyzed against carbohydrate-active enzyme database and a self-curated list of putative lignin degradative genes. Out of 19 genes predicted to function in lignin degradation, several genes encoding laccase, dye-decolorizing peroxidase, vanillate
O
-demethylase oxygenase and reductase, and biphenyl 2,3-dioxygenase were up-regulated > 2.0-fold in RNA-seq. This induction was further confirmed by qRT-PCR, validating the likely involvement of these genes in the degradation of HA. |
| doi_str_mv | 10.1007/s12223-017-0573-0 |
| format | Article |
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Pseudomonas
sp. PAMC 26793 cells time-dependently induced in the presence of HA in a lab flask. Out of 6288 genes, 299 (microarray) and 585 (RNA-seq) were up-regulated by > 2.0-fold in HA-induced cells, compared with controls. A significant portion (9.7% in microarray and 24.1% in RNA-seq) of these genes are predicted to function in the transport and metabolism of small molecule compounds, which could result from microbial HA degradation. To further identify lignin (a surrogate for HA)-degradative genes, 6288 protein sequences were analyzed against carbohydrate-active enzyme database and a self-curated list of putative lignin degradative genes. Out of 19 genes predicted to function in lignin degradation, several genes encoding laccase, dye-decolorizing peroxidase, vanillate
O
-demethylase oxygenase and reductase, and biphenyl 2,3-dioxygenase were up-regulated > 2.0-fold in RNA-seq. This induction was further confirmed by qRT-PCR, validating the likely involvement of these genes in the degradation of HA.</description><identifier>ISSN: 0015-5632</identifier><identifier>EISSN: 1874-9356</identifier><identifier>DOI: 10.1007/s12223-017-0573-0</identifier><identifier>PMID: 29196950</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Acids ; Applied Microbiology ; Bacteria ; Biodegradation ; Biological activity ; Biomedical and Life Sciences ; Biphenyl ; Biphenyl 2,3-dioxygenase ; Carbohydrates ; Catalysis ; Decoloring ; Degradation ; DNA microarrays ; Environmental Engineering/Biotechnology ; Gene expression ; Gene sequencing ; Genes ; Humic acids ; Immunology ; Laccase ; Life Sciences ; Lignin ; Metabolism ; Microbiology ; Microorganisms ; Original Article ; Oxygenase ; Peroxidase ; Pseudomonas ; Reductase ; Ribonucleic acid ; RNA ; Soils ; Taiga & tundra ; Tundra ; Uncertainty analysis ; Vanillate O-demethylase</subject><ispartof>Folia microbiologica, 2018-05, Vol.63 (3), p.315-323</ispartof><rights>Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i. 2017</rights><rights>Folia Microbiologica is a copyright of Springer, (2017). All Rights Reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c438t-c6565bc2f7a479dbe2c262c8bc336cdb85e9eba0df125a98e72d0230687c69b03</citedby><cites>FETCH-LOGICAL-c438t-c6565bc2f7a479dbe2c262c8bc336cdb85e9eba0df125a98e72d0230687c69b03</cites><orcidid>0000-0001-7504-6247</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s12223-017-0573-0$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s12223-017-0573-0$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27923,27924,41487,42556,51318</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29196950$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kim, Dockyu</creatorcontrib><creatorcontrib>Park, Ha Ju</creatorcontrib><creatorcontrib>Sul, Woo Jun</creatorcontrib><creatorcontrib>Park, Hyun</creatorcontrib><title>Transcriptome analysis of Pseudomonas sp. from subarctic tundra soil: pathway description and gene discovery for humic acids degradation</title><title>Folia microbiologica</title><addtitle>Folia Microbiol</addtitle><addtitle>Folia Microbiol (Praha)</addtitle><description>Although humic acids (HA) are involved in many biological processes in soils and thus their ecological importance has received much attention, the degradative pathways and corresponding catalytic genes underlying the HA degradation by bacteria remain unclear. To unveil those uncertainties, we analyzed transcriptomes extracted from
Pseudomonas
sp. PAMC 26793 cells time-dependently induced in the presence of HA in a lab flask. Out of 6288 genes, 299 (microarray) and 585 (RNA-seq) were up-regulated by > 2.0-fold in HA-induced cells, compared with controls. A significant portion (9.7% in microarray and 24.1% in RNA-seq) of these genes are predicted to function in the transport and metabolism of small molecule compounds, which could result from microbial HA degradation. To further identify lignin (a surrogate for HA)-degradative genes, 6288 protein sequences were analyzed against carbohydrate-active enzyme database and a self-curated list of putative lignin degradative genes. Out of 19 genes predicted to function in lignin degradation, several genes encoding laccase, dye-decolorizing peroxidase, vanillate
O
-demethylase oxygenase and reductase, and biphenyl 2,3-dioxygenase were up-regulated > 2.0-fold in RNA-seq. This induction was further confirmed by qRT-PCR, validating the likely involvement of these genes in the degradation of HA.</description><subject>Acids</subject><subject>Applied Microbiology</subject><subject>Bacteria</subject><subject>Biodegradation</subject><subject>Biological activity</subject><subject>Biomedical and Life Sciences</subject><subject>Biphenyl</subject><subject>Biphenyl 2,3-dioxygenase</subject><subject>Carbohydrates</subject><subject>Catalysis</subject><subject>Decoloring</subject><subject>Degradation</subject><subject>DNA microarrays</subject><subject>Environmental Engineering/Biotechnology</subject><subject>Gene expression</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Humic acids</subject><subject>Immunology</subject><subject>Laccase</subject><subject>Life Sciences</subject><subject>Lignin</subject><subject>Metabolism</subject><subject>Microbiology</subject><subject>Microorganisms</subject><subject>Original Article</subject><subject>Oxygenase</subject><subject>Peroxidase</subject><subject>Pseudomonas</subject><subject>Reductase</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>Soils</subject><subject>Taiga & tundra</subject><subject>Tundra</subject><subject>Uncertainty analysis</subject><subject>Vanillate O-demethylase</subject><issn>0015-5632</issn><issn>1874-9356</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp1kc1u1TAQRi1ERS8tD8AGWWLDJmVsx3bMDlX8SZXool1bju3cpkri4EmK7hvw2PiSghASK1vy-T6P5hDyksEFA9BvkXHORQVMVyB1uTwhO9boujJCqqdkB8BkJZXgp-Q54j2AglrwZ-SUG2aUkbAjP26ym9Dnfl7SGKmb3HDAHmnq6DXGNaQxTQ4pzhe0y2mkuLYu-6X3dFmnkB3F1A_v6OyWu-_uQEPcuvo0la5A93GKNPTo00PMB9qlTO_WsaSd7wMWfJ9dcEf8nJx0bsD44vE8I7cfP9xcfq6uvn76cvn-qvK1aJbKK6lk63mnXa1NaCP3XHHftF4I5UPbyGhi6yB0jEtnmqh5AC5ANdor04I4I2-23jmnb2vExY5lvDgMboppRcuMZkqZki7o63_Q-7TmsqFfFJRFN7UoFNsonxNijp2dcz-6fLAM7FGT3TTZoskeNdnjEK8em9d2jOFP4reXAvANwPI07WP-6-v_tv4EsiKftQ</recordid><startdate>20180501</startdate><enddate>20180501</enddate><creator>Kim, Dockyu</creator><creator>Park, Ha 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acids</topic><topic>Immunology</topic><topic>Laccase</topic><topic>Life Sciences</topic><topic>Lignin</topic><topic>Metabolism</topic><topic>Microbiology</topic><topic>Microorganisms</topic><topic>Original Article</topic><topic>Oxygenase</topic><topic>Peroxidase</topic><topic>Pseudomonas</topic><topic>Reductase</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>Soils</topic><topic>Taiga & tundra</topic><topic>Tundra</topic><topic>Uncertainty analysis</topic><topic>Vanillate O-demethylase</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kim, Dockyu</creatorcontrib><creatorcontrib>Park, Ha Ju</creatorcontrib><creatorcontrib>Sul, Woo Jun</creatorcontrib><creatorcontrib>Park, Hyun</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts 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(Praha)</addtitle><date>2018-05-01</date><risdate>2018</risdate><volume>63</volume><issue>3</issue><spage>315</spage><epage>323</epage><pages>315-323</pages><issn>0015-5632</issn><eissn>1874-9356</eissn><abstract>Although humic acids (HA) are involved in many biological processes in soils and thus their ecological importance has received much attention, the degradative pathways and corresponding catalytic genes underlying the HA degradation by bacteria remain unclear. To unveil those uncertainties, we analyzed transcriptomes extracted from
Pseudomonas
sp. PAMC 26793 cells time-dependently induced in the presence of HA in a lab flask. Out of 6288 genes, 299 (microarray) and 585 (RNA-seq) were up-regulated by > 2.0-fold in HA-induced cells, compared with controls. A significant portion (9.7% in microarray and 24.1% in RNA-seq) of these genes are predicted to function in the transport and metabolism of small molecule compounds, which could result from microbial HA degradation. To further identify lignin (a surrogate for HA)-degradative genes, 6288 protein sequences were analyzed against carbohydrate-active enzyme database and a self-curated list of putative lignin degradative genes. Out of 19 genes predicted to function in lignin degradation, several genes encoding laccase, dye-decolorizing peroxidase, vanillate
O
-demethylase oxygenase and reductase, and biphenyl 2,3-dioxygenase were up-regulated > 2.0-fold in RNA-seq. This induction was further confirmed by qRT-PCR, validating the likely involvement of these genes in the degradation of HA.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>29196950</pmid><doi>10.1007/s12223-017-0573-0</doi><tpages>9</tpages><orcidid>https://orcid.org/0000-0001-7504-6247</orcidid></addata></record> |
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| ispartof | Folia microbiologica, 2018-05, Vol.63 (3), p.315-323 |
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| subjects | Acids Applied Microbiology Bacteria Biodegradation Biological activity Biomedical and Life Sciences Biphenyl Biphenyl 2,3-dioxygenase Carbohydrates Catalysis Decoloring Degradation DNA microarrays Environmental Engineering/Biotechnology Gene expression Gene sequencing Genes Humic acids Immunology Laccase Life Sciences Lignin Metabolism Microbiology Microorganisms Original Article Oxygenase Peroxidase Pseudomonas Reductase Ribonucleic acid RNA Soils Taiga & tundra Tundra Uncertainty analysis Vanillate O-demethylase |
| title | Transcriptome analysis of Pseudomonas sp. from subarctic tundra soil: pathway description and gene discovery for humic acids degradation |
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