In Silico Analysis of the Phylogenetic and Physiological Characteristics of Sphingobium indicum B90A: A Hexachlorocyclohexane-Degrading Bacterium
The study focuses on the in silico genomic characterization of Sphingobium indicum B90A, revealing a wealth of genes involved in stress response, carbon monoxide oxidation, β-carotene biosynthesis, heavy metal resistance, and aromatic compound degradation, suggesting its potential as a bioremediatio...
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| Veröffentlicht in: | Current microbiology 2024-08, Vol.81 (8), p.233, Article 233 |
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| creator | Kaur, Jasvinder Verma, Helianthous Kaur, Jaspreet Lata, Pushp Dhingra, Gauri Garg Lal, Rup |
| description | The study focuses on the in silico genomic characterization of
Sphingobium indicum
B90A, revealing a wealth of genes involved in stress response, carbon monoxide oxidation, β-carotene biosynthesis, heavy metal resistance, and aromatic compound degradation, suggesting its potential as a bioremediation agent. Furthermore, genomic adaptations among nine Sphingomonad strains were explored, highlighting shared core genes via pangenome analysis, including those related to the shikimate pathway and heavy metal resistance. The majority of genes associated with aromatic compound degradation, heavy metal resistance, and stress response were found within genomic islands across all strains.
Sphingobium indicum
UT26S exhibited the highest number of genomic islands, while
Sphingopyxis alaskensis
RB2256 had the maximum fraction of its genome covered by genomic islands. The distribution of
lin
genes varied among the strains, indicating diverse genetic responses to environmental pressures. Additionally, in silico evidence of horizontal gene transfer (HGT) between plasmids pSRL3 and pISP3 of the
Sphingobium
and
Sphingomonas
genera, respectively, has been provided. The manuscript offers novel insights into strain B90A, highlighting its role in horizontal gene transfer and refining evolutionary relationships among Sphingomonad strains. The discovery of stress response genes and the
czcABCD
operon emphasizes the potential of Sphingomonads in consortia development, supported by genomic island analysis. |
| doi_str_mv | 10.1007/s00284-024-03762-1 |
| format | Article |
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Sphingobium indicum
B90A, revealing a wealth of genes involved in stress response, carbon monoxide oxidation, β-carotene biosynthesis, heavy metal resistance, and aromatic compound degradation, suggesting its potential as a bioremediation agent. Furthermore, genomic adaptations among nine Sphingomonad strains were explored, highlighting shared core genes via pangenome analysis, including those related to the shikimate pathway and heavy metal resistance. The majority of genes associated with aromatic compound degradation, heavy metal resistance, and stress response were found within genomic islands across all strains.
Sphingobium indicum
UT26S exhibited the highest number of genomic islands, while
Sphingopyxis alaskensis
RB2256 had the maximum fraction of its genome covered by genomic islands. The distribution of
lin
genes varied among the strains, indicating diverse genetic responses to environmental pressures. Additionally, in silico evidence of horizontal gene transfer (HGT) between plasmids pSRL3 and pISP3 of the
Sphingobium
and
Sphingomonas
genera, respectively, has been provided. The manuscript offers novel insights into strain B90A, highlighting its role in horizontal gene transfer and refining evolutionary relationships among Sphingomonad strains. The discovery of stress response genes and the
czcABCD
operon emphasizes the potential of Sphingomonads in consortia development, supported by genomic island analysis.</description><identifier>ISSN: 0343-8651</identifier><identifier>ISSN: 1432-0991</identifier><identifier>EISSN: 1432-0991</identifier><identifier>DOI: 10.1007/s00284-024-03762-1</identifier><identifier>PMID: 38904756</identifier><language>eng</language><publisher>New York: Springer US</publisher><subject>Aromatic compounds ; Biodegradation, Environmental ; Biomedical and Life Sciences ; Bioremediation ; Biosynthesis ; Biotechnology ; Carbon monoxide ; Carotene ; Cellular stress response ; Computer Simulation ; Degradation ; Gene transfer ; Gene Transfer, Horizontal ; Genes ; Genetic diversity ; Genome, Bacterial ; Genomic analysis ; Genomic Islands ; Genomics ; Heavy metals ; Hexachlorocyclohexane ; Hexachlorocyclohexane - metabolism ; Horizontal transfer ; Islands ; Life Sciences ; Microbiology ; Oxidation resistance ; Phylogeny ; Plasmids ; Sphingobium indicum ; Sphingomonadaceae - classification ; Sphingomonadaceae - genetics ; Sphingomonadaceae - metabolism ; β-Carotene</subject><ispartof>Current microbiology, 2024-08, Vol.81 (8), p.233, Article 233</ispartof><rights>The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2024. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.</rights><rights>2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c256t-f68d40914cb2acc1c37c0c6a540cf01e80e0ec1941075376b5c75c08783f38003</cites><orcidid>0000-0003-1163-5039 ; 0000-0001-8364-8547</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/s00284-024-03762-1$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00284-024-03762-1$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38904756$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kaur, Jasvinder</creatorcontrib><creatorcontrib>Verma, Helianthous</creatorcontrib><creatorcontrib>Kaur, Jaspreet</creatorcontrib><creatorcontrib>Lata, Pushp</creatorcontrib><creatorcontrib>Dhingra, Gauri Garg</creatorcontrib><creatorcontrib>Lal, Rup</creatorcontrib><title>In Silico Analysis of the Phylogenetic and Physiological Characteristics of Sphingobium indicum B90A: A Hexachlorocyclohexane-Degrading Bacterium</title><title>Current microbiology</title><addtitle>Curr Microbiol</addtitle><addtitle>Curr Microbiol</addtitle><description>The study focuses on the in silico genomic characterization of
Sphingobium indicum
B90A, revealing a wealth of genes involved in stress response, carbon monoxide oxidation, β-carotene biosynthesis, heavy metal resistance, and aromatic compound degradation, suggesting its potential as a bioremediation agent. Furthermore, genomic adaptations among nine Sphingomonad strains were explored, highlighting shared core genes via pangenome analysis, including those related to the shikimate pathway and heavy metal resistance. The majority of genes associated with aromatic compound degradation, heavy metal resistance, and stress response were found within genomic islands across all strains.
Sphingobium indicum
UT26S exhibited the highest number of genomic islands, while
Sphingopyxis alaskensis
RB2256 had the maximum fraction of its genome covered by genomic islands. The distribution of
lin
genes varied among the strains, indicating diverse genetic responses to environmental pressures. Additionally, in silico evidence of horizontal gene transfer (HGT) between plasmids pSRL3 and pISP3 of the
Sphingobium
and
Sphingomonas
genera, respectively, has been provided. The manuscript offers novel insights into strain B90A, highlighting its role in horizontal gene transfer and refining evolutionary relationships among Sphingomonad strains. The discovery of stress response genes and the
czcABCD
operon emphasizes the potential of Sphingomonads in consortia development, supported by genomic island analysis.</description><subject>Aromatic compounds</subject><subject>Biodegradation, Environmental</subject><subject>Biomedical and Life Sciences</subject><subject>Bioremediation</subject><subject>Biosynthesis</subject><subject>Biotechnology</subject><subject>Carbon monoxide</subject><subject>Carotene</subject><subject>Cellular stress response</subject><subject>Computer Simulation</subject><subject>Degradation</subject><subject>Gene transfer</subject><subject>Gene Transfer, Horizontal</subject><subject>Genes</subject><subject>Genetic diversity</subject><subject>Genome, Bacterial</subject><subject>Genomic analysis</subject><subject>Genomic Islands</subject><subject>Genomics</subject><subject>Heavy metals</subject><subject>Hexachlorocyclohexane</subject><subject>Hexachlorocyclohexane - metabolism</subject><subject>Horizontal transfer</subject><subject>Islands</subject><subject>Life Sciences</subject><subject>Microbiology</subject><subject>Oxidation resistance</subject><subject>Phylogeny</subject><subject>Plasmids</subject><subject>Sphingobium indicum</subject><subject>Sphingomonadaceae - classification</subject><subject>Sphingomonadaceae - genetics</subject><subject>Sphingomonadaceae - metabolism</subject><subject>β-Carotene</subject><issn>0343-8651</issn><issn>1432-0991</issn><issn>1432-0991</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kcFu1DAQhi0EotvCC3BAlrhwCYxjO3G4bRdKK1UCqXC2vBNn48qJFzuRuo_BG-NtFpA4cLBGHn__P9b8hLxi8I4B1O8TQKlEAWU-vK7Kgj0hKyZ4WUDTsKdkBVzwQlWSnZHzlO4BWNkAe07OuGpA1LJakZ83I71z3mGg69H4Q3KJho5OvaVf-4MPOzvaySE1Y3tsJBdyz6HxdNObaHCy0aUMPKru9r0bd2Hr5oG6sXWY62UD6w90Ta_tg8HehxjwgD70-Tra4qPdRdNmEb1cvObhBXnWGZ_sy1O9IN-vPn3bXBe3Xz7fbNa3BZaymoquUq2AhgnclgaRIa8RsDJSAHbArAILFlkjGNQyb2crsZYIqla84wqAX5C3i-8-hh-zTZMeXELrff5XmJPmUIMSIKXK6Jt_0Pswx7yuE1XlEUeqXCiMIaVoO72PbjDxoBnoY2B6CUznwPRjYJpl0euT9bwdbPtH8juhDPAFSPlp3Nn4d_Z_bH8BqFShPA</recordid><startdate>20240801</startdate><enddate>20240801</enddate><creator>Kaur, Jasvinder</creator><creator>Verma, Helianthous</creator><creator>Kaur, Jaspreet</creator><creator>Lata, Pushp</creator><creator>Dhingra, Gauri Garg</creator><creator>Lal, Rup</creator><general>Springer US</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7T7</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-1163-5039</orcidid><orcidid>https://orcid.org/0000-0001-8364-8547</orcidid></search><sort><creationdate>20240801</creationdate><title>In Silico Analysis of the Phylogenetic and Physiological Characteristics of Sphingobium indicum B90A: A Hexachlorocyclohexane-Degrading Bacterium</title><author>Kaur, Jasvinder ; Verma, Helianthous ; Kaur, Jaspreet ; Lata, Pushp ; Dhingra, Gauri Garg ; Lal, Rup</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c256t-f68d40914cb2acc1c37c0c6a540cf01e80e0ec1941075376b5c75c08783f38003</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Aromatic compounds</topic><topic>Biodegradation, Environmental</topic><topic>Biomedical and Life Sciences</topic><topic>Bioremediation</topic><topic>Biosynthesis</topic><topic>Biotechnology</topic><topic>Carbon monoxide</topic><topic>Carotene</topic><topic>Cellular stress response</topic><topic>Computer Simulation</topic><topic>Degradation</topic><topic>Gene transfer</topic><topic>Gene Transfer, Horizontal</topic><topic>Genes</topic><topic>Genetic diversity</topic><topic>Genome, Bacterial</topic><topic>Genomic analysis</topic><topic>Genomic Islands</topic><topic>Genomics</topic><topic>Heavy metals</topic><topic>Hexachlorocyclohexane</topic><topic>Hexachlorocyclohexane - metabolism</topic><topic>Horizontal transfer</topic><topic>Islands</topic><topic>Life Sciences</topic><topic>Microbiology</topic><topic>Oxidation resistance</topic><topic>Phylogeny</topic><topic>Plasmids</topic><topic>Sphingobium indicum</topic><topic>Sphingomonadaceae - classification</topic><topic>Sphingomonadaceae - genetics</topic><topic>Sphingomonadaceae - metabolism</topic><topic>β-Carotene</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kaur, Jasvinder</creatorcontrib><creatorcontrib>Verma, Helianthous</creatorcontrib><creatorcontrib>Kaur, Jaspreet</creatorcontrib><creatorcontrib>Lata, Pushp</creatorcontrib><creatorcontrib>Dhingra, Gauri Garg</creatorcontrib><creatorcontrib>Lal, Rup</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Current microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kaur, Jasvinder</au><au>Verma, Helianthous</au><au>Kaur, Jaspreet</au><au>Lata, Pushp</au><au>Dhingra, Gauri Garg</au><au>Lal, Rup</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>In Silico Analysis of the Phylogenetic and Physiological Characteristics of Sphingobium indicum B90A: A Hexachlorocyclohexane-Degrading Bacterium</atitle><jtitle>Current microbiology</jtitle><stitle>Curr Microbiol</stitle><addtitle>Curr Microbiol</addtitle><date>2024-08-01</date><risdate>2024</risdate><volume>81</volume><issue>8</issue><spage>233</spage><pages>233-</pages><artnum>233</artnum><issn>0343-8651</issn><issn>1432-0991</issn><eissn>1432-0991</eissn><abstract>The study focuses on the in silico genomic characterization of
Sphingobium indicum
B90A, revealing a wealth of genes involved in stress response, carbon monoxide oxidation, β-carotene biosynthesis, heavy metal resistance, and aromatic compound degradation, suggesting its potential as a bioremediation agent. Furthermore, genomic adaptations among nine Sphingomonad strains were explored, highlighting shared core genes via pangenome analysis, including those related to the shikimate pathway and heavy metal resistance. The majority of genes associated with aromatic compound degradation, heavy metal resistance, and stress response were found within genomic islands across all strains.
Sphingobium indicum
UT26S exhibited the highest number of genomic islands, while
Sphingopyxis alaskensis
RB2256 had the maximum fraction of its genome covered by genomic islands. The distribution of
lin
genes varied among the strains, indicating diverse genetic responses to environmental pressures. Additionally, in silico evidence of horizontal gene transfer (HGT) between plasmids pSRL3 and pISP3 of the
Sphingobium
and
Sphingomonas
genera, respectively, has been provided. The manuscript offers novel insights into strain B90A, highlighting its role in horizontal gene transfer and refining evolutionary relationships among Sphingomonad strains. The discovery of stress response genes and the
czcABCD
operon emphasizes the potential of Sphingomonads in consortia development, supported by genomic island analysis.</abstract><cop>New York</cop><pub>Springer US</pub><pmid>38904756</pmid><doi>10.1007/s00284-024-03762-1</doi><orcidid>https://orcid.org/0000-0003-1163-5039</orcidid><orcidid>https://orcid.org/0000-0001-8364-8547</orcidid></addata></record> |
| fulltext | fulltext |
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| ispartof | Current microbiology, 2024-08, Vol.81 (8), p.233, Article 233 |
| issn | 0343-8651 1432-0991 1432-0991 |
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| source | MEDLINE; SpringerLink Journals |
| subjects | Aromatic compounds Biodegradation, Environmental Biomedical and Life Sciences Bioremediation Biosynthesis Biotechnology Carbon monoxide Carotene Cellular stress response Computer Simulation Degradation Gene transfer Gene Transfer, Horizontal Genes Genetic diversity Genome, Bacterial Genomic analysis Genomic Islands Genomics Heavy metals Hexachlorocyclohexane Hexachlorocyclohexane - metabolism Horizontal transfer Islands Life Sciences Microbiology Oxidation resistance Phylogeny Plasmids Sphingobium indicum Sphingomonadaceae - classification Sphingomonadaceae - genetics Sphingomonadaceae - metabolism β-Carotene |
| title | In Silico Analysis of the Phylogenetic and Physiological Characteristics of Sphingobium indicum B90A: A Hexachlorocyclohexane-Degrading Bacterium |
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