Shedding light on biofilm formation of Halobacterium salinarum R1 by SWATH‐LC/MS/MS analysis of planktonic and sessile cells
Early and mature biofilm formation in the extremely halophilic euryarchaeon Halobacterium salinarum strain R1 was characterized by SWATH‐LC/MS/MS. Using a simple surfactant‐assisted protein solubilization protocol and one‐dimensional ultra‐high performance nanoflow chromatography on the front end, 6...
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| Veröffentlicht in: | Proteomics (Weinheim) 2017-04, Vol.17 (7), p.np-n/a |
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| creator | Losensky, Gerald Jung, Klaus Urlaub, Henning Pfeifer, Felicitas Fröls, Sabrina Lenz, Christof |
| description | Early and mature biofilm formation in the extremely halophilic euryarchaeon Halobacterium salinarum strain R1 was characterized by SWATH‐LC/MS/MS. Using a simple surfactant‐assisted protein solubilization protocol and one‐dimensional ultra‐high performance nanoflow chromatography on the front end, 63.2 and 58.6% of the predicted H. salinarum R1 proteome could be detected and quantified, respectively. Analysis of biophysical protein properties, functional analysis and pathway mapping indicated comprehensive characterization of the proteome. Sixty point eight percent of the quantified proteins (or 34.5% of the predicted proteome) exhibited significant abundance changes between planktonic and sessile states, demonstrating that haloarchaeal biofilm formation represents a profound “lifestyle change” on the molecular level. Our results and analysis constitute the first comprehensive study to track molecular changes from planktonic cultures to initial and mature archaeal biofilms on the proteome level. Data are available via ProteomeXchange, identifier PXD003667. Proteins exemplifying different protein expression level profiles were selected, and their corresponding gene transcripts targeted by qRT‐PCR to test the feasibility of establishing rapid PCR‐based assays for archaeal biofilm formation. |
| doi_str_mv | 10.1002/pmic.201600111 |
| format | Article |
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Using a simple surfactant‐assisted protein solubilization protocol and one‐dimensional ultra‐high performance nanoflow chromatography on the front end, 63.2 and 58.6% of the predicted H. salinarum R1 proteome could be detected and quantified, respectively. Analysis of biophysical protein properties, functional analysis and pathway mapping indicated comprehensive characterization of the proteome. Sixty point eight percent of the quantified proteins (or 34.5% of the predicted proteome) exhibited significant abundance changes between planktonic and sessile states, demonstrating that haloarchaeal biofilm formation represents a profound “lifestyle change” on the molecular level. Our results and analysis constitute the first comprehensive study to track molecular changes from planktonic cultures to initial and mature archaeal biofilms on the proteome level. Data are available via ProteomeXchange, identifier PXD003667. Proteins exemplifying different protein expression level profiles were selected, and their corresponding gene transcripts targeted by qRT‐PCR to test the feasibility of establishing rapid PCR‐based assays for archaeal biofilm formation.</description><identifier>ISSN: 1615-9853</identifier><identifier>EISSN: 1615-9861</identifier><identifier>DOI: 10.1002/pmic.201600111</identifier><identifier>PMID: 27604596</identifier><language>eng</language><publisher>Germany: Wiley Subscription Services, Inc</publisher><subject>Archaea ; Archaeal Proteins - analysis ; Archaeal Proteins - genetics ; Archaeal Proteins - metabolism ; Biofilm ; Biofilms ; Biofilms - growth & development ; Chromatography, Liquid ; Functional analysis ; Gene Expression Regulation, Archaeal ; Haloarchaea ; Halobacterium salinarum ; Halobacterium salinarum - chemistry ; Halobacterium salinarum - genetics ; Halobacterium salinarum - metabolism ; Microbiology ; Peptide mapping ; Plankton - chemistry ; Plankton - growth & development ; Plankton - metabolism ; Polymerase chain reaction ; Proteins ; Proteome - analysis ; Proteomes ; Solubilization ; Strain analysis ; SWATH ; Tandem Mass Spectrometry</subject><ispartof>Proteomics (Weinheim), 2017-04, Vol.17 (7), p.np-n/a</ispartof><rights>2016 WILEY‐VCH Verlag GmbH & Co. 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KGaA, Weinheim</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4029-6832e84739f04c035650f898f1926640cb59cfda3462e29f5bcd3f1fe62fbeff3</citedby><cites>FETCH-LOGICAL-c4029-6832e84739f04c035650f898f1926640cb59cfda3462e29f5bcd3f1fe62fbeff3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fpmic.201600111$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fpmic.201600111$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,27903,27904,45553,45554</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27604596$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Losensky, Gerald</creatorcontrib><creatorcontrib>Jung, Klaus</creatorcontrib><creatorcontrib>Urlaub, Henning</creatorcontrib><creatorcontrib>Pfeifer, Felicitas</creatorcontrib><creatorcontrib>Fröls, Sabrina</creatorcontrib><creatorcontrib>Lenz, Christof</creatorcontrib><title>Shedding light on biofilm formation of Halobacterium salinarum R1 by SWATH‐LC/MS/MS analysis of planktonic and sessile cells</title><title>Proteomics (Weinheim)</title><addtitle>Proteomics</addtitle><description>Early and mature biofilm formation in the extremely halophilic euryarchaeon Halobacterium salinarum strain R1 was characterized by SWATH‐LC/MS/MS. Using a simple surfactant‐assisted protein solubilization protocol and one‐dimensional ultra‐high performance nanoflow chromatography on the front end, 63.2 and 58.6% of the predicted H. salinarum R1 proteome could be detected and quantified, respectively. Analysis of biophysical protein properties, functional analysis and pathway mapping indicated comprehensive characterization of the proteome. Sixty point eight percent of the quantified proteins (or 34.5% of the predicted proteome) exhibited significant abundance changes between planktonic and sessile states, demonstrating that haloarchaeal biofilm formation represents a profound “lifestyle change” on the molecular level. Our results and analysis constitute the first comprehensive study to track molecular changes from planktonic cultures to initial and mature archaeal biofilms on the proteome level. Data are available via ProteomeXchange, identifier PXD003667. Proteins exemplifying different protein expression level profiles were selected, and their corresponding gene transcripts targeted by qRT‐PCR to test the feasibility of establishing rapid PCR‐based assays for archaeal biofilm formation.</description><subject>Archaea</subject><subject>Archaeal Proteins - analysis</subject><subject>Archaeal Proteins - genetics</subject><subject>Archaeal Proteins - metabolism</subject><subject>Biofilm</subject><subject>Biofilms</subject><subject>Biofilms - growth & development</subject><subject>Chromatography, Liquid</subject><subject>Functional analysis</subject><subject>Gene Expression Regulation, Archaeal</subject><subject>Haloarchaea</subject><subject>Halobacterium salinarum</subject><subject>Halobacterium salinarum - chemistry</subject><subject>Halobacterium salinarum - genetics</subject><subject>Halobacterium salinarum - metabolism</subject><subject>Microbiology</subject><subject>Peptide mapping</subject><subject>Plankton - chemistry</subject><subject>Plankton - growth & development</subject><subject>Plankton - metabolism</subject><subject>Polymerase chain reaction</subject><subject>Proteins</subject><subject>Proteome - analysis</subject><subject>Proteomes</subject><subject>Solubilization</subject><subject>Strain analysis</subject><subject>SWATH</subject><subject>Tandem Mass Spectrometry</subject><issn>1615-9853</issn><issn>1615-9861</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkcFOGzEQhq2qqFDotcfKUi-9JHi8tnd9RBE0SEEgAupx5fXaYPCug72rKpeqj9Bn7JPUaWgOvYA00oxG3_yamR-hj0CmQAg9XnVOTykBQQgAvEEHIIBPZCXg7a7mxT56n9JDRspKlu_QPi0FYVyKA_RjeW_a1vV32Lu7-wGHHjcuWOc7bEPs1OByJ1g8Vz40Sg8murHDSXnXq5ira8DNGi-_ndzMf__8tZgdXyxzYNUrv04ubUZXXvWPQ-idzu0WJ5OS8wZr4306QntW-WQ-POdDdHt2ejObTxaXX89nJ4uJZoTKiagKaipWFtISpknBBSe2kpUFSYVgRDdcatuqgglqqLS80W1hwRpBbWOsLQ7Rl63uKoan0aSh7lzabKB6E8ZUQyWhKoES9gq04IzxUsqMfv4PfQhjzKf_FeSEipKXmZpuKR1DStHYehVdp-K6BlJvTKw3JtY7E_PAp2fZselMu8P_uZYBvgW-50euX5Crry7OZ0BZ3vcPd8yn8w</recordid><startdate>201704</startdate><enddate>201704</enddate><creator>Losensky, Gerald</creator><creator>Jung, Klaus</creator><creator>Urlaub, Henning</creator><creator>Pfeifer, Felicitas</creator><creator>Fröls, Sabrina</creator><creator>Lenz, Christof</creator><general>Wiley Subscription Services, Inc</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>7QO</scope><scope>7QP</scope><scope>7TK</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>201704</creationdate><title>Shedding light on biofilm formation of Halobacterium salinarum R1 by SWATH‐LC/MS/MS analysis of planktonic and sessile cells</title><author>Losensky, Gerald ; Jung, Klaus ; Urlaub, Henning ; Pfeifer, Felicitas ; Fröls, Sabrina ; Lenz, Christof</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4029-6832e84739f04c035650f898f1926640cb59cfda3462e29f5bcd3f1fe62fbeff3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Archaea</topic><topic>Archaeal Proteins - analysis</topic><topic>Archaeal Proteins - genetics</topic><topic>Archaeal Proteins - metabolism</topic><topic>Biofilm</topic><topic>Biofilms</topic><topic>Biofilms - growth & development</topic><topic>Chromatography, Liquid</topic><topic>Functional analysis</topic><topic>Gene Expression Regulation, Archaeal</topic><topic>Haloarchaea</topic><topic>Halobacterium salinarum</topic><topic>Halobacterium salinarum - chemistry</topic><topic>Halobacterium salinarum - genetics</topic><topic>Halobacterium salinarum - metabolism</topic><topic>Microbiology</topic><topic>Peptide mapping</topic><topic>Plankton - chemistry</topic><topic>Plankton - growth & development</topic><topic>Plankton - metabolism</topic><topic>Polymerase chain reaction</topic><topic>Proteins</topic><topic>Proteome - analysis</topic><topic>Proteomes</topic><topic>Solubilization</topic><topic>Strain analysis</topic><topic>SWATH</topic><topic>Tandem Mass Spectrometry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Losensky, Gerald</creatorcontrib><creatorcontrib>Jung, Klaus</creatorcontrib><creatorcontrib>Urlaub, Henning</creatorcontrib><creatorcontrib>Pfeifer, Felicitas</creatorcontrib><creatorcontrib>Fröls, Sabrina</creatorcontrib><creatorcontrib>Lenz, Christof</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</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>Proteomics (Weinheim)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Losensky, Gerald</au><au>Jung, Klaus</au><au>Urlaub, Henning</au><au>Pfeifer, Felicitas</au><au>Fröls, Sabrina</au><au>Lenz, Christof</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Shedding light on biofilm formation of Halobacterium salinarum R1 by SWATH‐LC/MS/MS analysis of planktonic and sessile cells</atitle><jtitle>Proteomics (Weinheim)</jtitle><addtitle>Proteomics</addtitle><date>2017-04</date><risdate>2017</risdate><volume>17</volume><issue>7</issue><spage>np</spage><epage>n/a</epage><pages>np-n/a</pages><issn>1615-9853</issn><eissn>1615-9861</eissn><abstract>Early and mature biofilm formation in the extremely halophilic euryarchaeon Halobacterium salinarum strain R1 was characterized by SWATH‐LC/MS/MS. Using a simple surfactant‐assisted protein solubilization protocol and one‐dimensional ultra‐high performance nanoflow chromatography on the front end, 63.2 and 58.6% of the predicted H. salinarum R1 proteome could be detected and quantified, respectively. Analysis of biophysical protein properties, functional analysis and pathway mapping indicated comprehensive characterization of the proteome. Sixty point eight percent of the quantified proteins (or 34.5% of the predicted proteome) exhibited significant abundance changes between planktonic and sessile states, demonstrating that haloarchaeal biofilm formation represents a profound “lifestyle change” on the molecular level. Our results and analysis constitute the first comprehensive study to track molecular changes from planktonic cultures to initial and mature archaeal biofilms on the proteome level. Data are available via ProteomeXchange, identifier PXD003667. 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| subjects | Archaea Archaeal Proteins - analysis Archaeal Proteins - genetics Archaeal Proteins - metabolism Biofilm Biofilms Biofilms - growth & development Chromatography, Liquid Functional analysis Gene Expression Regulation, Archaeal Haloarchaea Halobacterium salinarum Halobacterium salinarum - chemistry Halobacterium salinarum - genetics Halobacterium salinarum - metabolism Microbiology Peptide mapping Plankton - chemistry Plankton - growth & development Plankton - metabolism Polymerase chain reaction Proteins Proteome - analysis Proteomes Solubilization Strain analysis SWATH Tandem Mass Spectrometry |
| title | Shedding light on biofilm formation of Halobacterium salinarum R1 by SWATH‐LC/MS/MS analysis of planktonic and sessile cells |
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