Metabolic flexibility of D-ribose producer strain of Bacillus pumilus under environmental perturbations
The metabolic reaction rate vector is a bridge that links gene and protein expression alterations to the phenotypic endpoint. We present a simple approach for the estimation of flux distribution at key branch points in the metabolic network by using substrate uptake, metabolite secretion rate, and b...
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| Veröffentlicht in: | Journal of industrial microbiology & biotechnology 2012-08, Vol.39 (8), p.1227-1243 |
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| creator | Srivastava, Rajesh K Maiti, Soumen K Das, Debasish Bapat, Prashant M Batta, Kritika Bhushan, Mani Wangikar, Pramod P |
| description | The metabolic reaction rate vector is a bridge that links gene and protein expression alterations to the phenotypic endpoint. We present a simple approach for the estimation of flux distribution at key branch points in the metabolic network by using substrate uptake, metabolite secretion rate, and biomass growth rate for transketolase (tkt) deficient Bacillus pumilus ATCC 21951. We find that the glucose-6-phosphate (G6P) and pseudo catabolic/anabolic branch points are flexible in the D-ribose-producing tkt deficient strain of B. pumilus. The normalized flux through the pentose phosphate pathway (PPP) varied from 1.5 to 86 % under different growth conditions, thereby enabling substantial extracellular accumulation of D-ribose under certain conditions. Interestingly, the flux through PPP was affected by the extracellular phosphate concentration and dissolved oxygen concentration. This metabolic flexibility may have been the underlying reason for this strain being selected from thousands of others in a screening for D-ribose producers conducted in the 1970s. |
| doi_str_mv | 10.1007/s10295-012-1115-z |
| format | Article |
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We present a simple approach for the estimation of flux distribution at key branch points in the metabolic network by using substrate uptake, metabolite secretion rate, and biomass growth rate for transketolase (tkt) deficient Bacillus pumilus ATCC 21951. We find that the glucose-6-phosphate (G6P) and pseudo catabolic/anabolic branch points are flexible in the D-ribose-producing tkt deficient strain of B. pumilus. The normalized flux through the pentose phosphate pathway (PPP) varied from 1.5 to 86 % under different growth conditions, thereby enabling substantial extracellular accumulation of D-ribose under certain conditions. Interestingly, the flux through PPP was affected by the extracellular phosphate concentration and dissolved oxygen concentration. This metabolic flexibility may have been the underlying reason for this strain being selected from thousands of others in a screening for D-ribose producers conducted in the 1970s.</description><identifier>ISSN: 1367-5435</identifier><identifier>EISSN: 1476-5535</identifier><identifier>DOI: 10.1007/s10295-012-1115-z</identifier><identifier>PMID: 22438109</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer-Verlag</publisher><subject>Adenosine ; Amino acids ; Bacillus - classification ; Bacillus - enzymology ; Bacillus - growth & development ; Bacillus - metabolism ; Bacillus pumilus ; Biochemistry ; Bioinformatics ; Biological and medical sciences ; Biomass ; Biomedical and Life Sciences ; Biotechnology ; Carbon ; Dissolved oxygen ; Enzymes ; Fluctuations ; Fundamental and applied biological sciences. Psychology ; Gene expression ; genes ; Genetic Engineering ; Genotype & phenotype ; Glucose ; glucose 6-phosphate ; Growth conditions ; Inorganic Chemistry ; Life Sciences ; Linear programming ; Metabolic Engineering and Synthetic Biology ; Metabolic Networks and Pathways ; Metabolism ; Metabolites ; Microbiology ; Mutation ; Natural products ; Optimization ; Oxygen - metabolism ; pentose phosphate cycle ; Pentose Phosphate Pathway ; Potassium ; protein synthesis ; Ribose - biosynthesis ; screening ; secretion ; Studies ; transketolase ; Transketolase - genetics ; Transketolase - metabolism</subject><ispartof>Journal of industrial microbiology & biotechnology, 2012-08, Vol.39 (8), p.1227-1243</ispartof><rights>Society for Industrial Microbiology and Biotechnology 2012</rights><rights>2015 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c459t-8d2b90ac55939fd7518ebacc5b4a01f9dfa062301c52eef127313e339d5e38e03</citedby><cites>FETCH-LOGICAL-c459t-8d2b90ac55939fd7518ebacc5b4a01f9dfa062301c52eef127313e339d5e38e03</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10295-012-1115-z$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10295-012-1115-z$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,777,781,27905,27906,41469,42538,51300</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=26212275$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22438109$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Srivastava, Rajesh K</creatorcontrib><creatorcontrib>Maiti, Soumen K</creatorcontrib><creatorcontrib>Das, Debasish</creatorcontrib><creatorcontrib>Bapat, Prashant M</creatorcontrib><creatorcontrib>Batta, Kritika</creatorcontrib><creatorcontrib>Bhushan, Mani</creatorcontrib><creatorcontrib>Wangikar, Pramod P</creatorcontrib><title>Metabolic flexibility of D-ribose producer strain of Bacillus pumilus under environmental perturbations</title><title>Journal of industrial microbiology & biotechnology</title><addtitle>J Ind Microbiol Biotechnol</addtitle><addtitle>J Ind Microbiol Biotechnol</addtitle><description>The metabolic reaction rate vector is a bridge that links gene and protein expression alterations to the phenotypic endpoint. We present a simple approach for the estimation of flux distribution at key branch points in the metabolic network by using substrate uptake, metabolite secretion rate, and biomass growth rate for transketolase (tkt) deficient Bacillus pumilus ATCC 21951. We find that the glucose-6-phosphate (G6P) and pseudo catabolic/anabolic branch points are flexible in the D-ribose-producing tkt deficient strain of B. pumilus. The normalized flux through the pentose phosphate pathway (PPP) varied from 1.5 to 86 % under different growth conditions, thereby enabling substantial extracellular accumulation of D-ribose under certain conditions. Interestingly, the flux through PPP was affected by the extracellular phosphate concentration and dissolved oxygen concentration. This metabolic flexibility may have been the underlying reason for this strain being selected from thousands of others in a screening for D-ribose producers conducted in the 1970s.</description><subject>Adenosine</subject><subject>Amino acids</subject><subject>Bacillus - classification</subject><subject>Bacillus - enzymology</subject><subject>Bacillus - growth & development</subject><subject>Bacillus - metabolism</subject><subject>Bacillus pumilus</subject><subject>Biochemistry</subject><subject>Bioinformatics</subject><subject>Biological and medical sciences</subject><subject>Biomass</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>Carbon</subject><subject>Dissolved oxygen</subject><subject>Enzymes</subject><subject>Fluctuations</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene expression</subject><subject>genes</subject><subject>Genetic Engineering</subject><subject>Genotype & phenotype</subject><subject>Glucose</subject><subject>glucose 6-phosphate</subject><subject>Growth conditions</subject><subject>Inorganic Chemistry</subject><subject>Life Sciences</subject><subject>Linear programming</subject><subject>Metabolic Engineering and Synthetic Biology</subject><subject>Metabolic Networks and Pathways</subject><subject>Metabolism</subject><subject>Metabolites</subject><subject>Microbiology</subject><subject>Mutation</subject><subject>Natural products</subject><subject>Optimization</subject><subject>Oxygen - metabolism</subject><subject>pentose phosphate cycle</subject><subject>Pentose Phosphate Pathway</subject><subject>Potassium</subject><subject>protein synthesis</subject><subject>Ribose - biosynthesis</subject><subject>screening</subject><subject>secretion</subject><subject>Studies</subject><subject>transketolase</subject><subject>Transketolase - genetics</subject><subject>Transketolase - metabolism</subject><issn>1367-5435</issn><issn>1476-5535</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNqFkl2L1TAQhoMo7nr0B3ijBRG8qWaSpm0u1_UTVrzQvS5pOjlkSZNj0oi7v97UHj8QxKsZmOedzMwbQh4CfQ6Udi8SUCZFTYHVACDqm1vkFJqurYXg4nbJedvVouHihNxL6YpSKrqO3SUnjDW8BypPyf4DLmoMzurKOPxmR-vscl0FU72qox1DwuoQw5Q1xiotUVm_1l4qbZ3LqTrk2a4x-6kA6L_aGPyMflGuOmBcchzVYoNP98kdo1zCB8e4I5dvXn8-f1dffHz7_vzsotaNkEvdT2yUVGkhJJdm6gT0OCqtxdgoCkZORtGWcQpaMEQDrOPAkXM5CeQ9Ur4jz7a-ZeovGdMyzDZpdE55DDkNQFsJsmNF-H-UlyNL2cqCPvkLvQo5-rLIDwpArhfdEdgoHUNKEc1wiHZW8bpAw2rYsBk2FMOG1bDhpmgeHTvnccbpl-KnQwV4egRU0sqZqLy26TfXMijLiMKxjUul5PcY_xzx368_3kRGhUHtY2l8-YlRaMpXaST0kn8H2N-3ig</recordid><startdate>20120801</startdate><enddate>20120801</enddate><creator>Srivastava, Rajesh K</creator><creator>Maiti, Soumen K</creator><creator>Das, Debasish</creator><creator>Bapat, Prashant M</creator><creator>Batta, Kritika</creator><creator>Bhushan, Mani</creator><creator>Wangikar, Pramod P</creator><general>Springer-Verlag</general><general>Springer</general><general>Oxford University Press</general><scope>FBQ</scope><scope>IQODW</scope><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>3V.</scope><scope>7QL</scope><scope>7QR</scope><scope>7T7</scope><scope>7WY</scope><scope>7WZ</scope><scope>7X7</scope><scope>7XB</scope><scope>87Z</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8FL</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BEZIV</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FRNLG</scope><scope>FYUFA</scope><scope>F~G</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>HCIFZ</scope><scope>K60</scope><scope>K6~</scope><scope>K9.</scope><scope>L.-</scope><scope>LK8</scope><scope>M0C</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M2P</scope><scope>M7N</scope><scope>M7P</scope><scope>MBDVC</scope><scope>P64</scope><scope>PQBIZ</scope><scope>PQBZA</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><scope>7QO</scope></search><sort><creationdate>20120801</creationdate><title>Metabolic flexibility of D-ribose producer strain of Bacillus pumilus under environmental perturbations</title><author>Srivastava, Rajesh K ; 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Biotechnol</addtitle><date>2012-08-01</date><risdate>2012</risdate><volume>39</volume><issue>8</issue><spage>1227</spage><epage>1243</epage><pages>1227-1243</pages><issn>1367-5435</issn><eissn>1476-5535</eissn><abstract>The metabolic reaction rate vector is a bridge that links gene and protein expression alterations to the phenotypic endpoint. We present a simple approach for the estimation of flux distribution at key branch points in the metabolic network by using substrate uptake, metabolite secretion rate, and biomass growth rate for transketolase (tkt) deficient Bacillus pumilus ATCC 21951. We find that the glucose-6-phosphate (G6P) and pseudo catabolic/anabolic branch points are flexible in the D-ribose-producing tkt deficient strain of B. pumilus. The normalized flux through the pentose phosphate pathway (PPP) varied from 1.5 to 86 % under different growth conditions, thereby enabling substantial extracellular accumulation of D-ribose under certain conditions. Interestingly, the flux through PPP was affected by the extracellular phosphate concentration and dissolved oxygen concentration. This metabolic flexibility may have been the underlying reason for this strain being selected from thousands of others in a screening for D-ribose producers conducted in the 1970s.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer-Verlag</pub><pmid>22438109</pmid><doi>10.1007/s10295-012-1115-z</doi><tpages>17</tpages></addata></record> |
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| ispartof | Journal of industrial microbiology & biotechnology, 2012-08, Vol.39 (8), p.1227-1243 |
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| subjects | Adenosine Amino acids Bacillus - classification Bacillus - enzymology Bacillus - growth & development Bacillus - metabolism Bacillus pumilus Biochemistry Bioinformatics Biological and medical sciences Biomass Biomedical and Life Sciences Biotechnology Carbon Dissolved oxygen Enzymes Fluctuations Fundamental and applied biological sciences. Psychology Gene expression genes Genetic Engineering Genotype & phenotype Glucose glucose 6-phosphate Growth conditions Inorganic Chemistry Life Sciences Linear programming Metabolic Engineering and Synthetic Biology Metabolic Networks and Pathways Metabolism Metabolites Microbiology Mutation Natural products Optimization Oxygen - metabolism pentose phosphate cycle Pentose Phosphate Pathway Potassium protein synthesis Ribose - biosynthesis screening secretion Studies transketolase Transketolase - genetics Transketolase - metabolism |
| title | Metabolic flexibility of D-ribose producer strain of Bacillus pumilus under environmental perturbations |
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