A Genome-Scale Metabolic Model of <i>Anabaena</i> 33047 to Guide Genetic Modifications to Overproduce Nylon Monomers
Nitrogen fixing-cyanobacteria can significantly improve the economic feasibility of cyanobacterial production processes by eliminating the requirement for reduced nitrogen. <i>Anabaena</i> sp. ATCC 33047 is a marine, heterocyst forming, nitrogen fixing cyanobacteria with a very short dou...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-03-01
|
| Series: | Metabolites |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2218-1989/11/3/168 |
| _version_ | 1797541297187192832 |
|---|---|
| author | John I. Hendry Hoang V. Dinh Debolina Sarkar Lin Wang Anindita Bandyopadhyay Himadri B. Pakrasi Costas D. Maranas |
| author_facet | John I. Hendry Hoang V. Dinh Debolina Sarkar Lin Wang Anindita Bandyopadhyay Himadri B. Pakrasi Costas D. Maranas |
| author_sort | John I. Hendry |
| collection | DOAJ |
| description | Nitrogen fixing-cyanobacteria can significantly improve the economic feasibility of cyanobacterial production processes by eliminating the requirement for reduced nitrogen. <i>Anabaena</i> sp. ATCC 33047 is a marine, heterocyst forming, nitrogen fixing cyanobacteria with a very short doubling time of 3.8 h. We developed a comprehensive genome-scale metabolic (GSM) model, <i>i</i>AnC892, for this organism using annotations and content obtained from multiple databases. <i>i</i>AnC892 describes both the vegetative and heterocyst cell types found in the filaments of <i>Anabaena</i> sp. ATCC 33047. <i>i</i>AnC892 includes 953 unique reactions and accounts for the annotation of 892 genes. Comparison of <i>i</i>AnC892 reaction content with the GSM of <i>Anabaena</i> sp. PCC 7120 revealed that there are 109 reactions including uptake hydrogenase, pyruvate decarboxylase, and pyruvate-formate lyase unique to <i>i</i>AnC892. <i>i</i>AnC892 enabled the analysis of energy production pathways in the heterocyst by allowing the cell specific deactivation of light dependent electron transport chain and glucose-6-phosphate metabolizing pathways. The analysis revealed the importance of light dependent electron transport in generating ATP and NADPH at the required ratio for optimal N<sub>2</sub> fixation. When used alongside the strain design algorithm, OptForce, <i>i</i>AnC892 recapitulated several of the experimentally successful genetic intervention strategies that over produced valerolactam and caprolactam precursors. |
| first_indexed | 2024-03-10T13:13:57Z |
| format | Article |
| id | doaj.art-e1bf4db821ff400795df4a838120eea9 |
| institution | Directory Open Access Journal |
| issn | 2218-1989 |
| language | English |
| last_indexed | 2024-03-10T13:13:57Z |
| publishDate | 2021-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Metabolites |
| spelling | doaj.art-e1bf4db821ff400795df4a838120eea92023-11-21T10:33:46ZengMDPI AGMetabolites2218-19892021-03-0111316810.3390/metabo11030168A Genome-Scale Metabolic Model of <i>Anabaena</i> 33047 to Guide Genetic Modifications to Overproduce Nylon MonomersJohn I. Hendry0Hoang V. Dinh1Debolina Sarkar2Lin Wang3Anindita Bandyopadhyay4Himadri B. Pakrasi5Costas D. Maranas6Department of Chemical Engineering, The Pennsylvania State University, University Park, State College, PA 16802, USADepartment of Chemical Engineering, The Pennsylvania State University, University Park, State College, PA 16802, USADepartment of Chemical Engineering, The Pennsylvania State University, University Park, State College, PA 16802, USADepartment of Chemical Engineering, The Pennsylvania State University, University Park, State College, PA 16802, USADepartment of Biology, Washington University, St. Louis, MO 63130, USADepartment of Biology, Washington University, St. Louis, MO 63130, USADepartment of Chemical Engineering, The Pennsylvania State University, University Park, State College, PA 16802, USANitrogen fixing-cyanobacteria can significantly improve the economic feasibility of cyanobacterial production processes by eliminating the requirement for reduced nitrogen. <i>Anabaena</i> sp. ATCC 33047 is a marine, heterocyst forming, nitrogen fixing cyanobacteria with a very short doubling time of 3.8 h. We developed a comprehensive genome-scale metabolic (GSM) model, <i>i</i>AnC892, for this organism using annotations and content obtained from multiple databases. <i>i</i>AnC892 describes both the vegetative and heterocyst cell types found in the filaments of <i>Anabaena</i> sp. ATCC 33047. <i>i</i>AnC892 includes 953 unique reactions and accounts for the annotation of 892 genes. Comparison of <i>i</i>AnC892 reaction content with the GSM of <i>Anabaena</i> sp. PCC 7120 revealed that there are 109 reactions including uptake hydrogenase, pyruvate decarboxylase, and pyruvate-formate lyase unique to <i>i</i>AnC892. <i>i</i>AnC892 enabled the analysis of energy production pathways in the heterocyst by allowing the cell specific deactivation of light dependent electron transport chain and glucose-6-phosphate metabolizing pathways. The analysis revealed the importance of light dependent electron transport in generating ATP and NADPH at the required ratio for optimal N<sub>2</sub> fixation. When used alongside the strain design algorithm, OptForce, <i>i</i>AnC892 recapitulated several of the experimentally successful genetic intervention strategies that over produced valerolactam and caprolactam precursors.https://www.mdpi.com/2218-1989/11/3/168cyanobacteria<i>Anabaena</i> sp. ATCC 33047genome scale metabolic modelsflux balance analysisOptForcecaprolactam |
| spellingShingle | John I. Hendry Hoang V. Dinh Debolina Sarkar Lin Wang Anindita Bandyopadhyay Himadri B. Pakrasi Costas D. Maranas A Genome-Scale Metabolic Model of <i>Anabaena</i> 33047 to Guide Genetic Modifications to Overproduce Nylon Monomers Metabolites cyanobacteria <i>Anabaena</i> sp. ATCC 33047 genome scale metabolic models flux balance analysis OptForce caprolactam |
| title | A Genome-Scale Metabolic Model of <i>Anabaena</i> 33047 to Guide Genetic Modifications to Overproduce Nylon Monomers |
| title_full | A Genome-Scale Metabolic Model of <i>Anabaena</i> 33047 to Guide Genetic Modifications to Overproduce Nylon Monomers |
| title_fullStr | A Genome-Scale Metabolic Model of <i>Anabaena</i> 33047 to Guide Genetic Modifications to Overproduce Nylon Monomers |
| title_full_unstemmed | A Genome-Scale Metabolic Model of <i>Anabaena</i> 33047 to Guide Genetic Modifications to Overproduce Nylon Monomers |
| title_short | A Genome-Scale Metabolic Model of <i>Anabaena</i> 33047 to Guide Genetic Modifications to Overproduce Nylon Monomers |
| title_sort | genome scale metabolic model of i anabaena i 33047 to guide genetic modifications to overproduce nylon monomers |
| topic | cyanobacteria <i>Anabaena</i> sp. ATCC 33047 genome scale metabolic models flux balance analysis OptForce caprolactam |
| url | https://www.mdpi.com/2218-1989/11/3/168 |
| work_keys_str_mv | AT johnihendry agenomescalemetabolicmodelofianabaenai33047toguidegeneticmodificationstooverproducenylonmonomers AT hoangvdinh agenomescalemetabolicmodelofianabaenai33047toguidegeneticmodificationstooverproducenylonmonomers AT debolinasarkar agenomescalemetabolicmodelofianabaenai33047toguidegeneticmodificationstooverproducenylonmonomers AT linwang agenomescalemetabolicmodelofianabaenai33047toguidegeneticmodificationstooverproducenylonmonomers AT aninditabandyopadhyay agenomescalemetabolicmodelofianabaenai33047toguidegeneticmodificationstooverproducenylonmonomers AT himadribpakrasi agenomescalemetabolicmodelofianabaenai33047toguidegeneticmodificationstooverproducenylonmonomers AT costasdmaranas agenomescalemetabolicmodelofianabaenai33047toguidegeneticmodificationstooverproducenylonmonomers AT johnihendry genomescalemetabolicmodelofianabaenai33047toguidegeneticmodificationstooverproducenylonmonomers AT hoangvdinh genomescalemetabolicmodelofianabaenai33047toguidegeneticmodificationstooverproducenylonmonomers AT debolinasarkar genomescalemetabolicmodelofianabaenai33047toguidegeneticmodificationstooverproducenylonmonomers AT linwang genomescalemetabolicmodelofianabaenai33047toguidegeneticmodificationstooverproducenylonmonomers AT aninditabandyopadhyay genomescalemetabolicmodelofianabaenai33047toguidegeneticmodificationstooverproducenylonmonomers AT himadribpakrasi genomescalemetabolicmodelofianabaenai33047toguidegeneticmodificationstooverproducenylonmonomers AT costasdmaranas genomescalemetabolicmodelofianabaenai33047toguidegeneticmodificationstooverproducenylonmonomers |