Mechanism‐Guided Design of Highly Efficient Protein Secretion and Lipid Conversion for Biomanufacturing and Biorefining

Xie, Shangxian; Sun, Su; Lin, Furong; Li, Muzi; Pu, Yunqiao; Cheng, Yanbing; Xu, Bing; Liu, Zhihua; da Costa Sousa, Leonardo; Dale, Bruce E.; Ragauskas, Arthur J.; Dai, Susie Y.; Yuan, Joshua S.

doi:10.1002/advs.201801980

Title: Mechanism‐Guided Design of Highly Efficient Protein Secretion and Lipid Conversion for Biomanufacturing and Biorefining

Journal Article · Wed May 01 00:00:00 EDT 2019 · Advanced Science

DOI:https://doi.org/10.1002/advs.201801980· OSTI ID:1510339

^[1]; Sun, Su ^[1]; Lin, Furong ^[1]; Li, Muzi ^[1]; Pu, Yunqiao ^[2]; Cheng, Yanbing ^[1]; Xu, Bing ^[1]; Liu, Zhihua ^[1]; da Costa Sousa, Leonardo ^[3]; Dale, Bruce E. ^[3]; Ragauskas, Arthur J. ^[4]; Dai, Susie Y. ^[5];

^[1]

Synthetic and Systems Biology Innovation Hub and Department of Plant Pathology and MicrobiologyTexas A&,M University College Station TX 77843 USA
Joint Institute for Biological Sciences and Biosciences DivisionOak Ridge National Laboratory Oak Ridge TN 37831 USA
Department of Chemical Engineering and Materials ScienceMichigan State University East Lansing MI 48824 USA
Joint Institute for Biological Sciences and Biosciences DivisionOak Ridge National Laboratory Oak Ridge TN 37831 USA, Department of Chemical and Biomolecular Engineering &, Department of Forestry, Wildlife, and FisheriesUniversity of Tennessee Knoxville TN 37996 USA
Synthetic and Systems Biology Innovation Hub and Department of Plant Pathology and MicrobiologyTexas A&,M University College Station TX 77843 USA, State Hygienic LaboratoryUniversity of Iowa Coralville IA 52246 USA

Bacterial protein secretion represents a significant challenge in biotechnology, which is essential for the cost-effective production of therapeutics, enzymes, and other functional proteins. Here, it is demonstrated that proteomics-guided engineering of transcription, translation, secretion, and folding of ligninolytic laccase balances the process, minimizes the toxicity, and enables efficient heterologous secretion with a total protein yield of 13.7 g L^-1. The secretory laccase complements the biochemical limits on lignin depolymerization well in Rhodococcus opacus PD630. Further proteomics analysis reveals the mechanisms for the oleaginous phenotype of R. opacus PD630, where a distinct multiunit fatty acid synthase I drives the carbon partition to storage lipid. The discovery guides the design of efficient lipid conversion from lignin and carbohydrate. The proteomics-guided integration of laccase-secretion and lipid production modules enables a high titer in converting lignin-enriched biorefinery waste to lipid. The fundamental mechanisms, engineering components, and design principle can empower transformative platforms for biomanufacturing and biorefining.

View Journal Article

Cite

Export

Save

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE)

Grant/Contract Number:: EE0006112; EE0007104; EE0008250; AC05-00OR22725

OSTI ID:: 1510339

Alternate ID(s):: OSTI ID: 1510340; OSTI ID: 1530062; OSTI ID: 1606678

Journal Information:: Advanced Science, Journal Name: Advanced Science; ISSN 2198-3844

Publisher:: WileyCopyright Statement

Country of Publication:: Germany

Language:: English

Citation Metrics:

Cited by: 45 works

Citation information provided by
Web of Science

References (36)

Lignin Valorization: Improving Lignin Processing in the Biorefinery Ragauskas, A. J.; Beckham, G. T.; Biddy, M. J. Science, Vol. 344, Issue 6185, p. 1246843-1246843 https://doi.org/10.1126/science.1246843	journal	May 2014
The missing piece of the type II fatty acid synthase system from Mycobacterium tuberculosis Sacco, E.; Covarrubias, A. S.; O'Hare, H. M. Proceedings of the National Academy of Sciences, Vol. 104, Issue 37 https://doi.org/10.1073/pnas.0704132104	journal	September 2007
Bacterial expression systems for recombinant protein production: E. coli and beyond Chen, Rachel Biotechnology Advances, Vol. 30, Issue 5 https://doi.org/10.1016/j.biotechadv.2011.09.013	journal	September 2012
Production of recombinant proteins by microbes and higher organisms Demain, Arnold L.; Vaishnav, Preeti Biotechnology Advances, Vol. 27, Issue 3 https://doi.org/10.1016/j.biotechadv.2009.01.008	journal	May 2009
Application of quantitative 31P NMR in biomass lignin and biofuel precursors characterization Pu, Yunqiao; Cao, Shilin; Ragauskas, Arthur J. Energy & Environmental Science, Vol. 4, Issue 9 https://doi.org/10.1039/c1ee01201k	journal	January 2011
Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast Huang, Mingtao; Bai, Yunpeng; Sjostrom, Staffan L. Proceedings of the National Academy of Sciences, Vol. 112, Issue 34 https://doi.org/10.1073/pnas.1506460112	journal	August 2015
Exploration of Natural Biomass Utilization Systems (NBUS) for advanced biofuel—from systems biology to synthetic design Xie, Shangxian; Syrenne, Ryan; Sun, Su Current Opinion in Biotechnology, Vol. 27 https://doi.org/10.1016/j.copbio.2014.02.007	journal	June 2014
Preparative expression of secreted proteins in bacteria: status report and future prospects Georgiou, G.; Segatori, L. Current Opinion in Biotechnology, Vol. 16, Issue 5 https://doi.org/10.1016/j.copbio.2005.07.008	journal	October 2005
Production of Soluble Recombinant Proteins in Bacteria Schein, Catherine H. Nature Biotechnology, Vol. 7, Issue 11 https://doi.org/10.1038/nbt1189-1141	journal	November 1989
Towards lignin consolidated bioprocessing: simultaneous lignin depolymerization and product generation by bacteria Salvachúa, Davinia; Karp, Eric M.; Nimlos, Claire T. Green Chemistry, Vol. 17, Issue 11 https://doi.org/10.1039/C5GC01165E	journal	January 2015
Enzymatic conversion of lignin into renewable chemicals Bugg, Timothy DH; Rahmanpour, Rahman Current Opinion in Chemical Biology, Vol. 29 https://doi.org/10.1016/j.cbpa.2015.06.009	journal	December 2015
The twin-arginine translocation pathway is a major route of protein export in Streptomyces coelicolor Widdick, D. A.; Dilks, K.; Chandra, G. Proceedings of the National Academy of Sciences, Vol. 103, Issue 47 https://doi.org/10.1073/pnas.0607025103	journal	November 2006
Lignin Conversion: Opportunities and Challenges for the Integrated Biorefinery Xie, Shangxian; Ragauskas, Arthur J.; Yuan, Joshua S. Industrial Biotechnology, Vol. 12, Issue 3 https://doi.org/10.1089/ind.2016.0007	journal	June 2016
Efficient expression of full-length antibodies in the cytoplasm of engineered bacteria Robinson, Michael-Paul; Ke, Na; Lobstein, Julie Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms9072	journal	August 2015
The Crystal Structure of Yeast Fatty Acid Synthase, a Cellular Machine with Eight Active Sites Working Together Lomakin, Ivan B.; Xiong, Yong; Steitz, Thomas A. Cell, Vol. 129, Issue 2 https://doi.org/10.1016/j.cell.2007.03.013	journal	April 2007
The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse McLeod, M. P.; Warren, R. L.; Hsiao, W. W. L. Proceedings of the National Academy of Sciences, Vol. 103, Issue 42, p. 15582-15587 https://doi.org/10.1073/pnas.0607048103	journal	October 2006
Understanding Pulp Delignification by Laccase–Mediator Systems through Isolation and Characterization of Lignin–Carbohydrate Complexes Du, Xueyu; Li, Jiebing; Gellerstedt, Göran Biomacromolecules, Vol. 14, Issue 9 https://doi.org/10.1021/bm4006936	journal	August 2013
Development of a genetic transformation system for benzene-tolerant Rhodococcus opacus strains Na, Kyung-su; Nagayasu, Kan; Kuroda, Akio Journal of Bioscience and Bioengineering, Vol. 99, Issue 4 https://doi.org/10.1263/jbb.99.408	journal	April 2005
Integration of shot-gun proteomics and bioinformatics analysis to explore plant hormone responses Zhang, Yixiang; Liu, Sanmin; Dai, Susie Y. BMC Bioinformatics, Vol. 13, Issue Suppl 15 https://doi.org/10.1186/1471-2105-13-S15-S8	journal	January 2012
The Crystal Structure of a Mammalian Fatty Acid Synthase Maier, T.; Leibundgut, M.; Ban, N. Science, Vol. 321, Issue 5894 https://doi.org/10.1126/science.1161269	journal	September 2008
Synergistic enzymatic and microbial lignin conversion Zhao, Cheng; Xie, Shangxian; Pu, Yunqiao Green Chemistry, Vol. 18, Issue 5 https://doi.org/10.1039/C5GC01955A	journal	January 2016
Establishment of a gene transfer system for Rhodococcus opacus PD630 based on electroporation and its application for recombinant biosynthesis of poly(3-hydroxyalkanoic acids) Kalscheuer, R.; Arenskötter, M.; Steinbüchel, A. Applied Microbiology and Biotechnology, Vol. 52, Issue 4 https://doi.org/10.1007/s002530051553	journal	October 1999
Characterization of SLAC: A small laccase from Streptomyces coelicolor with unprecedented activity Machczynski, Michael C.; Vijgenboom, Erik; Samyn, Bart Protein Science, Vol. 13, Issue 9 https://doi.org/10.1110/ps.04759104	journal	September 2004
Recombinant protein folding and misfolding in Escherichia coli Baneyx, François; Mujacic, Mirna Nature Biotechnology, Vol. 22, Issue 11 https://doi.org/10.1038/nbt1029	journal	November 2004
Lignin valorization through integrated biological funneling and chemical catalysis Linger, J. G.; Vardon, D. R.; Guarnieri, M. T. Proceedings of the National Academy of Sciences, Vol. 111, Issue 33, p. 12013-12018 https://doi.org/10.1073/pnas.1410657111	journal	August 2014
Engineering xylose metabolism in triacylglycerol-producing Rhodococcus opacus for lignocellulosic fuel production Kurosawa, Kazuhiko; Wewetzer, Sandra J.; Sinskey, Anthony J. Biotechnology for Biofuels, Vol. 6, Issue 1 https://doi.org/10.1186/1754-6834-6-134	journal	January 2013
Translational level is a critical factor for the secretion of heterologous proteins in Escherichia coli Simmons, Laura C.; Yansura, Daniel G. Nature Biotechnology, Vol. 14, Issue 5 https://doi.org/10.1038/nbt0596-629	journal	May 1996
Cellulosic ethanol production from AFEX-treated corn stover using Saccharomyces cerevisiae 424A(LNH-ST) Lau, M. W.; Dale, B. E. Proceedings of the National Academy of Sciences, Vol. 106, Issue 5, p. 1368-1373 https://doi.org/10.1073/pnas.0812364106	journal	January 2009
Advanced Chemical Design for Efficient Lignin Bioconversion Xie, Shangxian; Sun, Qining; Pu, Yunqiao ACS Sustainable Chemistry & Engineering, Vol. 5, Issue 3 https://doi.org/10.1021/acssuschemeng.6b02401	journal	January 2017
Application of an Improved Proteomics Method for Abundant Protein Cleanup: Molecular and Genomic Mechanisms Study in Plant Defense Zhang, Yixiang; Gao, Peng; Xing, Zhuo Molecular & Cellular Proteomics, Vol. 12, Issue 11 https://doi.org/10.1074/mcp.M112.025213	journal	August 2013
A fungal metabolite mediates degradation of non-phenolic lignin structures and synthetic lignin by laccase Eggert, Claudia; Temp, Ulrike; Dean, Jeffrey F. D. FEBS Letters, Vol. 391, Issue 1-2 https://doi.org/10.1016/0014-5793(96)00719-3	journal	August 1996
Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development Holder, Jason W.; Ulrich, Jil C.; DeBono, Anthony C. PLoS Genetics, Vol. 7, Issue 9 https://doi.org/10.1371/journal.pgen.1002219	journal	September 2011
The emerging role for bacteria in lignin degradation and bio-product formation Bugg, Timothy DH; Ahmad, Mark; Hardiman, Elizabeth M. Current Opinion in Biotechnology, Vol. 22, Issue 3 https://doi.org/10.1016/j.copbio.2010.10.009	journal	June 2011
The twin-arginine translocation (Tat) protein export pathway Palmer, Tracy; Berks, Ben C. Nature Reviews Microbiology, Vol. 10, Issue 7 https://doi.org/10.1038/nrmicro2814	journal	June 2012
Microbial Type I Fatty Acid Synthases (FAS): Major Players in a Network of Cellular FAS Systems Schweizer, E.; Hofmann, J. Microbiology and Molecular Biology Reviews, Vol. 68, Issue 3 https://doi.org/10.1128/MMBR.68.3.501-517.2004	journal	September 2004
Optimization of the ammonia fiber explosion (AFEX) treatment parameters for enzymatic hydrolysis of corn stover Teymouri, Farzaneh; Laureano-Perez, Lizbeth; Alizadeh, Hasan Bioresource Technology, Vol. 96, Issue 18, p. 2014-2018 https://doi.org/10.1016/j.biortech.2005.01.016	journal	December 2005

Similar Records

A Unique Bacterial Pelletized Cultivation Platform in Rhodococcus opacus PD630 Enhanced Lipid Productivity and Simplified Harvest for Lignin Bioconversion

Journal Article · Mon Jan 10 00:00:00 EST 2022 · ACS Sustainable Chemistry & Engineering · OSTI ID:1510339

Xu, Bing; Li, Qiang; Pu, Yuanqiao Joseph; +5 more

Combinatorial pretreatment and fermentation optimization enabled a record yield on lignin bioconversion

Journal Article · Mon Jan 29 00:00:00 EST 2018 · Biotechnology for Biofuels · OSTI ID:1510339

Liu, Zhi -Hua; Xie, Shangxian; Lin, Furong; +2 more

Production of single cell protein from agro-waste using Rhodococcus opacus

Journal Article · Sat Sep 01 00:00:00 EDT 2018 · Journal of Industrial Microbiology and Biotechnology · OSTI ID:1510339

Mahan, Kristina M.; Le, Rosemary K.; Wells, Jr., Tyrone; +6 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
applied microbiology
heterologous protein secretion expression
lignin valorization
lipid biosynthesis
metabolic engineering

Title: Mechanism‐Guided Design of Highly Efficient Protein Secretion and Lipid Conversion for Biomanufacturing and Biorefining

Citation Formats

References (36)

Similar Records

Related Subjects