Development of Chemical and Metabolite Sensors for Rhodococcus opacus PD630

DeLorenzo, Drew M.; Henson, William R.; Moon, Tae Seok

doi:10.1021/acssynbio.7b00192

Development of Chemical and Metabolite Sensors for Rhodococcus opacus PD630

Journal Article · Wed Jul 26 00:00:00 EDT 2017 · ACS Synthetic Biology

DOI:https://doi.org/10.1021/acssynbio.7b00192· OSTI ID:1417982

DeLorenzo, Drew M. ^[1]; Henson, William R. ^[2]; ^[2]

Washington Univ., St. Louis, MO (United States); Washington University in St. Louis
Washington Univ., St. Louis, MO (United States)

Rhodococcus opacus PD630 is a non-model, gram positive bacterium that possesses desirable traits for biomass conversion, including consumption capabilities for lignocellulose-based sugars and toxic lignin-derived aromatic compounds, significant triacylglycerol accumulation, relatively rapid growth rate, and genetic tractability. However, few genetic elements have been directly characterized in R. opacus, limiting its application for lignocellulose bioconversion. Here, we report the characterization and development of genetic tools for tunable gene expression in R. opacus, including: 1) six fluorescent reporters for quantifying promoter output, 2) three chemically inducible promoters for variable gene expression, and 3) two classes of metabolite sensors derived from native R. opacus promoters that detect nitrogen levels or aromatic compounds. Using these tools, we also provide insights into native aromatic consumption pathways in R. opacus. Overall, this work expands the ability to control and characterize gene expression in R. opacus for future lignocellulose-based fuel and chemical production.

View Accepted Manuscript (DOE)

Research Organization:: Washington Univ., St. Louis, MO (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: SC0012705

OSTI ID:: 1417982

Journal Information:: ACS Synthetic Biology, Journal Name: ACS Synthetic Biology Journal Issue: 10 Vol. 6; ISSN 2161-5063

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

References (32)

Formation of intracytoplasmic lipid inclusions by Rhodococcus opacus strain PD630 Alvarez, Hector M.; Mayer, Frank; Fabritius, Dirk Archives of Microbiology, Vol. 165, Issue 6 https://doi.org/10.1007/s002030050341	journal	June 1996
Induction and carbon catabolite repression of phenol degradation genes in Rhodococcus erythropolis and Rhodococcus jostii Szőköl, Juraj; Rucká, Lenka; Šimčíková, Michaela Applied Microbiology and Biotechnology, Vol. 98, Issue 19 https://doi.org/10.1007/s00253-014-5881-6	journal	June 2014
Programmable genetic circuits for pathway engineering Hoynes-O’Connor, Allison; Moon, Tae Seok Current Opinion in Biotechnology, Vol. 36 https://doi.org/10.1016/j.copbio.2015.08.007	journal	December 2015
Metabolic engineering strategies to bio-adipic acid production Kruyer, Nicholas S.; Peralta-Yahya, Pamela Current Opinion in Biotechnology, Vol. 45 https://doi.org/10.1016/j.copbio.2017.03.006	journal	June 2017
Enhancing muconic acid production from glucose and lignin-derived aromatic compounds via increased protocatechuate decarboxylase activity Johnson, Christopher W.; Salvachúa, Davinia; Khanna, Payal Metabolic Engineering Communications, Vol. 3 https://doi.org/10.1016/j.meteno.2016.04.002	journal	December 2016
Engineering l-arabinose metabolism in triacylglycerol-producing Rhodococcus opacus for lignocellulosic fuel production Kurosawa, Kazuhiko; Plassmeier, Jens; Kalinowski, Jörn Metabolic Engineering, Vol. 30 https://doi.org/10.1016/j.ymben.2015.04.006	journal	July 2015
Expression-level optimization of a multi-enzyme pathway in the absence of a high-throughput assay Lee, Michael E.; Aswani, Anil; Han, Audrey S. Nucleic Acids Research, Vol. 41, Issue 22 https://doi.org/10.1093/nar/gkt809	journal	September 2013
Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulating Rhodococcus opacus PD630 Yoneda, Aki; Henson, William R.; Goldner, Nicholas K. Nucleic Acids Research, Vol. 44, Issue 5 https://doi.org/10.1093/nar/gkw055	journal	February 2016
Controlling gene expression in mycobacteria with anhydrotetracycline and Tet repressor Ehrt, S. Nucleic Acids Research, Vol. 33, Issue 2 https://doi.org/10.1093/nar/gni013	journal	January 2005
Review of US and EU initiatives toward development, demonstration, and commercialization of lignocellulosic biofuels Balan, Venkatesh; Chiaramonti, David; Kumar, Sandeep Biofuels, Bioproducts and Biorefining, Vol. 7, Issue 6 https://doi.org/10.1002/bbb.1436	journal	August 2013
The new forestry biofuels sector Pu, Yunqiao; Zhang, Dongcheng; Singh, Preet M. Biofuels, Bioproducts and Biorefining, Vol. 2, Issue 1 https://doi.org/10.1002/bbb.48	journal	January 2008
Rapid metabolic analysis of Rhodococcus opacus PD630 via parallel ¹³ C-metabolite fingerprinting Hollinshead, Whitney D.; Henson, William R.; Abernathy, Mary Biotechnology and Bioengineering, Vol. 113, Issue 1 https://doi.org/10.1002/bit.25702	journal	September 2015
Physical, chemical, and metabolic state sensors expand the synthetic biology toolbox for Synechocystis sp. PCC 6803 : New Sensors for Immethun, Cheryl M.; DeLorenzo, Drew M.; Focht, Caroline M. Biotechnology and Bioengineering, Vol. 114, Issue 7 https://doi.org/10.1002/bit.26275	journal	March 2017
Biological Production of Muconic Acid via a Prokaryotic 2,3-Dihydroxybenzoic Acid Decarboxylase Sun, Xinxiao; Lin, Yuheng; Yuan, Qipeng ChemSusChem, Vol. 7, Issue 9 https://doi.org/10.1002/cssc.201402092	journal	July 2014
Methods in Lignin Chemistry Timell, T. E.; Lin, Stephen Y.; Dence, Carlton W. Springer Series in Wood Science https://doi.org/10.1007/978-3-642-74065-7	book	January 1992
Control of the acetamidase gene of Mycobacterium smegmatis by multiple regulators Roberts, Gretta; Muttucumaru, D. G. Niranjala; Parish, Tanya FEMS Microbiology Letters, Vol. 221, Issue 1 https://doi.org/10.1016/S0378-1097(03)00177-0	journal	April 2003
Microbial production of fatty acid-derived fuels and chemicals Lennen, Rebecca M.; Pfleger, Brian F. Current Opinion in Biotechnology, Vol. 24, Issue 6 https://doi.org/10.1016/j.copbio.2013.02.028	journal	December 2013
Opportunities and challenges in biological lignin valorization Beckham, Gregg T.; Johnson, Christopher W.; Karp, Eric M. Current Opinion in Biotechnology, Vol. 42 https://doi.org/10.1016/j.copbio.2016.02.030	journal	December 2016
High-cell-density batch fermentation of Rhodococcus opacus PD630 using a high glucose concentration for triacylglycerol production Kurosawa, Kazuhiko; Boccazzi, Paolo; de Almeida, Naomi M. Journal of Biotechnology, Vol. 147, Issue 3-4 https://doi.org/10.1016/j.jbiotec.2010.04.003	journal	June 2010
Biodiesel production potential of oleaginous Rhodococcus opacus grown on biomass gasification wastewater Goswami, Lalit; Tejas Namboodiri, M. M.; Vinoth Kumar, R. Renewable Energy, Vol. 105 https://doi.org/10.1016/j.renene.2016.12.044	journal	May 2017
Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform Rock, Jeremy M.; Hopkins, Forrest F.; Chavez, Alejandro Nature Microbiology, Vol. 2, Issue 4 https://doi.org/10.1038/nmicrobiol.2016.274	journal	February 2017
Adipic acid production from lignin Vardon, Derek R.; Franden, Mary Ann; Johnson, Christopher W. Energy & Environmental Science, Vol. 8, Issue 2 https://doi.org/10.1039/C4EE03230F	journal	January 2015
Conversion of corn stover alkaline pre-treatment waste streams into biodiesel via Rhodococci Le, Rosemary K.; Wells Jr., Tyrone; Das, Parthapratim RSC Advances, Vol. 7, Issue 7 https://doi.org/10.1039/C6RA28033A	journal	January 2017
Lignin to lipid bioconversion by oleaginous Rhodococci Kosa, Matyas; Ragauskas, Arthur J. Green Chemistry, Vol. 15, Issue 8 https://doi.org/10.1039/c3gc40434j	journal	January 2013
Improving fatty acids production by engineering dynamic pathway regulation and metabolic control Xu, P.; Li, L.; Zhang, F. Proceedings of the National Academy of Sciences, Vol. 111, Issue 31 https://doi.org/10.1073/pnas.1406401111	journal	July 2014
Isolation and characterization of the Rhodococcus opacus thiostrepton-inducible genes tipAL and tipAS : application for recombinant protein expression in Rhodococcus Dong, Li; Nakashima, Nobutaka; Tamura, Noriko FEMS Microbiology Letters, Vol. 237, Issue 1 https://doi.org/10.1111/j.1574-6968.2004.tb09675.x	journal	August 2004
Saccharification of Cellulose by Recombinant Rhodococcus opacus PD630 Strains Hetzler, Stephan; Bröker, Daniel; Steinbüchel, Alexander Applied and Environmental Microbiology, Vol. 79, Issue 17 https://doi.org/10.1128/AEM.01214-13	journal	June 2013
Establishment of Cellobiose Utilization for Lipid Production in Rhodococcus opacus PD630 Hetzler, Stephan; Steinbüchel, Alexander Applied and Environmental Microbiology, Vol. 79, Issue 9 https://doi.org/10.1128/AEM.03678-12	journal	February 2013
Catabolism of Benzoate and Phthalate in Rhodococcus sp. Strain RHA1: Redundancies and Convergence Patrauchan, M. A.; Florizone, C.; Dosanjh, M. Journal of Bacteriology, Vol. 187, Issue 12, p. 4050-4063 https://doi.org/10.1128/JB.187.12.4050-4063.2005	journal	June 2005
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
Tolerance and adaptive evolution of triacylglycerol-producing Rhodococcus opacus to lignocellulose-derived inhibitors Kurosawa, Kazuhiko; Laser, Josephine; Sinskey, Anthony J. Biotechnology for Biofuels, Vol. 8, Issue 1 https://doi.org/10.1186/s13068-015-0258-3	journal	January 2015
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

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Selection of stable reference genes for RT-qPCR in Rhodococcus opacus PD630 DeLorenzo, Drew M.; Moon, Tae Seok Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-24486-w	journal	April 2018
Boosting Secondary Metabolite Production and Discovery through the Engineering of Novel Microbial Biosensors de Frias, Ulysses Amancio; Pereira, Greicy Kelly Bonifacio; Guazzaroni, María-Eugenia BioMed Research International, Vol. 2018 https://doi.org/10.1155/2018/7021826	journal	July 2018
Lipid metabolism of phenol-tolerant Rhodococcus opacus strains for lignin bioconversion Henson, William R.; Hsu, Fong-Fu; Dantas, Gautam Biotechnology for Biofuels, Vol. 11, Issue 1 https://doi.org/10.1186/s13068-018-1337-z	journal	December 2018
Discovery of potential pathways for biological conversion of poplar wood into lipids by co-fermentation of Rhodococci strains Li, Xiaolu; He, Yucai; Zhang, Libing Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1395-x	journal	March 2019
Development of Rhodococcus opacus as a chassis for lignin valorization and bioproduction of high-value compounds Anthony, Winston E.; Carr, Rhiannon R.; DeLorenzo, Drew M. Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1535-3	journal	August 2019

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