A comprehensive metabolic map for production of bio-based chemicals

Lee, Sang Yup; Kim, Hyun Uk; Chae, Tong Un; Cho, Jae Sung; Kim, Je Woong; Shin, Jae Ho; Kim, Dong In; Ko, Yoo sung; Jang, Woo Dae; Jang, Yu‐Sin

doi:10.1038/s41929-018-0212-4

Cited by 411 publications

(237 citation statements)

References 187 publications

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“…A sustainable alternative to produce these products is through engineering microbial cell factories that can directly use renewable and cost‐effective feedstocks, such as lignocellulose, atmospheric CO 2 , and syngas (Peralta‐Yahya et al, 2012). A vast number of chemicals have been successfully produced in various microbes that feature diverse chemical structures and functional groups (Borodina et al, 2015; Jiang, Qiao, Bentley, Liu, & Zhang, 2017; Lee et al, 2019; Luo, Cho, & Lee, 2019; Wehrs et al, 2019). Recent advances in metabolic engineering and synthetic biology have provided a greatly expanded set of tools necessary to assemble and optimize metabolic pathways for improved titers, productivities and yields (D. Liu, Evans, & Zhang, 2015; Y. Liu & Nielsen, 2019; Salis, Mirsky, & Voigt, 2009).…”

Section: Introductionmentioning

confidence: 99%

Exploiting nonionic surfactants to enhance fatty alcohol production in Rhodosporidium toruloides

Liu

Geiselman

Coradetti

et al. 2020

Biotech & Bioengineering

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Fatty alcohols (FOHs) are important feedstocks in the chemical industry to produce detergents, cosmetics, and lubricants. Microbial production of FOHs has become an attractive alternative to production in plants and animals due to growing energy demands and environmental concerns. However, inhibition of cell growth caused by intracellular FOH accumulation is one major issue that limits FOH titers in microbial hosts. In addition, identification of FOH‐specific exporters remains a challenge and previous studies towards this end are limited. To alleviate the toxicity issue, we exploited nonionic surfactants to promote the export of FOHs in Rhodosporidium toruloides, an oleaginous yeast that is considered an attractive next‐generation host for the production of fatty acid‐derived chemicals. Our results showed FOH export efficiency was dramatically improved and the growth inhibition was alleviated in the presence of small amounts of tergitol and other surfactants. As a result, FOH titers increase by 4.3‐fold at bench scale to 352.6 mg/L. With further process optimization in a 2‐L bioreactor, the titer was further increased to 1.6 g/L. The method we show here can potentially be applied to other microbial hosts and may facilitate the commercialization of microbial FOH production.

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Section: Introductionmentioning

confidence: 99%

Exploiting nonionic surfactants to enhance fatty alcohol production in Rhodosporidium toruloides

Liu

Geiselman

Coradetti

et al. 2020

Biotech & Bioengineering

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“…Diacids, polyamine, and lactams are all used to produce various polyester and nylon fibers which are currently derived from petrochemicals 7,8 . In an effort to make production of these chemicals sustainable, many groups have developed engineered microbes to synthesize these precursors [9][10][11][12] . The L-lysine metabolism of Pseudomonas putida has been leveraged to produce valerolactam 13 , as well as the diacid glutarate both in the native host and heterologously 14,15 .…”

Section: Introductionmentioning

confidence: 99%

Glutarate metabolism in Pseudomonas putida is regulated by two distinct glutarate sensing transcription factors

Thompson

Cruz-Morales

Krishna

et al. 2019

Preprint

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A significant bottleneck in synthetic biology involves screening the large genetically encoded libraries enabled by the latest technologies for desirable phenotypes such as chemical production. However, transcription factor based biosensors can be leveraged to screen thousands of genetic designs for optimal chemical production in engineered microbes. In this study we characterize two glutarate sensing transcription factors (CsiR and GcdR) from Pseudomonas putida. The genomic contexts of csiR homologs were analyzed and DNA binding sites were bioinformatically predicted. Both CsiR and GcdR were purified and shown to bind upstream of their coding sequencing in vitro. CsiR was shown to dissociate from DNA in vitro when exogenous glutarate was added confirming it acts as a genetic repressor. Both transcription factors and cognate promoters were then cloned into broad host range vectors to create two glutarate biosensors. Their respective sensing performance features were characterized, and more sensitive derivatives of the GcdR biosensor were created by manipulating the expression of the transcription factor. Sensor vectors were then reintroduced into P. putida and were evaluated for their ability to respond to glutarate as well as various lysine metabolites. Additionally, we developed a novel mathematical approach to describe the usable range of detection for genetically encoded biosensors which may be broadly useful to future efforts to better characterize biosensor performance.

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“…Therefore, the enzymes of these pathways are promising targets for the development of new antibiotics—an increasingly important mission due to the rise of antibiotic resistance in recent years . Additionally, aromatic amino acids and their derivatives are used in the production of pharmaceuticals, opioids, food additives, dietary supplements, aromatic polymers, and petrochemical aromatics, which makes the pathways that produce them highly attractive for environmentally friendly biotechnological applications . For many plants and microorganisms, these anabolic pathways start with the shikimate pathway to produce chorismate, a precursor for the biosynthesis of aromatic amino acids and other aromatic compounds, including secondary metabolites in plants, siderophores in microorganisms, and certain antibiotics in fungi .…”

Section: Introductionmentioning

confidence: 99%

Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain

et al. 2019

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Tyrosine biosynthesis via the shikimate pathway is absent in humans and other animals, making it an attractive target for next‐generation antibiotics, which is increasingly important due to the looming proliferation of multidrug‐resistant pathogens. Tyrosine biosynthesis is also of commercial importance for the environmentally friendly production of numerous compounds, such as pharmaceuticals, opioids, aromatic polymers, and petrochemical aromatics. Prephenate dehydrogenase (PDH) catalyzes the penultimate step of tyrosine biosynthesis in bacteria: the oxidative decarboxylation of prephenate to 4‐hydroxyphenylpyruvate. The majority of PDHs are competitively inhibited by tyrosine and consist of a nucleotide‐binding domain and a dimerization domain. Certain PDHs, including several from pathogens on the World Health Organization priority list of antibiotic‐resistant bacteria, possess an additional ACT domain. However, biochemical and structural knowledge was lacking for these enzymes. In this study, we successfully established a recombinant protein expression system for PDH from Bacillus anthracis (BaPDH), the causative agent of anthrax, and determined the structure of a BaPDH ternary complex with NAD+ and tyrosine, a binary complex with tyrosine, and a structure of an isolated ACT domain dimer. We also conducted detailed kinetic and biophysical analyses of the enzyme. We show that BaPDH is allosterically regulated by tyrosine binding to the ACT domains, resulting in an asymmetric conformation of the BaDPH dimer that sterically prevents prephenate binding to either active site. The presented mode of allosteric inhibition is unique compared to both the competitive inhibition established for other PDHs and to the allosteric mechanisms for other ACT‐containing enzymes. This study provides new structural and mechanistic insights that advance our understanding of tyrosine biosynthesis in bacteria. Enzymes Prephenate dehydrogenase from Bacillus anthracis (PDH): EC database ID: https://www.brenda-enzymes.org/enzyme.php?ecno=1.3.1.12. Databases Coordinates and structure factors have been deposited in the Protein Data Bank (PDB) with accession numbers PDB ID: http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6U60 (BaPDH complex with NAD+ and tyrosine), PDB ID: http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5UYY (BaPDH complex with tyrosine), and PDB ID: http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5V0S (BaPDH isolated ACT domain dimer). The diffraction images are available at http://proteindiffraction.org with DOIs: https://doi.org/10.18430/M35USC, https://doi.org/10.18430/M35UYY, and https://doi.org/10.18430/M35V0S.

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A comprehensive metabolic map for production of bio-based chemicals

Cited by 411 publications

References 187 publications

Exploiting nonionic surfactants to enhance fatty alcohol production in Rhodosporidium toruloides

Exploiting nonionic surfactants to enhance fatty alcohol production in Rhodosporidium toruloides

Glutarate metabolism in Pseudomonas putida is regulated by two distinct glutarate sensing transcription factors

Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain

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