1
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Stukenberg D, Faber A, Becker A. Graded-CRISPRi, a Tool for Tuning the Strengths of CRISPRi-Mediated Knockdowns in Vibrio natriegens Using gRNA Libraries. ACS Synth Biol 2024; 13:2091-2104. [PMID: 38916455 DOI: 10.1021/acssynbio.4c00056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
In recent years, the fast-growing bacterium Vibrio natriegens has gained increasing attention as it has the potential to become a next-generation chassis for synthetic biology. A wide range of genetic parts and genome engineering methods have already been developed. However, there is still a need for a well-characterized tool to effectively and gradually reduce the expression levels of native genes. To bridge this gap, we created graded-CRISPRi, a system utilizing gRNA variants that lead to varying levels of repression strength. By incorporating multiple gRNA sequences into our design, we successfully extended this concept to simultaneously repress four distinct reporter genes. Furthermore, we demonstrated the capability of using graded-CRISPRi to target native genes, thereby examining the effect of various knockdown levels on growth.
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Affiliation(s)
- Daniel Stukenberg
- Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg 35037, Germany
- Department of Biology, Philipps-Universität Marburg, Marburg 35037, Germany
| | - Anna Faber
- Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg 35037, Germany
- Department of Biology, Philipps-Universität Marburg, Marburg 35037, Germany
| | - Anke Becker
- Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg 35037, Germany
- Department of Biology, Philipps-Universität Marburg, Marburg 35037, Germany
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2
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Holbrook-Smith D, Trouillon J, Sauer U. Metabolomics and Microbial Metabolism: Toward a Systematic Understanding. Annu Rev Biophys 2024; 53:41-64. [PMID: 38109374 DOI: 10.1146/annurev-biophys-030722-021957] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Over the past decades, our understanding of microbial metabolism has increased dramatically. Metabolomics, a family of techniques that are used to measure the quantities of small molecules in biological samples, has been central to these efforts. Advances in analytical chemistry have made it possible to measure the relative and absolute concentrations of more and more compounds with increasing levels of certainty. In this review, we highlight how metabolomics has contributed to understanding microbial metabolism and in what ways it can still be deployed to expand our systematic understanding of metabolism. To that end, we explain how metabolomics was used to (a) characterize network topologies of metabolism and its regulation networks, (b) elucidate the control of metabolic function, and (c) understand the molecular basis of higher-order phenomena. We also discuss areas of inquiry where technological advances should continue to increase the impact of metabolomics, as well as areas where our understanding is bottlenecked by other factors such as the availability of statistical and modeling frameworks that can extract biological meaning from metabolomics data.
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Affiliation(s)
| | - Julian Trouillon
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland;
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland;
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3
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Berkvens A, Salinas L, Remeijer M, Planqué R, Teusink B, Bruggeman FJ. Understanding and computational design of genetic circuits of metabolic networks. Essays Biochem 2024; 68:41-51. [PMID: 38662439 PMCID: PMC11065555 DOI: 10.1042/ebc20230045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 05/01/2024]
Abstract
The expression of metabolic proteins is controlled by genetic circuits, matching metabolic demands and changing environmental conditions. Ideally, this regulation brings about a competitive level of metabolic fitness. Understanding how cells can achieve a robust (close-to-optimal) functioning of metabolism by appropriate control of gene expression aids synthetic biology by providing design criteria of synthetic circuits for biotechnological purposes. It also extends our understanding of the designs of genetic circuitry found in nature such as metabolite control of transcription factor activity, promoter architectures and transcription factor dependencies, and operon composition (in bacteria). Here, we review, explain and illustrate an approach that allows for the inference and design of genetic circuitry that steers metabolic networks to achieve a maximal flux per unit invested protein across dynamic conditions. We discuss how this approach and its understanding can be used to rationalize Escherichia coli's strategy to regulate the expression of its ribosomes and infer the design of circuitry controlling gene expression of amino-acid biosynthesis enzymes. The inferred regulation indeed resembles E. coli's circuits, suggesting that these have evolved to maximize amino-acid production fluxes per unit invested protein. We end by an outlook of the use of this approach in metabolic engineering applications.
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Affiliation(s)
- Alicia Berkvens
- Systems Biology Lab, A-LIFE, AIMMS, VU University, Amsterdam, NL
| | - Luis Salinas
- Systems Biology Lab, A-LIFE, AIMMS, VU University, Amsterdam, NL
| | - Maaike Remeijer
- Systems Biology Lab, A-LIFE, AIMMS, VU University, Amsterdam, NL
| | - Robert Planqué
- Department of Mathematics, Amsterdam Center for Dynamics and Computation, VU University, Amsterdam, NL
| | - Bas Teusink
- Systems Biology Lab, A-LIFE, AIMMS, VU University, Amsterdam, NL
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4
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Liu J, Liu J, Li J, Zhao X, Sun G, Qiao Q, Shi T, Che B, Chen J, Zhuang Q, Wang Y, Sun J, Zhu D, Zheng P. Reconstruction the feedback regulation of amino acid metabolism to develop a non-auxotrophic L-threonine producing Corynebacterium glutamicum. BIORESOUR BIOPROCESS 2024; 11:43. [PMID: 38664309 PMCID: PMC11045695 DOI: 10.1186/s40643-024-00753-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
L-Threonine is an important feed additive with the third largest market size among the amino acids produced by microbial fermentation. The GRAS (generally regarded as safe) industrial workhorse Corynebacterium glutamicum is an attractive chassis for L-threonine production. However, the present L-threonine production in C. glutamicum cannot meet the requirement of industrialization due to the relatively low production level of L-threonine and the accumulation of large amounts of by-products (such as L-lysine, L-isoleucine, and glycine). Herein, to enhance the L-threonine biosynthesis in C. glutamicum, releasing the aspartate kinase (LysC) and homoserine dehydrogenase (Hom) from feedback inhibition by L-lysine and L-threonine, respectively, and overexpressing four flux-control genes were performed. Next, to reduce the formation of by-products L-lysine and L-isoleucine without the cause of an auxotrophic phenotype, the feedback regulation of dihydrodipicolinate synthase (DapA) and threonine dehydratase (IlvA) was strengthened by replacing the native enzymes with heterologous analogues with more sensitive feedback inhibition by L-lysine and L-isoleucine, respectively. The resulting strain maintained the capability of synthesizing enough amounts of L-lysine and L-isoleucine for cell biomass formation but exhibited almost no extracellular accumulation of these two amino acids. To further enhance L-threonine production and reduce the by-product glycine, L-threonine exporter and homoserine kinase were overexpressed. Finally, the rationally engineered non-auxotrophic strain ZcglT9 produced 67.63 g/L (17.2% higher) L-threonine with a productivity of 1.20 g/L/h (108.0% higher) in fed-batch fermentation, along with significantly reduced by-product accumulation, representing the record for L-threonine production in C. glutamicum. In this study, we developed a strategy of reconstructing the feedback regulation of amino acid metabolism and successfully applied this strategy to de novo construct a non-auxotrophic L-threonine producing C. glutamicum. The main end by-products including L-lysine, L-isoleucine, and glycine were almost eliminated in fed-batch fermentation of the engineered C. glutamicum strain. This strategy can also be used for engineering producing strains for other amino acids and derivatives.
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Affiliation(s)
- Jianhang Liu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Shandong Provincial Key Laboratory of Microbial Engineering, School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353, China
| | - Jiao Liu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Jiajun Li
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353, China
- Shandong Provincial Key Laboratory of Microbial Engineering, School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353, China
| | - Xiaojia Zhao
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Guannan Sun
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Qianqian Qiao
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Tuo Shi
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Bin Che
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Jiuzhou Chen
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Qianqian Zhuang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353, China
- Shandong Provincial Key Laboratory of Microbial Engineering, School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353, China
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Yu Wang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Jibin Sun
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Deqiang Zhu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353, China.
- Shandong Provincial Key Laboratory of Microbial Engineering, School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353, China.
| | - Ping Zheng
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China.
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5
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Wang W, Xiang Y, Yin G, Hu S, Cheng J, Chen J, Du G, Kang Z, Wang Y. Construction of 5-Aminolevulinic Acid Microbial Cell Factories through Identification of Novel Synthases and Metabolic Pathway Screens and Transporters. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8006-8017. [PMID: 38554273 DOI: 10.1021/acs.jafc.4c00903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/01/2024]
Abstract
5-Aminolevulinic acid (5-ALA) plays a pivotal role in the biosynthesis of heme and chlorophyll and has garnered great attention for its agricultural applications. This study explores the multifaceted construction of 5-ALA microbial cell factories. Evolutionary analysis-guided screening identified a novel 5-ALA synthase from Sphingobium amiense as the best synthase. An sRNA library facilitated global gene screening that demonstrated that trpC and ilvA repression enhanced 5-ALA production by 74.3% and 102%, respectively. Subsequently, efflux of 5-ALA by the transporter Gdx increased 5-ALA biosynthesis by 25.7%. To mitigate oxidative toxicity, DNA-binding proteins from starved cells were employed, enhancing cell density and 5-ALA titer by 21.1 and 4.1%, respectively. Combining these strategies resulted in an Escherichia coli strain that produced 5-ALA to 1.51 g·L-1 in shake flask experiments and 6.19 g·L-1 through fed-batch fermentation. This study broadens the repertoire of available 5-ALA synthases and transporters and provides a new platform for optimizing 5-ALA bioproduction.
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Affiliation(s)
- Wenqiu Wang
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiaxing Institute of Future Food, Jiaxing 314050, China
| | - Yulong Xiang
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Guobin Yin
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Shan Hu
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiaxing Institute of Future Food, Jiaxing 314050, China
| | - Jian Cheng
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhen Kang
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yang Wang
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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6
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Doranga S, Conway T. Nitrogen assimilation by E. coli in the mammalian intestine. mBio 2024; 15:e0002524. [PMID: 38380942 PMCID: PMC10936423 DOI: 10.1128/mbio.00025-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 02/22/2024] Open
Abstract
Nitrogen is an essential element for all living organisms, including Escherichia coli. Potential nitrogen sources are abundant in the intestine, but knowledge of those used specifically by E. coli to colonize remains limited. Here, we sought to determine the specific nitrogen sources used by E. coli to colonize the streptomycin-treated mouse intestine. We began by investigating whether nitrogen is limiting in the intestine. The NtrBC two-component system upregulates approximately 100 genes in response to nitrogen limitation. We showed that NtrBC is crucial for E. coli colonization, although most genes of the NtrBC regulon are not induced, which indicates that nitrogen is not limiting in the intestine. RNA-seq identified upregulated genes in colonized E. coli involved in transport and catabolism of seven amino acids, dipeptides and tripeptides, purines, pyrimidines, urea, and ethanolamine. Competitive colonization experiments revealed that L-serine, N-acetylneuraminic acid, N-acetylglucosamine, and di- and tripeptides serve as nitrogen sources for E. coli in the intestine. Furthermore, the colonization defect of a L-serine deaminase mutant was rescued by excess nitrogen in the drinking water but not by an excess of carbon and energy, demonstrating that L-serine serves primarily as a nitrogen source. Similar rescue experiments showed that N-acetylneuraminic acid serves as both a carbon and nitrogen source. To a minor extent, aspartate and ammonia also serve as nitrogen sources. Overall, these findings demonstrate that E. coli utilizes multiple nitrogen sources for successful colonization of the mouse intestine, the most important of which is L-serine. IMPORTANCE While much is known about the carbon and energy sources that are used by E. coli to colonize the mammalian intestine, very little is known about the sources of nitrogen. Interrogation of colonized E. coli by RNA-seq revealed that nitrogen is not limiting, indicating an abundance of nitrogen sources in the intestine. Pathways for assimilation of nitrogen from several amino acids, dipeptides and tripeptides, purines, pyrimidines, urea, and ethanolamine were induced in mice. Competitive colonization assays confirmed that mutants lacking catabolic pathways for L-serine, N-acetylneuraminic acid, N-acetylglucosamine, and di- and tripeptides had colonization defects. Rescue experiments in mice showed that L-serine serves primarily as a nitrogen source, whereas N-acetylneuraminic acid provides both carbon and nitrogen. Of the many nitrogen assimilation mutants tested, the largest colonization defect was for an L-serine deaminase mutant, which demonstrates L-serine is the most important nitrogen source for colonized E. coli.
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Affiliation(s)
- Sudhir Doranga
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, Ohio, USA
| | - Tyrrell Conway
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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7
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Matsuyama C, Seike T, Okahashi N, Niide T, Hara KY, Hirono-Hara Y, Ishii J, Shimizu H, Toya Y, Matsuda F. Metabolome analysis of metabolic burden in Escherichia coli caused by overexpression of green fluorescent protein and delta-rhodopsin. J Biosci Bioeng 2024; 137:187-194. [PMID: 38281859 DOI: 10.1016/j.jbiosc.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/18/2023] [Accepted: 12/04/2023] [Indexed: 01/30/2024]
Abstract
Overexpression of proteins by introducing a DNA vector is among the most important tools for the metabolic engineering of microorganisms such as Escherichia coli. Protein overexpression imposes a burden on metabolism because metabolic pathways must supply building blocks for protein and DNA synthesis. Different E. coli strains have distinct metabolic capacities. In this study, two proteins were overexpressed in four E. coli strains (MG1655(DE3), W3110(DE3), BL21star(DE3), and Rosetta(DE3)), and their effects on metabolic burden were investigated. Metabolomic analysis showed that E. coli strains overexpressing green fluorescent protein had decreased levels of several metabolites, with a positive correlation between the number of reduced metabolites and green fluorescent protein expression levels. Moreover, nucleic acid-related metabolites decreased, indicating a metabolic burden in the E. coli strains, and the growth rate and protein expression levels were improved by supplementation with the five nucleosides. In contrast, two strains overexpressing delta rhodopsin, a microbial membrane rhodopsin from Haloterrigena turkmenica, led to a metabolic burden and decrease in the amino acids Ala, Val, Leu, Ile, Thr, Phe, Asp, and Trp, which are the most frequent amino acids in the delta rhodopsin protein sequence. The metabolic burden caused by protein overexpression was influenced by the metabolic capacity of the host strains and the sequences of the overexpressed proteins. Detailed characterization of the effects of protein expression on the metabolic state of engineered cells using metabolomics will provide insights into improving the production of target compounds.
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Affiliation(s)
- Chinatsu Matsuyama
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Taisuke Seike
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Nobuyuki Okahashi
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, Osaka 565-0871, Japan
| | - Teppei Niide
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Kiyotaka Y Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | | | - Jun Ishii
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo 657-8501, Japan
| | - Hiroshi Shimizu
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Yoshihiro Toya
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Fumio Matsuda
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, Osaka 565-0871, Japan.
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8
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Liu X, Liu J, Liu Z, Qiao Q, Ni X, Yang J, Sun G, Li F, Zhou W, Guo X, Chen J, Jia S, Zheng Y, Zheng P, Sun J. Engineering allosteric inhibition of homoserine dehydrogenase by semi-rational saturation mutagenesis screening. Front Bioeng Biotechnol 2024; 11:1336215. [PMID: 38234301 PMCID: PMC10791936 DOI: 10.3389/fbioe.2023.1336215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
Allosteric regulation by pathway products plays a vital role in amino acid metabolism. Homoserine dehydrogenase (HSD), the key enzyme for the biosynthesis of various aspartate family amino acids, is subject to feedback inhibition by l-threonine and l-isoleucine. The desensitized mutants with the potential for amino acid production remain limited. Herein, a semi-rational approach was proposed to relieve the feedback inhibition. HSD from Corynebacterium glutamicum (CgHSD) was first characterized as a homotetramer, and nine conservative sites at the tetramer interface were selected for saturation mutagenesis by structural simulations and sequence analysis. Then, we established a high-throughput screening (HTS) method based on resistance to l-threonine analog and successfully acquired two dominant mutants (I397V and A384D). Compared with the best-ever reported desensitized mutant G378E, both new mutants qualified the engineered strains with higher production of CgHSD-dependent amino acids. The mutant and wild-type enzymes were purified and assessed in the presence or absence of inhibitors. Both purified mutants maintained >90% activity with 10 mM l-threonine or 25 mM l-isoleucine. Moreover, they showed >50% higher specific activities than G378E without inhibitors. This work provides two competitive alternatives for constructing cell factories of CgHSD-related amino acids and derivatives. Moreover, the proposed approach can be applied to engineering other allosteric enzymes in the amino acid synthesis pathway.
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Affiliation(s)
- Xinyang Liu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, China
| | - Jiao Liu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Zhemin Liu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Qianqian Qiao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, China
| | - Xiaomeng Ni
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Jinxing Yang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Guannan Sun
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Fanghe Li
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Wenjuan Zhou
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Xuan Guo
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Jiuzhou Chen
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Shiru Jia
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, China
| | - Yu Zheng
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, China
| | - Ping Zheng
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Jibin Sun
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
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9
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Stegmüller J, Rodríguez Estévez M, Shu W, Gläser L, Myronovskyi M, Rückert-Reed C, Kalinowski J, Luzhetskyy A, Wittmann C. Systems metabolic engineering of the primary and secondary metabolism of Streptomyces albidoflavus enhances production of the reverse antibiotic nybomycin against multi-resistant Staphylococcus aureus. Metab Eng 2024; 81:123-143. [PMID: 38072358 DOI: 10.1016/j.ymben.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/17/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024]
Abstract
Nybomycin is an antibiotic compound with proven activity against multi-resistant Staphylococcus aureus, making it an interesting candidate for combating these globally threatening pathogens. For exploring its potential, sufficient amounts of nybomycin and its derivatives must be synthetized to fully study its effectiveness, safety profile, and clinical applications. As native isolates only accumulate low amounts of the compound, superior producers are needed. The heterologous cell factory S. albidoflavus 4N24, previously derived from the cluster-free chassis S. albidoflavus Del14, produced 860 μg L-1 of nybomycin, mainly in the stationary phase. A first round of strain development modulated expression of genes involved in supply of nybomycin precursors under control of the common Perm* promoter in 4N24, but without any effect. Subsequent studies with mCherry reporter strains revealed that Perm* failed to drive expression during the product synthesis phase but that use of two synthetic promoters (PkasOP* and P41) enabled strong constitutive expression during the entire process. Using PkasOP*, several rounds of metabolic engineering successively streamlined expression of genes involved in the pentose phosphate pathway, the shikimic acid pathway, supply of CoA esters, and nybomycin biosynthesis and export, which more than doubled the nybomycin titer to 1.7 mg L-1 in the sixth-generation strain NYB-6B. In addition, we identified the minimal set of nyb genes needed to synthetize the molecule using single-gene-deletion strains. Subsequently, deletion of the regulator nybW enabled nybomycin production to begin during the growth phase, further boosting the titer and productivity. Based on RNA sequencing along the created strain genealogy, we discovered that the nyb gene cluster was unfavorably downregulated in all advanced producers. This inspired removal of a part and the entire set of the four regulatory genes at the 3'-end nyb of the cluster. The corresponding mutants NYB-8 and NYB-9 exhibited marked further improvement in production, and the deregulated cluster was combined with all beneficial targets from primary metabolism. The best strain, S. albidoflavus NYB-11, accumulated up to 12 mg L-1 nybomycin, fifteenfold more than the basic strain. The absence of native gene clusters in the host and use of a lean minimal medium contributed to a selective production process, providing an important next step toward further development of nybomycin.
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Affiliation(s)
- Julian Stegmüller
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Wei Shu
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Maksym Myronovskyi
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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10
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Li L, Li N, Wang X, Gao S, Zhang J, Zhou J, Wu Z, Zeng W. Metabolic engineering combined with enzyme engineering for overproduction of ectoine in Escherichia coli. BIORESOURCE TECHNOLOGY 2023; 390:129862. [PMID: 37839643 DOI: 10.1016/j.biortech.2023.129862] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
Ectoine, a natural protective agent, is naturally synthesized at low titers by some extreme environment microorganisms that are usually difficult to culture. There is a need for an efficient and eco-friendly ectoine production process. In this study, Escherichia coli BL21(DE3) with the ectABC gene cluster from Halomonas venusta achieved 1.7 g/L ectoine. After optimizing the expression plasmid, 2.1 g/L ectoine was achieved. Besides, the aspartate kinase mutant LysCT311I from Corynebacterium glutamicum and aspartate semialdehyde dehydrogenase from Halomonas elongata were overexpressed to increase precursors supply. Furthermore, the rate-limiting enzyme EctB was semirationally engineered, and the E407D mutation enhanced ectoine production by 13.8 %. To improve acetyl-CoA supply, the non-oxidative glycolysis pathway was introduced. Overall, the optimized strain ECT9-5 produced 67.1 g/L ectoine by fed-batch fermentation with a 0.3 g/g of glucose and the kinetic model resulted in a good fit.
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Affiliation(s)
- Lihong Li
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Ning Li
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xinglong Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Song Gao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Juan Zhang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhimeng Wu
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Weizhu Zeng
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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11
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Alam S, Doherty E, Ortega-Prieto P, Arizanova J, Fets L. Membrane transporters in cell physiology, cancer metabolism and drug response. Dis Model Mech 2023; 16:dmm050404. [PMID: 38037877 PMCID: PMC10695176 DOI: 10.1242/dmm.050404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023] Open
Abstract
By controlling the passage of small molecules across lipid bilayers, membrane transporters influence not only the uptake and efflux of nutrients, but also the metabolic state of the cell. With more than 450 members, the Solute Carriers (SLCs) are the largest transporter super-family, clustering into families with different substrate specificities and regulatory properties. Cells of different types are, therefore, able to tailor their transporter expression signatures depending on their metabolic requirements, and the physiological importance of these proteins is illustrated by their mis-regulation in a number of disease states. In cancer, transporter expression is heterogeneous, and the SLC family has been shown to facilitate the accumulation of biomass, influence redox homeostasis, and also mediate metabolic crosstalk with other cell types within the tumour microenvironment. This Review explores the roles of membrane transporters in physiological and malignant settings, and how these roles can affect drug response, through either indirect modulation of sensitivity or the direct transport of small-molecule therapeutic compounds into cells.
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Affiliation(s)
- Sara Alam
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Emily Doherty
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Paula Ortega-Prieto
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Julia Arizanova
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Louise Fets
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
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12
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Miao R, Jahn M, Shabestary K, Peltier G, Hudson EP. CRISPR interference screens reveal growth-robustness tradeoffs in Synechocystis sp. PCC 6803 across growth conditions. THE PLANT CELL 2023; 35:3937-3956. [PMID: 37494719 PMCID: PMC10615215 DOI: 10.1093/plcell/koad208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/01/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023]
Abstract
Barcoded mutant libraries are a powerful tool for elucidating gene function in microbes, particularly when screened in multiple growth conditions. Here, we screened a pooled CRISPR interference library of the model cyanobacterium Synechocystis sp. PCC 6803 in 11 bioreactor-controlled conditions, spanning multiple light regimes and carbon sources. This gene repression library contained 21,705 individual mutants with high redundancy over all open reading frames and noncoding RNAs. Comparison of the derived gene fitness scores revealed multiple instances of gene repression being beneficial in 1 condition while generally detrimental in others, particularly for genes within light harvesting and conversion, such as antennae components at high light and PSII subunits during photoheterotrophy. Suboptimal regulation of such genes likely represents a tradeoff of reduced growth speed for enhanced robustness to perturbation. The extensive data set assigns condition-specific importance to many previously unannotated genes and suggests additional functions for central metabolic enzymes. Phosphoribulokinase, glyceraldehyde-3-phosphate dehydrogenase, and the small protein CP12 were critical for mixotrophy and photoheterotrophy, which implicates the ternary complex as important for redirecting metabolic flux in these conditions in addition to inactivation of the Calvin cycle in the dark. To predict the potency of sgRNA sequences, we applied machine learning on sgRNA sequences and gene repression data, which showed the importance of C enrichment and T depletion proximal to the PAM site. Fitness data for all genes in all conditions are compiled in an interactive web application.
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Affiliation(s)
- Rui Miao
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, SE-17165,Sweden
| | - Michael Jahn
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, SE-17165,Sweden
- Max Planck Unit for the Science of Pathogens, 10117 Berlin,Germany
| | - Kiyan Shabestary
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, SE-17165,Sweden
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ,UK
| | - Gilles Peltier
- Aix Marseille Univ, CEA, CNRS, Institut de Biosciences et Biotechnologies Aix-Marseille, CEA Cadarache, 13108 Saint Paul-Lez-Durance,France
| | - Elton P Hudson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, SE-17165,Sweden
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13
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Wan X, Chou WK, Brynildsen MP. Amino acids can deplete ATP and impair nitric oxide detoxification by Escherichia coli. Free Radic Biol Med 2023; 205:90-99. [PMID: 37253411 DOI: 10.1016/j.freeradbiomed.2023.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/18/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2023]
Abstract
Nitric oxide (·NO) is a prevalent antimicrobial that is known to damage iron-containing enzymes in amino acid (AA) biosynthesis pathways. With Escherichia coli, ·NO is detoxified in aerobic environments by Hmp, which is an enzyme that is synthesized de novo in response to ·NO. With this knowledgebase, it is expected that the availability of AAs in the extracellular environment would enhance ·NO detoxification, because AAs would foster translation of Hmp. However, we observed that ·NO detoxification by E. coli was far slower in populations grown and treated in the presence of AAs (AA+) in comparison to those grown and stressed in the absence of AAs (AA-). Further experiments revealed that AA+ populations had difficulty translating proteins under ·NO stress, and that ·NO activated the stringent response in AA+ populations. Additional work revealed significant ATP depletion in ·NO-stressed AA+ cultures that far exceeded that of ·NO-stressed AA- populations. Transcription, translation, and RelA were not found to be significant contributors to the ATP depletion observed, whereas AA import was implicated as a significant ATP consumption pathway. Alleviating ATP depletion while maintaining access to AAs partially restored ·NO detoxification, which suggested that ATP depletion contributed to the translational difficulties observed in ·NO-stressed AA+ populations. These data reveal an unexpected interaction within the ·NO response network of E. coli that stimulates a stringent response by RelA in conditions where AAs are plentiful.
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Affiliation(s)
- Xuanqing Wan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Wen Kang Chou
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Mark P Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA.
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14
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Mohler K, Moen JM, Rogulina S, Rinehart J. System-wide optimization of an orthogonal translation system with enhanced biological tolerance. Mol Syst Biol 2023; 19:e10591. [PMID: 37477096 PMCID: PMC10407733 DOI: 10.15252/msb.202110591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 07/05/2023] [Accepted: 07/05/2023] [Indexed: 07/22/2023] Open
Abstract
Over the past two decades, synthetic biological systems have revolutionized the study of cellular physiology. The ability to site-specifically incorporate biologically relevant non-standard amino acids using orthogonal translation systems (OTSs) has proven particularly useful, providing unparalleled access to cellular mechanisms modulated by post-translational modifications, such as protein phosphorylation. However, despite significant advances in OTS design and function, the systems-level biology of OTS development and utilization remains underexplored. In this study, we employ a phosphoserine OTS (pSerOTS) as a model to systematically investigate global interactions between OTS components and the cellular environment, aiming to improve OTS performance. Based on this analysis, we design OTS variants to enhance orthogonality by minimizing host process interactions and reducing stress response activation. Our findings advance understanding of system-wide OTS:host interactions, enabling informed design practices that circumvent deleterious interactions with host physiology while improving OTS performance and stability. Furthermore, our study emphasizes the importance of establishing a pipeline for systematically profiling OTS:host interactions to enhance orthogonality and mitigate mechanisms underlying OTS-mediated host toxicity.
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Affiliation(s)
- Kyle Mohler
- Department of Cellular & Molecular PhysiologyYale School of MedicineNew HavenCTUSA
- Systems Biology InstituteYale UniversityNew HavenCTUSA
| | - Jack M Moen
- Quantitative Biosciences Institute (QBI)University of California, San FranciscoSan FranciscoCAUSA
- 2QBI Coronavirus Research Group (QCRG)San FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Svetlana Rogulina
- Department of Cellular & Molecular PhysiologyYale School of MedicineNew HavenCTUSA
- Systems Biology InstituteYale UniversityNew HavenCTUSA
| | - Jesse Rinehart
- Department of Cellular & Molecular PhysiologyYale School of MedicineNew HavenCTUSA
- Systems Biology InstituteYale UniversityNew HavenCTUSA
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15
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Weiland P, Dempwolff F, Steinchen W, Freibert S, Tian H, Glatter T, Martin R, Thomma BPHJ, Bange G, Altegoer F. Structural and functional analysis of the cerato-platanin-like protein Cpl1 suggests diverging functions in smut fungi. MOLECULAR PLANT PATHOLOGY 2023; 24:768-787. [PMID: 37171083 PMCID: PMC10257043 DOI: 10.1111/mpp.13349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 03/28/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
Abstract
Plant-pathogenic fungi are causative agents of the majority of plant diseases and can lead to severe crop loss in infected populations. Fungal colonization is achieved by combining different strategies, such as avoiding and counteracting the plant immune system and manipulating the host metabolome. Of major importance are virulence factors secreted by fungi, which fulfil diverse functions to support the infection process. Most of these proteins are highly specialized, with structural and biochemical information often absent. Here, we present the atomic structures of the cerato-platanin-like protein Cpl1 from Ustilago maydis and its homologue Uvi2 from Ustilago hordei. Both proteins adopt a double-Ψβ-barrel architecture reminiscent of cerato-platanin proteins, a class so far not described in smut fungi. Our structure-function analysis shows that Cpl1 binds to soluble chitin fragments via two extended grooves at the dimer interface of the two monomer molecules. This carbohydrate-binding mode has not been observed previously and expands the repertoire of chitin-binding proteins. Cpl1 localizes to the cell wall of U. maydis and might synergize with cell wall-degrading and decorating proteins during maize infection. The architecture of Cpl1 harbouring four surface-exposed loop regions supports the idea that it might play a role in the spatial coordination of these proteins. While deletion of cpl1 has only mild effects on the virulence of U. maydis, a recent study showed that deletion of uvi2 strongly impairs U. hordei virulence. Our structural comparison between Cpl1 and Uvi2 reveals sequence variations in the loop regions that might explain a diverging function.
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Affiliation(s)
- Paul Weiland
- Center for Synthetic Microbiology (SYNMIKRO), Faculty of ChemistryPhilipps‐University MarburgMarburgGermany
| | - Felix Dempwolff
- Center for Synthetic Microbiology (SYNMIKRO), Faculty of ChemistryPhilipps‐University MarburgMarburgGermany
| | - Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO), Faculty of ChemistryPhilipps‐University MarburgMarburgGermany
| | - Sven‐Andreas Freibert
- Center for Synthetic Microbiology (SYNMIKRO), Institute of CytobiologyPhilipps‐University MarburgMarburgGermany
- Protein Biochemistry and Spectroscopy Core Facility, Institute of CytobiologyPhilipps‐University MarburgMarburgGermany
| | - Hui Tian
- Institute for Plant SciencesUniversity of CologneCologneGermany
| | - Timo Glatter
- Max‐Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Roman Martin
- Faculty of Mathematics and Computer SciencePhilipps‐University MarburgMarburgGermany
| | - Bart P. H. J. Thomma
- Institute for Plant SciencesUniversity of CologneCologneGermany
- Cluster of Excellence on Plant Sciences (CEPLAS)CologneGermany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Faculty of ChemistryPhilipps‐University MarburgMarburgGermany
- Max‐Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Florian Altegoer
- Center for Synthetic Microbiology (SYNMIKRO), Faculty of ChemistryPhilipps‐University MarburgMarburgGermany
- Max‐Planck Institute for Terrestrial MicrobiologyMarburgGermany
- Institute of MicrobiologyHeinrich‐Heine‐UniversityDüsseldorfGermany
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16
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Lewis J, Scott NE. CRISPRi-Mediated Silencing of Burkholderia O-Linked Glycosylation Systems Enables the Depletion of Glycosylation Yet Results in Modest Proteome Impacts. J Proteome Res 2023; 22:1762-1778. [PMID: 36995114 PMCID: PMC10243306 DOI: 10.1021/acs.jproteome.2c00790] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Indexed: 03/31/2023]
Abstract
The process of O-linked protein glycosylation is highly conserved across the Burkholderia genus and mediated by the oligosaccharyltransferase PglL. While our understanding of Burkholderia glycoproteomes has increased in recent years, little is known about how Burkholderia species respond to modulations in glycosylation. Utilizing CRISPR interference (CRISPRi), we explored the impact of silencing of O-linked glycosylation across four species of Burkholderia; Burkholderia cenocepacia K56-2, Burkholderia diffusa MSMB375, Burkholderia multivorans ATCC17616, and Burkholderia thailandensis E264. Proteomic and glycoproteomic analyses revealed that while CRISPRi enabled inducible silencing of PglL, this did not abolish glycosylation, nor recapitulate phenotypes such as proteome changes or alterations in motility that are associated with glycosylation null strains, despite inhibition of glycosylation by nearly 90%. Importantly, this work also demonstrated that CRISPRi induction with high levels of rhamnose leads to extensive impacts on the Burkholderia proteomes, which without appropriate controls mask the impacts specifically driven by CRISPRi guides. Combined, this work revealed that while CRISPRi allows the modulation of O-linked glycosylation with reductions up to 90% at a phenotypic and proteome levels, Burkholderia appears to demonstrate a robust tolerance to fluctuations in glycosylation capacity.
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Affiliation(s)
- Jessica
M. Lewis
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute
for Infection and Immunity, Melbourne 3000, Australia
| | - Nichollas E. Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute
for Infection and Immunity, Melbourne 3000, Australia
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17
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Zhang X, Wang X, Zhang Y, Wang F, Zhang C, Li X. Development of isopentenyl phosphate kinases and their application in terpenoid biosynthesis. Biotechnol Adv 2023; 64:108124. [PMID: 36863457 DOI: 10.1016/j.biotechadv.2023.108124] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/20/2023] [Accepted: 02/26/2023] [Indexed: 03/04/2023]
Abstract
As the largest class of natural products, terpenoids (>90,000) have multiple biological activities and a wide range of applications (e.g., pharmaceutical, agricultural, personal care and food industries). Therefore, the sustainable production of terpenoids by microorganisms is of great interest. Microbial terpenoid production depends on two common building blocks: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In addition to the natural biosynthetic pathways, mevalonate and methyl-D-erythritol-4-phosphate pathways, IPP and DMAPP can be produced through the conversion of isopentenyl phosphate and dimethylallyl monophosphate by isopentenyl phosphate kinases (IPKs), offering an alternative route for terpenoid biosynthesis. This review summarizes the properties and functions of various IPKs, novel IPP/DMAPP synthesis pathways involving IPKs, and their applications in terpenoid biosynthesis. Furthermore, we have discussed strategies to exploit novel pathways and unleash their potential for terpenoid biosynthesis.
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Affiliation(s)
- Xinyi Zhang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xun Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Yu Zhang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Fei Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| | - Xun Li
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China.
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18
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Fulton RL, Downs DM. Modulators of a robust and efficient metabolism: Perspective and insights from the Rid superfamily of proteins. Adv Microb Physiol 2023; 83:117-179. [PMID: 37507158 PMCID: PMC10642521 DOI: 10.1016/bs.ampbs.2023.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Metabolism is an integrated network of biochemical pathways that assemble to generate the robust, responsive physiologies of microorganisms. Despite decades of fundamental studies on metabolic processes and pathways, our understanding of the nuance and complexity of metabolism remains incomplete. The ability to predict and model metabolic network structure, and its influence on cellular fitness, is complicated by the persistence of genes of unknown function, even in the best-studied model organisms. This review describes the definition and continuing study of the Rid superfamily of proteins. These studies are presented with a perspective that illustrates how metabolic complexity can complicate the assignment of function to uncharacterized genes. The Rid superfamily of proteins has been divided into eight subfamilies, including the well-studied RidA subfamily. Aside from the RidA proteins, which are present in all domains of life and prevent metabolic stress, most members of the Rid superfamily have no demonstrated physiological role. Recent progress on functional assignment supports the hypothesis that, overall, proteins in the Rid superfamily modulate metabolic processes to ensure optimal organismal fitness.
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Affiliation(s)
- Ronnie L Fulton
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, GA, United States.
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19
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Muralidhara P, Ewald JC. Protein-Metabolite Interactions Shape Cellular Metabolism and Physiology. Methods Mol Biol 2023; 2554:1-10. [PMID: 36178616 DOI: 10.1007/978-1-0716-2624-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein-metabolite interactions regulate many important cellular processes but still remain understudied. Recent technological advancements are gradually uncovering the complexity of the protein-metabolite interactome. Here, we highlight some classic and recent examples of how protein metabolite interactions regulate metabolism, both locally and globally, and how this contributes to cellular physiology. We also discuss the importance of these interactions in diseases such as cancer.
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Affiliation(s)
| | - Jennifer C Ewald
- Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany
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20
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Han B, Dai Z, Li Z. Computer-Based Design of a Cell Factory for High-Yield Cytidine Production. ACS Synth Biol 2022; 11:4123-4133. [PMID: 36442151 DOI: 10.1021/acssynbio.2c00431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyrimidine ribonucleotide de novo biosynthesis pathway (PRdnBP) is an important pathway to produce pyrimidine nucleosides. We attempted to systematically investigate PRdnBP in Escherichia coli with genome-scale metabolic models and utilized the models to guide strain design. The balance of central carbon metabolism and PRdnBP affected the production of cytidine from glucose. Using Bayesian metabolic flux analysis, the effect of modified PRdnBP on the metabolic network was analyzed. The acetate overflow became coupled with PRdnBP flux, while they were originally independent under oxygen-sufficient conditions. The coupling between cytidine production and acetate secretion in the modified strain was weakened by arcA deletion, which resulted in further improving the efficient accumulation of cytidine. In total, 1.28 g/L of cytidine with a yield of 0.26 g/g glucose was produced. The yield of cytidine produced by E. coli is higher than previous reports. Our strategy provides an effective attempt to find metabolic bottlenecks in genetically engineered bacteria by using flux coupling analysis.
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Affiliation(s)
- Bin Han
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai200237, China
| | - Zeyu Dai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai200237, China
| | - Zhimin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai200237, China.,Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai200237, China
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21
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Schwan M, Khaledi A, Willger S, Papenfort K, Glatter T, Häußler S, Thormann KM. FlrA-independent production of flagellar proteins is required for proper flagellation in Shewanella putrefaciens. Mol Microbiol 2022; 118:670-682. [PMID: 36285560 DOI: 10.1111/mmi.14993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 01/18/2023]
Abstract
Flagella are multiprotein complexes whose assembly and positioning require complex spatiotemporal control. Flagellar assembly is thought to be controlled by several transcriptional tiers, which are mediated through various master regulators. Here, we revisited the regulation of flagellar genes in polarly flagellated gammaproteobacteria by the regulators FlrA, RpoN (σ54 ) and FliA (σ28 ) in Shewanella putrefaciens CN-32 at the transcript and protein level. We found that a number of regulatory and structural proteins were present in the absence of the main regulators, suggesting that initiation of flagella assembly and motor activation relies on the abundance control of only a few structural key components that are required for the formation of the MS- and C-ring and the flagellar type III secretion system. We identified FlrA-independent promoters driving expression of the regulators of flagellar number and positioning, FlhF and FlhG. Reduction of the gene expression levels from these promoters resulted in the emergence of hyperflagellation. This finding indicates that basal expression is required to adjust the flagellar counter in Shewanella. This is adding a deeper layer to the regulation of flagellar synthesis and assembly.
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Affiliation(s)
- Meike Schwan
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Ariane Khaledi
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sven Willger
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Kai Papenfort
- Institute for Microbiology, Friedrich Schiller University, Jena, Germany
| | - Timo Glatter
- Max Planck Institute for Terrestrial Microbiology, Mass Spectrometry and Proteomics, Marburg, Germany
| | - Susanne Häußler
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Kai M Thormann
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
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22
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Castillo-Alfonso F, Quintana-Menéndez A, Vigueras-Ramírez G, Sales-Cruz AM, Rosales-Colunga LM, Olivares-Hernández R. Analysis of the Propionate Metabolism in Bacillus subtilis during 3-Indolacetic Production. Microorganisms 2022; 10:microorganisms10122352. [PMID: 36557605 PMCID: PMC9782769 DOI: 10.3390/microorganisms10122352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022] Open
Abstract
The genera Bacillus belongs to the group of microorganisms that are known as plant growth-promoting bacteria, their metabolism has evolved to produce molecules that benefit the growth of the plant, and the production of 3-indole acetic acid (IAA) is part of its secondary metabolism. In this work, Bacillus subtilis was cultivated in a bioreactor to produce IAA using propionate and glucose as carbon sources in an M9-modified media; in both cases, tryptophan was added as a co-substrate. The yield of IAA using propionate is 17% higher compared to glucose. After 48 h of cultivation, the final concentration was 310 mg IAA/L using propionate and 230 mg IAA/L using glucose, with a concentration of 500 mg Trp/L. To gain more insight into propionate metabolism and its advantages, the genome-scale metabolic model of B. subtilis (iBSU 1147) and computational analysis were used to calculate flux distribution and evaluate the metabolic capabilities to produce IAA using propionate. The metabolic fluxes demonstrate that propionate uptake favors the production of precursors needed for the synthesis of the hormone, and the sensitivity analysis shows that the control of a specific growth rate has a positive impact on the production of IAA.
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Affiliation(s)
- Freddy Castillo-Alfonso
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana Unidad Cuajimalpa, Ciudad de México 05370, Mexico
| | - Alejandro Quintana-Menéndez
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana Unidad Cuajimalpa, Ciudad de México 05370, Mexico
| | - Gabriel Vigueras-Ramírez
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Cuajimalpa de Morelos, Ciudad de México 05348, Mexico
| | - Alfonso Mauricio Sales-Cruz
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Cuajimalpa de Morelos, Ciudad de México 05348, Mexico
| | - Luis Manuel Rosales-Colunga
- Facultad de Ingeniería, Universidad Autónoma de San Luis Potosí, Av. Dr Manuel Nava 8, Zona Universitaria, San Luis Potosí 78290, Mexico
| | - Roberto Olivares-Hernández
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Cuajimalpa de Morelos, Ciudad de México 05348, Mexico
- Correspondence:
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23
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Hurbain J, Thommen Q, Anquez F, Pfeuty B. Quantitative modeling of pentose phosphate pathway response to oxidative stress reveals a cooperative regulatory strategy. iScience 2022; 25:104681. [PMID: 35856027 PMCID: PMC9287814 DOI: 10.1016/j.isci.2022.104681] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/12/2022] [Accepted: 06/23/2022] [Indexed: 01/22/2023] Open
Abstract
Living cells use signaling and regulatory mechanisms to adapt to environmental stresses. Adaptation to oxidative stress involves the regulation of many enzymes in both glycolysis and pentose phosphate pathways (PPP), so as to support PPP-driven NADPH recycling for antioxidant defense. The underlying regulatory logic is investigated by developing a kinetic modeling approach fueled with metabolomics and 13C-fluxomics datasets from human fibroblast cells. Bayesian parameter estimation and phenotypic analysis of models highlight complementary roles for several metabolite-enzyme regulations. Specifically, carbon flux rerouting into PPP involves a tight coordination between the upregulation of G6PD activity concomitant to a decreased NADPH/NADP+ ratio and the differential control of downward and upward glycolytic fluxes through the joint inhibition of PGI and GAPD enzymes. Such functional interplay between distinct regulatory feedbacks promotes efficient detoxification and homeostasis response over a broad range of stress level, but can also explain paradoxical pertubation phenotypes for instance reported for 6PGD modulation in mammalian cells.
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Affiliation(s)
- Julien Hurbain
- CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, University of Lille, 59000 Lille, France
| | - Quentin Thommen
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, University of Lille, 59000 Lille, France
| | - Francois Anquez
- CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, University of Lille, 59000 Lille, France
| | - Benjamin Pfeuty
- CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, University of Lille, 59000 Lille, France
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24
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Ahn-Horst TA, Mille LS, Sun G, Morrison JH, Covert MW. An expanded whole-cell model of E. coli links cellular physiology with mechanisms of growth rate control. NPJ Syst Biol Appl 2022; 8:30. [PMID: 35986058 PMCID: PMC9391491 DOI: 10.1038/s41540-022-00242-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022] Open
Abstract
Growth and environmental responses are essential for living organisms to survive and adapt to constantly changing environments. In order to simulate new conditions and capture dynamic responses to environmental shifts in a developing whole-cell model of E. coli, we incorporated additional regulation, including dynamics of the global regulator guanosine tetraphosphate (ppGpp), along with dynamics of amino acid biosynthesis and translation. With the model, we show that under perturbed ppGpp conditions, small molecule feedback inhibition pathways, in addition to regulation of expression, play a role in ppGpp regulation of growth. We also found that simulations with dysregulated amino acid synthesis pathways provide average amino acid concentration predictions that are comparable to experimental results but on the single-cell level, concentrations unexpectedly show regular fluctuations. Additionally, during both an upshift and downshift in nutrient availability, the simulated cell responds similarly with a transient increase in the mRNA:rRNA ratio. This additional simulation functionality should support a variety of new applications and expansions of the E. coli Whole-Cell Modeling Project.
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Affiliation(s)
- Travis A Ahn-Horst
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | | | - Gwanggyu Sun
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Jerry H Morrison
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
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25
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Wang HD, Xu JZ, Zhang WG. Metabolic engineering of Escherichia coli for efficient production of L-arginine. Appl Microbiol Biotechnol 2022; 106:5603-5613. [PMID: 35931894 DOI: 10.1007/s00253-022-12109-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/15/2022] [Accepted: 07/27/2022] [Indexed: 11/02/2022]
Abstract
As an important semi-essential amino acid, L-arginine (L-Arg) has important application prospects in medicine and health care. However, it remains a challenge to efficiently produce L-Arg by Escherichia coli (E. coli). In the present study, we obtained an E. coli A1 with L-Arg accumulation ability, and carried out a series of metabolic engineering on it, and finally obtained an E. coli strain A7 with high L-Arg production ability. First, genome analysis of strain A1 was performed to explore the related genes affecting L-Arg accumulation. We found that gene speC and gene speF played an important role in the accumulation of L-Arg. Second, we used two strategies to solve the feedback inhibition of the L-Arg pathway in E. coli. One was the combination of a mutation of the gene argA and the deletion of the gene argR, and the other was the combination of a heterologous insertion of the gene argJ and the deletion of the gene argR. The combination of exogenous argJ gene insertion and argR gene deletion achieved higher titer accumulation with less impact on strain growth. Finally, we inserted the gene cluster argCJBDF of Corynebacterium glutamicum (C. glutamicum) to enhance the metabolic flux of the L-Arg pathway in E. coli. The final strain obtained 70.1 g/L L-Arg in a 5-L bioreactor, with a yield of 0.326 g/g glucose and a productivity of 1.17 g/(L· h). This was the highest level of L-Arg production by E. coli ever reported. Collectively, our findings provided valuable insights into the possibility of the industrial production of L-Arg by E. coli. KEY POINTS: • Genetic background of E. coli A1 genome analysis. • Heterologous argJ substitution of argA mutation promoted excessive accumulation of L-Arg in E. coli A1. • The overexpression of L-Arg synthesis gene cluster argCJBDF of Corynebacterium glutamicum (C. glutamate) promoted the accumulation of L-Arg, and 70.1 g/L L-Arg was finally obtained in fed-batch fermentation.
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Affiliation(s)
- Hai-De Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1,800# Lihu Road, 214122, WuXi, People's Republic of China
| | - Jian-Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1,800# Lihu Road, 214122, WuXi, People's Republic of China.
| | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1,800# Lihu Road, 214122, WuXi, People's Republic of China.
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26
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Radoš D, Donati S, Lempp M, Rapp J, Link H. Homeostasis of the biosynthetic E. coli metabolome. iScience 2022; 25:104503. [PMID: 35754712 PMCID: PMC9218372 DOI: 10.1016/j.isci.2022.104503] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/19/2022] [Accepted: 05/26/2022] [Indexed: 11/22/2022] Open
Abstract
Metabolite concentrations vary across conditions and such metabolome changes are relevant for metabolic and gene regulation. Here, we used LC-MS/MS to explore metabolite concentration changes in Escherichia coli. We measured 101 primary metabolites in 19 experimental conditions that include various nutrients and stresses. Many metabolites showed little variation across conditions and only few metabolites correlated with the growth rate. The least varying metabolites were nucleotides (e.g. UTP had 10% variation) and amino acids (e.g. methionine had 13% variation). These results show that E. coli maintains protein and RNA building blocks within narrow concentration ranges, thus indicating that many feedback mechanisms in biosynthetic pathways contribute to end-product homeostasis. 101 E coli metabolites were measured in 19 conditions Biosynthetic end-products vary little between conditions Few metabolites correlate with the growth rate Metabolome data identify active regulatory metabolites
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Affiliation(s)
- Dušica Radoš
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Stefano Donati
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Martin Lempp
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Johanna Rapp
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
| | - Hannes Link
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
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27
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Berry S, Müller M, Rai A, Pelkmans L. Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells. Cell Syst 2022; 13:454-470.e15. [PMID: 35613616 DOI: 10.1016/j.cels.2022.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 12/13/2021] [Accepted: 04/21/2022] [Indexed: 12/18/2022]
Abstract
RNA concentration homeostasis involves coordinating RNA abundance and synthesis rates with cell size. Here, we study this in human cells by combining genome-wide perturbations with quantitative single-cell measurements. Despite relative ease in perturbing RNA synthesis, we find that RNA concentrations generally remain highly constant. Perturbations that would be expected to increase nuclear mRNA levels, including those targeting nuclear mRNA degradation or export, result in downregulation of RNA synthesis. This is associated with reduced abundance of transcription-associated proteins and protein states that are normally coordinated with RNA production in single cells, including RNA polymerase II (RNA Pol II) itself. Acute perturbations, elevation of nuclear mRNA levels, and mathematical modeling indicate that mammalian cells achieve robust mRNA concentration homeostasis by the mRNA-based negative feedback on transcriptional activity in the nucleus. This ultimately acts to coordinate RNA Pol II abundance with nuclear mRNA degradation and export rates and may underpin the scaling of mRNA abundance with cell size.
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Affiliation(s)
- Scott Berry
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland; EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.
| | - Micha Müller
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Arpan Rai
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
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28
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Kremer DM, Lyssiotis CA. Targeting allosteric regulation of cancer metabolism. Nat Chem Biol 2022; 18:441-450. [PMID: 35484254 DOI: 10.1038/s41589-022-00997-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 02/14/2022] [Indexed: 12/13/2022]
Abstract
Metabolic reprogramming is observed across all cancer types. Indeed, the success of many classic chemotherapies stems from their targeting of cancer metabolism. Contemporary research in this area has refined our understanding of tumor-specific metabolic mechanisms and has revealed strategies for exploiting these vulnerabilities selectively. Based on this growing understanding, new small-molecule tools and drugs have been developed to study and target tumor metabolism. Here, we highlight allosteric modulation of metabolic enzymes as an attractive mechanism of action for small molecules that target metabolic enzymes. We then discuss the mechanistic insights garnered from their application in cancer studies and highlight the achievements of this approach in targeting cancer metabolism. Finally, we discuss technological advances in drug discovery for allosteric modulators of enzyme activity.
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Affiliation(s)
- Daniel M Kremer
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA.,Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA.,Department of Chemistry, the Scripps Research Institute, La Jolla, CA, USA
| | - Costas A Lyssiotis
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA. .,Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI, USA. .,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
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29
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Losa J, Leupold S, Alonso-Martinez D, Vainikka P, Thallmair S, Tych KM, Marrink SJ, Heinemann M. Perspective: a stirring role for metabolism in cells. Mol Syst Biol 2022; 18:e10822. [PMID: 35362256 PMCID: PMC8972047 DOI: 10.15252/msb.202110822] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/05/2022] [Accepted: 03/09/2022] [Indexed: 11/24/2022] Open
Abstract
Based on recent findings indicating that metabolism might be governed by a limit on the rate at which cells can dissipate Gibbs energy, in this Perspective, we propose a new mechanism of how metabolic activity could globally regulate biomolecular processes in a cell. Specifically, we postulate that Gibbs energy released in metabolic reactions is used to perform work, allowing enzymes to self‐propel or to break free from supramolecular structures. This catalysis‐induced enzyme movement will result in increased intracellular motion, which in turn can compromise biomolecular functions. Once the increased intracellular motion has a detrimental effect on regulatory mechanisms, this will establish a feedback mechanism on metabolic activity, and result in the observed thermodynamic limit. While this proposed explanation for the identified upper rate limit on cellular Gibbs energy dissipation rate awaits experimental validation, it offers an intriguing perspective of how metabolic activity can globally affect biomolecular functions and will hopefully spark new research.
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Affiliation(s)
- José Losa
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Simeon Leupold
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Diego Alonso-Martinez
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Petteri Vainikka
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Sebastian Thallmair
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Katarzyna M Tych
- Chemical Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Siewert J Marrink
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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30
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Hai-De W, Shuai L, Bing-Bing W, Jie L, Jian-Zhong X, Wei-Guo Z. Metabolic engineering of Escherichia coli for efficient production of l-arginine. ADVANCES IN APPLIED MICROBIOLOGY 2022; 122:127-150. [PMID: 37085192 DOI: 10.1016/bs.aambs.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
As a semi-essential amino acid, l-arginine (l-Arg) plays an important role in food, health care, and medical treatment. At present, the main method of producing l-Arg is the use of microbial fermentation. Therefore, the selection and breeding of high-efficiency microbial strains is the top priority. To continuously improve the l-Arg production performance of the strains, a series of metabolic engineering strategies have been tried to transform the strains. The production of l-Arg by metabolically engineered Corynebacterium glutamicum (C. glutamicum) reached a relatively high level. Escherichia coli (E. coli), as a strain with great potential for l-Arg production, also has a large number of research strategies aimed at screening effective E. coli for producing l-Arg. E. coli also has a number of advantages over C. glutamicum in producing l-Arg. Therefore, it is of great significance to screen out excellent and stable E. coli to produce l-Arg. Here, based on recent research results, we review the metabolic pathways of l-Arg production in E. coli, the research progress of l-Arg production in E. coli, and various regulatory strategies implemented in E. coli.
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31
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ElyC and Cyclic Enterobacterial Common Antigen Regulate Synthesis of Phosphoglyceride-Linked Enterobacterial Common Antigen. mBio 2021; 12:e0284621. [PMID: 34809459 PMCID: PMC8609368 DOI: 10.1128/mbio.02846-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Gram-negative cell envelope is a complex structure delineating the cell from its environment. Recently, we found that enterobacterial common antigen (ECA) plays a role maintaining the outer membrane (OM) permeability barrier, which excludes toxic molecules including many antibiotics. ECA is a conserved carbohydrate found throughout Enterobacterales (e.g., Salmonella, Klebsiella, and Yersinia). There are two OM forms of ECA (phosphoglyceride-linked ECAPG and lipopolysaccharide-linked ECALPS) and one periplasmic form of ECA (cyclic ECACYC). ECAPG, found in the outer leaflet of the OM, consists of a linear ECA oligomer attached to phosphoglyceride through a phosphodiester linkage. The process through which ECAPG is produced from polymerized ECA is unknown. Therefore, we set out to identify genes interacting genetically with ECAPG biosynthesis in Escherichia coli K-12 using the competition between ECA and peptidoglycan biosynthesis. Through transposon-directed insertion sequencing, we identified an interaction between elyC and ECAPG biosynthesis. ElyC is an inner membrane protein previously shown to alter peptidoglycan biosynthesis rates. We found ΔelyC was lethal specifically in strains producing ECAPG without other ECA forms, suggesting ECAPG biosynthesis impairment or dysregulation. Further characterization suggested ElyC inhibits ECAPG synthesis in a posttranscriptional manner. Moreover, the full impact of ElyC on ECA levels requires the presence of ECACYC. Our data demonstrate ECACYC can regulate ECAPG synthesis in strains wild type for elyC. Overall, our data demonstrate ElyC and ECACYC act in a novel pathway that regulates the production of ECAPG, supporting a model in which ElyC provides feedback regulation of ECAPG production based on the periplasmic levels of ECACYC.
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32
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Shimizu K, Matsuoka Y. Feedback regulation and coordination of the main metabolism for bacterial growth and metabolic engineering for amino acid fermentation. Biotechnol Adv 2021; 55:107887. [PMID: 34921951 DOI: 10.1016/j.biotechadv.2021.107887] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/05/2021] [Accepted: 12/09/2021] [Indexed: 12/28/2022]
Abstract
Living organisms such as bacteria are often exposed to continuous changes in the nutrient availability in nature. Therefore, bacteria must constantly monitor the environmental condition, and adjust the metabolism quickly adapting to the change in the growth condition. For this, bacteria must orchestrate (coordinate and integrate) the complex and dynamically changing information on the environmental condition. In particular, the central carbon metabolism (CCM), monomer synthesis, and macromolecular synthesis must be coordinately regulated for the efficient growth. It is a grand challenge in bioscience, biotechnology, and synthetic biology to understand how living organisms coordinate the metabolic regulation systems. Here, we consider the integrated sensing of carbon sources by the phosphotransferase system (PTS), and the feed-forward/feedback regulation systems incorporated in the CCM in relation to the pool sizes of flux-sensing metabolites and αketoacids. We also consider the metabolic regulation of amino acid biosynthesis (as well as purine and pyrimidine biosyntheses) paying attention to the feedback control systems consisting of (fast) enzyme level regulation with (slow) transcriptional regulation. The metabolic engineering for the efficient amino acid production by bacteria such as Escherichia coli and Corynebacterium glutamicum is also discussed (in relation to the regulation mechanisms). The amino acid synthesis is important for determining the rate of ribosome biosynthesis. Thus, the growth rate control (growth law) is further discussed on the relationship between (p)ppGpp level and the ribosomal protein synthesis.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan; Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan.
| | - Yu Matsuoka
- Department of Fisheries Distribution and Management, National Fisheries University, Shimonoseki, Yamaguchi 759-6595, Japan
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33
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Jahn M, Crang N, Janasch M, Hober A, Forsström B, Kimler K, Mattausch A, Chen Q, Asplund-Samuelsson J, Hudson EP. Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator. eLife 2021; 10:69019. [PMID: 34723797 PMCID: PMC8591527 DOI: 10.7554/elife.69019] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 10/30/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria must balance the different needs for substrate assimilation, growth
functions, and resilience in order to thrive in their environment. Of all
cellular macromolecules, the bacterial proteome is by far the most important
resource and its size is limited. Here, we investigated how the highly versatile
'knallgas' bacterium Cupriavidus necator reallocates protein
resources when grown on different limiting substrates and with different growth
rates. We determined protein quantity by mass spectrometry and estimated enzyme
utilization by resource balance analysis modeling. We found that C.
necator invests a large fraction of its proteome in functions that
are hardly utilized. Of the enzymes that are utilized, many are present in
excess abundance. One prominent example is the strong expression of CBB cycle
genes such as Rubisco during growth on fructose. Modeling and mutant competition
experiments suggest that CO2-reassimilation through Rubisco does not
provide a fitness benefit for heterotrophic growth, but is rather an investment
in readiness for autotrophy.
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Affiliation(s)
- Michael Jahn
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Nick Crang
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Markus Janasch
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Andreas Hober
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Björn Forsström
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Kyle Kimler
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Alexander Mattausch
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Qi Chen
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Johannes Asplund-Samuelsson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Elton Paul Hudson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
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34
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Zakataeva NP. Microbial 5'-nucleotidases: their characteristics, roles in cellular metabolism, and possible practical applications. Appl Microbiol Biotechnol 2021; 105:7661-7681. [PMID: 34568961 PMCID: PMC8475336 DOI: 10.1007/s00253-021-11547-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 11/25/2022]
Abstract
5′-Nucleotidases (EC 3.1.3.5) are enzymes that catalyze the hydrolytic dephosphorylation of 5′-ribonucleotides and 5′-deoxyribonucleotides to their respective nucleosides and phosphate. Most 5′-nucleotidases have broad substrate specificity and are multifunctional enzymes capable of cleaving phosphorus from not only mononucleotide phosphate molecules but also a variety of other phosphorylated metabolites. 5′-Nucleotidases are widely distributed throughout all kingdoms of life and found in different cellular locations. The well-studied vertebrate 5′-nucleotidases play an important role in cellular metabolism. These enzymes are involved in purine and pyrimidine salvage pathways, nucleic acid repair, cell-to-cell communication, signal transduction, control of the ribo- and deoxyribonucleotide pools, etc. Although the first evidence of microbial 5′-nucleotidases was obtained almost 60 years ago, active studies of genetic control and the functions of microbial 5′-nucleotidases started relatively recently. The present review summarizes the current knowledge about microbial 5′-nucleotidases with a focus on their diversity, cellular localizations, molecular structures, mechanisms of catalysis, physiological roles, and activity regulation and approaches to identify new 5′-nucleotidases. The possible applications of these enzymes in biotechnology are also discussed. Key points • Microbial 5′-nucleotidases differ in molecular structure, hydrolytic mechanism, and cellular localization. • 5′-Nucleotidases play important and multifaceted roles in microbial cells. • Microbial 5′-nucleotidases have wide range of practical applications.
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Affiliation(s)
- Natalia P Zakataeva
- Ajinomoto-Genetika Research Institute, 1st Dorozhny Proezd, b.1-1, Moscow, 117545, Russia.
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35
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Ali S, Alam M, Hasan GM, Hassan MI. Potential therapeutic targets of Klebsiella pneumoniae: a multi-omics review perspective. Brief Funct Genomics 2021; 21:63-77. [PMID: 34448478 DOI: 10.1093/bfgp/elab038] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/15/2022] Open
Abstract
The multidrug resistance developed in many organisms due to the prolonged use of antibiotics has been an increasing global health crisis. Klebsiella pneumoniae is a causal organism for various infections, including respiratory, urinary tract and biliary diseases. Initially, immunocompromised individuals are primarily affected by K. pneumoniae. Due to the emergence of hypervirulent strains recently, both healthy and immunocompetent individuals are equally susceptible to K. pneumoniae infections. The infections caused by multidrug-resistant and hypervirulent K. pneumoniae strains are complicated to treat, illustrating an urgent need to develop novel and more practical approaches to combat the pathogen. We focused on the previously performed high-throughput analyses by other groups to discover several novel enzymes that may be considered attractive drug targets of K. pneumoniae. These targets qualify most of the selection criteria for drug targeting, including an absence of its homolog's gene in the host. The capsule, lipopolysaccharide, fimbriae, siderophores and essential virulence factors facilitate the pathogen entry, infection and survival inside the host. This review discusses K. pneumoniae pathophysiology, including its virulence determinants and further the potential drug targets that might facilitate the discovery of novel drugs and effective treatment regimens shortly.
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Affiliation(s)
- Sabeeha Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
| | - Manzar Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
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36
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Metabolome and proteome analyses reveal transcriptional misregulation in glycolysis of engineered E. coli. Nat Commun 2021; 12:4929. [PMID: 34389727 PMCID: PMC8363753 DOI: 10.1038/s41467-021-25142-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 07/21/2021] [Indexed: 01/24/2023] Open
Abstract
Synthetic metabolic pathways are a burden for engineered bacteria, but the underlying mechanisms often remain elusive. Here we show that the misregulated activity of the transcription factor Cra is responsible for the growth burden of glycerol overproducing E. coli. Glycerol production decreases the concentration of fructose-1,6-bisphoshate (FBP), which then activates Cra resulting in the downregulation of glycolytic enzymes and upregulation of gluconeogenesis enzymes. Because cells grow on glucose, the improper activation of gluconeogenesis and the concomitant inhibition of glycolysis likely impairs growth at higher induction of the glycerol pathway. We solve this misregulation by engineering a Cra-binding site in the promoter controlling the expression of the rate limiting enzyme of the glycerol pathway to maintain FBP levels sufficiently high. We show the broad applicability of this approach by engineering Cra-dependent regulation into a set of constitutive and inducible promoters, and use one of them to overproduce carotenoids in E. coli. Synthetic pathways represent a metabolic burden on host cells. Here the authors engineer Cra-binding sites to prevent misregulation in glycerol and carotenoid overproducing E. coli strains.
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37
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Wu X, Xu H, Luo F, Wang J, Zhao L, Zhou X, Yang Y, Cai H, Sun P, Zhou H. Sizes and ligands tuned gold nanocluster acting as a new type of monoamine oxidase B inhibitor. Biosens Bioelectron 2021; 189:113377. [PMID: 34090156 DOI: 10.1016/j.bios.2021.113377] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/10/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022]
Abstract
Monoamine oxidase inhibitors (MAOIs) are a class of drugs that can be used in the treatment of Parkinson's disease, clinical depression, and anxiety by targeting monoamine oxidase B (MAO). However, the side effects of MAOIs drive the requirement of a new framework of enzyme inhibitors development. In this context, a new type of MAOI has been built on the framework of gold nanoclusters (AuNCs), realizing the transformation from no function of small molecules to MAOI function of ligand-modified AuNCs. The MAOI activity of fabricated AuNCs can be achieved by size control and specific ligands modification. In this work, AuNCs modified with cysteamine or 4-aminothiophenol, about 1-3 nm in size, were found to have MAOI activity (MAOI-like AuNCs) and their characterization has been extensively described. Meanwhile, the possible mechanism behind this MAOI activity has been explored and it is believed that the proper size of AuNCs with ligands containing amino groups can bind tightly with the entrance to active sites of MAO, blocking the enzyme interacting with its substrates, thereby realizing the function of MAOI. Last, the antimicrobial activity and the performance of the MAOI-like AuNCs in the human blood sample were explored and suggested that MAOI-like AuNCs do not possess strong antimicrobial activity and have no visualized side effect on blood cells, although the by-product peroxide of MAO reaction may reshape the white blood cells. The research in this work may shed some light on the development of a new type of enzyme inhibitor based on the framework of nanomaterials.
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Affiliation(s)
- Xueqiang Wu
- College of Pharmacy, Jinan University, Guangzhou, 510632, PR China
| | - Heng Xu
- College of Life Sciences, Jiaying University, Meizhou, 514015, PR China
| | - Fazeng Luo
- College of Pharmacy, Jinan University, Guangzhou, 510632, PR China
| | - Jinhua Wang
- College of Pharmacy, Jinan University, Guangzhou, 510632, PR China
| | - Li Zhao
- College of Pharmacy, Jinan University, Guangzhou, 510632, PR China
| | - Xia Zhou
- College of Pharmacy, Jinan University, Guangzhou, 510632, PR China; First Affiliated Hospital of Jinan University, Guangzhou, 510632, PR China
| | - Ying Yang
- First Affiliated Hospital of Jinan University, Guangzhou, 510632, PR China
| | - Huaihong Cai
- College of Chemistry and Materials Science, Jinan University, Guangzhou, 510632, PR China.
| | - Pinghua Sun
- College of Pharmacy, Jinan University, Guangzhou, 510632, PR China; First Affiliated Hospital of Jinan University, Guangzhou, 510632, PR China.
| | - Haibo Zhou
- College of Pharmacy, Jinan University, Guangzhou, 510632, PR China; First Affiliated Hospital of Jinan University, Guangzhou, 510632, PR China.
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38
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Kochanowski K, Okano H, Patsalo V, Williamson J, Sauer U, Hwa T. Global coordination of metabolic pathways in Escherichia coli by active and passive regulation. Mol Syst Biol 2021; 17:e10064. [PMID: 33852189 PMCID: PMC8045939 DOI: 10.15252/msb.202010064] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 12/15/2022] Open
Abstract
Microorganisms adjust metabolic activity to cope with diverse environments. While many studies have provided insights into how individual pathways are regulated, the mechanisms that give rise to coordinated metabolic responses are poorly understood. Here, we identify the regulatory mechanisms that coordinate catabolism and anabolism in Escherichia coli. Integrating protein, metabolite, and flux changes in genetically implemented catabolic or anabolic limitations, we show that combined global and local mechanisms coordinate the response to metabolic limitations. To allocate proteomic resources between catabolism and anabolism, E. coli uses a simple global gene regulatory program. Surprisingly, this program is largely implemented by a single transcription factor, Crp, which directly activates the expression of catabolic enzymes and indirectly reduces the expression of anabolic enzymes by passively sequestering cellular resources needed for their synthesis. However, metabolic fluxes are not controlled by this regulatory program alone; instead, fluxes are adjusted mostly through passive changes in the local metabolite concentrations. These mechanisms constitute a simple but effective global regulatory program that coarsely partitions resources between different parts of metabolism while ensuring robust coordination of individual metabolic reactions.
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Affiliation(s)
- Karl Kochanowski
- Institute of Molecular Systems BiologyETH ZurichZurichSwitzerland
- Life Science Zurich PhD Program on Systems BiologyZurichSwitzerland
| | - Hiroyuki Okano
- Department of PhysicsUniversity of California at San DiegoLa JollaCAUSA
| | - Vadim Patsalo
- Department of Integrative Structural and Computational Biology, and The Skaggs Institute for Chemical BiologyThe Scripps Research InstituteLa JollaCAUSA
| | - James Williamson
- Department of Integrative Structural and Computational Biology, and The Skaggs Institute for Chemical BiologyThe Scripps Research InstituteLa JollaCAUSA
| | - Uwe Sauer
- Institute of Molecular Systems BiologyETH ZurichZurichSwitzerland
| | - Terence Hwa
- Department of PhysicsUniversity of California at San DiegoLa JollaCAUSA
- Institute for Theoretical ScienceETH ZurichZurichSwitzerland
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39
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Abstract
It is generally recognized that proteins constitute the key cellular component in shaping microbial phenotypes. Due to limited cellular resources and space, optimal allocation of proteins is crucial for microbes to facilitate maximum proliferation rates while allowing a flexible response to environmental changes. To account for the growth condition-dependent proteome in the constraint-based metabolic modeling of Escherichia coli, we consolidated a coarse-grained protein allocation approach with the explicit consideration of enzymatic constraints on reaction fluxes. Besides representing physiologically relevant wild-type phenotypes and flux distributions, the resulting protein allocation model (PAM) advances the predictability of the metabolic responses to genetic perturbations. A main driver of mutant phenotypes was ascribed to inherited regulation patterns in protein distribution among metabolic enzymes. Moreover, the PAM correctly reflected metabolic responses to an augmented protein burden imposed by the heterologous expression of green fluorescent protein. In summary, we were able to model the effects of important and frequently applied metabolic engineering approaches on microbial metabolism. Therefore, we want to promote the integration of protein allocation constraints into classical constraint-based models to foster their predictive capabilities and application for strain analysis and engineering purposes. IMPORTANCE Predictive metabolic models are important, e.g., for generating biological knowledge and designing microbes with superior performance for target compound production. Yet today’s whole-cell models either show insufficient predictive capabilities or are computationally too expensive to be applied to metabolic engineering purposes. By linking the inherent genotype-phenotype relationship to a complete representation of the proteome, the PAM advances the accuracy of simulated phenotypes and intracellular flux distributions of E. coli. Being equally computationally lightweight as classical stoichiometric models and allowing for the application of established in silico tools, the PAM and related simulation approaches will foster the use of a model-driven metabolic research. Applications range from the investigation of mechanisms of microbial evolution to the determination of optimal strain design strategies in metabolic engineering, thus supporting basic scientists and engineers alike.
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40
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Adaptive laboratory evolution of methylotrophic Escherichia coli enables synthesis of all amino acids from methanol-derived carbon. Appl Microbiol Biotechnol 2021; 105:869-876. [PMID: 33404828 DOI: 10.1007/s00253-020-11058-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/21/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023]
Abstract
Recent attempts to create synthetic Escherichia coli methylotrophs identified that de novo biosynthesis of amino acids, in the presence of methanol, presents significant challenges in achieving autonomous methylotrophic growth. Previously engineered methanol-dependent strains required co-utilization of stoichiometric amounts of co-substrates and methanol. As such, these strains could not be evolved to grow on methanol alone. In this work, we have explored an alternative approach to enable biosynthesis of all amino acids from methanol-derived carbon in minimal media without stoichiometric coupling. First, we identified that biosynthesis of threonine was limiting the growth of our methylotrophic E. coli. To address this, we performed adaptive laboratory evolution to generate a strain that grew efficiently in minimal medium with methanol and threonine. Methanol assimilation and growth of the evolved strain were analyzed, and, interestingly, we found that the evolved strain synthesized all amino acids, including threonine, from methanol-derived carbon. The evolved strain was then further engineered through overexpression of an optimized threonine biosynthetic pathway. We show that the resulting methylotrophic E. coli strain has a methanol-dependent growth phenotype with homoserine as co-substrate. In contrast to previous methanol-dependent strains, co-utilization of homoserine is not stoichiometrically linked to methanol assimilation. As such, future engineering of this strain and successive adaptive evolution could enable autonomous growth on methanol as the sole carbon source. KEY POINTS: • Adaptive evolution of E. coli enables biosynthesis of all amino acids from methanol. • Overexpression of threonine biosynthesis pathway improves methanol assimilation. • Methanol-dependent growth is seen in minimal media with homoserine as co-substrate.
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41
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Castillo Alfonso F, Vigueras-Ramírez G, Rosales-Colunga LM, Del Monte-Martínez A, Olivares Hernández R. Propionate as the preferred carbon source to produce 3-indoleacetic acid in B. subtilis: comparative flux analysis using five carbon sources. Mol Omics 2021; 17:554-564. [PMID: 33972977 DOI: 10.1039/d1mo00039j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
3-Indoleacetic acid (IAA) is a phytohormone that promotes plant root growth, improving the use of nutrients and crop yield and it is been reported that bacteria of the genus Bacillus are capable of producing this phytohormone under various growth conditions. Considering this metabolic capability, in this work, Bacillus subtilis was cultivated in five different carbon sources: glucose, acetate, propionate, citrate and glycerol; and l-tryptophan (Trp) was used as an inducer for the IAA production. Based on the experimental results it was observed that the highest growth rate was achieved using glucose as a carbon source (μ = 0.12 h-1) and the lowest value was for citrate (μ = 0.08 h-1). On the other hand, the highest IAA production was obtained using propionate Yp/s = 0.975 (gIAA gTrp-1) and the lowest was when glucose was the substrate Yp/s = 0.803 (gIAA gTrp-1). In order to explore the metabolism and understand these differences, the experimental data was used to calculate the flux distribution using the genomic-scale metabolic model of Bacillus subtilis. Performing a comparative analysis it is observed that the fluxes towards precursors increase when propionate is the carbon source.
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Affiliation(s)
- Freddy Castillo Alfonso
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Delegación Cuajimalpa, Ciudad de Mexico, 05348, Mexico
| | - Gabriel Vigueras-Ramírez
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Delegación Cuajimalpa, Ciudad de Mexico, 05348, Mexico.
| | - Luis Manuel Rosales-Colunga
- Facultad de Ingeniería, Universidad Autónoma de San Luis Potosí, Av. Dr Manuel Nava 8, Zona Universitaria, 78290, San Luis Potosí, S.L.P, Mexico
| | - Alberto Del Monte-Martínez
- Centro de Estudios de Proteínas, Univerisdad de La Habana, Calle 25 #455, e/J e I, vedado, 10400, Havana, Cuba
| | - Roberto Olivares Hernández
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Delegación Cuajimalpa, Ciudad de Mexico, 05348, Mexico.
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42
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Donati S, Kuntz M, Pahl V, Farke N, Beuter D, Glatter T, Gomes-Filho JV, Randau L, Wang CY, Link H. Multi-omics Analysis of CRISPRi-Knockdowns Identifies Mechanisms that Buffer Decreases of Enzymes in E. coli Metabolism. Cell Syst 2020; 12:56-67.e6. [PMID: 33238135 DOI: 10.1016/j.cels.2020.10.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 09/23/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022]
Abstract
Enzymes maintain metabolism, and their concentration affects cellular fitness: high enzyme levels are costly, and low enzyme levels can limit metabolic flux. Here, we used CRISPR interference (CRISPRi) to study the consequences of decreasing E. coli enzymes below wild-type levels. A pooled CRISPRi screen with 7,177 strains demonstrates that metabolism buffers fitness defects for hours after the induction of CRISPRi. We characterized the metabolome and proteome responses in 30 CRISPRi strains and elucidated three gene-specific buffering mechanisms: ornithine buffered the knockdown of carbamoyl phosphate synthetase (CarAB) by increasing CarAB activity, S-adenosylmethionine buffered the knockdown of homocysteine transmethylase (MetE) by de-repressing expression of the methionine pathway, and 6-phosphogluconate buffered the knockdown of 6-phosphogluconate dehydrogenase (Gnd) by activating a bypass. In total, this work demonstrates that CRISPRi screens can reveal global sources of metabolic robustness and identify local regulatory mechanisms that buffer decreases of specific enzymes. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
- Stefano Donati
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Michelle Kuntz
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Vanessa Pahl
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Niklas Farke
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Dominik Beuter
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Lennart Randau
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Chun-Ying Wang
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Hannes Link
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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43
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Boon R, Silveira GG, Mostoslavsky R. Nuclear metabolism and the regulation of the epigenome. Nat Metab 2020; 2:1190-1203. [PMID: 33046909 DOI: 10.1038/s42255-020-00285-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022]
Abstract
Cellular metabolism has emerged as a major biological node governing cellular behaviour. Metabolic pathways fuel cellular energy needs, providing basic chemical molecules to sustain cellular homeostasis, proliferation and function. Changes in nutrient consumption or availability therefore can result in complete reprogramming of cellular metabolism towards stabilizing core metabolite pools, such as ATP, S-adenosyl methionine, acetyl-CoA, NAD/NADP and α-ketoglutarate. Because these metabolites underlie a variety of essential metabolic reactions, metabolism has evolved to operate in separate subcellular compartments through diversification of metabolic enzyme complexes, oscillating metabolic activity and physical separation of metabolite pools. Given that these same core metabolites are also consumed by chromatin modifiers in the establishment of epigenetic signatures, metabolite consumption on and release from chromatin directly influence cellular metabolism and gene expression. In this Review, we highlight recent studies describing the mechanisms determining nuclear metabolism and governing the redistribution of metabolites between the nuclear and non-nuclear compartments.
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Affiliation(s)
- Ruben Boon
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Giorgia G Silveira
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Raul Mostoslavsky
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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44
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Treuner-Lange A, Chang YW, Glatter T, Herfurth M, Lindow S, Chreifi G, Jensen GJ, Søgaard-Andersen L. PilY1 and minor pilins form a complex priming the type IVa pilus in Myxococcus xanthus. Nat Commun 2020; 11:5054. [PMID: 33028835 PMCID: PMC7541494 DOI: 10.1038/s41467-020-18803-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 09/14/2020] [Indexed: 01/05/2023] Open
Abstract
Type IVa pili are ubiquitous and versatile bacterial cell surface filaments that undergo cycles of extension, adhesion and retraction powered by the cell-envelope spanning type IVa pilus machine (T4aPM). The overall architecture of the T4aPM and the location of 10 conserved core proteins within this architecture have been elucidated. Here, using genetics, cell biology, proteomics and cryo-electron tomography, we demonstrate that the PilY1 protein and four minor pilins, which are widely conserved in T4aP systems, are essential for pilus extension in Myxococcus xanthus and form a complex that is an integral part of the T4aPM. Moreover, these proteins are part of the extended pilus. Our data support a model whereby the PilY1/minor pilin complex functions as a priming complex in T4aPM for pilus extension, a tip complex in the extended pilus for adhesion, and a cork for terminating retraction to maintain a priming complex for the next round of extension.
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Affiliation(s)
- Anke Treuner-Lange
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Yi-Wei Chang
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Boulevard, Pasadena, CA, 91125, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 422 Curie Boulevard, Philadelphia, PA, 19104, USA
| | - Timo Glatter
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Marco Herfurth
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Steffi Lindow
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Georges Chreifi
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Boulevard, Pasadena, CA, 91125, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Boulevard, Pasadena, CA, 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Lotte Søgaard-Andersen
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany.
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45
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Kyle Bennett R, Agee A, Har JRG, von Hagel B, Antoniewicz MR, Papoutsakis ET. Regulatory interventions improve the biosynthesis of limiting amino acids from methanol carbon to improve synthetic methylotrophy in Escherichia coli. Biotechnol Bioeng 2020; 118:43-57. [PMID: 32876943 DOI: 10.1002/bit.27549] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/29/2020] [Accepted: 08/26/2020] [Indexed: 12/30/2022]
Abstract
Synthetic methylotrophy aims to engineer methane and methanol utilization pathways in platform hosts like Escherichia coli for industrial bioprocessing of natural gas and biogas. While recent attempts to engineer synthetic methylotrophs have proved successful, autonomous methylotrophy, that is, the ability to utilize methane or methanol as sole carbon and energy substrates, has not yet been realized. Here, we address an important limitation of autonomous methylotrophy in E. coli: the inability of the organism to synthesize several amino acids when grown on methanol. We targeted global and local amino acid regulatory networks. Those include removal of amino acid allosteric feedback inhibition (argAH15Y , ilvAL447F , hisGE271K , leuAG462D , proBD107N , thrAS345F , trpES40F ), knockouts of transcriptional repressors (ihfA, metJ); and overexpression of amino acid biosynthetic operons (hisGDCBHAFI, leuABCD, thrABC, trpEDCBA) and transcriptional regulators (crp, purR). Compared to the parent methylotrophic E. coli strain that was unable to synthesize these amino acids from methanol carbon, these strategies resulted in improved biosynthesis of limiting proteinogenic amino acids (histidine, leucine, lysine, methionine, phenylalanine, threonine, tyrosine) from methanol carbon. In several cases, improved amino acid biosynthesis from methanol carbon led to improvements in methylotrophic growth in methanol minimal medium supplemented with a small amount of yeast extract. This study addresses a key limitation currently preventing autonomous methylotrophy in E. coli and possibly other synthetic methylotrophs and provides insight as to how this limitation can be alleviated via global and local regulatory modifications.
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Affiliation(s)
- Robert Kyle Bennett
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA.,The Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Alec Agee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA.,The Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Jie R G Har
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
| | - Bryan von Hagel
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA.,The Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
| | - Eleftherios T Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA.,The Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
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46
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Parker DJ, Lalanne JB, Kimura S, Johnson GE, Waldor MK, Li GW. Growth-Optimized Aminoacyl-tRNA Synthetase Levels Prevent Maximal tRNA Charging. Cell Syst 2020; 11:121-130.e6. [PMID: 32726597 DOI: 10.1016/j.cels.2020.07.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 05/07/2020] [Accepted: 07/02/2020] [Indexed: 01/28/2023]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) serve a dual role in charging tRNAs. Their enzymatic activities both provide protein synthesis flux and reduce uncharged tRNA levels. Although uncharged tRNAs can negatively impact bacterial growth, substantial concentrations of tRNAs remain deacylated even under nutrient-rich conditions. Here, we show that tRNA charging in Bacillus subtilis is not maximized due to optimization of aaRS production during rapid growth, which prioritizes demands in protein synthesis over charging levels. The presence of uncharged tRNAs is alleviated by precisely tuned translation kinetics and the stringent response, both insensitive to aaRS overproduction but sharply responsive to underproduction, allowing for just enough aaRS production atop a "fitness cliff." Notably, we find that the stringent response mitigates fitness defects at all aaRS underproduction levels even without external starvation. Thus, adherence to minimal, flux-satisfying protein production drives limited tRNA charging and provides a basis for the sensitivity and setpoints of an integrated growth-control network.
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Affiliation(s)
- Darren J Parker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jean-Benoît Lalanne
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Satoshi Kimura
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Grace E Johnson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Fermentative N-Methylanthranilate Production by Engineered Corynebacterium glutamicum. Microorganisms 2020; 8:microorganisms8060866. [PMID: 32521697 PMCID: PMC7356990 DOI: 10.3390/microorganisms8060866] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/02/2020] [Accepted: 06/05/2020] [Indexed: 12/20/2022] Open
Abstract
The N-functionalized amino acid N-methylanthranilate is an important precursor for bioactive compounds such as anticancer acridone alkaloids, the antinociceptive alkaloid O-isopropyl N-methylanthranilate, the flavor compound O-methyl-N-methylanthranilate, and as a building block for peptide-based drugs. Current chemical and biocatalytic synthetic routes to N-alkylated amino acids are often unprofitable and restricted to low yields or high costs through cofactor regeneration systems. Amino acid fermentation processes using the Gram-positive bacterium Corynebacterium glutamicum are operated industrially at the million tons per annum scale. Fermentative processes using C. glutamicum for N-alkylated amino acids based on an imine reductase have been developed, while N-alkylation of the aromatic amino acid anthranilate with S-adenosyl methionine as methyl-donor has not been described for this bacterium. After metabolic engineering for enhanced supply of anthranilate by channeling carbon flux into the shikimate pathway, preventing by-product formation and enhancing sugar uptake, heterologous expression of the gene anmt encoding anthranilate N-methyltransferase from Ruta graveolens resulted in production of N-methylanthranilate (NMA), which accumulated in the culture medium. Increased SAM regeneration by coexpression of the homologous adenosylhomocysteinase gene sahH improved N-methylanthranilate production. In a test bioreactor culture, the metabolically engineered C. glutamicum C1* strain produced NMA to a final titer of 0.5 g·L−1 with a volumetric productivity of 0.01 g·L−1·h−1 and a yield of 4.8 mg·g−1 glucose.
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48
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Bacterial Glycogen Provides Short-Term Benefits in Changing Environments. Appl Environ Microbiol 2020; 86:AEM.00049-20. [PMID: 32111592 DOI: 10.1128/aem.00049-20] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/26/2020] [Indexed: 11/20/2022] Open
Abstract
Changing nutritional conditions challenge microbes and shape their evolutionary optimization. Here, we used real-time metabolomics to investigate the role of glycogen in the dynamic physiological adaptation of Escherichia coli to fluctuating nutrients following carbon starvation. After the depletion of environmental glucose, we found significant metabolic activity remaining, which was linked to rapid utilization of intracellular glycogen. Glycogen was depleted by 80% within minutes of glucose starvation and was similarly replenished within minutes of glucose availability. These fast time scales of glycogen utilization correspond to the short-term benefits that glycogen provided to cells undergoing various physiological transitions. Cells capable of utilizing glycogen exhibited shorter lag times than glycogen mutants when starved between periods of exposure to different carbon sources. The ability to utilize glycogen was also important for the transition between planktonic and biofilm lifestyles and enabled increased glucose uptake during pulses of limited glucose availability. While wild-type and mutant strains exhibited comparable growth rates in steady environments, mutants deficient in glycogen utilization grew more poorly in environments that fluctuated on minute scales between carbon availability and starvation. Taken together, these results highlight an underappreciated role of glycogen in rapidly providing carbon and energy in changing environments, thereby increasing survival and competition capabilities under fluctuating and nutrient-poor conditions.IMPORTANCE Nothing is constant in life, and microbes in particular have to adapt to frequent and rapid environmental changes. Here, we used real-time metabolomics and single-cell imaging to demonstrate that the internal storage polymer glycogen plays a crucial role in such dynamic adaptations. Glycogen is depleted within minutes of glucose starvation and similarly is replenished within minutes of glucose availability. Cells capable of utilizing glycogen exhibited shorter lag times than glycogen mutants when starved between periods of exposure to different carbon sources. While wild-type and mutant strains exhibited comparable growth rates in steady environments, mutants deficient in glycogen utilization grew more poorly in environments that fluctuated on minute scales between carbon availability and starvation. These results highlight an underappreciated role of glycogen in rapidly providing carbon and energy in changing environments, thereby increasing survival and competition capabilities under fluctuating and nutrient-poor conditions.
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Schramm T, Lempp M, Beuter D, Sierra SG, Glatter T, Link H. High-throughput enrichment of temperature-sensitive argininosuccinate synthetase for two-stage citrulline production in E. coli. Metab Eng 2020; 60:14-24. [PMID: 32179161 PMCID: PMC7225747 DOI: 10.1016/j.ymben.2020.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/03/2020] [Accepted: 03/08/2020] [Indexed: 12/20/2022]
Abstract
Controlling metabolism of engineered microbes is important to modulate cell growth and production during a bioprocess. For example, external parameters such as light, chemical inducers, or temperature can act on metabolism of production strains by changing the abundance or activity of enzymes. Here, we created temperature-sensitive variants of an essential enzyme in arginine biosynthesis of Escherichia coli (argininosuccinate synthetase, ArgG) and used them to dynamically control citrulline overproduction and growth of E. coli. We show a method for high-throughput enrichment of temperature-sensitive ArgG variants with a fluorescent TIMER protein and flow cytometry. With 90 of the thus derived ArgG variants, we complemented an ArgG deletion strain showing that 90% of the strains exhibit temperature-sensitive growth and 69% of the strains are auxotrophic for arginine at 42 °C and prototrophic at 30 °C. The best temperature-sensitive ArgG variant enabled precise and tunable control of cell growth by temperature changes. Expressing this variant in a feedback-dysregulated E. coli strain allowed us to realize a two-stage bioprocess: a 33 °C growth-phase for biomass accumulation and a 39 °C stationary-phase for citrulline production. With this two-stage strategy, we produced 3 g/L citrulline during 45 h cultivation in a 1-L bioreactor. These results show that temperature-sensitive enzymes can be created en masse and that they may function as metabolic valves in engineered bacteria. Method to enrich temperature-sensitive enzymes en masse. Temperature-sensitive enzymes function as metabolic valve. Temperature controlled two-stage production of citrulline.
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Affiliation(s)
- Thorben Schramm
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany
| | - Martin Lempp
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany
| | - Dominik Beuter
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany
| | - Silvia González Sierra
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany
| | - Timo Glatter
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany
| | - Hannes Link
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany.
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50
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Lempp M, Farke N, Kuntz M, Freibert SA, Lill R, Link H. Systematic identification of metabolites controlling gene expression in E. coli. Nat Commun 2019; 10:4463. [PMID: 31578326 PMCID: PMC6775132 DOI: 10.1038/s41467-019-12474-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/11/2019] [Indexed: 01/07/2023] Open
Abstract
Metabolism controls gene expression through allosteric interactions between metabolites and transcription factors. These interactions are usually measured with in vitro assays, but there are no methods to identify them at a genome-scale in vivo. Here we show that dynamic transcriptome and metabolome data identify metabolites that control transcription factors in E. coli. By switching an E. coli culture between starvation and growth, we induce strong metabolite concentration changes and gene expression changes. Using Network Component Analysis we calculate the activities of 209 transcriptional regulators and correlate them with metabolites. This approach captures, for instance, the in vivo kinetics of CRP regulation by cyclic-AMP. By testing correlations between all pairs of transcription factors and metabolites, we predict putative effectors of 71 transcription factors, and validate five interactions in vitro. These results show that combining transcriptomics and metabolomics generates hypotheses about metabolism-transcription interactions that drive transitions between physiological states. Interactions between metabolites and transcription factors are known to control gene expression but analyzing these events at genome-scale is challenging. Here, the authors integrate dynamic metabolome and transcriptome data from E.coli to predict regulatory metabolite-transcription factor interactions.
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Affiliation(s)
- Martin Lempp
- Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Niklas Farke
- Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Michelle Kuntz
- Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Sven Andreas Freibert
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, 35033, Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, 35033, Marburg, Germany.,LOEWE Zentrum für Synthetische Mikrobiologie SYNMIKRO, Philipps-Universität Marburg, 35032, Marburg, Germany
| | - Hannes Link
- Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany. .,LOEWE Zentrum für Synthetische Mikrobiologie SYNMIKRO, Philipps-Universität Marburg, 35032, Marburg, Germany.
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