1
|
Tian S, Zhao G, Lv G, Wu C, Su R, Wang F, Wang Z, Liu Y, Chen N, Li Y. Efficient Fermentative Production of d-Alanine and Other d-Amino Acids by Metabolically Engineered Corynebacterium glutamicum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8039-8051. [PMID: 38545740 DOI: 10.1021/acs.jafc.4c00914] [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: 04/11/2024]
Abstract
d-Amino acids (d-AAs) have wide applications in industries such as pharmaceutical, food, and cosmetics due to their unique properties. Currently, the production of d-AAs has relied on chemical synthesis or enzyme catalysts, and it is challenging to produce d-AAs via direct fermentation from glucose. We observed that Corynebacterium glutamicum exhibits a remarkable tolerance to high concentrations of d-Ala, a crucial characteristic for establishing a successful fermentation process. By optimizing meso-diaminopilmelate dehydrogenases in different C. glutamicum strains and successively deleting l-Ala biosynthetic pathways, we developed an efficient d-Ala fermentation system. The d-Ala titer was enhanced through systems metabolic engineering, which involved strengthening glucose assimilation and pyruvate supply, reducing the formation of organic acid byproducts, and attenuating the TCA cycle. During fermentation in a 5-L bioreactor, a significant accumulation of l-Ala was observed in the broth, which was subsequently diminished by introducing an l-amino acid deaminase. Ultimately, the engineered strain DA-11 produced 85 g/L d-Ala with a yield of 0.30 g/g glucose, accompanied by an optical purity exceeding 99%. The fermentation platform has the potential to be extended for the synthesis of other d-AAs, as demonstrated by the production of d-Val and d-Glu.
Collapse
Affiliation(s)
- Siyu Tian
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Guihong Zhao
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Gengcheng Lv
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Chen Wu
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Rui Su
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Feiao Wang
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Zeting Wang
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Yuexiang Liu
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Ning Chen
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Yanjun Li
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| |
Collapse
|
2
|
Raevsky A, Kovalenko O, Bulgakov E, Sharifi M, Volochnyuk D, Tukalo M. Developing a comprehensive solution aimed to disrupt LARS1/RagD protein-protein interaction. J Biomol Struct Dyn 2024; 42:747-758. [PMID: 36995308 DOI: 10.1080/07391102.2023.2194996] [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: 12/27/2022] [Accepted: 03/18/2023] [Indexed: 03/31/2023]
Abstract
Aminoacyl-tRNA synthetases are crucial enzymes involved in protein synthesis and various cellular physiological reactions. Aside from their standard role in linking amino acids to the corresponding tRNAs, they also impact protein homeostasis by controlling the level of soluble amino acids within the cell. For instance, leucyl-tRNA synthetase (LARS1) acts as a leucine sensor for the mammalian target of rapamycin complex 1 (mTORC1), and may also function as a probable GTPase-activating protein (GAP) for the RagD subunit of the heteromeric activator of mTORC1. In turn, mTORC1 regulates cellular processes, such as protein synthesis, autophagy, and cell growth, and is implicated in various human diseases including cancer, obesity, diabetes, and neurodegeneration. Hence, inhibitors of mTORC1 or a deregulated mTORC1 pathway may offer potential cancer therapies. In this study, we investigated the structural requirements for preventing the sensing and signal transmission from LARS to mTORC1. Building upon recent studies on mTORC1 regulation activation by leucine, we lay the foundation for the development of chemotherapeutic agents against mTORC1 that can overcome resistance to rapamycin. Using a combination of in-silico approaches to develop and validate an alternative interaction model, discussing its benefits and advancements. Finally, we identified a set of compounds ready for testing to prevent LARS1/RagD protein-protein interactions. We establish a basis for creating chemotherapeutic drugs targeting mTORC1, which can conquer resistance to rapamycin. We utilize in-silico methods to generate and confirm an alternative interaction model, outlining its advantages and improvements, and pinpoint a group of novel substances that can prevent LARS1/RagD interactions.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Alexey Raevsky
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Enamine Ltd, Kyiv, Ukraine
| | - Oksana Kovalenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Elijah Bulgakov
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | | | - Dmityi Volochnyuk
- Enamine Ltd, Kyiv, Ukraine
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Michael Tukalo
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| |
Collapse
|
3
|
Aboelnga MM, Gauld JW. Screening a library of potential competitive inhibitors against bacterial threonyl-tRNA synthetase: DFT calculations. J Biomol Struct Dyn 2023:1-9. [PMID: 37909495 DOI: 10.1080/07391102.2023.2276878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/24/2023] [Indexed: 11/03/2023]
Abstract
Due to the growing interest in directing aminoacyl-tRNA synthetases for antimicrobial therapies, evaluating the binding proficiency of potential inhibitors against this target holds significant importance. In this work, we proposed potential ligands that could properly bind to the crucial Zn(II) cofactor located in the active site of Threonyl-tRNA synthetases (ThrRS), potentially functioning as competitive inhibitors. Initially, detailed DFT quantum chemical study was conducted to examine the binding ability of threonine against unnatural amino acids to cofactor Zn(II). Then, the binding energy value for each suggested ligand has been determined and compared to the value determined for the native substrate, threonine. Our screening investigation showed that the native threonine should coordinate in a bidentate fashion to this Zn(II) which lead to the highest (binding energy) BE Thereby, the synthetic site of ThrRS rejects unnatural amino acids that cannot afford this type of coordination to Zn(II) ion which has been supported by our calculations. Moreover, based on their binding to the Zn(II) and the obtained BE values compared to the cognate threonine, many potent ligands have been suggested. Importantly, ligands with deprotonated warheads showed the highest binding ability amongst a list of potential hits. Further investigation on the selected ligands using molecular docking and QM/MM calculations confirmed our findings of the suggested ligands being able to bind efficiently in the active site of ThrRS. The suggested hits from this study should be valuable in paving routs for developing candidates as competitive inhibitors against the bacterial ThrRS.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Mohamed M Aboelnga
- Department of Chemistry, Faculty of Science, Damietta University, New Damietta, Egypt
| | - James W Gauld
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Canada
| |
Collapse
|
4
|
Jiang HK, Weng JH, Wang YH, Tsou JC, Chen PJ, Ko ALA, Söll D, Tsai MD, Wang YS. Rational design of the genetic code expansion toolkit for in vivo encoding of D-amino acids. Front Genet 2023; 14:1277489. [PMID: 37904728 PMCID: PMC10613524 DOI: 10.3389/fgene.2023.1277489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/18/2023] [Indexed: 11/01/2023] Open
Abstract
Once thought to be non-naturally occurring, D-amino acids (DAAs) have in recent years been revealed to play a wide range of physiological roles across the tree of life, including in human systems. Synthetic biologists have since exploited DAAs' unique biophysical properties to generate peptides and proteins with novel or enhanced functions. However, while peptides and small proteins containing DAAs can be efficiently prepared in vitro, producing large-sized heterochiral proteins poses as a major challenge mainly due to absence of pre-existing DAA translational machinery and presence of endogenous chiral discriminators. Based on our previous work demonstrating pyrrolysyl-tRNA synthetase's (PylRS') remarkable substrate polyspecificity, this work attempts to increase PylRS' ability in directly charging tRNAPyl with D-phenylalanine analogs (DFAs). We here report a novel, polyspecific Methanosarcina mazei PylRS mutant, DFRS2, capable of incorporating DFAs into proteins via ribosomal synthesis in vivo. To validate its utility, in vivo translational DAA substitution were performed in superfolder green fluorescent protein and human heavy chain ferritin, successfully altering both proteins' physiochemical properties. Furthermore, aminoacylation kinetic assays further demonstrated aminoacylation of DFAs by DFRS2 in vitro.
Collapse
Affiliation(s)
- Han-Kai Jiang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Taiwan International Graduate Program Chemical Biology and Molecular Biophysics, Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Jui-Hung Weng
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yi-Hui Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Jo-Chu Tsou
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Pei-Jung Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - An-Li Andrea Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yane-Shih Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Taiwan International Graduate Program Chemical Biology and Molecular Biophysics, Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
5
|
Gill B, Schwecht I, Rahman N, Dhawan T, Verschoor C, Nazli A, Kaushic C. Metabolic signature for a dysbiotic microbiome in the female genital tract: A systematic review and meta-analysis. Am J Reprod Immunol 2023; 90:e13781. [PMID: 37766408 DOI: 10.1111/aji.13781] [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: 04/14/2023] [Revised: 07/06/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND The vaginal microbiome (VMB) is a critical determinant of reproductive health, where a microbial shift towards a dysbiotic environment has implications for susceptibility to, and clinical presentation of sexually transmitted infections (STIs). Metabolomic profiling of the vaginal microenvironment has led to the identification of metabolic responses to clinical conditions of dysbiosis. However, no studies have examined metabolic markers that are common across conditions and can serve as a signature for vaginal dysbiosis. METHOD OF STUDY We have conducted a comprehensive systematic review and meta-analysis to identify consistently deregulated metabolites along with their impact on host and microbial metabolism during dysbiosis. We employed two complementary approaches including a vote counting analysis for all eligible studies identified in the systematic review, in addition to a meta-analysis for a subset of studies with sufficient available data. Significantly deregulated metabolites were then selected for pathway enrichment analysis. RESULTS Our results revealed a total of 502 altered metabolites reported across 10 dysbiotic conditions from 16 studies. Following a rigorous, collective analysis, six metabolites which were consistently downregulated and could be generalized to all dysbiotic conditions were identified. In addition, five downregulated and one upregulated metabolite was identified from a bacterial vaginosis (BV) focused sub-analysis. These metabolites have the potential to serve as a metabolic signature for vaginal dysbiosis. Their role in eight altered metabolic pathways indicates a disruption of amino acid, carbohydrate, and energy metabolism during dysbiosis. CONCLUSION Based on this analysis, we propose a schematic model outlining the common metabolic perturbations associated with vaginal dysbiosis, which can be potential targets for therapeutics and prophylaxis.
Collapse
Affiliation(s)
- Biban Gill
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Center, Michael G. DeGroote Center for Learning and Discovery, McMaster University, Hamilton, ON, Canada
| | - Ingrid Schwecht
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Center, Michael G. DeGroote Center for Learning and Discovery, McMaster University, Hamilton, ON, Canada
| | - Nuzhat Rahman
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Center, Michael G. DeGroote Center for Learning and Discovery, McMaster University, Hamilton, ON, Canada
| | - Tushar Dhawan
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Center, Michael G. DeGroote Center for Learning and Discovery, McMaster University, Hamilton, ON, Canada
| | - Chris Verschoor
- Health Sciences North Research Institute, Northern Ontario School of Medicine, Sudbury, ON, Canada
| | - Aisha Nazli
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Center, Michael G. DeGroote Center for Learning and Discovery, McMaster University, Hamilton, ON, Canada
| | - Charu Kaushic
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Center, Michael G. DeGroote Center for Learning and Discovery, McMaster University, Hamilton, ON, Canada
| |
Collapse
|
6
|
Giegé R, Eriani G. The tRNA identity landscape for aminoacylation and beyond. Nucleic Acids Res 2023; 51:1528-1570. [PMID: 36744444 PMCID: PMC9976931 DOI: 10.1093/nar/gkad007] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 02/07/2023] Open
Abstract
tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.
Collapse
Affiliation(s)
- Richard Giegé
- Correspondence may also be addressed to Richard Giegé.
| | | |
Collapse
|
7
|
Rayevsky A, Sharifi M, Demianenko E, Volochnyuk D, Tukalo M. Effect of Charge Distribution in a Modified tRNA Substrate on Pre-Reaction Protein-tRNA Complex Geometry. ACS OMEGA 2021; 6:4227-4235. [PMID: 33644545 PMCID: PMC7906584 DOI: 10.1021/acsomega.0c05143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
An important aspect of molecular mechanics simulations of a protein structure and ligand binding often involves the generation of reliable force fields for nonstandard residues and ligands. We consider the aminoacyl-tRNA synthetase (AaRS) system that involves nucleic acid and amino acid derivatives, obtaining force field atomic charges using the restrained electrostatic potential (RESP) approach. These charges are shown to predict observed properties of the post-transfer editing reaction in this system, in contrast to simulations performed using approximate charges conceived based upon standard charges for related systems present in force field databases. In particular, the simulations predicted key properties induced by mutation. The approach taken for generating the RESP charges retains established charges for known fragments, defining new charges only for the novel chemical features present in the modified residues. This approach is of general relevance for the design of force fields for pharmacological applications, and indeed the AaRS target system is itself relevant to antibiotics development.
Collapse
Affiliation(s)
- Alexey Rayevsky
- Department
of Protein Synthesis Enzymology, Institute
of Molecular Biology and Genetics National Academy of Sciences of
Ukraine, Osipovskogo
st. 2a, Kyiv, UA 03143, Ukraine
- Laboratory
of Bioinformatics and Structural Biology, Institute of Food Biotechnology and Genomics National Academy of
Sciences, Osipovskogo 2a Str., Kyiv, 04123, Ukraine
| | - Mohsen Sharifi
- RockGen
Therapeutics, #831 Bioventure,
4301 W. Markham St., Little Rock, Arkansas 72205, United
States
| | - Eugeniy Demianenko
- Chuiko
Institute of Surface Chemistry of National Academy of Sciences of
Ukraine, 17 General Naumov Str., Kyiv 03164, Ukraine
| | - Dmitriy Volochnyuk
- Department
of Biologically Active Compounds, Institute
of Organic Chemistry NASU, Murmanskaya 5 str, Kyiv, 02660, Ukraine
- Enamine
Ltd, 78 Chervonotkatska
Str, Kyiv, UA 02660, Ukraine
| | - Michael Tukalo
- Department
of Protein Synthesis Enzymology, Institute
of Molecular Biology and Genetics National Academy of Sciences of
Ukraine, Osipovskogo
st. 2a, Kyiv, UA 03143, Ukraine
| |
Collapse
|