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Hernández-Herreros N, Rodríguez A, Galán B, Auxiliadora Prieto M. Boosting hydrogen production in Rhodospirillum rubrum by syngas-driven photoheterotrophic adaptive evolution. BIORESOURCE TECHNOLOGY 2024; 406:130972. [PMID: 38876276 DOI: 10.1016/j.biortech.2024.130972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 06/16/2024]
Abstract
Rhodospirillum rubrum is a photosynthetic purple non-sulphur bacterium with great potential to be used for complex waste valorisation in biotechnological applications due to its metabolic versatility. This study investigates the production of hydrogen (H2) and polyhydroxyalkanoates (PHA) by R. rubrum from syngas under photoheterotrophic conditions. An adaptive laboratory evolution strategy (ALE) has been carried out to improve the yield of the process. After 200 generations, two evolved strains were selected that showed reduced lag phase and enhanced poly-3-hydroxybutyrate (PHB) and H2 synthesis compared to the parental strain. Genomic analysis of the photo-adapted (PA) variants showed four genes with single point mutations, including the photosynthesis gene expression regulator PpsR. The proteome of the variants suggested that the adapted variants overproduced H2 due to a more efficient CO oxidation through the CO-dehydrogenase enzyme complex and confirmed that energy acquisition was enhanced through overexpression of the photosynthetic system and metal cofactors essential for pigment biosynthesis.
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Affiliation(s)
- Natalia Hernández-Herreros
- Microbial & Plant Biotechnology Department, Polymer Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Alberto Rodríguez
- Microbial & Plant Biotechnology Department, Polymer Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Beatriz Galán
- Microbial & Plant Biotechnology Department, Environmental Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
| | - M Auxiliadora Prieto
- Microbial & Plant Biotechnology Department, Polymer Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain.
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Aleshina YA, Aleshin VA. Evolutionary Changes in Primate Glutamate Dehydrogenases 1 and 2 Influence the Protein Regulation by Ligands, Targeting and Posttranslational Modifications. Int J Mol Sci 2024; 25:4341. [PMID: 38673928 PMCID: PMC11050691 DOI: 10.3390/ijms25084341] [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: 03/15/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
There are two paralogs of glutamate dehydrogenase (GDH) in humans encoded by the GLUD1 and GLUD2 genes as a result of a recent retroposition during the evolution of primates. The two human GDHs possess significantly different regulation by allosteric ligands, which is not fully characterized at the structural level. Recent advances in identification of the GDH ligand binding sites provide a deeper perspective on the significance of the accumulated substitutions within the two GDH paralogs. In this review, we describe the evolution of GLUD1 and GLUD2 after the duplication event in primates using the accumulated sequencing and structural data. A new gibbon GLUD2 sequence questions the indispensability of ancestral R496S and G509A mutations for GLUD2 irresponsiveness to GTP, providing an alternative with potentially similar regulatory features. The data of both GLUD1 and GLUD2 evolution not only confirm substitutions enhancing GLUD2 mitochondrial targeting, but also reveal a conserved mutation in ape GLUD1 mitochondrial targeting sequence that likely reduces its transport to mitochondria. Moreover, the information of GDH interactors, posttranslational modification and subcellular localization are provided for better understanding of the GDH mutations. Medically significant point mutations causing deregulation of GDH are considered from the structural and regulatory point of view.
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Affiliation(s)
- Yulia A. Aleshina
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Vasily A. Aleshin
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Sechenov First Moscow State Medical University, 119048 Moscow, Russia
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CryoEM structural exploration of catalytically active enzyme pyruvate carboxylase. Nat Commun 2022; 13:6185. [PMID: 36261450 PMCID: PMC9581989 DOI: 10.1038/s41467-022-33987-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/04/2022] [Indexed: 12/24/2022] Open
Abstract
Pyruvate carboxylase (PC) is a tetrameric enzyme that contains two active sites per subunit that catalyze two consecutive reactions. A mobile domain with an attached prosthetic biotin links both reactions, an initial biotin carboxylation and the subsequent carboxyl transfer to pyruvate substrate to produce oxaloacetate. Reaction sites are at long distance, and there are several co-factors that play as allosteric regulators. Here, using cryoEM we explore the structure of active PC tetramers focusing on active sites and on the conformational space of the oligomers. The results capture the mobile domain at both active sites and expose catalytic steps of both reactions at high resolution, allowing the identification of substrates and products. The analysis of catalytically active PC tetramers reveals the role of certain motions during enzyme functioning, and the structural changes in the presence of additional cofactors expose the mechanism for allosteric regulation.
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Aleshin VA, Bunik VI, Bruch EM, Bellinzoni M. Structural Basis for the Binding of Allosteric Activators Leucine and ADP to Mammalian Glutamate Dehydrogenase. Int J Mol Sci 2022; 23:ijms231911306. [PMID: 36232607 PMCID: PMC9570180 DOI: 10.3390/ijms231911306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Glutamate dehydrogenase (GDH) plays a key role in the metabolism of glutamate, an important compound at a cross-road of carbon and nitrogen metabolism and a relevant neurotransmitter. Despite being one of the first discovered allosteric enzymes, GDH still poses challenges for structural characterization of its allosteric sites. Only the structures with ADP, and at low (3.5 Å) resolution, are available for mammalian GDH complexes with allosteric activators. Here, we aim at deciphering a structural basis for the GDH allosteric activation using bovine GDH as a model. For the first time, we report a mammalian GDH structure in a ternary complex with the activators leucine and ADP, co-crystallized with potassium ion, resolved to 2.45 Å. An improved 2.4-angstrom resolution of the GDH complex with ADP is also presented. The ternary complex with leucine and ADP differs from the binary complex with ADP by the conformation of GDH C-terminus, involved in the leucine binding and subunit interactions. The potassium site, identified in this work, may mediate interactions between the leucine and ADP binding sites. Our data provide novel insights into the mechanisms of GDH activation by leucine and ADP, linked to the enzyme regulation by (de)acetylation.
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Affiliation(s)
- Vasily A. Aleshin
- Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Sechenov University, 119048 Moscow, Russia
| | - Victoria I. Bunik
- Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Sechenov University, 119048 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Correspondence: (V.I.B.); (M.B.); Tel.: +7-495-9394484 (V.I.B.); +33-1-45688608 (M.B.)
| | - Eduardo M. Bruch
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75724 Paris, France
| | - Marco Bellinzoni
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75724 Paris, France
- Correspondence: (V.I.B.); (M.B.); Tel.: +7-495-9394484 (V.I.B.); +33-1-45688608 (M.B.)
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Zheng X, Lin Z, Lu J, Ye R, Qu M, Wang J, Xu G, Ying Z, Chen S. De novo transcriptome analysis reveals the molecular regulatory mechanism underlying the response to excess nitrogen in Azolla spp. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 248:106202. [PMID: 35623198 DOI: 10.1016/j.aquatox.2022.106202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 03/30/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Phytoremediation potential of Azolla in removal of nitrogen from wastewater has been promising. However, little is known about the response of Azolla to high concentrations of nitrogen. In this study, the responses of four Azolla species to different concentrations of total nitrogen ranging from 0 to 180 mg L-1 were examined. The responses varied among different species, and the high nitrogen-tolerant species A. caroliniana and A. microphylla could remove nitrogen from aqueous solutions with higher efficiencies. We further performed transcriptome analysis to explore the molecular mechanism underlying the response to high nitrogen stress in Azolla. RNA-seq analysis revealed a synergistic regulatory network of differentially expressed genes (DEGs) involved in nitrogen transport and metabolism in A. microphylla, mainly in the roots. Under high nitrogen treatment, the DEGs encoding nitrate transporters or nitrate transporter 1/peptide transporters (NRTs/NPFs), ammonium transporters (AMTs), nitrate reductase (NIA), nitrite reductase (NIR) and glutamine synthetases/glutamate synthases (GSs/GOGATs) were down-regulated, and the DEGs encoding glutamate dehydrogenases (GDHs) were up-regulated, suggesting that A. microphylla possessed high tolerance against excess nitrogen through down-regulation of nitrate and ammonium uptake and fine regulation of nitrogen assimilation in the roots. Our results provided a theoretical foundation for better utilization of Azolla for wastewater treatment.
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Affiliation(s)
- Xiangli Zheng
- National Azolla Germplasm Center, Agricultural Ecology Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Zhongyuan Lin
- Marine Biotechnology Center, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China; Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Jianjun Lu
- Marine Biotechnology Center, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China; Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Rongrong Ye
- Marine Biotechnology Center, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China; Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Mengyu Qu
- Marine Biotechnology Center, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China; Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Junhong Wang
- National Azolla Germplasm Center, Agricultural Ecology Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Guozhong Xu
- National Azolla Germplasm Center, Agricultural Ecology Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Zhaoyang Ying
- National Azolla Germplasm Center, Agricultural Ecology Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China.
| | - Songbiao Chen
- Marine Biotechnology Center, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China; Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China.
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