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Gaspari M, Ghiotto G, Centurion VB, Kotsopoulos T, Santinello D, Campanaro S, Treu L, Kougias PG. Decoding Microbial Responses to Ammonia Shock Loads in Biogas Reactors through Metagenomics and Metatranscriptomics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:591-602. [PMID: 38112274 PMCID: PMC10785759 DOI: 10.1021/acs.est.3c07840] [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: 09/21/2023] [Revised: 11/17/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023]
Abstract
The presence of elevated ammonia levels is widely recognized as a significant contributor to process inhibition in biogas production, posing a common challenge for biogas plant operators. The present study employed a combination of biochemical, genome-centric metagenomic and metatranscriptomic data to investigate the response of the biogas microbiome to two shock loads induced by single pulses of elevated ammonia concentrations (i.e., 1.5 g NH4+/LR and 5 g NH4+/LR). The analysis revealed a microbial community of high complexity consisting of 364 Metagenome Assembled Genomes (MAGs). The hydrogenotrophic pathway was the primary route for methane production during the entire experiment, confirming its efficiency even at high ammonia concentrations. Additionally, metatranscriptomic analysis uncovered a metabolic shift in the methanogens Methanothrix sp. MA6 and Methanosarcina flavescens MX5, which switched their metabolism from the acetoclastic to the CO2 reduction route during the second shock. Furthermore, multiple genes associated with mechanisms for maintaining osmotic balance in the cell were upregulated, emphasizing the critical role of osmoprotection in the rapid response to the presence of ammonia. Finally, this study offers insights into the transcriptional response of an anaerobic digestion community, specifically focusing on the mechanisms involved in recovering from ammonia-induced stress.
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Affiliation(s)
- Maria Gaspari
- Soil
and Water Resources Institute, Hellenic Agricultural Organisation
Dimitra, Thermi, Thessaloniki 57001, Greece
- Department
of Hydraulics, Soil Science and Agricultural Engineering, School of
Agriculture, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Gabriele Ghiotto
- Department
of Biology, University of Padova, Padova 35121, Italy
| | | | - Thomas Kotsopoulos
- Department
of Hydraulics, Soil Science and Agricultural Engineering, School of
Agriculture, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | | | | | - Laura Treu
- Department
of Biology, University of Padova, Padova 35121, Italy
| | - Panagiotis G. Kougias
- Soil
and Water Resources Institute, Hellenic Agricultural Organisation
Dimitra, Thermi, Thessaloniki 57001, Greece
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Morita Y, Yoshida A, Ye S, Tomita T, Yoshida M, Kosono S, Nishiyama M. Protein-protein interaction-mediated regulation of lysine biosynthesis of Thermus thermophilus through the function-unknown protein LysV. J GEN APPL MICROBIOL 2023; 69:91-101. [PMID: 37357393 DOI: 10.2323/jgam.2023.06.003] [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] [Indexed: 06/27/2023]
Abstract
Thermus thermophilus biosynthesizes lysine via α-aminoadipate as an intermediate using the amino-group carrier protein, LysW, to transfer the attached α-aminoadipate and its derivatives to biosynthetic enzymes. A gene named lysV, which encodes a hypothetical protein similar to LysW, is present in the lysine biosynthetic gene cluster. Although the knockout of lysV did not affect lysine auxotrophy, lysV homologs are conserved in the lysine biosynthetic gene clusters of microorganisms belonging to the phylum Deinococcus-Thermus, suggesting a functional role for LysV in lysine biosynthesis. Pulldown assays and crosslinking experiments detected interactions between LysV and all of the biosynthetic enzymes requiring LysW for reactions, and the activities of most of all these enzymes were affected by LysV. These results suggest that LysV modulates the lysine biosynthesis through protein-protein interactions.
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Affiliation(s)
- Yutaro Morita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Ayako Yoshida
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | - Siyan Ye
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Takeo Tomita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | - Minoru Yoshida
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science
| | - Saori Kosono
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | - Makoto Nishiyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
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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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Li D, Wang X, Xu X, Gu J, Yang Y, Liu T, Wang S, Chen S, Li J. Duck Complement Factor H Binds to Outer Membrane Protein Omp24 of Riemerella anatipestifer. Avian Dis 2021; 65:261-268. [PMID: 34412457 DOI: 10.1637/0005-2086-65.2.261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 03/29/2021] [Indexed: 11/05/2022]
Abstract
The resistance to serum complement-mediated killing is a vital virulence property of microbial pathogens. Complement factor H (FH) is a key negative regulator of the complement alternative pathway (AP) that prevents formation and accelerates the decay of AP C3 convertase and acts as a cofactor in the inactivation of C3b. Pathogens can recruit host FH through their surface proteins to escape the clearance of the complement system. Riemerella anatipestifer could also evade the complement system attack to achieve host infection, but the mechanism is still unclear. In this study, the R. anatipestifer proteins that could interact with FH in host serum were screened and analyzed, and the functions were determined. Affinity chromatography with a Ni-nitrilotriacetic acid Sefinose column and mass spectrometry identified three outer membrane proteins (Omp) of R. anatipestifer, Omp54, Omp53, and Omp24, as potential FH-binding proteins. We then successfully conducted the prokaryotic expression and polyclonal antibody preparation of three candidate proteins. Indirect immunofluorescence assay showed that three candidate proteins were all present in R. anatipestifer. The affinity blotting assay, anti-serum-inhibiting assay, and serum bactericidal assay presented evidence that Omp24 could bind FH. Moreover, FH bound to Omp24 was associated with resistance to the alternative pathway and functional for R. anatipestifer survival in the normal duck serum. These results suggested that R. anatipestifer Omp24 was a FH-binding protein and the interaction with FH blocked the alternative pathway. Recruitment of complement regulatory proteins may facilitate better R. anatipestifer resistance to this vital line of host defense.
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Affiliation(s)
- Delong Li
- College of Veterinary Medicine, Southwest University, Chongqing 402460, People's Republic of China.,Immunology Research Center, Medical Research Institute, Southwest University, Chongqing 402460, People's Republic of China
| | - Xiangli Wang
- College of Veterinary Medicine, Southwest University, Chongqing 402460, People's Republic of China
| | - Xingsheng Xu
- College of Veterinary Medicine, Southwest University, Chongqing 402460, People's Republic of China
| | - Jiulong Gu
- College of Veterinary Medicine, Southwest University, Chongqing 402460, People's Republic of China
| | - Yunchuan Yang
- College of Veterinary Medicine, Southwest University, Chongqing 402460, People's Republic of China
| | - Ting Liu
- College of Veterinary Medicine, Southwest University, Chongqing 402460, People's Republic of China
| | - Siyuan Wang
- College of Veterinary Medicine, Southwest University, Chongqing 402460, People's Republic of China
| | - Sihuai Chen
- College of Veterinary Medicine, Southwest University, Chongqing 402460, People's Republic of China.,Immunology Research Center, Medical Research Institute, Southwest University, Chongqing 402460, People's Republic of China
| | - Jixiang Li
- College of Veterinary Medicine, Southwest University, Chongqing 402460, People's Republic of China, .,Immunology Research Center, Medical Research Institute, Southwest University, Chongqing 402460, People's Republic of China
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Espina G, Atalah J, Blamey JM. Extremophilic Oxidoreductases for the Industry: Five Successful Examples With Promising Projections. Front Bioeng Biotechnol 2021; 9:710035. [PMID: 34458243 PMCID: PMC8387880 DOI: 10.3389/fbioe.2021.710035] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 06/30/2021] [Indexed: 11/29/2022] Open
Abstract
In a global context where the development of more environmentally conscious technologies is an urgent need, the demand for enzymes for industrial processes is on the rise. Compared to conventional chemical catalysts, the implementation of biocatalysis presents important benefits including higher selectivity, increased sustainability, reduction in operating costs and low toxicity, which translate into cleaner production processes, lower environmental impact as well as increasing the safety of the operating staff. Most of the currently available commercial enzymes are of mesophilic origin, displaying optimal activity in narrow ranges of conditions, which limits their actual application under industrial settings. For this reason, enzymes from extremophilic microorganisms stand out for their specific characteristics, showing higher stability, activity and robustness than their mesophilic counterparts. Their unique structural adaptations allow them to resist denaturation at high temperatures and salinity, remain active at low temperatures, function at extremely acidic or alkaline pHs and high pressure, and participate in reactions in organic solvents and unconventional media. Because of the increased interest to replace chemical catalysts, the global enzymes market is continuously growing, with hydrolases being the most prominent type of enzymes, holding approximately two-third share, followed by oxidoreductases. The latter enzymes catalyze electron transfer reactions and are one of the most abundant classes of enzymes within cells. They hold a significant industrial potential, especially those from extremophiles, as their applications are multifold. In this article we aim to review the properties and potential applications of five different types of extremophilic oxidoreductases: laccases, hydrogenases, glutamate dehydrogenases (GDHs), catalases and superoxide dismutases (SODs). This selection is based on the extensive experience of our research group working with these particular enzymes, from the discovery up to the development of commercial products available for the research market.
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Affiliation(s)
| | | | - Jenny M. Blamey
- Fundación Biociencia, Santiago, Chile
- Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
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Zhao Y, Gao J, Su S, Shan X, Li S, Liu H, Yuan Y, Li H. Regulation of the activity of maize glutamate dehydrogenase by ammonium and potassium. Biosci Biotechnol Biochem 2021; 85:262-271. [PMID: 33604622 DOI: 10.1093/bbb/zbaa020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/18/2020] [Indexed: 11/14/2022]
Abstract
Glutamate dehydrogenase (GDH) is an important enzyme in ammonium metabolism, the activity of which is regulated by multiple factors. In this study, we investigate the effects of ammonium and potassium on the activity of maize GDH. Our results show that both ammonium and potassium play multiple roles in regulating the activity of maize GDH, with the specific roles depending on the concentration of potassium. Together with the structural information of GDH, we propose models for the substrate inhibition of ammonium, and the elimination of substrate inhibition by potassium. These models are supported by the analysis of statistic thermodynamics. We also analyze the binding sites of ammonium and potassium on maize GDH, and the conformational changes of maize GDH. The findings provide insight into the regulation of maize GDH activity by ammonium and potassium and reveal the importance of the dose and ratio of nitrogen and potassium in crop cultivation.
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Affiliation(s)
- Yanjie Zhao
- College of Plant Science, Jilin University, Changchun, China
| | - Jie Gao
- College of Plant Science, Jilin University, Changchun, China
| | - Shengzhong Su
- College of Plant Science, Jilin University, Changchun, China
| | - Xiaohui Shan
- College of Plant Science, Jilin University, Changchun, China
| | - Shipeng Li
- College of Plant Science, Jilin University, Changchun, China
| | - Hongkui Liu
- College of Plant Science, Jilin University, Changchun, China
| | - Yaping Yuan
- College of Plant Science, Jilin University, Changchun, China
| | - He Li
- College of Plant Science, Jilin University, Changchun, China
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Iacobucci I, Monaco V, Cozzolino F, Monti M. From classical to new generation approaches: An excursus of -omics methods for investigation of protein-protein interaction networks. J Proteomics 2020; 230:103990. [PMID: 32961344 DOI: 10.1016/j.jprot.2020.103990] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/11/2020] [Accepted: 08/31/2020] [Indexed: 01/24/2023]
Abstract
Functional Proteomics aims to the identification of in vivo protein-protein interaction (PPI) in order to piece together protein complexes, and therefore, cell pathways involved in biological processes of interest. Over the years, proteomic approaches used for protein-protein interaction investigation have relied on classical biochemical protocols adapted to a global overview of protein-protein interactions, within so-called "interactomics" investigation. In particular, their coupling with advanced mass spectrometry instruments and innovative analytical methods led to make great strides in the PPIs investigation in proteomics. In this review, an overview of protein complexes purification strategies, from affinity purification approaches, including proximity-dependent labeling techniques and cross-linking strategy for the identification of transient interactions, to Blue Native Gel Electrophoresis (BN-PAGE) and Size Exclusion Chromatography (SEC) employed in the "complexome profiling", has been reported, giving a look to their developments, strengths and weakness and providing to readers several recent applications of each strategy. Moreover, a section dedicated to bioinformatic databases and platforms employed for protein networks analyses was also included.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Vittoria Monaco
- CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Flora Cozzolino
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.
| | - Maria Monti
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.
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