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Thitiprasert S, Jaiaue P, Amornbunchai N, Thammakes J, Piluk J, Srimongkol P, Tanasupawat S, Thongchul N. Association between organic nitrogen substrates and the optical purity of D-lactic acid during the fermentation by Sporolactobacillus terrae SBT-1. Sci Rep 2024; 14:10522. [PMID: 38719898 PMCID: PMC11079031 DOI: 10.1038/s41598-024-61247-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 05/03/2024] [Indexed: 05/12/2024] Open
Abstract
The development of biotechnological lactic acid production has attracted attention to the potential production of an optically pure isomer of lactic acid, although the relationship between fermentation and the biosynthesis of highly optically pure D-lactic acid remains poorly understood. Sporolactobacillus terrae SBT-1 is an excellent D-lactic acid producer that depends on cultivation conditions. Herein, three enzymes responsible for synthesizing optically pure D-lactic acid, including D-lactate dehydrogenase (D-LDH; encoded by ldhDs), L-lactate dehydrogenase (L-LDH; encoded by ldhLs), and lactate racemase (Lar; encoded by larA), were quantified under different organic nitrogen sources and concentration to study the relationship between fermentation conditions and synthesis pathway of optically pure lactic acid. Different organic nitrogen sources and concentrations significantly affected the quantity and quality of D-lactic acid produced by strain SBT-1 as well as the synthetic optically pure lactic acid pathway. Yeast extract is a preferred organic nitrogen source for achieving high catalytic efficiency of D-lactate dehydrogenase and increasing the transcription level of ldhA2, indicating that this enzyme plays a major role in D-lactic acid formation in S. terrae SBT-1. Furthermore, lactate racemization activity could be regulated by the presence of D-lactic acid. The results of this study suggest that specific nutrient requirements are necessary to achieve a stable and highly productive fermentation process for the D-lactic acid of an individual strain.
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Affiliation(s)
- Sitanan Thitiprasert
- Center of Excellence in Bioconversion and Bioseparation for Platform Chemical Production, Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand.
- Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand.
| | - Phetcharat Jaiaue
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand
| | - Nichakorn Amornbunchai
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand
| | - Jesnipit Thammakes
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand
| | - Jirabhorn Piluk
- Center of Excellence in Bioconversion and Bioseparation for Platform Chemical Production, Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand
- Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand
| | - Piroonporn Srimongkol
- Center of Excellence in Bioconversion and Bioseparation for Platform Chemical Production, Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand
- Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand
| | - Somboon Tanasupawat
- Center of Excellence in Bioconversion and Bioseparation for Platform Chemical Production, Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand
| | - Nuttha Thongchul
- Center of Excellence in Bioconversion and Bioseparation for Platform Chemical Production, Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand.
- Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand.
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Schütterle DM, Hegner R, Temovska M, Ortiz-Ardila AE, Angenent LT. Exclusive D-lactate-isomer production during a reactor-microbiome conversion of lactose-rich waste by controlling pH and temperature. WATER RESEARCH 2024; 250:121045. [PMID: 38159537 DOI: 10.1016/j.watres.2023.121045] [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: 10/11/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
Lactate is among the top-ten-biobased products. It occurs naturally as D- or L-isomer and as a racemic mixture (DL-lactate). Generally, lactate with a high optical purity is more valuable. In searching for suitable renewable feedstocks for lactate production, unutilized organic waste streams are increasingly coming into focus. Here, we investigated acid whey, which is a lactose-rich byproduct of yogurt production, that represents a considerable environmental footprint for the dairy industry. We investigated the steering of the lactate-isomer composition in a continuous and open culture system (HRT = 0.6 d) at different pH values (pH 5.0 vs. pH 6.5) and process temperatures (38°C to 50°C). The process startup was achieved by autoinoculation. At a pH of 5.0 and a temperature of 47°C-50°C, exclusive D-lactate production occurred because of the dominance of Lactobacillus spp. (> 95% of relative abundance). The highest volumetric D-lactate production rate of 722 ± 94.6 mmol C L-1 d-1 (0.90 ± 0.12 g L-1 h-1), yielding 0.93 ± 0.15 mmol C mmol C-1, was achieved at a pH of 5.0 and a temperature of 44°C (n = 18). At a pH of 6.5 and a temperature of 44°C, we found a mixture of DL-lactate (average D-to-L-lactate production rate ratio of 1.69 ± 0.90), which correlated with a high abundance of Streptococcus spp. and Enterococcus spp. However, exclusive L-lactate production could not be achieved. Our results show that for the continuous conversion of lactose-rich dairy waste streams, the pH was a critical process parameter to control the yield of lactate isomers by influencing the composition of the microbiota. In contrast, temperature adjustments allowed the improvement of bioprocess kinetics.
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Affiliation(s)
- Dorothea M Schütterle
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
| | - Richard Hegner
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
| | - Monika Temovska
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstr. 94-96, Tübingen 72076, Germany; AG Angenent, Max Planck Institute for Biology, Max Planck Ring 5, Tübingen 72076, Germany
| | - Andrés E Ortiz-Ardila
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
| | - Largus T Angenent
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstr. 94-96, Tübingen 72076, Germany; AG Angenent, Max Planck Institute for Biology, Max Planck Ring 5, Tübingen 72076, Germany; Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds vej 10D, Aarhus C 8000, Denmark; The Novo Nordisk Foundation CO2 Research Center (CORC), Aarhus University, Gustav Wieds vej 10C, Aarhus C 8000, Denmark; Cluster of Excellence - Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, Tübingen 72074, Germany.
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Zecchin P, Pecqueur L, Oltmanns J, Velours C, Schünemann V, Fontecave M, Golinelli‐Pimpaneau B. Structure-based insights into the mechanism of [4Fe-4S]-dependent sulfur insertase LarE. Protein Sci 2024; 33:e4874. [PMID: 38100250 PMCID: PMC10806937 DOI: 10.1002/pro.4874] [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: 09/05/2023] [Revised: 11/28/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Several essential cellular metabolites, such as enzyme cofactors, contain sulfur atoms and their biosynthesis requires specific thiolation enzymes. LarE is an ATP-dependent sulfur insertase, which catalyzes the sequential conversion of the two carboxylate groups of the precursor of the lactate racemase cofactor into thiocarboxylates. Two types of LarE enzymes are known, one that uses a catalytic cysteine as a sacrificial sulfur donor, and the other one that uses a [4Fe-4S] cluster as a cofactor. Only the crystal structure of LarE from Lactobacillus plantarum (LpLarE) from the first class has been solved. We report here the crystal structure of LarE from Methanococcus maripaludis (MmLarE), belonging to the second class, in the cluster-free (apo-) and cluster-bound (holo-) forms. The structure of holo-MmLarE shows that the [4Fe-4S] cluster is chelated by three cysteines only, leaving an open coordination site on one Fe atom. Moreover, the fourth nonprotein-bonded iron atom was able to bind an anionic ligand such as a phosphate group or a chloride ion. Together with the spectroscopic analysis of holo-MmLarE and the previously reported biochemical investigations of holo-LarE from Thermotoga maritima, these crystal structures support the hypothesis of a reaction mechanism, in which the [4Fe-4S] cluster binds a hydrogenosulfide ligand in place of the chloride anion, thus generating a [4Fe-5S] intermediate, and transfers it to the substrate, as in the case of [4Fe-4S]-dependent tRNA thiolation enzymes.
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Affiliation(s)
- Paolo Zecchin
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8829Sorbonne UniversitéParis cedex 05France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8829Sorbonne UniversitéParis cedex 05France
| | - Jonathan Oltmanns
- Universität of Kaiserslautern‐LandauDepartment of PhysicsKaiserslauternGermany
| | - Christophe Velours
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRSUniversité Paris‐SaclayGif‐sur‐Yvette cedexFrance
- Present address:
Fundamental Microbiology and Pathogenicity LaboratoryUMR 5234 CNRS‐University of Bordeaux, SFR TransBioMedBordeauxFrance
| | - Volker Schünemann
- Universität of Kaiserslautern‐LandauDepartment of PhysicsKaiserslauternGermany
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8829Sorbonne UniversitéParis cedex 05France
| | - Béatrice Golinelli‐Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8829Sorbonne UniversitéParis cedex 05France
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Ev LD, Poloni JF, Damé-Teixeira N, Arthur RA, Corralo DJ, Henz SL, DO T, Maltz M, Parolo CCF. Biofilm dysbiosis and caries activity: a surface or an individual issue? J Appl Oral Sci 2023; 31:e20230214. [PMID: 37970886 PMCID: PMC10697669 DOI: 10.1590/1678-7757-2023-0214] [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: 07/18/2023] [Revised: 08/28/2023] [Accepted: 09/19/2023] [Indexed: 11/19/2023] Open
Abstract
OBJECTIVE This study aimed to analyze the functional profile of supragingival biofilm from sound (CAs), active (CAa), and inactive (CAi) enamel caries lesions from caries-active individuals to provide insights into the diversity of biological processes regarding biofilm dysbiosis. METHODOLOGY A metatranscriptome analysis was performed in biofilm samples collected from five caries-active individuals. Total RNA was extracted, and the microbial cDNAs were obtained and sequenced (Illumina HiSeq3000). Trimmed data were submitted to the SqueezeMeta pipeline in the co-assembly mode for functional analysis and further differential gene expression analysis (DESeq2). RESULTS Bioinformatics analysis of mRNAs revealed a similar functional profile related to all analyzed conditions (CAa, CAi, and CAs). However, active and inactive surfaces share up-regulated genes (gtsA; qrtT; tqsA; pimB; EPHX1) related to virulence traits that were not overrepresented in sound surfaces. From a functional perspective, what matters most is the individual carious status rather than the surface condition. Therefore, pooling samples from various sites can be carried out using naturally developed oral biofilms but should preferably include carious surfaces. CONCLUSION Metatranscriptome data from subjects with caries activity have shown that biofilms from sound, arrested, and active lesions are similar in composition and function.
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Affiliation(s)
- Laís Daniela Ev
- Universidade Federal do Rio Grande do Sul, Faculdade de Odontologia, Departamento de Odontologia Preventiva e Social, Porto Alegre, RS, Brasil
| | - Joice Faria Poloni
- Instituto Nacional de Ciência e Tecnologia - Ciências Forense, Pontifica Universidade Católica do Rio Grande do Sul, Escola de Ciências da Saúde e da Vida, Porto Alegre, Brasil
| | - Nailê Damé-Teixeira
- Universidade de Brasília, Faculdade de Ciências da Saúde, Departamento de Odontologia, Brasília, DF, Brasil
| | - Rodrigo Alex Arthur
- Universidade Federal do Rio Grande do Sul, Faculdade de Odontologia, Departamento de Odontologia Preventiva e Social, Porto Alegre, RS, Brasil
| | - Daniela Jorge Corralo
- Universidade de Passo Fundo, Escola de Odontologia, Departamento de Odontologia, RS, Passo Fundo, Brasil
| | - Sandra Liana Henz
- Universidade Federal do Rio Grande do Sul, Faculdade de Odontologia, Departamento de Odontologia Preventiva e Social, Porto Alegre, RS, Brasil
| | - Thuy DO
- University of Leeds, School of Dentistry, Division of Oral Biology, Leeds, UK
| | - Marisa Maltz
- Universidade Federal do Rio Grande do Sul, Faculdade de Odontologia, Departamento de Odontologia Preventiva e Social, Porto Alegre, RS, Brasil
| | - Clarissa Cavalcanti Fatturi Parolo
- Universidade Federal do Rio Grande do Sul, Faculdade de Odontologia, Departamento de Odontologia Preventiva e Social, Porto Alegre, RS, Brasil
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Ajaykamal T, Palaniandavar M. Mononuclear nickel(ii)-flavonolate complexes of tetradentate tripodal 4N ligands as structural and functional models for quercetin 2,4-dioxygenase: structures, spectra, redox and dioxygenase activity. RSC Adv 2023; 13:24674-24690. [PMID: 37601601 PMCID: PMC10436029 DOI: 10.1039/d3ra04834a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 08/01/2023] [Indexed: 08/22/2023] Open
Abstract
Three new nickel(ii)-flavonolate complexes of the type [Ni(L)(fla)](ClO4) 1-3, where L is the tripodal 4N ligand tris(pyrid-2-ylmethyl)amine (tpa, L1) or (pyrid-2-ylmethyl)bis(6-methylpyrid-2-ylmethyl)amine (6-Me2-tpa, L2) or tris(N-Et-benzimidazol-2-ylmethyl)amine (Et-ntb, L3), have been isolated as functional models for Ni(ii)-containing quercetin 2,4-dioxygenase. Single crystal X-ray structures of 1 and 3 reveal that Ni(ii) is involved in π-back bonding with flavonolate (fla-), as evident from enhancement in C[double bond, length as m-dash]O bond length upon coordination [H(fla), 1.232(3); 1, 1.245(7); 3, 1.262(8) Å]. More asymmetric chelation of fla- in 3 than in 1 [Δd = (Ni-Ocarbonyl - Ni-Oenolate): 1, 0.126; 3, 0.182 Å] corresponds to lower π-delocalization in 3 with electron-releasing N-Et substituent. The optimized structures of 1-3 and their geometrical isomers have been computed by DFT methods. The HOMO and LUMO, both localized on Ni(ii)-bound fla-, are highly conjugated bonding π- and antibonding π*-orbitals respectively. They are located higher in energy than the Ni(ii)-based MOs (HOMO-1, dx2-y2; HOMO-2/6, dz2), revealing that the Ni(ii)-bound fla- rather than Ni(ii) would undergo oxidation upon exposure to dioxygen. The results of computational studies, in combination with spectral and electrochemical studies, support the involvement of redox-inactive Ni(ii) in π-back bonding with fla-, tuning the π-delocalization in fla- and hence its activation. Upon exposure to dioxygen, all the flavonolate adducts in DMF solution decompose to produce CO and depside, which then is hydrolyzed to give the corresponding acids at 70 °C. The highest rate of dioxygenase reactivity of 3 (kO2: 3 (29.10 ± 0.16) > 1 (16.67 ± 0.70) > 2 (1.81 ± 0.04 × 10-1 M-1 s-1)), determined by monitoring the disappearance of the LMCT band in the range 440-450 nm, is ascribed to the electron-releasing N-Et substituent on bzim ring, which decreases the π-delocalization in fla- and enhances its activation.
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Affiliation(s)
- Tamilarasan Ajaykamal
- Department of Chemistry, Bharathidasan University Tiruchirapalli 620 024 Tamil Nadu India +91-431-2407043 +91-431-2407125
| | - Mallayan Palaniandavar
- Department of Chemistry, Bharathidasan University Tiruchirapalli 620 024 Tamil Nadu India +91-431-2407043 +91-431-2407125
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Jang HY, Kim MJ, Bae M, Hwang IM, Lee JH. Transcriptional analysis of the molecular mechanism underlying the response of Lactiplantibacillus plantarum to lactic acid stress conditions. Heliyon 2023; 9:e16520. [PMID: 37303574 PMCID: PMC10250755 DOI: 10.1016/j.heliyon.2023.e16520] [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: 12/07/2022] [Revised: 05/02/2023] [Accepted: 05/19/2023] [Indexed: 06/13/2023] Open
Abstract
Lactic acid bacteria (LAB) present various benefits to humans; they play key roles in the fermentation of food and as probiotics. Acidic conditions are common to both LAB in the intestinal tract as well as fermented foods. Lactiplantibacillus plantarum is a facultative homofermentative bacterium, and lactic acid is the end metabolite of glycolysis. To characterize how L. plantarum responds to lactic acid, we investigated its transcriptome following treatment with hydrochloride (HCl) or dl-lactic acid at an early stage of growth. Bacterial growth was more attenuated in the presence of lactic acid than in the presence of HCl at the same pH range. Bacterial transcriptome analysis showed that the expression of 67 genes was significantly altered (log2FC > 2 or < 2). A total of 31 genes were up- or downregulated under both conditions: 19 genes in the presence of HCl and 17 genes in the presence of dl-lactic acid. The fatty acid synthesis-related genes were upregulated in both acidic conditions, whereas the lactate racemization-related gene (lar) was only upregulated following treatment with dl-lactic acid. In particular, lar expression increased following l-lactic acid treatment but did not increase following HCl or d-lactic acid treatment. Expression of lar and production of d-lactic acid were investigated with malic and acetic acid; the results revealed a higher expression of lar and production of d-lactic acid in the presence of malic acid than that in the presence of acetic acid.
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Hausinger RP, Hu J, Desguin B. The nickel-pincer coenzyme of lactate racemase: A case study of uncovering cofactor structure and biosynthesis. Methods Enzymol 2023; 685:341-371. [PMID: 37245907 PMCID: PMC10626555 DOI: 10.1016/bs.mie.2023.03.006] [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: 05/30/2023]
Abstract
Cofactors are essential components of numerous enzymes, therefore their characterization by structural, biophysical, and biochemical approaches is crucial for understanding the resulting catalytic and regulatory mechanisms. In this chapter, we present a case study of a recently discovered cofactor, the nickel-pincer nucleotide (NPN), by demonstrating how we identified and thoroughly characterized this unprecedented nickel-containing coenzyme that is tethered to lactase racemase from Lactiplantibacillus plantarum. In addition, we describe how the NPN cofactor is biosynthesized by a panel of proteins encoded in the lar operon and describe the properties of these novel enzymes. Comprehensive protocols for conducting functional and mechanistic studies of NPN-containing lactate racemase (LarA) and the carboxylase/hydrolase (LarB), sulfur transferase (LarE), and metal insertase (LarC) used for NPN biosynthesis are provided for potential applications towards characterizing enzymes in the same or homologous families.
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Affiliation(s)
- Robert P Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States.
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States; Department of Chemistry, Michigan State University, East Lansing, MI, United States
| | - Benoît Desguin
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-La-Neuve, Belgium
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Gatreddi S, Urdiain-Arraiza J, Desguin B, Hausinger RP, Hu J. Structural and mutational characterization of a malate racemase from the LarA superfamily. Biometals 2023; 36:303-313. [PMID: 35182264 PMCID: PMC9388697 DOI: 10.1007/s10534-022-00372-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/07/2022] [Indexed: 01/13/2023]
Abstract
The LarA superfamily consists of nickel-dependent enzymes catalyzing racemization/epimerization reactions using a variety of α-hydroxy acids. The first-characterized LarA, a lactate racemase from Lactobacillus plantarum, led to the discovery of the nickel-pincer nucleotide (NPN) cofactor that is utilized by family members with alternative substrates, including malate racemase from Thermoanaerobacterium thermosaccharolyticum (Mar2). In this work, a higher resolution crystal structure of Mar2 was obtained with better data quality that revealed new structural and dynamic characteristics of the protein. A model of the Mar2 structure with bound cofactor and substrate was generated to uncover the common and the unique features among two distinct subgroups in the LarA superfamily. In addition, structure-guided mutational studies were used to examine the importance of residues that are modeled to interact with NPN and to explore which residues were critical for conferring specificity for malate. In particular, substitution of two residues involved in substrate binding in Mar2 to match the corresponding residues in LarA led to the acquisition of low levels of lactate racemase activity. Of additional interest, the substrate spectrum was expanded to include tartrate, an analog of malate. These new findings will help to better understand structure-function relationships of many other LarA homologs that are broadly distributed in bacterial and archaeal species.
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Affiliation(s)
- Santhosh Gatreddi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Julian Urdiain-Arraiza
- Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348, Louvain-La-Neuve, Belgium
| | - Benoît Desguin
- Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348, Louvain-La-Neuve, Belgium
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA.
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Kronen M, Vázquez-Campos X, Wilkins MR, Lee M, Manefield MJ. Evidence for a Putative Isoprene Reductase in Acetobacterium wieringae. mSystems 2023; 8:e0011923. [PMID: 36943133 PMCID: PMC10134865 DOI: 10.1128/msystems.00119-23] [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: 03/23/2023] Open
Abstract
Recent discoveries of isoprene-metabolizing microorganisms suggest they might play an important role in the global isoprene budget. Under anoxic conditions, isoprene can be used as an electron acceptor and is reduced to methylbutene. This study describes the proteogenomic profiling of an isoprene-reducing bacterial culture to identify organisms and genes responsible for the isoprene hydrogenation reaction. A metagenome-assembled genome (MAG) of the most abundant (89% relative abundance) lineage in the enrichment, Acetobacterium wieringae, was obtained. Comparative proteogenomics and reverse transcription-PCR (RT-PCR) identified a putative five-gene operon from the A. wieringae MAG upregulated during isoprene reduction. The operon encodes a putative oxidoreductase, three pleiotropic nickel chaperones (2 × HypA, HypB), and one 4Fe-4S ferredoxin. The oxidoreductase is proposed as the putative isoprene reductase with a binding site for NADH, flavin adenine dinucleotide (FAD), two pairs of canonical [4Fe-4S] clusters, and a putative iron-sulfur cluster site in a Cys6-bonding environment. Well-studied Acetobacterium strains, such as A. woodii DSM 1030, A. wieringae DSM 1911, or A. malicum DSM 4132, do not encode the isoprene-regulated operon but encode, like many other bacteria, a homolog of the putative isoprene reductase (~47 to 49% amino acid sequence identity). Uncharacterized homologs of the putative isoprene reductase are observed across the Firmicutes, Spirochaetes, Tenericutes, Actinobacteria, Chloroflexi, Bacteroidetes, and Proteobacteria, suggesting the ability of biohydrogenation of unfunctionalized conjugated doubled bonds in other unsaturated hydrocarbons. IMPORTANCE Isoprene was recently shown to act as an electron acceptor for a homoacetogenic bacterium. The focus of this study is the molecular basis for isoprene reduction. By comparing a genome from our isoprene-reducing enrichment culture, dominated by Acetobacterium wieringae, with genomes of other Acetobacterium lineages that do not reduce isoprene, we shortlisted candidate genes for isoprene reduction. Using comparative proteogenomics and reverse transcription-PCR we have identified a putative five-gene operon encoding an oxidoreductase referred to as putative isoprene reductase.
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Affiliation(s)
- Miriam Kronen
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Xabier Vázquez-Campos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Matthew Lee
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Michael J Manefield
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
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10
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Site Specialization of Human Oral Veillonella Species. Microbiol Spectr 2023; 11:e0404222. [PMID: 36695592 PMCID: PMC9927086 DOI: 10.1128/spectrum.04042-22] [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] [Indexed: 01/26/2023] Open
Abstract
Veillonella species are abundant members of the human oral microbiome with multiple interspecies commensal relationships. Examining the distribution patterns of Veillonella species across the oral cavity is fundamental to understanding their oral ecology. In this study, we used a combination of pangenomic analysis and oral metagenomic information to clarify Veillonella taxonomy and to test the site specialist hypothesis for the Veillonella genus, which contends that most oral bacterial species are adapted to live at specific oral sites. Using isolate genome sequences combined with shotgun metagenomic sequence data, we showed that Veillonella species have clear, differential site specificity: Veillonella parvula showed strong preference for supra- and subgingival plaque, while closely related V. dispar, as well as more distantly related V. atypica, preferred the tongue dorsum, tonsils, throat, and hard palate. In addition, the provisionally named Veillonella sp. Human Microbial Taxon 780 showed strong site specificity for keratinized gingiva. Using comparative genomic analysis, we identified genes associated with thiamine biosynthesis and the reductive pentose phosphate cycle that may enable Veillonella species to occupy their respective habitats. IMPORTANCE Understanding the microbial ecology of the mouth is fundamental for understanding human physiology. In this study, metapangenomics demonstrated that different Veillonella species have clear ecological preferences in the oral cavity of healthy humans, validating the site specialist hypothesis. Furthermore, the gene pool of different Veillonella species was found to be reflective of their ecology, illuminating the potential role of vitamins and carbohydrates in determining Veillonella distribution patterns and interspecies interactions.
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Gatreddi S, Sui D, Hausinger RP, Hu J. Irreversible inactivation of lactate racemase by sodium borohydride reveals reactivity of the nickel-pincer nucleotide cofactor. ACS Catal 2023; 13:1441-1448. [PMID: 37886035 PMCID: PMC10599654 DOI: 10.1021/acscatal.2c05461] [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] [Indexed: 01/11/2023]
Abstract
The nickel-pincer nucleotide (NPN) cofactor discovered in lactate racemase from Lactiplantibacillus plantarum (LarALp) is essential for the activities of racemases/epimerases in the highly diverse LarA superfamily. Prior mechanistic studies have established a proton-coupled hydride-transfer mechanism for LarALp, but direct evidence showing that hydride attacks the C4 atom in the pyridinium ring of NPN has been lacking. Here, we show that sodium borohydride (NaBH4) irreversibly inactivates LarALp accompanied by a rapid color change of the enzyme. The altered ultraviolet-visible spectra during NaBH4 titration supported hydride transfer to C4 of NPN, and the concomitant Ni loss unraveled by mass spectrometry experiments accounted for the irreversible inactivation. High resolution structures of LarALp revealed a substantially weakened C-Ni bond in the metastable sulfite-NPN adduct where the NPN cofactor is in the reduced state. These findings allowed us to propose a mechanism of LarALp inactivation by NaBH4 that provides key insights into the enzyme-catalyzed reaction and sheds light on the reactivity of small molecule NPN mimetics.
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Affiliation(s)
- Santhosh Gatreddi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, United States
| | - Dexin Sui
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
| | - Robert P. Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, United States
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, United States
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12
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Zhou X, Zhang N, Hossain F, Kandalai S, Tian H, Zheng Q. Biosynthesis of D/L-lactate from methylglyoxal. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.133087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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13
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Chatterjee S, Gatreddi S, Gupta S, Nevarez JL, Rankin JA, Turmo A, Hu J, Hausinger RP. Unveiling the mechanisms and biosynthesis of a novel nickel-pincer enzyme. Biochem Soc Trans 2022; 50:1187-1196. [PMID: 35960008 PMCID: PMC9880988 DOI: 10.1042/bst20220490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 01/31/2023]
Abstract
The nickel-pincer nucleotide (NPN) coenzyme, a substituted pyridinium mononucleotide that tri-coordinates nickel, was first identified covalently attached to a lysine residue in the LarA protein of lactate racemase. Starting from nicotinic acid adenine dinucleotide, LarB carboxylates C5 of the pyridinium ring and hydrolyzes the phosphoanhydride, LarE converts the C3 and C5 carboxylates to thiocarboxylates, and LarC incorporates nickel to form a C-Ni and two S-Ni bonds, during the biosynthesis of this cofactor. LarB uses a novel carboxylation mechanism involving the transient formation of a cysteinyl-pyridinium adduct. Depending on the source of the enzyme, LarEs either catalyze a sacrificial sulfur transfer from a cysteinyl side chain resulting in the formation of dehydroalanine or they utilize a [4Fe-4S] cluster bound by three cysteine residues to accept and transfer a non-core sulfide atom. LarC is a CTP-dependent enzyme that cytidinylylates its substrate, adds nickel, then hydrolyzes the product to release NPN and CMP. Homologs of the four lar genes are widely distributed in microorganisms, with some species containing multiple copies of larA whereas others lack this gene, consistent with the cofactor serving other functions. Several LarA-like proteins were shown to catalyze racemase or epimerase activities using 2-hydroxyacid substrates other than lactic acid. Thus, lactate racemase is the founding member of a large family of NPN-containing enzymes.
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Affiliation(s)
- Shramana Chatterjee
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Santhosh Gatreddi
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Swati Gupta
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Jorge L. Nevarez
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Joel A. Rankin
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Aiko Turmo
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Robert P. Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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14
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Chatterjee S, Parson KF, Ruotolo BT, McCracken J, Hu J, Hausinger RP. Characterization of a [4Fe-4S]-dependent LarE sulfur insertase that facilitates nickel-pincer nucleotide cofactor biosynthesis in Thermotoga maritima. J Biol Chem 2022; 298:102131. [PMID: 35700827 PMCID: PMC9283937 DOI: 10.1016/j.jbc.2022.102131] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 11/10/2022] Open
Abstract
Sulfur-insertion reactions are essential for the biosynthesis of several cellular metabolites, including enzyme cofactors. In Lactobacillus plantarum, a sulfur-containing nickel-pincer nucleotide (NPN) cofactor is used as a coenzyme of lactic acid racemase, LarA. During NPN biosynthesis in L. plantarum, sulfur is transferred to a nicotinic acid-derived substrate by LarE, which sacrifices the sulfur atom of its single cysteinyl side chain, forming a dehydroalanine residue. Most LarE homologs contain three conserved cysteine residues that are predicted to cluster at the active site; however, the function of this cysteine cluster is unclear. In this study, we characterized LarE from Thermotoga maritima (LarETm) and show that it uses these three conserved cysteine residues to bind a [4Fe-4S] cluster that is required for sulfur transfer. Notably, we found LarETm retains all side chain sulfur atoms, in contrast to LarELp. We also demonstrate that when provided with L-cysteine and cysteine desulfurase from Escherichia coli (IscSEc), LarETm functions catalytically with IscSEc transferring sulfane sulfur atoms to LarETm. Native mass spectrometry results are consistent with a model wherein the enzyme coordinates sulfide at the nonligated iron atom of the [4Fe-4S] cluster, forming a [4Fe-5S] species, and transferring the noncore sulfide to the activated substrate. This proposed mechanism is like that of TtuA that catalyzes sulfur transfer during 2-thiouridine synthesis. In conclusion, we found that LarE sulfur insertases associated with NPN biosynthesis function either by sacrificial sulfur transfer from the protein or by transfer of a noncore sulfide bound to a [4Fe-4S] cluster.
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Affiliation(s)
- Shramana Chatterjee
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - John McCracken
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Jian Hu
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Robert P Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA.
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15
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Turmo A, Hu J, Hausinger RP. Characterization of the nickel-inserting cyclometallase LarC from Moorella thermoacetica and identification of a cytidinylylated reaction intermediate. Metallomics 2022; 14:6539348. [PMID: 35225337 PMCID: PMC8962377 DOI: 10.1093/mtomcs/mfac014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/19/2022] [Indexed: 11/13/2022]
Abstract
LarC catalyzes the CTP-dependent insertion of nickel ion into pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN), the final biosynthetic step for generating the nickel-pincer nucleotide (NPN) enzyme cofactor. In this study, we characterized a LarC homolog from Moorella thermoacetica (LarCMt) and characterized selected properties of the protein. We ruled out the hypothesis that enzyme inhibition by its product pyrophosphate accounts for its apparent single-turnover activity. Most notably, we identified a cytidinylylated-substrate intermediate that is formed during the reaction of LarCMt. Selected LarCMt variants with substitutions at the predicted CTP-binding site retained substantial amounts of activity, but exhibited greatly reduced levels of the CMP-P2TMN intermediate. In contrast, enhanced amounts of the CMP-P2TMN intermediate were generated when using LarCMt from cells grown on medium without supplemental nickel. On the basis of these results, we propose a functional role for CTP in the unprecedented nickel-insertase reaction during NPN biosynthesis.
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Affiliation(s)
- Aiko Turmo
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA,Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Robert P Hausinger
- Correspondence: 567 Wilson Rd, Room 2215, Biomedical Physical Sciences, East Lansing, MI 48824, USA. E-mail:
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Kaswan P, Oswal P, Kumar A, Mohan Srivastava C, Vaya D, Rawat V, Nayan Sharma K, Kumar Rao G. SNS donors as mimic to enzymes, chemosensors, and imaging agents. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2021.109140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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Uddin R, Arif A. Potential Drug Targets Identification Against Clostridioides Difficile (CD)
and Characterization of Indispensable Proteins by a Subtractive Genomics
Approach Followed by Virtual Screening. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180818666210930160128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Clostridioides difficile (CD) is an enteric multi-drug resistant pathogenic bacterium.
CD-associated infections are the leading cause of nosocomial diarrhea that can further lead to pseudomembranous
colitis, toxic mega-colon or sepsis with greater mortality and morbidity risks. CD infection
possesses higher rates of recurrence due to its greater resistance to antibiotics. Considering its higher
rates of recurrence, it has become a major burden on healthcare facilities. Therefore, there is a dire need
to identify novel drug targets to combat antibiotic resistance of Clostridioides difficile.
Objective:
To identify and propose new and novel drug targets against the Clostridioides difficile.
Methods:
In the current study, a computational subtractive genomics approach was applied to obtain a set
of potential drug targets that exist in the multi-drug resistant strain of Clostridioides difficile. Here, the
uncharacterized proteins were studied as potential drug targets. The methodology involved several bioinformatics
databases and tools. The druggable proteins sequences were retrieved based on non-homology
with host proteome and essentiality for the survival of the pathogen. The uncharacterized proteins were
functionally characterized using different computational tools, and sub-cellular localization was also predicted.
The metabolic pathways were analyzed using the KEGG database. Eventually, the druggable proteome
has been fetched using sequence similarity with the already available drug targets present in the
DrugBank database. These druggable proteins were further explored for the structural details to identify
drug candidates.
Results :
A priority list of potential drug targets was provided with the help of the applied method on the
complete proteome set of the C. difficile. Moreover, the drug-like compounds have been screened against
the potential drug targets to prioritize potential drug candidates. To facilitate the need for drug targets and
therapies, the study proposed five potential protein drug targets, out of which three proposed drug targets
were subjected to homology modeling to explore their structural and functional activities
Conclusion:
In conclusion, we proposed three unique, unexplored drug targets against C. difficile. The
structure-based methods were applied and resulted in a list of top-scoring compounds as potential inhibitors
to proposed drug targets.
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Affiliation(s)
- Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological
Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Alina Arif
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological
Sciences, University of Karachi, Karachi 75270, Pakistan
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18
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Treviño RE, Shafaat HS. Protein-based models offer mechanistic insight into complex nickel metalloenzymes. Curr Opin Chem Biol 2022; 67:102110. [PMID: 35101820 DOI: 10.1016/j.cbpa.2021.102110] [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: 09/24/2021] [Revised: 11/22/2021] [Accepted: 12/06/2021] [Indexed: 11/03/2022]
Abstract
There are ten nickel enzymes found across biological systems, each with a distinct active site and reactivity that spans reductive, oxidative, and redox-neutral processes. We focus on the reductive enzymes, which catalyze reactions that are highly germane to the modern-day climate crisis: [NiFe] hydrogenase, carbon monoxide dehydrogenase, acetyl coenzyme A synthase, and methyl coenzyme M reductase. The current mechanistic understanding of each enzyme system is reviewed along with existing knowledge gaps, which are addressed through the development of protein-derived models, as described here. This opinion is intended to highlight the advantages of using robust protein scaffolds for modeling multiscale contributions to reactivity and inspire the development of novel artificial metalloenzymes for other small molecule transformations.
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Affiliation(s)
- Regina E Treviño
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.
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19
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The LarB carboxylase/hydrolase forms a transient cysteinyl-pyridine intermediate during nickel-pincer nucleotide cofactor biosynthesis. Proc Natl Acad Sci U S A 2021; 118:2106202118. [PMID: 34548397 DOI: 10.1073/pnas.2106202118] [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] [Accepted: 08/23/2021] [Indexed: 11/18/2022] Open
Abstract
Enzymes possessing the nickel-pincer nucleotide (NPN) cofactor catalyze C2 racemization or epimerization reactions of α-hydroxyacid substrates. LarB initiates synthesis of the NPN cofactor from nicotinic acid adenine dinucleotide (NaAD) by performing dual reactions: pyridinium ring C5 carboxylation and phosphoanhydride hydrolysis. Here, we show that LarB uses carbon dioxide, not bicarbonate, as the substrate for carboxylation and activates water for hydrolytic attack on the AMP-associated phosphate of C5-carboxylated-NaAD. Structural investigations show that LarB has an N-terminal domain of unique fold and a C-terminal domain homologous to aminoimidazole ribonucleotide carboxylase/mutase (PurE). Like PurE, LarB is octameric with four active sites located at subunit interfaces. The complex of LarB with NAD+, an analog of NaAD, reveals the formation of a covalent adduct between the active site Cys221 and C4 of NAD+, resulting in a boat-shaped dearomatized pyridine ring. The formation of such an intermediate with NaAD would enhance the reactivity of C5 to facilitate carboxylation. Glu180 is well positioned to abstract the C5 proton, restoring aromaticity as Cys221 is expelled. The structure of as-isolated LarB and its complexes with NAD+ and the product AMP identify additional residues potentially important for substrate binding and catalysis. In combination with these findings, the results from structure-guided mutagenesis studies lead us to propose enzymatic mechanisms for both the carboxylation and hydrolysis reactions of LarB that are distinct from that of PurE.
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Detman A, Laubitz D, Chojnacka A, Kiela PR, Salamon A, Barberán A, Chen Y, Yang F, Błaszczyk MK, Sikora A. Dynamics of dark fermentation microbial communities in the light of lactate and butyrate production. MICROBIOME 2021; 9:158. [PMID: 34261525 PMCID: PMC8281708 DOI: 10.1186/s40168-021-01105-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 05/28/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND This study focuses on the processes occurring during the acidogenic step of anaerobic digestion, especially resulting from nutritional interactions between dark fermentation (DF) bacteria and lactic acid bacteria (LAB). Previously, we have confirmed that DF microbial communities (MCs) that fed on molasses are able to convert lactate and acetate to butyrate. The aims of the study were to recognize the biodiversity of DF-MCs able and unable to convert lactate and acetate to butyrate and to define the conditions for the transformation. RESULTS MCs sampled from a DF bioreactor were grown anaerobically in mesophilic conditions on different media containing molasses or sucrose and/or lactate and acetate in five independent static batch experiments. The taxonomic composition (based on 16S_rRNA profiling) of each experimental MC was analysed in reference to its metabolites and pH of the digestive liquids. In the samples where the fermented media contained carbohydrates, the two main tendencies were observed: (i) a low pH (pH ≤ 4), lactate and ethanol as the main fermentation products, MCs dominated with Lactobacillus, Bifidobacterium, Leuconostoc and Fructobacillus was characterized by low biodiversity; (ii) pH in the range 5.0-6.0, butyrate dominated among the fermentation products, the MCs composed mainly of Clostridium (especially Clostridium_sensu_stricto_12), Lactobacillus, Bifidobacterium and Prevotella. The biodiversity increased with the ability to convert acetate and lactate to butyrate. The MC processing exclusively lactate and acetate showed the highest biodiversity and was dominated by Clostridium (especially Clostridium_sensu_stricto_12). LAB were reduced; other genera such as Terrisporobacter, Lachnoclostridium, Paraclostridium or Sutterella were found. Butyrate was the main metabolite and pH was 7. Shotgun metagenomic analysis of the selected butyrate-producing MCs independently on the substrate revealed C.tyrobutyricum as the dominant Clostridium species. Functional analysis confirmed the presence of genes encoding key enzymes of the fermentation routes. CONCLUSIONS Batch tests revealed the dynamics of metabolic activity and composition of DF-MCs dependent on fermentation conditions. The balance between LAB and the butyrate producers and the pH values were shown to be the most relevant for the process of lactate and acetate conversion to butyrate. To close the knowledge gaps is to find signalling factors responsible for the metabolic shift of the DF-MCs towards lactate fermentation. Video Abstract.
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Affiliation(s)
- Anna Detman
- Institute of Biochemistry and Biophysics – Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Daniel Laubitz
- Department of Pediatrics at Steel Children’s Research Center College of Medicine, University of Arizona, 1501 N. Campbell Avenue, Room 3301, PO Box 245073, Tucson, Arizona 85724-5073 USA
| | - Aleksandra Chojnacka
- Institute of Biochemistry and Biophysics – Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
- Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Pawel R. Kiela
- Department of Pediatrics at Steel Children’s Research Center College of Medicine, University of Arizona, 1501 N. Campbell Avenue, Room 3301, PO Box 245073, Tucson, Arizona 85724-5073 USA
| | - Agnieszka Salamon
- Institute of Agricultural and Food Biotechnology, Rakowiecka 36, 02-532 Warsaw, Poland
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, 1177 E. 4th Street, P.O. Box 210038, Tucson, Arizona 85721-0038 USA
| | - Yongjian Chen
- Department of Environmental Science, University of Arizona, 1177 E. 4th Street, P.O. Box 210038, Tucson, Arizona 85721-0038 USA
| | - Fei Yang
- Department of Environmental Science, University of Arizona, 1177 E. 4th Street, P.O. Box 210038, Tucson, Arizona 85721-0038 USA
| | - Mieczysław K. Błaszczyk
- Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Anna Sikora
- Institute of Biochemistry and Biophysics – Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
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21
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Contreras-Dávila CA, Esveld J, Buisman CJN, Strik DPBTB. nZVI Impacts Substrate Conversion and Microbiome Composition in Chain Elongation From D- and L-Lactate Substrates. Front Bioeng Biotechnol 2021; 9:666582. [PMID: 34211964 PMCID: PMC8239352 DOI: 10.3389/fbioe.2021.666582] [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] [Received: 02/10/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022] Open
Abstract
Medium-chain carboxylates (MCC) derived from biomass biorefining are attractive biochemicals to uncouple the production of a wide array of products from the use of non-renewable sources. Biological conversion of biomass-derived lactate during secondary fermentation can be steered to produce a variety of MCC through chain elongation. We explored the effects of zero-valent iron nanoparticles (nZVI) and lactate enantiomers on substrate consumption, product formation and microbiome composition in batch lactate-based chain elongation. In abiotic tests, nZVI supported chemical hydrolysis of lactate oligomers present in concentrated lactic acid. In fermentation experiments, nZVI created favorable conditions for either chain-elongating or propionate-producing microbiomes in a dose-dependent manner. Improved lactate conversion rates and n-caproate production were promoted at 0.5-2 g nZVI⋅L-1 while propionate formation became relevant at ≥ 3.5 g nZVI⋅L-1. Even-chain carboxylates (n-butyrate) were produced when using enantiopure and racemic lactate with lactate conversion rates increased in nZVI presence (1 g⋅L-1). Consumption of hydrogen and carbon dioxide was observed late in the incubations and correlated with acetate formation or substrate conversion to elongated products in the presence of nZVI. Lactate racemization was observed during chain elongation while isomerization to D-lactate was detected during propionate formation. Clostridium luticellarii, Caproiciproducens, and Ruminococcaceae related species were associated with n-valerate and n-caproate production while propionate was likely produced through the acrylate pathway by Clostridium novyi. The enrichment of different potential n-butyrate producers (Clostridium tyrobutyricum, Lachnospiraceae, Oscillibacter, Sedimentibacter) was affected by nZVI presence and concentrations. Possible theories and mechanisms underlying the effects of nZVI on substrate conversion and microbiome composition are discussed. An outlook is provided to integrate (bio)electrochemical systems to recycle (n)ZVI and provide an alternative reducing power agent as durable control method.
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Affiliation(s)
| | - Johan Esveld
- Environmental Technology, Wageningen University & Research, Wageningen, Netherlands
| | - Cees J N Buisman
- Environmental Technology, Wageningen University & Research, Wageningen, Netherlands
| | - David P B T B Strik
- Environmental Technology, Wageningen University & Research, Wageningen, Netherlands
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22
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Al Bataineh MT, Dash NR, Elkhazendar M, Alnusairat DMH, Darwish IMI, Al-Hajjaj MS, Hamid Q. Revealing oral microbiota composition and functionality associated with heavy cigarette smoking. J Transl Med 2020; 18:421. [PMID: 33167991 PMCID: PMC7653996 DOI: 10.1186/s12967-020-02579-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/24/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Heavy tobacco smoking, a hallmark feature of lung cancer, is drastically predominant in Middle Eastern populations. The precise links between nicotine dependence and the functional contribution of the oral microbiota remain unknown in these populations. METHODS We evaluated the composition and functional capabilities of oral microbiota with relation to cigarette smoking in 105 adults through shotgun metagenomics using buccal swabs. RESULTS The oral microbiota composition in our study subjects was dominated by the phyla Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes, in addition to the genera Prevotella and Veillonella, similar to previously described westernized cohorts. Furthermore, the smoker's oral microbiota represented a significant abundance of Veillonella dispar, Leptotrichia spp. and Prevotella pleuritidis when compared to non-smokers. Within the smoking groups, differential relative abundance testing unveiled relative abundance of Streptobacillus hongkongensis, Fusobacterium massiliense, Prevotella bivia in high nicotine dependent compared to low nicotine dependent profiles based on Fagerström Test for Nicotine Dependence. Functional profiling showed marked differences between smokers and non-smokers. Smokers exhibited an enrichment of Tricarballylate utilization and Lactate racemization when compared to the non-smokers. According to their nicotine dependence, enrichment of Xanthosine utilization, p-Aminobenzoyl-Glutamate utilization, and multidrug efflux pump in Campylobacter jejuni biosynthesis modules were detected in the high nicotine dependent group. CONCLUSIONS These compositional and functional differences may provide critical insight on how variations in the oral microbiota could predispose to respiratory illnesses and smoke cessation relapse in cigarette smokers. In particular, the observed enrichment of Fusobacterium and Prevotella in the oral microbiota possibly suggests an intriguing linkage to gut and lung cancers.
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Affiliation(s)
- Mohammad Tahseen Al Bataineh
- Clinical Sciences Department, College of Medicine, University of Sharjah, 27272, Sharjah, United Arab Emirates. .,Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.
| | - Nihar Ranjan Dash
- Clinical Sciences Department, College of Medicine, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Mohammed Elkhazendar
- Clinical Sciences Department, College of Medicine, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | | | | | - Mohamed Saleh Al-Hajjaj
- Clinical Sciences Department, College of Medicine, University of Sharjah, 27272, Sharjah, United Arab Emirates.,University Hospital Sharjah, Sharjah, United Arab Emirates
| | - Qutayba Hamid
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,Meakins-Christie Laboratories, McGill University, Montreal, QC, Canada
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23
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Desguin B, Urdiain-Arraiza J, Da Costa M, Fellner M, Hu J, Hausinger RP, Desmet T, Hols P, Soumillion P. Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases. Sci Rep 2020; 10:18123. [PMID: 33093595 PMCID: PMC7583248 DOI: 10.1038/s41598-020-74802-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/06/2020] [Indexed: 12/13/2022] Open
Abstract
Isomerization reactions are fundamental in biology. Lactate racemase, which isomerizes L- and D-lactate, is composed of the LarA protein and a nickel-containing cofactor, the nickel-pincer nucleotide (NPN). In this study, we show that LarA is part of a superfamily containing many different enzymes. We overexpressed and purified 13 lactate racemase homologs, incorporated the NPN cofactor, and assayed the isomerization of different substrates guided by gene context analysis. We discovered two malate racemases, one phenyllactate racemase, one α-hydroxyglutarate racemase, two D-gluconate 2-epimerases, and one short-chain aliphatic α-hydroxyacid racemase among the tested enzymes. We solved the structure of a malate racemase apoprotein and used it, along with the previously described structures of lactate racemase holoprotein and D-gluconate epimerase apoprotein, to identify key residues involved in substrate binding. This study demonstrates that the NPN cofactor is used by a diverse superfamily of α-hydroxyacid racemases and epimerases, widely expanding the scope of NPN-dependent enzymes.
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Affiliation(s)
- Benoît Desguin
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348, Louvain-La-Neuve, Belgium.
| | - Julian Urdiain-Arraiza
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348, Louvain-La-Neuve, Belgium
| | | | - Matthias Fellner
- Biochemistry, University of Otago, PO Box 56, Dunedin, Otago, 9054, New Zealand.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.,Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Tom Desmet
- Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Pascal Hols
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348, Louvain-La-Neuve, Belgium
| | - Patrice Soumillion
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348, Louvain-La-Neuve, Belgium
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24
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Shetty SA, Boeren S, Bui TPN, Smidt H, de Vos WM. Unravelling lactate-acetate and sugar conversion into butyrate by intestinal Anaerobutyricum and Anaerostipes species by comparative proteogenomics. Environ Microbiol 2020; 22:4863-4875. [PMID: 33001550 PMCID: PMC7702098 DOI: 10.1111/1462-2920.15269] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 11/28/2022]
Abstract
The d- and l-forms of lactate are important fermentation metabolites produced by intestinal bacteria but are found to negatively affect mucosal barrier function and human health. Both enantiomers of lactate can be converted with acetate into the presumed beneficial butyrate by a phylogenetically related group of anaerobes, including Anaerobutyricum and Anaerostipes spp. This is a low energy yielding process with a partially unknown pathway in Anaerobutyricum and Anaerostipes spp. and hence, we sought to address this via a comparative genomics, proteomics and physiology approach. We compared growth of Anaerobutyricum soehngenii on lactate with that on sucrose and sorbitol. Comparative proteomics revealed complete pathway of butyrate formation from sucrose, sorbitol and lactate. Notably, a gene cluster, lctABCDEF was abundantly expressed when grown on lactate. This gene cluster encodes a lactate dehydrogenase (lctD), electron transport proteins A and B (lctCB), nickel-dependent racemase (lctE), lactate permease (lctF) and short-chain acyl-CoA dehydrogenase (lctG). Investigation of available genomes of intestinal bacteria revealed this new gene cluster to be highly conserved in only Anaerobutyricum and Anaerostipes spp. Present study demonstrates that A. soehngenii and several related Anaerobutyricum and Anaerostipes spp. are highly adapted for a lifestyle involving lactate plus acetate utilization in the human intestinal tract.
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Affiliation(s)
- Sudarshan A Shetty
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, The Netherlands
| | - Thi P N Bui
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.,No Caelus Pharmaceuticals, Armsterdam, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.,Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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25
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Abstract
Background and objectives: Sepsis is defined as a life-threatening organ dysfunction syndrome, which occurs when the body's immune response to infection is impaired. The aim of the present study was to investigate serum Iron, Copper, Zinco, Cobalt, Chromium, Selenium, Vanadium, Nickel, Cadmium, and Aliminium levels in patients with sepsis.Materials and methods: This prospective and observational study was conducted at a tertiary care university hospital of Turkey from 2015 to 2016, and comprised patients with sepsis. Serum concentrations of 10 elements were analyzed using inductively coupled plasma mass spectrometry. Analyses were performed at the laboratory of Düzce University Scientific and Technological Research Application and Research Center. A total of 87 participants (52 men, 35 women; average age, 74.11 ± 14.26) were enrolled.Results: When evaluated in terms of trace elements, a significant difference was noted between the sepsis and control groups in terms of the levels of the five elements. Chromium, Iron, Nickel, Copper, and Cadmium levels were significantly higher in the sepsis group.Conclusion: Our study indicated in particular, Iron, Copper, Chromium, Nickel, and Cadmium levels were elevated in patients with sepsis.
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Affiliation(s)
- İdris Akkaş
- Department of Infectious Diseases, Oltu State Hospital, Ministry of Health, Erzurum, Turkey
| | - Nevin Ince
- Department of Infectious Diseases and Clinical Microbiology, Duzce University Faculty of Medicine, Duzce, Turkey
| | - Mehmet Ali Sungur
- Department of Biostatistics, Düzce University Faculty of Medicine, Düzce, Turkey
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26
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Abstract
At least two types of pincer complexes are known to exist in biology. A metal-pyrroloquinolone quinone (PQQ) cofactor was first identified in bacterial methanol dehydrogenase, and later also found in selected short-chain alcohol dehydrogenases of other microorganisms. The PQQ-associated metal can be calcium, magnesium, or a rare earth element depending on the enzyme sequence. Synthesis of this organic ligand requires a series of accessory proteins acting on a small peptide, PqqA. Binding of metal to PQQ yields an ONO-type pincer complex. More recently, a nickel-pincer nucleotide (NPN) cofactor was discovered in lactate racemase, LarA. This cofactor derives from nicotinic acid adenine dinucleotide via action of a carboxylase/hydrolase, sulfur transferase, and nickel insertase, resulting in an SCS-type pincer complex. The NPN cofactor likely occurs in selected other racemases and epimerases of bacteria, archaea, and a few eukaryotes.
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Affiliation(s)
- Jorge Nevarez
- Department of Chemistry, 578 South Shaw Lane, Michigan State University, East Lansing, Michigan 48824 (USA)
| | - Aiko Turmo
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Michigan State University, East Lansing, Michigan 48824 (USA)
| | - Jian Hu
- Department of Chemistry, 578 South Shaw Lane, Michigan State University, East Lansing, Michigan 48824 (USA).,Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Michigan State University, East Lansing, Michigan 48824 (USA)
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Michigan State University, East Lansing, Michigan 48824 (USA).,Department of Microbiology and Molecular Genetics, 567 Wilson Road, 2215 Biomedical Physical Sciences, Michigan State University, East Lansing, Michigan 48824 (USA)
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27
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Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE. Sci Rep 2020; 10:5830. [PMID: 32242052 PMCID: PMC7118094 DOI: 10.1038/s41598-020-62847-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/20/2020] [Indexed: 11/16/2022] Open
Abstract
Detailed crystallographic characterization of a tri-aspartate metal-binding site previously identified on the three-fold symmetry axis of a hexameric enzyme, LarE from Lactobacillus plantarum, was conducted. By screening an array of monovalent, divalent, and trivalent metal ions, we demonstrated that this metal binding site stoichiometrically binds Ca2+, Mn2+, Fe2+/Fe3+, Co2+, Ni2+, Cu2+, Zn2+, and Cd2+, but not monovalent metal ions, Cr3+, Mg2+, Y3+, Sr2+ or Ba2+. Extensive database searches resulted in only 13 similar metal binding sites in other proteins, indicative of the rareness of tri-aspartate architectures, which allows for engineering such a selective multivalent metal ion binding site into target macromolecules for structural and biophysical characterization.
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28
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Alfano M, Cavazza C. Structure, function, and biosynthesis of nickel-dependent enzymes. Protein Sci 2020; 29:1071-1089. [PMID: 32022353 DOI: 10.1002/pro.3836] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 01/23/2020] [Accepted: 01/23/2020] [Indexed: 12/17/2022]
Abstract
Nickel enzymes, present in archaea, bacteria, plants, and primitive eukaryotes are divided into redox and nonredox enzymes and play key functions in diverse metabolic processes, such as energy metabolism and virulence. They catalyze various reactions by using active sites of diverse complexities, such as mononuclear nickel in Ni-superoxide dismutase, glyoxylase I and acireductone dioxygenase, dinuclear nickel in urease, heteronuclear metalloclusters in [NiFe]-carbon monoxide dehydrogenase, acetyl-CoA decarbonylase/synthase and [NiFe]-hydrogenase, and even more complex cofactors in methyl-CoM reductase and lactate racemase. The presence of metalloenzymes in a cell necessitates a tight regulation of metal homeostasis, in order to maintain the appropriate intracellular concentration of nickel while avoiding its toxicity. As well, the biosynthesis and insertion of nickel active sites often require specific and elaborated maturation pathways, allowing the correct metal to be delivered and incorporated into the target enzyme. In this review, the phylogenetic distribution of nickel enzymes will be briefly described. Their tridimensional structures as well as the complexity of their active sites will be discussed. In view of the latest findings on these enzymes, a special focus will be put on the biosynthesis of their active sites and nickel activation of apo-enzymes.
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Affiliation(s)
- Marila Alfano
- University of Grenoble Alpes, CEA, CNRS, IRIG, CBM, Grenoble, France
| | - Christine Cavazza
- University of Grenoble Alpes, CEA, CNRS, IRIG, CBM, Grenoble, France
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29
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Shi R, Wodrich MD, Pan H, Tirani FF, Hu X. Functional Models of the Nickel Pincer Nucleotide Cofactor of Lactate Racemase. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Renyi Shi
- Laboratory of Inorganic Synthesis and CatalysisInstitute of Chemical Sciences and EngineeringÉcole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI BCH 3305 Lausanne 1015 Switzerland
| | - Matthew D. Wodrich
- Laboratory of Inorganic Synthesis and CatalysisInstitute of Chemical Sciences and EngineeringÉcole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI BCH 3305 Lausanne 1015 Switzerland
- Laboratory for Computational Molecular DesignInstitute of Chemical Science and EngineeringEcole Polytechnique Fédérale de Lausanne (EPFL) Lausanne 1015 Switzerland
| | - Hui‐Jie Pan
- Laboratory of Inorganic Synthesis and CatalysisInstitute of Chemical Sciences and EngineeringÉcole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI BCH 3305 Lausanne 1015 Switzerland
| | - Farzaneh Fadaei Tirani
- Laboratory of Inorganic Synthesis and CatalysisInstitute of Chemical Sciences and EngineeringÉcole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI BCH 3305 Lausanne 1015 Switzerland
| | - Xile Hu
- Laboratory of Inorganic Synthesis and CatalysisInstitute of Chemical Sciences and EngineeringÉcole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI BCH 3305 Lausanne 1015 Switzerland
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30
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Shi R, Wodrich MD, Pan HJ, Tirani FF, Hu X. Functional Models of the Nickel Pincer Nucleotide Cofactor of Lactate Racemase. Angew Chem Int Ed Engl 2019; 58:16869-16872. [PMID: 31535787 DOI: 10.1002/anie.201910490] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Indexed: 11/06/2022]
Abstract
A novel nickel pincer cofactor was recently discovered in lactate racemase. Reported here are three synthetic nickel pincer complexes that are both structural and functional models of the pincer cofactor in lactate racemase. DFT computations suggest the ipso-carbon atom of the pyridinium pincer ligands act as a hydride acceptor for lactate isomerization, whereas an organometallic pathway involving nickel-mediated β-hydride elimination is less favored.
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Affiliation(s)
- Renyi Shi
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305, Lausanne, 1015, Switzerland
| | - Matthew D Wodrich
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305, Lausanne, 1015, Switzerland.,Laboratory for Computational Molecular Design, Institute of Chemical Science and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Hui-Jie Pan
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305, Lausanne, 1015, Switzerland
| | - Farzaneh Fadaei Tirani
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305, Lausanne, 1015, Switzerland
| | - Xile Hu
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305, Lausanne, 1015, Switzerland
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31
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Abstract
The advancements of quantum chemical methods and computer power allow detailed mechanistic investigations of metalloenzymes. In particular, both quantum chemical cluster and combined QM/MM approaches have been used, which have been proven to successfully complement experimental studies. This review starts with a brief introduction of nickel-dependent enzymes and then summarizes theoretical studies on the reaction mechanisms of these enzymes, including NiFe hydrogenase, methyl-coenzyme M reductase, nickel CO dehydrogenase, acetyl CoA synthase, acireductone dioxygenase, quercetin 2,4-dioxygenase, urease, lactate racemase, and superoxide dismutase.
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32
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Xu S, Li J, Li J, Wu Y, Xiao Y, Hu C. D-Excess-LaA Production Directly from Biomass by Trivalent Yttrium Species. iScience 2019; 12:132-140. [PMID: 30682625 PMCID: PMC6352709 DOI: 10.1016/j.isci.2019.01.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/20/2018] [Accepted: 01/04/2019] [Indexed: 11/29/2022] Open
Abstract
D-lactic acid (D-LaA) synthesis directly from actual biomass via chemocatalytic conversion has shown high potential for satisfying its enormous demand in widespread applications. Here we report yttrium (Y(III))-species-catalyzed conversion of xylose and raw lignocelluloses to LaA with the highest yield of 87.3% (20% ee to D-LaA, ee%=(moles of D-LaA - moles of L-LaA)/(moles of D-LaA + moles of L-LaA) × 100). Combining experiments with theoretical modeling, we reveal that [Y(OH)2(H2O)2]+ is the possible catalytically active species, enabling the unconventional cleavage of C3-C4 in xylulose and the subsequent dehydration of glyceraldehyde to pyruvaldehyde (PRA). The distinct interactions between hydrated-PRA and [Y(OH)2(H2O)2]+ species contribute to the formation of different enantiomers, wherein H-migration via re-face attack leads to L-LaA and that via si-face attack yields D-LaA. The lower strain energy barrier is the origin of excess D-enantiomer formation. Y(III) exhibited outstanding efficiency for biomass conversion to lactic acid A high yield of D-excess-lactic acid with 20% ee value was obtained from xylose Reaction mechanism was successfully revealed by isotopic labeling and DFT study The lower strain energy induced the enantioselective formation of D-lactic acid
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Affiliation(s)
- Shuguang Xu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Jing Li
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Jianmei Li
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, PR China.
| | - Yi Wu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Yuan Xiao
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Changwei Hu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, PR China.
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33
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Hausmann B, Pelikan C, Rattei T, Loy A, Pester M. Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member. mBio 2019; 10:e02189-18. [PMID: 30755506 PMCID: PMC6372793 DOI: 10.1128/mbio.02189-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/04/2019] [Indexed: 01/05/2023] Open
Abstract
Microbial diversity in the environment is mainly concealed within the rare biosphere (all species with <0.1% relative abundance). While dormancy explains a low-abundance state very well, the mechanisms leading to rare but active microorganisms remain elusive. We used environmental systems biology to genomically and transcriptionally characterize "Candidatus Desulfosporosinus infrequens," a low-abundance sulfate-reducing microorganism cosmopolitan to freshwater wetlands, where it contributes to cryptic sulfur cycling. We obtained its near-complete genome by metagenomics of acidic peat soil. In addition, we analyzed anoxic peat soil incubated under in situ-like conditions for 50 days by Desulfosporosinus-targeted qPCR and metatranscriptomics. The Desulfosporosinus population stayed at a constant low abundance under all incubation conditions, averaging 1.2 × 106 16S rRNA gene copies per cm³ soil. In contrast, transcriptional activity of "Ca. Desulfosporosinus infrequens" increased at day 36 by 56- to 188-fold when minor amendments of acetate, propionate, lactate, or butyrate were provided with sulfate, compared to the no-substrate-control. Overall transcriptional activity was driven by expression of genes encoding ribosomal proteins, energy metabolism, and stress response but not by expression of genes encoding cell growth-associated processes. Since our results did not support growth of these highly active microorganisms in terms of biomass increase or cell division, they had to invest their sole energy for maintenance, most likely counterbalancing acidic pH conditions. This finding explains how a rare biosphere member can contribute to a biogeochemically relevant process while remaining in a zero-growth state over a period of 50 days.IMPORTANCE The microbial rare biosphere represents the largest pool of biodiversity on Earth and constitutes, in sum of all its members, a considerable part of a habitat's biomass. Dormancy or starvation is typically used to explain the persistence of low-abundance microorganisms in the environment. We show that a low-abundance microorganism can be highly transcriptionally active while remaining in a zero-growth state for at least 7 weeks. Our results provide evidence that this zero growth at a high cellular activity state is driven by maintenance requirements. We show that this is true for a microbial keystone species, in particular a cosmopolitan but permanently low-abundance sulfate-reducing microorganism in wetlands that is involved in counterbalancing greenhouse gas emissions. In summary, our results provide an important step forward in understanding time-resolved activities of rare biosphere members relevant for ecosystem functions.
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Affiliation(s)
- Bela Hausmann
- Research Network Chemistry meets Microbiology, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Claus Pelikan
- Research Network Chemistry meets Microbiology, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Research Network Chemistry meets Microbiology, Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Alexander Loy
- Research Network Chemistry meets Microbiology, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Michael Pester
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Microorganisms, Leibniz Institute DSMZ, Braunschweig, Germany
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
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34
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Fellner M, Rankin JA, Desguin B, Hu J, Hausinger RP. Analysis of the Active Site Cysteine Residue of the Sacrificial Sulfur Insertase LarE from Lactobacillus plantarum. Biochemistry 2018; 57:5513-5523. [PMID: 30157639 DOI: 10.1021/acs.biochem.8b00601] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
LarE from Lactobacillus plantarum is an ATP-dependent sulfur transferase that sacrifices its Cys176 sulfur atom to form a dehydroalanine (Dha) side chain during biosynthesis of the covalently linked nickel-pincer nucleotide (NPN) cofactor (pyridinium 3-thioamide-5-thiocarboxylic acid mononucleotide) of lactate racemase. Coenzyme A (CoA) stabilizes LarE and forms a CoA-Cys176 mixed disulfide with the protein. This study presents the crystal structure of the LarE/CoA complex, revealing protein interactions with CoA that mimic those for binding ATP. CoA weakly inhibits LarE activity, and the persulfide of CoA is capable of partially regenerating functional LarE from the Dha176 form of the protein. The physiological relevance of this cycling reaction is unclear. A new form of LarE was discovered, an NPN-LarE covalent adduct, explaining prior results in which activation of the lactate racemase apoprotein required only the isolated LarE. The crystal structure of the inactive C176A variant revealed a fold essentially identical to that of wild-type LarE. Additional active site variants of LarE were created and their activities characterized, with all LarE variants analyzed in terms of the structure. Finally, the L. plantarum LarE structure was compared to a homology model of Thermoanaerobacterium thermosaccharolyticum LarE, predicted to contain three cysteine residues at the active site, and to other proteins with a similar fold and multiple active site cysteine residues. These findings suggest that some LarE orthologs may not be sacrificial but instead may catalyze sulfur transfer by using a persulfide mechanism or from a labile site on a [4Fe-4S] cluster at this position.
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Affiliation(s)
- Matthias Fellner
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Joel A Rankin
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Benoît Desguin
- Institute of Life Sciences , Université catholique de Louvain , B-1348 Louvain-La-Neuve , Belgium
| | - Jian Hu
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States.,Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States.,Department of Microbiology and Molecular Genetics , Michigan State University , East Lansing , Michigan 48824 , United States
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35
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Hausinger RP, Desguin B, Fellner M, Rankin JA, Hu J. Nickel-pincer nucleotide cofactor. Curr Opin Chem Biol 2018; 47:18-23. [PMID: 30015232 DOI: 10.1016/j.cbpa.2018.06.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 06/15/2018] [Accepted: 06/19/2018] [Indexed: 10/28/2022]
Abstract
A novel organometallic cofactor, nickel pyridinium-3,5-dithiocarboxylic acid mononucleotide, was recently discovered in lactate racemase (LarA) of Lactobacillus plantarum. This review summarizes the substantial progress made in uncovering the function of this cofactor as a transient hydride acceptor in the LarA mechanism. The latest developments related to cofactor biosynthesis reveal insights into a pathway in which LarB serves as a nicotinic acid adenine dinucleotide hydrolase/carboxylase, LarE acts as a sacrificial sulfur transferase, and LarC functions as a nickel insertase, forming the nickel-pincer nucleotide cofactor that becomes covalently tethered to LarA in some bacteria. Bioinformatic studies reveal a widespread occurrence of larA, larB, larC, and larE orthologs in microorganisms, and additional roles for the cofactor are considered.
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Affiliation(s)
- Robert P Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
| | - Benoît Desguin
- Institute of Life Sciences, Université catholique de Louvain, B-1348 Louvain-La-Neuve, Belgium
| | - Matthias Fellner
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Joel A Rankin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
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36
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Desguin B, Fellner M, Riant O, Hu J, Hausinger RP, Hols P, Soumillion P. Biosynthesis of the nickel-pincer nucleotide cofactor of lactate racemase requires a CTP-dependent cyclometallase. J Biol Chem 2018; 293:12303-12317. [PMID: 29887527 DOI: 10.1074/jbc.ra118.003741] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/29/2018] [Indexed: 11/06/2022] Open
Abstract
Bacterial lactate racemase is a nickel-dependent enzyme that contains a cofactor, nickel pyridinium-3,5-bisthiocarboxylic acid mononucleotide, hereafter named nickel-pincer nucleotide (NPN). The LarC enzyme from the bacterium Lactobacillus plantarum participates in NPN biosynthesis by inserting nickel ion into pyridinium-3,5-bisthiocarboxylic acid mononucleotide. This reaction, known in organometallic chemistry as a cyclometalation, is characterized by the formation of new metal-carbon and metal-sulfur σ bonds. LarC is therefore the first cyclometallase identified in nature, but the molecular mechanism of LarC-catalyzed cyclometalation is unknown. Here, we show that LarC activity requires Mn2+-dependent CTP hydrolysis. The crystal structure of the C-terminal domain of LarC at 1.85 Å resolution revealed a hexameric ferredoxin-like fold and an unprecedented CTP-binding pocket. The loss-of-function of LarC variants with alanine variants of acidic residues leads us to propose a carboxylate-assisted mechanism for nickel insertion. This work also demonstrates the in vitro synthesis and purification of the NPN cofactor, opening new opportunities for the study of this intriguing cofactor and of NPN-utilizing enzymes.
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Affiliation(s)
| | | | - Olivier Riant
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, B-1348 Louvain-La-Neuve, Belgium and
| | - Jian Hu
- the Departments of Biochemistry and Molecular Genetics.,Chemistry, and
| | - Robert P Hausinger
- the Departments of Biochemistry and Molecular Genetics.,Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
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David B, Duchêne MC, Haustenne GL, Pérez-Núñez D, Chapot-Chartier MP, De Bolle X, Guédon E, Hols P, Hallet B. PBP2b plays a key role in both peripheral growth and septum positioning in Lactococcus lactis. PLoS One 2018; 13:e0198014. [PMID: 29791496 PMCID: PMC5965867 DOI: 10.1371/journal.pone.0198014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 05/11/2018] [Indexed: 12/11/2022] Open
Abstract
Lactococcus lactis is an ovoid bacterium that forms filaments during planktonic and biofilm lifestyles by uncoupling cell division from cell elongation. In this work, we investigate the role of the leading peptidoglycan synthase PBP2b that is dedicated to cell elongation in ovococci. We show that the localization of a fluorescent derivative of PBP2b remains associated to the septal region and superimposed with structural changes of FtsZ during both vegetative growth and filamentation indicating that PBP2b remains intimately associated to the division machinery during the whole cell cycle. In addition, we show that PBP2b-negative cells of L. lactis are not only defective in peripheral growth; they are also affected in septum positioning. This septation defect does not simply result from the absence of the protein in the cell growth machinery since it is also observed when PBP2b-deficient cells are complemented by a catalytically inactive variant of PBP2b. Finally, we show that round cells resulting from β-lactam treatment are not altered in septation, suggesting that shape elongation as such is not a major determinant for selection of the division site. Altogether, we propose that the specific PBP2b transpeptidase activity at the septum plays an important role for tagging future division sites during L. lactis cell cycle.
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Affiliation(s)
- Blandine David
- Institut des Sciences de la Vie (ISV), Université catholique de Louvain (UCL), Louvain-la-Neuve, Belgium
| | - Marie-Clémence Duchêne
- Institut des Sciences de la Vie (ISV), Université catholique de Louvain (UCL), Louvain-la-Neuve, Belgium
| | - Gabrielle Laurie Haustenne
- Institut des Sciences de la Vie (ISV), Université catholique de Louvain (UCL), Louvain-la-Neuve, Belgium
| | - Daniel Pérez-Núñez
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Xavier De Bolle
- Microorganisms Biology Research Unit (URBM), University of Namur (UNamur), Namur, Belgium
| | - Eric Guédon
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- STLO, INRA, Agrocampus Ouest, Rennes, France
| | - Pascal Hols
- Institut des Sciences de la Vie (ISV), Université catholique de Louvain (UCL), Louvain-la-Neuve, Belgium
- * E-mail: (BH); (PH)
| | - Bernard Hallet
- Institut des Sciences de la Vie (ISV), Université catholique de Louvain (UCL), Louvain-la-Neuve, Belgium
- * E-mail: (BH); (PH)
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38
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Xue G, Lai S, Li X, Zhang W, You J, Chen H, Qian Y, Gao P, Liu Z, Liu Y. Efficient bioconversion of organic wastes to high optical activity of l-lactic acid stimulated by cathode in mixed microbial consortium. WATER RESEARCH 2018; 131:1-10. [PMID: 29253664 DOI: 10.1016/j.watres.2017.12.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/27/2017] [Accepted: 12/12/2017] [Indexed: 06/07/2023]
Abstract
Lactic acid is one of the emerging top biomass derived platform chemicals that can be fermented from organic wastes. This study evaluated the potential of Cathodic Electro-Fermentation (CEF) as a novel approach to enhance the yield of high optical activity (OA) of l-lactic acid from organic wastes using mixed microbial consortium. The fermentation process was stimulated through the cathode applied with -100 mV versus standard hydrogen electrode (SHE), which contributed to 4.73 times higher lactic acid productivity (0.6578 g L-1 h-1) compared to that in the open circuit control (0.1392 g L-1 h-1), and an improved OA of l-lactic acid was also observed (42.3% vs. 3.6% of the open circuit control). The study elucidated that the optimal voltage at -100 mV promoted the conversion of pyruvate to l-lactate by 77.9% compared to the Blank, which triggered the generation of l-lactic acid to occur rapidly even at low concentration of pyruvate. The significant variation of microbial community in family- and genus-level distributions were observed in CEF system. Furthermore, the open-circuit operation test demonstrated that the cathode providing in-situ electron supply was essential to achieve high efficient bioconversion of organic wastes to lactic acid. Our work highlights the feasibility of CEF to steer high value-added fermentation products deriving from organic wastes by the mixed microbial consortium.
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Affiliation(s)
- Gang Xue
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Sizhou Lai
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Xiang Li
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China.
| | - Wenjuan Zhang
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Jiguang You
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Hong Chen
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Yajie Qian
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Pin Gao
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Zhenhong Liu
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Yanan Liu
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
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Zhang T, Zhang X, Chung LW. Computational Insights into the Reaction Mechanisms of Nickel-Catalyzed Hydrofunctionalizations and Nickel-Dependent Enzymes. ASIAN J ORG CHEM 2018. [DOI: 10.1002/ajoc.201700645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Tonghuan Zhang
- Department of Chemistry; South University of Science and Technology of China (SUSTech); Shenzhen 518055 China
- Lab of Computational Chemistry and Drug Design; Key Laboratory of Chemical Genomics; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Xiaoyong Zhang
- Department of Chemistry; South University of Science and Technology of China (SUSTech); Shenzhen 518055 China
| | - Lung Wa Chung
- Department of Chemistry; South University of Science and Technology of China (SUSTech); Shenzhen 518055 China
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40
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Rankin JA, Mauban RC, Fellner M, Desguin B, McCracken J, Hu J, Varganov SA, Hausinger RP. Lactate Racemase Nickel-Pincer Cofactor Operates by a Proton-Coupled Hydride Transfer Mechanism. Biochemistry 2018; 57:3244-3251. [PMID: 29489337 DOI: 10.1021/acs.biochem.8b00100] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lactate racemase (LarA) of Lactobacillus plantarum contains a novel organometallic cofactor with nickel coordinated to a covalently tethered pincer ligand, pyridinium-3-thioamide-5-thiocarboxylic acid mononucleotide, but its function in the enzyme mechanism has not been elucidated. This study presents direct evidence that the nickel-pincer cofactor facilitates a proton-coupled hydride transfer (PCHT) mechanism during LarA-catalyzed lactate racemization. No signal was detected by electron paramagnetic resonance spectroscopy for LarA in the absence or presence of substrate, consistent with a +2 metal oxidation state and inconsistent with a previously proposed proton-coupled electron transfer mechanism. Pyruvate, the predicted intermediate for a PCHT mechanism, was observed in quenched solutions of LarA. A normal substrate kinetic isotope effect ( kH/ kD of 3.11 ± 0.17) was established using 2-α-2H-lactate, further supporting a PCHT mechanism. UV-visible spectroscopy revealed a lactate-induced perturbation of the cofactor spectrum, notably increasing the absorbance at 340 nm, and demonstrated an interaction of the cofactor with the inhibitor sulfite. A crystal structure of LarA provided greater resolution (2.4 Å) than previously reported and revealed sulfite binding to the pyridinium C4 atom of the reduced pincer cofactor, mimicking hydride reduction during a PCHT catalytic cycle. Finally, computational modeling supports hydride transfer to the cofactor at the C4 position or to the nickel atom, but with formation of a nickel-hydride species requiring dissociation of the His200 metal ligand. In aggregate, these studies provide compelling evidence that the nickel-pincer cofactor acts by a PCHT mechanism.
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Affiliation(s)
| | - Robert C Mauban
- Department of Chemistry , University of Nevada , Reno , Nevada 89557 , United States
| | | | - Benoît Desguin
- Institute of Life Sciences , Université catholique de Louvain , B-1348 Louvain-La-Neuve , Belgium
| | | | | | - Sergey A Varganov
- Department of Chemistry , University of Nevada , Reno , Nevada 89557 , United States
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41
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Li H, Wang X, Tian G, Liu Y. Insights into the dioxygen activation and catalytic mechanism of the nickel-containing quercetinase. Catal Sci Technol 2018. [DOI: 10.1039/c8cy00187a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The catalytic mechanism of Ni-QueDFLA was elucidated by QM/MM calculations, and the different reactivities of nickel and iron were illuminated.
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Affiliation(s)
- Hong Li
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Xiya Wang
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Ge Tian
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
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43
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Mügge C, Kourist R. Practical Considerations Regarding the Choice of the Best High-Throughput Assay. Methods Mol Biol 2018; 1685:189-208. [PMID: 29086310 DOI: 10.1007/978-1-4939-7366-8_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
All protein engineering studies include the stage of identifying and characterizing variants within a mutant library by employing a suitable assay or selection method. A large variety of different assay approaches for different enzymes have been developed in the last few decades, and the throughput performance of these assays vary considerably. Thus, the concept of a protein engineering study must be adapted to the available assay methods. This introductory review chapter describes different assay concepts on selected examples, including selection and screening approaches, detection of pH and cosubstrate changes, coupled enzyme assays, methods using surrogate substrates and selective derivatization. The given examples should guide and inspire the reader when choosing and developing own high-throughput screening approaches.
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Affiliation(s)
- Carolin Mügge
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Robert Kourist
- Institute of Molecular Biotechnology, TU Graz, Petersgasse 14, A8010, Graz, Austria.
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Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H 2 and CO 2 compared to organotrophic growth with fructose. Sci Rep 2017; 7:13135. [PMID: 29030620 PMCID: PMC5640608 DOI: 10.1038/s41598-017-12712-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/14/2017] [Indexed: 01/13/2023] Open
Abstract
Clostridium ljungdahlii derives energy by lithotrophic and organotrophic acetogenesis. C. ljungdahlii was grown organotrophically with fructose and also lithotrophically, either with syngas - a gas mixture containing hydrogen (H2), carbon dioxide (CO2), and carbon monoxide (CO), or with H2 and CO2. Gene expression was compared quantitatively by microarrays using RNA extracted from all three conditions. Gene expression with fructose and with H2/CO2 was compared by RNA-Seq. Upregulated genes with both syngas and H2/CO2 (compared to fructose) point to the urea cycle, uptake and degradation of peptides and amino acids, response to sulfur starvation, potentially NADPH-producing pathways involving (S)-malate and ornithine, quorum sensing, sporulation, and cell wall remodeling, suggesting a global and multicellular response to lithotrophic conditions. With syngas, the upregulated (R)-lactate dehydrogenase gene represents a route of electron transfer from ferredoxin to NAD. With H2/CO2, flavodoxin and histidine biosynthesis genes were upregulated. Downregulated genes corresponded to an intracytoplasmic microcompartment for disposal of methylglyoxal, a toxic byproduct of glycolysis, as 1-propanol. Several cytoplasmic and membrane-associated redox-active protein genes were differentially regulated. The transcriptomic profiles of C. ljungdahlii in lithotrophic and organotrophic growth modes indicate large-scale physiological and metabolic differences, observations that may guide biofuel and commodity chemical production with this species.
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Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE. Proc Natl Acad Sci U S A 2017; 114:9074-9079. [PMID: 28784764 DOI: 10.1073/pnas.1704967114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The lar operon in Lactobacillus plantarum encodes five Lar proteins (LarA/B/C/D/E) that collaboratively synthesize and incorporate a niacin-derived Ni-containing cofactor into LarA, an Ni-dependent lactate racemase. Previous studies have established that two molecules of LarE catalyze successive thiolation reactions by donating the sulfur atom of their exclusive cysteine residues to the substrate. However, the catalytic mechanism of this very unusual sulfur-sacrificing reaction remains elusive. In this work, we present the crystal structures of LarE in ligand-free and several ligand-bound forms, demonstrating that LarE is a member of the N-type ATP pyrophosphatase (PPase) family with a conserved N-terminal ATP PPase domain and a unique C-terminal domain harboring the putative catalytic site. Structural analysis, combined with structure-guided mutagenesis, leads us to propose a catalytic mechanism that establishes LarE as a paradigm for sulfur transfer through sacrificing its catalytic cysteine residue.
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46
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Desguin B, Soumillion P, Hausinger RP, Hols P. Unexpected complexity in the lactate racemization system of lactic acid bacteria. FEMS Microbiol Rev 2017; 41:S71-S83. [DOI: 10.1093/femsre/fux021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/11/2017] [Indexed: 12/30/2022] Open
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47
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Yu MJ, Chen SL. From NAD + to Nickel Pincer Complex: A Significant Cofactor Evolution Presented by Lactate Racemase. Chemistry 2017; 23:7545-7557. [PMID: 28374531 DOI: 10.1002/chem.201700405] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Indexed: 02/02/2023]
Abstract
Lactate racemase (LarA), a new nickel enzyme discovered recently, catalyzes the racemization between d- and l-lactates with a novel nickel pincer cofactor (Ni-PTTMN) derived from nicotinic acid. In this study, by using DFT and a 200-atom active-site model, LarA is revealed to employ a modified proton-coupled hydride-transfer mechanism in which a hydride is transferred to a cofactor pyridine carbon from the substrate α-carbon along with proton transfer from the substrate hydroxy group to a histidine, and then moved back from the opposite side. Tyr294 and Lys298 provide significant acceleration effects by orientating substrates and stabilizing the negative charge developing at the substrate hydroxy oxygen. The barrier was determined to be 12.0 kcal mol-1 , which reveals enhanced racemase activity relative to the LarA reaction using NAD+ -like cofactors. Compared with NAD+ , Ni-PTTMN has a stronger hydride-addition reactivity in moderate and high environmental polarity and may fit perfectly the moderately polar active site of LarA.
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Affiliation(s)
- Ming-Jia Yu
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P.R. China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P.R. China
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48
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Xia W, Li H, Sun H. Nickel Metallochaperones: Structure, Function, and Nickel-Binding Properties. THE BIOLOGICAL CHEMISTRY OF NICKEL 2017. [DOI: 10.1039/9781788010580-00284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Nickel-containing enzymes catalyze a series of important biochemical processes in both prokaryotes and eukaryotes. The maturation of the enzymes requires the proper assembly of the nickel-containing active sites, which involves a battery of nickel metallochaperones that exert metal delivery and storage functions. “Cross-talk” also exists between different nickel enzyme maturation processes. This chapter summarizes the updated knowledge about the nickel chaperones based on biochemical and structural biology research, and discusses the possible nickel delivery mechanisms.
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Affiliation(s)
- Wei Xia
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry Sun Yat-sen University Guangzhou 510275 China
| | - Hongyan Li
- Department of Chemistry, The University of Hong Kong Hong Kong SAR China
| | - Hongzhe Sun
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry Sun Yat-sen University Guangzhou 510275 China
- Department of Chemistry, The University of Hong Kong Hong Kong SAR China
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49
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Structure and mechanism of a group-I cobalt energy coupling factor transporter. Cell Res 2017; 27:675-687. [PMID: 28322252 DOI: 10.1038/cr.2017.38] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/08/2017] [Accepted: 02/15/2017] [Indexed: 12/20/2022] Open
Abstract
Energy-coupling factor (ECF) transporters are a large family of ATP-binding cassette transporters recently identified in microorganisms. Responsible for micronutrient uptake from the environment, ECF transporters are modular transporters composed of a membrane substrate-binding component EcfS and an ECF module consisting of an integral membrane scaffold component EcfT and two cytoplasmic ATP binding/hydrolysis components EcfA/A'. ECF transporters are classified into groups I and II. Currently, the molecular understanding of group-I ECF transporters is very limited, partly due to a lack of transporter complex structural information. Here, we present structures and structure-based analyses of the group-I cobalt ECF transporter CbiMNQO, whose constituting subunits CbiM/CbiN, CbiQ, and CbiO correspond to the EcfS, EcfT, and EcfA components of group-II ECF transporters, respectively. Through reconstitution of different CbiMNQO subunits and determination of related ATPase and transporter activities, the substrate-binding subunit CbiM was found to stimulate CbiQO's basal ATPase activity. The structure of CbiMQO complex was determined in its inward-open conformation and that of CbiO in β, γ-methyleneadenosine 5'-triphosphate-bound closed conformation. Structure-based analyses revealed interactions between different components, substrate-gating function of the L1 loop of CbiM, and conformational changes of CbiO induced by ATP binding and product release within the CbiMNQO transporter complex. These findings enabled us to propose a working model of the CbiMNQO transporter, in which the transport process requires the rotation or toppling of both CbiQ and CbiM, and CbiN might function in coupling conformational changes between CbiQ and CbiM.
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50
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Dannheim H, Riedel T, Neumann-Schaal M, Bunk B, Schober I, Spröer C, Chibani CM, Gronow S, Liesegang H, Overmann J, Schomburg D. Manual curation and reannotation of the genomes of Clostridium difficile 630Δerm and C. difficile 630. J Med Microbiol 2017; 66:286-293. [DOI: 10.1099/jmm.0.000427] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Henning Dannheim
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig and Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Meina Neumann-Schaal
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig and Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover–Braunschweig, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Isabel Schober
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover–Braunschweig, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cynthia Maria Chibani
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Georg-August-University Göttingen, Grisebachstraße 8, 37077 Göttingen, Germany
| | - Sabine Gronow
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover–Braunschweig, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Heiko Liesegang
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Georg-August-University Göttingen, Grisebachstraße 8, 37077 Göttingen, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover–Braunschweig, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig and Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany
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