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Xu J, Zhao R, Liu A, Li L, Li S, Li Y, Qu M, Di Y. To live or die: "Fine-tuning" adaptation revealed by systemic analyses in symbiotic bathymodiolin mussels from diverse deep-sea extreme ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170434. [PMID: 38278266 DOI: 10.1016/j.scitotenv.2024.170434] [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: 10/16/2023] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
Hydrothermal vents (HVs) and cold seeps (CSs) are typical deep-sea extreme ecosystems with their own geochemical characteristics to supply the unique living conditions for local communities. Once HVs or CSs stop emission, the dramatic environmental change would pose survival risks to deep-sea organisms. Up to now, limited knowledge has been available to understand the biological responses and adaptive strategy to the extreme environments and their transition from active to extinct stage, mainly due to the technical difficulties and lack of representative organisms. In this study, bathymodiolin mussels, the dominant and successful species surviving in diverse deep-sea extreme ecosystems, were collected from active and extinct HVs (Southwest Indian Ocean) or CSs (South China Sea) via two individual cruises. The transcriptomic analysis and determination of multiple biological indexes in stress defense and metabolic systems were conducted in both gills and digestive glands of mussels, together with the metagenomic analysis of symbionts in mussels. The results revealed the ecosystem- and tissue-specific transcriptional regulation in mussels, addressing the autologous adaptations in antioxidant defense, energy utilization and key compounds (i.e. sulfur) metabolism. In detail, the successful antioxidant defense contributed to conquering the oxidative stress induced during the unavoidable metabolism of xenobiotics commonly existing in the extreme ecosystems; changes in metabolic rate functioned to handle toxic matters in different surroundings; upregulated gene expression of sulfide:quinone oxidoreductase indicated an active sulfide detoxification in mussels from HVs and active stage of HVs & CSs. Coordinately, a heterologous adaptation, characterized by the functional compensation between symbionts and mussels in energy utilization, sulfur and carbon metabolism, was also evidenced by the bacterial metagenomic analysis. Taken together, a new insight was proposed that symbiotic bathymodiolin mussels would develop a "finetuning" strategy combining the autologous and heterologous regulations to fulfill the efficient and effective adaptations for successful survival.
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Affiliation(s)
- Jianzhou Xu
- Ocean College, Zhejiang University, Zhoushan 316000, China; Hainan Institute of Zhejiang University, Sanya 572024, China
| | - Ruoxuan Zhao
- Ocean College, Zhejiang University, Zhoushan 316000, China
| | - Ao Liu
- Ocean College, Zhejiang University, Zhoushan 316000, China
| | - Liya Li
- Ocean College, Zhejiang University, Zhoushan 316000, China; Hainan Institute of Zhejiang University, Sanya 572024, China
| | - Shuimei Li
- Ocean College, Zhejiang University, Zhoushan 316000, China
| | - Yichen Li
- Ocean College, Zhejiang University, Zhoushan 316000, China
| | - Mengjie Qu
- Ocean College, Zhejiang University, Zhoushan 316000, China; Hainan Institute of Zhejiang University, Sanya 572024, China
| | - Yanan Di
- Ocean College, Zhejiang University, Zhoushan 316000, China; Hainan Institute of Zhejiang University, Sanya 572024, China.
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Wang J, Cheng Z, Wang J, Chen D, Chen J, Yu J, Qiu S, Dionysiou DD. Enhancement of bio-S 0 recovery and revealing the inhibitory effect on microorganisms under high sulfide loading. ENVIRONMENTAL RESEARCH 2023; 238:117214. [PMID: 37783332 DOI: 10.1016/j.envres.2023.117214] [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: 07/22/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023]
Abstract
Biodesulfurization is a mature technology, but obtaining biosulfur (S0) that can be easily settled naturally is still a challenge. Increasing the sulfide load is one of the known methods to obtain better settling of S0. However, the inhibitory effect of high levels of sulfide on microbes has also not been well studied. We constructed a high loading sulfide (1.55-10.86 kg S/m3/d) biological removal system. 100% sulfide removal and 0.56-2.53 kg S/m3/d S0 (7.0 ± 0.09-16.4 ± 0.25 μm) recovery were achieved at loads of 1.55-7.75 kg S/m3/d. Under the same load, S0 in the reflux sedimentation tank, which produced larger S0 particles (24.2 ± 0.73-53.8 ± 0.70 μm), increased the natural settling capacity and 45% recovery. For high level sulfide inhibitory effect, we used metagenomics and metatranscriptomics analyses. The increased sulfide load significantly inhibited the expression of flavin cytochrome c sulfide dehydrogenase subunit B (fccB) (Decreased from 615 ± 75 to 30 ± 5 TPM). At this time sulfide quinone reductase (SQR) (324 ± 185-1197 ± 51 TPM) was mainly responsible for sulfide oxidation and S0 production. When the sulfide load reached 2800 mg S/L, the SQR (730 ± 100 TPM) was also suppressed. This resulted in the accumulation of sulfide, causing suppression of carbon sequestration genes (Decreased from 3437 ± 842 to 665 ± 175 TPM). Other inhibitory effects included inhibition of microbial respiration, production of reactive oxygen species, and DNA damage. More sulfide-oxidizing bacteria (SOB) and newly identified potential SOB (99.1%) showed some activity (77.6%) upon sulfide accumulation. The main microorganisms in the sulfide accumulation environment were Thiomicrospiracea and Burkholderiaceae, whose sulfide oxidation capacity and respiration were not significantly inhibited. This study provides a new approach to enhance the natural sedimentation of S0 and describes new microbial mechanisms for the inhibitory effects of sulfide.
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Affiliation(s)
- Junjie Wang
- College of Environment, Zhejiang University of Technology, 18 Chao-wang Road, Hangzhou, 310014, China; Key Laboratory of Environmental Pollution Control Technology Research of Zhejiang Province, Eco-environmental Science Research & Design Institute of Zhejiang Province, Hangzhou, 310007, China
| | - Zhuowei Cheng
- College of Environment, Zhejiang University of Technology, 18 Chao-wang Road, Hangzhou, 310014, China; Key Laboratory of Environmental Pollution Control Technology Research of Zhejiang Province, Eco-environmental Science Research & Design Institute of Zhejiang Province, Hangzhou, 310007, China.
| | - Jiade Wang
- College of Environment, Zhejiang University of Technology, 18 Chao-wang Road, Hangzhou, 310014, China
| | - Dongzhi Chen
- School of Petrochemical Engineering & Environment, Zhejiang Ocean University, Zhoushan 316004, China
| | - Jianmeng Chen
- College of Environment, Zhejiang University of Technology, 18 Chao-wang Road, Hangzhou, 310014, China
| | - Jianming Yu
- College of Environment, Zhejiang University of Technology, 18 Chao-wang Road, Hangzhou, 310014, China
| | - Songkai Qiu
- College of Environment, Zhejiang University of Technology, 18 Chao-wang Road, Hangzhou, 310014, China; Haina-Water Engineering Research Center, Yangtze Delta Region Institute of Tsinghua University, Zhejiang, Jiaxing 314000, China
| | - Dionysios D Dionysiou
- Environmental Engineering and Science Program, University of Cincinnati, Cincinnati, OH, 45221, USA
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Sun K, Yu M, Zhu XY, Xue CX, Zhang Y, Chen X, Yao P, Chen L, Fu L, Yang Z, Zhang XH. Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole. Microbiol Spectr 2023; 11:e0114923. [PMID: 37623326 PMCID: PMC10580873 DOI: 10.1128/spectrum.01149-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/13/2023] [Indexed: 08/26/2023] Open
Abstract
The Sansha Yongle Blue Hole (SYBH), the deepest blue hole in the world, is an excellent habitat for revealing biogeochemical cycles in the anaerobic environment. However, how sulfur cycling is mediated by microorganisms in the SYBH hasn't been fully understood. In this study, the water layers of the SYBH were divided into oxic zone, hypoxic zone, anoxic zone I and II, and microbial-mediated sulfur cycling in the SYBH was comprehensively interpreted. The 16S rRNA genes/transcripts analyses showed that the microbial community structures associated with the sulfur cycling in each zone had distinctive features. Sulfur-oxidizing bacteria were mostly constituted by Gammaproteobacteria, Alphaproteobacteria, Campylobacterota, and Chlorobia above the anoxic zone I and sulfate-reducing bacteria were dominated by Desulfobacterota in anoxic zones. Metagenomic analyses showed that the sulfide-oxidation-related gene sqr and genes encoding the Sox system were mainly distributed in the anoxic zone I, while genes related to dissimilatory sulfate reduction and sulfur intermediate metabolite reduction were mainly distributed in the anoxic zone II, indicating different sulfur metabolic processes between these two zones. Moreover, sulfur-metabolism-related genes were identified in 81 metagenome-assembled genomes (MAGs), indicating a high diversity of microbial communities involved in sulfur cycling. Among them, three MAGs from the candidate phyla JdFR-76 and AABM5-125-24 with genes related to dissimilatory sulfate reduction exhibited distinctive metabolic features. Our results showed unique and novel microbial populations in the SYBH sulfur cycle correlated to the sharp redox gradients, revealing complex biogeochemical processes in this extreme environment. IMPORTANCE Oxygen-deficient regions in the global ocean are expanding rapidly and affect the growth, reproduction and ecological processes of marine organisms. The anaerobic water body of about 150 m in the Sansha Yongle Blue Hole (SYBH) provided a suitable environment to study the specific microbial metabolism in anaerobic seawater. Here, we found that the vertical distributions of the total and active communities of sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) were different in each water layer of the SYBH according to the dissolved oxygen content. Genes related to sulfur metabolism also showed distinct stratification characteristics. Furthermore, we have obtained diverse metagenome-assembled genomes, some of which exhibit special sulfur metabolic characteristics, especially candidate phyla JdFR-76 and AABM5-125-24 were identified as potential novel SRB. The results of this study will promote further understanding of the sulfur cycle in extreme environments, as well as the environmental adaptability of microorganisms in blue holes.
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Affiliation(s)
- Kai Sun
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Min Yu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiao-Yu Zhu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chun-Xu Xue
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yunhui Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xing Chen
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Lin Chen
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Liang Fu
- Sansha Track Ocean Coral Reef Conservation Research Institute, Sansha, China
| | - Zuosheng Yang
- College of Marine Geosciences, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
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Sousa FM, Fernandes B, Pereira MM. The protein family of pyruvate:quinone oxidoreductases: Amino acid sequence conservation and taxonomic distribution. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148958. [PMID: 36758662 DOI: 10.1016/j.bbabio.2023.148958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/24/2022] [Accepted: 02/01/2023] [Indexed: 02/11/2023]
Abstract
Pyruvate:quinone oxidoreductases (PQOs) catalyse the oxidative decarboxylation of pyruvate to acetate and concomitant reduction of quinone to quinol with the release of CO2. They are thiamine pyrophosphate (TPP) and flavin-adenine dinucleotide (FAD) containing enzymes, which interact with the membrane in a monotopic way. PQOs are considered as part of alternatives to most recognized pyruvate catabolizing pathways, and little is known about their taxonomic distribution and structural/functional relationship. In this bioinformatics work we tackled these gaps in PQO knowledge. We used the KEGG database to identify PQO coding genes, performed a multiple sequence analysis which allowed us to study the amino acid conservation on these enzymes, and looked at their possible cellular function. We observed that PQOS are enzymes exclusively present in prokaryotes with most of the sequences identified in bacteria. Regarding the amino acid sequence conservation, we found that 75 amino acid residues (out of 570, on average) have a conservation over 90 %, and that the most conserved regions in the protein are observed around the TPP and FAD binding sites. We systematized the presence of conserved features involved in Mg2+, TPP and FAD binding, as well as residues directly linked to the catalytic mechanism. We also established the presence of a new motif named "HEH lock", possibly involved in the dimerization process. The results here obtained for the PQO protein family contribute to a better understanding of the biochemistry of these respiratory enzymes.
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Affiliation(s)
- Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal; BioISI-Biosystems & Integrative Sciences Institute and Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Bárbara Fernandes
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal; BioISI-Biosystems & Integrative Sciences Institute and Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal; BioISI-Biosystems & Integrative Sciences Institute and Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal.
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Degli Esposti M. The bacterial origin of mitochondria: Incorrect phylogenies and the importance of metabolic traits. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 374:1-35. [PMID: 36858653 DOI: 10.1016/bs.ircmb.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
This article provides an updated review on the evolution of mitochondria from bacteria, which were likely related to extant alphaproteobacteria. Particular attention is given to the timeline of oxygen history on Earth and the entwined phases of eukaryotic evolution that produced the animals that still populate our planet. Mitochondria of early-branching unicellular eukaryotes and plants appear to retain partial or vestigial traits that were directly inherited from the alphaproteobacterial ancestors of the organelles. Most of such traits define the current aerobic physiology of mitochondria. Conversely, the anaerobic traits that would be essential in the syntrophic associations postulated for the evolution of eukaryotic cells are scantly present in extant alphaproteobacteria, and therefore cannot help defining from which bacterial lineage the ancestors of mitochondria originated. This question has recently been addressed quantitatively, reaching the novel conclusion that marine bacteria related to Iodidimonas may be the living relatives of protomitochondria. Additional evidence is presented that either support or does not contrast this novel view of the bacterial origin of mitochondria.
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Chen Y, Lyu Y, Zhang J, Li Q, Lyu L, Zhou Y, Kong J, Zeng X, Zhang S, Li J. Riddles of Lost City: Chemotrophic Prokaryotes Drives Carbon, Sulfur, and Nitrogen Cycling at an Extinct Cold Seep, South China Sea. Microbiol Spectr 2023; 11:e0333822. [PMID: 36511717 PMCID: PMC9927161 DOI: 10.1128/spectrum.03338-22] [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: 08/24/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Deep-sea cold seeps are one of the most productive ecosystems that sustained by hydrocarbons carried by the fluid. Once the seep fluid ceases, the thriving autotrophic communities die out, terming as the extinct seep. But heterotrophic fauna can still survive even for thousands of years. The critical role of prokaryotes in active seeps are well defined, but their functions in extinct seeps are poorly understood to date. Here, we clarified the diversity, taxonomic specificity, interspecies correlation, and metabolic profiles of sediment prokaryotes at an extinct seep site of Haima cold seep, South China Sea. Alpha diversity of archaea significantly increased, while that of bacteria remained unchanged in extinct seep compared to active seep. However, archaea composition did not differ significantly at extinct seep from active or nonseep sites based on weighted-unifrac dissimilarity, while bacteria composition exhibited significant difference. Distribution of archaea and bacteria showed clear specificity to extinct seeps, indicating the unique life strategies here. Prokaryotes might live chemolithoautotrophically on cycling of inorganic carbon, sulfur, and nitrogen, or chemoorganotrophically on recycling of hydrocarbons. Notably, many of the extinct seep specific species and networked keystone lineages are classified as Proteobacteria. Regarding the functional diversity and metabolic flexibility of this clade, Proteobacteria is supposed to integrate the geochemical cycles and play a critical role in energy and resource supplement for microbiome in extinct seep. Collectively, our findings shed lights on the microbial ecology and functional diversity in extinct seeps, providing new understanding of biogeochemical cycling after fluid cessation. IMPORTANCE This research paper uncovered the potential mechanisms for microbiota mediated geochemical cycling in extinct cold seep, advancing our understanding in deep sea microbiology ecology.
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Affiliation(s)
- Yu Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
| | - Yuanjiao Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Jian Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Qiqi Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Lina Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Yingli Zhou
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
| | - Jie Kong
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
| | - Xinyang Zeng
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
| | - Si Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Jie Li
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
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Zhong YW, Zhou P, Cheng H, Zhou YD, Pan J, Xu L, Li M, Tao CH, Wu YH, Xu XW. Metagenomic Features Characterized with Microbial Iron Oxidoreduction and Mineral Interaction in Southwest Indian Ridge. Microbiol Spectr 2022; 10:e0061422. [PMID: 36286994 PMCID: PMC9769843 DOI: 10.1128/spectrum.00614-22] [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: 02/17/2022] [Accepted: 07/25/2022] [Indexed: 01/05/2023] Open
Abstract
The Southwest Indian Ridge (SWIR) is one of the typical representatives of deep-sea ultraslow-spreading ridges, and has increasingly become a hot spot of studying subsurface geological activities and deep-sea mining management. However, the understanding of microbial activities is still limited on active hydrothermal vent chimneys in SWIR. In this study, samples from an active black smoker and a diffuse vent located in the Longqi hydrothermal region were collected for deep metagenomic sequencing, which yielded approximately 290 GB clean data and 295 mid-to-high-quality metagenome-assembled genomes (MAGs). Sulfur oxidation conducted by a variety of Gammaproteobacteria, Alphaproteobacteria, and Campylobacterota was presumed to be the major energy source for chemosynthesis in Longqi hydrothermal vents. Diverse iron-related microorganisms were recovered, including iron-oxidizing Zetaproteobacteria, iron-reducing Deferrisoma, and magnetotactic bacterium. Twenty-two bacterial MAGs from 12 uncultured phyla harbored iron oxidase Cyc2 homologs and enzymes for organic carbon degradation, indicated novel chemolithoheterotrophic iron-oxidizing bacteria that affected iron biogeochemistry in hydrothermal vents. Meanwhile, potential interactions between microbial communities and chimney minerals were emphasized as enriched metabolic potential of siderophore transportation, and extracellular electron transfer functioned by multi-heme proteins was discovered. Composition of chimney minerals probably affected microbial iron metabolic potential, as pyrrhotite might provide more available iron for microbial communities. Collectively, this study provides novel insights into microbial activities and potential mineral-microorganism interactions in hydrothermal vents. IMPORTANCE Microbial activities and interactions with minerals and venting fluid in active hydrothermal vents remain unclear in the ultraslow-spreading SWIR (Southwest Indian Ridge). Understanding about how minerals influence microbial metabolism is currently limited given the obstacles in cultivating microorganisms with sulfur or iron oxidoreduction functions. Here, comprehensive descriptions on microbial composition and metabolic profile on 2 hydrothermal vents in SWIR were obtained based on cultivation-free metagenome sequencing. In particular, autotrophic sulfur oxidation supported by minerals was presumed, emphasizing the role of chimney minerals in supporting chemosynthesis. Presence of novel heterotrophic iron-oxidizing bacteria was also indicated, suggesting overlooked biogeochemical pathways directed by microorganisms that connected sulfide mineral dissolution and organic carbon degradation in hydrothermal vents. Our findings offer novel insights into microbial function and biotic interactions on minerals in ultraslow-spreading ridges.
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Affiliation(s)
- Ying-Wen Zhong
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Peng Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Hong Cheng
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Ya-Dong Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, PR China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Chun-Hui Tao
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, PR China
- Key Laboratory of Submarine Geosciences, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Yue-Hong Wu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Xue-Wei Xu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
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Li X, Zhai W, Duan X, Gou C, Li M, Wang L, Basang W, Zhu Y, Gao Y. Extraction, Purification, Characterization and Application in Livestock Wastewater of S Sulfur Convertase. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:16368. [PMID: 36498440 PMCID: PMC9740322 DOI: 10.3390/ijerph192316368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Sulfide is a toxic pollutant in the farming environment. Microbial removal of sulfide always faces various biochemical challenges, and the application of enzymes for agricultural environmental remediation has promising prospects. In this study, a strain of Cellulosimicrobium sp. was isolated: numbered strain L1. Strain L1 can transform S2-, extracellular enzymes play a major role in this process. Next, the extracellular enzyme was purified, and the molecular weight of the purified sulfur convertase was about 70 kDa. The sulfur convertase is an oxidase with thermal and storage stability, and the inhibitor and organic solvent have little effect on its activity. In livestock wastewater, the sulfur convertase can completely remove S2-. In summary, this study developed a sulfur convertase and provides a basis for the application in environmental remediation.
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Affiliation(s)
- Xintian Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130000, China
| | - Wei Zhai
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130000, China
| | - Xinran Duan
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130000, China
| | - Changlong Gou
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao 028000, China
| | - Min Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130000, China
| | - Lixia Wang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Wangdui Basang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China
| | - Yanbin Zhu
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China
| | - Yunhang Gao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130000, China
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Miklovics N, Duzs Á, Balogh F, Paragi G, Rákhely G, Tóth A. Quinone binding site in a type VI sulfide:quinone oxidoreductase. Appl Microbiol Biotechnol 2022; 106:7505-7517. [PMID: 36219222 DOI: 10.1007/s00253-022-12202-8] [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: 07/01/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 11/26/2022]
Abstract
Monotopic membrane-bound flavoproteins, sulfide:quinone oxidoreductases (SQRs), have a variety of physiological functions, including sulfide detoxification. SQR enzymes are classified into six groups. SQRs use the flavin adenine dinucleotide (FAD) cofactor to transfer electrons from sulfide to quinone. A type VI SQR of the photosynthetic purple sulfur bacterium, Thiocapsa roseopersicina (TrSqrF), has been previously characterized, and the mechanism of sulfide oxidation has been proposed. This paper reports the characterization of quinone binding site (QBS) of TrSqrF composed of conserved aromatic and apolar amino acids. Val331, Ile333, and Phe366 were identified near the benzoquinone ring of enzyme-bound decylubiquinone (dUQ) using the TrSqrF homology model. In silico analysis revealed that Val331 and Ile333 alternately connected with the quinone head group via hydrogen bonds, and Phe366 and Trp369 bound the quinones via hydrophobic interactions. TrSqrF variants containing alanine (V331A, I333A, F366A) and aromatic amino acid (V331F, I333F, F366Y), as well as a C-terminal α-helix deletion (CTD) mutant were generated. These amino acids are critical for quinone binding and, thus, catalysis. Spectroscopic analyses proved that all mutants contained FAD. I333F replacement resulted in the lack of the charge transfer complex. In summary, the interactions described above maintain the quinone molecule's head in an optimal position for direct electron transfer from FAD. Surprisingly, the CTD mutant retained a relatively high level of specific activity while remaining membrane-anchored. This is a unique study because it focuses on the QBS and the oxidative stage of a type VI sulfide-dependent quinone reduction. KEY POINTS: • V331, I333, F366, and W369 were shown to interact with decylubiquinone in T. roseopersicina SqrF • These amino acids are involved in proper positioning of quinones next to FAD • I333 is essential in formation of a charge transfer complex from FAD to quinone.
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Affiliation(s)
- Nikolett Miklovics
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Ágnes Duzs
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Fanni Balogh
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Paragi
- Institute of Physics, University of Pécs, Pécs, Hungary
- Department of Theoretical Physics, University of Szeged, Szeged, Hungary
| | - Gábor Rákhely
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary.
- Department of Biotechnology, University of Szeged, Szeged, Hungary.
| | - András Tóth
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
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10
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Tanabe TS, Dahl C. HMS-S-S: a tool for the identification of sulfur metabolism-related genes and analysis of operon structures in genome and metagenome assemblies. Mol Ecol Resour 2022; 22:2758-2774. [PMID: 35579058 DOI: 10.1111/1755-0998.13642] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/25/2022] [Accepted: 05/11/2022] [Indexed: 11/26/2022]
Abstract
Sulfur compounds are used in a variety of biological processes including respiration and photosynthesis. Sulfide and sulfur compounds of intermediary oxidation state can serve as electron donors for lithotrophic growth while sulfate, thiosulfate and sulfur are used as electron acceptors in anaerobic respiration. The biochemistry underlying the manifold transformations of inorganic sulfur compounds occurring in sulfur metabolizing prokaryotes is astonishingly complex and knowledge about it has immensely increased over the last years. The advent of next-generation sequencing approaches as well as the significant increase of data availability in public databases has driven focus of environmental microbiology to probing the metabolic capacity of microbial communities by analysis of this sequence data. To facilitate these analyses, we created HMS-S-S, a comprehensive equivalogous hidden Markov model (HMM)-supported tool. Protein sequences related to sulfur compound oxidation, reduction, transport and intracellular transfer are efficiently detected and related enzymes involved in dissimilatory sulfur oxidation as opposed to sulfur compound reduction can be confidently distinguished. HMM search results are coupled to corresponding genes, which allows analysis of co-occurrence, synteny and genomic neighborhood. The HMMs were validated on an annotated test dataset and by cross-validation. We also proved its performance by exploring meta-assembled genomes isolated from samples from environments with active sulfur cycling, including members of the cable bacteria, novel Acidobacteria and assemblies from a sulfur-rich glacier, and were able to replicate and extend previous reports.
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Affiliation(s)
- Tomohisa Sebastian Tanabe
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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11
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Sun Y, Wang M, Zhong Z, Chen H, Wang H, Zhou L, Cao L, Fu L, Zhang H, Lian C, Sun S, Li C. Adaption to hydrogen sulfide-rich environments: Strategies for active detoxification in deep-sea symbiotic mussels, Gigantidas platifrons. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150054. [PMID: 34509839 DOI: 10.1016/j.scitotenv.2021.150054] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/10/2021] [Accepted: 08/27/2021] [Indexed: 05/27/2023]
Abstract
The deep-sea mussel Gigantidas platifrons is a representative species that relies on nutrition provided by chemoautotrophic endosymbiotic bacteria to survive in both hydrothermal vent and methane seep environments. However, vent and seep habitats have distinct geochemical features, with vents being more harsh than seeps because of abundant toxic chemical substances, particularly hydrogen sulfide (H2S). Until now, the adaptive strategies of G. platifrons in a heterogeneous environment and their sulfide detoxification mechanisms are still unclear. Herein, we conducted 16S rDNA sequencing and metatranscriptome sequencing of G. platifrons collected from a methane seep at Formosa Ridge in the South China Sea and a hydrothermal vent at Iheya North Knoll in the Mid-Okinawa Trough to provide a model for understanding environmental adaption and sulfide detoxification mechanisms, and a three-day laboratory controlled Na2S stress experiment to test the transcriptomic responses under sulfide stress. The results revealed the active detoxification of sulfide in G. platifrons gills. First, epibiotic Campylobacterota bacteria were more abundant in vent mussels and contributed to environmental adaptation by active oxidation of extracellular H2S. Notably, a key sulfide-oxidizing gene, sulfide:quinone oxidoreductase (sqr), derived from the methanotrophic endosymbiont, was significantly upregulated in vent mussels, indicating the oxidization of intracellular sulfide by the endosymbiont. In addition, transcriptomic comparison further suggested that genes involved in oxidative phosphorylation and mitochondrial sulfide oxidization pathway played important roles in the sulfide tolerance of the host mussels. Moreover, transcriptomic analysis of Na2S stressed mussels confirmed the upregulation of oxidative phosphorylation and sulfide oxidization genes in response to sulfide exposure. Overall, this study provided a systematic transcriptional analysis of both the active bacterial community members and the host mussels, suggesting that the epibionts, endosymbionts, and mussel host collaborated on sulfide detoxification from extracellular to intracellular space to adapt to harsh H2S-rich environments.
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Affiliation(s)
- Yan Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Minxiao Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhaoshan Zhong
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Hao Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Hao Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Li Zhou
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Lei Cao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Lulu Fu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Huan Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Chao Lian
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Song Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 10049, China.
| | - Chaolun Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 10049, China.
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12
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Liu LJ, Jiang Z, Wang P, Qin YL, Xu W, Wang Y, Liu SJ, Jiang CY. Physiology, Taxonomy, and Sulfur Metabolism of the Sulfolobales, an Order of Thermoacidophilic Archaea. Front Microbiol 2021; 12:768283. [PMID: 34721370 PMCID: PMC8551704 DOI: 10.3389/fmicb.2021.768283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/22/2021] [Indexed: 11/13/2022] Open
Abstract
The order Sulfolobales (phylum Crenarchaeota) is a group of thermoacidophilic archaea. The first member of the Sulfolobales was discovered in 1972, and current 23 species are validly named under the International Code of Nomenclature of Prokaryotes. The majority of members of the Sulfolobales is obligately or facultatively chemolithoautotrophic. When they grow autotrophically, elemental sulfur or reduced inorganic sulfur compounds are their energy sources. Therefore, sulfur metabolism is the most important physiological characteristic of the Sulfolobales. The functions of some enzymes and proteins involved in sulfur reduction, sulfur oxidation, sulfide oxidation, thiosulfate oxidation, sulfite oxidation, tetrathionate hydrolysis, and sulfur trafficking have been determined. In this review, we describe current knowledge about the physiology, taxonomy, and sulfur metabolism of the Sulfolobales, and note future challenges in this field.
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Affiliation(s)
- Li-Jun Liu
- School of Basic Medical Science, the Xi'an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, China.,Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Pei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ya-Ling Qin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen Xu
- School of Basic Medical Science, the Xi'an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, China.,Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Yang Wang
- School of Basic Medical Science, the Xi'an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, China.,Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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13
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Zhang M, Xue Q, Zhang S, Zhou H, Xu T, Zhou J, Zheng Y, Li M, Kumar S, Zhao D, Xiang H. Development of whole-cell catalyst system for sulfide biotreatment based on the engineered haloalkaliphilic bacterium. AMB Express 2021; 11:142. [PMID: 34693461 PMCID: PMC8542531 DOI: 10.1186/s13568-021-01302-9] [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: 09/29/2021] [Accepted: 10/12/2021] [Indexed: 11/10/2022] Open
Abstract
Microorganisms play an essential role in sulfide removal. Alkaline absorption solution facilitates the sulfide’s dissolution and oxidative degradation, so haloalkaliphile is a prospective source for environmental-friendly and cost-effective biodesulfurization. In this research, 484 sulfide oxidation genes were identified from the metagenomes of the soda-saline lakes and a haloalkaliphilic heterotrophic bacterium Halomonas salifodinae IM328 (=CGMCC 22183) was isolated from the same habitat as the host for expression of a representative sequence. The genetic manipulation was successfully achieved through the conjugation transformation method, and sulfide: quinone oxidoreductase gene (sqr) was expressed via pBBR1MCS derivative plasmid. Furthermore, a whole-cell catalyst system was developed by using the engineered strain that exhibited a higher rate of sulfide oxidation under the optimal alkaline pH of 9.0. The whole-cell catalyst could be recycled six times to maintain the sulfide oxidation rates from 41.451 to 80.216 µmol·min−1·g−1 dry cell mass. To summarize, a whole-cell catalyst system based on the engineered haloalkaliphilic bacterium is potentiated to be applied in the sulfide treatment at a reduced cost.
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14
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Li W, Gao J, Zhuang JL, Yao GJ, Zhang X, Liu YD, Liu QK, Shapleigh JP, Ma L. Metagenomics and metatranscriptomics uncover the microbial community associated with high S 0 production in a denitrifying desulfurization granular sludge reactor. WATER RESEARCH 2021; 203:117505. [PMID: 34384948 DOI: 10.1016/j.watres.2021.117505] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 07/08/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
The denitrification desulfurization process is a promising technology for elemental sulfur (S0) production from sulfide containing wastewater. However, the microbial community associated with high S0 production still is not well studied. This study describes an efficient denitrification S0 production bioreactor based on inoculation with anaerobic granular sludge. At an optimal S/N molar ratio of 7:2, 80 % of the influent sulfide was transformed to high quality elemental sulfur with a purity of 92.5% while the total inorganic nitrogen removal efficiency was stable at ∼80%. Metatranscriptomic analysis found that community expression of the gene encoding the sulfide-quinone reductase (SQR) was 10-fold greater than that of the flavocytochrome-c sulfide dehydrogenase subunit B (fccB). Moreover, the expression level of SQR was also significantly higher than the Dsr gene encoding for dissimilatory sulfate reductase, which encodes a critical S0 oxidation enzyme. Metagenomic binning analysis confirmed that sulfide-oxidizing bacteria (SOB) utilizing SQR were common in the community and most likely accounted for high S0 production. An unexpected enrichment in methanogens and high expression activity of bacteria carrying out Stickland fermentation as well as in other bacteria with reduced genomes indicated a complex community supporting stable sulfide oxidation to S0, likely aiding in performance stability. This study establishes this treatment approach as an alternative biotechnology for sulfide containing wastewater treatment and sheds light on the microbial interactions associated with high S0 production.
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Affiliation(s)
- Wei Li
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, China
| | - Jian Gao
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Jin-Long Zhuang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Gen-Ji Yao
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Xu Zhang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Yong-di Liu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Qi-Kai Liu
- Nishihara Environment Engineering (Shanghai) Co., Ltd., Shanghai, China
| | | | - Liang Ma
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China.
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15
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Peng SY, Wu X, Lu T, Cui G, Chen G. Research progress of hydrogen sulfide in Alzheimer's disease from laboratory to hospital: a narrative review. Med Gas Res 2021; 10:125-129. [PMID: 33004710 PMCID: PMC8086622 DOI: 10.4103/2045-9912.296043] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Alzheimer's disease is a neurodegenerative disease that mainly occurs in old age and early stages. Its main manifestations are memory impairment, aphasia, apraxia, loss of identity, abstract thinking and impairment of computing power, personality and behavior changes, etc. At present, the treatment of Alzheimer's disease only stays on reducing the disease and delaying the development, which is also a difficult problem to overcome in clinical practice. Hydrogen sulfide, as a third gaseous signal molecule after carbon monoxide and nitrogen monoxide, has become very popular in recent years. It shows very promising prospects in the Alzheimer's disease model. It can protect the nerve function and prevent the progress of the disease by affecting the amyloid precursor protein metabolism, anti-apoptosis, anti-inflammatory, and antioxidant pathways. Therefore, this article summarizes the relevant basic and clinical research of hydrogen sulfide in Alzheimer's disease, and discusses its progress and findings and mechanism characteristics.
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Affiliation(s)
- Song-Yang Peng
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Xin Wu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Ting Lu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Gang Cui
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Gang Chen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
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16
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Wang L, Shao Z. Aerobic Denitrification and Heterotrophic Sulfur Oxidation in the Genus Halomonas Revealed by Six Novel Species Characterizations and Genome-Based Analysis. Front Microbiol 2021; 12:652766. [PMID: 33815342 PMCID: PMC8014003 DOI: 10.3389/fmicb.2021.652766] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/09/2021] [Indexed: 11/16/2022] Open
Abstract
Bacteria of Halomonas are widely distributed in various environments and play a substantial role in the nutrient cycle. In this report, 14 strains capable of aerobic denitrification and heterotrophic sulfur oxidation were isolated from different habitats. Based on the phenotypic, genotypic, and chemotaxonomic analyses, these strains were considered to represent six novel species of the genus Halomonas, for which the names Halomonas zhangzhouensis sp. nov. type strain CXT3-11T ( = MCCC 1A11036T = KCTC 72087T), Halomonas aerodenitrificans sp. nov. CYD-9T ( = MCCC 1A11058T = KCTC 72088T), Halomonas sulfidoxydans sp. nov. CYN-1-2T ( = MCCC 1A11059T = KCTC 72089T), Halomonas ethanolica sp. nov. CYT3-1-1T ( = MCCC 1A11081T = KCTC 72090T), Halomonas sulfidivorans sp. nov. NLG_F1ET ( = MCCC 1A13718T = KCTC 72091T), and Halomonas tianxiuensis sp. nov. BC-M4-5T ( = MCCC 1A14433T = KCTC 72092T) are proposed. Intriguingly, they formed a unique group with 11 other species designated as the "H. desiderata group." To better understand their featured metabolisms, genes involved in denitrification and sulfur oxidation were analyzed, along with 193 other available genomes of the whole genus. Consistently, complete denitrification pathways were confirmed in the "H. desiderata group," in which napA, narG, nirS, norB, and nosZ genes coexist. Their nitrite reductase NirS formed a unique evolutionary lineage, distinguished from other denitrifiers in Halomonas. In addition, diverse occurrence patterns of denitrification genes were also observed in different phylogenetic clades of Halomonas. With respect to sulfur oxidation, fccAB genes involved in sulfide oxidation commonly exist in the "H. desiderata group," while sqr genes are diverse and can be found in more species; sqr genes co-occurred with fccAB in eight strains of this study, contributing to more active sulfide oxidation. Besides, the tsdA gene, which encodes an enzyme that oxidizes thiosulfate to tetrathionate, is ubiquitous in the genus Halomonas. The widespread presence of sqr/fccAB, pdo, and tsdA in Halomonas suggests that many Halomonas spp. can act as heterotrophic sulfur oxidizers. These results provide comprehensive insights into the potential of denitrification and sulfur oxidation in the whole genus of Halomonas. With regard to the global distribution of Halomonas, this report implies their unneglectable role in the biogeochemical cycle.
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Affiliation(s)
- Liping Wang
- School of Environment, Harbin Institute of Technology, Harbin, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Zongze Shao
- School of Environment, Harbin Institute of Technology, Harbin, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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17
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Landry AP, Ballou DP, Banerjee R. Hydrogen Sulfide Oxidation by Sulfide Quinone Oxidoreductase. Chembiochem 2021; 22:949-960. [PMID: 33080111 PMCID: PMC7969369 DOI: 10.1002/cbic.202000661] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/19/2020] [Indexed: 02/05/2023]
Abstract
Hydrogen sulfide (H2 S) is an environmental toxin and a heritage of ancient microbial metabolism that has stimulated new interest following its discovery as a neuromodulator. While many physiological responses have been attributed to low H2 S levels, higher levels inhibit complex IV in the electron transport chain. To prevent respiratory poisoning, a dedicated set of enzymes that make up the mitochondrial sulfide oxidation pathway exists to clear H2 S. The committed step in this pathway is catalyzed by sulfide quinone oxidoreductase (SQOR), which couples sulfide oxidation to coenzyme Q10 reduction in the electron transport chain. The SQOR reaction prevents H2 S accumulation and generates highly reactive persulfide species as products; these can be further oxidized or can modify cysteine residues in proteins by persulfidation. Here, we review the kinetic and structural characteristics of human SQOR, and how its unconventional redox cofactor configuration and substrate promiscuity lead to sulfide clearance and potentially expand the signaling potential of H2 S. This dual role of SQOR makes it a promising target for H2 S-based therapeutics.
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Affiliation(s)
- Aaron P. Landry
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - David P. Ballou
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
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18
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Wang S, Jiang L, Hu Q, Cui L, Zhu B, Fu X, Lai Q, Shao Z, Yang S. Characterization of Sulfurimonas hydrogeniphila sp. nov., a Novel Bacterium Predominant in Deep-Sea Hydrothermal Vents and Comparative Genomic Analyses of the Genus Sulfurimonas. Front Microbiol 2021; 12:626705. [PMID: 33717015 PMCID: PMC7952632 DOI: 10.3389/fmicb.2021.626705] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/11/2021] [Indexed: 11/13/2022] Open
Abstract
Bacteria of the genus Sulfurimonas within the class Campylobacteria are predominant in global deep-sea hydrothermal environments and widespread in global oceans. However, only few bacteria of this group have been isolated, and their adaptations for these extreme environments remain poorly understood. Here, we report a novel mesophilic, hydrogen- and sulfur-oxidizing bacterium, strain NW10T, isolated from a deep-sea sulfide chimney of Northwest Indian Ocean.16S rRNA gene sequence analysis showed that strain NW10T was most closely related to the vent species Sulfurimonas paralvinellae GO25T with 95.8% similarity, but ANI and DDH values between two strains were only 19.20 and 24.70%, respectively, indicating that strain NW10 represents a novel species. Phenotypic characterization showed strain NW10T is an obligate chemolithoautotroph utilizing thiosulfate, sulfide, elemental sulfur, or molecular hydrogen as energy sources, and molecular oxygen, nitrate, or elemental sulfur as electron acceptors. Moreover, hydrogen supported a better growth than reduced sulfur compounds. During thiosulfate oxidation, the strain can produce extracellular sulfur of elemental α-S8 with an unknown mechanism. Polyphasic taxonomy results support that strain NW10T represents a novel species of the genus Sulfurimonas, and named as Sulfurimonas hydrogeniphila sp. nov. Genome analyses revealed its diverse energy metabolisms driving carbon fixation via rTCA cycling, including pathways of sulfur/hydrogen oxidation, coupled oxygen/sulfur respiration and denitrification. Comparative analysis of the 11 available genomes from Sulfurimonas species revealed that vent bacteria, compared to marine non-vent strains, possess unique genes encoding Type V Sqr, Group II, and Coo hydrogenase, and are selectively enriched in genes related to signal transduction and inorganic ion transporters. These phenotypic and genotypic features of vent Sulfurimonas may explain their thriving in hydrothermal environments and help to understand the ecological role of Sulfurimonas bacteria in hydrothermal ecosystems.
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Affiliation(s)
- Shasha Wang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Qitao Hu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Liang Cui
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
| | - Bitong Zhu
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
| | - Xiaoteng Fu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Suping Yang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
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Liu ZX, Yang MH, Mu TZ, Liu JL, Zhang X, Xing JM. Transcriptional response of Thialkalivibrio versutus D301 to different sulfur sources and identification of the sulfur oxidation pathways. J Biotechnol 2021; 329:160-169. [PMID: 33592216 DOI: 10.1016/j.jbiotec.2021.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/26/2021] [Accepted: 02/07/2021] [Indexed: 12/27/2022]
Abstract
The genus Thialkalivibrio plays an essential role in the biological desulfurization system. However, to date, the sulfur oxidation pathways of Thialkalivibrio are not clearly understood. Here, we performed transcriptomic analysis on Thialkalivibrio versutus D301 with either thiosulfate or chemical sulfur as the sulfur source to understand it. The results show that T. versutus D301 has a higher growth rate and sulfur oxidation activity when thiosulfate is utilized. The use of chemical sulfur as sulfur source leads to decreased expression of genes involved in carbon metabolism, ribosome synthesis and oxidative phosphorylation in T. versutus D301. Potentially due to the adsorption to sulfur particles, the genes related to flagellum assembly and motivation are significantly induced in T. versutus D301 in the presence of chemical sulfur. In the periplasm, both thiosulfate and polysulfide from the chemical sulfur are oxidized to sulfate via the similar truncated Sox system (SoxAXYZB). Then, part of polysulfide reached to cytoplasm through an unidentified route is oxidized to sulfite by the Dsr-like system. The sulfite in the cytoplasm is further catalyzed to sulfate by SoxB or SoeABC. Overall, the difference in the oxidation rates of D301 can be mainly attributed to the bioavailability of the two sulfur sources, not the sulfur oxidation pathways.
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Affiliation(s)
- Zhi-Xia Liu
- CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China; School of Biology and Engineering, Hebei University of Science and Technology, Shijiazhuang, Hebei Province 050018, China
| | - Mao-Hua Yang
- CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Ting-Zhen Mu
- CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jin-Long Liu
- School of Biology and Engineering, Hebei University of Science and Technology, Shijiazhuang, Hebei Province 050018, China.
| | - Xiang Zhang
- Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, 250100, China
| | - Jian-Min Xing
- CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
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20
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Duzs Á, Miklovics N, Paragi G, Rákhely G, Tóth A. Insights into the catalytic mechanism of type VI sulfide:quinone oxidoreductases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148337. [PMID: 33202220 DOI: 10.1016/j.bbabio.2020.148337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/09/2020] [Accepted: 11/03/2020] [Indexed: 10/23/2022]
Abstract
Sulfide oxidation is catalyzed by ancient membrane-bound sulfide:quinone oxidoreductases (SQR) which are classified into six different types. For catalysis of sulfide oxidation, all SQRs require FAD cofactor and a redox-active centre in the active site, usually formed between conserved essential cysteines. SQRs of different types have variation in the number and position of cysteines, highlighting the potential for diverse catalytic mechanisms. The photosynthetic purple sulfur bacterium, Thiocapsa roseopersicina contains a type VI SQR enzyme (TrSqrF) having unusual catalytic parameters and four cysteines likely involved in the catalysis. Site-directed mutagenesis was applied to identify the role of cysteines in the catalytic process of TrSqrF. Based on biochemical and kinetic characterization of these TrSqrF variants, Cys121 is identified as crucial for enzyme activity. The cofactor is covalently bound via a heterodisulfide bridge between Cys121 and the C8M group of FAD. Mutation of another cysteine present in all SQRs (Cys332) causes remarkably decreased enzyme activity (14.6% of wild type enzyme) proving important, but non-essential role of this residue in enzyme catalysis. The sulfhydril-blocking agent, iodoacetamide can irreversibly inactivate TrSqrF but only if substrates are present and the enzyme is actively catalyzing its reaction. When the enzyme is inhibited by iodoacetamide, the FAD cofactor is released. The inhibition studies support a mechanism that entails opening and reforming of the heterodisulfide bridge during the catalytic cycle of TrSqrF. Our study thus reports the first detailed structure-function analysis of a type VI SQR enzyme which enables the proposal of a distinct mechanism of sulfide oxidation for this class.
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Affiliation(s)
- Ágnes Duzs
- Institute of Biophysics, Biological Research Centre, Temesvári krt 62., H-6726 Szeged, Hungary; Department of Biotechnology, University of Szeged, Közép fasor 52., H-6726 Szeged, Hungary
| | - Nikolett Miklovics
- Institute of Biophysics, Biological Research Centre, Temesvári krt 62., H-6726 Szeged, Hungary; Department of Biotechnology, University of Szeged, Közép fasor 52., H-6726 Szeged, Hungary; Doctoral School in Biology, University of Szeged, Közép fasor 52., H-6726 Szeged, Hungary
| | - Gábor Paragi
- Institute of Physics, University of Pécs, Ifjúság útja 6., H-7624 Pécs, Hungary; MTA-SZTE Biomimetic Systems Research Group, Department of Medical Chemistry, University of Szeged, Dóm square 8, H-6720 Szeged, Hungary
| | - Gábor Rákhely
- Institute of Biophysics, Biological Research Centre, Temesvári krt 62., H-6726 Szeged, Hungary; Department of Biotechnology, University of Szeged, Közép fasor 52., H-6726 Szeged, Hungary.
| | - András Tóth
- Institute of Biophysics, Biological Research Centre, Temesvári krt 62., H-6726 Szeged, Hungary; Department of Biotechnology, University of Szeged, Közép fasor 52., H-6726 Szeged, Hungary
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21
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Investigating the amino acid sequences of membrane bound dihydroorotate:quinone oxidoreductases (DHOQOs): Structural and functional implications. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148321. [PMID: 32991846 DOI: 10.1016/j.bbabio.2020.148321] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/14/2020] [Accepted: 09/23/2020] [Indexed: 12/26/2022]
Abstract
Dihydroorotate:quinone oxidoreductases (DHOQOs) are membrane bound enzymes responsible for oxidizing dihydroorotate (DHO) to orotate with concomitant reduction of quinone to quinol. They have FMN as prosthetic group and are part of the monotopic quinone reductase superfamily. These enzymes are also members of the dihydroorotate dehydrogenases (DHODHs) family, which besides membrane bound DHOQOs, class 2, includes soluble enzymes which reduce either NAD+ or fumarate, class 1. As key enzymes in both the de novo pyrimidine biosynthetic pathway as well as in the energetic metabolism, inhibitors of DHOQOs have been investigated as leads for therapeutics in cancer, immunological disorders and bacterial/viral infections. This work is a thorough bioinformatic approach on the structural conservation and taxonomic distribution of DHOQOs. We explored previously established structural/functional hallmarks of these enzymes, while searching for uncharacterized common elements. We also discuss the cellular role of DHOQOs and organize the identified protein sequences within six sub-classes 2A to 2F, according to their taxonomic origin and sequence traits. We concluded that DHOQOs are present in Archaea, Eukarya and Bacteria, including the first recognition in Gram-positive organisms. DHOQOs can be the single dihydroorotate dehydrogenase encoded in the genome of a species, or they can coexist with other DHODHs, as the NAD+ or fumarate reducing enzymes. Furthermore, we show that the type of catalytic base present in the active site is not an absolute criterium to distinguish between class 1 and class 2 enzymes. We propose the existence of a quinone binding motif ("ExAH") adjacent to a hydrophobic cavity present in the membrane interacting N-terminal domain.
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22
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Shimizu T, Masuda S. Persulphide-responsive transcriptional regulation and metabolism in bacteria. J Biochem 2020; 167:125-132. [PMID: 31385583 DOI: 10.1093/jb/mvz063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/02/2019] [Indexed: 12/17/2022] Open
Abstract
Hydrogen sulphide (H2S) impacts on bacterial growth both positively and negatively; it is utilized as an electron donor for photosynthesis and respiration, and it inactivates terminal oxidases and iron-sulphur clusters. Therefore, bacteria have evolved H2S-responsive detoxification mechanisms for survival. Sulphur assimilation in bacteria has been well studied, and sulphide:quinone oxidoreductase, persulphide dioxygenase, rhodanese and sulphite oxidase were reported as major sulphide-oxidizing enzymes of sulphide assimilation and detoxification pathways. However, how bacteria sense sulphide availability to control H2S and sulphide metabolism remains largely unknown. Recent studies have identified several bacterial (per)sulphide-sensitive transcription factors that change DNA-binding affinity through persulphidation of specific cysteine residues in response to highly reactive sulphur-containing chemicals and reactive sulphur species (RSS). This review focuses on current understanding of the persulphide-responsive transcription factors and RSS metabolism regulated by RSS sensory proteins.
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Affiliation(s)
- Takayuki Shimizu
- Department of General Systems Studies, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komana, Meguro-ku, Tokyo 153-8902, Japan
| | - Shinji Masuda
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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23
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Bonanata J, Coitiño EL. Understanding the mechanism of H 2S oxidation by flavin-dependent sulfide oxidases: a DFT/IEF-PCM study. J Mol Model 2019; 25:308. [PMID: 31502063 DOI: 10.1007/s00894-019-4197-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 08/28/2019] [Indexed: 12/18/2022]
Abstract
In the last years, H2S has been recognized as a signaling molecule in mammals, which can synthesize and catabolize (by oxidation) such species. The latter process is accelerated by a sulfide:quinone oxidoreductase (SQR, E.C. 1.8.5.4), a flavin-dependent sulfide oxidase (FDSO). FDSOs catalyze electron transfer from H2S to an acceptor in catalytic cycles involving two phases: (I) reduction of FAD by H2S (SH-) and (II) electron transfer from FADH- to the electron acceptor. The first step of FAD reduction consists on the reaction of SH- with a catalytic disulfide at the active site of the enzyme, to yield a thiolate and a persulfide in the protein. This step is ca. 106 times faster than the analogous reaction with low-molecular-weight disulfides (LMWDs) and the causes of such extraordinary acceleration remain unknown. Using the IEF-PCM(ε ≈ 10)/M06-2X-D3/6-31+G(d,p) level of theory, we have modeled the reaction of SH- with a disulfide as located in a representative model of the active site extracted from a prokaryotic SQR, assessing the effects of partial covalent interactions (PCIs) between the leaving sulfur atom and flavin ring on the activation Gibbs free-energy barrier at 298 K (∆‡G298K). To also evaluate the importance of entropic penalties on the first step, we have modeled at the same level of theory the reaction of (bis)hydroxyethyl disulfide in aqueous solution, a LMWD for which experimental data is available. Our results show that PCIs between the leaving sulfur atom and the flavin group only have a minor effect (∆‡G298K reduced by 1.6 kcal mol-1) while compensating entropic penalties could have a much larger effect (up to 8.3 kcal mol-1). Finally, we also present here a first model of some of further steps in the phase I of the catalytic cycle as in mammalian FDSOs, providing some light about their detailed mechanism. Graphical abstract .
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Affiliation(s)
- Jenner Bonanata
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias and Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay.
| | - E Laura Coitiño
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias and Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay.
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24
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Berben T, Overmars L, Sorokin DY, Muyzer G. Diversity and Distribution of Sulfur Oxidation-Related Genes in Thioalkalivibrio, a Genus of Chemolithoautotrophic and Haloalkaliphilic Sulfur-Oxidizing Bacteria. Front Microbiol 2019; 10:160. [PMID: 30837958 PMCID: PMC6382920 DOI: 10.3389/fmicb.2019.00160] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/22/2019] [Indexed: 12/20/2022] Open
Abstract
Soda lakes are saline alkaline lakes characterized by high concentrations of sodium carbonate/bicarbonate which lead to a stable elevated pH (>9), and moderate to extremely high salinity. Despite this combination of extreme conditions, biodiversity in soda lakes is high, and the presence of diverse microbial communities provides a driving force for highly active biogeochemical cycles. The sulfur cycle is one of the most important of these and bacterial sulfur oxidation is dominated by members of the obligately chemolithoautotrophic genus Thioalkalivibrio. Currently, 10 species have been described in this genus, but over one hundred isolates have been obtained from soda lake samples. The genomes of 75 strains were sequenced and annotated previously, and used in this study to provide a comprehensive picture of the diversity and distribution of genes related to dissimilatory sulfur metabolism in Thioalkalivibrio. Initially, all annotated genes in 75 Thioalkalivibrio genomes were placed in ortholog groups and filtered by bi-directional best BLAST analysis. Investigation of the ortholog groups containing genes related to sulfur oxidation showed that flavocytochrome c (fcc), the truncated sox system, and sulfite:quinone oxidoreductase (soe) are present in all strains, whereas dissimilatory sulfite reductase (dsr; which catalyzes the oxidation of elemental sulfur) was found in only six strains. The heterodisulfide reductase system (hdr), which is proposed to oxidize sulfur to sulfite in strains lacking both dsr and soxCD, was detected in 73 genomes. Hierarchical clustering of strains based on sulfur gene repertoire correlated closely with previous phylogenomic analysis. The phylogenetic analysis of several sulfur oxidation genes showed a complex evolutionary history. All in all, this study presents a comprehensive investigation of sulfur metabolism-related genes in cultivated Thioalkalivibrio strains and provides several avenues for future research.
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Affiliation(s)
- Tom Berben
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Lex Overmars
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Dimitry Y Sorokin
- Winogradsky Institute for Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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25
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Wang R, Lin JQ, Liu XM, Pang X, Zhang CJ, Yang CL, Gao XY, Lin CM, Li YQ, Li Y, Lin JQ, Chen LX. Sulfur Oxidation in the Acidophilic Autotrophic Acidithiobacillus spp. Front Microbiol 2019; 9:3290. [PMID: 30687275 PMCID: PMC6335251 DOI: 10.3389/fmicb.2018.03290] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022] Open
Abstract
Sulfur oxidation is an essential component of the earth's sulfur cycle. Acidithiobacillus spp. can oxidize various reduced inorganic sulfur compounds (RISCs) with high efficiency to obtain electrons for their autotrophic growth. Strains in this genus have been widely applied in bioleaching and biological desulfurization. Diverse sulfur-metabolic pathways and corresponding regulatory systems have been discovered in these acidophilic sulfur-oxidizing bacteria. The sulfur-metabolic enzymes in Acidithiobacillus spp. can be categorized as elemental sulfur oxidation enzymes (sulfur dioxygenase, sulfur oxygenase reductase, and Hdr-like complex), enzymes in thiosulfate oxidation pathways (tetrathionate intermediate thiosulfate oxidation (S4I) pathway, the sulfur oxidizing enzyme (Sox) system and thiosulfate dehydrogenase), sulfide oxidation enzymes (sulfide:quinone oxidoreductase) and sulfite oxidation pathways/enzymes. The two-component systems (TCSs) are the typical regulation elements for periplasmic thiosulfate metabolism in these autotrophic sulfur-oxidizing bacteria. Examples are RsrS/RsrR responsible for S4I pathway regulation and TspS/TspR for Sox system regulation. The proposal of sulfur metabolic and regulatory models provide new insights and overall understanding of the sulfur-metabolic processes in Acidithiobacillus spp. The future research directions and existing barriers in the bacterial sulfur metabolism are also emphasized here and the breakthroughs in these areas will accelerate the research on the sulfur oxidation in Acidithiobacillus spp. and other sulfur oxidizers.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Jian-Qun Lin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Lin-Xu Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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26
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Refojo PN, Sena FV, Calisto F, Sousa FM, Pereira MM. The plethora of membrane respiratory chains in the phyla of life. Adv Microb Physiol 2019; 74:331-414. [PMID: 31126533 DOI: 10.1016/bs.ampbs.2019.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The diversity of microbial cells is reflected in differences in cell size and shape, motility, mechanisms of cell division, pathogenicity or adaptation to different environmental niches. All these variations are achieved by the distinct metabolic strategies adopted by the organisms. The respiratory chains are integral parts of those strategies especially because they perform the most or, at least, most efficient energy conservation in the cell. Respiratory chains are composed of several membrane proteins, which perform a stepwise oxidation of metabolites toward the reduction of terminal electron acceptors. Many of these membrane proteins use the energy released from the oxidoreduction reaction they catalyze to translocate charges across the membrane and thus contribute to the establishment of the membrane potential, i.e. they conserve energy. In this work we illustrate and discuss the composition of the respiratory chains of different taxonomic clades, based on bioinformatic analyses and on biochemical data available in the literature. We explore the diversity of the respiratory chains of Animals, Plants, Fungi and Protists kingdoms as well as of Prokaryotes, including Bacteria and Archaea. The prokaryotic phyla studied in this work are Gammaproteobacteria, Betaproteobacteria, Epsilonproteobacteria, Deltaproteobacteria, Alphaproteobacteria, Firmicutes, Actinobacteria, Chlamydiae, Verrucomicrobia, Acidobacteria, Planctomycetes, Cyanobacteria, Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Aquificae, Thermotogae, Deferribacteres, Nitrospirae, Euryarchaeota, Crenarchaeota and Thaumarchaeota.
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Affiliation(s)
- Patrícia N Refojo
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipa Calisto
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal; University of Lisboa, Faculty of Sciences, BIOISI- Biosystems & Integrative Sciences Institute, Lisboa, Portugal
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