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Zhao S, Deng D, Wan T, Feng J, Deng L, Tian Q, Wang J, Aiman UE, Mukhaddi B, Hu X, Chen S, Qiu L, Huang L, Wei Y. Lignin bioconversion based on genome mining for ligninolytic genes in Erwinia billingiae QL-Z3. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:25. [PMID: 38360683 PMCID: PMC10870720 DOI: 10.1186/s13068-024-02470-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/02/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND Bioconversion of plant biomass into biofuels and bio-products produces large amounts of lignin. The aromatic biopolymers need to be degraded before being converted into value-added bio-products. Microbes can be environment-friendly and efficiently degrade lignin. Compared to fungi, bacteria have some advantages in lignin degradation, including broad tolerance to pH, temperature, and oxygen and the toolkit for genetic manipulation. RESULTS Our previous study isolated a novel ligninolytic bacterial strain Erwinia billingiae QL-Z3. Under optimized conditions, its rate of lignin degradation was 25.24% at 1.5 g/L lignin as the sole carbon source. Whole genome sequencing revealed 4556 genes in the genome of QL-Z3. Among 4428 protein-coding genes are 139 CAZyme genes, including 54 glycoside hydrolase (GH) and 16 auxiliary activity (AA) genes. In addition, 74 genes encoding extracellular enzymes are potentially involved in lignin degradation. Real-time PCR quantification demonstrated that the expression of potential ligninolytic genes were significantly induced by lignin. 8 knock-out mutants and complementary strains were constructed. Disruption of the gene for ELAC_205 (laccase) as well as EDYP_48 (Dyp-type peroxidase), ESOD_1236 (superoxide dismutase), EDIO_858 (dioxygenase), EMON_3330 (monooxygenase), or EMCAT_3587 (manganese catalase) significantly reduced the lignin-degrading activity of QL-Z3 by 47-69%. Heterologously expressed and purified enzymes further confirmed their role in lignin degradation. Fourier transform infrared spectroscopy (FTIR) results indicated that the lignin structure was damaged, the benzene ring structure and groups of macromolecules were opened, and the chemical bond was broken under the action of six enzymes encoded by genes. The abundant enzymatic metabolic products by EDYP_48, ELAC_205 and ESOD_1236 were systematically analyzed via liquid chromatography-mass spectrometry (LC-MS) analysis, and then provide a speculative pathway for lignin biodegradation. Finally, The activities of ligninolytic enzymes from fermentation supernatant, namely, LiP, MnP and Lac were 367.50 U/L, 839.50 U/L, and 219.00 U/L by orthogonal optimization. CONCLUSIONS Our findings provide that QL-Z3 and its enzymes have the potential for industrial application and hold great promise for the bioconversion of lignin into bioproducts in lignin valorization.
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Affiliation(s)
- Shuting Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Dongtao Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Tianzheng Wan
- Vrije University Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, Netherlands
| | - Jie Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Lei Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Qianyi Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jiayu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Umm E Aiman
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Balym Mukhaddi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xiaofeng Hu
- Shanghai Personal Biotechnology Co., Ltd, Shanghai, 20030, People's Republic of China
| | - Shaolin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Ling Qiu
- College of Mechanical and Electronic Engineering, The West Scientific Observing and Experimental Station of Rural Renewable Energy Exploitation and Utilization of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Yahong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Hamre AG, Al-Sadawi R, Johannesen KM, Bisarro B, Kjendseth ÅR, Leiros HKS, Sørlie M. Initial characterization of an iron superoxide dismutase from Thermobifida fusca. J Biol Inorg Chem 2023; 28:689-698. [PMID: 37725277 PMCID: PMC10520107 DOI: 10.1007/s00775-023-02019-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 08/24/2023] [Indexed: 09/21/2023]
Abstract
Superoxide dismutases (SODs) are enzymes that catalyze the dismutation of the superoxide radical anion into O2 and H2O2 in a two-step reaction. They are ubiquitous to all forms of life and four different types of metal centers are detected, dividing this class of enzymes into Cu-/Zn-, Ni-, Mn-, and Fe-SODs. In this study, a superoxide dismutase from the thermophilic bacteria Thermobifida fusca (TfSOD) was cloned and expressed before the recombinant enzyme was characterized. The enzyme was found to be active for superoxide dismutation measured by inhibition of cytochrome c oxidation and the inhibition of the autoxidation of pyrogallol. Its pH-optimum was determined to be 7.5, while it has a broad temperature optimum ranging from 20 to 90 °C. Combined with the Tm that was found to be 78.5 ± 0.5 °C at pH 8.0, TfSOD can be defined as a thermostable enzyme. Moreover, the crystal structure of TfSOD was determined and refined to 1.25 Å resolution. With electron paramagnetic resonance spectroscopy, it was confirmed that iron is the metal co-factor of TfSOD. The cell potential (Em) for the TfSOD-Fe3+/TfSOD-Fe2+ redox couple was determined to be 287 mV.
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Affiliation(s)
- Anne Grethe Hamre
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO 5003, 1432, Ås, Norway
| | - Rim Al-Sadawi
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO 5003, 1432, Ås, Norway
| | - Kirsti Merete Johannesen
- Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, 9037, Tromsö, Norway
| | - Bastien Bisarro
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO 5003, 1432, Ås, Norway
| | - Åsmund Røhr Kjendseth
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO 5003, 1432, Ås, Norway
| | - Hanna-Kirsti S Leiros
- Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, 9037, Tromsö, Norway
| | - Morten Sørlie
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO 5003, 1432, Ås, Norway.
- Department for Physics and Technology, Faculty of Science and Technology, UiT The Arctic University of Norway, 9037, Tromsö, Norway.
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3
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Dong L, Chen Y, Gu L, Gan M, Carrier A, Oakes K, Zhang X, Dong Z. Oral delivery of a highly stable superoxide dismutase as a skin aging inhibitor. Biomed Pharmacother 2023; 164:114878. [PMID: 37209626 DOI: 10.1016/j.biopha.2023.114878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/25/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023] Open
Abstract
As an effective antioxidant enzyme, superoxide dismutase (SOD) has been widely used as a food supplement, cosmetic additive, and therapeutic agent. However, oral delivery of SOD is challenging due to its relative instability, limited bioavailability, and low absorption efficiency in the gastrointestinal (GI) tract. We addressed these issues using a highly stable superoxide dismutase (hsSOD) generated from a hot spring microbial sample. This SOD exhibited a specific activity of 5000 IU/mg while retaining its enzymatic activity under low pH environments of an artificial GI system and in the presence of surfactants and various proteolytic enzymes. The inhibitory effects of hsSOD against skin-aging was evaluated under both in vitro and in vivo experiments using fibroblast cell and D-galactose induced aging-mouse models, respectively. Effective oral delivery of hsSOD promises wide applicability in pharmaceutical and food industries.
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Affiliation(s)
- Liang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, P.O. Box 2714, Beijing 100080, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongli Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, P.O. Box 2714, Beijing 100080, China; Shenzhen Siyomicro BIO-TECH CO., Ltd., Shenzhen 518116, China
| | - Lihong Gu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, P.O. Box 2714, Beijing 100080, China; Shenzhen Siyomicro BIO-TECH CO., Ltd., Shenzhen 518116, China
| | - Miao Gan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, P.O. Box 2714, Beijing 100080, China; Shenzhen Siyomicro BIO-TECH CO., Ltd., Shenzhen 518116, China
| | - Andrew Carrier
- Department of Chemistry, Cape Breton University, 1250 Grand Lake Road, Sydney, Nova Scotia B1P 6L2, Canada
| | - Ken Oakes
- Department of Biology, Cape Breton University, 1250 Grand Lake Road, Sydney, Nova Scotia B1P 6L2, Canada
| | - Xu Zhang
- Department of Chemistry, Cape Breton University, 1250 Grand Lake Road, Sydney, Nova Scotia B1P 6L2, Canada.
| | - Zhiyang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, P.O. Box 2714, Beijing 100080, China.
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Huang X, Qin B, Qin L, Peng Z, Xia S, Su Y, Sun K, Peng K. A comparative study on photosynthetic characteristics and flavonoid metabolism between Camellia petelotii (Merr.) Sealy and Camellia impressinervis Chang &Liang. FRONTIERS IN PLANT SCIENCE 2022; 13:1071458. [PMID: 36544877 PMCID: PMC9762238 DOI: 10.3389/fpls.2022.1071458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
Camellia petelotii (Merr.) Sealy and Camellia impressinervis Chang & Liang belong to the golden subgroup of Camellia (Theaceae). This subgroup contains the yellow-flowering species of the genus, which have high medicinal and ornamental value and a narrow geographical distribution. These species differ in their tolerance to high light intensity. This study aimed to explore the differences in their light-stress responses and light damage repair processes, and the effect of these networks on secondary metabolite synthesis. Two-year-old plants of both species grown at 300 µmol·m-2·s-1 photosynthetically active radiation (PAR) were shifted to 700 µmol·m-2·s-1 PAR for 5 days shifting back to 300 µmol·m-2·s-1 PAR for recovery for 5 days. Leaf samples were collected at the start of the experiment and 2 days after each shift. Data analysis included measuring photosynthetic indicators, differential transcriptome expression, and quantifying plant hormones, pigments, and flavonoids. Camellia impressinervis showed a weak ability to recover from photodamage that occurred at 700 µmol·m-2·s-1 compared with C. petelotii. Photodamage led to decreased photosynthesis, as shown by repressed transcript abundance for photosystem II genes psbA, B, C, O, and Q, photosystem I genes psaB, D, E, H, and N, electron transfer genes petE and F, and ATP synthesis genes ATPF1A and ATPF1B. High-light stress caused more severe damage to C. impressinervis, which showed a stronger response to reactive oxygen species than C. petelotii. In addition, high-light stress promoted the growth and development of high zeatin signalling and increased transcript abundance of adenylate dimethylallyl transferase (IPT) and histidine-containing phosphotransferase (AHP). The identification of transcriptional differences in the regulatory networks that respond to high-light stress and activate recovery of light damage in these two rare species adds to the resources available to conserve them and improve their value through molecular breeding.
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Affiliation(s)
- Xin Huang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, China
- Forestry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Bo Qin
- Forestry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Lei Qin
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, China
| | - Zhihong Peng
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, China
| | - Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, China
| | - Yi Su
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, China
| | - Kaidao Sun
- Forestry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Keqin Peng
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, China
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5
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Huang X, Qin B, Xia S, Su Y, Ku W, Chen R, Peng K. A comparative study on the effects of strong light stress on the photosynthetic characteristics of the shade plant Camellia petelotii (Merr.) Sealy. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01172-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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6
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Dong X, Wang W, Li S, Han H, Lv P, Yang C. Thermoacidophilic Alicyclobacillus Superoxide Dismutase: Good Candidate as Additives in Food and Medicine. Front Microbiol 2021; 12:577001. [PMID: 33815303 PMCID: PMC8014015 DOI: 10.3389/fmicb.2021.577001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 02/26/2021] [Indexed: 11/30/2022] Open
Abstract
Thermoacidophilic Alicyclobacillus strains attract great interests as the resource of thermostable or acidic enzymes. In this study, a putative gene encoding superoxide dismutase (AaSOD) was identified in a thermoacidophilic Alicyclobacillus strain. With a 16-fold activity observed, the AaSOD activity expressing in the medium of manganese enrichment was much higher than that in the iron medium. In addition, the purified AaSOD can be reconstituted exclusively with either Fe2+ or Mn2+, with its Mn-bound protein showing 25-fold activity than that of Fe-bound form. The optimal temperature for AaSOD reaction was 35°C, and was highly stable at any certain temperature up to 80°C. Of particular interest, the enzyme is found to be very stable across a wide pH range spanning from 2.0 to 10.0, which confers its robust stability in the acidic stomach environment and implies striking potentials as food additive and for medical use.
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Affiliation(s)
- Xueqian Dong
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China.,Shandong Food Ferment Industry Research & Design Institute, QiLu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Wei Wang
- Shandong Food Ferment Industry Research & Design Institute, QiLu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Shannan Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Hongyu Han
- Shandong Food Ferment Industry Research & Design Institute, QiLu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Peiwen Lv
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Chunyu Yang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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7
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Lin L, Wang X, Cao L, Xu M. Lignin catabolic pathways reveal unique characteristics of dye-decolorizing peroxidases in Pseudomonas putida. Environ Microbiol 2020; 21:1847-1863. [PMID: 30882973 DOI: 10.1111/1462-2920.14593] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 03/11/2019] [Accepted: 03/15/2019] [Indexed: 11/28/2022]
Abstract
Lignin is one of the largest carbon reservoirs in the environment, playing an important role in the global carbon cycle. However, lignin degradation in bacteria, especially non-model organisms, has not been well characterized either enzymatically or genetically. Here, a lignin-degrading bacterial strain, Pseudomonas putida A514, was used as the research model. Genomic and proteomic analyses suggested that two B subfamily dye-decolorizing peroxidases (DypBs) were prominent in lignin depolymerization, while the classic O2 -dependent ring cleavage strategy was utilized in central pathways to catabolize lignin-derived aromatic compounds that were funnelled by peripheral pathways. These enzymes, together with a range of transporters, sequential and expression-dose dependent regulation and stress response systems coordinated for lignin metabolism. Catalytic assays indicated these DypBs show unique Mn2+ independent lignin depolymerization activity, while Mn2+ oxidation activity is absent. Furthermore, a high synergy between DypB enzymes and A514 cells was observed to promote cell growth (5 × 1012 cfus/ml) and lignin degradation (27%). This suggested DypBs are competitive lignin biocatalysts and pinpointed limited extracellular secretion capacity as the rate-limiting factor in bacterial lignin degradation. DypB production was, therefore, optimized in recombinant strains and a 14,141-fold increase in DypB activity (56,565 U/l) was achieved, providing novel insights for lignin bioconversion.
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Affiliation(s)
- Lu Lin
- Institute of Marine Science and Technology, Shandong University, Jinan, China.,Ocean College, Zhejiang University, Hangzhou, China
| | | | - Lanfang Cao
- Ocean College, Zhejiang University, Hangzhou, China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou, China
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8
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Wang S, Dong ZY, Yan YB. Semiholoenzyme optimizes activity and stability of a hyperthermostable iron-superoxide dismutase. Biochem Biophys Res Commun 2019; 519:93-99. [PMID: 31477266 DOI: 10.1016/j.bbrc.2019.08.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 08/24/2019] [Indexed: 10/26/2022]
Abstract
Metal ion coordination is an essential step for the maturation of metalloenzymes. Generally, the metal coordination sites are thought to be fully occupied to achieve the maximum activity and stability. In this research, we compared the structural features, activity and stability of the apo-, semiholo- and holo-forms of a hyperthermostable tetrameric Fe-superoxide dismutase (SOD). Strikingly, the three forms of enzymes had similar compact tetrameric structures. Removal of iron ions destabilized subunit-subunit interactions during guanidine hydrochloride-induced unfolding. The partially metalized semiholoenzyme possessed most of the activity and identical hyperthermostability of the holoenzyme, but weaker propensity to aggregate. Furthermore, both of the iron content and activity of the semiholoenzyme were unaffected by a 200-fold excess iron ions in solutions, suggesting that conformation of the apo-subunits were forced to the close state by the iron-containing subunits. These observations suggest that fully metalized enzyme is probably nonessential for multimeric metalloenzymes and the semiholoenzyme may be a better choice. The unique properties of semiholoenzyme also provide the organisms a compromised solution to survival under metal deficiency conditions.
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Affiliation(s)
- Sha Wang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100081, China
| | - Zhi-Yang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100081, China
| | - Yong-Bin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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Padilla-Del Valle R, Morales-Vale LR, Ríos-Velázquez C. Unraveling the microbial and functional diversity of Coamo thermal spring in Puerto Rico using metagenomic library generation and shotgun sequencing. GENOMICS DATA 2016; 11:98-101. [PMID: 28070487 PMCID: PMC5219636 DOI: 10.1016/j.gdata.2016.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 12/17/2016] [Indexed: 11/17/2022]
Abstract
In Puerto Rico, the microbial diversity of the thermal spring (ThS) in Coamo has never been studied using metagenomics. The focus of our research was to generate a metagenomic library from the ThS of Coamo, Puerto Rico and explore the microbial and functional diversity. The metagenomic library from the ThS waters was generated using direct DNA isolation. High molecular weight (40 kbp) DNA was end-repaired, electro eluted and ligated into a fosmid vector (pCCFOS1); then transduced into Escherichia coli EPI300-T1R using T1 bacteriophages. The library consisted of approximately 6000 clones, 90% containing metagenomic DNA. Next-Generation-Sequencing technology (Illumina MiSeq) was used to process the ThS metagenome. After removing the cloning vector, 122,026 sequences with 33.10 Mbps size and 64% of G + C content were annotated and analyzed using the MG-RAST online server. Bacteria showed to be the most abundant domain (95.84%) followed by unidentified sequences (2.28%), viruses (1.67%), eukaryotes (0.15%), and archaea (0.01%). The most abundant phyla were Proteobacteria (95.03%), followed by unidentified (2.28%), unclassified from viruses (1.74%), Firmicutes (0.20%) and Actinobacteria (0.18%). The most abundant species were Escherichia coli, Polaromonas naphthalenivorans, Albidiferax ferrireducens and Acidovorax sp. Subsystem functional analysis showed that 20% of genes belong to transposable elements, 10% to clustering-based subsystems, and 8% to the production of cofactors. Functional analysis using NOG annotation showed that 82.79% of proteins are poorly characterized indicating the possibility of novel microbial functions and with potential biomedical and biotechnological applications. Metagenomic data was deposited into the NCBI database under the accession number SAMN06131862.
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Affiliation(s)
- Ricky Padilla-Del Valle
- Biology Department, University of Puerto Rico at Mayaguez, 108 Street Bo. Miradero Km 1.3, Zoo Entrance, Mayagüez 00680, Puerto Rico
| | - Luis R Morales-Vale
- Biology Department, University of Puerto Rico at Mayaguez, 108 Street Bo. Miradero Km 1.3, Zoo Entrance, Mayagüez 00680, Puerto Rico
| | - Carlos Ríos-Velázquez
- Biology Department, University of Puerto Rico at Mayaguez, 108 Street Bo. Miradero Km 1.3, Zoo Entrance, Mayagüez 00680, Puerto Rico
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Rashid GMM, Taylor CR, Liu Y, Zhang X, Rea D, Fülöp V, Bugg TDH. Identification of Manganese Superoxide Dismutase from Sphingobacterium sp. T2 as a Novel Bacterial Enzyme for Lignin Oxidation. ACS Chem Biol 2015. [PMID: 26198187 DOI: 10.1021/acschembio.5b00298] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The valorization of aromatic heteropolymer lignin is an important unsolved problem in the development of a biomass-based biorefinery, for which novel high-activity biocatalysts are needed. Sequencing of the genomic DNA of lignin-degrading bacterial strain Sphingobacterium sp. T2 revealed no matches to known lignin-degrading genes. Proteomic matches for two manganese superoxide dismutase proteins were found in partially purified extracellular fractions. Recombinant MnSOD1 and MnSOD2 were both found to show high activity for oxidation of Organosolv and Kraft lignin, and lignin model compounds, generating multiple oxidation products. Structure determination revealed that the products result from aryl-Cα and Cα-Cβ bond oxidative cleavage and O-demethylation. The crystal structure of MnSOD1 was determined to 1.35 Å resolution, revealing a typical MnSOD homodimer harboring a five-coordinate trigonal bipyramidal Mn(II) center ligated by three His, one Asp, and a water/hydroxide in each active site. We propose that the lignin oxidation reactivity of these enzymes is due to the production of a hydroxyl radical, a highly reactive oxidant. This is the first demonstration that MnSOD is a microbial lignin-oxidizing enzyme.
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Affiliation(s)
- Goran M. M. Rashid
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Charles R. Taylor
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Yangqingxue Liu
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Xiaoyang Zhang
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Dean Rea
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Vilmos Fülöp
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Timothy D. H. Bugg
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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Ding Y, Wang X, Mou Z. Communities in the iron superoxide dismutase amino acid network. J Theor Biol 2015; 367:278-285. [PMID: 25500180 DOI: 10.1016/j.jtbi.2014.11.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 11/24/2014] [Accepted: 11/28/2014] [Indexed: 10/24/2022]
Abstract
Amino acid networks (AANs) analysis is a new way to reveal the relationship between protein structure and function. We constructed six different types of AANs based on iron superoxide dismutase (Fe-SOD) three-dimensional structure information. These Fe-SOD AANs have clear community structures when they were modularized by different methods. Especially, detected communities are related to Fe-SOD secondary structures. Regular structures show better correlations with detected communities than irregular structures, and loops weaken these correlations, which suggest that secondary structure is the unit element in Fe-SOD folding process. In addition, a comparative analysis of mesophilic and thermophilic Fe-SOD AANs' communities revealed that thermostable Fe-SOD AANs had more highly associated community structures than mesophilic one. Thermophilic Fe-SOD AANs also had more high similarity between communities and secondary structures than mesophilic Fe-SOD AANs. The communities in Fe-SOD AANs show that dense interactions in modules can help to stabilize thermophilic Fe-SOD.
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Affiliation(s)
- Yanrui Ding
- School of Digital Media, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China; Key Laboratory of Industrial Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China.
| | - Xueqin Wang
- School of Digital Media, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Zhaolin Mou
- School of Digital Media, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
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12
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Wang S, Dong ZY, Yan YB. Formation of high-order oligomers by a hyperthemostable Fe-superoxide dismutase (tcSOD). PLoS One 2014; 9:e109657. [PMID: 25313557 PMCID: PMC4196948 DOI: 10.1371/journal.pone.0109657] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 09/02/2014] [Indexed: 12/20/2022] Open
Abstract
Hyperthermostable proteins are highly resistant to various extreme conditions. Many factors have been proposed to contribute to their ultrahigh structural stability. Some thermostable proteins have larger oligomeric size when compared to their mesophilic homologues. The formation of compact oligomers can minimize the solvent accessible surface area and increase the changes of Gibbs free energy for unfolding. Similar to mesophilic proteins, hyperthermostable proteins also face the problem of unproductive aggregation. In this research, we investigated the role of high-order oligomerization in the fight against aggregation by a hyperthermostable superoxide dismutase identified from Tengchong, China (tcSOD). Besides the predominant tetramers, tcSOD could also form active high-order oligomers containing at least eight subunits. The dynamic equilibrium between tetramers and high-order oligomers was not significantly affected by pH, salt concentration or moderate temperature. The secondary and tertiary structures of tcSOD remained unchanged during heating, while cross-linking experiments showed that there were conformational changes or structural fluctuations at high temperatures. Mutational analysis indicated that the last helix at the C-terminus was involved in the formation of high-order oligomers, probably via domain swapping. Based on these results, we proposed that the reversible conversion between the active tetramers and high-order oligomers might provide a buffering system for tcSOD to fight against the irreversible protein aggregation pathway. The formation of active high-order oligomers not only increases the energy barrier between the native state and unfolded/aggregated state, but also provides the enzyme the ability to reproduce the predominant oligomers from the active high-order oligomers.
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Affiliation(s)
- Sha Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhi-Yang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (YBY); (ZYD)
| | - Yong-Bin Yan
- State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Life Sciences, Tsinghua University, Beijing, China
- * E-mail: (YBY); (ZYD)
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13
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Cloning and characterization of a new manganese superoxide dismutase from deep-sea thermophile Geobacillus sp. EPT3. World J Microbiol Biotechnol 2013; 30:1347-57. [DOI: 10.1007/s11274-013-1536-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 10/21/2013] [Indexed: 10/26/2022]
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14
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López-López O, Cerdán ME, González-Siso MI. Hot spring metagenomics. Life (Basel) 2013; 3:308-20. [PMID: 25369743 PMCID: PMC4187134 DOI: 10.3390/life3020308] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 04/11/2013] [Accepted: 04/15/2013] [Indexed: 12/14/2022] Open
Abstract
Hot springs have been investigated since the XIX century, but isolation and examination of their thermophilic microbial inhabitants did not start until the 1950s. Many thermophilic microorganisms and their viruses have since been discovered, although the real complexity of thermal communities was envisaged when research based on PCR amplification of the 16S rRNA genes arose. Thereafter, the possibility of cloning and sequencing the total environmental DNA, defined as metagenome, and the study of the genes rescued in the metagenomic libraries and assemblies made it possible to gain a more comprehensive understanding of microbial communities—their diversity, structure, the interactions existing between their components, and the factors shaping the nature of these communities. In the last decade, hot springs have been a source of thermophilic enzymes of industrial interest, encouraging further study of the poorly understood diversity of microbial life in these habitats.
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Affiliation(s)
- Olalla López-López
- Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain.
| | - María Esperanza Cerdán
- Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain.
| | - María Isabel González-Siso
- Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain.
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15
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Li Y, Hu F, Wang X, Cao H, Liu D, Yao D. A rational design for trypsin-resistant improvement of Armillariella tabescens β-mannanase MAN47 based on molecular structure evaluation. J Biotechnol 2013; 163:401-7. [DOI: 10.1016/j.jbiotec.2012.12.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 12/20/2012] [Accepted: 12/21/2012] [Indexed: 11/27/2022]
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16
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Ding Y, Cai Y, Han Y, Zhao B, Zhu L. Application of principal component analysis to determine the key structural features contributing to iron superoxide dismutase thermostability. Biopolymers 2012; 97:864-72. [PMID: 22899361 DOI: 10.1002/bip.22093] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Iron superoxide dismutase (Fe-SOD) is predominantly found in bacteria and mitochondria. The thermal stability of Fe-SOD from different sources can vary dramatically. We have studied the influence of structural parameters on Fe-SOD thermostability by principal component analysis (PCA). The results show that an increased α-helical and turn content, an increased α-helix and loop length, an increase in the number of main-main chains and charged-uncharged hydrogen bonds, a decrease in the 3(10) -helix content, and a decreased β-strand and loop length are all important factors for Fe-SOD thermostability. Interestingly, the use of charged residues to form salt bridges is tendentious in thermophilic Fe-SOD. Negatively charged Arg and positively charged Glu are efficiently used to form salt bridges. The cooperative action of the exposed area, the hydrogen bonds, and the secondary structure plays a crucial role in resisting high temperatures, which demonstrates that the increased stability of thermophilic Fe-SOD is provided by several structural factors acting together.
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Affiliation(s)
- Yanrui Ding
- Jiangnan University, Wuxi, People's Republic of China.
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17
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Song C, Sheng L, Zhang X. Preparation and characterization of a thermostable enzyme (Mn-SOD) immobilized on supermagnetic nanoparticles. Appl Microbiol Biotechnol 2012; 96:123-32. [DOI: 10.1007/s00253-011-3835-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 12/04/2011] [Accepted: 12/09/2011] [Indexed: 11/24/2022]
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18
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19
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Tuffin M, Anderson D, Heath C, Cowan DA. Metagenomic gene discovery: how far have we moved into novel sequence space? Biotechnol J 2010; 4:1671-83. [PMID: 19946882 DOI: 10.1002/biot.200900235] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Metagenomics emerged in the late 1990s as a tool for accessing and studying the collective microbial genetic material in the environment. The advent of the technology generated great excitement, as it has provided new opportunities and technologies for studying the wealth of microbial genetic diversity in the environment. Metagenomics has been widely predicted to access new dimensions of protein sequence space. A decade on, we review how far we have actually moved into new sequence space (and other aspects of protein space) using metagenomic tools. While several novel enzyme activities and protein structures have been identified through metagenomic strategies, the greatest advancement has been made in the isolation of novel protein sequences, some of which have no close relatives, form deeply branched lineages and even represent novel families. This is particularly true for glycosyl hydrolases and lipase/esterases, despite the fact that these activities are frequently screened for in metagenomic studies. However, there is much room for improvement in the methods employed and they will need to be addressed so that access to novel biocatalytic activities can be widened.
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Affiliation(s)
- Marla Tuffin
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of Western Cape, Cape town, South Africa
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20
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Contributions of the C-terminal helix to the structural stability of a hyperthermophilic Fe-superoxide dismutase (TcSOD). Int J Mol Sci 2009; 10:5498-5512. [PMID: 20054483 PMCID: PMC2802007 DOI: 10.3390/ijms10125498] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Revised: 12/16/2009] [Accepted: 12/17/2009] [Indexed: 11/17/2022] Open
Abstract
Hyperthermophilic superoxide dismutases (SODs) are of particular interest due to their potential industrial importance and scientific merit in studying the molecular mechanisms of protein folding and stability. Compared to the mesophilic SODs, the hyperthermostable Fe-SODs (TcSOD and ApSOD) have an extended C-terminal helix, which forms an additional ion-pairing network. In this research, the role of the extended C-terminus in the structural stability of TcSOD was studied by investigating the properties of two deletion mutants. The results indicated that the ion-pairing network at the C-terminus had limited contributions to the stability of TcSOD against heat- and GdnHCl-induced inactivation. The intactness of the C-terminal helix had dissimilar impact on the two stages of TcSOD unfolding induced by guanidinium chloride. The mutations slightly decreased the Gibbs free energy of the dissociation of the tetrameric enzymes, while greatly affected the stability of the molten globule-like intermediate. These results suggested that the additional ion-pairing network mainly enhanced the structural stability of TcSOD by stabilizing the monomers.
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21
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García Echauri SA, Gidekel M, Moraga AG, Ordóñez LG, Rojas Contreras JA, Barba de la Rosa AP, De León Rodríguez A. Heterologous expression of a novel psychrophilic Cu/Zn superoxide dismutase from Deschampsia antarctica. Process Biochem 2009. [DOI: 10.1016/j.procbio.2009.04.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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22
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Soulère L, Bernard J. Design, solid phase synthesis and evaluation of cationic ferrocenoyl peptide bioconjugates as potential antioxidant enzyme mimics. Bioorg Med Chem Lett 2009; 19:1173-6. [DOI: 10.1016/j.bmcl.2008.12.084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 12/16/2008] [Accepted: 12/19/2008] [Indexed: 11/16/2022]
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23
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Kwasigroch JM, Wintjens R, Gilis D, Rooman M. SODa: an Mn/Fe superoxide dismutase prediction and design server. BMC Bioinformatics 2008; 9:257. [PMID: 18518943 PMCID: PMC2442099 DOI: 10.1186/1471-2105-9-257] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Accepted: 06/02/2008] [Indexed: 11/17/2022] Open
Abstract
Background Superoxide dismutases (SODs) are ubiquitous metalloenzymes that play an important role in the defense of aerobic organisms against oxidative stress, by converting reactive oxygen species into nontoxic molecules. We focus here on the SOD family that uses Fe or Mn as cofactor. Results The SODa webtool predicts if a target sequence corresponds to an Fe/Mn SOD. If so, it predicts the metal ion specificity (Fe, Mn or cambialistic) and the oligomerization mode (dimer or tetramer) of the target. In addition, SODa proposes a list of residue substitutions likely to improve the predicted preferences for the metal cofactor and oligomerization mode. The method is based on residue fingerprints, consisting of residues conserved in SOD sequences or typical of SOD subgroups, and of interaction fingerprints, containing residue pairs that are in contact in SOD structures. Conclusion SODa is shown to outperform and to be more discriminative than traditional techniques based on pairwise sequence alignments. Moreover, the fact that it proposes selected mutations makes it a valuable tool for rational protein design.
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Affiliation(s)
- Jean Marc Kwasigroch
- Unité de Bioinformatique génomique et structurale, Université Libre de Bruxelles, CP 165/61, avenue Roosevelt 50, B-1050 Brussels, Belgium.
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24
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Multistate folding of a hyperthermostable Fe-superoxide dismutase (TcSOD) in guanidinium hydrochloride: The importance of the quaternary structure. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:445-54. [DOI: 10.1016/j.bbapap.2007.12.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Revised: 11/15/2007] [Accepted: 12/03/2007] [Indexed: 11/22/2022]
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25
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Clark AT, Smith K, Muhandiram R, Edmondson SP, Shriver JW. Carboxyl pK(a) values, ion pairs, hydrogen bonding, and the pH-dependence of folding the hyperthermophile proteins Sac7d and Sso7d. J Mol Biol 2007; 372:992-1008. [PMID: 17692336 PMCID: PMC2083566 DOI: 10.1016/j.jmb.2007.06.089] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Revised: 06/19/2007] [Accepted: 06/29/2007] [Indexed: 10/23/2022]
Abstract
Sac7d and Sso7d are homologous, hyperthermophile proteins with a high density of charged surface residues and potential ion pairs. To determine the relative importance of specific amino acid side-chains in defining the stability and function of these Archaeal chromatin proteins, pK(a) values were measured for the acidic residues in both proteins using (13)C NMR chemical shifts. The stability of Sso7d enabled titrations to pH 1 under low-salt conditions. Two aspartate residues in Sso7d (D16 and D35) and a single glutamate residue (G54) showed significantly perturbed pK(a) values in low salt, indicating that the observed pH-dependence of stability was primarily due to these three residues. The pH-dependence of backbone amide NMR resonances demonstrated that perturbation of all three pK(a) values was primarily the result of side-chain to backbone amide hydrogen bonds. Few of the significantly perturbed acidic pK(a) values in Sac7d and Sso7d could be attributed to primarily ion pair or electrostatic interactions. A smaller perturbation of E48 (E47 in Sac7d) was ascribed to an ion pair interaction that may be important in defining the DNA binding surface. The small number (three) of significantly altered pK(a) values was in good agreement with a linkage analysis of the temperature, pH, and salt-dependence of folding. The linkage of the ionization of two or more side-chains to protein folding led to apparent cooperativity in the pH-dependence of folding, although each group titrated independently with a Hill coefficient near unity. These results demonstrate that the acid pH-dependence of protein stability in these hyperthermophile proteins is due to independent titration of acidic residues with pK(a) values perturbed primarily by hydrogen bonding of the side-chain to the backbone. This work demonstrates the need for caution in using structural data alone to argue the importance of ion pairs in stabilizing hyperthermophile proteins.
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Affiliation(s)
- Andrew T Clark
- Alabama High Field NMR Laboratory, Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Kelley Smith
- Alabama High Field NMR Laboratory, Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Ranjith Muhandiram
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Stephen P Edmondson
- Alabama High Field NMR Laboratory, Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
| | - John W Shriver
- Alabama High Field NMR Laboratory, Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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