1
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Zhang Q, Charles PD, Bendif EM, Hester SS, Mohammad S, Rickaby REM. Stimulating and toxic effect of chromium on growth and photosynthesis of a marine chlorophyte. THE NEW PHYTOLOGIST 2024; 241:676-686. [PMID: 37974482 DOI: 10.1111/nph.19376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023]
Abstract
Marine phytoplankton can interchange trace metals in various biochemical functions, particularly under metal-limiting conditions. Here, we investigate the stimulating and toxicity effect of chromium (Cr) on a marine Chlorophyceae Osetreococcus tauri under Fe-replete and Fe-deficient conditions. We determined the growth, photosynthesis, and proteome expressions of Osetreococcus tauri cultured under different Cr and Fe concentrations. In Fe-replete conditions, the presence of Cr(VI) stimulated significantly the growth rate and the maximum yield of photochemistry of photosystem II (Fv /Fm ) of the phytoplankton, while the functional absorption cross-section of photosystem II (σPSII ) did not change. Minor additions of Cr(VI) partially rescued phytoplankton growth under Fe-limited conditions. Proteomic analysis of this alga grown in Fe-replete normal and Fe-replete with Cr addition media (10 μM Cr) showed that the presence of Cr significantly decreased the expression of phosphate-transporting proteins and photosynthetic proteins, while increasing the expression of proteins related to carbon assimilation. Cr can stimulate the growth and photosynthesis of O. tauri, but the effects are dependent on both the Cr(VI) concentration and the availability of Fe. The proteomic results further suggest that Cr(VI) addition might significantly increase starch production and carbon fixation.
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Affiliation(s)
- Qiong Zhang
- Department of Ocean Science and Center for Ocean Research in Hong Kong and Macau (CORE), The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, 999077, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Tang Qi Road, Zhuhai, 519000, China
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, OX1 3AN, UK
| | - Philip D Charles
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - El Mahdi Bendif
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, OX1 3AN, UK
- Institut des sciences de la mer de Rimouski (ISMER), Université du Québec à Rimouski, Rimouski, G5L 3A1, QC, Canada
| | - Svenja S Hester
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Shabaz Mohammad
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Rosalind E M Rickaby
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, OX1 3AN, UK
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2
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Pereira AFM, Sani AA, Zapata TB, de Sousa DSM, Rossini BC, dos Santos LD, Rall VLM, Riccardi CDS, Fernandes Júnior A. Synergistic Antibacterial Efficacy of Melittin in Combination with Oxacillin against Methicillin-Resistant Staphylococcus aureus (MRSA). Microorganisms 2023; 11:2868. [PMID: 38138012 PMCID: PMC10745785 DOI: 10.3390/microorganisms11122868] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) often cause infections with high mortality rates. Antimicrobial peptides are a source of molecules for developing antimicrobials; one such peptide is melittin, a fraction from the venom of the Apis mellifera bee. This study aimed to evaluate the antibacterial and antibiofilm activities of melittin and its association with oxacillin (mel+oxa) against MRSA isolates, and to investigate the mechanisms of action of the treatments on MRSA. Minimum inhibitory concentrations (MICs) were determined, and synergistic effects of melittin with oxacillin and cephalothin were assessed. Antibiofilm and cytotoxic activities, as well as their impact on the cell membrane, were evaluated for melittin, oxacillin, and mel+oxa. Proteomics evaluated the effects of the treatments on MRSA. Melittin mean MICs for MRSA was 4.7 μg/mL and 12 μg/mL for oxacillin. Mel+oxa exhibited synergistic effects, reducing biofilm formation, and causing leakage of proteins, nucleic acids, potassium, and phosphate ions, indicating action on cell membrane. Melittin and mel+oxa, at MIC values, did not induce hemolysis and apoptosis in HaCaT cells. The treatments resulted in differential expression of proteins associated with protein synthesis and energy metabolism. Mel+oxa demonstrated antibacterial activity against MRSA, suggesting a potential as a candidate for the development of new antibacterial agents against MRSA.
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Affiliation(s)
- Ana Flávia Marques Pereira
- The Center for the Study of Venoms and Venomous Animals of UNESP (CEVAP), São Paulo State University (UNESP), Botucatu 18619-002, São Paulo, Brazil;
| | - Alessandra Aguirra Sani
- Department of Chemical and Biological Sciences, Microbiology and Immunology Sector, Institute of Biosciences of Botucatu (IBB), São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (A.A.S.); (T.B.Z.); (D.S.M.d.S.); (V.L.M.R.)
| | - Tatiane Baptista Zapata
- Department of Chemical and Biological Sciences, Microbiology and Immunology Sector, Institute of Biosciences of Botucatu (IBB), São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (A.A.S.); (T.B.Z.); (D.S.M.d.S.); (V.L.M.R.)
| | - Débora Silva Marques de Sousa
- Department of Chemical and Biological Sciences, Microbiology and Immunology Sector, Institute of Biosciences of Botucatu (IBB), São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (A.A.S.); (T.B.Z.); (D.S.M.d.S.); (V.L.M.R.)
| | - Bruno César Rossini
- Institute of Biotechnology (IBTEC), São Paulo State University (UNESP), Botucatu 18607-440, São Paulo, Brazil; (B.C.R.); (L.D.d.S.)
| | - Lucilene Delazari dos Santos
- Institute of Biotechnology (IBTEC), São Paulo State University (UNESP), Botucatu 18607-440, São Paulo, Brazil; (B.C.R.); (L.D.d.S.)
- Graduate Program in Tropical Diseases and Graduate Program in Research and Development (Medical Biotechnology), Botucatu Medical School (FMB), São Paulo State University (UNESP), Botucatu 18618-687, São Paulo, Brazil
| | - Vera Lúcia Mores Rall
- Department of Chemical and Biological Sciences, Microbiology and Immunology Sector, Institute of Biosciences of Botucatu (IBB), São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (A.A.S.); (T.B.Z.); (D.S.M.d.S.); (V.L.M.R.)
| | - Carla dos Santos Riccardi
- Department of Bioprocesses and Biotechnology, Faculty of Agricultural Sciences (FCA), São Paulo State University (UNESP), Botucatu 18610-034, São Paulo, Brazil;
| | - Ary Fernandes Júnior
- Department of Chemical and Biological Sciences, Microbiology and Immunology Sector, Institute of Biosciences of Botucatu (IBB), São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (A.A.S.); (T.B.Z.); (D.S.M.d.S.); (V.L.M.R.)
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3
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Mao Q, Jiang J, Wu X, Ma Y, Zhang Y, Zhao Y, Zhang Y, Wang Q. Bifunctional alcohol/aldehyde dehydrogenase AdhE controls phospho-transferase system sugar utilization and virulence gene expression by interacting PtsH in Edwardsiella piscicida. Microbiol Res 2022; 260:127018. [DOI: 10.1016/j.micres.2022.127018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/26/2022] [Accepted: 03/29/2022] [Indexed: 10/18/2022]
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4
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Shanbhag AP, Ghatak A, Rajagopal S. Industrial light at the end of the Iron-containing (group III) alcohol dehydrogenase tunnel. Biotechnol Appl Biochem 2022; 70:537-552. [PMID: 35751426 DOI: 10.1002/bab.2376] [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: 02/05/2022] [Accepted: 06/10/2022] [Indexed: 11/05/2022]
Abstract
There are three prominent alcohol dehydrogenases superfamilies: Short-chain, Medium-chain, and Iron-containing alcohol dehydrogenases (FeADHs). Many members are valuable catalysts for producing industrially relevant products such as Active pharmaceutical Intermediates, Chiral synthons, Biopolymers, Biofuels and secondary metabolites. However, FeADHs are the least explored enzymes among the superfamilies for commercial tenacities. They portray a conserved structure having a 'tunnel-like' cofactor and substrate binding site with particular functions, despite representing high sequence diversity. Interestingly, phylogenetic analysis demarcates enzymes catalyzing distinct native substrates where closely related clades convert similar molecules. Further, homologs from various mesophilic and thermophilic microbes have been explored for designing a solvent and temperature resistant enzyme for industrial purposes. The review explores different Iron-containing alcohol dehydrogenases potential engineering of the enzymes and substrates helpful in manufacturing commercial products. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Anirudh P Shanbhag
- Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK Campus, Bangalore, 560065.,Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, India
| | - Arindam Ghatak
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, India.,Biomoneta Research Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK Campus, Bangalore, 560065
| | - Sreenath Rajagopal
- Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK Campus, Bangalore, 560065
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5
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Adewara OA, Ogunbanwo ST. Acid stress responses of Lactobacillus amylovorus and Candida kefyr isolated from fermented sorghum gruel and their application in food fermentation. Can J Microbiol 2022; 68:269-280. [PMID: 35038286 DOI: 10.1139/cjm-2021-0118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Exposure of Lactic Acid Bacteria (LAB) and yeasts to adverse fluctuations during fermentation causes stress, consequently, microbes develop adaptive responses. In this study, the physiological and proteomic responses of LAB and yeast to acid stress, and their application in food fermentation was investigated. The physiological and proteomic responses of Lactobacillus amylovorus LS07 and Candida kefyr YS12 to acid stress were measured using turbidimetry method, SDS-PAGE and LC-MS/MS respectively. The technique previously reported by Association of Official Analytical Chemists (AOAC) were employed for evaluation of the physiocochemical and organoleptic properties of the sorghum gruel fermented using the LAB and yeast in singly and combination as starter cultures and spontaneous fermentation as control. Growth of L. amylovorus LS07 was optimal at pH 1.0 and C. kefyr YSI2 at pH 4. An increased intensity of 30S ribosomal protein S2 (L. amylovorus LS07) and 6-phosphogluconate dehydrogenase (C. kefyr YS12) was noted at pH 1 and 4 respectively suggesting increased microbial metabolism thereby reducing stress encountered. Sorghum gruel produced with combined starters had the highest crude protein (10.94 %), Iron content (0.0085 %), organoleptic acceptability (7.29) significantly different from products produced with the single starters and control. The combined starter's (L. amylovorus LS07 and C. kefyr YSI2 as starter) adapted stress yielded foods with improved sensory properties, mineral and reduced anti-nutrient contents.
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Affiliation(s)
- Oluwaseun Adeola Adewara
- University of Ibadan, 58987, Microbiology, Ibadan, Ibadan, Nigeria.,Caleb University, 202110, Biological Sciences and Biotechnology, Lagos, Lagos, Nigeria;
| | - S T Ogunbanwo
- University of Ibadan, Microbiology, P.O. Box 22346, University of Ibadan, Ibadan, Nigeria, Ibadan, Oyo, Nigeria, +234;
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6
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Fragkopoulos AA, Vachier J, Frey J, Le Menn FM, Mazza MG, Wilczek M, Zwicker D, Bäumchen O. Self-generated oxygen gradients control collective aggregation of photosynthetic microbes. J R Soc Interface 2021; 18:20210553. [PMID: 34847792 PMCID: PMC8633776 DOI: 10.1098/rsif.2021.0553] [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] [Indexed: 12/02/2022] Open
Abstract
For billions of years, photosynthetic microbes have evolved under the variable exposure to sunlight in diverse ecosystems and microhabitats all over our planet. Their abilities to dynamically respond to alterations of the luminous intensity, including phototaxis, surface association and diurnal cell cycles, are pivotal for their survival. If these strategies fail in the absence of light, the microbes can still sustain essential metabolic functionalities and motility by switching their energy production from photosynthesis to oxygen respiration. For suspensions of motile C. reinhardtii cells above a critical density, we demonstrate that this switch reversibly controls collective microbial aggregation. Aerobic respiration dominates over photosynthesis in conditions of low light, which causes the microbial motility to sensitively depend on the local availability of oxygen. For dense microbial populations in self-generated oxygen gradients, microfluidic experiments and continuum theory based on a reaction–diffusion mechanism show that oxygen-regulated motility enables the collective emergence of highly localized regions of high and low cell densities.
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Affiliation(s)
- Alexandros A Fragkopoulos
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Am Faßberg 17, 37077 Göttingen, Germany
| | - Jérémy Vachier
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Am Faßberg 17, 37077 Göttingen, Germany.,Nordita, KTH Royal Institute of Technology and Stockholm University, Hannes Alfvéns väg 12, 106 91 Stockholm, Sweden
| | - Johannes Frey
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Am Faßberg 17, 37077 Göttingen, Germany
| | - Flora-Maud Le Menn
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Am Faßberg 17, 37077 Göttingen, Germany
| | - Marco G Mazza
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Am Faßberg 17, 37077 Göttingen, Germany.,Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, UK
| | - Michael Wilczek
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Am Faßberg 17, 37077 Göttingen, Germany
| | - David Zwicker
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Am Faßberg 17, 37077 Göttingen, Germany
| | - Oliver Bäumchen
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Am Faßberg 17, 37077 Göttingen, Germany.,Experimental Physics V, University of Bayreuth, Universitätsstr. 30, 95447 Bayreuth, Germany
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7
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Bioconversion of Lignocellulosic Biomass into Value Added Products under Anaerobic Conditions: Insight into Proteomic Studies. Int J Mol Sci 2021; 22:ijms222212249. [PMID: 34830131 PMCID: PMC8624197 DOI: 10.3390/ijms222212249] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 01/14/2023] Open
Abstract
Production of biofuels and other value-added products from lignocellulose breakdown requires the coordinated metabolic activity of varied microorganisms. The increasing global demand for biofuels encourages the development and optimization of production strategies. Optimization in turn requires a thorough understanding of the microbial mechanisms and metabolic pathways behind the formation of each product of interest. Hydrolysis of lignocellulosic biomass is a bottleneck in its industrial use and often affects yield efficiency. The accessibility of the biomass to the microorganisms is the key to the release of sugars that are then taken up as substrates and subsequently transformed into the desired products. While the effects of different metabolic intermediates in the overall production of biofuel and other relevant products have been studied, the role of proteins and their activity under anaerobic conditions has not been widely explored. Shifts in enzyme production may inform the state of the microorganisms involved; thus, acquiring insights into the protein production and enzyme activity could be an effective resource to optimize production strategies. The application of proteomic analysis is currently a promising strategy in this area. This review deals on the aspects of enzymes and proteomics of bioprocesses of biofuels production using lignocellulosic biomass as substrate.
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8
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Hounslow E, Evans CA, Pandhal J, Sydney T, Couto N, Pham TK, Gilmour DJ, Wright PC. Quantitative proteomic comparison of salt stress in Chlamydomonas reinhardtii and the snow alga Chlamydomonas nivalis reveals mechanisms for salt-triggered fatty acid accumulation via reallocation of carbon resources. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:121. [PMID: 34022944 PMCID: PMC8141184 DOI: 10.1186/s13068-021-01970-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/13/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Chlamydomonas reinhardtii is a model green alga strain for molecular studies; its fully sequenced genome has enabled omic-based analyses that have been applied to better understand its metabolic responses to stress. Here, we characterised physiological and proteomic changes between a low-starch C. reinhardtii strain and the snow alga Chlamydomonas nivalis, to reveal insights into their contrasting responses to salinity stress. RESULTS Each strain was grown in conditions tailored to their growth requirements to encourage maximal fatty acid (as a proxy measure of lipid) production, with internal controls to allow comparison points. In 0.2 M NaCl, C. nivalis accumulates carbohydrates up to 10.4% DCW at 80 h, and fatty acids up to 52.0% dry cell weight (DCW) over 12 days, however, C. reinhardtii does not show fatty acid accumulation over time, and shows limited carbohydrate accumulation up to 5.5% DCW. Analysis of the C. nivalis fatty acid profiles showed that salt stress improved the biofuel qualities over time. Photosynthesis and respiration rates are reduced in C. reinhardtii relative to C. nivalis in response to 0.2 M NaCl. De novo sequencing and homology matching was used in conjunction with iTRAQ-based quantitative analysis to identify and relatively quantify proteomic alterations in cells exposed to salt stress. There were abundance differences in proteins associated with stress, photosynthesis, carbohydrate and lipid metabolism proteins. In terms of lipid synthesis, salt stress induced an increase in dihydrolipoyl dehydrogenase in C. nivalis (1.1-fold change), whilst levels in C. reinhardtii remained unaffected; this enzyme is involved in acetyl CoA production and has been linked to TAG accumulation in microalgae. In salt-stressed C. nivalis there were decreases in the abundance of UDP-sulfoquinovose (- 1.77-fold change), which is involved in sulfoquinovosyl diacylglycerol metabolism, and in citrate synthase (- 2.7-fold change), also involved in the TCA cycle. Decreases in these enzymes have been shown to lead to increased TAG production as fatty acid biosynthesis is favoured. Data are available via ProteomeXchange with identifier PXD018148. CONCLUSIONS These differences in protein abundance have given greater understanding of the mechanism by which salt stress promotes fatty acid accumulation in the un-sequenced microalga C. nivalis as it switches to a non-growth state, whereas C. reinhardtii does not have this response.
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Affiliation(s)
- E Hounslow
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - C A Evans
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK.
| | - J Pandhal
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - T Sydney
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK
| | - N Couto
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - T K Pham
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - D James Gilmour
- Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - P C Wright
- University of Southampton, University Road, Southampton, SO17 1BJ, UK
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9
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van Lis R, Couté Y, Brugière S, Tourasse NJ, Laurent B, Nitschke W, Vallon O, Atteia A. Phylogenetic and functional diversity of aldehyde-alcohol dehydrogenases in microalgae. PLANT MOLECULAR BIOLOGY 2021; 105:497-511. [PMID: 33415608 DOI: 10.1007/s11103-020-01105-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/10/2020] [Indexed: 06/12/2023]
Abstract
The study shows the biochemical and enzymatic divergence between the two aldehyde-alcohol dehydrogenases of the alga Polytomella sp., shedding light on novel aspects of the enzyme evolution amid unicellular eukaryotes. Aldehyde-alcohol dehydrogenases (ADHEs) are large metalloenzymes that typically perform the two-step reduction of acetyl-CoA into ethanol. These enzymes consist of an N-terminal acetylating aldehyde dehydrogenase domain (ALDH) and a C-terminal alcohol dehydrogenase (ADH) domain. ADHEs are present in various bacterial phyla as well as in some unicellular eukaryotes. Here we focus on ADHEs in microalgae, a diverse and polyphyletic group of plastid-bearing unicellular eukaryotes. Genome survey shows the uneven distribution of the ADHE gene among free-living algae, and the presence of two distinct genes in various species. We show that the non-photosynthetic Chlorophyte alga Polytomella sp. SAG 198.80 harbors two genes for ADHE-like enzymes with divergent C-terminal ADH domains. Immunoblots indicate that both ADHEs accumulate in Polytomella cells growing aerobically on acetate or ethanol. ADHE1 of ~ 105-kDa is found in particulate fractions, whereas ADHE2 of ~ 95-kDa is mostly soluble. The study of the recombinant enzymes revealed that ADHE1 has both the ALDH and ADH activities, while ADHE2 has only the ALDH activity. Phylogeny shows that the divergence occurred close to the root of the Polytomella genus within a clade formed by the majority of the Chlorophyte ADHE sequences, next to the cyanobacterial clade. The potential diversification of function in Polytomella spp. unveiled here likely took place after the loss of photosynthesis. Overall, our study provides a glimpse at the complex evolutionary history of the ADHE in microalgae which includes (i) acquisition via different gene donors, (ii) gene duplication and (iii) independent evolution of one of the two enzymatic domains.
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Affiliation(s)
- Robert van Lis
- Aix Marseille Université, CNRS, BIP UMR 7281, Marseille, France
- LBE, Univ Montpellier, INRAE, Narbonne, France
| | - Yohann Couté
- Univ Grenoble Alpes, CEA, INSERM, IRIG, Grenoble, BGE, France
| | - Sabine Brugière
- Univ Grenoble Alpes, CEA, INSERM, IRIG, Grenoble, BGE, France
| | - Nicolas J Tourasse
- UMR7141 CNRS-Sorbonne Université, Institut de Biologie Physico-Chimique, Paris, France
| | - Benoist Laurent
- FR 550 CNRS, Institut de Biologie Physico-Chimique, Paris, France
| | | | - Olivier Vallon
- UMR7141 CNRS-Sorbonne Université, Institut de Biologie Physico-Chimique, Paris, France
| | - Ariane Atteia
- Aix Marseille Université, CNRS, BIP UMR 7281, Marseille, France.
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France.
- MARBEC, Station Ifremer, Avenue Jean Monnet, Sète, France.
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10
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Cho S, Kim G, Song JJ, Cho C. Cryo-EM structure of Vibrio cholerae aldehyde-alcohol dehydrogenase spirosomes. Biochem Biophys Res Commun 2020; 536:38-44. [PMID: 33360541 DOI: 10.1016/j.bbrc.2020.12.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 12/13/2020] [Indexed: 01/10/2023]
Abstract
Aldehyde-alcohol dehydrogenase (AdhE) is a metabolic enzyme and virulence factor in bacteria. E. coli AdhE (eAdhE) multimerizes into spirosomes that are essential for enzymatic activity. However, it is unknown whether AdhE structure is conserved in divergent bacteria. Here, we present the cryo-EM structure of AdhE (vAdhE) from Vibrio cholerae to 4.31 Å resolution. Overall, vAdhE spirosomes are similar to eAdhE with conserved subunit arrangement. However, divergences in key oligomerization residues cause vAdhE to form labile spirosomes with lower enzymatic activity. Mutating the vAdhE oligomerization interface to mimic eAdhE increases spirosome stability and enzymatic activity to levels comparable to eAdhE. These results support the generality of AdhE spirosome structures, and provide a structural basis to target vAdhE to attenuate bacterial virulence.
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Affiliation(s)
- Saehyun Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Republic of Korea
| | - Gijeong Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Republic of Korea
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Republic of Korea.
| | - Carol Cho
- Center for Natural Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Republic of Korea.
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11
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Thangaraj S, Sun J. Transcriptomic reprogramming of the oceanic diatom Skeletonema dohrnii under warming ocean and acidification. Environ Microbiol 2020; 23:980-995. [PMID: 32975013 DOI: 10.1111/1462-2920.15248] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 09/14/2020] [Accepted: 09/20/2020] [Indexed: 12/19/2022]
Abstract
Under ocean warming and acidification, diatoms use a unique acclimation and adaptation strategy by saving energy and utilizing it for other cellular processes. However, the molecular mechanisms that underlie this reprogramming of energy utilization are currently unknown. Here, we investigate the metabolic reprogramming of the ecologically important diatom Skeletonema dohrnii grown under two different temperature (21°C and 25°C) and pCO2 (400 and 1000 ppm) levels, utilizing global transcriptomic analysis. We find that evolutionary changes in the baseline gene expression, which we termed transcriptional up- and downregulation, is the primary mechanism used by diatoms to acclimate to the combined conditions of ocean warming and acidification. This transcriptional regulation shows that under higher temperature and pCO2 conditions, photosynthesis, electron transport and carboxylation were modified with increasing abundances of genes encoding ATP, NADPH and carbon gaining for the carbon-dioxide-concentrating mechanisms (CCMs). Our results also indicate that changes in the transcriptional regulation of CCMs led to a decrease in the metabolic cost to save energy by promoting amino acid synthesis and nitrogen assimilation for the active protein processing machinery to adapt to warming and ocean acidification. This study generated unique metabolic insights into diatoms and suggests that future climate change conditions will cause evolutionary changes in oceanic diatoms that will facilitate their acclimation strategy.
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Affiliation(s)
- Satheeswaran Thangaraj
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan, Hubei, 430074, China
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan, Hubei, 430074, China
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12
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Filamentation of the bacterial bi-functional alcohol/aldehyde dehydrogenase AdhE is essential for substrate channeling and enzymatic regulation. Nat Commun 2020; 11:1426. [PMID: 32188856 PMCID: PMC7080775 DOI: 10.1038/s41467-020-15214-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/26/2020] [Indexed: 11/08/2022] Open
Abstract
Acetaldehyde-alcohol dehydrogenase (AdhE) enzymes are a key metabolic enzyme in bacterial physiology and pathogenicity. They convert acetyl-CoA to ethanol via an acetaldehyde intermediate during ethanol fermentation in an anaerobic environment. This two-step reaction is associated to NAD+ regeneration, essential for glycolysis. The bifunctional AdhE enzyme is conserved in all bacterial kingdoms but also in more phylogenetically distant microorganisms such as green microalgae. It is found as an oligomeric form called spirosomes, for which the function remains elusive. Here, we use cryo-electron microscopy to obtain structures of Escherichia coli spirosomes in different conformational states. We show that spirosomes contain active AdhE monomers, and that AdhE filamentation is essential for its activity in vitro and function in vivo. The detailed analysis of these structures provides insight showing that AdhE filamentation is essential for substrate channeling within the filament and for the regulation of enzyme activity.
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Kim G, Azmi L, Jang S, Jung T, Hebert H, Roe AJ, Byron O, Song JJ. Aldehyde-alcohol dehydrogenase forms a high-order spirosome architecture critical for its activity. Nat Commun 2019; 10:4527. [PMID: 31586059 PMCID: PMC6778083 DOI: 10.1038/s41467-019-12427-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/10/2019] [Indexed: 02/07/2023] Open
Abstract
Aldehyde-alcohol dehydrogenase (AdhE) is a key enzyme in bacterial fermentation, converting acetyl-CoA to ethanol, via two consecutive catalytic reactions. Here, we present a 3.5 Å resolution cryo-EM structure of full-length AdhE revealing a high-order spirosome architecture. The structure shows that the aldehyde dehydrogenase (ALDH) and alcohol dehydrogenase (ADH) active sites reside at the outer surface and the inner surface of the spirosome respectively, thus topologically separating these two activities. Furthermore, mutations disrupting the helical structure abrogate enzymatic activity, implying that formation of the spirosome structure is critical for AdhE activity. In addition, we show that this spirosome structure undergoes conformational change in the presence of cofactors. This work presents the atomic resolution structure of AdhE and suggests that the high-order helical structure regulates its enzymatic activity. Aldehyde-alcohol dehydrogenase (AdhE) converts acetyl-CoA to ethanol and plays an important role in bacterial fermentation. Here the authors present the 3.5 Å cryo-EM structure of full-length E. coli AdhE, which reveals a right-handed helical spirosome structure and they show that the helical structure is required for AdhE activity.
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Affiliation(s)
- Gijeong Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Liyana Azmi
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Seongmin Jang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Taeyang Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea.,School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Novum, SE-141 57, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, S-141 83, Huddinge, Sweden
| | - Hans Hebert
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Novum, SE-141 57, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, S-141 83, Huddinge, Sweden
| | - Andrew J Roe
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Olwyn Byron
- School of Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea.
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van Lis R, Brugière S, Baffert C, Couté Y, Nitschke W, Atteia A. Hybrid cluster proteins in a photosynthetic microalga. FEBS J 2019; 287:721-735. [PMID: 31361397 DOI: 10.1111/febs.15025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/21/2019] [Accepted: 07/28/2019] [Indexed: 11/30/2022]
Abstract
Hybrid cluster proteins (HCPs) are metalloproteins characterized by the presence of an iron-sulfur-oxygen cluster. These proteins occur in all three domains of life. In eukaryotes, HCPs have so far been found only in a few anaerobic parasites and photosynthetic microalgae. With respect to all species harboring an HCP, the green microalga Chlamydomonas reinhardtii stands out by the presence of four HCP genes. The study of the gene and protein structures as well as the phylogenetic analyses strongly support a model in which the HCP family in the alga has emerged from a single gene of alpha proteobacterial origin and then expanded by several rounds of duplications. The spectra and redox properties of HCP1 and HCP3, produced heterologously in Escherichia coli, were analyzed by electron paramagnetic resonance spectroscopy on redox-titrated samples. Both proteins contain a [4Fe-4S]-cluster as well as a [4Fe-2O-2S]-hybrid cluster with paramagnetic properties related to those of HCPs from Desulfovibrio species. Immunoblotting experiments combined with mass spectrometry-based proteomics showed that both nitrate and darkness contribute to the strong upregulation of the HCP levels in C. reinhardtii growing under oxic conditions. The link to the nitrate metabolism is discussed in the light of recent data on the potential role of HCP in S-nitrosylation in bacteria.
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Affiliation(s)
- Robert van Lis
- Aix Marseille Univ, CNRS, Unité de Bioénergétique et Ingénierie des Protéines, UMR 7281, Marseille, France.,LBE, Univ Montpellier, INRA, Narbonne, France
| | - Sabine Brugière
- Univ Grenoble Alpes, CEA and INSERM, BIG-BGE, Grenoble, France
| | - Carole Baffert
- Aix Marseille Univ, CNRS, Unité de Bioénergétique et Ingénierie des Protéines, UMR 7281, Marseille, France
| | - Yohann Couté
- Univ Grenoble Alpes, CEA and INSERM, BIG-BGE, Grenoble, France
| | - Wolfgang Nitschke
- Aix Marseille Univ, CNRS, Unité de Bioénergétique et Ingénierie des Protéines, UMR 7281, Marseille, France
| | - Ariane Atteia
- Aix Marseille Univ, CNRS, Unité de Bioénergétique et Ingénierie des Protéines, UMR 7281, Marseille, France.,MARBEC CNRS, IFREMER, IRD, Univ. Montpellier, UMR 9091, Sète, France
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Salomé PA, Merchant SS. A Series of Fortunate Events: Introducing Chlamydomonas as a Reference Organism. THE PLANT CELL 2019; 31:1682-1707. [PMID: 31189738 PMCID: PMC6713297 DOI: 10.1105/tpc.18.00952] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/20/2019] [Accepted: 06/08/2019] [Indexed: 05/13/2023]
Abstract
The unicellular alga Chlamydomonas reinhardtii is a classical reference organism for studying photosynthesis, chloroplast biology, cell cycle control, and cilia structure and function. It is also an emerging model for studying sensory cilia, the production of high-value bioproducts, and in situ structural determination. Much of the early appeal of Chlamydomonas was rooted in its promise as a genetic system, but like other classic model organisms, this rise to prominence predated the discovery of the structure of DNA, whole-genome sequences, and molecular techniques for gene manipulation. The haploid genome of C. reinhardtii facilitates genetic analyses and offers many of the advantages of microbial systems applied to a photosynthetic organism. C. reinhardtii has contributed to our understanding of chloroplast-based photosynthesis and cilia biology. Despite pervasive transgene silencing, technological advances have allowed researchers to address outstanding lines of inquiry in algal research. The most thoroughly studied unicellular alga, C. reinhardtii, is the current standard for algal research, and although genome editing is still far from efficient and routine, it nevertheless serves as a template for other algae. We present a historical retrospective of the rise of C. reinhardtii to illuminate its past and present. We also present resources for current and future scientists who may wish to expand their studies to the realm of microalgae.
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Affiliation(s)
- Patrice A Salomé
- University of California, Los Angeles, Department of Chemistry and Biochemistry, Los Angeles, CA 90095
| | - Sabeeha S Merchant
- University of California, Los Angeles, Department of Chemistry and Biochemistry, Los Angeles, CA 90095
- University of California, Berkeley, Departments of Plant and Microbial Biology and Molecular and Cell Biology, Berkeley, CA 94720
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Genome-wide characterization of ALDH Superfamily in Brassica rapa and enhancement of stress tolerance in heterologous hosts by BrALDH7B2 expression. Sci Rep 2019; 9:7012. [PMID: 31065035 PMCID: PMC6505040 DOI: 10.1038/s41598-019-43332-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 04/22/2019] [Indexed: 12/17/2022] Open
Abstract
Aldehyde dehydrogenase (ALDH) carries out oxidation of toxic aldehydes using NAD+/NADP+ as cofactors. In the present study, we performed a genome-wide identification and expression analysis of genes in the ALDH gene family in Brassica rapa. A total of 23 ALDH genes in the superfamily have been identified according to the classification of ALDH Gene Nomenclature Committee (AGNC). They were distributed unevenly across all 10 chromosomes. All the 23 Brassica rapa ALDH (BrALDH) genes exhibited varied expression patterns during treatments with abiotic stress inducers and hormonal treatments. The relative expression profiles of ALDH genes in B. rapa showed that they are predominantly expressed in leaves and stem suggesting their function in the vegetative tissues. BrALDH7B2 showed a strong response to abiotic stress and hormonal treatments as compared to other ALDH genes; therefore, it was overexpressed in heterologous hosts, E. coli and yeast to study its possible function under abiotic stress conditions. Over-expression of BrALDH7B2 in heterologous systems, E. coli and yeast cells conferred significant tolerance to abiotic stress treatments. Results from this work demonstrate that BrALDH genes are a promising and untapped genetic resource for crop improvement and could be deployed further in the development of drought and salinity tolerance in B. rapa and other economically important crops.
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Multiomics resolution of molecular events during a day in the life of Chlamydomonas. Proc Natl Acad Sci U S A 2019; 116:2374-2383. [PMID: 30659148 PMCID: PMC6369806 DOI: 10.1073/pnas.1815238116] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The unicellular green alga Chlamydomonas reinhardtii displays metabolic flexibility in response to a changing environment. We analyzed expression patterns of its three genomes in cells grown under light-dark cycles. Nearly 85% of transcribed genes show differential expression, with different sets of transcripts being up-regulated over the course of the day to coordinate cellular growth before undergoing cell division. Parallel measurements of select metabolites and pigments, physiological parameters, and a subset of proteins allow us to infer metabolic events and to evaluate the impact of the transcriptome on the proteome. Among the findings are the observations that Chlamydomonas exhibits lower respiratory activity at night compared with the day; multiple fermentation pathways, some oxygen-sensitive, are expressed at night in aerated cultures; we propose that the ferredoxin, FDX9, is potentially the electron donor to hydrogenases. The light stress-responsive genes PSBS, LHCSR1, and LHCSR3 show an acute response to lights-on at dawn under abrupt dark-to-light transitions, while LHCSR3 genes also exhibit a later, second burst in expression in the middle of the day dependent on light intensity. Each response to light (acute and sustained) can be selectively activated under specific conditions. Our expression dataset, complemented with coexpression networks and metabolite profiling, should constitute an excellent resource for the algal and plant communities.
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Düner M, Lambertz J, Mügge C, Hemschemeier A. The soluble guanylate cyclase CYG12 is required for the acclimation to hypoxia and trophic regimes in Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:311-337. [PMID: 29161457 DOI: 10.1111/tpj.13779] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 11/03/2017] [Accepted: 11/09/2017] [Indexed: 05/27/2023]
Abstract
Oxygenic phototrophs frequently encounter environmental conditions that result in intracellular energy crises. Growth of the unicellular green alga Chlamydomonas reinhardtii in hypoxia in the light depends on acclimatory responses of which the induction of photosynthetic cyclic electron flow is essential. The microalga cannot grow in the absence of molecular oxygen (O2 ) in the dark, although it possesses an elaborate fermentation metabolism. Not much is known about how the microalga senses and signals the lack of O2 or about its survival strategies during energy crises. Recently, nitric oxide (NO) has emerged to be required for the acclimation of C. reinhardtii to hypoxia. In this study, we show that the soluble guanylate cyclase (sGC) CYG12, a homologue of animal NO sensors, is also involved in this response. CYG12 is an active sGC, and post-transcriptional down-regulation of the CYG12 gene impairs hypoxic growth and gene expression in C. reinhardtii. However, it also results in a disturbed photosynthetic apparatus under standard growth conditions and the inability to grow heterotrophically. Transcriptome profiles indicate that the mis-expression of CYG12 results in a perturbation of responses that, in the wild-type, maintain the cellular energy budget. We suggest that CYG12 is required for the proper operation of the photosynthetic apparatus which, in turn, is essential for survival in hypoxia and darkness.
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Affiliation(s)
- Melis Düner
- Department of Plant Biochemistry, Workgroup Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Jan Lambertz
- Department of Plant Biochemistry, Workgroup Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Carolin Mügge
- Junior Research Group for Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Anja Hemschemeier
- Department of Plant Biochemistry, Workgroup Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitätsstr. 150, 44801, Bochum, Germany
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