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Carrión O, Zhu XY, Williams BT, Wang J, Zhang XH, Todd JD. Molecular discoveries in microbial DMSP synthesis. Adv Microb Physiol 2023; 83:59-116. [PMID: 37507162 DOI: 10.1016/bs.ampbs.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Dimethylsulfoniopropionate (DMSP) is one of the Earth's most abundant organosulfur compounds because many marine algae, bacteria, corals and some plants produce it to high mM intracellular concentrations. In these organisms, DMSP acts an anti-stress molecule with purported roles to protect against salinity, temperature, oxidative stress and hydrostatic pressure, amongst many other reported functions. However, DMSP is best known for being a major precursor of the climate-active gases and signalling molecules dimethylsulfide (DMS), methanethiol (MeSH) and, potentially, methane, through microbial DMSP catabolism. DMSP catabolism has been extensively studied and the microbes, pathways and enzymes involved have largely been elucidated through the application of molecular research over the last 17 years. In contrast, the molecular biology of DMSP synthesis is a much newer field, with the first DMSP synthesis enzymes only being identified in the last 5 years. In this review, we discuss how the elucidation of key DMSP synthesis enzymes has greatly expanded our knowledge of the diversity of DMSP-producing organisms, the pathways used, and what environmental factors regulate production, as well as to inform on the physiological roles of DMSP. Importantly, the identification of key DMSP synthesis enzymes in the major groups of DMSP producers has allowed scientists to study the distribution and predict the importance of different DMSP-producing organisms to global DMSP production in diverse marine and sediment environments. Finally, we highlight key challenges for future molecular research into DMSP synthesis that need addressing to better understand the cycling of this important marine organosulfur compound, and its magnitude in the environment.
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Affiliation(s)
- Ornella Carrión
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
| | - Xiao-Yu Zhu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Beth T Williams
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Jinyan Wang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
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Lu Q, Zhou X, Liu R, Shi G, Zheng N, Gao G, Wang Y. Impacts of a bacterial algicide on metabolic pathways in Chlorella vulgaris. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 249:114451. [PMID: 38321670 DOI: 10.1016/j.ecoenv.2022.114451] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 10/04/2022] [Accepted: 12/16/2022] [Indexed: 02/08/2024]
Abstract
Chlorella is a dominant species during harmful algal blooms (HABs) worldwide, which bring about great environmental problems and are also a serious threat to drinking water safety. Application of bacterial algicides is a promising way to control HABs. However, the identified bacterial algicides against Chlorella and the understanding of their effects on algal metabolism are very limited. Here, we isolated a novel bacterium Microbacterium paraoxydans strain M1 that has significant algicidal activities against Chlorella vulgaris (algicidal rate 64.38 %, at 120 h). Atrazine-desethyl (AD) was then identified from strain M1 as an effective bacterial algicide, with inhibition or algae-lysing concentration values (EC50) of 1.64 μg/mL and 1.38 μg/mL, at 72 h and 120 h, respectively. LAD (2 μg/mL AD) or HAD (20 μg/mL AD) causes morphology alteration and ultrastructure damage, chlorophyll a reduction, gene expression regulation (for example, psbA, 0.05 fold at 24 h, 2.97 fold at 72 h, and 0.23 fold of the control in HAD), oxidative stress, lipid oxidation (MDA, 2.09 and 3.08 fold of the control in LAD and HAD, respectively, at 120 h) and DNA damage (average percentage of tail DNA 6.23 % at 120 h in HAD, slight damage: 5∼20 %) in the algal cells. The impacts of AD on algal metabolites and metabolic pathways, as well as the algal response to the adverse effects were investigated. The results revealed that amino acids, amines, glycosides and urea decreased significantly compared to the control after 24 h exposure to AD (p < 0.05). The main up-regulated metabolic pathways implied metabonomic resistance and defense against osmotic pressure, oxidative stress, photosynthesis inhibition or partial cellular structure damage, such as phenylalanine metabolism, arginine biosynthesis. The down-regulated glycine, serine and threonine metabolism is a major lead in the algicidal mechanism according to the value of pathway impact. The down-regulated glycine, and serine are responsible for the downregulation of glyoxylate and dicarboxylate metabolism, aminoacyl-tRNA biosynthesis, glutathione metabolism, and sulfur metabolism, which strengthen the algae-lysing effect. It is the first time to highlight the pivotal role of glycine, serine and threonine metabolism in algicidal activities, which provided a new perspective for understanding the mechanism of bacterial algicides exerting on algal cells at the metabolic level.
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Affiliation(s)
- Qianqian Lu
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300371, China
| | - Xinzhu Zhou
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300371, China
| | - Ruidan Liu
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300371, China
| | - Guojing Shi
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300371, China
| | - Ningning Zheng
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300371, China
| | - Guanghai Gao
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300371, China; State key Laboratory of Hydroscience and Engineering, Tsinghua University, China.
| | - Yingying Wang
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300371, China; Nankai International Advanced Research Institute (Shenzhen Futian), Shenzhen, China.
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Li C, Crack JC, Newton‐Payne S, Murphy ARJ, Chen X, Pinchbeck BJ, Zhou S, Williams BT, Peng M, Zhang X, Chen Y, Le Brun NE, Todd JD, Zhang Y. Mechanistic insights into the key marine dimethylsulfoniopropionate synthesis enzyme DsyB/DSYB. MLIFE 2022; 1:114-130. [PMID: 38817677 PMCID: PMC10989797 DOI: 10.1002/mlf2.12030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 06/01/2024]
Abstract
Marine algae and bacteria produce approximately eight billion tonnes of the organosulfur molecule dimethylsulfoniopropionate (DMSP) in Earth's surface oceans annually. DMSP is an antistress compound and, once released into the environment, a major nutrient, signaling molecule, and source of climate-active gases. The methionine transamination pathway for DMSP synthesis is used by most known DMSP-producing algae and bacteria. The S-directed S-adenosylmethionine (SAM)-dependent 4-methylthio-2-hydroxybutyrate (MTHB) S-methyltransferase, encoded by the dsyB/DSYB gene, is the key enzyme of this pathway, generating S-adenosylhomocysteine (SAH) and 4-dimethylsulfonio-2-hydroxybutyrate (DMSHB). DsyB/DSYB, present in most haptophyte and dinoflagellate algae with the highest known intracellular DMSP concentrations, is shown to be far more abundant and transcribed in marine environments than any other known S-methyltransferase gene in DMSP synthesis pathways. Furthermore, we demonstrate in vitro activity of the bacterial DsyB enzyme from Nisaea denitrificans and provide its crystal structure in complex with SAM and SAH-MTHB, which together provide the first important mechanistic insights into a DMSP synthesis enzyme. Structural and mutational analyses imply that DsyB adopts a proximity and desolvation mechanism for the methyl transfer reaction. Sequence analysis suggests that this mechanism may be common to all bacterial DsyB enzymes and also, importantly, eukaryotic DSYB enzymes from e.g., algae that are the major DMSP producers in Earth's surface oceans.
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Affiliation(s)
- Chun‐Yang Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life SciencesOcean University of ChinaQingdaoChina
- State Key Laboratory of Microbial TechnologyMarine Biotechnology Research Center, Shandong UniversityQingdaoChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoShandongChina
| | - Jason C. Crack
- School of Chemistry, Centre for Molecular and Structural BiochemistryUniversity of East Anglia, Norwich Research ParkNorwichUK
| | | | | | - Xiu‐Lan Chen
- State Key Laboratory of Microbial TechnologyMarine Biotechnology Research Center, Shandong UniversityQingdaoChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoShandongChina
| | | | - Shun Zhou
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life SciencesOcean University of ChinaQingdaoChina
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | | | - Ming Peng
- State Key Laboratory of Microbial TechnologyMarine Biotechnology Research Center, Shandong UniversityQingdaoChina
| | - Xiao‐Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Yin Chen
- School of Life SciencesUniversity of WarwickCoventryUK
| | - Nick E. Le Brun
- School of Chemistry, Centre for Molecular and Structural BiochemistryUniversity of East Anglia, Norwich Research ParkNorwichUK
| | - Jonathan D. Todd
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life SciencesOcean University of ChinaQingdaoChina
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Yu‐Zhong Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life SciencesOcean University of ChinaQingdaoChina
- State Key Laboratory of Microbial TechnologyMarine Biotechnology Research Center, Shandong UniversityQingdaoChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoShandongChina
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Giraud D, Lima O, Rousseau-Gueutin M, Salmon A, Aïnouche M. Gene and Transposable Element Expression Evolution Following Recent and Past Polyploidy Events in Spartina (Poaceae). Front Genet 2021; 12:589160. [PMID: 33841492 PMCID: PMC8027259 DOI: 10.3389/fgene.2021.589160] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 02/23/2021] [Indexed: 12/18/2022] Open
Abstract
Gene expression dynamics is a key component of polyploid evolution, varying in nature, intensity, and temporal scales, most particularly in allopolyploids, where two or more sub-genomes from differentiated parental species and different repeat contents are merged. Here, we investigated transcriptome evolution at different evolutionary time scales among tetraploid, hexaploid, and neododecaploid Spartina species (Poaceae, Chloridoideae) that successively diverged in the last 6-10 my, at the origin of differential phenotypic and ecological traits. Of particular interest are the recent (19th century) hybridizations between the two hexaploids Spartina alterniflora (2n = 6x = 62) and S. maritima (2n = 6x = 60) that resulted in two sterile F1 hybrids: Spartina × townsendii (2n = 6x = 62) in England and Spartina × neyrautii (2n = 6x = 62) in France. Whole genome duplication of S. × townsendii gave rise to the invasive neo-allododecaploid species Spartina anglica (2n = 12x = 124). New transcriptome assemblies and annotations for tetraploids and the enrichment of previously published reference transcriptomes for hexaploids and the allododecaploid allowed identifying 42,423 clusters of orthologs and distinguishing 21 transcribed transposable element (TE) lineages across the seven investigated Spartina species. In 4x and 6x mesopolyploids, gene and TE expression changes were consistent with phylogenetic relationships and divergence, revealing weak expression differences in the tetraploid sister species Spartina bakeri and Spartina versicolor (<2 my divergence time) compared to marked transcriptome divergence between the hexaploids S. alterniflora and S. maritima that diverged 2-4 mya. Differentially expressed genes were involved in glycolysis, post-transcriptional protein modifications, epidermis development, biosynthesis of carotenoids. Most detected TE lineages (except SINE elements) were found more expressed in hexaploids than in tetraploids, in line with their abundance in the corresponding genomes. Comparatively, an astonishing (52%) expression repatterning and deviation from parental additivity were observed following recent reticulate evolution (involving the F1 hybrids and the neo-allododecaploid S. anglica), with various patterns of biased homoeologous gene expression, including genes involved in epigenetic regulation. Downregulation of TEs was observed in both hybrids and accentuated in the neo-allopolyploid. Our results reinforce the view that allopolyploidy represents springboards to new regulatory patterns, offering to worldwide invasive species, such as S. anglica, the opportunity to colonize stressful and fluctuating environments on saltmarshes.
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Affiliation(s)
- Delphine Giraud
- UMR CNRS 6553 Ecosystèmes, Biodiversité, Evolution (ECOBIO), Université de Rennes 1, Rennes, France
| | - Oscar Lima
- UMR CNRS 6553 Ecosystèmes, Biodiversité, Evolution (ECOBIO), Université de Rennes 1, Rennes, France
| | | | - Armel Salmon
- UMR CNRS 6553 Ecosystèmes, Biodiversité, Evolution (ECOBIO), Université de Rennes 1, Rennes, France
| | - Malika Aïnouche
- UMR CNRS 6553 Ecosystèmes, Biodiversité, Evolution (ECOBIO), Université de Rennes 1, Rennes, France
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Liao C, Seebeck FP. In Vitro Reconstitution of Bacterial DMSP Biosynthesis. Angew Chem Int Ed Engl 2019; 58:3553-3556. [DOI: 10.1002/anie.201814662] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Cangsong Liao
- Department for Chemistry; University of Basel; Mattenstrasse 24a 4002 Basel Switzerland
| | - Florian P. Seebeck
- Department for Chemistry; University of Basel; Mattenstrasse 24a 4002 Basel Switzerland
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Affiliation(s)
- Cangsong Liao
- Department for Chemistry; University of Basel; Mattenstrasse 24a 4002 Basel Switzerland
| | - Florian P. Seebeck
- Department for Chemistry; University of Basel; Mattenstrasse 24a 4002 Basel Switzerland
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