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Vilarrasa-Blasi J, Vellosillo T, Jinkerson RE, Fauser F, Xiang T, Minkoff BB, Wang L, Kniazev K, Guzman M, Osaki J, Barrett-Wilt GA, Sussman MR, Jonikas MC, Dinneny JR. Multi-omics analysis of green lineage osmotic stress pathways unveils crucial roles of different cellular compartments. Nat Commun 2024; 15:5988. [PMID: 39013881 PMCID: PMC11252407 DOI: 10.1038/s41467-024-49844-3] [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: 10/19/2022] [Accepted: 06/21/2024] [Indexed: 07/18/2024] Open
Abstract
Maintenance of water homeostasis is a fundamental cellular process required by all living organisms. Here, we use the single-celled green alga Chlamydomonas reinhardtii to establish a foundational understanding of osmotic-stress signaling pathways through transcriptomics, phosphoproteomics, and functional genomics approaches. Comparison of pathways identified through these analyses with yeast and Arabidopsis allows us to infer their evolutionary conservation and divergence across these lineages. 76 genes, acting across diverse cellular compartments, were found to be important for osmotic-stress tolerance in Chlamydomonas through their functions in cytoskeletal organization, potassium transport, vesicle trafficking, mitogen-activated protein kinase and chloroplast signaling. We show that homologs for five of these genes have conserved functions in stress tolerance in Arabidopsis and reveal a novel PROFILIN-dependent stage of acclimation affecting the actin cytoskeleton that ensures tissue integrity upon osmotic stress. This study highlights the conservation of the stress response in algae and land plants, and establishes Chlamydomonas as a unicellular plant model system to dissect the osmotic stress signaling pathway.
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Affiliation(s)
- Josep Vilarrasa-Blasi
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA.
| | - Tamara Vellosillo
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
| | - Robert E Jinkerson
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Friedrich Fauser
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Tingting Xiang
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Benjamin B Minkoff
- Department of Biochemistry and Center for Genomics Science Innovation, University of Wisconsin, Madison, WI, 53706, USA
| | - Lianyong Wang
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Kiril Kniazev
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Michael Guzman
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
| | - Jacqueline Osaki
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
| | | | - Michael R Sussman
- Department of Biochemistry and Center for Genomics Science Innovation, University of Wisconsin, Madison, WI, 53706, USA
| | - Martin C Jonikas
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA.
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Su M, Liu N, Zhang Z, Zhang J. Osmoregulatory strategies of estuarine fish Scatophagus argus in response to environmental salinity changes. BMC Genomics 2022; 23:545. [PMID: 35907798 PMCID: PMC9339187 DOI: 10.1186/s12864-022-08784-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 07/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Scatophagus argus, an estuarine inhabitant, can rapidly adapt to different salinity environments. However, the knowledge of the molecular mechanisms underlying its strong salinity tolerance remains unclear. The gill, as the main osmoregulatory organ, plays a vital role in the salinity adaptation of the fish, and thus relative studies are constructive to reveal unique osmoregulatory mechanisms in S. argus. RESULTS In the present study, iTRAQ coupled with nanoLC-MS/MS techniques were employed to explore branchial osmoregulatory mechanisms in S. argus acclimated to different salinities. Among 1,604 identified proteins, 796 differentially expressed proteins (DEPs) were detected. To further assess osmoregulatory strategies in the gills under different salinities, DEPs related to osmoregulatory (22), non-directional (18), hypo- (52), and hypersaline (40) stress responses were selected. Functional annotation analysis of these selected DEPs indicated that the cellular ion regulation (e.g. Na+-K+-ATPase [NKA] and Na+-K+-2Cl- cotransporter 1 [NKCC1]) and ATP synthesis were deeply involved in the osmoregulatory process. As an osmoregulatory protein, NKCC1 expression was inhibited under hyposaline stress but showed the opposite trend in hypersaline conditions. The expression levels of NKA α1 and β1 were only increased under hypersaline challenge. However, hyposaline treatments could enhance branchial NKA activity, which was inhibited under hypersaline environments, and correspondingly, reduced ATP content was observed in gill tissues exposed to hyposaline conditions, while its contents were increased in hypersaline groups. In vitro experiments indicated that Na+, K+, and Cl- ions were pumped out of branchial cells under hypoosmotic stress, whereas they were absorbed into cells under hyperosmotic conditions. Based on our results, we speculated that NKCC1-mediated Na+ influx was inhibited, and proper Na+ efflux was maintained by improving NKA activity under hyposaline stress, promoting the rapid adaptation of branchial cells to the hyposaline condition. Meanwhile, branchial cells prevented excessive loss of ions by increasing NKA internalization and reducing ATP synthesis. In contrast, excess ions in cells exposed to the hyperosmotic medium were excreted with sufficient energy supply, and reduced NKA activity and enhanced NKCC1-mediated Na+ influx were considered a compensatory regulation. CONCLUSIONS S. argus exhibited divergent osmoregulatory strategies in the gills when encountering hypoosmotic and hyperosmotic stresses, facilitating effective adaptabilities to a wide range of environmental salinity fluctuation.
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Affiliation(s)
- Maoliang Su
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Nanxi Liu
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Zhengqi Zhang
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Junbin Zhang
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
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Single-cell visualization and quantification of trace metals in Chlamydomonas lysosome-related organelles. Proc Natl Acad Sci U S A 2021; 118:2026811118. [PMID: 33879572 DOI: 10.1073/pnas.2026811118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The acidocalcisome is an acidic organelle in the cytosol of eukaryotes, defined by its low pH and high calcium and polyphosphate content. It is visualized as an electron-dense object by transmission electron microscopy (TEM) or described with mass spectrometry (MS)-based imaging techniques or multimodal X-ray fluorescence microscopy (XFM) based on its unique elemental composition. Compared with MS-based imaging techniques, XFM offers the additional advantage of absolute quantification of trace metal content, since sectioning of the cell is not required and metabolic states can be preserved rapidly by either vitrification or chemical fixation. We employed XFM in Chlamydomonas reinhardtii to determine single-cell and organelle trace metal quotas within algal cells in situations of trace metal overaccumulation (Fe and Cu). We found up to 70% of the cellular Cu and 80% of Fe sequestered in acidocalcisomes in these conditions and identified two distinct populations of acidocalcisomes, defined by their unique trace elemental makeup. We utilized the vtc1 mutant, defective in polyphosphate synthesis and failing to accumulate Ca, to show that Fe sequestration is not dependent on either. Finally, quantitation of the Fe and Cu contents of individual cells and compartments via XFM, over a range of cellular metal quotas created by nutritional and genetic perturbations, indicated excellent correlation with bulk data from corresponding cell cultures, establishing a framework to distinguish the nutritional status of single cells.
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Horn KM, Anderson FE. Spiralian Genomes Reveal Gene Family Expansions Associated with Adaptation to Freshwater. J Mol Evol 2020; 88:463-472. [PMID: 32388714 DOI: 10.1007/s00239-020-09949-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 05/02/2020] [Indexed: 10/24/2022]
Abstract
The colonization of freshwater habitats by marine-adapted organisms represents a major transition that has only occurred a few times in the evolution of animals. Only around half of the extant animal phyla have representatives in both marine and freshwater environments and even within those phyla some major clades are restricted to marine environments. Moving from marine to freshwater environments can create severe osmotic and ionic stresses and the mechanisms that animals have used to adapt to those stresses are still not well understood. In this study, we downloaded amino acid sequence data from 11 spiralian animal genomes (four freshwater taxa representing four different phyla as well as 7 marine taxa) and identified a number of gene family expansions that have occurred exclusively in the freshwater lineages. Further investigation of these gene families and the timing and nature of their expansions will illuminate one of the major evolutionary transitions in the history of life on Earth.
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Affiliation(s)
- Kevin M Horn
- Division of Natural Sciences and Mathematics, Kentucky Wesleyan College, Owensboro, KY, 42301, USA. .,School of Biological Sciences, Southern Illinois University, Carbondale, IL, 62901, USA.
| | - Frank E Anderson
- School of Biological Sciences, Southern Illinois University, Carbondale, IL, 62901, USA
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