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Kamakura S, Bilcke G, Sato S. Transcriptional responses to salinity-induced changes in cell wall morphology of the euryhaline diatom Pleurosira laevis. JOURNAL OF PHYCOLOGY 2024; 60:308-326. [PMID: 38446079 DOI: 10.1111/jpy.13437] [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: 09/29/2023] [Revised: 01/23/2024] [Accepted: 02/05/2024] [Indexed: 03/07/2024]
Abstract
Diatoms are unicellular algae with morphologically diverse silica cell walls, which are called frustules. The mechanism of frustule morphogenesis has attracted attention in biology and nanomaterials engineering. However, the genetic regulation of the morphology remains unclear. We therefore used transcriptome sequencing to search for genes involved in frustule morphology in the centric diatom Pleurosira laevis, which exhibits morphological plasticity between flat and domed valve faces in salinity 2 and 7, respectively. We observed differential expression of transposable elements (TEs) and transporters, likely due to osmotic response. Up-regulation of mechanosensitive ion channels and down-regulation of Ca2+-ATPases in cells with flat valves suggested that cytosolic Ca2+ levels were changed between the morphologies. Calcium signaling could be a mechanism for detecting osmotic pressure changes and triggering morphological shifts. We also observed an up-regulation of ARPC1 and annexin, involved in the regulation of actin filament dynamics known to affect frustule morphology, as well as the up-regulation of genes encoding frustule-related proteins such as BacSETs and frustulin. Taken together, we propose a model in which salinity-induced morphogenetic changes are driven by upstream responses, such as the regulation of cytosolic Ca2+ levels, and downstream responses, such as Ca2+-dependent regulation of actin dynamics and frustule-related proteins. This study highlights the sensitivity of euryhaline diatoms to environmental salinity and the role of active cellular processes in controlling gross valve morphology under different osmotic pressures.
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Affiliation(s)
- Shiho Kamakura
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, Obama, Fukui, Japan
| | - Gust Bilcke
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Shinya Sato
- Faculty of Marine Science and Technology, Fukui Prefectural University, Obama, Fukui, Japan
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Liu Q, Xing Y, Li Y, Wang H, Mi T, Zhen Y, Yu Z. Carbon fixation gene expression in Skeletonema marinoi in nitrogen-, phosphate-, silicate-starvation, and low-temperature stress exposure. JOURNAL OF PHYCOLOGY 2020; 56:310-323. [PMID: 31628865 DOI: 10.1111/jpy.12936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Diatoms are unicellular algae with a set of extraordinary genes, metabolic pathways, and physiological functions acquired by secondary endosymbiosis, especially for their efficient photosynthetic carbon fixation mechanisms, which can be a reason for their successful environmental adaptation and great contribution to primary production. Based on the available genomic information, the expression patterns of carbon fixation genes were analyzed using transcriptomic sequencing and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in Skeletonema marinoi. Meanwhile, suitable reference genes applying to specific experimental treatments were selected. In our results, carbon fixation genes were standardized by actin and TATA box-binding protein-coding genes in growth phase samples and stress conditions, respectively. It was found that a series of carbon fixation genes, such as the pyruvate orthophosphate dikinase (PPDK)-coding gene, had significantly up-regulated expression in nitrogen-starvation, phosphate-starvation, and low-temperature conditions, but consistently down-regulated in silicate-starvation treatment. These carbon fixation genes exhibited variable expression levels in different conditions and will be useful for investigating gene expression mechanisms in S. marinoi and improve our understanding of diatom carbon fixation pathways.
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Affiliation(s)
- Qian Liu
- Key laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Yongze Xing
- Key laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Sciences Academy, Beihai, 536000, China
| | - Ying Li
- Key laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Hualong Wang
- Key laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Tiezhu Mi
- Key laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Yu Zhen
- Key laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Zhigang Yu
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- Key Laboratory of Marine Chemical Theory and Technology, Ministry of Education, Qingdao, 266100, China
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Bates SS, Hubbard KA, Lundholm N, Montresor M, Leaw CP. Pseudo-nitzschia, Nitzschia, and domoic acid: New research since 2011. HARMFUL ALGAE 2018; 79:3-43. [PMID: 30420013 DOI: 10.1016/j.hal.2018.06.001] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 05/11/2023]
Abstract
Some diatoms of the genera Pseudo-nitzschia and Nitzschia produce the neurotoxin domoic acid (DA), a compound that caused amnesic shellfish poisoning (ASP) in humans just over 30 years ago (December 1987) in eastern Canada. This review covers new information since two previous reviews in 2012. Nitzschia bizertensis was subsequently discovered to be toxigenic in Tunisian waters. The known distribution of N. navis-varingica has expanded from Vietnam to Malaysia, Indonesia, the Philippines and Australia. Furthermore, 15 new species (and one new variety) of Pseudo-nitzschia have been discovered, bringing the total to 52. Seven new species were found to produce DA, bringing the total of toxigenic species to 26. We list all Pseudo-nitzschia species, their ability to produce DA, and show their global distribution. A consequence of the extended distribution and increased number of toxigenic species worldwide is that DA is now found more pervasively in the food web, contaminating new marine organisms (especially marine mammals), affecting their physiology and disrupting ecosystems. Recent findings highlight how zooplankton grazers can induce DA production in Pseudo-nitzschia and how bacteria interact with Pseudo-nitzschia. Since 2012, new discoveries have been reported on physiological controls of Pseudo-nitzschia growth and DA production, its sexual reproduction, and infection by an oomycete parasitoid. Many advances are the result of applying molecular approaches to discovering new species, and to understanding the population genetic structure of Pseudo-nitzschia and mechanisms used to cope with iron limitation. The availability of genomes from three Pseudo-nitzschia species, coupled with a comparative transcriptomic approach, has allowed advances in our understanding of the sexual reproduction of Pseudo-nitzschia, its signaling pathways, its interactions with bacteria, and genes involved in iron and vitamin B12 and B7 metabolism. Although there have been no new confirmed cases of ASP since 1987 because of monitoring efforts, new blooms have occurred. A massive toxic Pseudo-nitzschia bloom affected the entire west coast of North America during 2015-2016, and was linked to a 'warm blob' of ocean water. Other smaller toxic blooms occurred in the Gulf of Mexico and east coast of North America. Knowledge gaps remain, including how and why DA and its isomers are produced, the world distribution of potentially toxigenic Nitzschia species, the prevalence of DA isomers, and molecular markers to discriminate between toxigenic and non-toxigenic species and to discover sexually reproducing populations in the field.
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Affiliation(s)
- Stephen S Bates
- Fisheries and Oceans Canada, Gulf Fisheries Centre, P.O. Box 5030, Moncton, New Brunswick, E1C 9B6, Canada.
| | - Katherine A Hubbard
- Fish and Wildlife Research Institute (FWRI), Florida Fish and Wildlife Conservation Commission (FWC), 100 Eighth Avenue SE, St. Petersburg, FL 33701 USA; Woods Hole Center for Oceans and Human Health, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA, 02543 USA
| | - Nina Lundholm
- Natural History Museum of Denmark, University of Copenhagen, Sølvgade 83S, DK-1307 Copenhagen K, Denmark
| | - Marina Montresor
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Chui Pin Leaw
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
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Morozov AA, Bedoshvili YD, Popova MS, Likhoshway YV. Novel subfamilies of actin-regulating proteins. Mar Genomics 2017; 37:128-134. [PMID: 29074263 DOI: 10.1016/j.margen.2017.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 07/28/2017] [Accepted: 10/11/2017] [Indexed: 02/07/2023]
Abstract
Ability of actin to polymerise and depolymerise makes it essential to key functions of eukaryotic cell. The functioning of actin is controlled by a host of regulatory proteins, the repertoire of which in diatoms is known to remarkably differ from other organisms. We have performed a phylogenetic analysis of 521 actin and actin-related proteins' aminoacid sequences, as well as 190 sequences of gelsolin family proteins from various genomic and transcriptomic datasets. Based on the results of this analysis, as well as on the presence of clade-specific indels in some of the actin-related proteins, we describe a novel ARP subfamily, dubbed ARP12, which is specific to heterokonts and related organisms. We also describe two novel diatom-specific subfamilies, dGRC1 and dGRC2, among short gelsolin repeat-containing proteins.
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Affiliation(s)
- A A Morozov
- Cell Ultrastructure Dept., Limnological Institute SB RAS, Irkutsk, Russia.
| | - Ye D Bedoshvili
- Cell Ultrastructure Dept., Limnological Institute SB RAS, Irkutsk, Russia
| | - M S Popova
- Cell Ultrastructure Dept., Limnological Institute SB RAS, Irkutsk, Russia
| | - Ye V Likhoshway
- Cell Ultrastructure Dept., Limnological Institute SB RAS, Irkutsk, Russia
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Tesson B, Lerch SJL, Hildebrand M. Characterization of a New Protein Family Associated With the Silica Deposition Vesicle Membrane Enables Genetic Manipulation of Diatom Silica. Sci Rep 2017; 7:13457. [PMID: 29044150 PMCID: PMC5647440 DOI: 10.1038/s41598-017-13613-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/25/2017] [Indexed: 01/27/2023] Open
Abstract
Diatoms are known for their intricate, silicified cell walls (frustules). Silica polymerization occurs in a compartment called the silica deposition vesicle (SDV) and it was proposed that the cytoskeleton influences silica patterning through the SDV membrane (silicalemma) via interactions with transmembrane proteins. In this work we identify a family of proteins associated with the silicalemma, named SAPs for Silicalemma Associated Proteins. The T. pseudonana SAPs (TpSAPs) are characterized by their motif organization; each contains a transmembrane domain, serine rich region and a conserved cytoplasmic domain. Fluorescent tagging demonstrated that two of the TpSAPs were localized to the silicalemma and that the intralumenal region of TpSAP3 remained embedded in the silica while the cytoplasmic region was cleaved. Knockdown lines of TpSAP1 and 3 displayed malformed valves; which confirmed their roles in frustule morphogenesis. This study provides the first demonstration of altering silica structure through manipulation of a single gene.
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Affiliation(s)
- Benoit Tesson
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America.
| | - Sarah J L Lerch
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Mark Hildebrand
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America.
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