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Shimada M, Hayakawa MM, Suzaki T, Ishida H. Morphological reconstruction during cell regeneration in the ciliate Spirostomum ambiguum. Eur J Protistol 2024; 94:126079. [PMID: 38593565 DOI: 10.1016/j.ejop.2024.126079] [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: 11/17/2023] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/11/2024]
Abstract
When the ciliate Spirostomum ambiguum is transected into two pieces, both fragments regenerate and proliferate. In the anterior fragments, which have lost their contractile vacuoles due to transection, new contractile vacuoles were formed at their posterior ends in a few minutes. When the cells were cut into three pieces, new contractile vacuoles were formed in the anterior and middle fragments, both at their posterior ends. Thus, the anterior-posterior axis of S. ambiguum was maintained after transection. Morphological repair, including the formation of the contractile vacuole, was also observed when only the anteriormost portion was transected to cut out a small fragment that did not contain part of the macronucleus. Scanning electron microscopy was performed to observe changes in the shape of the cleavage surface of S. ambiguum during the wound healing process. Within minutes after cutting, the cut surface was covered with a cilia-free membrane, preventing leakage of cytoplasmic contents. The surface of the cut area then rounded with time and was covered with cilia, completing the repair of the cut area in about one day.
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Affiliation(s)
- Maho Shimada
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu-cho, Matsue 690-8504, Japan
| | - Masashi M Hayakawa
- Graduate School of Human Sciences, Osaka University, 1-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshinobu Suzaki
- Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Hideki Ishida
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu-cho, Matsue 690-8504, Japan.
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Šafranek M, Shumbusho A, Johansen W, Šarkanová J, Voško S, Bokor B, Jásik J, Demko V. Membrane-anchored calpains - hidden regulators of growth and development beyond plants? FRONTIERS IN PLANT SCIENCE 2023; 14:1289785. [PMID: 38173928 PMCID: PMC10762896 DOI: 10.3389/fpls.2023.1289785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
Calpains are modulatory proteases that modify diverse cellular substrates and play essential roles in eukaryots. The best studied are animal cytosolic calpains. Here, we focus on enigmatic membrane-anchored calpains, their structural and functional features as well as phylogenetic distribution. Based on domain composition, we identified four types of membrane-anchored calpains. Type 1 and 2 show broad phylogenetic distribution among unicellular protists and streptophytes suggesting their ancient evolutionary origin. Type 3 and 4 diversified early and are present in brown algae and oomycetes. The plant DEK1 protein is the only representative of membrane-anchored calpains that has been functionally studied. Here, we present up to date knowledge about its structural features, putative regulation, posttranslational modifications, and biological role. Finally, we discuss potential model organisms and available tools for functional studies of membrane-anchored calpains with yet unknown biological role. Mechanistic understanding of membrane-anchored calpains may provide important insights into fundamental principles of cell polarization, cell fate control, and morphogenesis beyond plants.
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Affiliation(s)
- Martin Šafranek
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Alain Shumbusho
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Wenche Johansen
- Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Júlia Šarkanová
- Comenius University Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - Stanislav Voško
- Comenius University Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - Boris Bokor
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
- Comenius University Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - Ján Jásik
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Viktor Demko
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
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Albright AR, Angeles-Albores D, Marshall W. Genome-wide analysis of anterior-posterior mRNA localization in Stentor coeruleus reveals a role for the microtubule cytoskeleton. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523364. [PMID: 36711710 PMCID: PMC9882060 DOI: 10.1101/2023.01.09.523364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Cells have complex and beautiful structures that are important for their function, but understanding the molecular mechanisms that produce these structures is a challenging problem due to the gap in size scales between molecular interactions and cellular structures. The giant ciliate Stentor coeruleus is a unicellular model organism whose large size, reproducible structure, and ability to heal wounds and regenerate has historically allowed the formation of structure in a single cell to be addressed using methods of experimental embryology. Such studies have shown that specific cellular structures, such as the oral apparatus, always form in specific regions of the cell, which raises the question: what is the source of positional information within this organism? By analogy with embryonic development, in which localized mRNA is often used to mark position, we asked whether position along the anterior-posterior axis of Stentor might be marked by specific regionalized mRNAs. By physically bisecting cells and conducting half-cell RNA sequencing, we were able to identify sets of messages enriched in either the anterior or posterior half. We repeated this analysis in cells in which a set of longitudinal microtubule bundles running down the whole length of the cell, known as KM-fibers, were disrupted by RNAi of b-tubulin. We found that many messages either lost their regionalized distribution or switched to an opposite distribution, such that anterior-enriched messages in control became posterior-enriched in the RNAi cells, or vice versa. This study indicates that mRNA can be regionalized within a single giant cell and that microtubules may play a role, possibly by serving as tracks for the movement of the messages.
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Affiliation(s)
- Ashley R. Albright
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Center for Cellular Construction, University of California, San Francisco, San Francisco, CA, USA
| | | | - Wallace Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Center for Cellular Construction, University of California, San Francisco, San Francisco, CA, USA
- Twitter: @WallaceUCSF
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Sood P, Lin A, Yan C, McGillivary R, Diaz U, Makushok T, Nadkarni A, Tang SKY, Marshall WF. Modular, cascade-like transcriptional program of regeneration in Stentor. eLife 2022; 11:80778. [PMID: 35924891 PMCID: PMC9371601 DOI: 10.7554/elife.80778] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/04/2022] [Indexed: 11/15/2022] Open
Abstract
The giant ciliate Stentor coeruleus is a classical model system for studying regeneration and morphogenesis in a single cell. The anterior of the cell is marked by an array of cilia, known as the oral apparatus, which can be induced to shed and regenerate in a series of reproducible morphological steps, previously shown to require transcription. If a cell is cut in half, each half regenerates an intact cell. We used RNA sequencing (RNAseq) to assay the dynamic changes in Stentor’s transcriptome during regeneration, after both oral apparatus shedding and bisection, allowing us to identify distinct temporal waves of gene expression including kinases, RNA -binding proteins, centriole biogenesis factors, and orthologs of human ciliopathy genes. By comparing transcriptional profiles of different regeneration events, we identified distinct modules of gene expression corresponding to oral apparatus regeneration, posterior holdfast regeneration, and recovery after wounding. By measuring gene expression after blocking translation, we show that the sequential waves of gene expression involve a cascade mechanism in which later waves of expression are triggered by translation products of early-expressed genes. Among the early-expressed genes, we identified an E2F transcription factor and the RNA-binding protein Pumilio as potential regulators of regeneration based on the expression pattern of their predicted target genes. RNAi-mediated knockdown experiments indicate that Pumilio is required for regenerating oral structures of the correct size. E2F is involved in the completion of regeneration but is dispensable for earlier steps. This work allows us to classify regeneration genes into groups based on their potential role for regeneration in distinct cell regeneration paradigms, and provides insight into how a single cell can coordinate complex morphogenetic pathways to regenerate missing structures.
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Affiliation(s)
- Pranidhi Sood
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Athena Lin
- Department of Biochemistry and BioPhysics, University of California, San Francisco, San Francisco, United States
| | - Connie Yan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Rebecca McGillivary
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Ulises Diaz
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Tatyana Makushok
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Ambika Nadkarni
- Department of Mechanical Engineering, Stanford University, palo alto, United States
| | - Sindy K Y Tang
- Department of Mechanical Engineering, Stanford University, Palo Alto, United States
| | - Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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