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Liu Y, Niu J, Ye F, Solberg T, Lu B, Wang C, Nowacki M, Gao S. Dynamic DNA N 6-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus. Genome Res 2024; 34:256-271. [PMID: 38471739 PMCID: PMC10984389 DOI: 10.1101/gr.278796.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
The formation of resting cysts commonly found in unicellular eukaryotes is a complex and highly regulated survival strategy against environmental stress that involves drastic physiological and biochemical changes. Although most studies have focused on the morphology and structure of cysts, little is known about the molecular mechanisms that control this process. Recent studies indicate that DNA N 6-adenine methylation (6mA) could be dynamically changing in response to external stimuli; however, its potential role in the regulation of cyst formation remains unknown. We used the ciliate Pseudocohnilembus persalinus, which can be easily induced to form cysts to investigate the dynamic pattern of 6mA in trophonts and cysts. Single-molecule real-time (SMRT) sequencing reveals high levels of 6mA in trophonts that decrease in cysts, along with a conversion of symmetric 6mA to asymmetric 6mA. Further analysis shows that 6mA, a mark of active transcription, is involved in altering the expression of encystment-related genes through changes in 6mA levels and 6mA symmetric-to-asymmetric conversion. Most importantly, we show that reducing 6mA levels by knocking down the DNA 6mA methyltransferase PpAMT1 accelerates cyst formation. Taken together, we characterize the genome-wide 6mA landscape in P. persalinus and provide insights into the role of 6mA in gene regulation under environmental stress in eukaryotes. We propose that 6mA acts as a mark of active transcription to regulate the encystment process along with symmetric-to-asymmetric conversion, providing important information for understanding the molecular response to environmental cues from the perspective of 6mA modification.
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Affiliation(s)
- Yongqiang Liu
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Junhua Niu
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Fei Ye
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Therese Solberg
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
- Department of Molecular Biology, Keio University School of Medicine, 160-8582 Tokyo, Japan
- Human Biology Microbiome Quantum Research Center (WPI-Bio2Q), Keio University, 108-8345 Tokyo, Japan
| | - Borong Lu
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Chundi Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
| | - Shan Gao
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China;
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
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Jin D, Li C, Chen X, Wang Y, Al-Rasheid KAS, Stover NA, Shao C, Zhang T. Decryption of the survival "black box": gene family expansion promotes the encystment in ciliated protists. BMC Genomics 2024; 25:286. [PMID: 38500030 PMCID: PMC10946202 DOI: 10.1186/s12864-024-10207-3] [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: 12/12/2023] [Accepted: 03/11/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Encystment is an important survival strategy extensively employed by microbial organisms to survive unfavorable conditions. Single-celled ciliated protists (ciliates) are popular model eukaryotes for studying encystment, whereby these cells degenerate their ciliary structures and develop cyst walls, then reverse the process under more favorable conditions. However, to date, the evolutionary basis and mechanism for encystment in ciliates is largely unknown. With the rapid development of high-throughput sequencing technologies, genome sequencing and comparative genomics of ciliates have become effective methods to provide insights into above questions. RESULTS Here, we profiled the MAC genome of Pseudourostyla cristata, a model hypotrich ciliate for encystment studies. Like other hypotrich MAC genomes, the P. cristata MAC genome is extremely fragmented with a single gene on most chromosomes, and encodes introns that are generally small and lack a conserved branch point for pre-mRNA splicing. Gene family expansion analyses indicate that multiple gene families involved in the encystment are expanded during the evolution of P. cristata. Furthermore, genomic comparisons with other five representative hypotrichs indicate that gene families of phosphorelay sensor kinase, which play a role in the two-component signal transduction system that is related to encystment, show significant expansion among all six hypotrichs. Additionally, cyst wall-related chitin synthase genes have experienced structural changes that increase them from single-exon to multi-exon genes during evolution. These genomic features potentially promote the encystment in hypotrichs and enhance their ability to survive in adverse environments during evolution. CONCLUSIONS We systematically investigated the genomic structure of hypotrichs and key evolutionary phenomenon, gene family expansion, for encystment promotion in ciliates. In summary, our results provided insights into the evolutionary mechanism of encystment in ciliates.
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Affiliation(s)
- Didi Jin
- Laboratory of Biodiversity and Evolution of Protozoa in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Chao Li
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xiao Chen
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, 264209, China
- Suzhou Research Institute, Shandong University, Suzhou, 215123, China
| | - Yurui Wang
- Laboratory of Biodiversity and Evolution of Protozoa in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Khaled A S Al-Rasheid
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Naomi A Stover
- Department of Biology, Bradley University, Peoria, 61625, USA
| | - Chen Shao
- Laboratory of Biodiversity and Evolution of Protozoa in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
| | - Tengteng Zhang
- Laboratory of Biodiversity and Evolution of Protozoa in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
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Deng H, He C, Worden AZ, Gong J. Employing a triple metabarcoding approach to differentiate active, dormant and dead microeukaryotes in sediments. Environ Microbiol 2024; 26:e16615. [PMID: 38501240 DOI: 10.1111/1462-2920.16615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/08/2024] [Indexed: 03/20/2024]
Abstract
Microbial communities are commonly characterised through the metabarcoding of environmental DNA. This DNA originates from both viable (including dormant and active) and dead organisms, leading to recent efforts to distinguish between these states. In this study, we further these approaches by distinguishing not only between viable and dead cells but also between dormant and actively growing cells. This is achieved by sequencing both rRNA and rDNA, in conjunction with propidium monoazide cross-linked rDNA, to partition the active, dormant and relic fractions in environmental samples. We apply this method to characterise the diversity and assemblage structure of these fractions of microeukaryotes in intertidal sediments during a wet-dry-rewet incubation cycle. Our findings indicate that a significant proportion of microeukaryotic phylotypes detected in the total rDNA pools originate from dormant and relic microeukaryotes in the sediments, both in terms of richness (dormant, 13 ± 2%; relic, 47 ± 5%) and read abundance (dormant, 20 ± 7%; relic, 14 ± 5%). The richness and sequence proportion of dormant microeukaryotes notably increase during the transition from wet to dry conditions. Statistical analyses suggest that the dynamics of diversity and assemblage structure across different activity fractions are influenced by various environmental drivers. Our strategy offers a versatile approach that can be adapted to characterise other microbes in a wide range of environments.
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Affiliation(s)
- Huiwen Deng
- School of Marine Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China
| | - Cui He
- School of Marine Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Alexandra Z Worden
- Marine Biological Laboratory, Woods Hole, Massachusetts, USA
- Department of Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Jun Gong
- School of Marine Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China
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Xu J, Shen Z, Yu M, Sheng Y, Yi Z. Novel insights into molecular mechanisms of vegetative cell cycle and resting cyst formation in Apodileptus cf. visscheri (Alveolata, Ciliophora). J Eukaryot Microbiol 2023; 70:e12958. [PMID: 36458427 DOI: 10.1111/jeu.12958] [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: 07/30/2022] [Revised: 10/13/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022]
Abstract
Ciliates usually with big cell sizes, complex morphological structures, and diverse life cycles, are good model organisms for studying cell proliferation regulation of eukaryotes. Up to date, the molecular regulation mechanisms for the vegetative cell cycle and encystment of these ciliates are poorly understood. Here, transcriptomes of Apodileptus cf. visscheri, which has an asexual vegetative cell cycle and is apt to encyst when environmental conditions become unfavorable, were sequenced to enrich our related knowledge. In this study, three replicates were sequenced for each of four cell stages, including initial period of growth, morphogenesis, cell division, and resting cyst. The significant transcription differences, involving cell cycle, biosynthesis, and energy metabolism pathways, were revealed between the resting cyst and vegetative cell cycle. Further investigations showed that the cell cycle pathway was enriched during morphogenesis stage and cell division stage. Compared to the initial period of growth stage, the differentially expressed genes involved in cellular components and molecular function were significantly enriched during cell division stage, while cellular components and biological processes were significantly enriched during morphogenesis stage. These provide novel insights into a comprehensive understanding at the molecular level of the survival and adaptive mechanism of unicellular eukaryotes.
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Affiliation(s)
- Jiahui Xu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou, Guangdong, China
| | - Zhuo Shen
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, Guangdong, China.,Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai, Guangdong, China
| | - Minjie Yu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou, Guangdong, China
| | - Yalan Sheng
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou, Guangdong, China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou, Guangdong, China
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Ganser MH, Bartel H, Weißenbacher B, Andosch A, Lütz-Meindl U, Radacher P, Agatha S. A light and electron microscopical study on the resting cyst of the tintinnid Schmidingerella (Alveolata, Ciliophora) including a phylogeny-aware comparison. Eur J Protistol 2022; 86:125922. [PMID: 36155308 DOI: 10.1016/j.ejop.2022.125922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/29/2022] [Accepted: 09/01/2022] [Indexed: 01/26/2023]
Abstract
Resting cysts protect ciliates against adverse environmental conditions. The morphology and ultrastructure of resting cysts has been described in very few Oligotrichea, a group of mainly marine planktonic ciliates. The present study provides the first ultrastructural data for loricate choreotrichids, applying light and electron microscopy on the cysts of the tintinnid Schmidingerella meunieri (Kofoid and Campbell, 1929) Agatha and Strüder-Kypke, 2012. The morphology of live cysts and the wall ultrastructure of cryofixed cysts were morphometrically analysed. The resting cyst is roughly flask-shaped, broadening to a slightly concave, laterally protruding anterior plate. An emergence pore closed by a skull cap-shaped papula is directed to the bottom of the lorica on the opposite side of the cyst. The cyst wall consists of an ectocyst, mesocyst, and endocyst differing in thickness, structure, and nitrogen concentration as revealed by conventional transmission electron microscopy, electron energy loss spectroscopy, and electron spectroscopic imaging. The cysts of S. meunieri belong to the kinetosome-resorbing type, which also occurs in the majority of hypotrich ciliates. Two main features (flask-shape and presence of an emergence pore) are shared with the closely related aloricate choreotrichids and oligotrichids, distinguishing the Oligotrichea from the hypotrich and the more distantly related euplotid ciliates.
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Affiliation(s)
- Maximilian H Ganser
- Department of Environment & Biodiversity, Paris Lodron University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria.
| | - Heidi Bartel
- Department of Environment & Biodiversity, Paris Lodron University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
| | - Birgit Weißenbacher
- Department of Environment & Biodiversity, Paris Lodron University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
| | - Ancuela Andosch
- Department of Biosciences & Medical Biology, Paris Lodron University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
| | - Ursula Lütz-Meindl
- Department of Environment & Biodiversity, Paris Lodron University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria; Department of Biosciences & Medical Biology, Paris Lodron University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
| | - Peter Radacher
- Department of Environment & Biodiversity, Paris Lodron University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
| | - Sabine Agatha
- Department of Environment & Biodiversity, Paris Lodron University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria.
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