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Zhou Z, Li C, Yuan Q, Chi Y, Li Y, Yan Y, Al-Farraj SA, Stover NA, Chen Z, Chen X. Single-cell transcriptomic analysis reveals genome evolution in predatory litostomatean ciliates. Eur J Protistol 2024; 93:126062. [PMID: 38368736 DOI: 10.1016/j.ejop.2024.126062] [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] [Received: 11/23/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
Many ciliated protists prey on other large microbial organisms, including other protists and microscopic metazoans. The ciliate class Litostomatea unites both predatory and endosymbiotic species. The evolution of predation ability in ciliates remains poorly understood, in part, due to a lack of genomic data. To fill this gap, we acquired the transcriptome profiles of six predatory litostomateans using single-cell sequencing technology and investigated their transcriptomic features. Our results show that: (1) in contrast to non-predatory ciliates, the predatory litostomateans have expanded gene families associated with transmembrane activity and reactive oxidative stress response pathways, potentially as a result of cellular behaviors such as fast contraction and extension; (2) the expansion of the calcium-activated BK potassium channel gene family, which hypothetically regulates cell contractility, is an ancient evolutionary event for the class Litostomatea, suggesting a rewired metabolism associated with the hunting behavior of predatory ciliates; and (3) three whole genome duplication (WGD) events have been detected in litostomateans, with genes associated with biosynthetic processes, transmembrane activity, and calcium-activated potassium channel activity being retained during the WGD events. In addition, we explored the evolutionary relationships among 17 ciliate species, including eight litostomateans, and provided a rich foundational dataset for future in-depth phylogenomic studies of Litostomatea. Our comprehensive analyses suggest that the rewired cellular metabolism via expanded gene families and WGD events might be the potential genetic basis for the predation ability of raptorial ciliates.
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Affiliation(s)
- Zhaorui Zhou
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Chao Li
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Qingxiang Yuan
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yong Chi
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yuqing Li
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Ying Yan
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Naomi A Stover
- Department of Biology, Bradley University, Peoria 61625, USA.
| | - Zigui Chen
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, 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.
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Osipov AV, Cheremnykh EG, Ziganshin RH, Starkov VG, Nguyen TTT, Nguyen KC, Le DT, Hoang AN, Tsetlin VI, Utkin YN. The Potassium Channel Blocker β-Bungarotoxin from the Krait Bungarus multicinctus Venom Manifests Antiprotozoal Activity. Biomedicines 2023; 11:biomedicines11041115. [PMID: 37189733 DOI: 10.3390/biomedicines11041115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/17/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023] Open
Abstract
Protozoal infections are a world-wide problem. The toxicity and somewhat low effectiveness of the existing drugs require the search for new ways of protozoa suppression. Snake venom contains structurally diverse components manifesting antiprotozoal activity; for example, those in cobra venom are cytotoxins. In this work, we aimed to characterize a novel antiprotozoal component(s) in the Bungarus multicinctus krait venom using the ciliate Tetrahymena pyriformis as a model organism. To determine the toxicity of the substances under study, surviving ciliates were registered automatically by an original BioLaT-3.2 instrument. The krait venom was separated by three-step liquid chromatography and the toxicity of the obtained fractions against T. pyriformis was analyzed. As a result, 21 kDa protein toxic to Tetrahymena was isolated and its amino acid sequence was determined by MALDI TOF MS and high-resolution mass spectrometry. It was found that antiprotozoal activity was manifested by β-bungarotoxin (β-Bgt) differing from the known toxins by two amino acid residues. Inactivation of β-Bgt phospholipolytic activity with p-bromophenacyl bromide did not change its antiprotozoal activity. Thus, this is the first demonstration of the antiprotozoal activity of β-Bgt, which is shown to be independent of its phospholipolytic activity.
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Affiliation(s)
- Alexey V Osipov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | | | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Vladislav G Starkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | | | - Khoa Cuu Nguyen
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, Ho Chi Minh City 700000, Vietnam
| | - Dung Tien Le
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, Ho Chi Minh City 700000, Vietnam
| | - Anh Ngoc Hoang
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, Ho Chi Minh City 700000, Vietnam
| | - Victor I Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Yuri N Utkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
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Van Houten J. A Review for the Special Issue on Paramecium as a Modern Model Organism. Microorganisms 2023; 11:microorganisms11040937. [PMID: 37110360 PMCID: PMC10143506 DOI: 10.3390/microorganisms11040937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023] Open
Abstract
This review provides background and perspective for the articles contributing to the Special Issue of MDPI Micro-organisms on Paramecium as a Modern Model Organism. The six articles cover a variety of topics, each taking advantage of an important aspect of Paramecium biology: peripheral surface proteins that are developmentally regulated, endosymbiont algae and bacteria, ion channel regulation by calmodulin, regulation of cell mating reactivity and senescence, and the introns that dwell in the large genome. Each article highlights a significant aspect of Paramecium and its versatility.
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Affiliation(s)
- Judith Van Houten
- Department of Biology, University of Vermont, Burlington, VT 05405, USA
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Valentine M, Yano J, Lodh S, Nabi A, Deng B, Van Houten J. Methods for Paramecium tetraurelia ciliary membrane protein identification and function. Methods Cell Biol 2023; 175:177-219. [PMID: 36967141 DOI: 10.1016/bs.mcb.2022.12.003] [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] [Indexed: 01/25/2023]
Abstract
In this chapter we provide some tools to study the ciliary proteins that make it possible for Paramecium cells to swim by beating their cilia. These proteins include many ion channels, accessory proteins, peripheral proteins, structural proteins, rootlets of cilia, and enzymes. Some of these proteins are also found in the soma membrane, but their distinct and critical functions are in the cilia. Paramecium has 4000 or more cilia per cell, giving it an advantage for biochemical studies over cells that have one primarily cilium per cell. Nonetheless, a challenge for studies of many ciliary proteins in Paramecium is their low abundance. We discuss here several strategies to overcome this challenge and other challenges such as working with very large channel proteins. We also include for completeness other techniques that are critical to the study of swimming behavior, such as genetic crosses, recording of swimming patterns, electrical recordings, expression of very large channel proteins, RNA Interference, among others.
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Affiliation(s)
- Megan Valentine
- State University of New York, Plattsburgh, NY, United States
| | - Junji Yano
- University of Vermont, Burlington, VT, United States
| | - Sukanya Lodh
- Marquette University, Milwaukee, WI, United States
| | | | - Bin Deng
- Vermont Biomedical Research Network, University of Vermont, Burlington, VT, United States
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Paramecium bursaria as a Potential Tool for Evaluation of Microplastics Toxicity. BIOLOGY 2022; 11:biology11121852. [PMID: 36552361 PMCID: PMC9775370 DOI: 10.3390/biology11121852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/08/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022]
Abstract
Microplastics (MPs) are normally defined as small plastic wastes with a size of 1 μm to 5 mm in diameter. This tiny plastic debris is abundant in aquatic systems and poses a great threat to aquatic biota. To date, toxicological assessment of MPs is predominantly dependent on metazoan animals, although their applications are sometimes limited due to the high cost, narrow ecological niche, or ethical considerations. In this regard, unicellular eukaryotes (i.e., protozoa) that are ubiquitously present in nature represent a promising alternative for evaluating the toxicity of MPs. In this study, we selected Paramecium bursaria (P. bursaria) as a representative of protozoa and further investigated behavioral and molecular changes in MPs-exposed P. bursaria. Our results showed that following MPs uptake, P. bursaria exhibited various changes, including anomalies in swimming patterns, reduction in moving speed, impairment of avoidance behavior, elevation of oxidative stress, and potential disturbance of endosymbiosis. These elicited changes in P. bursaria in response to MPs exposure were pronounced and measurable. Overall, this study demonstrated that P. bursaria could serve as a promising alternative for the toxicological assessment of MPs and may be further applied to evaluate the toxicity of other environmental contaminants.
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Calmodulin in Paramecium: Focus on Genomic Data. Microorganisms 2022; 10:microorganisms10101915. [PMID: 36296191 PMCID: PMC9608856 DOI: 10.3390/microorganisms10101915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/14/2022] [Accepted: 09/22/2022] [Indexed: 11/26/2022] Open
Abstract
Calcium (Ca2+) is a universal second messenger that plays a key role in cellular signaling. However, Ca2+ signals are transduced with the help of Ca2+-binding proteins, which serve as sensors, transducers, and elicitors. Among the collection of these Ca2+-binding proteins, calmodulin (CaM) emerged as the prototypical model in eukaryotic cells. This is a small protein that binds four Ca2+ ions and whose functions are multiple, controlling many essential aspects of cell physiology. CaM is universally distributed in eukaryotes, from multicellular organisms, such as human and land plants, to unicellular microorganisms, such as yeasts and ciliates. Here, we review most of the information gathered on CaM in Paramecium, a group of ciliates. We condense the information here by mentioning that mature Paramecium CaM is a 148 amino acid-long protein codified by a single gene, as in other eukaryotic microorganisms. In these ciliates, the protein is notoriously localized and regulates cilia function and can stimulate the activity of some enzymes. When Paramecium CaM is mutated, cells show flawed locomotion and/or exocytosis. We further widen this and additional information in the text, focusing on genomic data.
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