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Microorganisms
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Paramecium as Modern Model System
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Paramecium as Modern Model System

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Molecular Microbiology and Immunology".

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 20321

Special Issue Editor

Prof. Dr. Judith Van Houten

E-Mail Website
Guest Editor
Department of Biology, University of Vermont, 120 Marsh Life Science, 109 Carrigan Drive, Burlington, VT 05405, USA
Interests: signal transduction; cell biology; cells; ciliate; Paramecium; cloning; neuroscience

Special Issue Information

Dear Colleagues,

Studies that focus on Paramecium have provided important data about genetics (transmission and non-Mendelian), mating and conjugation, autogamy, genome duplication, cilia and basal bodies, ion channels, swimming behaviors, whole genome duplications, division of labor in two types of nuclei, tubulin function and modifications, RNA-mediated epigenetic controls, regulated secretion, osmoregulation, intracellular cortical networks, and much more. Usually, a model organism’s usefulness is much narrower and more specialized than this. Some of these studies can be traced back for over 100 years, and their results remain fresh and informative. Therefore, it is important that an appreciation for Paramecium as a model is refreshed and modern results from studies of this highly useful organism are brought together as in this Special Issue.

Some of its focal points (Potential Subtopics) include but are not limited to the following:

  • Cilia structure analyzed by cryotomography
  • Proteomic analysis of cilia
  • Whole genome sequencing combined with forward mutagenesis
  • Exocytosis, regulated secretion
  • Tubulin’s many tasks in the cell
  • Genome rearrangements, including duplications
  • Intracellular trafficking
  • Intracellular functions and regulation of Calcium
  • Syntaxins, locations, and functions
  • Regulation of ciliary motion

Prof. Dr. Judith Van Houten
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • cilia
  • genome evolution
  • tubulin
  • proteomics
  • trafficking
  • calcium
  • secretion

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Published Papers (7 papers)

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Research

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14 pages, 2140 KiB  
Article
A 63-kDa Periplasmic Protein of the Endonuclear Symbiotic Bacterium Holospora obtusa Secreted to the Outside of the Bacterium during the Early Infection Process Binds Weakly to the Macronuclear DNA of the Host Paramecium caudatum
by Masahiro Fujishima, Hideaki Kawano and Isamu Miyakawa
Microorganisms 2023, 11(1), 155; https://doi.org/10.3390/microorganisms11010155 - 7 Jan 2023
Cited by 3 | Viewed by 2494
Abstract
The Gram-negative bacterium Holospora obtusa is a macronucleus-specific symbiont of the ciliate Paramecium caudatum. It is known that an infection of this bacterium induces high level expressions of the host hsp60 and hsp70 genes, and the host cell acquires both heat-shock and [...] Read more.
The Gram-negative bacterium Holospora obtusa is a macronucleus-specific symbiont of the ciliate Paramecium caudatum. It is known that an infection of this bacterium induces high level expressions of the host hsp60 and hsp70 genes, and the host cell acquires both heat-shock and high salt resistances. In addition, an infectious form of H. obtusa-specific 63-kDa periplasmic protein with a DNA-binding domain in its amino acid sequence is secreted into the host macronucleus after invasion into the macronucleus and remain within the nucleus. These facts suggest that binding of the 63-kDa protein to the host macronuclear DNA causes changes in the host gene expressions and enhances an environmental adaptability of the host cells. This 63-kDa protein was renamed as periplasmic region protein 1 (PRP1) to distinguish it from other proteins with similar molecular weights. To confirm whether PRP1 indeed binds to the host DNA, SDS-DNA PAGE and DNA affinity chromatography with calf thymus DNA and P. caudatum DNA were conducted and confirmed that PRP1 binds weakly to the P. caudatum DNA with a monoclonal antibody raised for the 63-kDa protein. Full article
(This article belongs to the Special Issue Paramecium as Modern Model System)
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15 pages, 3246 KiB  
Article
Immaturin-Nuclease as a Model System for a Gene-Programmed Sexual Development and Rejuvenescence in Paramecium Life History
by Nobuyuki Haga, Toshinori Usui, Yasuhiro Takenaka, Yuta Chiba and Tomoaki Abe
Microorganisms 2023, 11(1), 82; https://doi.org/10.3390/microorganisms11010082 - 28 Dec 2022
Cited by 2 | Viewed by 2085
Abstract
Fertilization-initiated development and adult-onset aging are standard features in the life history of eukaryotes. In Paramecium, the number of cell divisions after the birth of a new generation is an essential parameter of sexual phase transition and aging. However, the gene driving [...] Read more.
Fertilization-initiated development and adult-onset aging are standard features in the life history of eukaryotes. In Paramecium, the number of cell divisions after the birth of a new generation is an essential parameter of sexual phase transition and aging. However, the gene driving this process and its evolutionary origin have not yet been elucidated. Here we report several critical outcomes obtained by molecular genetics, immunofluorescence microscopy, transformation by microinjection, and enzymological analysis. The cloned immaturin gene induces sexual rejuvenation in both mature and senescent cells by microinjection. The immaturin gene originated from proteobacteria’s glutathione-S-transferase (GST) gene. However, immaturin has been shown to lose GST activity and instead acquire nuclease activity. In vitro substrates for immaturin-nuclease are single- and double-stranded DNA, linear and circular DNA, and single-stranded viral genome RNA such as coronavirus. Anti-immaturin antibodies have shown that the subcellular localizations of immaturin are the macronucleus, cytoplasm, cell surface area, and cilia. The phase transition of sexuality is related to a decrease in the intracellular abundance of immaturin. We propose that sexual maturation and rejuvenation is a process programmed by the immaturin gene, and the sexual function of each age is defined by both the abundance and the intracellular localization mode of the immaturin-nuclease. Full article
(This article belongs to the Special Issue Paramecium as Modern Model System)
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16 pages, 6034 KiB  
Article
Species-Specific Duplication of Surface Antigen Genes in Paramecium
by Marcello Pirritano, Yulia Yakovleva, Alexey Potekhin and Martin Simon
Microorganisms 2022, 10(12), 2378; https://doi.org/10.3390/microorganisms10122378 - 30 Nov 2022
Cited by 1 | Viewed by 1922
Abstract
Paramecium is a free-living ciliate that undergoes antigenic variation and still the functions of these variable surface antigen coats in this non-pathogenic ciliate remain elusive. Only a few surface antigen genes have been described, mainly in the two model species P. tetraurelia strain [...] Read more.
Paramecium is a free-living ciliate that undergoes antigenic variation and still the functions of these variable surface antigen coats in this non-pathogenic ciliate remain elusive. Only a few surface antigen genes have been described, mainly in the two model species P. tetraurelia strain 51 and P. primaurelia strain 156. Given the lack of suitable sequence data to allow for phylogenetics and deeper sequence comparisons, we screened the genomes of six different Paramecium species for serotype genes and isolated 548 candidates. Our approach identified the subfamilies of the isogenes of individual serotypes that were mostly represented by intrachromosomal gene duplicates. These showed different duplication levels, and chromosome synteny suggested rather young duplication events after the emergence of the P. aurelia species complex, indicating a rapid evolution of surface antigen genes. We were able to identify the different subfamilies of the surface antigen genes with internal tandem repeats, which showed consensus motifs across species. The individual isogene families showed additional consensus motifs, indicating that the selection pressure holds individual amino acids constant in these repeats. This may be a hint of the receptor function of these antigens rather than a presentation of random epitopes, generating the variability of these surface molecules. Full article
(This article belongs to the Special Issue Paramecium as Modern Model System)
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18 pages, 4139 KiB  
Article
Intronization Signatures in Coding Exons Reveal the Evolutionary Fluidity of Eukaryotic Gene Architecture
by Judith Ryll, Rebecca Rothering and Francesco Catania
Microorganisms 2022, 10(10), 1901; https://doi.org/10.3390/microorganisms10101901 - 25 Sep 2022
Cited by 3 | Viewed by 1636
Abstract
The conventionally clear distinction between exons and introns in eukaryotic genes is actually blurred. To illustrate this point, consider sequences that are retained in mature mRNAs about 50% of the time: how should they be classified? Moreover, although it is clear that RNA [...] Read more.
The conventionally clear distinction between exons and introns in eukaryotic genes is actually blurred. To illustrate this point, consider sequences that are retained in mature mRNAs about 50% of the time: how should they be classified? Moreover, although it is clear that RNA splicing influences gene expression levels and is an integral part of interdependent cellular networks, introns continue to be regarded as accidental insertions; exogenous sequences whose evolutionary origin is independent of mRNA-associated processes and somewhat still elusive. Here, we present evidence that aids to resolve this disconnect between conventional views about introns and current knowledge about the role of RNA splicing in the eukaryotic cell. We first show that coding sequences flanked by cryptic splice sites are negatively selected on a genome-wide scale in Paramecium. Then, we exploit selection intensity to infer splicing-related evolutionary dynamics. Our analyses suggest that intron gain begins as a splicing error, involves a transient phase of alternative splicing, and is preferentially completed at the 5’ end of genes, which through intron gain can become highly expressed. We conclude that relaxed selective constraints may promote biological complexity in Paramecium and that the relationship between exons and introns is fluid on an evolutionary scale. Full article
(This article belongs to the Special Issue Paramecium as Modern Model System)
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12 pages, 1704 KiB  
Article
Method for Stress Assessment of Endosymbiotic Algae in Paramecium bursaria as a Model System for Endosymbiosis
by Toshiyuki Takahashi
Microorganisms 2022, 10(6), 1248; https://doi.org/10.3390/microorganisms10061248 - 18 Jun 2022
Cited by 1 | Viewed by 2107
Abstract
Endosymbiosis between heterotrophic host and microalga often breaks down because of environmental conditions, such as temperature change and exposure to toxic substances. By the time of the apparent breakdown of endosymbiosis, it is often too late for the endosymbiotic system to recover. In [...] Read more.
Endosymbiosis between heterotrophic host and microalga often breaks down because of environmental conditions, such as temperature change and exposure to toxic substances. By the time of the apparent breakdown of endosymbiosis, it is often too late for the endosymbiotic system to recover. In this study, I developed a technique for the stress assessment of endosymbiotic algae using Paramecium bursaria as an endosymbiosis model, after treatment with the herbicide paraquat, an endosymbiotic collapse inducer. Microcapillary flow cytometry was employed to evaluate a large number of cells in an approach that is more rapid than microscopy evaluation. In the assay, red fluorescence of the chlorophyll reflected the number of endosymbionts within the host cell, while yellow fluorescence fluctuated in response to the deteriorating viability of the endosymbiont under stress. Hence, the yellow/red fluorescence intensity ratio can be used as an algal stress index independent of the algal number. An optical evaluation revealed that the viability of the endosymbiotic algae within the host cell decreased after treatment with paraquat and that the remaining endosymbionts were exposed to high stress. The devised assay is a potential environmental monitoring method, applicable not only to P. bursaria but also to multicellular symbiotic units, such as corals. Full article
(This article belongs to the Special Issue Paramecium as Modern Model System)
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Review

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14 pages, 1188 KiB  
Review
A Review for the Special Issue on Paramecium as a Modern Model Organism
by Judith Van Houten
Microorganisms 2023, 11(4), 937; https://doi.org/10.3390/microorganisms11040937 - 3 Apr 2023
Cited by 2 | Viewed by 6640
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Paramecium as Modern Model System)
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29 pages, 2145 KiB  
Review
Calmodulin in Paramecium: Focus on Genomic Data
by Eduardo Villalobo, Gabriel Gutiérrez and Antonio Villalobo
Microorganisms 2022, 10(10), 1915; https://doi.org/10.3390/microorganisms10101915 - 27 Sep 2022
Cited by 1 | Viewed by 1985
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Paramecium as Modern Model System)
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