Special Issue "Ciliates as Model Organisms: From ‘omics’ to Genetics, Ecology and Signaling"

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

Deadline for manuscript submissions: 31 December 2021.

Special Issue Editors

Prof. Dr. Cristina Miceli
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Guest Editor
School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032 Camerino, Italy
Interests: cell biology; protistology; genomics
Prof. Dr. Adriana Vallesi
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Guest Editor
School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032 Camerino, Italy
Interests: zoology; cell biology; protistology
Dr. Ronald Edward Pearlman
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Guest Editor
Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
Interests: molecular biology; cell biology; genetics; biochemistry; genomics; proteomics; chromatin; epigenetics; gene expression; ciliates

Special Issue Information

Dear Colleagues,

Ciliates represent a group of unicellular eukaryotes widespread in nature, living in aquatic habitats, in soil, and as symbionts of animals. They are adapted to different conditions; from very cold to hot temperatures, and from clean to polluted environments, and possess complex molecular systems for many processes such as ciliary beating, for self-/non-self-recognition, sexual phenomena, and predator–prey interactions. To effect these processes, ciliates are able to manage different signals which can be classified in three categories: (i) intercellular signals produced by other cells/organisms; (ii) environmental signals not produced by other organisms; and (iii) intracellular signals produced inside the cell body.

Ciliates are nuclear dimorphic, with two types of genome in a common cytoplasm. The diploid small germline micronucleus (MIC) is mostly transcriptionally silent and the repository of genetic information. The polyploid large somatic macronucleus (MAC) is responsible for gene transcription during cell growth. In the last 15 years, MAC genomes of many species have been investigated and disclosed, and the MIC genomes of a selected group of species are also under investigation. Comparative genomics, together with the analysis of transcriptomic and proteomic data, provides essential information to understand genetics, cell biology, and ecology of ciliates. Unraveling signaling systems in ciliates can provide important knowledge for understanding similar systems in other eukaryotes, including multicellular organisms. For example, ciliates are very useful biological models to study processes such as the evolution of calcium signaling. In addition, the hippo-signaling pathway, known to control the size of organs in animals, has been demonstrated to control cell polarity in ciliates and to specify the relative dimensions of the anterior and posterior daughter cells during division. Protein pheromones, which control self-/non-self-recognition and mating in ciliates, are considered the evolutionary precursors of animal growth factors.

This Special Issue is open to reporting all studies on ciliates as model organisms, seeking to understand their genetics, cell biology, biochemistry, evolution, ecological adaptation, and the complex mechanisms of signaling systems, from the genes involved to the changes in gene expression during cell response, and from the structure and involved evolution of signal molecules to the membrane traffic in the cells.

We look forward to receiving your contributions.

Prof. Dr. Cristina Miceli
Prof. Dr. Adriana Vallesi
Dr. Ronald Edward Pearlman
Guest Editors

Manuscript Submission Information

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Published Papers (4 papers)

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Research

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Open AccessArticle
Characterization of Simple Sequence Repeats (SSRs) in Ciliated Protists Inferred by Comparative Genomics
Microorganisms 2020, 8(5), 662; https://doi.org/10.3390/microorganisms8050662 - 01 May 2020
Cited by 1 | Viewed by 948
Abstract
Simple sequence repeats (SSRs) are prevalent in the genomes of all organisms. They are widely used as genetic markers, and are insertion/deletion mutation hotspots, which directly influence genome evolution. However, little is known about such important genomic components in ciliated protists, a large [...] Read more.
Simple sequence repeats (SSRs) are prevalent in the genomes of all organisms. They are widely used as genetic markers, and are insertion/deletion mutation hotspots, which directly influence genome evolution. However, little is known about such important genomic components in ciliated protists, a large group of unicellular eukaryotes with extremely long evolutionary history and genome diversity. With recent publications of multiple ciliate genomes, we start to get a chance to explore perfect SSRs with motif size 1–100 bp and at least three motif repeats in nine species of two ciliate classes, Oligohymenophorea and Spirotrichea. We found that homopolymers are the most prevalent SSRs in these A/T-rich species, with AAA (lysine, charged amino acid; also seen as an SSR with one-adenine motif repeated three times) being the codons repeated at the highest frequencies in coding SSR regions, consistent with the widespread alveolin proteins rich in lysine repeats as found in Tetrahymena. Micronuclear SSRs are universally more abundant than the macronuclear ones of the same motif-size, except for the 8-bp-motif SSRs in extensively fragmented chromosomes. Both the abundance and A/T content of SSRs decrease as motif-size increases, while the abundance is positively correlated with the A/T content of the genome. Also, smaller genomes have lower proportions of coding SSRs out of all SSRs in Paramecium species. This genome-wide and cross-species analysis reveals the high diversity of SSRs and reflects the rapid evolution of these simple repetitive elements in ciliate genomes. Full article
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Open AccessArticle
Comparative Transcriptomics Reveals Distinct Gene Expressions of a Model Ciliated Protozoan Feeding on Bacteria-Free Medium, Digestible, and Digestion-Resistant Bacteria
Microorganisms 2020, 8(4), 559; https://doi.org/10.3390/microorganisms8040559 - 13 Apr 2020
Cited by 1 | Viewed by 1151
Abstract
Bacterivory is an important ecological function of protists in natural ecosystems. However, there are diverse bacterial species resistant to protistan digestion, which reduces the carbon flow to higher trophic levels. So far, a molecular biological view of metabolic processes in heterotrophic protists during [...] Read more.
Bacterivory is an important ecological function of protists in natural ecosystems. However, there are diverse bacterial species resistant to protistan digestion, which reduces the carbon flow to higher trophic levels. So far, a molecular biological view of metabolic processes in heterotrophic protists during predation of bacterial preys of different digestibility is still lacking. In this study, we investigated the growth performance a ciliated protozoan Tetrahymena thermophila cultivated in a bacteria-free Super Proteose Peptone (SPP) medium (control), and in the media mixed with either a digestion-resistant bacterial species (DRB) or a digestible strain of E. coli (ECO). We found the protist population grew fastest in the SPP and slowest in the DRB treatment. Fluorescence in situ hybridization confirmed that there were indeed non-digested, viable bacteria in the ciliate cells fed with DRB, but none in other treatments. Comparative analysis of RNA-seq data showed that, relative to the control, 637 and 511 genes in T. thermophila were significantly and differentially expressed in the DRB and ECO treatments, respectively. The protistan expression of lysosomal proteases (especially papain-like cysteine proteinases), GH18 chitinases, and an isocitrate lyase were upregulated in both bacterial treatments. The genes encoding protease, glycosidase and involving glycolysis, TCA and glyoxylate cycles of carbon metabolic processes were higher expressed in the DRB treatment when compared with the ECO. Nevertheless, the genes for glutathione metabolism were more upregulated in the control than those in both bacterial treatments, regardless of the digestibility of the bacteria. The results of this study indicate that not only bacterial food but also digestibility of bacterial taxa modulate multiple metabolic processes in heterotrophic protists, which contribute to a better understanding of protistan bacterivory and bacteria-protists interactions on a molecular basis. Full article
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Open AccessArticle
Comparative Transcriptome Analyses during the Vegetative Cell Cycle in the Mono-Cellular Organism Pseudokeronopsis erythrina (Alveolata, Ciliophora)
Microorganisms 2020, 8(1), 108; https://doi.org/10.3390/microorganisms8010108 - 12 Jan 2020
Cited by 2 | Viewed by 1043
Abstract
Studies focusing on molecular mechanisms of cell cycles have been lagging in unicellular eukaryotes compared to other groups. Ciliates, a group of unicellular eukaryotes, have complex cell division cycles characterized by multiple events. During their vegetative cell cycle, ciliates undergo macronuclear amitosis, micronuclear [...] Read more.
Studies focusing on molecular mechanisms of cell cycles have been lagging in unicellular eukaryotes compared to other groups. Ciliates, a group of unicellular eukaryotes, have complex cell division cycles characterized by multiple events. During their vegetative cell cycle, ciliates undergo macronuclear amitosis, micronuclear mitosis, stomatogenesis and somatic cortex morphogenesis, and cytokinesis. Herein, we used the hypotrich ciliate Pseudokeronopsis erythrina, whose morphogenesis has been well studied, to examine molecular mechanisms of ciliate vegetative cell cycles. Single-cell transcriptomes of the growth (G) and cell division (D) stages were compared. The results showed that (i) More than 2051 significantly differentially expressed genes (DEGs) were detected, among which 1545 were up-regulated, while 256 were down-regulated at the D stage. Of these, 11 randomly picked DEGs were validated by reverse transcription quantitative polymerase chain reaction (RT-qPCR); (ii) Enriched DEGs during the D stage of the vegetative cell cycle of P. erythrina were involved in development, cortex modifications, and several organelle-related biological processes, showing correspondence of molecular evidence to morphogenetic changes for the first time; (iii) Several individual components of molecular mechanisms of ciliate vegetative division, the sexual cell cycle and cellular regeneration overlap; and (iv) The P. erythrina cell cycle and division have the same essential components as other eukaryotes, including cyclin-dependent kinases (CDKs), cyclins, and genes closely related to cell proliferation, indicating the conserved nature of this biological process. Further studies are needed focusing on detailed inventory and gene interactions that regulate specific ciliated cell-phase events. Full article
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Review

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Open AccessReview
Natural Function and Structural Modification of Climacostol, a Ciliate Secondary Metabolite
Microorganisms 2020, 8(6), 809; https://doi.org/10.3390/microorganisms8060809 - 27 May 2020
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Abstract
The review highlights the main results of two decades of research on climacostol (5-[(2Z)-non-2-en-1-yl]benzene-1,3-diol), the resorcinolic lipid produced and used by the ciliated protozoan Climacostomum virens for chemical defense against a wide range of predators, and to assist its carnivorous feeding. [...] Read more.
The review highlights the main results of two decades of research on climacostol (5-[(2Z)-non-2-en-1-yl]benzene-1,3-diol), the resorcinolic lipid produced and used by the ciliated protozoan Climacostomum virens for chemical defense against a wide range of predators, and to assist its carnivorous feeding. After the first studies on the physiological function of climacostol, the compound and some analogues were chemically synthesized, thus allowing us to explore both its effect on different prokaryotic and eukaryotic biological systems, and the role of its relevant structural traits. In particular, the results obtained in the last 10 years indicate climacostol is an effective antimicrobial and anticancer agent, bringing new clues to the attempt to design and synthesize additional novel analogues that can increase or optimize its pharmacological properties. Full article
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

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