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Annual Review of Biophysics May 2017Telomerase is an RNA-protein complex that extends the 3' ends of linear chromosomes, using a unique telomerase reverse transcriptase (TERT) and template in the... (Review)
Review
Telomerase is an RNA-protein complex that extends the 3' ends of linear chromosomes, using a unique telomerase reverse transcriptase (TERT) and template in the telomerase RNA (TR), thereby helping to maintain genome integrity. TR assembles with TERT and species-specific proteins, and telomerase function in vivo requires interaction with telomere-associated proteins. Over the past two decades, structures of domains of TR and TERT as well as other telomerase- and telomere-interacting proteins have provided insights into telomerase function. A recently reported 9-Å cryo-electron microscopy map of the Tetrahymena telomerase holoenzyme has provided a framework for understanding how TR, TERT, and other proteins from ciliate as well as vertebrate telomerase fit and function together as well as unexpected insight into telomerase interaction at telomeres. Here we review progress in understanding the structural basis of human and Tetrahymena telomerase activity, assembly, and interactions.
Topics: Humans; Models, Molecular; Protein Domains; Protozoan Proteins; RNA; Telomerase; Tetrahymena
PubMed: 28301767
DOI: 10.1146/annurev-biophys-062215-011140 -
The Journal of Eukaryotic Microbiology Jan 2023Mitochondrial cox1 689 bp barcodes are routinely used for identification of Tetrahymena species. Here, we examine whether two shorter nuclear sequences, the 5.8S rRNA...
Mitochondrial cox1 689 bp barcodes are routinely used for identification of Tetrahymena species. Here, we examine whether two shorter nuclear sequences, the 5.8S rRNA gene region and the intergenic region between H3 and H4 histone genes, might also be useful either singly or in combination with each other or cox1. We obtained sequences from ~300 wild isolates deposited at the Tetrahymena Stock Center and analyzed additional sequences obtained from GenBank. The 5.8S rRNA gene and portions of its transcribed flanks identify isolates as to their major clade and uniquely identify some, but not all, species. The ~330 bp H3/H4 intergenic region possesses low intraspecific variability and is unique for most species. However, it fails to distinguish between two pairs of common species and their rarer counterparts, and its use is complicated by the presence of duplicate genes in some species. The results show that while the cox1 sequence is the best single marker for Tetrahymena species identification, 5.8S rRNA, and the H3/H4 intergenic regions sequences are useful, singly or in combination, to confirm cox1 species assignments or as part of a preliminary survey of newly collected Tetrahymena. From our newly collected isolates, the results extend the biogeographical range of T. shanghaiensis and T. malaccensis and identify a new species, Tetrahymena arleneae n. sp. herein described.
Topics: Tetrahymena; Mitochondria; DNA, Intergenic; Phylogeny
PubMed: 35808858
DOI: 10.1111/jeu.12936 -
Genetics Jun 2016Tetrahymena thermophila is a ciliate model organism whose study has led to important discoveries and insights into both conserved and divergent biological processes. In... (Review)
Review
Tetrahymena thermophila is a ciliate model organism whose study has led to important discoveries and insights into both conserved and divergent biological processes. In this review, we describe the tools for the use of Tetrahymena as a model eukaryote, including an overview of its life cycle, orientation to its evolutionary roots, and methodological approaches to forward and reverse genetics. Recent genomic tools have expanded Tetrahymena's utility as a genetic model system. With the unique advantages that Tetrahymena provide, we argue that it will continue to be a model organism of choice.
Topics: Genes, Protozoan; Genetic Techniques; Tetrahymena
PubMed: 27270699
DOI: 10.1534/genetics.114.169748 -
Open Biology Oct 2017Programmed genome rearrangements in ciliates provide fascinating examples of flexible epigenetic genome regulations and important insights into the interaction between... (Review)
Review
Programmed genome rearrangements in ciliates provide fascinating examples of flexible epigenetic genome regulations and important insights into the interaction between transposable elements (TEs) and host genomes. DNA elimination in removes approximately 12 000 internal eliminated sequences (IESs), which correspond to one-third of the genome, when the somatic macronucleus (MAC) differentiates from the germline micronucleus (MIC). More than half of the IESs, many of which show high similarity to TEs, are targeted for elimination in by the small RNA-mediated genome comparison of the MIC to the MAC. Other IESs are targeted for elimination in by the same small RNAs through repetitive sequences. Furthermore, the small RNA-heterochromatin feedback loop ensures robust DNA elimination. Here, we review an updated picture of the DNA elimination mechanism, discuss the physiological and evolutionary roles of DNA elimination, and outline the key questions that remain unanswered.
Topics: DNA, Protozoan; Evolution, Molecular; Gene Rearrangement; Genome, Protozoan; RNA, Small Untranslated; Tetrahymena
PubMed: 29021213
DOI: 10.1098/rsob.170172 -
Nature Communications Apr 2023Cilia are ubiquitous eukaryotic organelles responsible for cellular motility and sensory functions. The ciliary axoneme is a microtubule-based cytoskeleton consisting of...
Cilia are ubiquitous eukaryotic organelles responsible for cellular motility and sensory functions. The ciliary axoneme is a microtubule-based cytoskeleton consisting of two central singlets and nine outer doublet microtubules. Cryo-electron microscopy-based studies have revealed a complex network inside the lumen of both tubules composed of microtubule-inner proteins (MIPs). However, the functions of most MIPs remain unknown. Here, we present single-particle cryo-EM-based analyses of the Tetrahymena thermophila native doublet microtubule and identify 42 MIPs. These data shed light on the evolutionarily conserved and diversified roles of MIPs. In addition, we identified MIPs potentially responsible for the assembly and stability of the doublet outer junction. Knockout of the evolutionarily conserved outer junction component CFAP77 moderately diminishes Tetrahymena swimming speed and beat frequency, indicating the important role of CFAP77 and outer junction stability in cilia beating generation and/or regulation.
Topics: Tetrahymena thermophila; Cryoelectron Microscopy; Microtubules; Axoneme; Cytoskeleton; Cilia; Microtubule Proteins; Tetrahymena
PubMed: 37061538
DOI: 10.1038/s41467-023-37868-0 -
Structure (London, England : 1993) Nov 2006Telomerase is a ribonucleoprotein complex that reverse transcribes a portion of its RNA subunit during the synthesis of G-rich DNA at the 3' end of each chromosome in... (Review)
Review
Telomerase is a ribonucleoprotein complex that reverse transcribes a portion of its RNA subunit during the synthesis of G-rich DNA at the 3' end of each chromosome in most eukaryotes. This activity compensates for the inability of the normal DNA replication machinery to fully replicate chromosome termini. The roles of telomerase in cellular immortality and tumor biology have catalyzed a significant interest in this unusual polymerase. Recently the first structures of two domains, the CR4/CR5 and pseudoknot, of human telomerase RNA (hTR) were reported, offering a structural basis for interpreting biochemical studies and possible roles of hTR mutations in human diseases. Structures of the stem II and stem IV domains of Tetrahymena thermophila TR as well as the N-terminal domain of the T. thermophila telomerase reverse transcriptase have also been determined. These studies complement previous biochemical studies, providing rich insight into the structural basis for telomerase activity.
Topics: Animals; DNA-Directed DNA Polymerase; Humans; Models, Molecular; Mutation; Nucleic Acid Conformation; Protein Structure, Secondary; Protein Structure, Tertiary; RNA; Saccharomyces; Telomerase; Tetrahymena; Tetrahymena thermophila
PubMed: 17098185
DOI: 10.1016/j.str.2006.09.004 -
Pharmacological Research Aug 2021This paper describes evidence establishing that ultra-low doses of diverse chemical agents at concentrations from 10 to 10 M (e.g., approaching and/or less than 1 atom... (Review)
Review
This paper describes evidence establishing that ultra-low doses of diverse chemical agents at concentrations from 10 to 10 M (e.g., approaching and/or less than 1 atom or molecule of a substance/cell based on Avogadro's constant - 6.022×10/mole) are capable of engaging receptor and intracellular signaling systems to elicit reproducible effects in a variety of species, from unicellular organisms to humans. Multiple experimental studies have shown that only one or very few molecules are needed to activate a cell and/or entire organism via cascade(s) of amplification mechanisms and processes. For example, ultra-low dose ligand exposure was able to activate both an individual cell, and ~3000 to 25,000 neighboring cells on average, by about 50%. Such activation of cells and whole organisms typically displayed hormetic-biphasic dose responses. These findings indicate that numerous, diverse phylogenetic systems have evolved highly sensitive detection and signaling mechanisms to enhance survival functions, such as defense against infectious agents, responses to diverse types of pheromone communications (e.g., alarm, sexual attraction), and development of several types of cellular protection/resilience processes. This suggests that ultra-low dose effects may be far more common than have been recognized to date. We posit that such findings have important implications for evolutionary theory, ecological and systems biology, and clinical medicine.
Topics: Animals; Dose-Response Relationship, Drug; Fullerenes; Hormesis; Humans; Ligands; Models, Biological; Oligopeptides; Phagocytosis; Pheromones; Receptors, G-Protein-Coupled; Signal Transduction; Tetrahymena
PubMed: 34157423
DOI: 10.1016/j.phrs.2021.105738 -
Cfap91-Dependent Stability of the RS2 and RS3 Base Proteins and Adjacent Inner Dynein Arms in Cilia.Cells Dec 2022Motile cilia and eukaryotic flagella are specific cell protrusions that are conserved from protists to humans. They are supported by a skeleton composed of uniquely...
Motile cilia and eukaryotic flagella are specific cell protrusions that are conserved from protists to humans. They are supported by a skeleton composed of uniquely organized microtubules-nine peripheral doublets and two central singlets (9 × 2 + 2). Microtubules also serve as docking sites for periodically distributed multiprotein ciliary complexes. Radial spokes, the T-shaped ciliary complexes, repeat along the outer doublets as triplets and transduce the regulatory signals from the cilium center to the outer doublet-docked dynein arms. Using the genetic, proteomic, and microscopic approaches, we have shown that lack of Cfap91 protein affects stable docking/positioning of the radial spoke RS3 and the base of RS2, and adjacent inner dynein arms, possibly due to the ability of Cfap91 to interact with a molecular ruler protein, Ccdc39. The localization studies confirmed that the level of RS3-specific proteins, Cfap61 and Cfap251, as well as RS2-associated Cfap206, are significantly diminished in CFAP91-KO cells. Cilia of cells with knocked-out beat in an uncoordinated manner and their beating frequency is dramatically reduced. Consequently, CFAP91-KO cells swam about a hundred times slower than wild-type cells. We concluded that Cfap91 localizes at the base of radial spokes RS2 and RS3 and likely plays a role in the radial spoke(s) positioning and stability.
Topics: Axoneme; Cilia; Dyneins; Proteomics; Tetrahymena
PubMed: 36552811
DOI: 10.3390/cells11244048 -
Biochemistry Nov 2021RNA-based machines are ubiquitous in Nature and increasingly important for medicines. They fold into complex, dynamic structures that process information and catalyze...
RNA-based machines are ubiquitous in Nature and increasingly important for medicines. They fold into complex, dynamic structures that process information and catalyze reactions, including reactions that generate new RNAs and proteins across biology. What are the experimental strategies and steps that are necessary to understand how these complex machines work? Two 1990 papers from Herschlag and Cech on "Catalysis of RNA Cleavage by the Ribozyme" provide a master class in dissecting an RNA machine through kinetics approaches. By showing how to propose a kinetic framework, fill in the numbers, do cross-checks, and make comparisons across mutants and different RNA systems, the papers illustrate how to take a mechanistic approach and distill the results into general insights that are difficult to attain through other means.
Topics: Biocatalysis; History, 20th Century; Introns; Kinetics; RNA Precursors; RNA Splicing; RNA, Catalytic; Tetrahymena
PubMed: 34492193
DOI: 10.1021/acs.biochem.1c00392 -
Seminars in Cell & Developmental Biology Jun 2016The molecular details of meiotic recombination have been determined for a small number of model organisms. From these studies, a general picture has emerged that shows... (Review)
Review
The molecular details of meiotic recombination have been determined for a small number of model organisms. From these studies, a general picture has emerged that shows that most, if not all, recombination is initiated by a DNA double-strand break (DSB) that is repaired in a recombinogenic process using a homologous DNA strand as a template. However, the details of recombination vary between organisms, and it is unknown which variant is representative of evolutionarily primordial meiosis or most prevalent among eukaryotes. To answer these questions and to obtain a better understanding of the range of recombination processes among eukaryotes, it is important to study a variety of different organisms. Here, the ciliate Tetrahymena thermophila is introduced as a versatile meiotic model system, which has the additional bonus of having the largest phylogenetic distance to all of the eukaryotes studied to date. Studying this organism can contribute to our understanding of the conservation and diversification of meiotic recombination processes.
Topics: Crossing Over, Genetic; DNA Breaks, Double-Stranded; DNA Repair; Meiosis; Models, Biological; Tetrahymena
PubMed: 26899715
DOI: 10.1016/j.semcdb.2016.02.021