Spontaneous mutation accumulation and reproductive strategies in free-living ciliates

Knowledge of the frequency and fitness effects of mutations is essential for understanding a diversity of issues in evolution; thus, many efforts have gone into elucidating the mutational process. However, our understanding of mutation is far from complete, largely due to the fact that mutations are rare and frequently eliminated by natural selection. This renders studies of the mutational process inherently difficult. The ciliate Tetrahymena thermophila provides a unique opportunity to overcome these difficulties by allowing the accumulation of mutations over many generations in the absence of selection on the germline genome. Estimates of the rate and fitness effect of mutations, the first from the eukaryotic supergroup Chromalveolata, are within the range of those of previously studied eukaryotes. Mutations are partially recessive on average and the rate of lethal mutations is substantially lower than the deleterious mutation rate. Germline mutation accumulation in T. thermophila used the reproductive idiosyncrasy that the germline genome only gets expressed during sexual reproductions; thus, germline mutations could be hidden from selection during asexual transfers. There might be other useful reproduction strategies for evolutionary genetics, so as a start, another marine free-living ciliate Glauconema trihymene was explored and shown to have diverse asexual reproductive strategies. Selfing was also observed with peculiar macronuclear events in G. trihymene.Biology and Biochemistry, Department o

Diverse modes of reproduction in the marine free-living ciliate Glauconema trihymene

<p>Abstract</p> <p>Background</p> <p>Most free-living ciliates reproduce by equal fission or budding during vegetative growth. In certain ciliates, reproduction occurs inside the cyst wall, <it>viz</it>. reproductive cysts, but more complex reproductive strategies have generally been thought to be confined to parasitic or symbiotic species, e.g. <it>Radiophrya </it>spp.</p> <p>Results</p> <p>In addition to equal fission, asymmetric binary division and reproductive cysts were discovered in the free-living bacterivorous scuticociliate <it>Glauconema trihymene </it>Thompson, 1966. Asymmetric division is an innate physiological state that can be induced by sufficient food, and the higher the food concentration, the longer the asymmetric division persists. During asymmetric division, nuclear and somatic structures divide with transiently arrested cytokinesis and variable positioning of macronuclei. Phylogenetic analysis, based on the small subunit of ribosomal DNA (SSU rDNA) sequences, showed that the <it>G. trihymene </it>isolate studied here nests with typical scuticociliates and is paraphyletic to both the symbiotic apostome and astome ciliates, some of which also produce progeny by asymmetric division.</p> <p>Conclusions</p> <p>The asymmetric division in <it>G. trihymene </it>has no precedent among undisturbed free-living ciliates. The coexistence of multiple modes of reproduction may represent a previously undescribed reproductive strategy for ciliates living on food patches in coastal waters. This may also be indicative of similar reproductive strategies among other polyphenic ciliates, which have not been intensively studied. Asymmetric division provides a special opportunity for studying ciliates' phenotypic plasticity and may also illuminate the origins of multicellularity.</p

Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila

Knowledge of the rate and fitness effects of mutations is essential for understanding the process of evolution. Mutations are inherently difficult to study because they are rare and are frequently eliminated by natural selection. In the ciliate Tetrahymena thermophila, mutations can accumulate in the germline genome without being exposed to selection. We have conducted a mutation accumulation (MA) experiment in this species. Assuming that all mutations are deleterious and have the same effect, we estimate that the deleterious mutation rate per haploid germline genome per generation is U = 0.0047 (95% credible interval: 0.0015, 0.0125), and that germline mutations decrease fitness by s = 11% when expressed in a homozygous state (95% CI: 4.4%, 27%). We also estimate that deleterious mutations are partially recessive on average (h = 0.26; 95% CI: –0.022, 0.62) and that the rate of lethal mutations is &lt;10% of the deleterious mutation rate. Comparisons between the observed evolutionary responses in the germline and somatic genomes and the results from individual-based simulations of MA suggest that the two genomes have similar mutational parameters. These are the first estimates of the deleterious mutation rate and fitness effects from the eukaryotic supergroup Chromalveolata and are within the range of those of other eukaryotes

The Glyphosate-Based Herbicide Roundup Does not Elevate Genome-Wide Mutagenesis of Escherichia coli

Mutations induced by pollutants may promote pathogen evolution, for example by accelerating mutations conferring antibiotic resistance. Generally, evaluating the genome-wide mutagenic effects of long-term sublethal pollutant exposure at single-nucleotide resolution is extremely difficult. To overcome this technical barrier, we use the mutation accumulation/whole-genome sequencing (MA/WGS) method as a mutagenicity test, to quantitatively evaluate genome-wide mutagenesis of Escherichia coli after long-term exposure to a wide gradient of the glyphosate-based herbicide (GBH) Roundup Concentrate Plus. The genome-wide mutation rate decreases as GBH concentration increases, suggesting that even long-term GBH exposure does not compromise the genome stability of bacteria

Supplemental Material for Long, Doak, and Lynch, 2018

Supplemental Tables S1 and S

Characterization of Simple Sequence Repeats (SSRs) in Ciliated Protists Inferred by Comparative Genomics

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&ndash;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

The Rate And Spectrum Of Spontaneous Mutations In Mycobacterium Smegmatis, A Bacterium Naturally Devoid Of The Postreplicative Mismatch Repair Pathway

Mycobacterium smegmatis is a bacterium that is naturally devoid of known postreplicative DNA mismatch repair (MMR) homologs, mutS and mutL, providing an opportunity to investigate how the mutation rate and spectrum has evolved in the absence of a highly conserved primary repair pathway. Mutation accumulation experiments of M. smegmatis yielded a base-substitution mutation rate of 5.27 × 10−10 per site per generation, or 0.0036 per genome per generation, which is surprisingly similar to the mutation rate in MMR-functional unicellular organisms. Transitions were found more frequently than transversions, with the A:T→G:C transition rate significantly higher than the G:C→A:T transition rate, opposite to what is observed in most studied bacteria. We also found that the transition-mutation rate of M. smegmatis is significantly lower than that of other naturally MMR-devoid or MMR-knockout organisms. Two possible candidates that could be responsible for maintaining high DNA fidelity in this MMR-deficient organism are the ancestral-like DNA polymerase DnaE1, which contains a highly efficient DNA proofreading histidinol phosphatase (PHP) domain, and/or the existence of a uracil-DNA glycosylase B (UdgB) homolog that might protect the GC-rich M. smegmatis genome against DNA damage arising from oxidation or deamination. Our results suggest that M. smegmatis has a noncanonical Dam (DNA adenine methylase) methylation system, with target motifs differing from those previously reported. The mutation features of M. smegmatis provide further evidence that genomes harbor alternative routes for improving replication fidelity, even in the absence of major repair pathways.PubMedWoSScopu

Two New Ciliates from the North China Seas, Schizocalyptra aeschtae nov. spec. and Sathrophilus holtae nov. spec., with New Definition of the Genus Sathrophilus (Ciliophora, Oligohymenophora)

1) Laboratory of Protozoology, KLM, Ocean University of China, Qingdao, P. R. China; 2) College of Life Science, South China Normal University, Guangzhou, P. R. China; 3) Department of Zoology, the Natural History Museum, London, UK; 4Zoology Department, King Saud University, Riyadh, Saudi Arabia.The living morphology, infraciliature, and silverline system of two marine ciliates, Schizocalyptra aeschtae nov. spec. and Sathrophilus holtae nov. spec. collected from sandy beaches near Qingdao, north China seas, were investigated. Schizocalyptra aeschtae is diagnosed as follows: 75–200 × 30–80 μm in vivo, bilaterally flattened about 1:2; about 15 prolonged cilia in posterior half of body; 60 somatic kineties on average; bases of membranelle 1 (M1) and M2b short; M3 about the same length as M2a; paroral membrane with 6–12 fragments at its posterior part; 2 to numerous macronuclear nodules in different shapes and sizes; one large contractile vacuole terminally located; marine habitat. Sathrophilus holtae nov. spec. is characterized by: in vivo 35–70 × 20–40 μm, cylindrical in outline; dorsoventrally flattened, with a conspicuously long caudal bristle; 21 somatic kineties on average; M1 three-rowed and bipartite with first row conspicuously long and separated from the other two; M2 two-rowed and L-shaped; ratio of lengths of M2 to M3 about 3:1; paroral membrane extending to above level of M2; one contractile vacuole pore at the end of SK1; marine habitat. Since no diagnosis according to modern investigation is available for the genus Sathrophilus, a new definition is supplied: dorsoventrally flattened, elongated Cinetochilidae with Tetrahymena-like buccal apparatus and bipartite M1; paroral membrane slightly curved, terminating anteriorly to about level of M1/M2; buccal field above the equatorial level; postoral kineties and groups of kinetosomes (scutica) present; having a distinctly long caudal bristle and one conspicuous, cilia-free apically plate. The systematic position of Sathrophilus is briefly discussed which, based on the morphological and morphogenetic characters of Sathrophilus holtae, appears to be a loxocephalid rather than a scuticociliate or a hymenostomatid. In addition, a synonym is recognized, i.e. Paradexiotricha, and a new combination is suggested: Sathrophilus puytoraci (Grolière 1975) nov. comb. [basionym: Paradexiotricha puytoraci Grolière, 1975]

Morphology and Small Subunit rDNA Gene Sequence of Pseudoamphisiella quadrinucleata n. sp. (Ciliophora, Urostylida) from the South China Sea

The urosylid genus Pseudoamphisiella was established by Song (1996) with hitherto only two known congeners. In the present work, the morphology and infraciliature of a new member, Pseudoamphisiella quadrinucleata n. sp., a form with conspicuous alveolar layer and four macronuclear nodules isolated from the coastal waters both near Hong Kong and near Guangzhou, South China were investigated using living observation and protargol silver impregnation methods. Pseudoamphisiella quadrinucleata differs from other two known forms mainly by the number of macronuclear nodules: constantly four vs. two in Pseudoamphisiella alveolata and 24–57 in Pseudoamphisiella lacazei. To support this, the sequence of the small subunit rDNA of P. quadrinucleata n. sp. showed 14 and 74 nucleotides in comparison with that of the two known congeners, respectively, which hence firmly supports the validity of the new species