The ciliate Tetrahymena thermophila has been a powerful model system for molecular and cellular biology.However,some investigations have been limited due to the incomplete closure and sequencing of the macronuclear ge...The ciliate Tetrahymena thermophila has been a powerful model system for molecular and cellular biology.However,some investigations have been limited due to the incomplete closure and sequencing of the macronuclear genome assembly,which for many years has been stalled at 1,158 scaffolds,with large sections of unknown sequences(available in Tetrahymena Genome Database,TGD,http://ciliate.org/).Here we completed the first chromosome-level Tetrahymena macronuclear genome assembly,with approximately 300×long Single Molecule,Real-Time reads of the wild-type SB210 cells—the reference strain for the initial macronuclear genome sequencing project.All 181 chromosomes were capped with two telomeres and gaps were entirely closed.The completed genome shows significant improvements over the current assembly(TGD 2014)in both chromosome structure and sequence integrity.The majority of previously identified gene models shown in TGD were retained,with the addition of 36 new genes and 883 genes with modified gene models.The new genome and annotation were incorporated into TGD.This new genome allows for pursuit in some underexplored areas that were far more challenging previously;two of them,genome scrambling and chromosomal copy number,were investigated in this study.We expect that the completed macronuclear genome will facilitate many studies in Tetrahymena biology,as well as multiple lines of research in other eukaryotes.展开更多
Histone modification and nucleosome assembly play important roles in chromatin-related processes.Histone chaperones form different complexes and coordinate histone transportation and assembly.Various histone chaperone...Histone modification and nucleosome assembly play important roles in chromatin-related processes.Histone chaperones form different complexes and coordinate histone transportation and assembly.Various histone chaperone complexes have been identified in different organisms.The ciliate protozoa(ciliates)have various chromatin structures and different nuclear morphology.However,histone chaperone components and functions of different subunits remain unclear in ciliates.Tet-rahymema thermophila contains a transcriptionally active macronucleus(MAC)and a transcriptionally inactive micronu-cleus(MIC)which exhibit multiple replication and various chromatin remodeling progresses during vegetative growth and sexual developmental stages.Here,we found histone chaperone RebL1 not only localized evenly in the transcriptionally active MAC but also dynamically changed in the MIC during vegetative growth and sexual developmental stages.REBL1 knockdown inhibited cellular proliferation.The macronuclear morphology became bigger in growing mutants.The abnormal macronuclear structure also occurred in the starvation stage.Furthermore,micronuclear meiosis was disturbed during sexual development,leading to a failure to generate new gametic nuclei.RebL1 potentially interacted with various factors involved in histone-modifying complexes and chromatin remodeling complexes in different developmental stages.REBL1 knockdown affected expression levels of the genes involved in chromatin organization and transcription.Taken together,RebL1 plays a vital role in maintaining macronuclear structure stability and gametogenesis in T.thermophila.展开更多
Understanding the adaptation of organisms to extreme environments is a fascinating topic in biology.Ciliated eukaryotes(ciliates)that inhabit high-salinity environments exhibit remarkable diversity.We revealed various...Understanding the adaptation of organisms to extreme environments is a fascinating topic in biology.Ciliated eukaryotes(ciliates)that inhabit high-salinity environments exhibit remarkable diversity.We revealed various structural and molecular adaptations through a comprehensive investigation of Schmidingerothrix,a ciliate tolerant to salinity levels of up to 25%.One key finding was the presence of a unique microtubule cytoskeleton under the pellicle of Schmidingerothrix,which significantly contributed to its high-salt adaptation.Our results highlight the essential role of coexisting halophilic bacteria in supporting the thriving of ciliates in culture.Contrary to previous studies,our findings indicated an inability to synthesize glycine betaine and ectoine in Schmidingerothrix.However,Schmidingerothrix appears to have expanded its repertoire of phagocytosis-related genes,suggesting a robust mechanism for the uptake and accumulation of compatible solutes via phagocytosis of halophilic bacteria.We expanded our investigation to other high-salt ciliates from different clades and discovered that microtubule cell-shape-supporting cytoskeletons and the phagocytic acquisition of compatible solutes were common strategies for high-salt adaptation.These findings significantly enhance our understanding of how ciliates adapt to high-salt environments and provide valuable insights into the high diversity of heterotrophic protists.展开更多
基金Supported by the Natural Science Foundation of Shandong Province (JQ201706)The Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao) (2018SDKJ0406-2)+2 种基金Fundamental Research Funds for the Central Universities (201841005)the Blue Life Breakthrough Program of LMBB of Qingdao National Laboratory for Marine Science and Technology (MS2018NO04)and National Institutes of Health (2P40OD010964).
文摘The ciliate Tetrahymena thermophila has been a powerful model system for molecular and cellular biology.However,some investigations have been limited due to the incomplete closure and sequencing of the macronuclear genome assembly,which for many years has been stalled at 1,158 scaffolds,with large sections of unknown sequences(available in Tetrahymena Genome Database,TGD,http://ciliate.org/).Here we completed the first chromosome-level Tetrahymena macronuclear genome assembly,with approximately 300×long Single Molecule,Real-Time reads of the wild-type SB210 cells—the reference strain for the initial macronuclear genome sequencing project.All 181 chromosomes were capped with two telomeres and gaps were entirely closed.The completed genome shows significant improvements over the current assembly(TGD 2014)in both chromosome structure and sequence integrity.The majority of previously identified gene models shown in TGD were retained,with the addition of 36 new genes and 883 genes with modified gene models.The new genome and annotation were incorporated into TGD.This new genome allows for pursuit in some underexplored areas that were far more challenging previously;two of them,genome scrambling and chromosomal copy number,were investigated in this study.We expect that the completed macronuclear genome will facilitate many studies in Tetrahymena biology,as well as multiple lines of research in other eukaryotes.
基金supported by the National Natural Science Foundation of China(32270450,32071449)Shanxi Key Program International S&T Cooperation Projects(202104041101011)Shanxi Scholarship Council of China(2020016).
文摘Histone modification and nucleosome assembly play important roles in chromatin-related processes.Histone chaperones form different complexes and coordinate histone transportation and assembly.Various histone chaperone complexes have been identified in different organisms.The ciliate protozoa(ciliates)have various chromatin structures and different nuclear morphology.However,histone chaperone components and functions of different subunits remain unclear in ciliates.Tet-rahymema thermophila contains a transcriptionally active macronucleus(MAC)and a transcriptionally inactive micronu-cleus(MIC)which exhibit multiple replication and various chromatin remodeling progresses during vegetative growth and sexual developmental stages.Here,we found histone chaperone RebL1 not only localized evenly in the transcriptionally active MAC but also dynamically changed in the MIC during vegetative growth and sexual developmental stages.REBL1 knockdown inhibited cellular proliferation.The macronuclear morphology became bigger in growing mutants.The abnormal macronuclear structure also occurred in the starvation stage.Furthermore,micronuclear meiosis was disturbed during sexual development,leading to a failure to generate new gametic nuclei.RebL1 potentially interacted with various factors involved in histone-modifying complexes and chromatin remodeling complexes in different developmental stages.REBL1 knockdown affected expression levels of the genes involved in chromatin organization and transcription.Taken together,RebL1 plays a vital role in maintaining macronuclear structure stability and gametogenesis in T.thermophila.
基金supported by the National Natural Science Foundation of China(32122015,31872221,31900339 and 31872206)the National Key Research and Development Program of China(2020YFA0907400)+3 种基金the Strategic Priority Research Program of the Chinese Academy of Sciences(XDPB18)the Natural Science Foundation of Hebei Province(C2025202025)supported by the Wuhan Branch,Supercomputing Center,Chinese Academy of Sciences,Chinasupported by the National Aquatic Biological Resource Center(NABRC).
文摘Understanding the adaptation of organisms to extreme environments is a fascinating topic in biology.Ciliated eukaryotes(ciliates)that inhabit high-salinity environments exhibit remarkable diversity.We revealed various structural and molecular adaptations through a comprehensive investigation of Schmidingerothrix,a ciliate tolerant to salinity levels of up to 25%.One key finding was the presence of a unique microtubule cytoskeleton under the pellicle of Schmidingerothrix,which significantly contributed to its high-salt adaptation.Our results highlight the essential role of coexisting halophilic bacteria in supporting the thriving of ciliates in culture.Contrary to previous studies,our findings indicated an inability to synthesize glycine betaine and ectoine in Schmidingerothrix.However,Schmidingerothrix appears to have expanded its repertoire of phagocytosis-related genes,suggesting a robust mechanism for the uptake and accumulation of compatible solutes via phagocytosis of halophilic bacteria.We expanded our investigation to other high-salt ciliates from different clades and discovered that microtubule cell-shape-supporting cytoskeletons and the phagocytic acquisition of compatible solutes were common strategies for high-salt adaptation.These findings significantly enhance our understanding of how ciliates adapt to high-salt environments and provide valuable insights into the high diversity of heterotrophic protists.
