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ribosome profiling analysis identified a KRAS-interacting microprotein that represses oncogenic signaling in hepatocellular carcinoma cells

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Science China(Life Sciences) 2020年第4期63卷 529-542页

作者： Wenli Xu Bing Deng Penghui Lin Chang Liu Bin Li Qiaojuan Huang Hui Zhou Jianhua Yang Lianghu Qu MOE Key Laboratory of Gene Function and Regulation State Key Laboratory for BiocontrolSchool of Life SciencesSun Yat-Sen UniversityGuangzhou 510275China The Fifth Affiliated Hospital Sun Yat-Sen UniversityZhuhai 519000China

The roles of concealed microproteins encoded by long noncoding RNAs(lncRNAs)are gradually being exposed,but their functions in tumorigenesis are still largely unclear.Here,we identify and characterize a conserved 99-amino acid microprotein named KRASIM that is encoded by the putative lncRNA NCBP2-AS2.KRASIM is differentially expressed in normal hepatocytes and hepatocellular carcinoma(HCC)cells and can suppress HCC cell growth and proliferation.Mechanistically,KRASIM interacts and colocalizes with the KRAS protein in the cytoplasm of human HuH-7 hepatoma cells.More importantly,the overexpression of KRASIM decreases the KRAS protein level,leading to the inhibition of ERK signaling activity in HCC cells.These results demonstrate a novel microprotein repressor of the KRAS pathway for the first time and provide new insights into the regulatory mechanisms of oncogenic signaling and HCC therapy.

关键词： KRAS lncRNA microprotein ribosome profiling hepatocellular carcinoma

Accommodating the bacterial decoding release factor as an alien protein among the RNAs at the active site of the ribosome

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Cell Research 2007年第7期17卷 591-607页

作者： Elizabeth S Poole David J Young Marjan E Askarian-Amiri Debbie-Jane G Scarlett Warren P Tate Department of Biochemistry University of Otago P.O.Box 56 Dunedin New Zealand Department of Biochemistry University of Otago

The decoding release factor (RF) triggers termination of protein synthesis by functionally mimicking a tRNA to spanthe decoding centre and the peptidyl transferase centre (PTC) of the ribosome. Structurally, it must fit into a site craftedfor a tRNA and surrounded by five other RNAs, namely the adjacent peptidyl tRNA carrying the completed polypeptide,the mRNA and the three rRNAs. This is achieved by extending a structural domain from the body of the protein thatresults in a critical conformational change allowing it to contact the PTC. A structural model of the bacterial terminationcomplex with the accommodated RF shows that it makes close contact with the first, second and third bases of the stopcodon in the mRNA with two separate loops of structure: the anticodon loop and the loop at the tip of helix α5. Theanticodon loop also makes contact with the base following the stop codon that is known to strongly influence termina-tion efficiency. It confirms the close contact of domain 3 of the protein with the key RNA structures of the PTC. ThemRNA signal for termination includes sequences upstream as well as downstream of the stop codon, and this may reflectstructural restrictions for specific combinations of tRNA and RF to be bound onto the ribosome together. An unbiasedSELEX approach has been investigated as a tool to identify potential rRNA-binding contacts of the bacterial RF in itsdifferent binding conformations within the active centre of the ribosome.

关键词： release factor protein synthesis termination tRNA functional mimicry molecular mimicry SELEX ribosome

Cryo-EM structure and rRNA modification sites of a plant ribosome

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Plant Communications 2022年第5期3卷 144-152页

作者： Patrick Cottilli Yuzuru Itoh Yuko Nobe Anton S.Petrov Purificacion Lison Masato Taoka Alexey Amunts Science for Life Laboratory Department of Biochemistry and BiophysicsStockholm University17165 SolnaSweden Department of Chemistry Graduate School of ScienceTokyo Metropolitan UniversityMinami-osawa 1-1Hachioji-shiTokyo 192-0397Japan School of Chemistry and Biochemistry Georgia Institute of TechnologyAtlantaGAUSA Instituto de Biologıa Molecular y Celular de Plantas Universitat Politecnica de Valencia(UPV)-Consejo Superior de Investigaciones Cientıficas(CSIC)Ciudad Politecnica de la Innovacion(CPI)Valencia 46022Spain

Protein synthesis in crop plants contributes to the balance of food and fuel on our planet,which influences human metabolic activity and lifespan.Protein synthesis can be regulated with respect to changing environmental cues via the deposition of chemical modifications into rRNA.Here,we present the structure of a plant ribosome from tomato and a quantitative mass spectrometry analysis of its rRNAs.The study reveals fine features of the ribosomal proteins and 71 plant-specific rRNA modifications,and it re-annotates 30 rRNA residues in the available sequence.At the protein level,isoAsp is found in position 137 of uS11,and a zinc finger previously believed to be universal is missing from eL34,suggesting a lower effect of zinc defi-ciency on protein synthesis in plants.At the rRNA level,the plant ribosome differs markedly from its human counterpart with respect to the spatial distribution of modifications.Thus,it represents an additional layer of gene expression regulation,highlighting the molecular signature of a plant ribosome.The results provide a reference model of a plant ribosome for structural studies and an accurate marker for molecular ecology.

关键词： plant tomato ribosome RNA structure

Interaction between Bms1 and Rcl1,two ribosome biogenesis factors,is evolutionally conserved in zebrafish and human

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Journal of Genetics and Genomics 2016年第7期43卷 467-469页

作者： Yong Wang Qinfang Zhu Ling Huang Yanqing Zhu Jun Chen Jinrong Peng Li Jan Lo MOE Key Laboratory for Molecular Animal -Nutrit-ion College of Animal Sciences Zhejiang University Hangzhou 310058 China College of Life Sciences Zhejiang University Hangzhou 310058 China

ribosomes are large RNA and protein complexes that function as the machinery for translation protein synthesis （Boisvert et al., 2007; Ben-Shem et al., 2011： Henras et al., 2015： Kbatter et al., 2015; McCann et al., 2015）. The eukaryotic ribosome is composed of two subunits, the 60S large subunit （LSU） and the 40S small sub- unit （SSU）, which collectively comprise of four different ribosomal RNA （rRNA） species and more than 70 proteins （Ben-Sbem et al., 2011： Henras et al., 2015; Khatter et al., 2015）. The LSU contains the 28S, 5.8S and 5S rRNAs and the SSU contains the 18S rRNA. The assembly of each subunit is initiated in the nucleolus using the respective rRNAs as backbones （Ben-Shem et al., 2011; Henras et al., 2015; Khatter et al., 2015）.

关键词： ribosome evolutionally human

Enhancement of salinomycin production by ribosome engineering in Streptomyces albus

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Science China(Life Sciences) 2019年第2期62卷 276-279页

作者： Dong Li Jihui Zhang Yuqing Tian Huarong Tan State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences College of Life Sciences University of Chinese Academy of Sciences

Dear Editor,Streptomyces can produce a large variety of secondary metabolites as a major source of anti-infective, antitumor or immune-suppressive agents widely applied in clinical treatment. Antibiotics-resistant bac... 详细信息

关键词： Enhancement of salinomycin production by ribosome engineering in Streptomyces albus

A Proposal for Bioactive Domain of Trichosanthin From Examining the Sequence Homology of Eleven ribosome-inactivating Proteins

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Chinese Science Bulletin 1993年第21期38卷 1847-1848页

作者：金善炜顾梓伟叶国杰 Shanghai Institute of Organic Chemistry Academia SinicaShanghcd 200032PRC

Trichosanthin, a protein isolated from the root tuber of Trichosanthes kirilowii Maxim(Cucurbitaceae), is the active proteinous principle of a Chinese medicine. It is able to induce abortion of mid-gestation and to terminate early pregnancy, and it is effective for treatment of benign, malignant hydatidiform moles and ectopic pregnancy. Recently it has also been found an inhibitor of human immunodeficiency virus(HIV) and a

关键词： Eleven Proteins abortion ectopic Trichosanthes Cucurbitaceae tuber Domain ribosome 王幻

Nucleolar histone deacetylases HDT1,HDT2,and HDT3 regulate plant reproductive development

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Journal of Genetics and Genomics 2022年第1期49卷 30-39页

作者： Yu Luo Dong-Qiao Shi Peng-Fei Jia Yuan Bao Hong-Ju Li Wei-Cai Yang State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China College of Advanced Agricultural Sciences University of Chinese Academy of SciencesBeijing 100049China

Nucleolus is a membrane-less organelle where ribosomes are assembled, and ribosomal RNAs(r RNAs)transcribed and processed. The assembled ribosomes composed of ribosomal proteins and r RNAs synthesize proteins for cell survival. In plants, the loss of nucleolar ribosomal proteins often causes gametophytically or embryonically lethality. The amount of r RNAs are under stringent regulation according to demand and partially switched off by epigenetic modifications. However, the molecular mechanism for the selective activation or silencing is still unclear, and the transcriptional coordination of r RNAs and ribosomal proteins is also unknown. Here, we report the critical role of three Arabidopsis nucleolar proteins HDT1,HDT2, and HDT3 in fertility and transcription of r DNAs and r RNA processing-related genes through histone acetylation. This study highlights the important roles of transcriptional repression of ribosome biogenesisrelated genes for plant reproductive development.

关键词： Histone deacetylase rRNAs ribosome Reproductive development

Transcriptional response of Microcystis aeruginosa to the recruitment promoting-benthic bacteria

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Journal of Oceanology and Limnology 2022年第1期40卷 153-162页

作者： Juan WANG Yuande PENG Zhi WANG Wansheng ZOU Xianjin PENG Qisheng SONG College of Life Sciences Hunan Normal UniversityChangsha 410081China Institute of Bast Fiber Crops Chinese Academy of Agricultural SciencesChangsha 410205China Department of Life Science Hunan University of Arts and ScienceChangde 415000China Division of Plant Sciences University of MissouriColumbia 65211MOUSA

Blooms of Microcystis aeruginosa occur frequently in many freshwater ecosystems around the world,but the mechanism of recovery has not been fully understood.In our previous study,three benthic bacterial species(E.sp013,Ba.spD06,and Ba.spD24)were identifi ed capable of promoting the recruitment of M.aeruginosa.Here,we further investigated the transcriptional response of M.aeruginosa to the benthic bacteria in early phase of recruitment by means of RNA-Seq analysis.In total,5803803 unigenes on average length of 404 bp were obtained from the transcriptome of M.aeruginosa.There were 54982 unigenes identifi ed as benthic bacteria-responsive unigenes based on the expression level analysis.Results of the protein-protein interaction analysis(PPI)show that the hub genes of the benthic bacteria responsive unigenes mediated network were ribosomal proteins of 30S and 50S,and the most signifi cant functional module of the network was related to the ribosome.Both the unigenes encoding the translation initiation factors(IF-2,IF-3)and elongation factors(lepA,fusA,and tufA)were up-regulated to respond benthic bacteria.Therefore,it indicates that the benthic bacteria have a positive infl uence on activating the ribosome during the early recovery stage of M.aeruginosa.

关键词： Microcystis aeruginosa ribosome benthic bacteria chlorophyll a

Characterization of a Novel Gene, srpA, Conferring Resistance to Streptogramin A, Pleuromutilins, and Lincosamides in Streptococcus suis

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Engineering 2022年第2期8卷 85-94页

作者： Chaoyang Zhang Lu Liu Peng Zhang Jingpo Cui Xiaoxia Qin Lichao Ma Kun Han Zhanhui Wang Shaolin Wang Shuangyang Ding Zhangqi Shen College of Veterinary Medicine China Agricultural UniversityBeijing 100193China Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety China Agricultural UniversityBeijing 100193China

Antimicrobial resistance is undoubtedly one of the greatest global health threats. The emergence of multidrug-resistant(MDR) Gram-positive pathogens, such as methicillin-resistant Staphylococcus aureus(MRSA), vancomycin-resistant Enterococcus faecium(VRE), and β-lactamase-resistant Streptococcus pneumonia, has severely limited our antibiotic arsenal. Numerous ribosome-targeting antibiotics, especially pleuromutilins, oxazolidinones, and streptogramins, are viewed as promising alternatives against aggressive MDR pathogens. In this study, we identified a new adenosine triphosphate(ATP)-binding cassete(ABC)-F family determinant, srp A, in Streptococcus suis(S. suis) by means of a comparative analysis of the whole-genome sequences of tiamulin(TIA)-resistant and TIA-sensitive bacteria. Functional cloning confirmed that the deduced gene can mediate cross-resistance to pleuromutilins, lincosamides, and streptogramin A in S. suis and S. aureus. A sequence alignment revealed that Srp A shares the highest amino acid identity with Vga(E)(36%) and shows canonical characteristics of ABC-F family members.In Srp A-ribosome docked compounds, the extended loop region of Srp A approaches the valnemulinbinding pocket in the ribosome peptidyl-transferase center and competes with bound valnemulin. A detailed mutational analysis of the loop residues confirmed that this domain is crucial for Srp A activity,as substitutions or truncations of this region affect the efficiency and specificity of antibiotic resistance.Intracellular antibiotics accumulation indicated that Srp A does not act as an efflux pump, while a ribosome binding assay supported the protective effects of Srp A on the ribosome by preventing antibiotic binding as well as displacing bound drugs. These findings clarify the mechanisms underlying resistance to ribosomal antibiotics.

关键词： SrpA Streptococcus suis Antibiotic resistance ribosome ABC-F family proteins