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Imatinib blocks tyrosine phosphorylation of Smad4 and restores TGF-β growth-suppressive signaling in BCR-ABL1-positive leukemia

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Signal Transduction and Targeted Therapy 2023年第4期8卷 1993-2006页

作者： Lijing Wang Shuchen Gu Fenfang Chen Yi Yu Jin Cao Xinran Li Chun Gao Yanzhen Chen Shuchong Yuan Xia Liu Jun Qin Bin Zhao Pinglong Xu Tingbo Liang Hongyan Tong Xia Lin Xin-Hua Feng The MOE Key Laboratory of Biosystems Homeostasis&Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology Life Sciences InstituteZhejiang UniversityHangzhouZhejiang 310058China Center for Life Sciences Shaoxing InstituteZhejiang UniversityShaoxingZhejiang 321000China Cancer Center Zhejiang UniversityHangzhouZhejiang 310058China ZJU-Hangzhou Global Scientific and Technological Innovation Center Zhejiang UniversityHangzhouZhejiang 311200China Department of Hematology The First Affiliated HospitalZhejiang University School of MedicineHangzhou 310003China Beijing Proteome Research Center National Center for Protein SciencesBeijingChina Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease The First Affiliated HospitalZhejiang University School of MedicineHangzhou 310003China The Second Affiliated Hospital Zhejiang UniversityHangzhouZhejiang 310009China

Loss of TGF-β-mediated growth suppression is a major contributor to the development of cancers,best exemplified by loss-offunction mutations in genes encoding components of the TGF-βsignaling pathway in colorectal and pancreatic cancers.Alternatively,gain-of-function oncogene mutations can also disrupt antiproliferative TGF-βsignaling.However,the molecular mechanisms underlying oncogene-induced modulation of TGF-βsignaling have not been extensively investigated.Here,we show that the oncogenic BCR-ABL1 of chronic myelogenous leukemia(CML)and the cellular ABL1 tyrosine kinases phosphorylate and inactivate Smad4 to block antiproliferative TGF-βsignaling.Mechanistically,phosphorylation of Smad4 at Tyr195,Tyr301,and Tyr322 in the linker region interferes with its binding to the transcription co-activator p300/CBP,thereby blocking the ability of Smad4 to activate the expression of cyclin-dependent kinase(CDK)inhibitors and induce cell cycle arrest.In contrast,the inhibition of BCR-ABL1 kinase with Imatinib prevented Smad4 tyrosine phosphorylation and re-sensitized CML cells to TGF-β-induced antiproliferative and pro-apoptotic responses.Furthermore,expression of phosphorylation-site-mutated Y195F/Y301F/Y322F mutant of Smad4 in Smad4-null CML cells enhanced antiproliferative responses to TGF-β,whereas the phosphorylation-mimicking Y195E/Y301E/Y322E mutant interfered with TGF-βsignaling and enhanced the in vivo growth of CML cells.These findings demonstrate the direct role of BCR-ABL1 tyrosine kinase in suppressing TGF-βsignaling in CML and explain how Imatinib-targeted therapy restored beneficial TGF-βanti-growth responses.

关键词： Smad4 phosphorylation thereby

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Blue light-induced phosphorylation of Arabidopsis cryptochrome 1 is essential for its photosensitivity

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Journal of Integrative Plant Biology 2022年第9期64卷 1724-1738页

作者： Lin Gao Qing Liu Ming Zhong Nannan Zeng Weixian Deng Yaxing Li Dong Wang Siyuan Liu Qin Wang College of Life Sciences Basic Forestry and Proteomics Research CenterFujian Agriculture and Forestry UniversityFuzhou350002 China School of Life Sciences State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesSouth China Agricultural UniversityGuangzhou510642 China Key Laboratory of Ministry of Education for Genetics Breeding and Multiple Utilization of CropsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhou350002 China Department of Biological Chemistry David Geffen School of MedicineUniversity of California Los AngelesLos AngelesCA90095 USA

Plants possess two cryptochrome photoreceptors,cryptochrome 1(CRY1)and cryptochrome 2(CRY2),that mediate overlapping and distinct physiological responses.Both CRY1 and CRY2 undergo blue light-induced phosphorylation,but the molecular details of CRY1 phosphorylation remain unclear.Here we identify 19 in vivo phosphorylation sites in CRY1 using mass spectrometry and systematically analyze the physiological and photobiochemical activities of CRY1 variants with phosphosite substitutions.We demonstrate that nonphosphorylatable CRY1 variants have impaired phosphorylation,degradation,and physiological functions,whereasphosphomimeticvariants mimic the physiological functions of phosphorylated CRY1 to constitutively inhibit hypocotyl elongation.We further demonstrate that phosphomimetic CRY1 variants exhibit enhanced interaction with the E3 ubiquitin ligase COP1(CONSTITUTIVELY PHOTOMORPHOGENIC 1).This finding is consistent with the hypothesis that phosphorylation of CRY1 is required for COP1-dependent signaling and regulation of CRY1.We also determine that PHOTOREGULATORY PROTEIN KINASEs(PPKs)phosphorylate CRY1 in a blue light-dependent manner and that this phosphorylation is critical for CRY1 signaling and regulation.These results indicate that,similar to CRY2,blue light-dependent phosphorylation of CRY1 determines its photosensitivity.

关键词： Arabidopsis blue light cryptochrome phosphorylation PPK

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Oxidative phosphorylation safeguards pluripotency via UDP-N-acetylglucosamine

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Protein & Cell 2023年第5期14卷 376-381页

作者： Jiani Cao Meng Li Kun Liu Xingxing Shi Ning Sui Yuchen Yao Xiaojing Wang Shiyu Li Yuchang Tian Shaojing Tan Qian Zhao Liang Wang Xiahua Chai Lin Zhang Chong Liu Xing Li Zhijie Chang Dong Li Tongbiao Zhao State Key Laboratory of Stem Cell and Reproductive Biology Institute for Stem Cell and RegenerationInstitute of ZoologyChinese Academy of SciencesBeijing 100101China State Key Laboratory of Membrane Biology School of MedicineCenter for Synthetic and Systems BiologyTsinghua UniversityBeijing 100084China Beijing Institute for Stem Cell and Regenerative Medicine Beijing 100101China National Laboratory of Biomacromolecules CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China Qufu Normal University Qufu 273165China University of Chinese Academy of Sciences Beijing 100049China

Dear Editor,Embryonic stem cells(ESCs)have been assumed to possess immature mitochondria and to favor anaerobic glycolysis over oxidative phosphorylation(OXPHOS)for energy production.This proposition is largely based on the findings that ESCs possess globular mitochondria with blurred cristae,and the facts that ESCs have higher glycolysis activity and lower mitochondrial respiration capacity than somatic cells(Kondoh et al.,2007;Folmes et al.,2011,2012;Zhang et al.,2012;Xu et al.,2013;Ito and Suda,2014;Gu et al.,2016).However,recent studies have shown that mitochondrial autophagy and mitochondrial dynamics are pivotal for ESC self-renewal and pluripotency(Todd et al.,2010;Liu et al.,2016,2020;Wang et al.,2019;Zhong et al.,2019).These studies have raised a fundamental question:what is the contribution and functional mechanism of mitochondrial respiration in pluripotency regulation?

关键词： Kondo phosphorylation raised

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Dynamic phosphorylation of CENP-N by CDK1 guides accurate chromosome segregation in mitosis

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Journal of Molecular Cell Biology 2023年第6期15卷 53-64页

作者： Ran Liu Zhen Dou Tian Tian Xinjiao Gao Lili Chen Xiao Yuan Chunyue Wang Jiahe Hao Ping Gui McKay Mullen Felix Aikhionbare Liwen Niu Guoqiang Bi Peng Zou Xuan Zhang Chuanhai Fu Xuebiao Yao Jianye Zang Xing Liu MOE Key Laboratory for Cellular Dynamics&Hefei National Research Center for Interdisciplinary Sciences at the Microscale University of Science and Technology of China School of Life SciencesHefei 230026China CAS Center for Excellence in Molecular and Cell Sciences Anhui Key Laboratory for Cellular Dynamics and Chemical BiologyHefei 230027China Keck Center for Cellular Dynamics Morehouse School of MedicineAtlantaGA 30310USA College of Chemistry and Molecular Engineering Peking UniversityBeĳing 100871China

In mitosis,accurate chromosome segregation depends on the kinetochore,a supermolecular machinery that couples dynamic spin-dle microtubules to centromeric chromatin.However,the structure–activity relationship of the constitutive centromere-associated network(CCAN)during mitosis remains uncharacterized.Building on our recent cryo-electron microscopic analyses of human CCAN structure,we investigated how dynamic phosphorylation of human CENP-N regulates accurate chromosome segregation.Our mass spectrometric analyses revealed mitotic phosphorylation of CENP-N by CDK1,which modulates the CENP-L–CENP-N interaction for accurate chromosome segregation and CCAN organization.Perturbation of CENP-N phosphorylation is shown to prevent proper chromosome alignment and activate the spindle assembly checkpoint.These analyses provide mechanistic insight into a previously undefined link between the centromere–kinetochore network and accurate chromosome segregation.

关键词： mitosis centromere CENP-N CDK1 phosphorylation

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Human cytomegalovirus RNA2.7 inhibits RNA polymeraseⅡ(PolⅡ)Serine-2 phosphorylation by reducing the interaction between PolⅡand phosphorylated cyclin-dependent kinase 9(pCDK9)

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Virologica Sinica 2022年第3期37卷 358-369页

作者： Yujing Huang Xin Guo Jing Zhang Jianming Li Mingyi Xu Qing Wang Zhongyang Liu Yanping Ma Ying Qi Qiang Ruan Virology Laboratory Shengjing Hospital of China Medical UniversityShenyang110004China Department of Pediatrics Shengjing Hospital of China Medical UniversityShenyang110004China Department of Obstetrics and Gynecology Shengjing Hospital of China Medical UniversityShenyang110004China Department of Pediatrics The Fourth Affiliated HospitalChina Medical UniversityShenyang110033China

Human cytomegalovirus(HCMV)is a ubiquitous pathogen belongs to betaherpesvirus subfamily.RNA2.7 is a highly conserved long non-coding RNA accounting for more than 20%of total viral transcripts.In our study,functions of HCMV RNA2.7 were investigated by comparison of host cellular transcriptomes between cells infected with HCMV clinical strain and RNA2.7 deleted mutant.It was demonstrated that RNA polymeraseⅡ(PolⅡ)-dependent host gene transcriptions were significantly activated when RNA2.7 was removed during infection.A145 nt-in-length motif within RNA2.7 was identified to inhibit the phosphorylation of PolⅡSerine-2(PolⅡS2)by reducing the interaction between PolⅡand phosphorylated cyclin-dependent kinase 9(pCDK9).Due to the loss of PolⅡS2 phosphorylation,cellular DNA pre-replication complex(pre-RC)factors,including Cdt1 and Cdc6,were significantly decreased,which prevented more cells from entering into S phase and facilitated viral DNA replication.Our results provide new insights of HCMV RNA2.7 functions in regulation of host cellular transcription.

关键词： Human cytomegalovirus(HCMV) RNA2.7 RNA polymeraseⅡ(PolⅡ) Cyclin-dependent kinase 9(CDK9) phosphorylation

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KinasePhos 3.0:Redesign and Expansion of the Prediction on Kinase-specific phosphorylation Sites

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Genomics, Proteomics & Bioinformatics 2023年第1期21卷 228-241页

作者： Renfei Ma Shangfu Li Wenshuo Li Lantian Yao Hsien-Da Huang Tzong-Yi Lee Warshel Institute for Computational Biology School of MedicineThe Chinese University of Hong KongShenzhen 518172China School of Life Sciences University of Science and Technology of ChinaHefei 230027China School of Science and Engineering The Chinese University of Hong KongShenzhen 518172China School of Life and Health Sciences School of MedicineThe Chinese University of Hong KongShenzhen 518172China

The purpose of this work is to enhance KinasePhos,a machine learning-based kinasespecific phosphorylation site prediction tool.Experimentally verified kinase-specific phosphorylation data were collected from PhosphoSitePlus,UniProtKB,the GPS 5.0,and Phospho.ELM.In total,41,421 experimentally verified kinase-specific phosphorylation sites were identified.A total of 1380 unique kinases were identified,including 753 with existing classification information from KinBase and the remaining 627 annotated by building a phylogenetic tree.Based on this kinase classification,a total of 771 predictive models were built at the individual,family,and group levels,using at least 15 experimentally verified substrate sites in positive training datasets.The improved models demonstrated their effectiveness compared with other prediction tools.For example,the prediction of sites phosphorylated by the protein kinase B,casein kinase 2,and protein kinase A families had accuracies of 94.5%,92.5%,and 90.0%,respectively.The average prediction accuracy for all 771 models was 87.2%.For enhancing interpretability,the SHapley Additive exPlanations(SHAP)method was employed to assess feature importance.The web interface of KinasePhos 3.0 has been redesigned to provide comprehensive annotations of kinase-specific phosphorylation sites on multiple proteins.Additionally,considering the large scale of phosphoproteomic data,a downloadable prediction tool is available at https://***/KinasePhos/download.html or https://***/tom-209/KinasePhos-3.0-executable-file.

关键词： Kinase-specific phosphorylation phosphorylation site prediction phosphorylation SHAP feature importance Kinase

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A Review of Machine Learning and Algorithmic Methods for Protein phosphorylation Site Prediction

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Genomics, Proteomics & Bioinformatics 2023年第6期21卷 1266-1285页

作者： Farzaneh Esmaili Mahdi Pourmirzaei Shahin Ramazi Seyedehsamaneh Shojaeilangari Elham Yavari Department of Information Technology Tarbiat Modares UniversityTehran 14115-111Iran Department of Biophysics Faculty of Biological SciencesTarbiat Modares UniversityTehran 14115-111Iran Biomedical Engineering Group Department of Electrical Engineering and Information TechnologyIranian Research Organization for Science and Technology(IROST)Tehran 33535-111Iran

Post-translational modifications(PTMs)have key roles in extending the functional diversity of proteins and,as a result,regulating diverse cellular processes in prokaryotic and eukaryotic organisms.phosphorylation modification is a vital PTM that occurs in most proteins and plays a significant role in many biological processes.Disorders in the phosphorylation process lead to multiple diseases,including neurological disorders and cancers.The purpose of this review is to organize this body of knowledge associated with phosphorylation site(p-site)prediction to facilitate future research in this field.At first,we comprehensively review all related databases and introduce all steps regarding dataset creation,data preprocessing,and method evaluation in p-site prediction.Next,we investigate p-site prediction methods,which are divided into two computational groups:algorithmic and machine learning(ML).Additionally,it is shown that there are basically two main approaches for p-site prediction by ML:conventional and end-to-end deep learning methods,both of which are given an overview.Moreover,this review introduces the most important feature extraction techniques,which have mostly been used in p-site prediction.Finally,we create three test sets from new proteins related to the released version of the database of protein post-translational modifications(dbPTM)in 2022 based on general and human species.Evaluating online p-site prediction tools on newly added proteins introduced in the dbPTM 2022 release,distinct from those in the dbPTM 2019 release,reveals their limitations.In other words,the actual performance of these online p-site prediction tools on unseen proteins is notably lower than the results reported in their respective research pape.

关键词： phosphorylation Machinelearning Deep learning Post-translational modification Database

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B-lymphoid tyrosine kinase-mediated FAM83A phosphorylation elevates pancreatic tumorigenesis through interacting with β-catenin

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Signal Transduction and Targeted Therapy 2023年第3期8卷 1251-1268页

作者： Cefan Zhou Xiaoting Zhu Nanxi Liu Xueying Dong Xuewen Zhang Huili Huang Yu Tang Shicheng Liu Mengyu Hu Ming Wang Xiaoling Deng Shi Li Rui Zhang Yuan Huang Hao Lyu Shuai Xiao Sang Luo Declan William Ali Marek Michalak Xing-Zhen Chen Zhentian Wang Jingfeng Tang National“111”Center for Cellular Regulation and Molecular Pharmaceutics Key Laboratory of Fermentation Engineering(Ministry of Education)Hubei University of TechnologyWuhan 430068China Membrane Protein Disease Research Group Department of PhysiologyFaculty of Medicine and DentistryUniversity of AlbertaEdmontonAB T6G2R3Canada Cooperative Innovation Center of Industrial Fermentation(Ministry of Education&Hubei Province) Hubei Key Laboratory of Industrial MicrobiologyHubei University of TechnologyWuhanChina Department of Systems Biology for Medicine School of Basic Medical SciencesFudan Universityand Shanghai Fifth People’s HospitalFudan UniversityShanghai 200433China Department of Clinical Laboratory Renmin Hospital of Wuhan UniversityWuhan 430060China Ningxia Key Laboratory of Stem Cell and Regenerative Medicine General Hospital of Ningxia Medical UniversityNingxia 750001China Department of Biological Sciences University of AlbertaEdmontonAB T6G2R3Canada Department of Biochemistry University of AlbertaEdmontonAB T6G2R3Canada

Abnormal activation of Wnt/β-catenin-mediated transcription is closely associated with the malignancy of pancreatic cancer.Family with sequence similarity 83 member A(FAM83A)was shown recently to have oncogenic effects in a variety of cancer types,but the biological roles and molecular mechanisms of FAM83A in pancreatic cancer need further investigation.Here,we newly discovered that FAM83A binds directly toβ-catenin and inhibits the assembly of the cytoplasmic destruction complex thus inhibiting the subsequent phosphorylation and degradation.FAM83A is mainly phosphorylated by the SRC non-receptor kinase family member BLK(B-lymphoid tyrosine kinase)at tyrosine 138 residue within the DUF1669 domain that mediates the FAM83A-β-catenin interaction.Moreover,FAM83A tyrosine 138 phosphorylation enhances oncogenic Wnt/β-catenin-mediated transcription through promotingβ-catenin-TCF4 interaction and showed an elevated nucleus translocation,which inhibits the recruitment of histone deacetylases by TCF4.We also showed that FAM83A is a direct downstream target of Wnt/β-catenin signaling and correlates with the levels of Wnt target genes in human clinical pancreatic cancer tissues.Notably,the inhibitory peptides that target the FAM83A-β-catenin interaction significantly suppressed pancreatic cancer growth and metastasis in vitro and in vivo.Our results revealed that blocking the FAM83A cascade signaling defines a therapeutic target in human pancreatic cancer.

关键词： FAM83A elevated phosphorylation

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Distinctive phosphorylation pattern during mitotic exit network(MEN)regulation is important for the development and pathogenicity of Magnaporthe oryzae

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Stress Biology 2022年第1期2卷 182-192页

作者： Wanzhen Feng Jiansheng Wang Xinyu Liu Haowen Wu Muxing Liu Haifeng Zhang Xiaobo Zheng Ping Wang Zhengguang Zhang Department of Plant Pathology College of Plant ProtectionNanjing Agricultural Universityand Key Laboratory of Integrated Management of Crop Diseases and PestsMinistry of EducationNanjing 210095China The Key Laboratory of Plant Immunity Nanjing Agricultural UniversityNanjing 210095China Plant Protection and Quarantine Station of Nanjing Nanjing 210095China Departments of Microbiology Immunologyand Parasitologyand PediatricsLouisiana State University Health Sciences CenterNew OrleansLouisiana 70112USA

The mitotic exit network(MEN)pathway is a vital kinase cascade regulating the timely and correct progress of cell division.In the rice blast fungus Magnaporthe oryzae,the MEN pathway,consisting of conserved protein kinases MoSep1 and MoMob1-MoDbf2,is important in the development and pathogenicity of the fungus.We found that deletion of MoSEP1 affects the phosphorylation of MoMob1,but not MoDbf2,in contrast to what was found in the buddy yeast Saccharomyces cerevisiae,and verified this finding by in vitro phosphorylation assay and mass spectrom-etry(MS)analysis.We also found that S43 residue is the critical phosphor-site of MoMob1 by MoSep1,and proved that MoSep1-dependent MoMob1 phosphorylation is essential for cell division during the development of M.oryzae.We further provided evidence demonstrating that MoSep1 phosphorylates MoMob1 to maintain the cell cycle during vegetative growth and infection.Taken together,our results revealed that the MEN pathway has both distinct and conservative functions in regulating the cell cycle during the development and pathogenesis of M.oryzae.

关键词： Mitotic exit network(MEN) phosphorylation Pathogenicity Rice blast

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The removal of nitrate reductase phosphorylation enhances tolerance to ammonium nitrogen deficiency in rice

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Journal of Integrative Agriculture 2022年第3期21卷 631-643页

作者： HAN Rui-cai XU Zhi-rong LI Chen-yan Adnan RASHEED PAN Xiao-hua SHI Qing-hua WU Zi-ming Key Laboratory of Crop Physiology Ecology and Genetic BreedingMinistry of Education/College of AgronomyJiangxi Agricultural UniversityNanchang 330045P.R.China Rice Research Institute Jiangxi Academyof Agricultural Sciences/Jiangxi Provincial Key Laboratory for Physiology and Genetics of RiceNanchang 330200P.R.China

Nitrate reductase(NR) is a key enzyme for nitrogen assimilation in plants,and its activity is regulated by posttranslational phosphorylation.To investigate the effects of dephosphorylation of the NIA1 protein on the growth and the physiological and biochemical characteristics of rice under different forms of nitrogen supplies,the phenotypes,nitrogen metabolism and reactive oxygen metabolism were measured in NIA1 phosphorylation site-directed mutant lines(S532 D and S532 A),an Os Nia1 over-expression line(OE) and Kitaake(wild type,WT).Compared with WT and OE,S532 D and S532 A have stronger nitrogen assimilation capacities.When ammonium nitrate served as the nitrogen source,the plant heights,dry weights of shoots and chlorophyll(Chl) contents of S532 D and S532 A were lower than those of the WT and OE,whereas hydrogen peroxide(H_(2)O_(2)),malondialdehyde(MDA) and nitrite contents were higher.When potassium nitrate served as the nitrogen source,the plant heights,dry weights of shoots and Chl contents of S532 D and S532 A were higher than those of the WT and OE,there were no significant differences in the contents of H_(2)O_(2) and MDA in the leaves of the test materials,and the difference in nitrite contents among different lines decreased.When ammonium sulfate served as the nitrogen source,there were no significant differences in the physiological indexes of the test materials,except NR activity.Compared with ammonium nitrate and ammonium sulfate,the content of NH_(4)^(+)-N in the leaves of each plant was lower when potassium nitrate was used as the nitrogen source.The q PCR results showed that Os GS and Os NGS1 were negatively regulated by downstream metabolites,and Os Nrt2.2 was induced by nitrate.In summary,when ammonium nitrate served as the nitrogen source,the weak growth of NIA1 phosphorylation site-directed mutant lines was due to the toxicity caused by the excessive accumulation of nitrite.When potassium nitrate served as the nitrogen source,the assimilation rates of nitrate,nitrite and ammonium salt were a

关键词： Oryza sativa L. nitrate reductase phosphorylation NR activity nitrogen utilization nitrite

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