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Identification,evolution,expression and protein interaction analysis of genes encoding B-box zinc-finger proteins in maize

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Journal of Integrative Agriculture 2023年第2期22卷 371-388页

作者： XU Xiao-hui LI Wen-lan YANG Shu-ke ZHU Xiang-zhen SUN Hong-wei LI Fan LU Xing-bo CUI Jin-jie Shandong Key Laboratory of Plant Virology/Institute of Plant Protection Shandong Academy of Agricultural SciencesJinan 250100P.R.China State Key Laboratory of Cotton Biology/Institute of Cotton Research Chinese Academy of Agricultural SciencesAnyang 455000P.R.China Maize Research Institute Shandong Academy of Agricultural SciencesJinan 250100P.R.China

The B-box(BBX)family of proteins consists of zinc-finger transcription factors with one or two highly conserved B-box motifs at their *** proteins play crucial roles in various aspects of plant growth and development,including seedling photomorphogenesis,shade avoidance,flowering time,and biotic and abiotic stress *** studies have identified many different BBXs from several plant species,although the BBX family members in maize are largely ***-wide identification and comprehensive analysis of maize BBX(ZmBBX)expression and interaction networks would therefore provide valuable information for understanding their *** this study,36 maize BBXs in three major clades were *** ZmBBXs within a given clade were found to share similar domains,motifs,and genomic *** duplication analyses revealed that the expansion of BBX proteins in maize has mainly occurred by segmental *** expression levels of ZmBBXs were analyzed in various organs and tissues,and under different abiotic stress ***–protein interaction networks of ZmBBXs were established using bioinformatic tools and verified by bimolecular fluorescence complementation(BiFC)*** findings can facilitate a greater understanding of the complexity of the ZmBBX family and provide novel clues for unravelling ZmBBX protein functions.

关键词： maize B-box family protein evolution expression protein interaction

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Selective recognition of PTRE1 transcripts mediated by protein-protein interaction between the m^(6)A reader ECT2 and PTRE1

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Plant Communications 2024年第11期5卷 144-156页

作者： Li Yang Bo Wang Duanmu Zhao Xuechun Li Yifei Qin Ning Ouyang Zhili Xiao Zhibing Zhang Gad Galili Jiayang Li Hadas Peled-Zehavi Jian Wu Guangdong Laboratory for Lingnan Modern Agriculture State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesKey Laboratory of Plant Molecular Breeding of Guangdong ProvinceCollege of AgricultureSouth China Agricultural UniversityGuangzhou 510642China Key Laboratory of Molecular Epigenetics of the Ministry of Education(MOE) Northeast Normal UniversityChangchun 130024China Department of Plant and Environmental Sciences Weizmann Institute of ScienceRehovot 76100Israel State Key Laboratory of Plant Genomics and National Center for Plant Gene Research Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China These authors contributed equally to this article

N^(6)-methyladenosine (m^(6)A) is a prevalent internal post-transcriptional modification in eukaryotic RNAs executed by m^(6)A-binding proteins known as “readers.” Our previous research demonstrated that the Arabidopsis m^(6)A reader ECT2 positively regulates transcript levels of the proteasome regulator PTRE1 and several 20S proteasome subunits, thereby enhancing 26S proteasome activity. However, mechanism underlying the selective recognition of m^(6)A targets by readers, such as ECT2, remains elusive. In this study, we further demonstrate that ECT2 physically interacts with PTRE1 and several 20S proteasome subunits. This interaction, which occurs on the ribosome, involves the N terminus of PTRE1, suggesting that ECT2 might bind to the nascent PTRE1 polypeptide. Deleting ECT2’s protein interaction domain impairs its mRNA-binding ability, whereas mutations in the m^(6)A-RNA-binding site do not affect protein-protein interactions. Moreover, introducing a novel protein-binding domain into ECT2 increases transcript levels of proteins interacting with this domain. Our findings indicate that interaction with the PTRE1 protein enhances ECT2’s binding to PTRE1 m^(6)A mRNAs during translation, thereby regulating PTRE1 mRNA levels.

关键词： ECT2 20S proteasome m^(6)A RNA protein interaction Arabidopsis

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Expression, subcellular localization and protein-protein interaction of four isoforms of EcR/USP in the common cutworm

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Insect Science 2015年第1期22卷 95-105页

作者： Li-Xia Huang Yan-Jun Gong Jun Gu Bao-Juan Zeng Li-Hua Huang Qi-Li Feng Laboratory of Molecular and Developmental Entomology Guangdong Provincial Key Laboratory of Biotechnology for Plant DevelopmentSchool of Life Sciences South China Normal University Guangzhou China

Ecdysone receptor （EcR） and ultraspiracle （USP） form heterodimers to mediate ecdysteroid signaling during molting and metamorphosis. Various EcR/USP heterodimers have been reported. However, it is unclear what kind of EcR/USP combination is adopted by lepidopteran insects during the larval-pupal metamorphosis and whether the EcR/USP heterodimer varies among different tissues. To address these questions, two isoforms of each EcR and USP were cloned from the common cutworm, their messenger RNA expression patterns were examined by real-time quantitative polymerase chain reaction in different tissues during the larval-pupal metamorphosis and in the midgut in response to hormonal induction. Furthermore, their subcellular localization and protein-protein interaction were explored by transient expression and far-western blotting, respectively. All the four genes were significantly up-regulated in prepuae and/or pupae. The expression profiles of EcRB1 and USP1 were nearly identical to each other in the epidermis, fat body and midgut, and a similar situation also applied to EcRA and USP2. The three genes responded to 20-hydroxyecdysone （20E） induction except for USP2, and USP1 could be up-regulated by both 20E and juvenile hormone. The four proteins mainly localized in the nucleus and the nuclear localization was promoted by 20E. The protein-protein interaction between each EcR and USP was found in vitro. These results suggest that two types of EcR/USP heterodimer （EeRA/USP2 and EcRB 1/USP1） may exist simultaneously in the common cutworm, and the latter should play more important roles during the larval-pupal metamorphosis. In addition, the types of EcR/USP heterodimer do not vary in the tissues which undergo histolysis and regeneration during metamorphosis.

关键词： ecdysone receptor protein interaction subcellular localization ultraspiracle

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protein interaction Between p53 and △113p53 Is Required for the Anti-Apoptotic Function of △113p53

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Journal of Genetics and Genomics 2014年第2期41卷 53-62页

作者： Zhao Ou Le Yin Changqing Chang Jinrong Peng Jun Chen College of Life Sciences Zhejiang University College of Natural Resources and Environment South China Agricultural University College of Animal Sciences Zhejiang University

Zebrafish △113p53, an N-terminal truncated p53 isoform, is a p53-target gene that antagonises p53-mediated apoptotic activity. Interestingly, △113p53 does not act on p53 in a dominant-negative manner, but rather interferes with the p53 function by differentially modulating p53-target gene expression to protect cells from apoptosis. Previous studies showed that over-expressed △113p53 and p53 proteins formed a complex. However, it is not known whether endogenous p53 and △113p53 proteins also interact with each other, and if this interaction is required for △113p53 to inhibit the apoptotic activity of full-length p53. In this study, we used two available zebrafish p53 antibodies to address these questions. One, Zfp53-N, only recognises full-length p53, whereas the other, Zfp53-A7C10, detects both full-length p53 and △113p53. Using Zfp53-N for immunoprecipitation and Zfp53-A7C 10 for detection, we demonstrated that endogenous △113p53 and full-length p53 induced by a DNA-damaging drug formed a complex in vivo. Furthermore, of the six △113p53 mutants we generated with different point mutations in the oligomerisation domain, two failed to interact with p53 and lost the ability to modulate p53-target gene expression and inhibit p53-induced cell apoptosis. However, those △113p53 mutants that could interact with p53 retained the ability to antagonise the apoptotic activity of p53. Therefore, our data demonstrated that protein--protein interaction between △113p53 and p53 is essential for the anti-apoptotic function of △113p53. In addition, the two △113p53 mutants that failed to interact with p53 are also useful for the study of the mechanisms of other functions of △113p53.

关键词： p53 △113p53 protein interaction Apoptosis Zebrafish

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Co-immunoprecipitation for identifying protein–protein interaction on lipid droplets

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Biophysics Reports 2024年第2期10卷 102-110页

作者： Xiaochuan Fu Shuyan Zhang Pingsheng Liu Institute of Biophysics Chinese Academy of Sciences University of Chinese Academy of Sciences Institute of Infectious Diseases Beijing Key Laboratory of Emerging Infectious Diseases Beijing Ditan HospitalCapital Medical University Beijing Institute of Infectious Diseases

The lipid droplet(LD) is a conserved organelle that exists in almost all organisms, ranging from bacteria to mammals. Dysfunctions in LDs are linked to a range of human metabolic syndromes. The formation of protein complexes on LDs is crucial for maintaining their function. Investigating how proteins interact on LDs is essential for understanding the role of LDs. We have developed an effective method to uncover protein–protein interactions and protein complexes specifically on LDs. In this method, we conduct co-immunoprecipitation(co-IP) experiments using LD proteins extracted directly from isolated LDs, rather than utilizing proteins from cell lysates. To elaborate, we begin by purifying LDs with high-quality and extracting LD-associated proteins. Subsequently, the co-IP experiment is performed on these LD-associated proteins directly, which would enhance the co-IP experiment specificity of LDassociated proteins. This method enables researchers to directly unveil protein complexes on LDs and gain deeper insights into the functional roles of proteins associated with LDs.

关键词： Co-immunoprecipitation Lipid droplet protein interaction

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interaction of Hsp40 with influenza virus M2 protein: implications for PKR signaling pathway

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protein & Cell 2010年第10期1卷 944-955页

作者： Zhenhong Guan Di Liu Shuofu Mi Jie Zhang Qinong Ye Ming Wang George F.Gao Jinghua Yan College of Veterinary Medicine China Agricultural UniversityBeijing 100094China CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Beijing Institute of Biotechnology Beijing 100850China Beijing Institutes of Life Science Chinese Academy of SciencesBeijing 100101China

Influenza virus contains three integral membrane proteins:haemagglutinin,neuraminidase,and matrix protein(M1 and M2).Among them,M2 protein functions as an ion channel,important for virus uncoating in endosomes of virus-infected cells and essential for virus *** an effort to explore potential new functions of M2 in the virus life cycle,we used yeast two-hybrid system to search for M2-associated cellular *** of the positive clones was identified as human Hsp40/Hdj1,a DnaJ/Hsp40 family ***,we report that both BM2(M2 of influenza B virus)and A/M2(M2 of influenza A virus)interacted with Hsp40 in vitro and in *** region of M2-Hsp40 interaction has been mapped to the CTD1 domain of ***40 has been reported to be a regulator of PKR signaling pathway by interacting with p58^(IPK) that is a cellular inhibitor of *** is a crucial component of the host defense response against virus *** therefore attempted to understand the relationship among M2,Hsp40 and p58^(IPK) by further *** results demonstrated that both A/M2 and BM2 are able to bind to p58^(IPK)in vitro and in vivo and enhance PKR autophosphorylation probably via forming a stable complex with Hsp40 and P58^(IPK),and consequently induce cell *** results suggest that influenza virus M2 protein is involved in p58^(IPK)mediated PKR regulation during influenza virus infection,therefore affecting infected-cell life cycle and virus replication.

关键词： M2 protein of influenza virus Hsp40 P58^(IPK) protein interaction PKR signal pathway

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Parameter selection of pocket extraction algorithm using interaction interface

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Journal of Zhejiang University-Science A(Applied Physics & Engineering) 2006年第9期7卷 1492-1499页

作者： KIM Chong-Min WON Chung-In RYU Joonghyun CHO Cheol-Hyung BHAK Jonghwa KIM Deok-Soo Department of Industrial Engineering Hanyang University Seoul 133-791 Korea Voronoi Diagram Research Center Hanyang University Seoul 133-791 Korea Samsung Electronics Suwon Gyeonggi-do 443-742 Korea Korean Bioinformation Center Korea Research Institute of Bioscience and Biotechnology Daejeon 305-806 Korea Department of Industrial Engineering Hanyang University Seoul 133-791 Korea)

Pockets in proteins have been known to be very important for the life process. There have been several studies in the past to automatically extract the pockets from the structure information of known proteins. However, it is difficult to find a study comparing the precision of the extracted pockets from known pockets on the protein. In this paper, we propose an algorithm for extracting pockets from structure data of proteins and analyze the quality of the algorithm by comparing the extracted pockets with some known pockets. These results in this paper can be used to set the parameter values of the pocket extraction algorithm for getting better results.

关键词： Pocket protein interaction interface protein interaction Voronoi diagram

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interaction of brassinosteroid and cytokinin promotes ovule initiation and increases seed number per silique in Arabidopsis

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Journal of Integrative Plant Biology 2022年第3期64卷 702-716页

作者： Song-Hao Zu Yu-Tong Jiang Jin-Hui Chang Yan-Jie Zhang Hong-Wei Xue Wen-Hui Lin School of Life Sciences and Biotechnology The Joint International Research Laboratory of Metabolic and Developmental SciencesJoint Center for Single Cell BiologyShanghai Jiao Tong UniversityShanghai 200240China School of Agriculture and Biology Joint Center for Single Cell BiologyShanghai Jiao Tong UniversityShanghai 200240China

Ovule initiation is a key step that strongly influences ovule number and seed ***,mutants with enhanced brassinosteroid(BR)and cytokinin(CK)signaling produce more ovules and have a higher seed number per silique(SNS)than wild-type ***,we crossed BR-and CKrelated mutants to test whether these phytohormones function together in ovule *** determined that simultaneously enhancing BR and CK contents led to higher ovule and seed numbers than enhancing BR or CK separately,and BR and CK enhanced each ***,the BR-response transcription factor BZR1 directly interacted with the CK-response transcription factor ARABIDOPSIS RESPONSE REGULATOR1(ARR1).Treatments with BR or BR plus CK strengthened this interaction and subsequent ARR1 targeting and induction of downstream genes to promote ovule *** CK signaling partially rescued the reduced SNS phenotype of BR-deficient/insensitive mutants whereas enhanced BR signaling failed to rescue the low SNS of CK-deficient mutants,suggesting that BR regulates ovule initiation and SNS through CK-mediated and-independent *** study thus reveals that interaction between BR and CK promotes ovule initiation and increases seed number,providing important clues for increasing the seed yield of dicot crops.

关键词： brassinosteroid cytokinin ovule initiation protein interaction seed number per silique

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A Cross-Domain Ontology Semantic Representation Based on NCBI-BlueBERT Embedding

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Chinese Journal of Electronics 2022年第5期31卷 860-869页

作者： ZHAO Lingling WANG Junjie WANG Chunyu GUO Maozu Faculty of Computing Harbin Institute of Technology Department of Medical Informatics School of Biomedical Engineering and InformaticsNanjing Medical University Beijing Key Laboratory of Intelligent Processing for Building Big Data School of Electrical and Information Engineering Beijing University of Civil Engineering and Architecture

A common but critical task in biological ontologies data analysis is to compare the difference between ontologies. There have been numerous ontologybased semantic-similarity measures proposed in specific ontology domain, but it still remains a challenge for crossdomain ontologies comparison. An ontology contains the scientific natural language description for the corresponding biological aspect. Therefore, we develop a new method based on natural language processing(NLP) representation model bidirectional encoder representations from transformers(BERT) for cross-domain semantic representation of biological ontologies. This article uses the BERT model to represent the word-level of the ontologies as a set of vectors, facilitating the semantic analysis or comparing the biomedical entities named in an ontology or associated with ontology terms. We evaluated the ability of our method in two experiments: calculating similarities of pair-wise disease ontology and human phenotype ontology terms and predicting the pair-wise of proteins interaction. The experimental results demonstrated the comparative performance. This gives promise to the development of NLP methods in biological data analysis.

关键词： human phenotype ontology cross-domain semantic representation natural language description pair-wise disease ontology data analysis bidirectional encoder representations NLP protein interaction diseases proteins natural language processing ontologies (artificial intelligence) natural language processing representation neural nets bioinformatics semantic-similarity measures cross-domain ontology semantic representation semantic analysis NCBI-BlueBERT embedding biological ontology data analysis

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Engineered polymer nanoparticles incorporating L-amino acid groups as affinity reagents for fibrinogen

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Journal of Pharmaceutical Analysis 2021年第5期11卷 596-602页

作者： Yongyan Zhu Ruixuan Liu Dengyu Wu Qianqian Yu Kenneth J.Shea Quanhong Zhu School of Traditional Chinese Medicine Southern Medical UniversityGuangzhou510515China Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics Guangzhou510515China Guangdong Provincial Engineering Laboratory of Chinese Medicine Preparation Technology Guangzhou510515China Department of Chemistry University of CaliforniaIrvineCA92697USA

Synthetic polymer hydrogel nanoparticles(NPs)were developed to function as abiotic affinity reagents for *** NPs were made using both temperature-sensitive N-isopropyl acrylamide(NIPAm)and L-amino acid *** kinds of L-amino acids were acryloylated to obtain functional monomers:L-phenylalanine(Phe)and L-leucine(Leu)with hydrophobic side chains,L-glutamic acid(Glu)with negative charges,and L-lysine(Lys)and L-arginine(Arg)with positive *** incubating the NPs with fibrinogen,g-globulin,and human serum albumin(HSA)respectively,the NPs that incorporated Nacryloyl-Arg monomers(AArg@NPs)showed the strongest and most specific binding affinity to fibrinogen,when compared with g-globulin and ***,the fibrinogen-AArg binding model had the best docking scores,and this may be due to the interaction of positively charged AArg@NPs and the negatively charged fibrinogen D domain and the hydrophobic interaction between *** specific adsorption of AArg@NPs to fibrinogen was also confirmed by the immunoprecipitation assay,as the AArg@NPs selectively trapped the fibrinogen from a human plasma protein ***@NPs had a strong selectivity for,and specificity to,fibrinogen and may be developed as a potential human fibrinogen-specific affinity reagent.

关键词： Synthetic polymer nanoparticles Amino-acid monomers Arginine Fibrinogen Affinity reagent protein interaction

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