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Systems understanding of plant-pathogen interactions through genome-wide protein-protein interaction networks

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Frontiers of Agricultural Science and Engineering 2016年第2期3卷 102-112页

作者： Hong LI Ziding ZHANG State Key Laboratory of Agrobiotechnology College of Biological SciencesChina Agricultural University

Plants are frequently affected by pathogen infections.To effectively defend against such infections,two major modes of innate immunity have evolved in plants;pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity.Although the molecular components as well as the corresponding pathways involved in these two processes have been identified,many aspects of the molecular mechanisms of the plant immune system remain elusive.Recently,the rapid development of omics techniques(e.g.,genomics,proteomics and transcriptomics) has provided a great opportunity to explore plant–pathogen interactions from a systems perspective and studies on protein–protein interactions(PPIs) between plants and pathogens have been carried out and characterized at the network level.In this review,we introduce experimental and computational identification methods of PPIs,popular PPI network analysis approaches,and existing bioinformatics resources/tools related to PPIs.Then,we focus on reviewing the progress in genome-wide PPI networks related to plant–pathogen interactions,including pathogen-centric PPI networks,plant-centric PPI networks and interspecies PPI networks between plants and pathogens.We anticipate genome-wide PPI network analysis will provide a clearer understanding of plant–pathogen interactions and will offer some new opportunities for crop protection and improvement.

关键词： plant–pathogen interactions systems biology omics plant immunity protein–protein interaction network

A Yeast BiFC-seq Method for Genome-wide Interactome Mapping

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Genomics, Proteomics & Bioinformatics 2022年第4期20卷 795-807页

作者： Limin Shang Yuehui Zhang Yuchen Liu Chaozhi Jin Yanzhi Yuan Chunyan Tian Ming Ni Xiaochen Bo Li Zhang Dong Li Fuchu He Jian Wang State Key Laboratory of Proteomics Beijing Proteome Research CenterNational Center for Protein Sciences(Beijing)Beijing Institute of LifeomicsBeijing 102206China Department of Biotechnology Beijing Institute of Radiation MedicineBeijing 100850China Department of Rehabilitation Medicine Nan LouKey Laboratory of Wound Repair and Regeneration of PLACollege of Life SciencesChinese PLA General HospitalBeijing 100853China School of Basic Medical Sciences Anhui Medical UniversityHefei 230032China

Genome-wide physical protein±protein interaction(PPI)mapping remains a major challenge for current technologies.Here,we reported a high-efficiency BiFC-seq method,yeastenhanced green fluorescent protein-based bimolecular fluorescence complementation(y EGFPBiFC)coupled with next-generation DNA sequencing,for interactome mapping.We first applied y EGFP-BiFC method to systematically investigate an intraviral network of the Ebola virus.Two-thirds(9/14)of known interactions of EBOV were recaptured,and five novel interactions were discovered.Next,we used the BiFC-seq method to map the interactome of the tumor protein p53.We identified 97 interactors of p53,more than three-quarters of which were novel.Furthermore,in a more complex background,we screened potential interactors by pooling two BiFC libraries together and revealed a network of 229 interactions among 205 proteins.These results show that BiFC-seq is a highly sensitive,rapid,and economical method for genome-wide interactome mapping.

关键词： Bimolecular fluorescence complementation protein–protein interaction High-throughput Next-generation sequencing

Newfound Coding Potential of Transcripts Unveils Missing Members of Human protein Communities

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Genomics, Proteomics & Bioinformatics 2023年第3期21卷 515-534页

作者： Se´bastien Leblanc Marie *** Jean-Franc¸ois Jacques Amina M.Lekehal Andre´a Duclos Alexia Tremblay Alexis Bruggeman-Gascon Sondos Samandi Myle`ne Brunelle Alan A.Cohen Michelle S.Scott Xavier Roucou Department of Biochemistry and Functional Genomics Universite´de SherbrookeSherbrookeQC J1E 4K8Canada PROTEO Quebec Network for Research on Protein FunctionStructureand EngineeringQuebec CityQC G1V 0A6Canada Department of Family Medicine Universite´de SherbrookeSherbrookeQC J1H 5N4Canada

Recent proteogenomic approaches have led to the discovery that regions of the transcriptome previously annotated as non-coding regions[i.e.,untranslated regions(UTRs),open reading frames overlapping annotated coding sequences in a different reading frame,and non-coding RNAs]frequently encode proteins,termed alternative proteins(altProts).This suggests that previously identified protein–protein interaction(PPI)networks are partially incomplete because altProts are not present in conventional protein databases.Here,we used the proteogenomic resource OpenProt and a combined spectrum-and peptide-centric analysis for the re-analysis of a highthroughput human network proteomics dataset,thereby revealing the presence of 261 altProts in the network.We found 19 genes encoding both an annotated(reference)and an alternative protein interacting with each other.Of the 117 altProts encoded by pseudogenes,38 are direct interactors of reference proteins encoded by their respective parental genes.Finally,we experimentally validate several interactions involving altProts.These data improve the blueprints of the human PPI network and suggest functional roles for hundreds of altProts.

关键词： Alternative protein protein network protein–protein interaction Pseudogene Affinity purification mass spectrometry

Global Landscape of Native protein Complexes in Synechocystis sp.PCC 6803

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Genomics, Proteomics & Bioinformatics 2022年第4期20卷 715-727页

作者： Chen Xu Bing Wang Lin Yang Lucas Zhongming Hu Lanxing Yi Yaxuan Wang Shenglan Chen Andrew Emili Cuihong Wan School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology Central China Normal UniversityWuhan 430079China Donnelly Centre for Cellular and Biomolecular Research University of TorontoTorontoON M5S 2E8Canada Departments of Biochemistry and Biology Boston UniversityBostonMA 02215USA

Synechocystis sp.PCC 6803(hereafter:Synechocystis)is a model organism for studying photosynthesis,energy metabolism,and environmental stress.Although known as the first fully sequenced phototrophic organism,Synechocystis still has almost half of its proteome without functional annotations.In this study,by using co-fractionation coupled with liquid chromatographytandem mass spectrometry(LC-MS/MS),we define 291 multi-protein complexes,encompassing24,092 protein±protein interactions(PPIs)among 2062 distinct gene products.This information not only reveals the roles of photosynthesis in metabolism,cell motility,DNA repair,cell division,and other physiological processes,but also shows how protein functions vary from bacteria to higher plants due to changes in interaction partners.It also allows us to uncover the functions of hypothetical proteins,such as Sll0445,Sll0446,and Sll0447 involved in photosynthesis and cell motility,and Sll1334 involved in regulation of fatty acid biogenesis.Here we present the most extensive PPI data for Synechocystis so far,which provide critical insights into fundamental molecular mechanisms in cyanobacteria.

关键词： protein–protein interaction Cyanobacterium Co-fractionation Photosynthesis Function prediction

Molecular glues modulate protein functions by inducing protein aggregation:A promising therapeutic strategy of small molecules for disease treatment

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Acta Pharmaceutica Sinica B 2022年第9期12卷 3548-3566页

作者： Hongyu Wu Hong Yao Chen He Yilin Jia Zheying Zhu Shengtao Xu Dahong Li Jinyi Xu State Key Laboratory of Natural Medicines Department of Medicinal ChemistryChina Pharmaceutical UniversityNanjing 210009China Division of Molecular Therapeutics&Formulation School of Pharmacythe University of NottinghamUniversity Park CampusNottingham NG72RDUK Key Laboratory of Structure-Based Drug Design&Discovery Ministry of EducationSchool of Traditional Chinese Materia MedicaShenyang Pharmaceutical UniversityShenyang 110016China

Molecular glues can specifically induce aggregation between two or more proteins to modulate biological functions.In recent years,molecular glues have been widely used as protein degraders.In addition,however,molecular glues play a variety of vital roles,such as complex stabilization,interactome modulation and transporter inhibition,enabling challenging therapeutic targets to be druggable and offering an exciting novel approach for drug discovery.Since most molecular glues are identified serendipitously,exploration of their systematic discovery and rational design are important.In this review,representative examples of molecular glues with various physiological functions are divided into those mediating homo-dimerization,homo-polymerization and hetero-dimerization according to their aggregation modes,and we attempt to elucidate their mechanisms of action.In particular,we aim to highlight some biochemical techniques typically exploited within these representative studies and classify them in terms of three stages of molecular glue development:starting point,optimization and identification.

关键词： Small molecule Molecular glue Dimerization Polymerization protein–protein interaction

NSD3S stabilizes MYC through hindering its interaction with FBXW7

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Journal of Molecular Cell Biology 2020年第6期12卷 438-447页

作者： Valentina Gonzalez-Pecchi Albert KKwan Sean Doyle Andrey AIvanov Yuhong Du Haian Fu Graduate Program in Cancer Biology Emory UniversityAtlantaGAUSA Department of Pharmacology and Chemical Biology Emory Chemical Biology Discovery CenterEmory UniversityAtlantaGAUSA Winship Cancer Institute Emory UniversityAtlantaGAUSA Department of Hematology&Medical Oncology Emory UniversityAtlantaGAUSA

The MYC transcription factor plays a key role in cell growth control. Enhanced MYC protein stability has been found to promote tumorigenesis. Thus, understanding how MYC stability is controlled may have significant implications for revealing MYC-driven growth regulatory mechanisms in physiological and pathological processes. Our previous work identified the histone lysine methyltransferase nuclear receptor binding SET domain protein 3 (NSD3) as a MYC modulator. NSD3S, a noncatalytic isoform of NSD3 with oncogenic activity, appears to bind, stabilize, and activate the transcriptional activity of MYC. However, the mechanism by which NSD3S stabilizes MYC remains to be elucidated. To uncover the nature of the interaction and the underlying mechanism of MYC regulation by NSD3S, we characterized the binding interface between both proteins by narrowing the interface to a 15-amino acid region in NSD3S that is partially required for MYC regulation. Mechanistically, NSD3S binds to MYC and reduces the association of F-box and WD repeat domain containing 7 (FBXW7) with MYC, which results in suppression of FBXW7-mediated proteasomal degradation of MYC and an increase in MYC protein half-life. These results support a critical role for NSD3S in the regulation of MYC function and provide a novel mechanism for NSD3S oncogenic function through inhibition of FBXW7-mediated degradation of MYC.

关键词： cancer FBXW7 MYC NSD3S protein–protein interaction

Second-generation DNA-encoded multiple display on a constant macrocyclic scaffold enabled by an orthogonal protecting group strategy

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Chinese Chemical Letters 2022年第5期33卷 2559-2563页

作者： Qigui Nie Shuting Zhong Yangfeng Li Gong Zhang Yizhou Li Chongqing Key Laboratory of Natural Product Synthesis and Drug Research School of Pharmaceutical SciencesChongqing UniversityChongqing 401331China Key Laboratory of Biorheological Science and Technology Ministry of EducationCollege of BioengineeringChongqing UniversityChongqing 401331China

DNA-encoded chemical library(DEL)represents an emerging drug discovery technology to construct com-pound libraries with abundant chemical combinations.While drug-like small molecule DELs facilitate the discovery of binders against targets with defined pockets,macrocyclic DELs harboring extended scaffolds enable targeting of the protein–protein interaction(PPI)interface.We previously demonstrated the design of the first-generation DNA-encoded multiple display based on a constant macrocyclic scaffold,which harvested binders against difficult targets such as tumor necrosis factor-α(TNF-α).Here,we developed a novel strategy which utilized four orthogonal amine-protecting groups on DNA,to explore larger chem-ical combinations on the same constant macrocyclic scaffold,following the parallel paradigm to mimic the versatile antibody-like multivalent epitope recognition patterns.We successfully integrated these or-thogonal protecting groups with acylation and made a mock second-generation DNA-encoded display combination.This work illustrates a strategy to produce larger encoded multiple display on a constant macrocyclic scaffold,which could facilitate potential binder discovery with enhanced affinity to clinically significant PPI targets.

关键词： DNA-encoded library Macrocyclic scaffold DNA-compatible protein–protein interaction Chemical probe

An Integrated Systems Biology Approach Identifies ZIKV and DENV Replication

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Genomics, Proteomics & Bioinformatics 2021年第1期19卷 108-122页

作者： Guang Song Emily M.Lee Jianbo Pan Miao Xu Hee-Sool Rho Yichen Cheng Nadia Whitt Shu Yang Jennifer Kouznetsova Carleen Klumpp-Thomas Samuel G.Michael Cedric Moore Ki-Jun Yoon Kimberly M.Christian Anton Simeonov Wenwei Huang Menghang Xia Ruili Huang Madhu Lal-Nag Hengli Tang Wei Zheng Jiang Qian Hongjun Song Guo-li Ming Heng Zhu Department of Pharmacology&Molecular Sciences Johns Hopkins School of MedicineBaltimoreMD 21205USA Department of Biological Science Florida State UniversityTallahasseeFL 32306USA Department of Ophthalmology Johns Hopkins School of MedicineBaltimoreMD 21205USA National Center for Advancing Translational Sciences National Institutes of HealthBethesdaMD 20892USA Sir Run Run Shaw Hospital Zhejiang University School of MedicineHangzhou 310016China Institute for Cell Engineering Johns Hopkins University School of MedicineBaltimoreMD 21205USA Department of Neuroscience and Mahoney Institute for Neurosciences Perelman School for MedicineUniversity of PennsylvaniaPhiladelphiaPA 19104USA Department of Cell and Developmental Biology Perelman School for MedicineUniversity of PennsylvaniaPhiladelphiaPA 19104USA Institute for Regenerative Medicine Perelman School for MedicineUniversity of PennsylvaniaPhiladelphiaPA 19104USA The Epigenetics Institute Perelman School for MedicineUniversity of PennsylvaniaPhiladelphiaPA 19104USA

The Zika virus(ZIKV)and dengue virus(DENV)flaviviruses exhibit similar replicative processes but have distinct clinical outcomes.A systematic understanding of virus–host protein–protein interaction networks can reveal cellular pathways critical to viral replication and disease pathogenesis.Here we employed three independent systems biology approaches toward this goal.First,protein array analysis of direct interactions between individual ZIKV/DENV viral proteins and20,240 human proteins revealed multiple conserved cellular pathways and protein complexes,including proteasome complexes.Second,an RNAi screen of 10,415 druggable genes identified the host proteins required for ZIKV infection and uncovered that proteasome proteins were crucial in this process.Third,high-throughput screening of 6016 bioactive compounds for ZIKV inhibition yielded 134 effective compounds,including six proteasome inhibitors that suppress both ZIKV and DENV replication.Integrative analyses of these orthogonal datasets pinpoint proteasomes as critical host machinery for ZIKV/DENV replication.Our study provides multi-omics datasets for further studies of flavivirus–host interactions,disease pathogenesis,and new drug targets.

关键词： protein–protein interaction RNAi screening Chemical genetics screening Multi-omics

Computational Screening of Phase-separating proteins

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Genomics, Proteomics & Bioinformatics 2021年第1期19卷 13-24页

作者： Boyan Shen Zhaoming Chen Chunyu Yu Taoyu Chen Minglei Shi Tingting Li Department of Biomedical Informatics School of Basic Medical SciencesPeking University Health Science CenterBeijing 100191China Institute of Systems Biomedicine School of Basic Medical SciencesPeking University Health Science CenterBeijing 100191China MOE Key Laboratory of Bioinformatics Bioinformatics Division and Center for Synthetic&Systems BiologyBNRistSchool of MedicineTsinghua UniversityBeijing 100084China

Phase separation is an important mechanism that mediates the compartmentalization of proteins in cells.proteins that can undergo phase separation in cells share certain typical sequence features,like intrinsically disordered regions(IDRs)and multiple modular domains.Sequencebased analysis tools are commonly used in the screening of these proteins.However,current phase separation predictors are mostly designed for IDR-containing proteins,thus inevitably overlook the phase-separating proteins with relatively low IDR content.Features other than amino acid sequence could provide crucial information for identifying possible phase-separating proteins:protein–protein interaction(PPI)networks show multivalent interactions that underlie phase separation process;post-translational modifications(PTMs)are crucial in the regulation of phase separation behavior;spherical structures revealed in immunofluorescence(IF)images indicate condensed droplets formed by phase-separating proteins,distinguishing these proteins from non-phaseseparating proteins.Here,we summarize the sequence-based tools for predicting phaseseparating proteins and highlight the importance of incorporating PPIs,PTMs,and IF images into phase separation prediction in future studies.

关键词： Phase separation Prediction protein–protein interaction protein post-translational modification Immunofluorescence image