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Functional Analysis of Semi-conserved Transit peptide Motifs and Mechanistic Implications in Precursor Targeting and Recognition

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Molecular Plant 2016年第9期9卷 1286-1301页

作者： Kristen Holbrook Chitra Subramanian Prakitchai Chotewutmontri L. Evan Reddick Sarah Wright Huixia Zhang Lily Moncrief Barry D. Bruce Department of biochemistry Cellular and Molecular Biology Graduate Program in Plant Physiology and Genetics Graduate School of Genome Science and Technology Department of Botany Department of BotanyUniversity of Tennessee Knoxville TN 37996 USA present address: Department of Infectious Disease St. Jude Children's Research Hospital Memphis TN 38105 USA present address: Institute of Molecular Biology University of Oregon Eugene OR 97403 USA present address: Department of Microbiology University of Texas Southwestern Medical Center 5323 Harry Hines Boulevard Dallas TX 75390 USA present address: Albert R. Mann Library Cornell University Ithaca NY 14850 USA present address: U.S. Food and Drug Administration 10903 New Hampshire Avenue Silver Spring MD 20993 USA

Over 95% of plastid proteins are nuclear-encoded as their precursors containing an N-terminal extension known as the transit peptide （TP）. Although highly variable, TPs direct the precursors through a conserved, posttranslational mechanism involving translocons in the outer （TOC） and inner envelope （TOC）. The organelle import specificity is mediated by one or more components of the Toc complex. However, the high TP diversity creates a paradox on how the sequences can be specifically recognized. An emerging model of TP design is that they contain multiple loosely conserved motifs that are recognized at different steps in the targeting and transport process. Bioinformatics has demonstrated that many TPs contain semiconserved physicochemical motifs, termed FGLK. In order to characterize FGLK motifs in TP recognition and import, we have analyzed two well-studied TPs from the precursor of RuBisCO small subunit （SStp） and ferredoxin （Fdtp）. Both SStp and Fdtp contain two FGLK motifs. Analysis of large set mutations （-85） in these two motifs using in vitro, in organello, and in vivo approaches support a model in which the FGLK domains mediate interaction with TOC34 and possibly other TOC components. In vivo import analysis suggests that multiple FGLK motifs are functionally redundant. Furthermore, we discuss how FGLK motifs are required for efficient precursor protein import and how these elements may permit a convergent function of this highly variable class of targeting sequences.

关键词： chloroplast biology protein translocation Toc34 transit peptide cell biology

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Defective Etioplasts Observed in Variegation Mutants May Reveal the Light-Independent Regulation of White/Yellow Sectors of Arabidopsis Leaves

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Journal of Integrative Plant Biology 2011年第11期53卷 846-857页

作者： Wenjuan Wu Nabil Elsheery Qing Wei Lingang Zhang Jirong Huang National Key Laboratory of Plant Molecular Genetics Institute of Plant-PhysTology and-Ecology Shanghai Institutesfor Biological Sciences the Chinese Academy of Sciences Shanghai 200032 China present address： division of Nephrology and Hypertension Mayo Clinic Rochester MN 55905 USA present address： Institute of Plant Science and Resources okayama University Kurashiki Okayama Japan

Leaf variegation resulting from nuclear gene mutations has been used as a model system to elucidate the molecular mechanisms of chloroplast development. Since most variegation genes also function in photosynthesis, it remains unknown whether their roles in photosynthesis and chloroplast development are distinct. Here, using the variegation mutant thylakoid formation1 （thfl） we show that variegation formation is light independent. It was found that slow and uneven chloroplast development in thfl can be attributed to defects in etioplast development in darkness. Ultrastructural analysis showed the coexistence of plastids with or without prolamellar bodies （PLB） in cells of thfl, but not of WT. Although THF1 mutation leads to significant decreases in the levels of Pchlide and Pchliide oxidoreductase （POR） expression, genetic and 5-aminolevulinic acid （ALA）-feeding analysis did not reveal Pchlide or POR to be critical factors for etioplast formation in thfl. Northern blot analysis showed that plastid gene expression is dramatically reduced in thfl compared with that in WT, particularly in the dark. Our results also indicate that chlorophyll biosynthesis and expression of plastidic genes are coordinately suppressed in thfl. Based on these results, we propose a model to explain leaf variegation formation from the plastid development perspective.

关键词： Arabidopsis chloroplast etioplast THF1/Psb29 variegation Pchllide oxidoreductase Pchlide oxidoreductase chloroplastdevelopment.

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NADPH oxidase family proteins:signaling dynamics to disease management

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Cellular & Molecular Immunology 2022年第6期19卷 660-686页

作者： Rizwana Begum Shilpa Thota Abubakar Abdulkadir Gagandeep Kaur Prathyusha Bagam Sanjay Batra present address:Department of Environmental Medicine University of RochesterSchool of Medicine and DentistryRochesterNY14642USA Laboratory of Pulmonary Immunotoxicology Department of Environmental ToxicologySouthern University and A&M CollegeBaton RougeLA70813USA present address:division of Systems Biology National Center for Toxicological ResearchJeffersonAR72079USA

Reactive oxygen species(ROS)are pervasive signaling molecules in biological *** humans,a lack of ROS causes chronic and extreme bacterial infections,while uncontrolled release of these factors causes pathologies due to excessive *** phagocytes such as neutrophils(PMNs),eosinophils,monocytes,and macrophages use superoxide-generating NADPH oxidase(NOX)as part of their arsenal of antimicrobial mechanisms to produce high levels of *** is a multisubunit enzyme complex composed of five essential subunits,two of which are localized in the membrane,while three are localized in the *** resting phagocytes,the oxidase complex is unassembled and inactive;however,it becomes activated after cytosolic components translocate to the membrane and are assembled into a functional *** NOX isoforms play a variety of roles in cellular differentiation,development,proliferation,apoptosis,cytoskeletal control,migration,and *** studies have identified NOX as a major contributor to disease pathologies,resulting in a shift in focus on inhibiting the formation of potentially harmful free ***,a better understanding of the molecular mechanisms and the transduction pathways involved in NOX-mediated signaling is essential for the development of new therapeutic agents that minimize the hyperproduction of *** current review provides a thorough overview of the various NOX enzymes and their roles in disease pathophysiology,highlights pharmacological strategies,and discusses the importance of computational modeling for future NOX-related studies.

关键词： NADPH oxidase Reactive oxygen species Inflammation Inhibitors In silico

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Surveying the Oligomeric State of Arabidopsis thaliana Chloroplasts

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Molecular Plant 2017年第1期10卷 197-211页

作者： Peter K. Lundquist Otho Mantegazza Anja Stefanski Kai Stuhler Andreas P.M. Weber institute for Plant biochemistry Molecular Proteomics La_boratory BMFZ Cluster of Excellence on Plant Sciences (CEPLAS) Heinrich-Heine-University UniversitatsstraBe 1 40225 Duseldorf Germany present address: Plant Biology division The Samuel Roberts Noble Foundation Ardmore OK 73401 USA

Blue native-PAGE （BN-PAGE） resolves protein complexes in their native state. When combined with immu- noblotting, it can be used to identify the presence of high molecular weight complexes at high resolution for any protein, given a suitable antibody. To identify proteins in high molecular weight complexes on a large scale and to bypass the requirement for specific antibodies, we applied a tandem mass spectrometry （MS/MS） approach to BN-PAGE-resolved chloroplasts. Fractionation of the gel into six bands allowed iden- tification and label-free quantification of 1000 chloroplast proteins with native molecular weight separation. Significantly, this approach achieves a depth of identification comparable with traditional shotgun proteo- mic analyses of chloroplasts, indicating much of the known chloroplast proteome is amenable to MS/MS identification under our fractionation scheme. By limiting the number of fractionation bands to six, we facil- itate scaled-up comparative analyses, as we demonstrate with the reticulata chloroplast mutant displaying a reticulated leaf phenotype. Our comparative proteomics approach identified a candidate interacting protein of RETICULATA as well as effects on lipid remodeling proteins, amino acid metabolic enzymes, and plastid division machinery. We additionally highlight selected proteins from each sub-compartment of the chloroplast that provide novel insight on known or hypothesized protein complexes to further illus- trate the utility of this approach. Our results demonstrate the high sensitivity and reproducibility of this technique, which is anticipated to be widely adaptable to other sub-cellular compartments.

关键词： chloroplast blue native-PAGE comparative proteomics protein complex oligomeric state,RETICULATA

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SYNTHESIS OF 11 α-HYDROXY-AND 11β-CHLORO-ARTEMISININ

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Chinese Chemical Letters 1993年第2期4卷 99-100页

作者： Ying Li De Wen LU Hui Bin ZHANG Shanghai Institute of Materia Medica Academia SinicaShanghai 200031 present address:Department of Chemistry Changshu College.Changshu 215500 present address:division of Medicinal Chemistry Chinese Pharmaceutical UniversityNanjing 210009

11α-Hydroxy-and 11β-chloro-artemisinin have been prepared from artemisinin

关键词： CHLORO-ARTEMISININ HYDROXY-AND 11 SYNTHESIS OF 11 OH 429

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Non-invasive photoacoustic computed tomography of rat heart anatomy and function

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Light(Science & Applications) 2023年第1期12卷 109-117页

作者： Li Lin Xin Tong Susana Cavallero Yide Zhang Shuai Na Rui Cao Tzung K.Hsiai Lihong V.Wang Caltech Optical Imaging Laboratory Andrew and Peggy Cherng Department of Medical EngineeringDepartment of Electrical EngineeringCalifornia Institute of TechnologyPasadenaCAUSA Department of Bioengineering UCLALos AngelesCAUSA division of Cardiology Department of MedicineUCLALos AngelesCAUSA present address:College of Biomedical Engineering and Instrument Science Zhejiang UniversityHangzhouChina present address:The First Affiliated Hospital Zhejiang University School of MedicineHangzhouChina

Complementary to mainstream cardiac imaging modalities for preclinical research,photoacoustic computed tomography(PACT)can provide functional optical contrast with high imaging speed and ***,PACT has not been demonstrated to reveal the dynamics of whole cardiac anatomy or vascular system without surgical procedure(thoracotomy)for tissue ***,we achieved non-invasive imaging of rat hearts using the recently developed three-dimensional PACT(3D-PACT)platform,demonstrating the regulated illumination and detection schemes to reduce the effects of optical attenuation and acoustic distortion through the chest wall;thereby,enabling unimpeded visualization of the cardiac anatomy and intracardiac hemodynamics following rapidly scanning the heart within 10 *** further applied 3D-PACT to reveal distinct cardiac structural and functional changes among the healthy,hypertensive,and obese rats,with optical contrast to uncover differences in cardiac chamber size,wall thickness,and ***,3D-PACT provides high imaging speed and nonionizing penetration to capture the whole heart for diagnosing the animal models,holding promises for clinical translation to cardiac imaging of human neonates.

关键词： anatomy hypertensive illumination

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Timing Is Everything： Highly Specific and Transient Expression of a MAP Kinase Determines Auxin-Induced Leaf Venation Patterns in Arabidopsis

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Molecular Plant 2014年第11期7卷 1637-1652页

作者： Vera Stanko Concetta Giuliani Katarzyna Retzer Armin Djamei Vanessa Wahl Bernhard Wurzinger Cathal Wilson Erwin Heberle-Bors Markus Teige Friedrich Kragler Department of Plant Molecular Biology Max. F. Perutz Laboratories University of Vienna Dr. Bohrgasse 9/4 Vienna A-1030 Austria present address: Felix-Klein-Gymnasium Bottingerstraβe 17 D-37073 Gottingen Germany present address: Austrian Centre of Industrial Biotechnology Muthgasse 11 A-1190 Vienna Austria present address: Department of Applied Genetics and Cell Biology University of Natural Resources and Life Sciences Muthgasse 18 A-1190 Vienna Austria present address: Gregor Mendel Institute of Molecular Plant Biology Dr. Bohr-Gasse 3 1030 Vienna Austria Max Planck Institute of Molecular Plant Physiology Wissenschaftspark Golm Am Muhlenberg 1 D-14476 Potsdam-Golm Germany Department of biochemistry Max. F. Perutz Laboratories University of Vienna Dr. Bohrgasse 9/5 Vienna A-1030 Austria present address: Department of Ecogenomics and Systems Biology University of Vienna Althanstr. 14 A-1090 Vienna Austria present address: Telethon Institute of Genetics and Medicine Via Pietro Castellino 11180131-Naples Italy Department of Ecogenomics and Systems Biology University of Vienna AIthanstr. 14 A-1090 Vienna Austria

Mitogen-activated protein kinase （MAPK） cascades are universal signal transduction modules present in all eukaryotes. In plants, MAPK cascades were shown to regulate cell division, developmental processes, stress responses, and hormone pathways. The subgroup A of Arabidopsis MAPKs consists of AtMPK3, AtMPK6, and AtMPK10. AtMPK3 and AtMPK6 are activated by their upstream MAP kinase kinases （MKKs） AtMKK4 and AtMKK5 in response to biotic and abiotic stress. In addition, they were identified as key regulators of stomatal development and patterning. AtMPKIO has long been considered as a pseudo-gene, derived from a gene duplication of AtMPK6. Here we show that AtMPKIO is expressed highly but very transiently in seedlings and at sites of local auxin maxima leaves. MPK10 encodes a functional kinase and interacts with the upstream MAP kinase kinase （MAPKK） AtMKK2. mpklO mutants are delayed in flowering in long-day conditions and in continuous light. Moreover, cotyledons of mpk10 and mkk2 mutants have reduced vein complexity, which can be reversed by inhibiting polar auxin transport （PAT）. Auxin does not affect AtMPKIO expression while treatment with the PAT inhibitor HFCA extends the expression in leaves and reverses the mpklO mutant phenotype. These results suggest that the AtMKK2-AtMPK10 MAPK module regulates venation complexity by altering PAT efficiency.

关键词： Arabidopsis MAP kinase leaf development polar auxin transport leaf venation pattern.

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Off-the-shelf deep learning is not enough,and requires parsimony,Bayesianity,and causality

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npj Computational Materials 2021年第1期7卷 133-138页

作者： Rama K.Vasudevan Maxim Ziatdinov Lukas Vlcek Sergei.V.Kalinin Center for Nanophase Materials Sciences Oak RidgeTN 37831USA Computational Sciences and Engineering division Oak RidgeTN 37831USA Materials Science and Technology division Oak Ridge National LaboratoryOak RidgeTN 37831USA present address:Bayer St.LouisMO 63141USA

Deep neural networks(‘deep learning’)have emerged as a technology of choice to tackle problems in speech recognition,computer vision,finance,***,adoption of deep learning in physical domains brings substantial challenges stemming from the correlative nature of deep learning methods compared to the causal,hypothesis driven nature of modern *** argue that the broad adoption of Bayesian methods incorporating prior knowledge,development of solutions with incorporated physical constraints and parsimonious structural descriptors and generative models,and ultimately adoption of causal models,offers a path forward for fundamental and applied research.

关键词： learning enough finance

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A Plant Immune Receptor Degraded by Selective Autophagy

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Molecular Plant 2019年第1期12卷 113-123页

作者： Fan Yang Athen N.Kimberlin Christian G.Elowsky Yunfeng Liu Ariadna Gonzalez-Solis Edgar B.Cahoon James R.Alfano Department of Plant Pathology University of NebraskaLincolnNE 68588-0722USA Center for Plant Science Innovation University of NebraskaLincolnNE 68588-0660USA Department of Bioohemistry University of NebraskaLincolnNE 68588-0664US Center for Biotechnology University of NebraskaLincolnNE 68588-0665USA present address:Department of biochemistry University of MissouriColumbiaMQ 65211USA present address:College of Life Science and Technology University of GuangxiNanning 530004China

Plants recycle non-activated immune receptors to maintain a functional immune *** Arabidopsis immune receptor kinase FLAGELLIN-SENSING 2 (FLS2)recognizes bacterial ***,the molecular mechanisms by which non-activated FLS2 and other non-activated plant PRRs are recycled remain not well ***,we provide evidence showing thatArabidopsis orosomucoid (ORM)proteins,which have been known to be negative regulators of sphingoUpid biosynthesis,act as selective autophagy receptors to mediate the degradation of *** plants overexpressing ORM 1 or ORM2 have undetectable or greatly diminished FLS2 accumulation,nearly lack FLS2 signaling,and are more susceptible to the bacterial pathogen Pseudomonas *** the other hand,ORM1/2 RNAi plants and orml or orrn2 mutants generated by the CRISPR/Cas9-mediated gene editing have increased FLS2 accumulation and enhanced FLS2 signaling,and are more resistant to *** proteins interact with FLS2 and the autophagy-related protein ***,overexpression of ORM1 or ORM2 in autophagydefective mutants showed FLS2 abundance that is comparable to that in wild-type ***, FLS2 levels were not decreased in Arabidopsis plants overexpressing ORM1/2 derivatives that do not interact with *** together,these results suggest that selective autophagy functions in maintaining the homeostasis of a plant immune receptor and that beyond sphingolipid metabolic regulation ORM proteins can also act as selective autophagy receptors.

关键词： Plant immunity selective autophagy pattern recognition receptor selective autophagy receptors

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nitiation of ER Body Formation and Indole Glucosinolate Metabolism by the Plastidia Retrograde Signaling Metabolite, MEcPP

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Molecular Plant 2017年第11期10卷 1400-1416页

作者： Jin-Zheng Wang Baohua Li Yanmei Xiao Yu Ni Haiyan Ke Panyu Yang Amancio de Souza Marta Bjornson Xiang He Zhouxin Shen Gerd Ulrich Balcke Steve P. Briggs Alain Tissier Daniel J. Kliebenstein Katayoon Dehesh Institute for Integrative Genome Biology and Department of Botany and Plant Sciences University of California Riverside CA 92521 USA Department of Plant Biology University of California Davis CA 95616 USA Department of Plant Sciences University of California Davis CA 95616 USA division of Biological Sciences University of California San Diego La Jolla CA 92093 USA Department of Cell and Metabolic Biology Leibniz-lnstitute of Plant Biochemistry Halle Germany present address: College of Agronomy and Biotechnology Southwest University Chongqing P.R. China present address: Rice Research Institute Sichuan Agricultural University Changdu Sichuan 611130 China

Plants have evolved tightly regulated signaling networks to respond and adapt to environmental perturbations, but the nature of the signaling hub（s） involved have remained an enigma. We have previously established that methylerythritol cyclodiphosphate （MEcPP）, a precursor of plastidial isoprenoids and a stress- specific retrograde signaling metabolite, enables cellular readjustments for high-order adaptive functions. Here, we specifically show that MEcPP promotes two Brassicaceae-specific traits, namely endoplasmic reticulum （ER） body formation and induction of indole glucosinolate （IGs） metabolism selectively, via tran- scriptional regulation of key regulators NAIl for ER body formation and MYB51/122 for IGs biosynthesis）. The specificity of MEcPP is further confirmed by the lack of induction of wound-inducible ER body genes as well as IGs by other altered methylerythritol phosphate pathway enzymes. Genetic analyses revealed MEcPP-mediated COil-dependent induction of these traits. Moreover, MEcPP signaling integrates the biosynthesis and hydrolysis of IGs through induction of nitrile-specifier protein1 and reduction of the sup- pressor, ESM1, and production of simple nitriles as the bioactive end product. The findings position the plastidial metabolite, MEcPP, as the initiation hub, transducing signals to adjust the activity of hard- wired gene circuitry to expand phytochemical diversity and alter the associated subcellular structure required for functionality of the secondary metabolites, thereby tailoring plant stress responses.

关键词： glucosinolates ER body retrograde signaling MEP pathway MEcPP stress

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