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Guo M.,CAS Wuhan Botanical Garden | Huang B.X.,U.S. National Institutes of Health
Proteomics | Year: 2013

Reversible phosphorylation, tightly controlled by protein kinases and phosphatases, plays a central role in mediating biological processes, such as protein-protein interactions, subcellular translocation, and activation of cellular enzymes. MS-based phosphoproteomics has now allowed the detection and quantification of tens of thousands of phosphorylation sites from a typical biological sample in a single experiment, which has posed new challenges in functional analysis of each and every phosphorylation site on specific signaling phosphoproteins of interest. In this article, we review recent advances in the functional analysis of targeted phosphorylation carried out by various chemical and biological approaches in combination with the MS-based phosphoproteomics. This review focuses on three types of strategies, including forward functional analysis, defined for the result-driven phosphoproteomics efforts in determining the substrates of a specific protein kinase; reverse functional analysis, defined for tracking the kinase(s) for specific phosphosite(s) derived from the discovery-driven phosphoproteomics efforts; and MS-based analysis on the structure-function relationship of phosphoproteins. It is expected that this review will provide a state-of-the-art overview of functional analysis of site-specific phosphorylation and explore new perspectives and outline future challenges. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Recent breakthrough on identification and characterization of PYR/PYLs as ABA receptors enables us to better understand the perception, signaling and transportation of ABA in plant. Based on publicly available microarray data, transcriptional levels of ABA signaling pathway core components were compared after stress and phytohormone treatments, including these involved in ABA metabolism, signal transduction, and catabolism. The results showed that both abiotic and biotic stress treatments increased the expression levels of ABA key metabolism and catabolism transcripts. The expression levels of PYR/PYLs were down-regulated and these of PP2Cs and ABFs were uniformly up-regulated after exogenous ABA application and under stress conditions. The results indicated that the increased ratio of PP2Cs:PYR/PYLs might be required for activation of the downstream ABA signal pathway under both abiotic and biotic stress conditions. We concluded that abiotic and biotic stress responses shared ABA signal pathway in Arabidopsis. © 2012 Elsevier Inc.

Wei X.,CAS Wuhan Botanical Garden | Jiang M.,CAS Wuhan Botanical Garden
New Phytologist | Year: 2012

• This study aimed to reveal species-genetic diversity correlations (SGDCs) and their underlying mechanisms in natural and disturbed forests. • A community survey and molecular analyses were carried out to compare species diversity (SD), the genetic diversity of the dominant tree species Euptelea pleiospermum (GD), the altitudinal patterns of SD and GD, SGDC, genetic differentiation (F ST), community divergence (F ST-C), effective population size (N e), and recent migration rate between mountain riparian forests along the Yandu (natural) and Nan (disturbed) rivers. • In natural forests, both SD and GD showed a unimodal altitudinal pattern and GD was positively correlated with SD, whereas a unimodal pattern and positive SGDC were not found in the disturbed forests. SD and F ST at the natural sites were higher than those at the disturbed sites. However, there were no significant differences in GD, F ST-C, N e or recent migration rate between the natural and disturbed sites. • A correlation between the patterns of SD and GD along a geographical gradient (e.g. altitude) is an important driver of positive SGDC. The absence of positive SGDC in the disturbed forests may result from reduced SD but unaffected GD, indicating nonparallel changes in SD and GD. This study furthermore cautions against generalizations about changes in SD and GD following disturbance. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.

Zhang Q.,CAS Wuhan Botanical Garden | Lou Z.,Chinese Academy of Sciences
Environmental Science and Policy | Year: 2011

The Three Gorges Dam (TGD) is by far the world's largest hydroelectric scheme. Due to its unprecedented magnitude, the TGD has been controversial ever since it was proposed in the early 20th century and building commenced in 1993. Recent problems, including geological disasters (e.g., landslides) in the uplands and algal blooms in the aquatic environment since the reservoir's partial filling to 156. m in 2006, suggest that the environmental challenge has never been greater than now. The environmental deterioration might be further intensified when the reservoir reaches its final water level of 175. m. Solving the environmental challenges will be essential for the sustainable development of the Three Gorges Reservoir region (TGRR), and environmental sustainability in the TGRR is a high priority for the nation considering its critical location in the Yangtze Basin, which contributes 40% of China's GDP. This article reviews primary environmental assessments for biodiversity conservation, the water environment, water level fluctuation zone, and the uplands after the partial filling in the reservoir region. It also discusses the success of mitigation efforts to date. Although there are successes in mitigation particularly in conservation of endangered plants and fishes, it seems likely that environmental conditions in the TGRR could only get worse in the short term. Building a partnership among the TGD stakeholders, including local residents, governments, and international communities is necessary to meet the mounting environmental challenge in the TGRR and beyond. © 2011 Elsevier Ltd.

Li S.,CAS Wuhan Botanical Garden | Zhang Q.,CAS Wuhan Botanical Garden
Journal of Hazardous Materials | Year: 2010

A data matrix (4032 observations), obtained during a 2-year monitoring period (2005-2006) from 42 sites in the upper Han River is subjected to various multivariate statistical techniques including cluster analysis, principal component analysis (PCA), factor analysis (FA), correlation analysis and analysis of variance to determine the spatial characterization of dissolved trace elements and heavy metals. Our results indicate that waters in the upper Han River are primarily polluted by Al, As, Cd, Pb, Sb and Se, and the potential pollutants include Ba, Cr, Hg, Mn and Ni. Spatial distribution of trace metals indicates the polluted sections mainly concentrate in the Danjiang, Danjiangkou Reservoir catchment and Hanzhong Plain, and the most contaminated river is in the Hanzhong Plain. Q-model clustering depends on geographical location of sampling sites and groups the 42 sampling sites into four clusters, i.e., Danjiang, Danjiangkou Reservoir region (lower catchment), upper catchment and one river in headwaters pertaining to water quality. The headwaters, Danjiang and lower catchment, and upper catchment correspond to very high polluted, moderate polluted and relatively low polluted regions, respectively. Additionally, PCA/FA and correlation analysis demonstrates that Al, Cd, Mn, Ni, Fe, Si and Sr are controlled by natural sources, whereas the other metals appear to be primarily controlled by anthropogenic origins though geogenic source contributing to them. © 2009 Elsevier B.V. All rights reserved.

He D.,CAS Wuhan Botanical Garden | Yang P.,CAS Wuhan Botanical Garden
Frontiers in Plant Science | Year: 2013

Seed is a condensed form of plant. Under suitable environmental conditions, it can resume the metabolic activity from physiological quiescent status, and mobilize the reserves, biosynthesize new proteins, regenerate organelles, and cell membrane, eventually protrude the radicle and enter into seedling establishment. So far, how these activities are regulated in a coordinated and sequential manner is largely unknown. With the availability of more and more genome sequence information and the development of mass spectrometry (MS) technology, proteomics has been widely applied in analyzing the mechanisms of different biological processes, and proved to be very powerful. Regulation of rice seed germination is critical for rice cultivation. In recent years, a lot of proteomic studies have been conducted in exploring the gene expression regulation, reserves mobilization and metabolisms reactivation, which brings us new insights on the mechanisms of metabolism regulation during this process. Nevertheless, it also invokes a lot of questions. In this mini-review, we summarized the progress in the proteomic studies of rice seed germination. The current challenges and future perspectives were also discussed, which might be helpful for the following studies. © 2013 He and Yang.

Chan Z.,CAS Wuhan Botanical Garden
Frontiers in Plant Science | Year: 2012

Fruits and vegetables are extremely susceptible to decay and easily lose commercial value after harvest. Different strategies have been developed to control postharvest decay and prevent quality deterioration during postharvest storage, including cold storage, controlled atmosphere (CA), and application of biotic and abiotic stimulus. In this review, mechanisms related to protein level responses of host side and pathogen side were characterized. Protein extraction protocols have been successfully developed for recalcitrant, low protein content fruit tissues. Comparative proteome profiling and functional analysis revealed that defense related proteins, energy metabolism, and antioxidant pathway played important roles in fruits in response to storage conditions and exogenous elicitor treatments. Secretome of pathogenic fungi has been well-investigated and the results indicated that hydrolytic enzymes were the key virulent factors for the pathogen infection. These protein level changes shed new light on interaction among fruits, pathogens, and environmental conditions. Potential postharvest strategies to reduce risk of fruit decay were further proposed based on currently available proteomic data. © 2013 Chan.

Li S.,CAS Wuhan Botanical Garden | Zhang Q.,CAS Wuhan Botanical Garden
Journal of Hazardous Materials | Year: 2010

Surface water samples were collected from 42 sampling sites throughout the upper Han River during the time period of 2005-2006. The concentrations of trace metals were determined using inductively coupled plasma-atomic emission spectrometry (ICP-AES) for the seasonal variability and preliminary risk assessment. The results demonstrated that concentrations of 11 heavy metals showed significant seasonality and most variables exhibited higher levels in the rainy season. Principal component analysis (PCA) and factor analysis (FA) revealed that variables governing water quality in one season may not be important in another season. Risk of metals on human health was then evaluated using Hazard Quotient (HQ) and carcinogenic risk, and indicated that As with HQ >1 and carcinogenic risk >10-4, was the most important pollutant leading to non-carcinogenic and carcinogenic concerns, in particular for children. The first five largest elements to chronic risks were As, Pb, V, Se and Sb, in the dry season, while they were As, V, Co, Pb and Sb in the rainy season. This assessment would help establish pollutant loading reduction goal and the total maximum daily loads, and consequently contribute to preserve public health in the Han River basin and develop water conservation strategy for the interbasin water transfer project. © 2010 Elsevier B.V.

Shi H.,CAS Wuhan Botanical Garden | Chan Z.,CAS Wuhan Botanical Garden
Journal of Integrative Plant Biology | Year: 2014

Polyamines (mainly putrescine (Put), spermidine (Spd), and spermine (Spm)) have been widely found in a range of physiological processes and in almost all diverse environmental stresses. In various plant species, abiotic stresses modulated the accumulation of polyamines and related gene expression. Studies using loss-of-function mutants and transgenic overexpression plants modulating polyamine metabolic pathways confirmed protective roles of polyamines during plant abiotic stress responses, and indicated the possibility to improve plant tolerance through genetic manipulation of the polyamine pathway. Additionally, putative mechanisms of polyamines involved in plant abiotic stress tolerance were thoroughly discussed and crosstalks among polyamine, abscisic acid, and nitric oxide in plant responses to abiotic stress were emphasized. Special attention was paid to the interaction between polyamine and reactive oxygen species, ion channels, amino acid and carbon metabolism, and other adaptive responses. Further studies are needed to elucidate the polyamine signaling pathway, especially polyamine-regulated downstream targets and the connections between polyamines and other stress responsive molecules. © 2013 Institute of Botany, Chinese Academy of Sciences.

Melatonin (N-acetyl-5-methoxytryptamine) is not only a widely known animal hormone, but also an important regulator in plant development and multiple abiotic stress responses. Recently, it has been revealed that melatonin alleviated cold stress through mediating several cold-related genes, including C-REPEAT-BINDING FACTORs (CBFs)/Drought Response Element Binding factors (DREBs), COR15a, and three transcription factors (CAMTA1, ZINC FINGER OF ARABIDOPSIS THALIANA 10 (ZAT10), and ZAT12). In this study, we quantified the endogenous melatonin level in Arabidopsis plant leaves and found the endogenous melatonin levels were significantly induced by cold stress (4C) treatment. In addition, we found one cysteine2/histidine2-type zinc finger transcription factor, ZAT6, was involved in melatonin-mediated freezing stress response in Arabidopsis. Interestingly, exogenous melatonin enhanced freezing stress resistance was largely alleviated in AtZAT6 knockdown plants, but was enhanced in AtZAT6 overexpressing plants. Moreover, the expression levels of AtZAT6 and AtCBFs were commonly upregulated by cold stress (4C) and exogenous melatonin treatments, and modulation of AtZAT6 expression significantly affected the induction AtCBFs transcripts by cold stress (4C) and exogenous melatonin treatments. Taken together, AtZAT6-activated CBF pathway might be essential for melatonin-mediated freezing stress response in Arabidopsis. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

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