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Proteomic Analysis Provides Insights into Arabidopsis thaliana Response Under Narrow-Wavelength LED of 595 nm light 蛋白质组学分析揭示拟南芥对595 nm窄波长LED光的响应
Pub Date : 2019-01-01 DOI: 10.35248/0974-276x.19.12.507
N. Yavari, M. Lefsrud
A growing body of evidence has highlighted that a wide range of plant processes including growth, photosynthesis, and stress response are regulated by 595 nm light. However, the molecular mechanisms underlying 595 nm-induced signals are not known. The aim of this work was to study the comparative proteomic changes in leaves of Arabidopsis thaliana Col-0 plants treated with narrow-wavelength 595 nm light or fluorescent light for 5 days. Harvested plant samples were analyzed using inline RP-SCX-RP liquid chromatography coupled with LTQ mass spectrometer, resulting in the identification of 1538 proteins. Linear regression modeling of proteins’ relative abundance revealed a total of 23 differentially abundant proteins (DAPs). Functional analysis of these DAPs demonstrated the role of several biological mechanisms in A. thaliana’s response to 595 nm light including stress response and metabolic processes. A network analysis of these DAPs revealed the importance of energy and redox regulation mechanisms. Further analyses determined potentially important roles for proteins associated with glycolysis, ATP synthase complex, cell wall modification, and thylakoid membrane that may modulate the plant’s adaptive response to 595 nm light. A significant enrichment of DAPs for PSII tolerance capacity, as well as associated Ca2+ and ROS signaling pathways were also identified. Collectively, this study provides an important insight into potential molecular pathways that sustain a plant’s response to 595 nm light.
越来越多的证据表明,包括生长、光合作用和应激反应在内的一系列植物过程都受到595纳米光的调控。然而,595纳米诱导信号的分子机制尚不清楚。本研究旨在研究拟南芥(Arabidopsis thaliana) col0型植株叶片在595 nm光和荧光处理5 d后蛋白质组学的变化。收获的植物样品采用内联RP-SCX-RP液相色谱联用LTQ质谱仪进行分析,鉴定出1538个蛋白。蛋白质相对丰度的线性回归模型显示,共有23个差异丰度蛋白(DAPs)。这些DAPs的功能分析表明,在拟南芥对595 nm光的响应中,存在胁迫响应和代谢过程等多种生物学机制。对这些DAPs的网络分析揭示了能量和氧化还原调节机制的重要性。进一步的分析确定了与糖酵解、ATP合成酶复合物、细胞壁修饰和类囊体膜相关的蛋白质可能在调节植物对595 nm光的适应性反应中发挥重要作用。DAPs的显著富集与PSII耐受能力以及相关的Ca2+和ROS信号通路有关。总的来说,这项研究为维持植物对595纳米光的反应的潜在分子途径提供了重要的见解。
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引用次数: 1
Redox Proteome Perturbation in Arabidopsis upon Pseudomonas syringae Infection 丁香假单胞菌感染对拟南芥氧化还原蛋白质组的影响
Pub Date : 2019-01-01 DOI: 10.4172/0974-276X.1000490
Pei Liu, Huoming Zhang, L. Xiong, Yiji Xia
Oxidative burst is one of the earliest plant cellular responses triggered by pathogen infection. Reactive oxygen species can cause oxidative modifications of redox-sensitive proteins to mediate the defense responses. Identification and characterization of proteins that undergo oxidative modifications in these processes is an important step toward understanding molecular mechanisms of plant defense responses. In this study, an in vivo 15N metabolic labeling method combined with a cysteine-containing peptide enrichment technique was applied to identify and quantify proteins and their redox states in Arabidopsis in response to infection by Pseudomonas syringae pv tomato DC3000 (Pst). Changes of peptide redox states were compared and corrected with the changes of protein levels. A total of forty peptides representing thirty-six non-redundant proteins showed significantly redox state changes in response to the infection by the virulent Pst strain and the avirulent Pst strain (Pst avrRpm1), of which 23 had previously not been recognized to undergo oxidative PTMs. The differentially expressed redox-sensitive proteins are involved in cell wall organization, primary metabolism, photosynthesis and stress responses. Interestingly, proteins located at extracellular were more susceptible to be regulated on the redox PTMs level. These findings provide a foundation for further investigation into the redox signaling during plant defense responses.
氧化爆发是植物细胞受病原菌感染后最早发生的反应之一。活性氧可以引起氧化还原敏感蛋白的氧化修饰,从而介导防御反应。鉴定和表征在这些过程中经历氧化修饰的蛋白质是了解植物防御反应分子机制的重要一步。本研究采用体内15N代谢标记法结合含半胱氨酸肽富集技术,鉴定和定量拟南芥对丁香假单胞菌pv番茄DC3000 (Pst)感染的蛋白及其氧化还原状态。将肽氧化还原状态的变化与蛋白水平的变化进行比较和校正。共有40个多肽代表36个非冗余蛋白在毒力Pst菌株和无毒Pst菌株(Pst avrRpm1)的感染下表现出明显的氧化还原状态变化,其中23个先前未被识别为发生氧化PTMs。差异表达的氧化还原敏感蛋白参与细胞壁组织、初级代谢、光合作用和胁迫反应。有趣的是,位于细胞外的蛋白质更容易受到氧化还原PTMs水平的调节。这些发现为进一步研究植物防御反应中的氧化还原信号提供了基础。
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引用次数: 0
A Method for Isolation and Proteomic Analysis of Outer Membrane Vesicles from Fecal Samples by LC-MS/MS. LC-MS/MS分离粪便外膜小泡及蛋白质组学分析方法
Pub Date : 2019-01-01 Epub Date: 2019-03-18 DOI: 10.4172/0974-276X.1000494
Jing Wu, Mingrui An, Jianhui Zhu, Zhijing Tan, Grace Y Chen, Ryan W Stidham, David M Lubman

Outer membrane vesicles (OMVs) are nanosized spheres secreted by bacteria that are similar to the vesicles known as exosomes, which are secreted by most mammalian cell types. In contrast to many studies focusing on optimizing methods for enriching exosomes from biological fluid, few studies have been conducted to investigate outer membrane vesicles from fecal samples. Herein, we have developed a pipeline comprised of membrane filtration and multiple cycles of ultracentrifugation (UC) to isolate OMVs from fecal samples for proteomics analysis, where multiple cycles of UC are required for removal of contaminants. By iTRAQ labeling quantitative proteomics analysis, different filter sizes (0.22 μm and 0.45 μm) were compared in terms of their performance in enriching OMVs and eliminating background fecal material. Using the 0.45 μm filter, a slightly higher protein yield was obtained but no additional contaminating proteins from bacteria were identified compared to those from the 0.22 μm filter. The 0.45 μm filter together with the multiple cycles of UC were thus used to isolate OMVs for proteomics analysis. To our knowledge, this is the first study profiling a large number of OMV proteins from fecal samples. Such capabilities may help provide valuable information in understanding the communication between the host and microbiota, which is critical in preventing cancer and disease development.

外膜囊泡(omv)是由细菌分泌的纳米级球体,类似于大多数哺乳动物细胞类型分泌的外泌体囊泡。与许多研究侧重于优化从生物体液中富集外泌体的方法相比,很少有研究对粪便样本中的外膜囊泡进行研究。在此,我们开发了一个由膜过滤和多次超离心(UC)组成的管道,从粪便样本中分离omv进行蛋白质组学分析,其中需要多次超离心来去除污染物。通过iTRAQ标记定量蛋白质组学分析,比较了不同过滤尺寸(0.22 μm和0.45 μm)在富集omv和去除背景粪便物质方面的性能。与0.22 μm过滤器相比,使用0.45 μm过滤器获得的蛋白质产量略高,但没有从细菌中鉴定出额外的污染蛋白质。利用0.45 μm滤镜和UC的多个循环分离omv进行蛋白质组学分析。据我们所知,这是第一个从粪便样本中分析大量OMV蛋白的研究。这种能力可能有助于为了解宿主和微生物群之间的交流提供有价值的信息,这对预防癌症和疾病的发展至关重要。
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引用次数: 6
Visual mass-spec share (vMS-Share): a new public web-based mass spectrometry visualization and data mining repository. 可视化质谱共享(vMS-Share):一个新的基于网络的公共质谱可视化和数据挖掘存储库。
Pub Date : 2019-01-01 DOI: 10.4172/0974-276X.1000495
Niksa Blonder, Benjamin C Orsburn, Josip Blonder, Carlos A Gonzalez

Herein we introduce the Visual Mass-Spec Share (vMS-Share), a new public mass spectrometric (MS) repository and data mining website/resource freely accessible at https://vmsshare.nist.gov. vMS-Share is a web-based application developed for instant visualization of raw MS data with integrated display of metadata optimized for the sharing of proteomics and metabolomics experimental results. Each MS-based identification is linked to a given experiment and the entire experimental data can then be viewed using the link associated with a given peptide and/or small molecule. Interactive and user-friendly visualizations are provided to the user via variety of easily accessible search filters.

本文介绍了一个新的公共质谱(MS)存储库和数据挖掘网站/资源,可免费访问https://vmsshare.nist.gov。vMS-Share是一个基于web的应用程序,用于即时可视化原始MS数据,并集成显示为共享蛋白质组学和代谢组学实验结果而优化的元数据。每个基于质谱的鉴定都与给定的实验相关联,然后可以使用与给定肽和/或小分子相关的链接查看整个实验数据。交互式和用户友好的可视化通过各种容易访问的搜索过滤器提供给用户。
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引用次数: 3
Engineering a Long Lasting Tethered, Multimeric Human Growth Hormone Protein to Improve Pharmacokinetic Half-Life and Potency 设计一种持久系留的多聚体人类生长激素蛋白以改善药代动力学半衰期和效力
Pub Date : 2019-01-01 DOI: 10.35248/0974-276x.19.12.497
Tianxing Wang, Bin Zhao, E. Foehr
Long-acting human growth hormone (hGH) is intended to improve compliance, adherence and efficacy for patients with growth hormone deficiency or other growth disorders. There is poor patient compliance with daily dosing and novel strategies for improving pharmacokinetic half-life and potency are under development. Subcutaneously and intramuscularly administered recombinant human growth hormone (aka somatropin) has a short half-life of just a few hours. Growth hormone is cleared by glomerular filtration based on its size and through receptor mediated uptake. By engineering a multimeric hGH, the clearance via glomerular filtration may be reduced and the receptor binding improved through multiple points of contact. A synthetic form of hGH was created by linking multiple hGH proteins together through bi-functional PEG linkers. In addition a recombinant form of hGH was created by expressing three hGH proteins tethered together by a repetitive amino acid linker sequence. These engineered proteins were evaluated for structure and function. The tethered hGH proteins were potent and increased weight gain in hypophysectomized rats.
长效人类生长激素(hGH)旨在改善生长激素缺乏症或其他生长障碍患者的依从性、依从性和疗效。患者对每日给药的依从性较差,改善药代动力学半衰期和效力的新策略正在开发中。皮下注射和肌肉注射重组人生长激素(又名生长激素)的半衰期很短,只有几个小时。生长激素根据其大小和受体介导的摄取通过肾小球滤过清除。通过设计多聚hGH,可以减少通过肾小球滤过的清除率,并通过多个接触点改善受体结合。通过双功能PEG连接物将多个hGH蛋白连接在一起,形成了一种合成形式的hGH。此外,通过表达由重复氨基酸连接序列连接在一起的三个hGH蛋白,构建了重组形式的hGH。对这些工程蛋白的结构和功能进行了评价。拴系的生长激素蛋白是有效的,并增加了垂体切除大鼠的体重增加。
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引用次数: 1
Neurocognitive Assessment Software for Enrichment Sensory Environments 丰富感官环境的神经认知评估软件
Pub Date : 2019-01-01 DOI: 10.4172/0974-276X.1000492
Chatzichronis Stylianos, Alexiou Athanasios, Simou Panagiota, Mantzavinos Vasileios, Tsiamis Vasileios, Asma Perveen, G. Ashraf
In cases with sensory processing dysfunctions like autism spectrum disorder (ASD) and cognitive decline like Alzheimer's disease (AD), optimistic neurological improvements have been recorded after systematic sensorimotor enrichment stimulation and art therapeutic procedures. While art therapy may offer a cognitive-behavioral breakthrough, several latest studies have explored the effectiveness of brain signals representations through audio and visual transformations of electroencephalography (EEG) measurements and the necessity of neurological evaluation of sensory integration therapies. In this technical report, new software based on the JAVA and processing programming language is presented, that detects, displays and analyzes EEG signals for individual or a group of patients. This neuroinformatics software offers a digital painting environment and a real time transformation of EEG signals into adjustable music volume and octave configuration per electrode, for the real time observation and evaluation of therapeutic procedures. The EEG acquisition is wireless, therefore, brain data can also be collected from the application of other sensory or sensorimotor therapeutic sessions as well. The Neurocognitive Assessment Software for Enrichment Sensory Environments (NASESE) includes two main functionalities, organized in five different modules. The first functionality includes recording, filtering and visualization of the EEG signals exported to a rotating 3D brain model and a real-time transformation of brain activity to sound sculptures, while the second functionality generates statistical tests and coherence calculation in a fully customizable computerized environment.
在像自闭症谱系障碍(ASD)这样的感觉处理功能障碍和像阿尔茨海默病(AD)这样的认知能力下降的病例中,经过系统的感觉运动增强刺激和艺术治疗程序后,神经系统得到了乐观的改善。虽然艺术疗法可能提供认知行为的突破,但一些最新的研究已经探索了通过脑电图(EEG)测量的音频和视觉转换来表达大脑信号的有效性,以及对感觉统合疗法进行神经学评估的必要性。在本技术报告中,介绍了一种基于JAVA和处理编程语言的新软件,用于检测、显示和分析个体或群体患者的脑电图信号。这个神经信息学软件提供了一个数字绘画环境和脑电图信号的实时转换成可调的音乐音量和每个电极的八度配置,用于实时观察和治疗过程的评估。脑电图采集是无线的,因此,大脑数据也可以从其他感觉或感觉运动治疗过程中收集。丰富感官环境的神经认知评估软件(NASESE)包括两个主要功能,分为五个不同的模块。第一个功能包括脑电图信号的记录,过滤和可视化输出到一个旋转的3D大脑模型和大脑活动的实时转换为声音雕塑,而第二个功能产生统计测试和连贯计算在一个完全可定制的计算机化环境。
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引用次数: 6
Quantitative Proteomics Using Formalin-fixed, Paraffin-embedded Biopsy Tissues in Inflammatory Disease. 利用炎症性疾病中的福尔马林固定、石蜡包埋活检组织进行定量蛋白质组学研究
Pub Date : 2019-01-01 Epub Date: 2019-10-03 DOI: 10.35248/0974-276X.12.19.503
Abhimanyu Amarnani, Joseph R Capri, Puneet Souda, David A Elashoff, Ivan A Lopez, Julian P Whitelegge, Ram R Singh

Background: Investigations in human disease pathogenesis have been hampered due to paucity of access to fresh-frozen tissues (FFT) for use in global, data-driven methodologies. As an alternative, formalin-fixed, paraffin-embedded (FFPE) tissues are readily available in pathology banks. However, the use of formalin for fixation can lead to the loss of proteins that appear during inflammation, thus introducing an inherent sample bias. To address this, we compared FF and FFPE tissue proteomics to determine whether FFPE-tissue can be used effectively in inflammatory diseases.

Methods: Adjacent kidney slices from lupus nephritic mice were processed as FFPE or FFTs. Their tissue lysates were run together using proteomics workflow involving filter-aided sample preparation, in-solution dimethyl isotope labeling, StageTip fractionation, and nano-LC MS/MS through an Orbitrap XL MS.

Results: We report a >97% concordance in protein identification between adjacent FFPE and FFTs in murine lupus nephritic kidneys. Specifically, proteins representing pathways, namely, 'systemic lupus erythematosus', 'interferon-α', 'TGF-β', and 'extracellular matrix', were reproducibly quantified between FFPE and FFTs. However, 12%-29% proteins were quantified differently in FFPE compared to FFTs, but the differences were consistent across experiments. In particular, certain proteins represented in pathways, including 'inflammatory response' and 'innate immune system' were quantified less in FFPE than in FFTs. In a pilot study of human FFPE tissues, we identified proteins relevant to pathogenesis in lupus nephritic kidney biopsies compared to control kidneys.

Conclusion: This is the first report of lupus nephritis kidney proteomics using FFPE tissue. We concluded that archived FFPE tissues can be reliably used for proteomic analyses in inflammatory diseases, with a caveat that certain proteins related to immunity and inflammation may be quantified less in FFPE than in FFTs.

背景:由于无法获得新鲜冷冻组织(FFT)用于全球数据驱动方法,人类疾病发病机制的研究受到了阻碍。病理库中有福尔马林固定、石蜡包埋(FFPE)组织可供选择。然而,使用福尔马林固定可能会导致炎症过程中出现的蛋白质丢失,从而带来固有的样本偏差。为了解决这个问题,我们比较了FF和FFPE组织蛋白质组学,以确定FFPE组织是否能有效地用于炎症性疾病:方法:狼疮肾炎小鼠的相邻肾切片被处理为全脂或全冻组织。采用蛋白质组学工作流程对它们的组织裂解液进行了处理,包括过滤辅助样品制备、溶液中二甲基同位素标记、StageTip分馏以及通过Orbitrap XL MS进行纳米LC MS/MS分析:结果:我们报告了小鼠狼疮肾炎肾脏中相邻FFPE和FFT蛋白质鉴定的一致性>97%。具体而言,代表 "系统性红斑狼疮"、"干扰素-α"、"TGF-β "和 "细胞外基质 "等通路的蛋白质在FFPE和FFT之间的定量具有可重复性。然而,12%-29%的蛋白质在全脂胎膜和全脂胎膜上的定量结果不同,但不同实验之间的差异是一致的。特别是,某些蛋白在 "炎症反应 "和 "先天免疫系统 "等通路中的定量在全纤维组织中比在全纤维组织中少。在一项针对人类全冻干组织的试验性研究中,与对照肾脏相比,我们在狼疮肾炎肾活检组织中发现了与发病机制相关的蛋白质:结论:这是第一份使用FFPE组织进行狼疮肾炎肾脏蛋白质组学研究的报告。我们的结论是,存档的 FFPE 组织可以可靠地用于炎症性疾病的蛋白质组学分析,但需要注意的是,某些与免疫和炎症相关的蛋白质在 FFPE 中的定量可能低于在 FFT 中的定量。
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引用次数: 0
Interactive Web Tool for Standardizing Proteomics Workflow for Liquid Chromatography-Mass Spectrometry Data. 用于标准化液相色谱-质谱数据的蛋白质组学工作流程的交互式Web工具。
Pub Date : 2019-01-01 Epub Date: 2019-05-23
Sudhir Srivastava, Michael Merchant, Anil Rai, Shesh N Rai

Introduction: The proteomics experiments involve several steps and there are many choices available for each step in the workflow. Therefore, standardization of proteomics workflow is an essential task for design of proteomics experiments. However, there are challenges associated with the quantitative measurements based on liquid chromatography-mass spectrometry such as heterogeneity due to technical variability and missing values.

Methods: We introduce a web application, Proteomics Workflow Standardization Tool (PWST) to standardize the proteomics workflow. The tool will be helpful in deciding the most suitable choice for each step of the experimentation. This is based on identifying steps/choices with least variability such as comparing Coefficient of Variation (CV). We demonstrate the tool on data with categorical and continuous variables. We have used the special cases of general linear model, analysis of covariance and analysis of variance with fixed effects to study the effects due to various sources of variability. We have provided various options that will aid in finding the contribution of sum of squares for each variable and the CV. The user can analyze the data variability at protein and peptide level even in the presence of missing values.

Availability and implementation: The source code for "PWST" is written in R and implemented as shiny web application that can be accessed freely from https://ulbbf.shinyapps.io/pwst/.

蛋白质组学实验涉及几个步骤,工作流程中的每个步骤都有许多选择。因此,标准化蛋白质组学工作流程是蛋白质组学实验设计的重要内容。然而,基于液相色谱-质谱法的定量测量存在挑战,如由于技术可变性和缺失值而导致的异质性。方法:引入蛋白质组学工作流程标准化工具(PWST),对蛋白质组学工作流程进行标准化。该工具将有助于为实验的每个步骤决定最合适的选择。这是基于识别具有最小可变性的步骤/选择,例如比较变异系数(CV)。我们在具有分类变量和连续变量的数据上演示了该工具。我们用一般线性模型、协方差分析和固定效应方差分析的特殊情况来研究各种变异性来源的影响。我们提供了各种选项,以帮助找到每个变量和CV的平方和的贡献。即使存在缺失值,用户也可以分析蛋白质和肽水平的数据变异性。可用性和实现:“PWST”的源代码是用R编写的,并实现为闪亮的web应用程序,可以从https://ulbbf.shinyapps.io/pwst/免费访问。
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引用次数: 0
Proteomic Effects of Magnesium Stress on Biofilm Associated Proteins Isolated from Cellulolytic Bacillus licheniformis YNP5-TSU 镁胁迫对纤维素分解芽孢杆菌YNP5-TSU生物膜相关蛋白的蛋白质组学影响
Pub Date : 2019-01-01 DOI: 10.35248/0974-276x.19.12.504
Joshua A. OHair, Hui Li, M. Rangu, S. Thapa, Yong Yang, T. Fish, S. Bhatti, T. Thannhauser, Suping Zhou
Optimization of cellulase activity is vital for synthesizing the end-products of second generation biofuel production. The slightest change in fermentation parameters can reduce the secretion of necessary enzymes to degrade cellulosic biomass. Determining the ecological effects of certain key media components is essential to understand how bacterial species will respond in a fluid environment. For our experiment a cellulosic media was designed to enhance the industrially important thermophile, Bacillus licheniformis YNP5-TSU. After several attempts to simplify the carboxymethylcellulose (CMC) media composition, impaired biofilm maturation and cellulase activity was noticed. This negative artifact occurred only when magnesium sulphate was removed from media. To analyze the shift in gene expression caused by magnesium stress, biofilm associated proteins were extracted from both control (4.0 mM MgSO4) and magnesium depleted (0.0 mM MgSO4) media at 24 hr and 48 hr incubation periods. These proteins were quantified through isobaric labeling and raw data generated from nanoLC-MS/MS identified over 2,000 proteins from the Bacillus licheniformis YNP5-TSU proteome (NCBI accession number MEDD00000000). After statistical normalization and false discovery rate were calculated, a total of 161 proteins from magnesium depleted media and 238 proteins from control media were deemed statistically relevant. A closer look through STRING interconnected webs, data mining, and NCBI annotations revealed several up/down regulated proteins that had linkage to biofilm formation and cellulase secretion. In this study we are able to provide significant evidence that; (1) biofilm maturation and cellulase production are highly correlated and (2), their optimization is dependent on the expression of several key proteins.
纤维素酶活性的优化对于合成第二代生物燃料的最终产物至关重要。发酵参数的微小变化可以减少降解纤维素生物质所需酶的分泌。确定某些关键介质成分的生态效应对于了解细菌物种如何在流体环境中做出反应至关重要。在我们的实验中,我们设计了一种纤维素培养基来增强工业上重要的嗜热菌地衣芽孢杆菌YNP5-TSU。在多次尝试简化羧甲基纤维素(CMC)培养基组成后,发现生物膜成熟和纤维素酶活性受损。只有当硫酸镁从介质中移除时,才会出现这种负面伪影。为了分析镁胁迫引起的基因表达变化,在24小时和48小时的孵育期,从对照(4.0 mM MgSO4)和缺镁(0.0 mM MgSO4)培养基中提取生物膜相关蛋白。这些蛋白通过等压标记和纳米lc -MS/MS生成的原始数据进行定量,从地衣芽孢杆菌YNP5-TSU蛋白质组中鉴定了2000多个蛋白(NCBI登录号MEDD00000000)。经过统计归一化和错误发现率的计算,缺镁培养基中的161个蛋白和对照培养基中的238个蛋白被认为具有统计学相关性。通过STRING互连网、数据挖掘和NCBI注释的进一步研究发现,一些上调/下调的蛋白与生物膜的形成和纤维素酶的分泌有关。在这项研究中,我们能够提供重要的证据;(1)生物膜的成熟和纤维素酶的产生是高度相关的;(2)它们的优化取决于几个关键蛋白的表达。
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引用次数: 5
In silico Mining of EST-SSRs from the Drought Tolerant ESTs in Safflower 红花抗旱est中EST-SSRs的硅挖掘
Pub Date : 2019-01-01 DOI: 10.35248/0974-276x.19.12.506
C. Sudhakar, M. Thippeswamy, M. Sivakumar, O. Sudhakarbabu, Mangesh Y. Dudhe
Drought stress is a major abiotic factor causing yield loss in safflower and limited studies have been carried out to dissect the molecular mechanism at EST-SSR level. In this study, a possible relationship between simple sequence repeats (SSRs) distribution and drought stress was studied using three EST libraries of safflower, Ct-D-EST, Ct-NEST and Co-EST. The Ct-D-EST was generated from drought tolerant safflower cultivar A-1; Ct-N-EST and Co-EST were the EST datasets of safflower and its wild progenitor C. oxycanthus, respectively. In total, 156 (45%), 1194 (5%) and 1550 (9%) EST-SSRs were mined from Ct-D-EST, Ct-N-EST and Co-EST libraries, respectively. Comparison of EST-SSRs from Ct-D-EST with that of SSRs from other two libraries showed reasonable differences for each class of repeats. Large variations were observed for dinucleotide repeats in all the libraries. In drought EST-SSRs, only one kind of amino acid was produced by repeat (ATG)14 which encodes met indicating the loci and repeat observed to be 100%. Since three ESTs with SSRs from Ct-D-EST, annotated to putative candidate genes, S-adenosylmethionine synthetase, one-helix protein and myo-inositol 1-phosphate synthetase, did not express with SSRs in the Ct-N-EST, these can be considered as potential candidate genes for drought tolerance. A trinuceotinde SSR, encoding met, was also found in the EST annotated to putative s-adenosylmethionine synthetase, hence, both can be considered as indices for drought tolerance. The genomic resources and the information generated in this study may be useful for the safflower breeders particularly for the development of drought tolerant cultivar.
干旱胁迫是造成红花产量损失的主要非生物因子,目前在EST-SSR水平上对其分子机制的研究还比较有限。以红花为研究对象,利用Ct-D-EST、Ct-NEST和Co-EST 3个EST文库,研究了ssr分布与干旱胁迫之间的关系。Ct-D-EST是从耐旱红花品种A-1中获得的;Ct-N-EST和Co-EST分别是红花及其野生祖植物赤荆芥的EST数据集。从Ct-D-EST、Ct-N-EST和Co-EST文库中分别挖掘出156个(45%)、1194个(5%)和1550个(9%)est - ssr。Ct-D-EST的EST-SSRs与其他两个文库的SSRs比较显示,每一类重复序列存在合理差异。在所有文库中,二核苷酸重复序列都有很大的差异。在干旱EST-SSRs中,重复序列(ATG)14只产生了一种编码符合的氨基酸,表明该位点和重复率为100%。由于Ct-D-EST中含有SSRs的3个est在被注释为候选基因(s -腺苷蛋氨酸合成酶、单螺旋蛋白和肌醇- 1-磷酸合成酶)的Ct-N-EST中没有表达SSRs,因此这些基因可以被认为是潜在的耐旱候选基因。编码met的三核苷酸SSR也在假定的s-腺苷蛋氨酸合成酶注释的EST中发现,因此两者都可以作为耐旱性的指标。本研究所获得的基因组资源和信息可为红花育种者特别是耐旱品种的培育提供参考。
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引用次数: 4
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Journal of proteomics & bioinformatics
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