Using the <i>Arabidopsis</i> Information Resource (TAIR) to Find Information About <i>Arabidopsis</i> Genes

Reiser, Leonore; Subramaniam, Sabarinath; Li, Donghui; Huala, Eva

doi:10.1002/cpbi.36

Cited by 48 publications

(18 citation statements)

References 51 publications

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“…ch/) [78], and Subcellular Localization Database for A. thaliana (SUBA4; http://suba.live/) [79]. Data from the primary literature and/or The Arabidopsis Information Resource site (TAIR; https ://www.arabi dopsi s.org/) [80], and Mercator and Mapman BIN ontologies (http://www. plabi pd.de/porta l/merca tor-seque nce-annot ation /) [81] also aided in protein curation.…”

Section: Proteomics Analysismentioning

confidence: 99%

“…Manual curation of these proteins was performed using our tomato chloroplast protein Atlas [68], which predicted tomato protein localization using five published algorithms [72][73][74][75][76]. In addition, TAIR and three protein databases (PPDB, plprot and SUBA4) provided theoretical predictions and/or empirical data of the Arabidopsis homolog's location [77][78][79][80].…”

Section: Nanolc-ms/ms Analysis Identifies 254 Non-plastid Co-isolatinmentioning

confidence: 99%

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Methodology: an optimized, high-yield tomato leaf chloroplast isolation and stroma extraction protocol for proteomics analyses and identification of chloroplast co-localizing proteins

2020

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Background Chloroplasts are critical organelles that perceive and convey metabolic and stress signals to different cellular components, while remaining the seat of photosynthesis and a metabolic factory. The proteomes of intact leaves, chloroplasts, and suborganellar fractions of plastids have been evaluated in the model plant Arabidopsis, however fewer studies have characterized the proteomes of plastids in crops. Tomato (Solanum lycopersicum) is an important world-wide crop and a model system for the study of wounding, herbivory and fruit ripening. While significant advances have been made in understanding proteome and metabolome changes in fruit ripening, far less is known about the tomato chloroplast proteome or its subcompartments. Results With the long-term goal of understanding chloroplast proteome dynamics in response to stress, we describe a high-yielding method to isolate intact tomato chloroplasts and stromal proteins for proteomic studies. The parameters that limit tomato chloroplast yields were identified and revised to increase yields. Compared to published data, our optimized method increased chloroplast yields by 6.7- and 4.3-fold relative to published spinach and Arabidopsis leaf protocols, respectively; furthermore, tomato stromal protein yields were up to 79-fold higher than Arabidopsis stromal proteins yields. We provide immunoblot evidence for the purity of the stromal proteome isolated using our enhanced methods. In addition, we leverage our nanoliquid chromatography tandem mass spectrometry (nanoLC–MS/MS) data to assess the quality of our stromal proteome. Using strict criteria, proteins detected by 1 peptide spectral match, by one peptide, or were sporadically detected were designated as low-level contaminating proteins. A set of 254 proteins that reproducibly co-isolated with the tomato chloroplast stroma were identified. The subcellular localization, frequency of detection, normalized spectral abundance, and functions of the co-isolating proteins are discussed. Conclusions Our optimized method for chloroplast isolation increased the yields of tomato chloroplasts eightfold enabling the proteomics analysis of the chloroplast stromal proteome. The set of 254 proteins that co-isolate with the chloroplast stroma provides opportunities for developing a better understanding of the extensive and dynamic interactions of chloroplasts with other organelles. These co-isolating proteins also have the potential for expanding our knowledge of proteins that are co-localized in multiple subcellular organelles.

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Section: Proteomics Analysismentioning

confidence: 99%

Section: Nanolc-ms/ms Analysis Identifies 254 Non-plastid Co-isolatinmentioning

confidence: 99%

Methodology: an optimized, high-yield tomato leaf chloroplast isolation and stroma extraction protocol for proteomics analyses and identification of chloroplast co-localizing proteins

2020

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“…The genome sequences and amino acid sequences of B. napus ‘Westar 10’ were obtained from the Brassica Database (Chalhoub et al , ; Cheng et al , ), and the sequences of Arabidopsis were downloaded from TAIR 10 database (Reiser et al , ). The 2000 bp upstream sequences from the start codons of BnaWRKY genes and B‐related genes were analysed to determine the cis ‐regulatory elements (W box).…”

Section: Methodsmentioning

confidence: 99%

Transcription factor BnaA9.WRKY47 contributes to the adaptation of Brassica napus to low boron stress by up‐regulating the boric acid channel gene BnaA3.NIP5;1

Feng

Cui

Wang

et al. 2019

Plant Biotechnology Journal

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Summary Boron (B) deficiency is one of the major causes of growth inhibition and yield reduction in Brassica napus (B. napus). However, the molecular mechanisms of low B adaptation in B. napus are largely unknown. Here, fifty‐one BnaWRKY transcription factors were identified as responsive to B deficiency in B. napus, in which BnaAn.WRKY26, BnaA9.WRKY47, BnaA1.WKRY53 and BnaCn.WRKY57 were tested in yeast one‐hybrid assays and showed strong binding activity with conserved sequences containing a W box in the promoters of the B transport‐related genes BnaNIP5;1s and BnaBOR1s. Green fluorescent protein fused to the target protein demonstrated the nuclear localization of BnaA9.WRKY47. CRISPR/Cas9‐mediated knockout lines of BnaA9.WRKY47 in B. napus had increased sensitivity to low B and lower contents of B than wild‐type plants. In contrast, overexpression of BnaA9.WRKY47 enhanced the adaptation to low B with higher B contents in tissues than in wild‐type plants. Consistent with the phenotypic response and B accumulation in these transgenic lines, the transcription activity of BnaA3.NIP5;1, a B efficiency candidate gene, was decreased in the knockout lines but was significantly increased in the overexpressing lines under low B conditions. Electrophoretic mobility shift assays, transient expression experiments in tobacco and in situ hybridizations showed that BnaA9.WRKY47 directly activated BnaA3.NIP5;1 expression through binding to the specific cis‐element. Taken together, our findings support BnaWRKYs as new participants in response to low B, and BnaA9.WRKY47 contributes to the adaptation of B. napus to B deficiency through up‐regulating BnaA3.NIP5;1 expression to facilitate efficient B uptake.

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“…We recognize there is a clear need for databases that are tailored for the communities that they serve. For example, SoyBase ( https://www.soybase.org ) ( 17 ) primarily focuses on resources and tools for soybean breeding, while TAIR ( 18 ) focuses on gene function for the Arabidopsis research community. However, as more organism genomes are sequenced, comparisons between and among species become more biologically informative.…”

Section: Biocurationmentioning

confidence: 99%

“…Significant work has been done in these areas. The curation tools for GO annotation include TAIR’s in-house curation tool PubSearch ( 35 ) and TAIR’s community portal the Online Annotation Submission Tool (TOAST) ( 18 ), PomBase’s Canto ( 36 ), the GO consortium’s Noctua ( http://noctua.berkeleybop.org ) and Table Editor ( http://bit.ly/table-editor ) ( Table 3 ). To facilitate sharing annotations among resources, there are some existing and emergent standards for ontology annotation data exchange.…”

Section: Ontologiesmentioning

confidence: 99%

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

et al. 2018

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The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require data management plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated and shared, so that they can be easily utilized in future analyses. AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development, curation and management, with the goal of creating database products that are more Findable, Accessible, Interoperable and Reusable. We strive to promote authentic, detailed, accurate and explicit communication between all parties involved in scientific data. As a step toward this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication and sustainability with regard to data curation. Each section describes challenges and opportunities for these topics, along with recommendations and best practices.

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Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes

Cited by 48 publications

References 51 publications

Methodology: an optimized, high-yield tomato leaf chloroplast isolation and stroma extraction protocol for proteomics analyses and identification of chloroplast co-localizing proteins

Methodology: an optimized, high-yield tomato leaf chloroplast isolation and stroma extraction protocol for proteomics analyses and identification of chloroplast co-localizing proteins

Transcription factor BnaA9.WRKY47 contributes to the adaptation of Brassica napus to low boron stress by up‐regulating the boric acid channel gene BnaA3.NIP5;1

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

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