Effective research, education, and outreach efforts by the
A key remit of the
- NSF-PAR ID:
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Plant Direct
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Effective research, education, and outreach efforts by the
Arabidopsis thalianacommunity, as well as other scientific communities that depend on Arabidopsis resources, depend vitally on easily available and publicly‐shared resources. These resources include reference genome sequence data and an ever‐increasing number of diverse data sets and data types. TAIR(The Arabidopsis Information Resource) and Araport (originally named the Arabidopsis Information Portal) are community informatics resources that provide tools, data, and applications to the more than 30,000 researchers worldwide that use in their work either Arabidopsis as a primary system of study or data derived from Arabidopsis. Four years after Araport's establishment, the IAICheld another workshop to evaluate the current status of Arabidopsis Informatics and chart a course for future research and development. The workshop focused on several challenges, including the need for reliable and current annotation, community‐defined common standards for data and metadata, and accessible and user‐friendly repositories/tools/methods for data integration and visualization. Solutions envisioned included (a) a centralized annotation authority to coalesce annotation from new groups, establish a consistent naming scheme, distribute this format regularly and frequently, and encourage and enforce its adoption. (b) Standards for data and metadata formats, which are essential, but challenging when comparing across diverse genotypes and in areas with less‐established standards (e.g., phenomics, metabolomics). Community‐established guidelines need to be developed. (c) A searchable, central repository for analysis and visualization tools. Improved versioning and user access would make tools more accessible. Workshop participants proposed a “one‐stop shop” website, an Arabidopsis “Super‐Portal” to link tools, data resources, programmatic standards, and best practice descriptions for each data type. This must have community buy‐in and participation in its establishment and development to encourage adoption.
The flowering plant
Arabidopsis thalianais a dicot model organism for research in many aspects of plant biology. A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, including mRNA, the various classes of non‐coding RNA, and small RNA. The TAIR10 annotation update had a profound impact on Arabidopsis research but was released more than 5 years ago. Maintaining the accuracy of the annotation continues to be a prerequisite for future progress. Using an integrative annotation pipeline, we assembled tissue‐specific RNA‐Seq libraries from 113 datasets and constructed 48 359 transcript models of protein‐coding genes in eleven tissues. In addition, we annotated various classes of non‐coding RNAincluding micro RNA, long intergenic RNA, small nucleolar RNA, natural antisense transcript, small nuclear RNA, and small RNAusing published datasets and in‐house analytic results. Altogether, we identified 635 novel protein‐coding genes, 508 novel transcribed regions, 5178 non‐coding RNAs, and 35 846 small RNAloci that were formerly unannotated. Analysis of the splicing events and RNA‐Seq based expression profiles revealed the landscapes of gene structures, untranslated regions, and splicing activities to be more intricate than previously appreciated. Furthermore, we present 692 uniformly expressed housekeeping genes, 43% of whose human orthologs are also housekeeping genes. This updated Arabidopsis genome annotation with a substantially increased resolution of gene models will not only further our understanding of the biological processes of this plant model but also of other species.
Light signal provides the spatial and temporal information for plants to adapt to the prevailing environmental conditions. Alterations in light quality and quantity can trigger robust changes in global gene expression. In
Arabidopsis thaliana, two groups of key factors regulating those changes in gene expression are CONSTITUTIVE PHOTOMORPHOGENESIS/ DEETIOLATED/ FUSCA( COP/ DET/ FUS) and a subset of basic helix‐loop‐helix transcription factors called PHYTOCHROME‐ INTERACTING FACTORS( PIFs). Recently, rapid progress has been made in characterizing the E3 ubiquitin ligases for the light‐induced degradation of PIF1, PIF3 and PIF4; however, the E3 ligase(s) for PIF5 remains unknown. Here, we show that the CUL4 COP1– SPAcomplex is necessary for the red light‐induced degradation of PIF5. Furthermore, COP1 and SPAproteins stabilize PIF5 in the dark, but promote the ubiquitination and degradation of PIF5 in response to red light through the 26S proteasome pathway. Genetic analysis illustrates that overexpression of can partially suppress both PIF5 cop1‐4and spaQseedling de‐etiolation phenotypes under dark and red‐light conditions. In addition, the PIF5 protein level cycles under both diurnal and constant light conditions, which is also defective in the cop1‐4and spaQbackgrounds. Both cop1‐4and spaQshow defects in diurnal growth pattern. Overexpression of partially restores growth defects in PIF5 cop1‐4and spaQunder diurnal conditions, suggesting that the COP1– SPAcomplex plays an essential role in photoperiodic hypocotyl growth, partly through regulating the PIF5 level. Taken together, our data illustrate how the CUL4 COP1– SPAE3 ligase dynamically controls the PIF5 level to regulate plant development.
BRs) are essential plant growth‐promoting hormones involved in many processes throughout plant development, from seed germination to flowering time. Since BRsdo not undergo long‐distance transport, cell‐ and tissue‐specific regulation of hormone levels involves both biosynthesis and inactivation. To date, ten BR‐inactivating enzymes, with at least five distinct biochemical activities, have been experimentally identified in the model plant Arabidopsis thaliana. Epigenetic interactions between T‐DNAinsertion alleles and genetic linkage have hindered analysis of higher‐order null mutants in these genes. A previous study demonstrated that the bas1‐2 sob7‐1 ben1‐1triple‐null mutant could not be characterized due to epigenetic interactions between the exonic T‐DNAinsertions in bas1‐2and sob7‐1,causing the intronic T‐DNAinsertion of ben1‐1to revert to a partial loss‐of‐function allele. We used CRISPR‐Cas9genome editing to avoid this problem and generated the bas1‐2 sob7‐1 ben1‐3triple‐null mutant. This triple‐null mutant resulted in an additive seedling long‐hypocotyl phenotype. We also uncovered a role for ‐mediated BEN1 BR‐inactivation in seedling cotyledon petiole elongation that was not observed in the single ben1‐2null mutant but only in the absence of both and BAS1 . In addition, genetic analysis demonstrated that SOB7 does not contribute to the early‐flowering phenotype, which BEN1 and BAS1 redundantly regulate. Our results show that SOB7 , BAS1 and BEN1, have overlapping and independent roles based on their differential spatiotemporal tissue expression patterns SOB7
The catalytic activity of mitogen‐activated protein kinases (
MAPKs) is dynamically modified in plants. Since MAPKs have been shown to play important roles in a wide range of signaling pathways, the ability to monitor MAPKactivity in living plant cells would be valuable. Here, we report the development of a genetically encoded MAPKactivity sensor for use in Arabidopsis thaliana. The sensor is composed of yellow and blue fluorescent proteins, a phosphopeptide binding domain, a MAPKsubstrate domain and a flexible linker. Using in vitrotesting, we demonstrated that phosphorylation causes an increase in the Förster resonance energy transfer ( FRET) efficiency of the sensor. The FRETefficiency can therefore serve as a readout of kinase activity. We also produced transgenic Arabidopsis lines expressing this sensor of MAPKactivity ( SOMA) and performed live‐cell imaging experiments using detached cotyledons. Treatment with NaCl, the synthetic flagellin peptide flg22 and chitin all led to rapid gains in FRETefficiency. Control lines expressing a version of SOMAin which the phosphosite was mutated to an alanine did not show any substantial changes in FRET. We also expressed the sensor in a conditional loss‐of‐function double‐mutant line for the Arabidopsis MAPKgenes and MPK3 . These experiments demonstrated that MPK6 MPK3/6 are necessary for the NaCl‐induced FRETgain of the sensor, while other MAPKs are probably contributing to the chitin and flg22‐induced increases in FRET. Taken together, our results suggest that SOMAis able to dynamically report MAPKactivity in living plant cells.