A high resolution map of the <i>Arabidopsis thaliana</i> developmental transcriptome based on <scp>RNA</scp>‐seq profiling

Klepikova, Anna V.; Kasianov, Artem S.; Gerasimov, Evgeny S.; Logacheva, Maria D.; Penin, Aleksey A.

doi:10.1111/tpj.13312

Cited by 600 publications

(702 citation statements)

References 49 publications

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“…A possible explanation could be that this is due to the differential expression of HCF222 in young and mature plants or leaves. The expression profile of HCF222 in the TRAVA database (Klepikova et al, 2016), which comprises RNA sequencing data for different stages and tissues of Arabidopsis, supports this assumption (Supplemental Fig. S5).…”

Section: Hcf222 Possibly Catalyzes Protein Maturation At the Thylakoidssupporting

confidence: 54%

The DnaJ-Like Zinc-Finger Protein HCF222 Is Required for Thylakoid Membrane Biogenesis in Plants

et al. 2017

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To understand the biogenesis of the thylakoid membrane in higher plants and to identify auxiliary proteins required to build up this highly complex membrane system, we have characterized the allelic nuclear mutants high chlorophyll fluorescence222-1 (hcf222-1) and hcf222-2 and isolated the causal gene by map-based cloning. In the ethyl methanesulfonate-induced mutant hcf222-1, the accumulation of the cytochrome b 6 f (Cytb6f) complex was reduced to 30% compared with the wild type. Other thylakoid membrane complexes accumulated to normal levels. The T-DNA knockout mutant hcf222-2 showed a more severe defect with respect to thylakoid membrane proteins and accumulated only 10% of the Cytb6f complex, accompanied by a reduction in photosystem II, the photosystem II light-harvesting complex, and photosystem I. HCF222 encodes a protein of 99 amino acids in Arabidopsis (Arabidopsis thaliana) that has similarities to the cysteine-rich zinc-binding domain of DnaJ chaperones. The insulin precipitation assay demonstrated that HCF222 has disulfide reductase activity in vitro. The protein is conserved in higher plants and bryophytes but absent in algae and cyanobacteria. Confocal fluorescence microscopy showed that a fraction of HCF222-green fluorescent protein was detectable in the endoplasmic reticulum but that it also could be recognized in chloroplasts. A fusion construct of HCF222 containing a plastid transit peptide targets the protein into chloroplasts and was able to complement the mutational defect. These findings indicate that the chloroplast-targeted HCF222 is indispensable for the maturation and/or assembly of the Cytb6f complex and is very likely involved in thiol-disulfide biochemistry at the thylakoid membrane.

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Section: Hcf222 Possibly Catalyzes Protein Maturation At the Thylakoidssupporting

confidence: 54%

The DnaJ-Like Zinc-Finger Protein HCF222 Is Required for Thylakoid Membrane Biogenesis in Plants

et al. 2017

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“…The Arabidopsis eFP Browser (http://www.bar.utoronto.ca/) 45 and Transcriptome Variation Analyses (TraVA; http://travadb.org) 46 databases indicate that the expression of ORB1 is most intense in above-ground tissues. To define the expression pattern of ORB1 more precisely, we generated an ORB1 pro :GUS construct.…”

Section: Resultsmentioning

confidence: 99%

Deficient glutamate biosynthesis triggers a concerted upregulation of ribosomal protein genes in Arabidopsis

Muñoz-Nortes

Pérez-Pérez

Sarmiento-Mañús

et al. 2017

Sci Rep

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Biomass production requires the coordination between growth and metabolism. In a large-scale screen for mutants affected in leaf morphology, we isolated the orbiculata1 (orb1) mutants, which exhibit a pale green phenotype and reduced growth. The combination of map-based cloning and next-generation sequencing allowed us to establish that ORB1 encodes the GLUTAMATE SYNTHASE 1 (GLU1) enzyme, also known as FERREDOXIN-DEPENDENT GLUTAMINE OXOGLUTARATE AMINOTRANSFERASE 1 (Fd-GOGAT1). We performed an RNA-seq analysis to identify global gene expression changes in the orb1–3 mutant. We found altered expression levels of genes encoding enzymes involved in nitrogen assimilation and amino acid biosynthesis, such as glutamine synthetases, asparagine synthetases and glutamate dehydrogenases, showing that the expression of these genes depends on the levels of glutamine and/or glutamate. In addition, we observed a concerted upregulation of genes encoding subunits of the cytosolic ribosome. A gene ontology (GO) analysis of the differentially expressed genes between Ler and orb1–3 showed that the most enriched GO terms were ‘translation’, ‘cytosolic ribosome’ and ‘structural constituent of ribosome’. The upregulation of ribosome-related functions might reflect an attempt to keep protein synthesis at optimal levels even when the pool of glutamate is reduced.

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“…It is possible that these epidermal regulators could be involved in the regulation of pigment biosynthesis and accumulation in the seed coat. While TRY has been identified as a potential regulator of pigment accumulation in the early Arabidopsis seed coat (Khan et al ), neither ETC1 nor ETC3 are expressed in Arabidopsis seed development (Belmonte et al ; Klepikova et al ). Given the presence of multiple homologues of both ETC1 and ETC3 in B. napus , it is possible that some homologues may have diverged and show greater involvement in seed coat development than their Arabidopsis counterparts.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome landscape of the early Brassica napus seed

Ziegler

Khan

Kalichuk

et al. 2019

JIPB

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Brassica napus L. (canola) is one of the world's most economically important oilseeds. Despite our growing knowledge of Brassica genetics, we still know little about the genes and gene regulatory networks underlying early seed development. In this work, we use laser microdissection coupled with RNA sequencing to profile gene activity of both the maternal and filial subregions of the globular seed. We find subregions of the chalazal end including the chalazal endosperm, chalazal proliferating tissue, and chalazal seed coat, have unique transcriptome profiles associated with hormone biosynthesis and polysaccharide metabolism. We confirm that the chalazal seed coat is uniquely enriched for sucrose biosynthesis and transport, and that the chalazal endosperm may function as an important regulator of the maternal region through brassinosteroid synthesis. The chalazal proliferating tissue, a poorly understood subregion, was specifically enriched in transcripts associated with megasporogenesis and trehalose biosynthesis, suggesting this ephemeral structure plays an important role in both sporophytic development and carbon nutrient balance, respectively. Finally, compartmentalization of transcription factors and their regulatory circuits has uncovered previously unknown roles for the chalazal pole in early seed development.

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A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA‐seq profiling

Cited by 600 publications

References 49 publications

The DnaJ-Like Zinc-Finger Protein HCF222 Is Required for Thylakoid Membrane Biogenesis in Plants

The DnaJ-Like Zinc-Finger Protein HCF222 Is Required for Thylakoid Membrane Biogenesis in Plants

Deficient glutamate biosynthesis triggers a concerted upregulation of ribosomal protein genes in Arabidopsis

Transcriptome landscape of the early Brassica napus seed

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