Functional Characterization of DEAD-Box RNA Helicases in Arabidopsis thaliana under Abiotic Stress Conditions

Kim, Jin Sun; Kim, Kyung-Ae; Oh, Tae Woo; Park, Chul Min; Kang, Hunseung

doi:10.1093/pcp/pcn125

Cited by 100 publications

(63 citation statements)

References 35 publications

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“…4 B-D). The importance of the MRH4-like RNA helicase for growth at cold temperature in N. crassa is consistent with work on RNA helicases in many other systems (40,46,47), although the relatively modest effect of deleting this locus may be a consequence of functional redundancy among the 18 known helicases in the N. crassa genome, as has been suggested in Arabidopsis (47).…”

Section: Genes Inside Divergence Islands Have Functions and Patterns Ofsupporting

confidence: 84%

Population genomics and local adaptation in wild isolates of a model microbial eukaryote

Ellison

Hall

Kowbel

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

239

291

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Elucidating the connection between genotype, phenotype, and adaptation in wild populations is fundamental to the study of evolutionary biology, yet it remains an elusive goal, particularly for microscopic taxa, which comprise the majority of life. Even for microbes that can be reliably found in the wild, defining the boundaries of their populations and discovering ecologically relevant phenotypes has proved extremely difficult. Here, we have circumvented these issues in the microbial eukaryote Neurospora crassa by using a "reverse-ecology" population genomic approach that is free of a priori assumptions about candidate adaptive alleles. We performed Illumina whole-transcriptome sequencing of 48 individuals to identify single nucleotide polymorphisms. From these data, we discovered two cryptic and recently diverged populations, one in the tropical Caribbean basin and the other endemic to subtropical Louisiana. We conducted high-resolution scans for chromosomal regions of extreme divergence between these populations and found two such genomic "islands." Through growthrate assays, we found that the subtropical Louisiana population has a higher fitness at low temperature (10°C) and that several of the genes within these distinct regions have functions related to the response to cold temperature. These results suggest the divergence islands may be the result of local adaptation to the 9°C difference in average yearly minimum temperature between these two populations. Remarkably, another of the genes identified using this unbiased, whole-genome approach is the well-known circadian oscillator frequency, suggesting that the 2.4°-10.6°difference in latitude between the populations may be another important environmental parameter.ecological genomics | genome scan | fungi | circadian clock D iscovering the genetic basis behind adaptive phenotypes has long been considered the holy grail of evolutionary genetics. Although there are now several studies that have succeeded in identifying genes responsible for such phenotypes, the majority of them use a "forward-ecology" approach whereby candidate genes are identified on the basis of their having a function related to conspicuous traits, such as pigmentation (1-4). A paucity of obvious phenotypic traits has been a major impediment for studying adaptation in microbes because these organisms are, by nature, inconspicuous. However, next-generation sequencing technology has made it possible for individual laboratories to acquire whole-genome sequence information across populations. This innovation has enabled an unbiased "reverse-ecology" approach whereby genes with functions related to ecologically relevant traits can be identified by examining patterns of genetic diversity within and between populations and identifying candidate genes as those showing the signature of recent positive selection and/or divergent adaptation between populations (5).

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Section: Genes Inside Divergence Islands Have Functions and Patterns Ofsupporting

confidence: 84%

Population genomics and local adaptation in wild isolates of a model microbial eukaryote

Ellison

Hall

Kowbel

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

239

291

View full text Add to dashboard Cite

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“…DEAD-box RNA helicases have been implicated to have a function during stress adaptation processes, but their functional roles in plant stress responses remain to be clearly elucidated (Owttrim, 2006). Kim et al (2008) found differential expression in transcript levels of two RNA helicases viz. AtRH9 and AtRH25 in Arabidopsis thaliana exposed to cold, drought or salt stress.…”

Section: Resultsmentioning

confidence: 99%

Proteome Analysis of Detached Fronds from a Resurrection Plant Selaginella Bryopteris - Response to Dehydration and Rehydration

Deeba¹,

Pandey²,

Pathre³

et al. 2009

J Proteomics Bioinform

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Selaginella bryopteris (L.) Bak is a resurrection plant. Uniquely, its detached fronds have the ability to survive desiccation similar to that of the whole plant. In order to understand the mechanisms of desiccation tolerance, proteome studies were carried out in this plant using detached fronds to reveal proteins that were differentially expressed in response to dehydration and rehydration. There was not much difference in electrolyte leakage between control, dehydrated and rehydrated fronds. During dehydration the plants showed only respiration and a drop in F v /F m values. Both fluorescence and photosynthesis regained totally after rehydration. About 250 protein spots were reproducibly detected and analyzed. From the putatively identified spots (proteins), it was observed that proteins involved in transport, targeting and degradation were expressed more in the desiccated fronds. These findings tentatively indicate that some of the proteins could contribute a physiological advantage to S. bryopteris under desiccation.

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“…RH7 plays a role in pre-18S rRNA processing and small ribosome subunit biogenesis, and promotes plant development at low temperatures Liu et al, 2016). The cytosolic RH5, RH9, and RH25 helicases are involved in the response to both salt and cold stresses (Kant et al, 2007;Kim et al, 2008), whereas the plastid-localized RH3, which is required for intron splicing, mediates salt-and cold-stress responses (Larkin et al, 2003;Gu et al, 2014). Moreover, RH50 associates with RNA-containing megadalton complexes that are RNase-sensitive and contain ribosomal proteins, suggesting that RH50 interacts with immature chloroplast ribosomes, possibly as a ribosomal biogenesis factor.…”

Section: Rh50 and Gun1: Coexpression And Colocalizationmentioning

confidence: 99%

“…In fact, the cytosolic RH7, which is involved in pre-18S rRNA processing and biogenesis of the small (40S) ribosomal subunit, is essential for plant development at low temperatures Liu et al, 2016). Moreover, the helicases RH5, RH9, and RH25 contribute to the response to salt and cold stresses (Kant et al, 2007;Kim et al, 2008), and the plastidlocated RH3, which is required for intron splicing, mediates salt-and cold-stress responses (Gu et al, 2014).…”

Section: Rh50 Promotes Biogenesis Of the Plastid Ribosome Bymentioning

confidence: 99%

The DEAD-box RNA Helicase RH50 Is a 23S-4.5S rRNA Maturation Factor that Functionally Overlaps with the Plastid Signaling Factor GUN1

Paieri

Tadini

Manavski³

et al. 2017

Plant Physiol.

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DEAD-box RNA helicases (DBRHs) modulate RNA secondary structure, allowing RNA molecules to adopt the conformations required for interaction with their target proteins. RH50 is a chloroplast-located DBRH that colocalizes and is coexpressed with GUN1, a central factor in chloroplast-to-nucleus signaling. When combined with mutations that impair plastid gene expression (prors1-1, prpl11-1, prps1-1, prps21-1, prps17-1, and prpl24-1), rh50 and gun1 mutations evoke similar patterns of epistatic effects. These observations, together with the synergistic growth phenotype of the double mutant rh50-1 gun1-102, suggest that RH50 and GUN1 are functionally related and that this function is associated with plastid gene expression, in particular ribosome functioning. However, rh50-1 itself is not a gun mutant, although-like gun1-102-the rh50-1 mutation suppresses the downregulation of nuclear genes for photosynthesis induced by the prors1-1 mutation. The RH50 protein comigrates with ribosomal particles, and is required for efficient translation of plastid proteins. RH50 binds to transcripts of the 23S-4.5S intergenic region and, in its absence, levels of the corresponding rRNA processing intermediate are strongly increased, implying that RH50 is required for the maturation of the 23S and 4.5S rRNAs. This inference is supported by the finding that loss of RH50 renders chloroplast protein synthesis sensitive to erythromycin and exposure to cold. Based on these results, we conclude that RH50 is a plastid rRNA maturation factor.

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Functional Characterization of DEAD-Box RNA Helicases in Arabidopsis thaliana under Abiotic Stress Conditions

Cited by 100 publications

References 35 publications

Population genomics and local adaptation in wild isolates of a model microbial eukaryote

Population genomics and local adaptation in wild isolates of a model microbial eukaryote

Proteome Analysis of Detached Fronds from a Resurrection Plant Selaginella Bryopteris - Response to Dehydration and Rehydration

The DEAD-box RNA Helicase RH50 Is a 23S-4.5S rRNA Maturation Factor that Functionally Overlaps with the Plastid Signaling Factor GUN1

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