Genome-wide Characterization of Brassica rapa Genes Encoding Serine/arginine-rich Proteins: Expression and Alternative Splicing Events by Abiotic Stresses

Yoon, Eun Kyung; Krishnamurthy, Panneerselvam; Kim, Jin A.; Jeong, Mi‐Jeong; Lee, Soo In

doi:10.1007/s12374-017-0391-6

Cited by 16 publications

(18 citation statements)

References 39 publications

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“…In this study, 4 TaSR and 2 BdSR protein genes were found to have undergone segmental duplication. Interestingly, no tandem duplication of TaSR and BdSR protein genes was detected, consistent with the report in Brassica rapa [34]. Moreover, 22 homologous gene pairs were found between 22 TaSR and 12 BdSR protein genes, and most TaSR and BdSR protein genes were highly expressed in inflorescences.…”

Section: Discussionsupporting

confidence: 88%

Genome-Wide Analysis of Serine/Arginine-Rich Protein Family in Wheat and Brachypodium distachyon

Chen

Liu

et al. 2019

Plants

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By regulating the pre-mRNA splicing of other genes and themselves, plant serine/arginine-rich (SR) proteins play important roles in development and in response to abiotic stresses. Presently, the functions of most plant SR protein genes remain unclear. Wheat (Triticum aestivum) and Brachypodium distachyon are closely related species. In this study, 40 TaSR and 18 BdSR proteins were identified respectively, and they were classified into seven subfamilies: SR, RS, SCL, RSZ, RS2Z, SC35, and SR45. Similar to Arabidopsis and rice SR protein genes, most TaSR and BdSR protein genes are expressed extensively. Surprisingly, real-time polymerase chain reaction (RT-PCR) analyses showed that no alternative splicing event was found in TaSR protein genes, and only six BdSR protein genes are alternatively spliced genes. The detected alternatively spliced BdSR protein genes and transcripts are much fewer than in Arabidopsis, rice, maize, and sorghum. In the promoter regions, 92 development-related, stress-related, and hormone-related cis-elements were detected, indicating their functions in development and in response to environmental stresses. Meanwhile, 19 TaSR and 16 BdSR proteins were predicted to interact with other SR proteins or non-SR proteins, implying that they are involved in other functions in addition to modulating pre-mRNA splicing as essential components of the spliceosome. These results lay a foundation for further analyses of these genes.

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Section: Discussionsupporting

confidence: 88%

Genome-Wide Analysis of Serine/Arginine-Rich Protein Family in Wheat and Brachypodium distachyon

Chen

Liu

et al. 2019

Plants

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“…Interestingly, SR45a homologs in Arabidopsis was unperturbed by reactive oxygen species [13] indicating possible shared functions for SR45a genes between these species. Furthermore, it is confirmed that BrSR45a do not alternatively spliced under hydrogen peroxide mediated oxidative stress while splice variants in B. rapa were reported [15] Seed germination is one of the most critical stages for plant survival [25] and germination rate under drought stress indicates the degree of basal tolerance mechanism [35]. The overexpression of BrSR45a in transgenic lines had germination rate around 22-34% while the germination of mutants and control was completely inhibited in 15% or 20% PEG-induced drought stress.…”

Section: Discussionmentioning

confidence: 60%

“…Our previous study showed that abiotic stresses-including salt, drought, oxidative and heat shock-upregulate the expression of BrSR45a in B. rapa [15]. Herein, we characterized the functional role of BrSR45a in drought and heat stress responses.…”

Section: Discussionmentioning

confidence: 90%

“…This result clearly indicates that BrSR45a overexpression resulted in heat-tolerant phenotypes in Arabidopsis seedlings. However, it is not clear BrSR45a or its splice isoforms induced during heat stress [15] contributing tolerance phenotypes, and characterization of heat stress derived splice variants will shed light on the precise role in thermotolerance.…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, some AS events in A. thaliana genes and in three Brassica species (B. rapa, B. oleracea, and B. napus) have been evolutionarily conserved [14]. The model plant Arabidopsis thaliana encodes 18 SR proteins, while Brassica rapa has 25 SR genes (BrSR) that are classified into six subfamilies, named SR, RSZ, SC, SCL, RS2Z, and RS according to their distinct domain organization; most of them are responsive to oxidative, cold, and heat stress [15]. The SR genes are known to be actively alternatively spliced under stress conditions [16].…”

Section: Introductionmentioning

confidence: 99%

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Brassica Rapa SR45a Regulates Drought Tolerance via the Alternative Splicing of Target Genes

Muthusamy

Yoon

Kim

et al. 2020

Genes

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The emerging evidence has shown that plant serine/arginine-rich (SR) proteins play a crucial role in abiotic stress responses by regulating the alternative splicing (AS) of key genes. Recently, we have shown that drought stress enhances the expression of SR45a (also known as SR-like 3) in Brassica rapa. Herein, we unraveled the hitherto unknown functions of BrSR45a in drought stress response by comparing the phenotypes, chlorophyll a fluorescence and splicing patterns of the drought-responsive genes of Arabidopsis BrSR45a overexpressors (OEs), homozygous mutants (SALK_052345), and controls (Col-0). Overexpression and loss of function did not result in aberrant phenotypes; however, the overexpression of BrSR45a was positively correlated with drought tolerance and the stress recovery rate in an expression-dependent manner. Moreover, OEs showed a higher drought tolerance index during seed germination (38.16%) than the control lines. Additionally, the overexpression of BrSR45a induced the expression of the drought stress-inducible genes RD29A, NCED3, and DREB2A under normal conditions. To further illustrate the molecular linkages between BrSR45a and drought tolerance, we investigated the AS patterns of key drought-tolerance and BrSR45a interacting genes in OEs, mutants, and controls under both normal and drought conditions. The splicing patterns of DCP5, RD29A, GOLS1, AKR, U2AF, and SDR were different between overexpressors and mutants under normal conditions. Furthermore, drought stress altered the splicing patterns of NCED2, SQE, UPF1, U4/U6-U5 tri-snRNP-associated protein, and UPF1 between OEs and mutants, indicating that both overexpression and loss of function differently influenced the splicing patterns of target genes. This study revealed that BrSR45a regulates the drought stress response via the alternative splicing of target genes in a concentration-dependent manner.

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Insights into established and emerging roles of SR protein family in plants and animals

et al. 2022

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Splicing of pre-mRNA is an essential part of eukaryotic gene expression.Serine-/arginine-rich (SR) proteins are highly conserved RNA-binding proteins present in all metazoans and plants. SR proteins are involved in constitutive and alternative splicing, thereby regulating the transcriptome and proteome diversity in the organism. In addition to their role in splicing, SR proteins are also involved in mRNA export, nonsense-mediated mRNA decay, mRNA stability, and translation. Due to their pivotal roles in mRNA metabolism, SR proteins play essential roles in normal growth and development. Hence, any misregulation of this set of proteins causes developmental defects in both plants and animals. SR proteins from the animal kingdom are extensively studied for their canonical and noncanonical functions. Compared with the animal kingdom, plant genomes harbor more SR protein-encoding genes and greater diversity of SR proteins, which are probably evolved for plant-specific functions. Evidence from both plants and animals confirms the essential role of SR proteins as regulators of gene expression influencing cellular processes, developmental stages, and disease conditions.

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Genome-wide Characterization of Brassica rapa Genes Encoding Serine/arginine-rich Proteins: Expression and Alternative Splicing Events by Abiotic Stresses

Cited by 16 publications

References 39 publications

Genome-Wide Analysis of Serine/Arginine-Rich Protein Family in Wheat and Brachypodium distachyon

Genome-Wide Analysis of Serine/Arginine-Rich Protein Family in Wheat and Brachypodium distachyon

Brassica Rapa SR45a Regulates Drought Tolerance via the Alternative Splicing of Target Genes

Insights into established and emerging roles of SR protein family in plants and animals

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