OsFCA Transcripts Show More Complex Alternative Processing Patterns than its Arabidopsis Counterparts

Jang, Yun Hee; Lee, Jeong‐Hwan; Park, Hyo Young; Kim, Soon Kap; Lee, Bo Young; Suh, Mi Chung; Kim, Jeong Kook

doi:10.1007/s12374-009-9018-x

Cited by 5 publications

(4 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Alternative splicing is a mechanism by which genes can produce multiple transcript variants protein products, which allows in turn to increase the diversity of gene functions. Alternative splicing plays an important role in various processes such as development, response to pathogen and to various abiotic stresses ( Bove et al, 2008 ; Gassmann, 2008 ; Jang et al, 2009 ; Reddy & Golovkin, 2010 ). A pair of splice variants ( BvSIP1;1 α and BvSIP1;1 β ) were found in BvAQPs.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris

Kong

Yang

Wang

et al. 2017

PeerJ

View full text Add to dashboard Cite

Aquaporins (AQPs) are essential channel proteins that execute multi-functions throughout plant growth and development, including water transport, uncharged solutes uptake, stress response, and so on. Here, we report the first genome-wide identification and characterization AQP (BvAQP) genes in sugar beet (Beta vulgaris), an important crop widely cultivated for feed, for sugar production and for bioethanol production. Twenty-eight sugar beet AQPs (BvAQPs) were identified and assigned into five subfamilies based on phylogenetic analyses: seven of plasma membrane (PIPs), eight of tonoplast (TIPs), nine of NOD26-like (NIPs), three of small basic (SIPs), and one of x-intrinsic proteins (XIPs). BvAQP genes unevenly mapped on all chromosomes, except on chromosome 4. Gene structure and motifs analyses revealed that BvAQP have conserved exon-intron organization and that they exhibit conserved motifs within each subfamily. Prediction of BvAQPs functions, based on key protein domains conservation, showed a remarkable difference in substrate specificity among the five subfamilies. Analyses of BvAQPs expression, by mean of RNA-seq, in different plant organs and in response to various abiotic stresses revealed that they were ubiquitously expressed and that their expression was induced by heat and salt stresses. These results provide a reference base to address further the function of sugar beet aquaporins and to explore future applications for plants growth and development improvements as well as in response to environmental stresses.

show abstract

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris

Kong

Yang

Wang

et al. 2017

PeerJ

View full text Add to dashboard Cite

show abstract

“…The GST pull‐down assay was performed as described previously (Jang et al ., ,b). The full‐length and truncated forms of two Arabidopsis U2AF65 isoforms, a and b (At4g36690 and At1g60900), were cloned into the pGEX5X–1 vector to generate GST‐tagged proteins.…”

Section: Methodsmentioning

confidence: 99%

“…Total RNA was extracted from whole plants or the appropriate plant materials using TRIzol reagent (Invitrogen, http://www.lifetechnologies.com/order/catalog/product/15596026). RT–PCR analysis was performed as described previously (Jang et al ., ,b). The primer sets used in this analysis are listed in Table S3.…”

Section: Methodsmentioning

confidence: 99%

A homolog of splicing factor SF1 is essential for development and is involved in the alternative splicing of pre‐mRNA in Arabidopsis thaliana

et al. 2014

Self Cite

View full text Add to dashboard Cite

SUMMARYDuring initial spliceosome assembly, SF1 binds to intron branch points and interacts with U2 snRNP auxiliary factor 65 (U2AF65). Here, we present evidence indicating that AtSF1, the Arabidopsis SF1 homolog, interacts with AtU2AF65a and AtU2AF65b, the Arabidopsis U2AF65 homologs. A mutant allele of AtSF1 (At5g51300) that contains a T-DNA insertion conferred pleiotropic developmental defects, including early flowering and abnormal sensitivity to abscisic acid. An AtSF1 promoter-driven GUS reporter assay showed that AtSF1 promoter activity was temporally and spatially altered, and that full AtSF1 promoter activity required a significant proportion of the coding region. DNA chip analyses showed that only a small proportion of the transcriptome was altered by more than twofold in either direction in the AtSF1 mutant. Expression of the mRNAs of many heat shock proteins was more than fourfold higher in the mutant strain; these mRNAs were among those whose expression was increased most in the mutant strain. An RT-PCR assay revealed an altered alternative splicing pattern for heat shock transcription factor HsfA2 (At2g26150) in the mutant; this altered splicing is probably responsible for the increased expression of the target genes induced by HsfA2. Altered alternative splicing patterns were also detected for the transcripts of other genes in the mutant strain. These results suggest that AtSF1 has functional similarities to its yeast and metazoan counterparts.

show abstract

“…Alternative splicing is a mechanism by which genes can produce multiple transcript variants protein products, which allows in turn to increase the diversity of gene functions. Alternative splicing plays an important role in various processes such as development, response to pathogen and to various abiotic stresses (Bove et al 2008;Gassmann 2008;Jang et al 2009;Reddy & Golovkin 2010). A pair of splice variants (BvSIP1;1α and BvSIP1;1β) were found in BvAQPs.…”

Section: Discussionmentioning

confidence: 99%

Peer Review #1 of "Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris (v0.2)"

2017

View full text Add to dashboard Cite

Aquaporins (AQPs) are essential channel proteins that execute multi-functions throughout plant growth and development, including water transport, uncharged solutes uptake, stress response, etc. Here, we report the first genome-wide identification and characterization AQP (BvAQP) genes in sugar beet (Beta vulgaris), an important crop widely cultivated for feed, for sugar production and for bioethanol production. 28 sugar beet AQPs (BvAQPs) were identified and assigned into five subfamilies based on phylogenetic analyses: 7 of plasma membrane (PIPs), 8 of tonoplast (TIPs), 9 of NOD26-like (NIPs), 3 of small basic (SIPs), and 1 of x-intrinsic proteins (XIPs). BvAQP genes unevenly mapped on all chromosomes, except on chromosome 4. Gene structure and motifs analyses revealed that BvAQP have conserved exon-intron organization and that they exhibit conserved motifs within each subfamily. Prediction of BvAQPs functions, based on key protein domains conservation, showed a remarkable difference in substrate specificity among the five subfamilies. Analyses of BvAQPs expression, by mean of RNA-seq, in different plant organs and in response to various abiotic stresses revealed that they were ubiquitously expressed and that their expression was induced by heat and salt stresses. These results provide a reference base to address further the function of sugar beet aquaporins and to explore future applications for plants growth and development improvements as well as in response to environmental stresses.

show abstract

OsFCA Transcripts Show More Complex Alternative Processing Patterns than its Arabidopsis Counterparts

Cited by 5 publications

References 17 publications

Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris

Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris

A homolog of splicing factor SF1 is essential for development and is involved in the alternative splicing of pre‐mRNA in Arabidopsis thaliana

Peer Review #1 of "Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris (v0.2)"

Contact Info

Product

Resources

About