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Abiotic stress regulates expression of galactinol synthase genes post-transcriptionally through intron retention in rice

  • Sritama Mukherjee
  • Sonali Sengupta
  • Abhishek Mukherjee
  • Papri Basak
  • Arun Lahiri Majumder
Original Article


Main conclusion

Expression of the Galactinol synthase genes in rice is regulated through post-transcriptional intron retention in response to abiotic stress and may be linked to Raffinose Family Oligosaccharide synthesis in osmotic perturbation.

Galactinol synthase (GolS) is the first committed enzyme in raffinose family oligosaccharide (RFO) synthesis pathway and synthesizes galactinol from UDP-galactose and inositol. Expression of GolS genes has long been implicated in abiotic stress, especially drought and salinity. A non-canonical regulation mechanism controlling the splicing and maturation of rice GolS genes was identified in rice photosynthetic tissue. We found that the two isoforms of Oryza sativa GolS (OsGolS) gene, located in chromosomes 3(OsGolS1) and 7(OsGolS2) are interspersed by conserved introns harboring characteristic premature termination codons (PTC). During abiotic stress, the premature and mature transcripts of both isoforms were found to accumulate in a rhythmic manner for very small time-windows interrupted by phases of complete absence. Reporter gene assay using GolS promoters under abiotic stress does not reflect this accumulation profile, suggesting that this regulation occurs post-transcriptionally. We suggest that this may be due to a surveillance mechanism triggering the degradation of the premature transcript preventing its accumulation in the cell. The suggested mechanism fits the paradigm of PTC-induced Nonsense-Mediated Decay (NMD). In support of our hypothesis, when we pharmacologically blocked NMD, the full-length pre-mRNAs were increasingly accumulated in cell. To this end, our work suggests that a combined transcriptional and post transcriptional control exists in rice to regulate GolS expression under stress. Concurrent detection and processing of prematurely terminating transcripts coupled to repressed splicing can be described as a form of Regulated Unproductive Splicing and Translation (RUST) and may be linked to the stress adaptation of the plant, which is an interesting future research possibility.


Rice GolS Abiotic stress RUST Splicing Regulation 



The project is supported by funds from Department of Biotechnology and the Raja Ramanna Fellowship Project of the Department of Atomic Energy, Government of India awarded to ALM, currently an INSA Senior Scientist. SM was supported by Fellowship from the Council of Scientific and Industrial Research (CSIR) and Department of Atomic Energy (DAE). SS was a Staff Scientist supported by DBT and Fast-Track young scientist scheme of Department of Science and Technology (DST), Government of India. AM is supported by the DBT project.


This study is funded by grants from the Department of Biotechnology (DBT654BT/AB/05/02/2007-III) and the Raja Ramanna Fellowship Project of the Department of Atomic Energy (D.O No. 10/25/2010/RRF-R & D-II/3118), both from the Government of India, awarded to ALM, currently an INSA Senior Scientist. SM and PB was supported by Fellowship from the Council of Scientific and Industrial Research (CSIR) and Department of Atomic Energy (DAE). AM is supported by the DBT project. SSG was a Staff Scientist supported by DBT and Fast-Track Young Scientist Scheme of Department of Science and Technology (DST), Government of India.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Supplementary material

425_2018_3046_MOESM1_ESM.pdf (89 kb)
Online Resource 1 (ESM_1.pdf): Primers and their sequences (PDF 89 kb)
425_2018_3046_MOESM2_ESM.pdf (91 kb)
Online Resource 2 (ESM_2.pdf): Splice site analysis of GolS genes in rice and wild rice relatives. Os: Oryza sativa, Ob: Oryza brachyantha, Om: Oryza minuta (PDF 90 kb)
425_2018_3046_MOESM3_ESM.tif (2.6 mb)
Online Resource 3 (ESM_3.pdf): Sequence alignment of OsGolS with wild rice relatives. Exon-exon junctions are represented with black boxes. Os: Oryza sativa, Ob: Oryza brachyantha, Or: Oryza rufipogon, Om: Oryza minuta (TIFF 2668 kb)
425_2018_3046_MOESM4_ESM.tif (1.5 mb)
Online Resource 4 (ESM_4.tif): a PCR amplification of GolS genes from cDNA of Porteresia coarctata (PcGolS1/PcGolS2) and Oryza sativa (OsGolS1/OsGolS2). Sequence alignment of OsGolS1 and PcGolS1 (b) and OsGolS2 and PcGolS2 (c) showing complete identity (TIFF 1585 kb)
425_2018_3046_MOESM5_ESM.tif (1.1 mb)
Online Resource 5 (ESM_5.tif): Semiquantitative RT-PCR of (a) OsGolS1 and (b) OsGolS2 in one month old seedlings. Red triangles show occurrence of pre-mRNA, green triangles show occurrence of mature mRNA. Days indicate the stress treatment. c Quantitative PCR for all the above conditions. ‘*’ represents p-value < 0.05 as calculated through student’s t-test. (TIFF 1143 kb)
425_2018_3046_MOESM6_ESM.tif (610 kb)
Online Resource 6 (ESM_6.tif): a–b Searching for an intronless OsGolS from different tissues. Pre-mRNAs were amplified only in mature leaves and germinated seedlings. c Quantitative PCR for all the above conditions. ‘*’ represents p value < 0.05 as calculated through student’s t-test (TIFF 610 kb)
425_2018_3046_MOESM7_ESM.tif (1.7 mb)
Online Resource 7 (ESM_7.tif): In planta expression of OsGolS proteins. a Schematic diagram of binary vector pCAMBIA-1301 construct used in transformation. Portion of T-DNA from Left border to Right border is shown in this figure. Gene of interest (OsGolS1/2; pre-mature/mature) was placed under the constitutive expression of CaMV 35S promoter and NOS terminator. Hygromycin resistant hptII gene is present in the vector backbone as plant selection and GUS is present as reporter gene. b Stages of callus initiation and Agrobacterium mediated transformation. (A) Dehusked seeds of rice IR64 cultivar kept on callus initiation medium (CIM), (B) Mature scutellar calli after 4 weeks of culture, ready for transformation, (C-D) Selection of infected calli in selection medium (CIM + Hyg-50 mg/L; two rounds, each for 15 days). c Immunoblot showing overexpression of his-tagged OsGolS1& OsGolS2 proteins (pre-mature and mature) in rice calli. Lane1: pre-mature OsGolS1, lane2: mature OsGolS1, lane3: pre-mature OsGolS2 and lane4: mature OsGolS2. Lane(s) 1&3 showed sign of degradation. Distinct bands of ~ 39.5 kDa and ~ 37 kDa full-length functional proteins were detected in lanes 2 and 4, respectively (TIFF 1782 kb)
425_2018_3046_MOESM8_ESM.tif (382 kb)
Online Resource 8 (ESM_8.tif): Quantitative RT-PCR expression of GUS in POsGolS1 and POsGolS2 in 7-day-old etiolated rice seedlings under a salt stress (0, 50 and 150 mM NaCl) and b dehydration stress (0, 10 and 20% PEG) (TIFF 382 kb)
425_2018_3046_MOESM9_ESM.tif (1.1 mb)
Online Resource 9 (ESM_9.tif): Semi-quantitative (a-b) and quantitative (c-d) PCR for first exons (OsGolS1: 326 bp; OsGolS2: 774 bp). The samples used were one-month old plants grown under normal photoperiod (16:8 light:dark) at control conditions treated with low salt (50 mM NaCl) for 8–11 days; each treated with cycloheximide with an untreated control. DAS—days after stress; D1—drug treatment1; FE—first exon. In drug treatment 1, whole seedlings were immersed in the drug. ‘*’ represent p-value < 0.05 as calculated through student’s t-test (TIFF 1169 kb)
425_2018_3046_MOESM10_ESM.tif (317 kb)
Online Resource 10 (ESM_10.tif): Quantitative RT-PCR from nuclear mRNA of leaves of 10 days old rice seedlings for the detection of NMD-sensitive transcripts (OsGolS1 and OsGolS2) (TIFF 316 kb)


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Authors and Affiliations

  1. 1.Division of Plant BiologyBose Institute (Centenary Campus)KolkataIndia
  2. 2.Botany DepartmentBethune CollegeKolkataIndia
  3. 3.School of Plant Environment and Soil SciencesLSUAg CenterBaton RougeUSA

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