Genome-wide characterization and expression profiling of PDI family gene reveals function as abiotic and biotic stress tolerance in Chinese cabbage (Brassica rapa ssp. pekinensis)

Abstract

BackgroundProtein disulfide isomerase (PDI) and PDI-like proteins contain thioredoxin domains that catalyze protein disulfide bond, inhibit aggregation of misfolded proteins, and function in isomerization during protein folding in endoplasmic reticulum and responses during abiotic stresses.Chinese cabbage is widely recognized as an economically important, nutritious vegetable, but its yield is severely hampered by various biotic and abiotic stresses. Because of, it is prime need to identify those genes whose are responsible for biotic and abiotic stress tolerance. PDI family genes are among of them.ResultsWe have identified 32 PDI genes from the Br135K microarray dataset, NCBI and BRAD database, and in silico characterized their sequences. Expression profiling of those genes was performed using cDNA of plant samples imposed to abiotic stresses; cold, salt, drought and ABA (Abscisic Acid) and biotic stress; Fusarium oxysporum f. sp. conglutinans infection. The Chinese cabbage PDI genes were clustered in eleven groups in phylogeny. Among them, 15 PDI genes were ubiquitously expressed in various organs, while 24 PDI genes were up-regulated under salt and drought stress. By contrast, cold and ABA stress responsive gene number were ten and nine, respectively. In case of F. oxysporum f. sp. conglutinans infection 14 BrPDI genes were highly up-regulated. Interestingly, BrPDI1–1 gene was identified as putative candidate against abiotic (salt and drought) and biotic stresses, BrPDI5–2 gene for ABA stress, and BrPDI1–4, 6–1 and 9–2 were putative candidate genes for both cold and chilling injury stresses.ConclusionsOur findings help to elucidate the involvement of PDI genes in stress responses, and they lay the foundation for functional genomics in future studies and molecular breeding of Brassica rapa crops. The stress-responsive PDI genes could be potential resources for molecular breeding of Brassica crops resistant to biotic and abiotic stresses.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4277-2) contains supplementary material, which is available to authorized users.

Comparative Proteomic Analysis of Nodulated and Non-Nodulated Casuarina glauca Sieb. ex Spreng. Grown under Salinity Conditions Using Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS)

“…A glycine-rich RNA binding protein, member of a protein family involved in various stress responses [57], was only upregulated in the KNO 3 + series while an annexin, a member of a family of calcium-and phospholipid-binding proteins that has been linked to various stress responses [58], was upregulated in both groups. A protein disulfide isomerase, which is involved in the endoplasmic reticulum stress response that is also linked to salt stress [59,60], was only upregulated under salt stress in the KNO 3 + group. In summary, while some stress response pathways seem to be active in both series, others were only active either in non-nodulated plants growing on nitrate as N source, or in nodulated plants.…”

In silico identification and expression analysis of superoxide dismutase (SOD) gene family in Medicago truncatula

“…The segmental gene duplication event was marked based on the previously described criteria: the sequence alignment length covered more than 80% of the longer gene, and the identity of the aligned regions was over 70% (Jia et al 2017;Song et al 2017). The tandem duplicated genes were defined as two or more homologous genes located on one single chromosome with a distance of 100 kb without any intervening gene (Kayum et al 2017).…”

Source-Sink Modifications Affect Leaf Senescence and Grain Mass in Wheat

“…Protein disulfide isomerases (PDIs) are enzymes found primarily in the endoplasmic reticulum (ER) in eukaryotes play a vital role in protein folding. The up-regulated levels of PDIs (A0A024FRN3, A0A1D5XQP7, A0A1D5XQP9, B9A8E3, F8THZ6, Q6JAB5, Q93XQ8) in the present study indicated the higher PDI activity (MF) and confirmed the active status of protein synthesis (Hayano et al ., 1995; Lv et al ., 2016; Kayum et al ., 2017) and higher resistance to abiotic stresses (Kayum et al ., 2017). This conclusion was strongly confirmed by the upregulation of 60S ribosomal protein L29 (A0A1D5RRD3), 40S ribosomal protein S12 (A0A1D5UFM0, A0A1D5UVS7) and Eukaryotic translation initiation factor 4B1 (Q9AUJ7) (Table S1).…”