Computational insights into GST gene family identification and characterization in Caffea canephora

Swati Vaish

Abstract


Glutathione S-transferases are a multifunctional protein super family that is involved in diverse plant functions such as defense mechanisms, signaling, stress response, secondary metabolism, plant growth and development [1]. GSTs are classified into three distinct superfamilies namely cytoplasmic, mitochondrial and microsomal. Cytopalsmic and mitochondrial GSTs are soluble; and microsomal GSTs (MAPEGs) are membrane associated proteins involved in eicosanoid and glutathione metabolism. Soluble plant GSTs are further categorized into 14 different classes based on sequence similarity, genomic organization, immunological cross reactivity and functions viz. tau (U), phi (F), theta (T), zeta (Z), lambda (L), Dehydroascorbate reductase (DHAR), Tetrachloro-hydroquinone dehalogenase (TCHQD), Elongation factor 1Bγ (EF1Bγ), microsomal prostaglandin E synthase type 2 (mPGES2), Glutathionyl hydroquinone reductase (GHR), iota, hemerythrin, metaxin and Ure2p [2]. GST gene family have been identified and characterized in various plant species such as 39 GSTs in Cucumis melo var. saccharinus [3], 92 GSTs in Medicago truncatula [4], 32 GSTs in Cucurbita maxima [5], 330 GSTs Triticum aestivum [6], 82 GSTs in Raphanus sativus [7], 51 GSTs in chickpea [8] and 31 GSTs in Vigna radiata [9].
Although the coffee whole genome sequence is available but the distribution of GST genes on coffee chromosomes, their subcellular localization, gene structure, their evolutionary relation with each other, conserved motifs and their roles are still unknown. A total of 71 GST genes with the canonical thioredoxin fold have been identified belonging to nine GST classes namely tau, phi, theta, zeta, lambda, DHAR, EF1G, mPGES2 and GHR. Tau and theta GST genes were highest in number. The 71 GST genes were distributed into 10 coffee chromosomes. The physicochemical features showed most of the CGST proteins as highly stable and hydrophilic protein, majorly localized in the cytoplasm. Gene architecture showed the conservation of exon numbers in each GST classes. MEME analyses revealed few class specific motifs and many motifs were found in all the GST classes. Multiple sequence alignment of coffee GST revealed the Ser and Cys as conserved catalytic residue. Gene duplication analyses showed both the tandem and segmental duplication as a driving force for GST gene family expansion in coffee. The phylogenetic analyses of coffee GST with angiosperm (Arabidopsis and rice), gymnosperm (L. kaempferi) and bryophyte (P. patens) revealed that the evolution of plant GSTs might be earlier than their division into individual groups such as bryophyte, pteridophyte, gymnosperm and angiosperm and also the each GST classes have diverged prior to the division of monocot and dicot. Additionally, the numbers of each class of GSTs expanded in a species specific manner independently and irrespective of their genome size. Cis-regulatory element analyses showed the dominance of light responsive element followed by stress and hormone responsive element. The comprehensive and organized studies of CcGST genes family provides groundwork for further functional analyses of CcGST genes in coffee at molecular level and further for plant breeding approaches.


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SWATI ET AL

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