Isolation and in silico characterization of cDNA encoding cyclophilin from etiolated Vigna mungo seedlings

SHORT COMMUNICATION

Isolation and in silico characterization of cDNA encoding cyclophilin from etiolated Vigna mungo seedlings

Kalika Kuhar^I; Varun Kumar Gupta^I; Rekha Kansal^II; Vijay Kumar GuptaI, ^*

^IDepartment of Biochemistry, Kurukshetra University, Kurukshetra, Haryana, India

^IINational Research Centre on Plant Biotechnology, Indian Agricultural Research Institute (PUSA), New Delhi, India

ABSTRACT

A full-length cDNA clone encoding cyclophilin gene of 848 bp, including a 519 bp open reading frame, has been isolated from the cDNA library constructed from etiolated seedlings of Vigna mungo (GenBank FN668732). The cDNA sequence showed 97% identity with Vigna radiata cyclophilin mRNA. The sequence was GC rich and lacked introns. The open reading frame encoded 172 amino acid polypeptide with molecular weight 18.3 kDa and theoretical pI 8.61. BlastP analysis indicated that its putative amino acid sequence shared 100% identity with several plant cyclophilins particularly legumes. The conserved seven amino acid residues region in V. mungo cyclophilin was RSGKPLH (present in legumes) instead of KSGKPLH, indicating its similarity to the cyclophilins of other legumes. This novel V. mungo cyclophilin gene will broaden the pool of plant cyclophilin genes for further studies.

Keywords: gene library, open reading frame

Cyclophilins (CyPs), first identified as the cellular receptors of the immunosuppressant drug cyclosporin A in mammalian cells (Handschumacher et al., 1984), constitute a family of highly conserved proteins which appear to be ubiquitous in organisms, ranging from bacteria to plants and animals (Galat, 1999). CyPs and FKBPs (receptors for the FK506 and rapamycin proteins) are collectively referred to as immunophilins. These proteins have peptidyl prolyl cis-trans isomerase activity that facilitates protein folding in vivo by catalyzing the isomerization of peptide bonds preceding proline residues (Brandts et al., 1975). Transcriptional analysis showed they are mostly 18 - 23 kDa proteins expressed throughout the plant, and different isoforms are present in all parts of the cell including cytosol, nucleus, mitochondria, secretory pathway, and chloroplast (Romano et al., 2004). The abundance and diversity of CyP isoforms suggests that plant CyPs are involved in a wide variety of cellular processes, including protein folding, mRNA processing, protein trafficking and maturation, signal transduction, and abiotic and biotic stress responses (Marivet et al., 1992; Chou and Gasser, 1997; Godoy et al., 2000; Sekhar et al., 2010; Que et al., 2011).

Plant CyPs were first identified in 1990 with the isolation of CyP cDNA sequences from tomato, maize, and Brassica napus (Gasser et al., 1990). Subsequently, CyP genes have been isolated from Vicia faba (Kinoshita and Shimazaki, 1999), Glycine max (Kan et al., 2002), Arabidopsis thaliana (Romano et al., 2004), maize (Marivet et al., 1995), rice (Kumari et al., 2009), Cajanus cajan (Sekhar et al., 2010) and sugarcane (Que et al., 2011). While the A. thaliana genome contains the largest number (29) of CyP genes (Romano et al., 2004), the number of plant CyPs available in databases is small compared to that of other organisms.

To our knowledge, there is no report on isolation of CyP genes from Vigna mungo, which is an important food legume crop of the Indian subcontinent and its tolerance to various stresses is a major concern because of the comparatively less genetic diversity in this crop. In this study, we report the isolation and in silico characterization of a cDNA clone encoding CyP gene from the etiolated seedlings of V. mungo.

Total RNA was isolated from 8-day-old etiolated seedlings of V. mungo by LiCl method (Menke et al., 1996) and used for purification of mRNA using Oligotex mRNA isolation Kit (Qiagen). cDNA was synthesized using SMART^TM PCR cDNA synthesis kit (Clontech). The cDNA fragments (0.5 - 2.0 kbp) were eluted from the gel, ligated to pGEMT Easy vector (Promega) and transformed into Escherichia coli DH5α competent cells to generate cDNA library. The transformants were spread on LA plates containing ampicillin, X-gal, and IPTG and incubated at 37°C for 18 to 24 hours. The screening of the cDNA library was carried out using pigeon pea protease inhibitor gene as probe according to the method of Sambrook et al. (1989). The positive colonies were got sequenced from Techno Concept, New Delhi, India and after analysis submitted to EMBL Nucleotide Data Base.

The nucleotide sequence was analyzed in silico using VecScreen program of National Center for Biotechnology Information (NCBI), Basic Local Alignment Search Tool (BLAST), FGENESH program of Softberry web server and BioEdit. Restriction map analysis of complete open reading frame (ORF) of V. mungo CyP gene sequence was generated using software available at www.nebcutter.com. Multiple sequence alignment was done on CLUSTAL W server (Thompson et al., 1994) available at www.genome.ad.jp. The physical and chemical parameters, exact mass and hydrophobic nature of the deduced protein sequence were computed using ExPASy web server. The phylogenetic tree of the deduced amino acid sequence was generated using software available on http://www.123genomics.com.

To isolate a full-length CyP gene from etiolated seedlings of V. mungo, a cDNA library was constructed which contained 95% recombinant colonies. On screening of this library by hybridization using the pigeon pea protease inhibitor as probe, four positive clones were identified and got sequenced. The BLASTN search analysis of these sequences revealed one unique full-length cDNA sequence of 848 bp, including an ORF of 519 bp in length with no introns (Figure 1). The sequence showed 97, 89, 85, 83, 82, 82, 80 and 79% identity with CyP mRNA (cDNA) of Vigna radiata (ABO20612.1), G. max (AF456323.1), Phaseolus vulgaris (X74403.1), soybean (BT092190.1), Arachis digoi (EU170616.1), V. faba (AB012947.1), Lupinus luteus (AF178458.1), and A. thaliana (AK226392.1) respectively indicating that the isolated gene belonged to a legume CyP gene family. The cDNA sequence encoding V. mungo CyP was submitted to the Genbank with the accession number (FN668732). The length of ORF (519 bp) for V. mungo CyP cDNA sequence was identical to the ORFs of pigeon pea (Sekhar et al., 2010), sugarcane (Que et al., 2011) and rice (Kumari et al., 2009). The nucleotide composition revealed that the V. mungo CyP gene was GC rich as it contained 21.39% A, 30.44% C, 29.87% G and 18.30% T residues. Restriction map analysis of the gene sequence showed the absence of restriction sites for commonly used restriction enzymes such as EcoRI, EcoRV, HindIII, HpaI, NotI, PstI, SalI, SmaI, XbaI, XmnI. The CyP gene was released from the clone using EcoRI and NotI enzymes as they were present at the flanking sites of MCS region but not internally in the ORF.

The ORF encoded 172 amino acid polypeptide (Figure 2) with molecular weight 18.3 kDa and theoretical pI 8.61. These values are in accordance with the previous reports on CyPs (Ye and Ng, 2001; Kumari et al., 2009). The putative CyP protein encoded by V. mungo cDNA had a highly conserved functional site Trp128 (W128) present in all CyPs in eukaryotes (Liu et al., 1991). The conserved seven amino acid residues region KSGKPLH (48 - 54), which was specific to cytoplasmic CyPs in plants (Lippuner et al., 1994), was also found but with one variation i.e. K (lysine) at position 48 being replaced by R (arginine). Similar to V. mungo, the CyPs of other legumes also contained RSGKPLH (48 - 54) sequence (Figure 2). In contrast, CyPs of non-legumes such as sugarcane contained the sequence KSGKPLH (Que et al., 2011). This observation implied that the seven conserved amino acid residues regions in CYPs of legumes were RSGKPLH.

BLASTP search analysis of the deduced V. mungo CyP amino acid sequence showed 100% homology to the CyPs of other legumes viz. V. radiata, P. vulgaris, G. max and so on. ClustalW analysis calculated the best match for the V. mungo cyp and lined them to identify their similarities and differences with the sequences available on NCBI Genbank (Figure 2). The sequence was found to be rich in glycine, threonine, valine, lysine and phenylalanine. The instability index depicted a value of 20.09, which suggested the stable nature of this protein. The hydropathy index predicted hydrophilic nature of this protein implying its cytosolic/extracellular location. A dendrogram displaying phylogenetic relationship showed that V. mungo CyP sequence was closely related to CyPs from V. radiata and P. vulgaris but distant from the CyPs of Triticum, Oryza, and maize (Figure 3). The close relationship among legume CyPs might be due to the presence of similar conserved region of seven amino acids in the region of 48-54. The role of V. mungo CyP gene needs investigation for its exploitation in improving plant characteristics.

Overall, a novel full-length cDNA (848 bp) containing 519 bp ORF encoding CyP has been isolated from the cDNA library generated from etiolated seedlings of V. mungo. This gene was characterized using bioinformatics tools. It showed substantial homology to CyP genes from other legumes. The ORF encoded 172 amino acids polypeptide having a highly conserved functional site Trp128 and RSGKPLH (48-54) sequence conserved in CyPs of legumes. Phylogenetic analysis also predicted close relationship among CyP genes of V. mungo, V. radiata and P. vulgaris. The isolated novel gene will add to the resource of plant CyP genes for further use after investigation of its role.

Received: 13 February, 2012

Accepted: 23 June, 2012

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Publication Dates

• Publication in this collection
  04 Oct 2012
• Date of issue
  2012

History

• Received
  13 Feb 2012
• Accepted
  23 June 2012