Deschampsia antarctica É.Desv.
2.1. Analysis of CHS gene from D. antarctica DaCHS full-length cDNA was obtained using the partial sequence of an EST as the template, designing primers for 5′- and 3′-RACE-PCR reactions. A sequence of 1741 bp with a poly (A) tail, containing 143 bp and 407 bp of 5′- and 3′ -UTR sequences respective...
| Main Authors: | , , , , , |
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| Format: | Other/Unknown Material |
| Language: | unknown |
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Zenodo
2020
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| Subjects: | |
| Online Access: | https://doi.org/10.5281/zenodo.8301817 http://treatment.plazi.org/id/03D71B6CFFFEFB63633EFD11FAF6C369 |
| Summary: | 2.1. Analysis of CHS gene from D. antarctica DaCHS full-length cDNA was obtained using the partial sequence of an EST as the template, designing primers for 5′- and 3′-RACE-PCR reactions. A sequence of 1741 bp with a poly (A) tail, containing 143 bp and 407 bp of 5′- and 3′ -UTR sequences respectively, was obtained as well as an ORF of 1191 bp with a deduced polypeptide sequence of 397 amino acids. This sequence was deposited in GenBank (accession number MG766286). Analysis of the predicted DaCHS protein demonstrated the typical conserved structural features among CHSs. The mature protein has an estimated molecular weight of 43.53 kDa (pI 6.44). Important residues for the active site motif can be observed in DaCHS (C167, F218, H306 and N339). Moreover, the active site motif is formed by a variety of residues typical of the chalcone synthase family, which are also observed in the Deschampsia protein sequence. It has two domains: the N-terminal domain ranges from amino acid 8 to 231 and the C-terminal domain ranges from amino acid 241 to 391. Multiple alignment analysis with fourteen other CHS sequences of representative monocotyledons showed a highly conserved pattern among sequences (Fig. 1). All these findings suggest that DaCHS belongs to the CHS family. 2.2. Phylogenetic analysis of DaCHS Fifteen other CHS amino acid sequences were considered for phylogenetic analysis of DaCHS, including proteins from O. sativa L, Z. mays L. and H. vulgare L. According to these results, DaCHS can be grouped together with H. vulgare CHS 1 (Fig. 2). Acetate kinase A from Streptococcus equi was used as the outlier. 2.3. DaCHS homology model Analysis of the DaCHS 3D-structure showed one pocket in the middle zone of the protein. Substrates interact with the catalytic amino acids in this location. It contains the typical residues C167, F218, F268, H306 and N339. The protein is composed of 12 α helices, 8α helices 310, 13β sheets and 23 loops (Fig. 3). The best coincidence in the pairwise alignment analysis was found with O. sativa ... |
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