Computational protocol: A stress inducible SUMO conjugating enzyme gene (SaSce9) from a grass halophyte Spartina alterniflora enhances salinity and drought stress tolerance in Arabidopsis

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Protocol publication

[…] An expressed sequence tag #968 (EST) of Spartina alterniflora from a salinity stressed EST library constructed previously in our laboratory [] was found to be similar with SUMO conjugate enzyme gene and was referred as ‘SaSce9’ in this report. It was used for multiple sequence alignment with orthologs from different organisms. Multiple alignments of SaSce9 were performed using ClustalW program [] using amino acids, and phylogenetic analyses were conducted in MEGA 4 []. Phylogenetic tree of these sequences were inferred using the Neighbor-Joining method []. The bootstrap consensus tree inferred from 1,000 replicates was used to represent the evolutionary history of the selected eukaryotic species. The tertiary structure of SaSce9 was predicted by homology modeling based on crystallographic data deposited on the Swissprot using SWISS-MODEL []. […]

Pipeline specifications

Software tools Clustal W, MEGA, SWISS-MODEL
Applications Phylogenetics, Protein structure analysis
Organisms Saccharomyces cerevisiae, Arabidopsis thaliana
Chemicals Oxygen