In vitro and in silico cloning of Xenopus laevis SOD2 cDNA and its phylogenetic analysis.
By using the methodology of both wet and dry biology (i.e., RT-PCR and cycle sequencing, and biocomputational technology, respectively) and the data obtained through the Genome Projects, we have cloned Xenopus laevis SOD2 (MnSOD) cDNA and determined its nucleotide sequence. These data and the deduced protein primary structure were compared with all the other SOD2 nucleotide and amino acid sequences from eukaryotes and prokaryotes, published in public databases. The analysis was performed by using both Clustal W, a well known and widely used program for sequence analysis, and AntiClustAl, a new algorithm recently created and implemented by our group. Our results demonstrate a very high conservation of the enzyme amino acid sequence during evolution, which proves a close structure-function relationship. This is to be expected for very ancient molecules endowed with critical biological functions, performed through a specific structural organization. The nucleotide sequence conservation is less pronounced: this too was foreseeable, due to neutral mutations and to the species-specific codon usage. The data obtained by using AntiClustAl are comparable with those produced with Clustal W, which validates this algorithm as an important new tool for biocomputational analysis. Finally, it is noteworthy that evolutionary trees, drawn by using all the available data on SOD2 nucleotide sequences and amino acid and either Clustal W or AntiClustAl, are comparable to those obtained through phylogenetic analysis based on fossil records.
Purrello
Michele
M
Dipartimento di Scienze Biomediche, Sezione di Biologia e Genetica, Università di Catania, Catania, Italy.
Di Pietro
Cinzia
C
Ragusa
Marco
M
Pulvirenti
Alfredo
A
Giugno
Rosalba
R
Di Pietro
Valentina
V
Emmanuele
Giovanni
G
Travali
Salvo
S
Scalia
Marina
M
Shasha
Dennis
D
Ferro
Alfredo
A
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D003001:Cloning, Molecular; D019295:Computational Biology; D018076:DNA, Complementary / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D013482:Superoxide Dismutase / Q000145:classification* / Q000235:genetics*; D014982:Xenopus laevis / Q000235:genetics*; D000099156:Superoxide Dismutase 2
D018076:DNA, Complementary; D013482:Superoxide Dismutase; D000099156:Superoxide Dismutase 2