Computational protocol: Nuclear Importation of Mariner Transposases among Eukaryotes: Motif Requirements and Homo-Protein Interactions

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Protocol publication

[…] In an attempt to locate putative monopartite and bipartite NLSs, we first conducted an in-silico analysis using the amino acid sequence of three active mariner transposases: MOS1, HIMAR1 and MCMAR1 belonging to the mauritiana, irritans and elegans sub-families, respectively. All the sequences of MLE transposases so far described are rich in basic residues (, red letters). As a consequence, they have a predicted high IEP (isoelectric point; ). Sequence analysis of the three transposases revealed that basic residues are not homogenously distributed, and two regions with very different IEP values can be distinguished (, ). The N-terminal regions spanning from residues 1-237/246 were richer in basic residues than the region consisting of the last 101–102 C-terminal residues. Taking into account the distribution of the basic residues in MLE transposases, motifs characteristic of NLSs, consisting of H, K and R located in the N-terminal region can be expected to be present. Moreover, sequence comparisons revealed that there was no stretch of basic residues, conserved in a sequence and location that would make it possible to consider them as common monopartite or bipartite NLSs shared by MOS1, HIMAR1 and MCMAR1. This therefore supports the hypothesis that no cardinal conserved monopartite or bipartite NLS was present in these three MLE transposases, and that each of them uses different NLSs. Searches for cardinal and degenerated NLSs were monitored using PredictNLS at http://cubic.bioc.columbia.edu/predictNLS/ or PSORTII at http://psort.ims.u-tokyo.ac.jp/form2.html. We detected 2 monopartite and 2 bipartite putative NLSs in MOS1 (, grey boxed letters, designated M2 and M4, and M1 and M3, respectively), 2 monopartite NLSs in HIMAR1 (, grey boxed letters, designated H1 and H2), and 1 in MCMAR1 (, grey boxed letters, designated N1). All these NLSs were degenerate, apart from M3, which was previously proposed to be an active bipartite NLS in MOS1 , and M4, which was very similar to that of the SV40 T antigen. Interestingly, taking into account the structure of MOS1 and the alignment of three sequences of transposase, we observed that M1, M3, H2 and N1 are included in with α-helix or β-sheet folds, what strongly impairs that they are functional NLS. […]

Pipeline specifications

Software tools PredictNLS, PSORT
Application Protein sequence analysis
Diseases Scleroderma, Localized