bioRxiv Science⌕ Search

Biology subjects

Takeuchi, I.

Publications and source records attributed to Takeuchi, I..

2 recordsLinked to original sources
bioRxiv2018

Analysis of phage-resistant mechanisms in Staphylococcus aureus SA003 reveals a different binding mechanism for the closely related Twort-like phages phiSA012 and phiSA039

We have previously generated strains of Staphylococcus aureus SA003 resistant to its specific phage {phi}SA012 through long-term coevolution experiment. However, the DNA mutations responsible for the phenotypic change of phage resistance are unknown. Whole-genome analysis revealed six genes that acquired unique point mutations: five missense mutations and one nonsense mutation. Moreover, one deletion, 1.779-bp, resulted in the deletion of the genes encoding glycosyltransferase, TarS, and iron-sulfure repair protein, ScdA. The deletion occurred from the second round of coculture (SA003R2) and remained through the last round. The {phi}SA012 infection toward SA003R2 had decreased to 79.77{+/-}7.50% according to plating efficiency. Complementation of the phage-resistant strain by the wild-type allele showed two mutated host genes were linked to the inhibition of post-adsorption, and five genes were linked to phage adsorption of {phi}SA012. Unlike {phi}SA012, infection by {phi}SA039, a close relative of {phi}SA012, onto SA003R2 was impaired drastically. Complementation of SA003R2 by wild-type tarS restores the infectivity of {phi}SA039. Thus, we concluded that {phi}SA039 requires {beta}-GlcNAc in Wall Teichoic Acid (WTA) for its binding. In silico analysis of the {phi}SA039 genome revealed that several proteins in the tail and baseplate region were different from {phi}SA012; notably the partial deletion of orf96 of {phi}SA039, a homolog of orf99 of {phi}SA012. Orf100 of {phi}SA039, a homolog of Orf103 of {phi}SA012, a previously reported receptor binding protein (RBP), had low similarity (86%) to that of {phi}SA012. The difference in tail and baseplate proteins might be the factor for specificity difference between {phi}SA012 and {phi}SA039.

microbiology↗
bioRxiv2017

Toward Machine Learning-based Data-driven Functional Protein Studies: Understanding Colour Tuning Rules and Predicting the Absorption Wavelengths of Microbial Rhodopsins

The light-dependent ion-transport function of microbial rhodopsin has been widely used in optogenetics for optical control of neural activity. In order to increase the variety of rhodopsin proteins having a wide range of absorption wavelengths, the light absorption properties of various wild-type rhodopsins and their artificially mutated variants were investigated in the literature. Here, we demonstrate that a machine-learning-based (ML-based) data-driven approach is useful for understanding and predicting the light-absorption properties of microbial rhodopsin proteins. We constructed a database of 796 proteins consisting of microbial rhodopsin wildtypes and their variants. We then proposed an ML method that produces a statistical model describing the relationship between amino-acid sequences and absorption wavelengths and demonstrated that the fitted statistical model is useful for understanding colour tuning rules and predicting absorption wavelengths. By applying the ML method to the database, two residues that were not considered in previous studies are newly identified to be important to colour shift.

biophysics↗