Deep dive into the diversity and properties of rhodopsins in actinomycetes of the family Geodermatophilaceae

Abstract

In recent decades, most studies of microbial rhodopsins have focused on their identification and characterization in aquatic bacteria. In 2021, actinomycetes of the family Geodermatophilaceae, commonly inhabiting terrestrial ecosystems in hot and arid regions, have been reported to contain rhodopsins with DTEW, DTEF and NDQ amino acid motifs. An advanced bioinformatics analysis performed in this work additionally revealed NTQ rhodopsin and heliorhodopsins. The absorption maxima identified for rhodopsins from the above five groups ranged from 513 nm (NTQ rhodopsin) to 559 nm (heliorhodopsin). An assessment of pumping specificity showed that DTEW and DTEF rhodopsins possessed outward H⁺-transport activities. Ca²⁺ ions were required for pumping if E. coli C43(DE3) was used as an expression strain, but were unnecessary in the case of E. coli BL21(DE3). For NDQ rhodopsin, outward H⁺-transport was detected in NaCl and KCl solutions at pH 5 and 6, but not at neutral pH. A weak Na⁺-efflux was observed for this rhodopsin at pH 6 and 7 in a NaCl solution only in the presence of proton ionophore. NTQ rhodopsin acted as an inward Cl⁻-, Br⁻-, and I⁻- pump, with a much weaker activity towards NO³⁻. No pumping activity was detected for the heliorhodopsin tested. The finding of rhodopsins with novel properties further expands the rhodopsin landscape.