Lokiarchaeota archaeon schizorhodopsin-2 (LaSzR2) is an inward proton pump displaying a characteristic feature of acid-induced spectral blue-shift

Keiichi Kojima,Masaki Nakama,Masumi Hasegawa,Susumu Yoshizawa,Marie Kurihara,Yuki Sudo,Takashi Kikukawa

doi:10.1038/s41598-020-77936-9

Keiichi Kojima, Masaki Nakama + Show 5 more

Open Access

https://doi.org/10.1038/s41598-020-77936-9

Copy DOI

Abstract

The photoreactive protein rhodopsin is widespread in microorganisms and has a variety of photobiological functions. Recently, a novel phylogenetically distinctive group named ‘schizorhodopsin (SzR)’ has been identified as an inward proton pump. We performed functional and spectroscopic studies on an uncharacterised schizorhodopsin from the phylum Lokiarchaeota archaeon. The protein, LaSzR2, having an all-trans-retinal chromophore, showed inward proton pump activity with an absorption maximum at 549 nm. The pH titration experiments revealed that the protonated Schiff base of the retinal chromophore (Lys188, pKa = 12.3) is stabilised by the deprotonated counterion (presumably Asp184, pKa = 3.7). The flash-photolysis experiments revealed the presence of two photointermediates, K and M. A proton was released and uptaken from bulk solution upon the formation and decay of the M intermediate. During the M-decay, the Schiff base was reprotonated by the proton from a proton donating residue (presumably Asp172). These properties were compared with other inward (SzRs and xenorhodopsins, XeRs) and outward proton pumps. Notably, LaSzR2 showed acid-induced spectral ‘blue-shift’ due to the protonation of the counterion, whereas outward proton pumps showed opposite shifts (red-shifts). Thus, we can distinguish between inward and outward proton pumps by the direction of the acid-induced spectral shift.

Highlights

Sunlight provides a fundamental source for organisms, including humans
Light signals received by sensory rhodopsin I (SRI) and sensory rhodopsin II (SRII) are transmitted to a cytoplasmic signal transduction cascade, which regulates the direction of rotation of the flagellar motor, resulting in phototaxis responses[8,13]
A phylogenetically distinctive rhodopsin clade, xenorhodopsin (XeR), has been identified from diverse eubacteria and archaea, such as Parvularcula oceani, Rubricoccus marinus and Nanosalina as a light-driven inward proton pump (Fig. 1A)[14,15,16]. These XeRs were named as Parvularcula oceani XeR (PoXeR), Rubricoccus marinus XeR (RmXeR) and Nanosalina XeR (NsXeR)

Summary

Introduction

Sunlight provides a fundamental source for organisms, including humans. Many organisms possess a variety of photoreceptor proteins that can capture sunlight. Since 2000, eubacterial and eukaryotic proton pump rhodopsins, such as proteorhodopsin (PR), thermophilic rhodopsin (TR) and Leptosphaeria rhodopsin (LR), have been identified by genomic analysis and characterised, in addition to HsBR2,8 These proton pumps convert light energy into available adenosine triphosphate (ATP) which provides chemical energy to the cells through the formation of a proton gradient across the cell membrane as a collaborative work with ATP synthase[9], suggesting these ‘outward’ proton pumps play an important role in the ecosystem. In addition to these outward proton pumps, other ion pumps which transport different substrate ions such as Cl− and N a+ have been identified in archaea, bacteria, viruses and eukarya (Fig. 1A, typical microbial rhodopsin)[2,8]. From the comparative study between LaSzR2, XeRs and outward proton pump rhodopsins such as BR and TR, we discuss a key characteristic of inward proton pumps, including LaSzR2

Methods

Results

Discussion

Conclusion