Archaeal rhodopsins

Bieszke, J. A., E. L. Braun et al. (1999). The nop-1 gene of Neurospora crassa encodes a seven transmembrane helix retinal-binding protein homologous to archaeal rhodopsins. Proc. Natl. Acad. Sci. 96(14) 8034-8039. 

Spudich, J.L. (1998) Variations on a molecular switch transport and sensory signalling by archaeal rhodopsins. Mol. Microbiol., 28, 1051-1058. 

Fig. 4.2 (A) Archaeal rhodopsins. (B) The chromophore of archaeal rhodopsins, protonated Schiff base of all-trans-retinal.

Figures 4.1B and 4.2B show that the isomeric compositions between visual and archaeal rhodopsins differ not only for the 01=02 double bond, but also for the C6-C7 single bond. In visual rhodopsins, the C6-C7 bond is in a cis form, and the...

Figure 4.3 shows photochemical reactions in visual (Fig. 4.3A) and archaeal (Fig. 4.3B) rhodopsins. In visual rhodopsins, the 11-as-retinal is isomerized into the a -trans form. The selectivity is 100%, and the quantum yield is 0.67 for bovine rhodopsin [20]. In archaeal rhodopsins, the all-trans-retinal is isomerized into the 13-cis form. The selectivity is 100%, and the quantum yield is 0.64 for bacteriorhodopsin [21]. Squid and octopus possess a photoisomerase called retino-chrome, which supplies the 11-ris-retinal for their rhodopsins through the specific photoreaction. Retinochrome possesses all-trans-retinal as the chromophore, and the all-trans-retinal is isomerized into the 11-cis form with a selectivity of 100% [22]. Thus, the photoproduct is different between archaeal rhodopsins and retinochrome, the aU-trans form being converted into the 13-cis and 11-cis forms, respectively. This fact implies that protein environment determines the reaction pathways of photoisomerization in their excited states. 

HPLC analysis also revealed that the protonated Schiff base of all-traws-retinal in solution is isomerized predominantly into the 11-cis form (82% 11-cis, 12% 9-cis, and 6% 13-ds in methanol) [23]. The 11-cis form as a photoproduct is the nature of retinochrome, not those of archaeal rhodopsins. This suggests that the protein environment of retinochrome serves as the intrinsic property of the photoisomerization of the retinal chromophore. In contrast, it seems that the protein environment of archaeal rhodopsins forces the reaction pathway of the isomerization to change into the 13-cis form. In this regard, it is interesting that the quantum yield of bacteriorhodopsin (0.64) is 4—5 times higher than that in solution (-0.15) [21,23], The altered excited state reaction pathways in archaeal rhodopsins never reduce the efficiency. Rather, archaeal rhodopsins discover the reaction pathway from the all-trans to 13-cis form efficiently. Consequently, the system of efficient isomerization reaction is achieved as well as in visual rhodopsins. Structural and spectroscopic studies on archaeal rhodopsins are also reviewed in Section 4.3. 

Halobacteria contain four rhodopsins bacteriorhodopsin, halorhodopsin, sensor-yrhodopsin, and phoborhodopsin (Fig. 4.2A) [11-17]. Bacteriorhodopsin and halorhodopsin are light-driven ion pumps, which act as an outward proton pump and an inward Ch pump, respectively. Sensoryrhodopsin and phoborhodopsin are photoreceptors that act to produce attractant and repellent responses in phototaxis, respectively. These four archaeal rhodopsins have similar structures seven helices constitute the transmembrane portion of the protein, and a retinal chromophore is bound to a lysine residue of the seventh helix via a protonated SchifF base linkage (Fig. 4.1). A negatively charged counterion is present to stabilize the positive charge inside the protein the counterion is an aspartate except for in halorhodopsin, which possesses a chloride ion. In sensoryrhodopsin, interaction with a transmembrane transducer protein raises the pKa of the aspartate, so that the aspartate is protonated at neutral pH. 

Unlike visual rhodopsins that bleach upon illumination, archaeal rhodopsins exhibit photocycle. This is highly advantageous in ultrafast spectroscopic studies and these techniques have been extensively applied in addition to low-temperature spectroscopy [2,12,13]. In particular, bacteriorhodopsin has been regarded historically as the model system to test new spectroscopic methods. As in visual rhodopsins, the light absorption of archaeal rhodopsins causes formation of red-shifted primary intermediates [68]. The primary K intermediate can be stabilized at 77 K. Time-resolved visible spectroscopy of bacteriorhodopsin reveals the presence of the precursor, called the J intermediate [12,13]. The J intermediate is more red-shifted (7.max -625 nm) than the K intermediate (2rn ix -590 nm). The excited state of bacteriorhodopsin possesses blue-shifted absorption, which decays nonexpo-nentially. The two components of the stimulated emission decay at about 200 and 500 fs [69]. The J intermediate is formed in <500 fs, and converted to the K intermediate within 3 ps [12,69]. 

This chapter has gathered together the current understanding of retinal photoisomerization in visual and archaeal rhodopsins mainly from the experimental point of view. Extensive studies by means of ultrafast spectroscopy of visual and archaeal rhodopsins have provided an answer to the question, What is the primary reaction in vision We now know that it is isomerization from 11-cis to all-trans form in visual rhodopsins and from all-trans to 13-cis form in archaeal rho-dopsin. Femtosecond spectroscopy of visual and archaeal rhodopsins eventually captured their excited states and, as a consequence, we now know that this unique photochemistry takes place in our eyes and in archaea. Such unique reactions are facilitated in the protein environment, and recent structural determinations have further improved our understanding on the basis of structure. In parallel, vibrational analysis of primary intermediates, such as resonance Raman and infrared spectroscopies, have provided insight into the isomerization mechanism. 

Due to constraints of space, I could not introduce many important theoretical studies here. Various important models have been proposed on the primary isomerization mechanism in rhodopsins, including the bicycle pedal model [101], sudden polarization [102], and the hula-twist model [103]. The finding of a conical intersection between the excited and ground states is also an important contribution [104]. Since the atomic structures of visual and archaeal rhodopsins are now available, theoretical investigations will become more important in the future. The combination of three methods - diffraction, spectroscopy, and theory - will lead to a real understanding of the isomerization mechanism in rhodopsins. 

Halobacterium salinurum membrane contains a family of four photoactive retinal proteins, called archaeal rhodopsins that are similar to our visual pigments in their... 

Microbial Rhodopsins Archaeal Rhodopsins Bacterial Rhodopsins Eukaryotic Rhodopsins. 124-2... 

SRIP). Many laboratories extensively characterized this family of proteins with a battery of diverse techniques, because they provide excellent model systems for the two fundamental functions of membranes active transport and sensory signaling. Twenty-nine variants of BR, HR, SRI, and SRII were documented in related extremely halophlHc archaea, such as Natronomonas pharaonis and Haloarcula vallismortis. Members of the archaeal rhodopsin family were generally assumed to be only in the haloarchaea and appeared to be restricted to the extreme halophilic environments of solar evaporation ponds and other regions of near-saturated salt concentration. 

Bieszke, J.A., Spudich, E.N., Scott, K.L., Borkovich, K.A., and Spudich, J.L., A eukaryotic protein, NOP-1, binds retinal to form an archaeal rhodopsin-like photochemically reactive pigment. Biochemistry, 38, 43, 14,138, 1999. 

Zhai, Y., Heijne, W.H., Smith, D.W., and Saier, M.H., Jr., Homologues of archaeal rhodopsins in plants, animals and fungi structural and functional predications for a putative fungal chaperone protein, Biochim. Biophys. Acta, 1511, 2,206, 2001. 

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