Archaerhodopsin proteins are a
family of
retinal-containing
photoreceptors found in the
archaeageneraHalobacterium and Halorubrum. Like the homologous bacteriorhodopsin (bR) protein, archaerhodopsins harvest energy from sunlight to pump H+ ions out of the cell, establishing a proton motive force that is used for
ATP synthesis. They have some structural similarities to the mammalian
G protein-coupled receptor protein
rhodopsin, but are not true homologs.
Archaerhodopsins differ from bR in that the claret membrane, in which they are expressed, includes
bacterioruberin, a second
chromophore thought to protect against
photobleaching. Also, bR lacks the
omega loop structure observed at the N-terminus of the structures of several archaerhodopsins.
Mutants of Archaerhodopsin-3 (AR3) are used as tools in
optogenetics for neuroscience research.[1]
archaea from
Ancient Greekἀρχαῖα (arkhaîa, "ancient"), the plural and neuter form of
ἀρχαῖος (arkhaîos, "ancient").[4]
rhodopsin from Ancient Greek
ῥόδον (rhódon, "rose"), because of its pinkish color, and
ὄψις (ópsis, "sight").[5]
History
In the 1960s, a light driven proton pump was discovered in Halobacterium salinarum, and called Bacteriorhodopsin. Over the following years, there were various studies of the membrane of H. salinarum to determine the mechanism of these light-driven proton pumps.
In 1988, another Manabu Yoshida's group at
Osaka University reported a novel light-sensitive proton pump from a strain of Halobacterium which they termed Archaerhodopsin.[3] A year later, the same group reported isolating the gene that encodes Archaerhodopsin.[6][7]
Family members
Seven members of the archaerhodopsin family have been identified to date.
Archaerhodopsin 1 and 2 (AR1 and AR2) were the first archaerhodopsins to be identified and are expressed by Halobacterium sp. Aus-1 and Aus-2 respectively. Both species were first isolated in
Western Australia in the late 1980s.[3][8][6] The
crystal structures of both proteins were solved by Kunio Ihara, Tsutomo Kouyama and co-workers at
Nagoya University, together with collaborators at the
Spring-8 synchrotron.[14]
Mutants of Archaerhodopsin-3 (AR3) are widely used as tools in
optogenetics for neuroscience research.[1]
AR3 has recently been introduced as a fluorescent voltage sensor.[17]
AR4
AR4 is expressed in Halobacterium species xz 515. The organism was first identified in a salt lake in
Tibet.[10][18] The gene encoding it was identified by H. Wang and colleagues in 2000.[19] In most bacteriorhodopsin homologs, H+ release to the extracellular medium takes place before a replacement ion is taken up from the cytosolic side of the membrane. Under the acidic conditions found in the organism's native habitat, the order of these stages in the AR4 photocycle is reversed.[20]
HeAR is expressed by Halorubrum ejinorense.[12] The organism was first isolated from Lake Ejinor in
Inner Mongolia,
China.[22]
AR-TP009/ArchT
AR-TP009 is expressed by Halorubrum sp. TP009. Its ability to act as a neural silencer has been investigated in mouse
cortical pyramidal neurons.[13]
General features
Occurrence
Like other members of the
microbial rhodopsin family, archaerhodopsins are expressed in specialised, protein-rich domains of the
cell surface membrane, commonly called the claret membrane. In addition to
ether lipids, the claret membrane contains bacterioruberin, (a 50-carbon
carotenoid pigment) which is thought to protect against photobleaching.
Atomic force microscope images of the claret membranes of several archaerhodopsins, show that the proteins are
trimeric and are arranged in a
hexagonal lattice.[23] Bacterioruberin has also been implicated in oligomerisation and may facilitate protein-protein interactions in the native membrane.[24][25]
Function
Archaerhodopsins are
active transporters, using the energy from
sunlight to pump H+ ions out of the cell to generate a proton motive force that is used for
ATP synthesis. Removal of the retinal cofactor (e.g. by treatment with
hydroxylamine) abolishes the transporter function and dramatically alters the absorption spectra of the proteins. The proton pumping ability of AR3 has been demonstrated in recombinant E. coli cells[26] and of AR4 in
liposomes.[20]
In the resting or ground state of archaerhodopsin, the bound retinal is in the all-trans form, but on absorption of a photon of light, it
isomerizes to 13-cis. The protein surrounding the chromophore reacts to the change of shape and undergoes an ordered sequence of
conformational changes, which are collectively known as the photocycle. These changes alter the
polarity of the local environment surrounding
titratableamino acid side chains inside the protein, enabling H+ to be pumped from the cytoplasm to the extracellular side of the membrane. The
intermediate states of the photocycle may be identified by their
absorption maxima.[20][27]
Structures
Crystal structures of the resting or ground states of AR1 (3.4 Å resolution), AR2 (1.8 Å resolution) and AR3 (1.07 and 1.3 Å) have been deposited in the
Protein Data Bank.[14][28][16] Proteins possess seven transmembrane
α-helices and a two-stranded extracellular-facing
β-sheet.
Retinal is covalently bonded via
Schiff base to a
lysine residue on helix G.[14][16][note 1] The conserved DLLxDGR sequence, close to the extracellular-facing
N-terminus of both proteins, forms a tightly curved
omega loop that has been implicated in bacterioruberin binding.[24] The cleavage of the first 6 amino acids and the conversion of Gln7 to a pyroglutamate (PCA) residue was also observed in AR3, as previously reported for bacteriorhodopsin.[16]
Use in research
Archaerhodopsins drive the
hyperpolarization of the cell membrane by secreting protons in presence of light, thereby inhibiting
action potential firing of neurons.[29] This process is associated with an increase in extracellular H+ (i.e. decreased
pH linked to the activity of these proteins. These characteristics allow for Archaerhodopsins to be commonly used tools for
optogenetic studies as they behave as transmission inhibition factors in presence of light.[30] When expressed within intracellular membranes, the proton pump activity increases the cytosolic
pH, this functionality can be used for optogenetic acidification of lysosomes and synaptic vesicles when targeted to these
organelles.[31]
Notes
^Helix G is the nearest transmembrane helix to the
C-terminus.
^
abcdMukohata Y, Sugiyama Y, Ihara K, Yoshida M (March 1988). "An Australian halobacterium contains a novel proton pump retinal protein: archaerhodopsin". Biochemical and Biophysical Research Communications. 151 (3): 1339–45.
doi:
10.1016/S0006-291X(88)80509-6.
PMID2833260.
^
abUegaki K, Sugiyama Y, Mukohata Y (April 1991). "Archaerhodopsin-2, from Halobacterium sp. aus-2 further reveals essential amino acid residues for light-driven proton pumps". Archives of Biochemistry and Biophysics. 286 (1): 107–10.
doi:
10.1016/0003-9861(91)90014-A.
PMID1654776.
^
abcIhara K, Umemura T, Katagiri I, Kitajima-Ihara T, Sugiyama Y, Kimura Y, Mukohata Y (January 1999). "Evolution of the archaeal rhodopsins: evolution rate changes by gene duplication and functional differentiation". Journal of Molecular Biology. 285 (1): 163–74.
doi:
10.1006/jmbi.1998.2286.
PMID9878396.
^
abLi Q, Sun Q, Zhao W, Wang H, Xu D (June 2000). "Newly isolated archaerhodopsin from a strain of Chinese halobacteria and its proton pumping behavior". Biochimica et Biophysica Acta (BBA) - Biomembranes. 1466 (1–2): 260–6.
doi:
10.1016/S0005-2736(00)00188-7.
PMID10825447.
^
abcEnami N, Yoshimura K, Murakami M, Okumura H, Ihara K, Kouyama T (2006). "Crystal Structures of Archaerhodopsin-1 and -2: Common structural motif in archaeal light-driven proton pumps". J. Mol. Biol. 358 (3): 675–685.
doi:
10.1016/j.jmb.2006.02.032.
PMID16540121.
^Wang, S. Zhan, Q. Sun, D. Xu, W. Zhao, W. Huang, Q. Li., 2000. Primary structure of helix C to helix G of a new retinal protein in H.sp.xz515. Chin. Sci. Bull., 45: 1108-1113.
^Tang L, Sun Q, Li Q, Huang Y, Wei Q, Zhang Y, Hu J, Zhang Z (2001). "Imaging bacteriorhodopsinlike molecules of claretmembranes from Tibet halobacteria xz515 by atomic force microscope". Chinese Science Bulletin. 46 (22): 1897–1900.
Bibcode:
2001ChSBu..46.1897T.
doi:
10.1007/BF02901167.
S2CID96378194.
^
abYoshimura K, Kouyama T (2008). "Structural Role of Bacterioruberin in the Trimeric Structure of Archaerhodopsin-2". Journal of Molecular Biology. 375 (5): 1267–81.
doi:
10.1016/j.jmb.2007.11.039.
PMID18082767.