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Archaerhodopsin (alternatively known as bacterio-opsin) is a family of light-driven outward proton pump retinal proteins found in Archaea such as Halobacterium and Halorubrum. They drive the hyperpolarization of the cell membrane by secreting protons in presence of light. This process is associated to an increase in 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. This family includes:

  • Archaerhodopsin-1 (AR-1)
  • Archaerhodopsin-2 (AR-2)
  • Archaerhodopsin-3 (AR-3)
  • Archaerhodopsin-BD1 (AR-BD1)
  • Archaerhodopsin-4 (AR-4)

Etymology

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Archaerhodopsin is named after Archaea, the domain in which the protein family was first found, and Rhodopsin (commonly known as visual purple), the protein family Archaerhodopsins belong to.

Archaea, from Ancient Greek ἀρχαῖα (arkhaîa, "ancient"), which is the plural and neuter form of ἀρχαῖος (arkhaîos, "ancient").[1]

History

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Gene

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Archaerhodopsins are light-driven outward proton pump retinal proteins, similar to bacteriorhodopsins[2] ,[3] . Archaerododhopsin 1 and 2 (aR1 and aR2) represent the first archaerhodopsins founded in Halobacterium family isolated from Australian strains by Mukahata et al., 1988, and Uegaki et al., 1991. Archaerododhopsin 1 and 2 (AR1 and AR2), are present in Halobacterial species, Halobacterium sp. Aus-1 [4] and Aus-2[5] respectively.

In addition to (aR1) and (aR2), Archaerhodopsin-3 (aR3), is another microbial rhodopsin proton pump founded in Halorubrum sodomense species. That has recently been introduced as a fluorescent voltage sensor[6]. The fourth Archaerhodopsin, Archaerodopsin-4 (aR4), represents a new member of the microbial rhodopsin family founded in Halobacterium species xz 515 collected from a salt take in Tibet[7],[8].

Archaerhodopsin proteins mentioned above carried the some ion pumps function but with different amino acid sequences which reflects difference in Halobacteria strains and related ecological habitats. For example, according to Sugiyama et al., 1989 and Ubgaki et al., 1991, the amino acid sequences which were deduced from the structural genes coding the polypeptides of both (aR1) an (aR2) indicated that all essential residues are conserved [9],[10].While Archaerhodopsin-3 protein encoded by aop3 gene is closely related to Archaerodopsin-1 (AaR1) and Archaerodopsin-2 (aR2) with over 90 % homology[11] .However, (aR4), was found membrane of Halobacterium species xz 515 collected from a salt take in Tibet , shows 87% sequence similarity to aR1, 97% to aR2 and 84% to aR3. Archaerhodopsin gene of xz 515 encoding the protein from helix C to helix G has been identified by H. Wang et al., 2000 [12]. The genes encoding archaerhodopsin proteins and its related Halobacterium strains, origins and subcelular location were illustrated in the present table:

Archaerhodopsin proteins (Short names) aR-1 aR-2 aR-3 aR-4
Organism (Halobacterium sp) Halorubrum chaoviator.Aus-1 Halobacterium sp. Aus-2 Halorubrum sodomense Halobacterium species xz 515
Gene -356 GGAGCTCCTCGATCGTCTCCTCGCGCTCCTGGACCG

-320 CGGTGGACAGCTCCTCGATGCGCTGCTCGTAGGCGTCTATCGCCTCGACGTCGATGGTGACGTCGTCGGTCTCCTCCGCT -240 TCCTGTTCCGCAGTGCTTTCGCTACGCTGTTCGGCTTCCGCCTCGGCGTCGTCGTCTGCCATACGAGACTGGTAGAGCCC -160 CAGGGTCATTACTTTCAGGCCGACAACGTCACCCCGACCCGCGGCCCGTCAGGGTCGACCGGCGCCGGACCCCGCGCCAG -80 AAGGGGGCGTCGTCACGGGGCGATACCTGACTAGGTTGGCATCGATCTAATAGAATATACACAGTATAACGAAGTGGGT 1 ATGGACCCGATAGCGCTAACCGCAGCCGTTGGAGCTGATCTGCTCGGGGACGGTCGCCCCGAGACGCTCTGGTTGGGCAT 81 AGGCACGCTACTGATGCTCATCGGGACCTTCTACTTCATCGTTAAAGGATGGGGGGTCACTGACAAGGAGGCCCGTGAGT 161 ACTACTCGATCACGATCCTCGTGCCGGGGATCGCGTCGGCAGCGTACCTGTCGATGTTCTTCGGCATCGGCCTGACGGAA 241 GTTCAGGTCGGCAGCGAAATGCTGGACATCTACTACGCGCGGTACGCGGACTGGCTGTTCACCACGCCGCTGCTGCTGCT 321 CGACCTCGCGCTGCTGGCGAAGGTCGACCGCGTGAGCATCGGCACGCTCGTCGGCGTCGACGCGCTGATGATCGTCACCG 401 GACTCGTCGGCGCGCTCTCGCACACGCCGCTCGCGCGGTACACGTGGTGGCTGTTCAGCACGATCTGCATGATCGTCGTG 481 CTGTACTTCCTCGCCACGAGCCTGCGCGCCGCTGCGAAGGAGCGCGGTCCGAGGTCGCGAGCACGTTCAACACCCTTAC 561 GGCGTTGGTGTTGGTGCTCTGGACGGCCTACCCGATCCTGTGGATCATCGGTACCGAGGGTGCCGGCGTCGTCGGCCTCG 641 GCATCGAGACCCTCCTGTTC ATGGTGCTCGACGTGACCGCCAAGGTCGGGTTCCGCTTCATCCTGCTCCGCAGCCGCGCG 721 ATCCTCGGCGACACCGAGGCACCGGAGCCCTCCGCGGGCGCCGAGGCCTCCGCCGCGGACTGATCGGCTAGCGACCCGA 801 CGCGGCAGAACAACACGGTTCAACCGTTTCCAGCGTTCATTTTTCGACATGACTGACACTACCACCGAACAGCCGCCAGT 881 GCTGCGTACACGGTCCGTCGTCGGACTCGCCGCCTGCGTCGTGACCGCGCTCGTCGGATATTCCTGATCCCGACGCTACA 961 GGAGCCGGGAGGCGGGTTCAACGCCCGGTTCTGGACGATGGCGGCCTTGGAGCTGGTCGCCATGATCGGCGTCGTCTACT 1041 TCGTCCTCAACCTCCATGAGGAGTCGCACTGAGGCGGGCGAGAAGCCGCTCGCTCGCACCGCCGATC

-60 CCATACCTGACTGGGTTGGCATCGTTCTCAATAGACTATATGCTTTACATAGAAGTGGGC

1 ATGGACCCGATAGCGCTACAGGCGGGATTCGACCTTCTTAACGACGGTCGTCCCGAGACA 61 CTCTGGTTGGGTATCGGCACGCTACTAATGCTTATTGGGACCTTCTACTTCATCGCCCGC 121 GGATGGGGCGTGACAGACAAGGAGGCCCGTGAGTACTACGCGATCACCATCCTCGTGCCG 181 GGATGGGGCGTGACAGACAAGGAGGCCCGTGAGTACTACGCGATCACCATCCTCGTGCCG 241 CTCGCCAGCGGAACGGTGCTCGACATCTACTACGCCCGGTACGCGGACTGGCTGTTCACG 301 ACGCCGCTGCTGCTACTCGACCTCGCGCTGCTGGCGAAGGTTGACCGCGTGACCATCGGG 361 ACGCTCATCGGCGTCGACGCGCTGATGATCGTCACCGGTCTCATCGGCGCGCTCTCGAAG 421 ACGCCGCTCGCGCGGTACACCTGGTGGCTGTTCAGCACGATCGCGTTCCTGTTCGTGCTG 481 TACTACCTCCTGACGAGCCTGCGCAGCGCCGCTGCGAAGCGCTCCGAGGAGGTCCGGAGT 541 ACCTTCAACACGCTGACCGCACTGGTCGCCGTCCTCTGGACGGCGTACCCGATCCTCTGG 601 ATCGTCGGGACCGAGGGTGCCGGTGTCGTCGGTCTGGGCATCGAGACCCTGGCGTTCATG 661 GTCCTCGACGTGACCGCGAAGGTCGGATTCGGGTTCGTCCTGCTCCGTAGCCGTGCGATC 721 CTCGGCGAGACCGAGGCCCCCGAGCCGTCGGCCGGGGCCGACGCCTCCGCCGCGGACTGA 781 TCGGCAGGCCGACCCGACGCGACCGAACAGCACGGTTCAACCGTTTTCACCCTTCATTTT 841 TCGACATGACTGACACCAATACCGAACAGACACCGGTGCTGAACACGCGGTCCGTCGTCG 901 GGCTCGCCGTCTGCCTCGTGATCGCTCTCTCCGGGATC [13]

N/A N/A
Gene name Bop N/A aop3 N/A

Structure

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Function

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Rhodopsin, from Ancient Greek ῥόδον (rhódon, "rose"), because of its pinkish color, and ὄψις (ópsis, "sight").[14]
  1. ^ Archaea in Wiktionary The free dictionary
  2. ^ Li, Q. G., Zhang, Y., Cheng, S. Y. et al., 1993. The detection of retinal protein similar to bacteriorhodopsin in four halobacterium species. Acta Biophysica Sinica (in Chinese). 9(2): 288.
  3. ^ Y. Wang, D. Ma, Y. Zhao, M. Ming, J. Wu, J. Ding. 2012. Light-driven proton pumps of archaerhodopsin and bacteriorhodopsin & polymer-matrix composite materials of those functional proteins. Acta Polym. Sin. pp. 698-713.
  4. ^ Mukohata Y,. Sugiyama Y,. ihara K, yoshida M,. 1988. An Australian halobacterium contains a novel proton pump retinal protein: archaerhodopsin. Biochemical and Biophysical Research Communications. 151: 1339-1345.
  5. ^ Uegaki K., Sugiyamya Y., Mukohatya Y,. 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: 107-1 10.
  6. ^ Kralj JM, Douglass AD, Hochbaum DR, Maclaurin D, Cohen AE. 2012. Optical recording of action potentials in mammalian neurons using a microbial rhodopsin. Nature methods. 9:90-95.
  7. ^ Q. Li, Q. Sun, W. Zhao, H. Wang, D. Xu. 2000. Newly isolated archaerhodopsin from a strain of Chinese halobacteria and its proton pumping behaviour . Biochim. Biophys. Acta, 1466: 260-266.
  8. ^ Y. Wang, D. Ma, Y. Zhao, M. Ming, J. Wu, J., 2012. Ding Light-driven proton pumps of archaerhodopsin and bacteriorhodopsin & polymer-matrix composite materials of those functional proteins. Acta Polym. Sin. 698-713.
  9. ^ Y Sugiyama, M Maeda, M Futai, Y Mukohata. 1989. Isolation of a gene that encodes a new retinal protein, archaerhodopsin, from Halobacterium sp. aus-1. The Journal of Biological Chemistry. 264: 20859-20862.
  10. ^ Uegakik, ., Sugiyamya., Mukohatya,. 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: 107-1 10.
  11. ^ Ihara, K., Umemura, T., Katagiri, I., Kitajima-Ihara, T., Sugiyama, Y., Kimura, Y., Mukohata, Y., 1999. Evolution of the archaeal rhodopsins: evolution rate changes by gene duplication and functional differentiation. J. Mol. Biol. 285: 163-174.
  12. ^ . 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.
  13. ^ Koichi Uegaki, Yasuo Sugiyama, and Yasuo Mukohata1990. 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): 107-110.
  14. ^ Rhodopsin in Wiktionary The free dictionary
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