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Ion-pumping microbial rhodopsins.

Kandori H - Front Mol Biosci (2015)

Bottom Line: Ion-transporting proteins can be found in microbial rhodopsins, such as light-gated channels and light-driven pumps, which are the main tools in optogenetics.On the other hand, different kinds of H(+) and Cl(-) pumps have been found in marine bacteria, such as proteorhodopsin (PR) and Fulvimarina pelagi rhodopsin (FR), respectively.In addition, a light-driven Na(+) pump was found, Krokinobacter eikastus rhodopsin 2 (KR2).

View Article: PubMed Central - PubMed

Affiliation: Department of Frontier Materials and OptoBioTechnology Research Center, Nagoya Institute of Technology Nagoya, Japan.

ABSTRACT
Rhodopsins are light-sensing proteins used in optogenetics. The word "rhodopsin" originates from the Greek words "rhodo" and "opsis," indicating rose and sight, respectively. Although the classical meaning of rhodopsin is the red-colored pigment in our eyes, the modern meaning of rhodopsin encompasses photoactive proteins containing a retinal chromophore in animals and microbes. Animal and microbial rhodopsins possess 11-cis and all-trans retinal, respectively, to capture light in seven transmembrane α-helices, and photoisomerizations into all-trans and 13-cis forms, respectively, initiate each function. Ion-transporting proteins can be found in microbial rhodopsins, such as light-gated channels and light-driven pumps, which are the main tools in optogenetics. Light-driven pumps, such as archaeal H(+) pump bacteriorhodopsin (BR) and Cl(-) pump halorhodopsin (HR), were discovered in the 1970s, and their mechanism has been extensively studied. On the other hand, different kinds of H(+) and Cl(-) pumps have been found in marine bacteria, such as proteorhodopsin (PR) and Fulvimarina pelagi rhodopsin (FR), respectively. In addition, a light-driven Na(+) pump was found, Krokinobacter eikastus rhodopsin 2 (KR2). These light-driven ion-pumping microbial rhodopsins are classified as DTD, TSA, DTE, NTQ, and NDQ rhodopsins for BR, HR, PR, FR, and KR2, respectively. Recent understanding of ion-pumping microbial rhodopsins is reviewed in this paper.

No MeSH data available.


Phylogenic tree of microbial rhodopsins. This figure is modified from Inoue et al. (2015). The scale bar represents the number of substitutions per site (0.1 indicates 10 nucleotides substitutions per 100 nucleotides). Marine bacterial H+ (yellow), Na+ (orange) and Cl− (cyan) pumps have the DTE (or DTX), NDQ, and NTQ motifs, respectively, while archaeal H+ and Cl− pumps have the DTD and TSA motifs, respectively. Sensory rhodopsins from halophilic archaea and eubacteria are also shown. AR1, Archaerhodopsin-1; AR2, Archaerhodopsin-2; AR3, Archaerhodopsin-3; HwBR, BR from Haloquadratum walsbyi; MR, Middle rhodopsin; NpHR, HsHR, SrHR, HR from Natronomonas pharaonis; H. salinarum and Salinibacter ruber; HsSRI, HvSRI, SrSRI, sensory rhodopsin I from H. salinarum, Haloarcula vallismortis and S. ruber; HsSRI, NpSRI, sensory rhodopsin I from H. salinarum and N. pharaonis; VsPR, GlPR, NdR1. proteorhodopsins from Vibrio sp. AND4, Gillisia limnaea DSM 15749, Nonlabens dokdonensis DSW-6; XR, xanthorhodopsin, TR, proteorhodopsin from Thermus thermophilus; CbClR, CsClR, SpClR, NmClR, ClR from Citromicrobium bathyomarinum, Citromicrobium sp. JLT1363, Sphingopyxis baekryungensis DSM 16222 and N. marinus; GlNaR, NdNaR, IaNaR, TrNaR1, TrNaR2, NaR from G. limnaea, Nonlabens dokdonensis, Indibacter alkaliphilus, and two NaRs from Truepera radiovictrix, respectively.
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Figure 3: Phylogenic tree of microbial rhodopsins. This figure is modified from Inoue et al. (2015). The scale bar represents the number of substitutions per site (0.1 indicates 10 nucleotides substitutions per 100 nucleotides). Marine bacterial H+ (yellow), Na+ (orange) and Cl− (cyan) pumps have the DTE (or DTX), NDQ, and NTQ motifs, respectively, while archaeal H+ and Cl− pumps have the DTD and TSA motifs, respectively. Sensory rhodopsins from halophilic archaea and eubacteria are also shown. AR1, Archaerhodopsin-1; AR2, Archaerhodopsin-2; AR3, Archaerhodopsin-3; HwBR, BR from Haloquadratum walsbyi; MR, Middle rhodopsin; NpHR, HsHR, SrHR, HR from Natronomonas pharaonis; H. salinarum and Salinibacter ruber; HsSRI, HvSRI, SrSRI, sensory rhodopsin I from H. salinarum, Haloarcula vallismortis and S. ruber; HsSRI, NpSRI, sensory rhodopsin I from H. salinarum and N. pharaonis; VsPR, GlPR, NdR1. proteorhodopsins from Vibrio sp. AND4, Gillisia limnaea DSM 15749, Nonlabens dokdonensis DSW-6; XR, xanthorhodopsin, TR, proteorhodopsin from Thermus thermophilus; CbClR, CsClR, SpClR, NmClR, ClR from Citromicrobium bathyomarinum, Citromicrobium sp. JLT1363, Sphingopyxis baekryungensis DSM 16222 and N. marinus; GlNaR, NdNaR, IaNaR, TrNaR1, TrNaR2, NaR from G. limnaea, Nonlabens dokdonensis, Indibacter alkaliphilus, and two NaRs from Truepera radiovictrix, respectively.

Mentions: We now know that nature uses three different ion pump rhodopsins (H+, Na+, and Cl− pumps). They can be distinguished by characteristic sequences (Figure 3). BR has two aspartic acid residues, D85 and D96, in helix C which function as the H+ acceptor and donor, respectively, for the retinal Schiff base during its H+ pumping photocycle (Figure 4). In addition, the former forms a hydrogen bond with T89. The DTD motif in BR (D85, T89, and D96) is well conserved for other archaeal H+-pumping rhodopsins. At the corresponding position, most PRs have a DTE motif in which the H+ donor is Glu instead of D96 in BR. However, there are some exceptions. Exiguobacterium sibiricum rhodopsin (ESR) has Lys instead of Glu (Petrovskaya et al., 2010), and the DTX motif may be more accurate for the marine bacterial H+ pump. Light-driven Cl− pump HR is a TSA rhodopsin, and light-driven Na+ and Cl− pumps have NDQ and NTQ motifs, respectively at the same position (Figure 3) (Inoue et al., 2013; Béjà and Lanyi, 2014; Yoshizawa et al., 2014). Thus, these three residues, which correspond to position 85, 89, and 96 of BR, are important for categorizing ion pump rhodopsins. The next section summarizes structural features of these light-driven pumps, followed by a mechanistic explanation on H+, Cl−, and Na+ pumps, one by one.


Ion-pumping microbial rhodopsins.

Kandori H - Front Mol Biosci (2015)

Phylogenic tree of microbial rhodopsins. This figure is modified from Inoue et al. (2015). The scale bar represents the number of substitutions per site (0.1 indicates 10 nucleotides substitutions per 100 nucleotides). Marine bacterial H+ (yellow), Na+ (orange) and Cl− (cyan) pumps have the DTE (or DTX), NDQ, and NTQ motifs, respectively, while archaeal H+ and Cl− pumps have the DTD and TSA motifs, respectively. Sensory rhodopsins from halophilic archaea and eubacteria are also shown. AR1, Archaerhodopsin-1; AR2, Archaerhodopsin-2; AR3, Archaerhodopsin-3; HwBR, BR from Haloquadratum walsbyi; MR, Middle rhodopsin; NpHR, HsHR, SrHR, HR from Natronomonas pharaonis; H. salinarum and Salinibacter ruber; HsSRI, HvSRI, SrSRI, sensory rhodopsin I from H. salinarum, Haloarcula vallismortis and S. ruber; HsSRI, NpSRI, sensory rhodopsin I from H. salinarum and N. pharaonis; VsPR, GlPR, NdR1. proteorhodopsins from Vibrio sp. AND4, Gillisia limnaea DSM 15749, Nonlabens dokdonensis DSW-6; XR, xanthorhodopsin, TR, proteorhodopsin from Thermus thermophilus; CbClR, CsClR, SpClR, NmClR, ClR from Citromicrobium bathyomarinum, Citromicrobium sp. JLT1363, Sphingopyxis baekryungensis DSM 16222 and N. marinus; GlNaR, NdNaR, IaNaR, TrNaR1, TrNaR2, NaR from G. limnaea, Nonlabens dokdonensis, Indibacter alkaliphilus, and two NaRs from Truepera radiovictrix, respectively.
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Figure 3: Phylogenic tree of microbial rhodopsins. This figure is modified from Inoue et al. (2015). The scale bar represents the number of substitutions per site (0.1 indicates 10 nucleotides substitutions per 100 nucleotides). Marine bacterial H+ (yellow), Na+ (orange) and Cl− (cyan) pumps have the DTE (or DTX), NDQ, and NTQ motifs, respectively, while archaeal H+ and Cl− pumps have the DTD and TSA motifs, respectively. Sensory rhodopsins from halophilic archaea and eubacteria are also shown. AR1, Archaerhodopsin-1; AR2, Archaerhodopsin-2; AR3, Archaerhodopsin-3; HwBR, BR from Haloquadratum walsbyi; MR, Middle rhodopsin; NpHR, HsHR, SrHR, HR from Natronomonas pharaonis; H. salinarum and Salinibacter ruber; HsSRI, HvSRI, SrSRI, sensory rhodopsin I from H. salinarum, Haloarcula vallismortis and S. ruber; HsSRI, NpSRI, sensory rhodopsin I from H. salinarum and N. pharaonis; VsPR, GlPR, NdR1. proteorhodopsins from Vibrio sp. AND4, Gillisia limnaea DSM 15749, Nonlabens dokdonensis DSW-6; XR, xanthorhodopsin, TR, proteorhodopsin from Thermus thermophilus; CbClR, CsClR, SpClR, NmClR, ClR from Citromicrobium bathyomarinum, Citromicrobium sp. JLT1363, Sphingopyxis baekryungensis DSM 16222 and N. marinus; GlNaR, NdNaR, IaNaR, TrNaR1, TrNaR2, NaR from G. limnaea, Nonlabens dokdonensis, Indibacter alkaliphilus, and two NaRs from Truepera radiovictrix, respectively.
Mentions: We now know that nature uses three different ion pump rhodopsins (H+, Na+, and Cl− pumps). They can be distinguished by characteristic sequences (Figure 3). BR has two aspartic acid residues, D85 and D96, in helix C which function as the H+ acceptor and donor, respectively, for the retinal Schiff base during its H+ pumping photocycle (Figure 4). In addition, the former forms a hydrogen bond with T89. The DTD motif in BR (D85, T89, and D96) is well conserved for other archaeal H+-pumping rhodopsins. At the corresponding position, most PRs have a DTE motif in which the H+ donor is Glu instead of D96 in BR. However, there are some exceptions. Exiguobacterium sibiricum rhodopsin (ESR) has Lys instead of Glu (Petrovskaya et al., 2010), and the DTX motif may be more accurate for the marine bacterial H+ pump. Light-driven Cl− pump HR is a TSA rhodopsin, and light-driven Na+ and Cl− pumps have NDQ and NTQ motifs, respectively at the same position (Figure 3) (Inoue et al., 2013; Béjà and Lanyi, 2014; Yoshizawa et al., 2014). Thus, these three residues, which correspond to position 85, 89, and 96 of BR, are important for categorizing ion pump rhodopsins. The next section summarizes structural features of these light-driven pumps, followed by a mechanistic explanation on H+, Cl−, and Na+ pumps, one by one.

Bottom Line: Ion-transporting proteins can be found in microbial rhodopsins, such as light-gated channels and light-driven pumps, which are the main tools in optogenetics.On the other hand, different kinds of H(+) and Cl(-) pumps have been found in marine bacteria, such as proteorhodopsin (PR) and Fulvimarina pelagi rhodopsin (FR), respectively.In addition, a light-driven Na(+) pump was found, Krokinobacter eikastus rhodopsin 2 (KR2).

View Article: PubMed Central - PubMed

Affiliation: Department of Frontier Materials and OptoBioTechnology Research Center, Nagoya Institute of Technology Nagoya, Japan.

ABSTRACT
Rhodopsins are light-sensing proteins used in optogenetics. The word "rhodopsin" originates from the Greek words "rhodo" and "opsis," indicating rose and sight, respectively. Although the classical meaning of rhodopsin is the red-colored pigment in our eyes, the modern meaning of rhodopsin encompasses photoactive proteins containing a retinal chromophore in animals and microbes. Animal and microbial rhodopsins possess 11-cis and all-trans retinal, respectively, to capture light in seven transmembrane α-helices, and photoisomerizations into all-trans and 13-cis forms, respectively, initiate each function. Ion-transporting proteins can be found in microbial rhodopsins, such as light-gated channels and light-driven pumps, which are the main tools in optogenetics. Light-driven pumps, such as archaeal H(+) pump bacteriorhodopsin (BR) and Cl(-) pump halorhodopsin (HR), were discovered in the 1970s, and their mechanism has been extensively studied. On the other hand, different kinds of H(+) and Cl(-) pumps have been found in marine bacteria, such as proteorhodopsin (PR) and Fulvimarina pelagi rhodopsin (FR), respectively. In addition, a light-driven Na(+) pump was found, Krokinobacter eikastus rhodopsin 2 (KR2). These light-driven ion-pumping microbial rhodopsins are classified as DTD, TSA, DTE, NTQ, and NDQ rhodopsins for BR, HR, PR, FR, and KR2, respectively. Recent understanding of ion-pumping microbial rhodopsins is reviewed in this paper.

No MeSH data available.