Limits...
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.


(A) Cl− transport pathway in HR and FR (NTQ rhodopsin). Cl− binds near the Schiff base region, as is seen from the Cl−-dependent color change. The KR2 structure is used in which T is replaced by D116. (B) Na+ transport pathway in KR2 (NDQ rhodopsin). Na+ does not bind near the chromophore in the dark, while a light-induced structural alteration accompanies the uptake of Na+ upon formation of the O intermediate. This is the structure of KR2 (PDB: 3X3C, Kato et al., 2015).
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4585134&req=5

Figure 11: (A) Cl− transport pathway in HR and FR (NTQ rhodopsin). Cl− binds near the Schiff base region, as is seen from the Cl−-dependent color change. The KR2 structure is used in which T is replaced by D116. (B) Na+ transport pathway in KR2 (NDQ rhodopsin). Na+ does not bind near the chromophore in the dark, while a light-induced structural alteration accompanies the uptake of Na+ upon formation of the O intermediate. This is the structure of KR2 (PDB: 3X3C, Kato et al., 2015).

Mentions: The first identified light-driven inward Cl− pump was HR in 1977 (Matsuno-Yagi and Mukohata, 1977). Interestingly, it was first believed to be an outward Na+ pump, whereas clear anion dependence revealed that HR is an inward Cl− pump (Schobert and Lanyi, 1982). While the overall architecture of HRs is BR-like, the crystal structures of two Cl− pumps from Halobacterium salinarum (HsHR; Kolbe et al., 2000) and from Natronomonas pharaonis (NpHR; Kouyama et al., 2010) clearly show the presence of a Cl− in the Schiff base region. HR has the TSA motif in which D85 in BR is replaced by Thr. This suggests that the electric quadrupole of the Schiff base with its counterion complex (D85, D212, and R82 in BR) lacks a negative charge and that the charge balance is compensated for by the binding of the negatively charged Cl−. This is also the case for NTQ rhodopsins such as Fulvimarina rhodopsin (FR), where D85 is replaced by Asn (Figure 11A). FR clearly shows Cl−-dependent color changes, indicating direct binding near the Schiff base as well as HR (Inoue et al., 2014).


Ion-pumping microbial rhodopsins.

Kandori H - Front Mol Biosci (2015)

(A) Cl− transport pathway in HR and FR (NTQ rhodopsin). Cl− binds near the Schiff base region, as is seen from the Cl−-dependent color change. The KR2 structure is used in which T is replaced by D116. (B) Na+ transport pathway in KR2 (NDQ rhodopsin). Na+ does not bind near the chromophore in the dark, while a light-induced structural alteration accompanies the uptake of Na+ upon formation of the O intermediate. This is the structure of KR2 (PDB: 3X3C, Kato et al., 2015).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4585134&req=5

Figure 11: (A) Cl− transport pathway in HR and FR (NTQ rhodopsin). Cl− binds near the Schiff base region, as is seen from the Cl−-dependent color change. The KR2 structure is used in which T is replaced by D116. (B) Na+ transport pathway in KR2 (NDQ rhodopsin). Na+ does not bind near the chromophore in the dark, while a light-induced structural alteration accompanies the uptake of Na+ upon formation of the O intermediate. This is the structure of KR2 (PDB: 3X3C, Kato et al., 2015).
Mentions: The first identified light-driven inward Cl− pump was HR in 1977 (Matsuno-Yagi and Mukohata, 1977). Interestingly, it was first believed to be an outward Na+ pump, whereas clear anion dependence revealed that HR is an inward Cl− pump (Schobert and Lanyi, 1982). While the overall architecture of HRs is BR-like, the crystal structures of two Cl− pumps from Halobacterium salinarum (HsHR; Kolbe et al., 2000) and from Natronomonas pharaonis (NpHR; Kouyama et al., 2010) clearly show the presence of a Cl− in the Schiff base region. HR has the TSA motif in which D85 in BR is replaced by Thr. This suggests that the electric quadrupole of the Schiff base with its counterion complex (D85, D212, and R82 in BR) lacks a negative charge and that the charge balance is compensated for by the binding of the negatively charged Cl−. This is also the case for NTQ rhodopsins such as Fulvimarina rhodopsin (FR), where D85 is replaced by Asn (Figure 11A). FR clearly shows Cl−-dependent color changes, indicating direct binding near the Schiff base as well as HR (Inoue et al., 2014).

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.