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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.


Typical photocycle of microbial rhodopsins showing isomeric and protonation state of retinal. X− represents the Schiff base counterion, and D85 in BR also acts as the H+ acceptor from the Schiff base. In a Cl− pump such as HR and FR, X− is a Cl−, so that the M intermediate is not formed because the Schiff base is not deprotonated. Instead, the Cl− is transported upwards (in this figure). In KR2, a Na+ pump, X− is a D116 acting as the Schiff base counterion and H+ acceptor from the Schiff base. CP and EC indicate cytoplasmic and extracellular domains, respectively. In the unphotolyzed state of microbial rhodopsins, the EC side is generally open through a hydrogen-bonding network but the CP side is closed. While this is persistent in the K and M states, the CP side is open in the N state. When the EC side is closed (black), the CP side is open, as is the case for an ion pump, as occurs in the N intermediate of BR. Such alternative access must work for all H+, Cl−, and Na+ pumps.
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Figure 9: Typical photocycle of microbial rhodopsins showing isomeric and protonation state of retinal. X− represents the Schiff base counterion, and D85 in BR also acts as the H+ acceptor from the Schiff base. In a Cl− pump such as HR and FR, X− is a Cl−, so that the M intermediate is not formed because the Schiff base is not deprotonated. Instead, the Cl− is transported upwards (in this figure). In KR2, a Na+ pump, X− is a D116 acting as the Schiff base counterion and H+ acceptor from the Schiff base. CP and EC indicate cytoplasmic and extracellular domains, respectively. In the unphotolyzed state of microbial rhodopsins, the EC side is generally open through a hydrogen-bonding network but the CP side is closed. While this is persistent in the K and M states, the CP side is open in the N state. When the EC side is closed (black), the CP side is open, as is the case for an ion pump, as occurs in the N intermediate of BR. Such alternative access must work for all H+, Cl−, and Na+ pumps.

Mentions: The H+ pathway across the membrane from the cytoplasmic to the extracellular side in BR is shown in Figure 8, together with protonatable groups and the order of respective H+ transfers. A summary of the photocycle is shown in Figure 9, which illustrates key intermediate states for most microbial rhodopsins. Although the photocycle of BR contains six intermediates, namely J, K, L, M, N, and O states that are named alphabetically, only three states (K, M, and N) are shown in Figure 7 to demonstrate the mechanism clearly. After light absorption, photoisomerization occurs from the all-trans- to 13-cis-form in 10−13 second. This ultrafast retinal isomerization yields the formation of red-shifted J and K intermediates, in which J is the precursor of the K state. The protein cavity, which accommodates retinal, cannot change its shape promptly, and the K intermediate contains twisted 13-cis retinal. An altered hydrogen-bonding network in the Schiff base region also contributes to higher free energy in K than in the original state, and such energy storage in the primary intermediate structure leads to subsequent protein structural changes upon relaxation.


Ion-pumping microbial rhodopsins.

Kandori H - Front Mol Biosci (2015)

Typical photocycle of microbial rhodopsins showing isomeric and protonation state of retinal. X− represents the Schiff base counterion, and D85 in BR also acts as the H+ acceptor from the Schiff base. In a Cl− pump such as HR and FR, X− is a Cl−, so that the M intermediate is not formed because the Schiff base is not deprotonated. Instead, the Cl− is transported upwards (in this figure). In KR2, a Na+ pump, X− is a D116 acting as the Schiff base counterion and H+ acceptor from the Schiff base. CP and EC indicate cytoplasmic and extracellular domains, respectively. In the unphotolyzed state of microbial rhodopsins, the EC side is generally open through a hydrogen-bonding network but the CP side is closed. While this is persistent in the K and M states, the CP side is open in the N state. When the EC side is closed (black), the CP side is open, as is the case for an ion pump, as occurs in the N intermediate of BR. Such alternative access must work for all H+, Cl−, and Na+ pumps.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
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Figure 9: Typical photocycle of microbial rhodopsins showing isomeric and protonation state of retinal. X− represents the Schiff base counterion, and D85 in BR also acts as the H+ acceptor from the Schiff base. In a Cl− pump such as HR and FR, X− is a Cl−, so that the M intermediate is not formed because the Schiff base is not deprotonated. Instead, the Cl− is transported upwards (in this figure). In KR2, a Na+ pump, X− is a D116 acting as the Schiff base counterion and H+ acceptor from the Schiff base. CP and EC indicate cytoplasmic and extracellular domains, respectively. In the unphotolyzed state of microbial rhodopsins, the EC side is generally open through a hydrogen-bonding network but the CP side is closed. While this is persistent in the K and M states, the CP side is open in the N state. When the EC side is closed (black), the CP side is open, as is the case for an ion pump, as occurs in the N intermediate of BR. Such alternative access must work for all H+, Cl−, and Na+ pumps.
Mentions: The H+ pathway across the membrane from the cytoplasmic to the extracellular side in BR is shown in Figure 8, together with protonatable groups and the order of respective H+ transfers. A summary of the photocycle is shown in Figure 9, which illustrates key intermediate states for most microbial rhodopsins. Although the photocycle of BR contains six intermediates, namely J, K, L, M, N, and O states that are named alphabetically, only three states (K, M, and N) are shown in Figure 7 to demonstrate the mechanism clearly. After light absorption, photoisomerization occurs from the all-trans- to 13-cis-form in 10−13 second. This ultrafast retinal isomerization yields the formation of red-shifted J and K intermediates, in which J is the precursor of the K state. The protein cavity, which accommodates retinal, cannot change its shape promptly, and the K intermediate contains twisted 13-cis retinal. An altered hydrogen-bonding network in the Schiff base region also contributes to higher free energy in K than in the original state, and such energy storage in the primary intermediate structure leads to subsequent protein structural changes upon relaxation.

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.