bop encodes bacterio-opsin, the apoprotein of bacteriorhodopsin, the light-driven outward proton pump of the extremely halophilic archaeon Halobacterium salinarum. The protein is made as a precursor with a 13-residue N-terminal propeptide and folds into seven transmembrane helices. Retinal is bound covalently as a protonated Schiff base to Lys216 (mature numbering). Bacteriorhodopsin is the only protein of the purple membrane, a specialised patch of the cell membrane in which homotrimers form a two-dimensional crystalline lattice with archaeal lipids. Light isomerises the all-trans retinal to 13-cis and drives a photocycle in which the Schiff base proton is passed to Asp85 and released to the outside, and the Schiff base is then reprotonated from the cytoplasm through Asp96. Each photocycle moves one proton out of the cell. The resulting proton motive force drives ATP synthesis by the cell's ATP synthase and lets cells grow phototrophically when oxygen is scarce; bop expression is induced by low oxygen and light through the Bat activator. The light-dependent change in proton motive force can also be sensed by the cell, so bacteriorhodopsin contributes a secondary photoreceptor input to phototaxis. Bacteriorhodopsin is among the most intensively studied membrane proteins, with more than a hundred crystal and cryo-EM structures, including time-resolved structures of photocycle intermediates.
Definition: Primary active transport of a proton across a membrane against its electrochemical gradient, driven by the energy of absorbed light, for example by a retinal-containing microbial rhodopsin.
Justification: GO:0015454 light-driven active monoatomic ion transmembrane transporter activity has no children, so the proton pumps (bacteriorhodopsin, proteorhodopsin, xanthorhodopsin) cannot be distinguished from the chloride pump halorhodopsin or the sodium-pumping rhodopsins. The activity of bacteriorhodopsin is fully characterised; currently the ion specificity has to be expressed by a second term (GO:0015078). A proton-specific child of GO:0015454 (and of GO:0015078) would also be the natural target for InterPro2GO mappings of the proton-pumping rhodopsin families, replacing the incorrect channel mapping.
Parent term: light-driven active monoatomic ion transmembrane transporter activity
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005216 monoatomic ion channel activity | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO mapping from IPR018229 (rhodopsin retinal-binding site signature). Bacteriorhodopsin is not a channel. It is a light-driven active transporter that moves protons outward against the electrochemical gradient, one proton per photocycle, through a sequence of protonation changes on the Schiff base, Asp85 and Asp96. Reason: GO:0005216 is defined as energy-independent facilitated diffusion through an aqueous pore. Bacteriorhodopsin does the opposite: it uses light energy to pump protons uphill and builds a proton gradient in starved or anaerobic cells. Its mutants affect pumping, not channel conductance. The mapping is wrong for this protein. The same IPR018229 mapping puts channel activity on the halorhodopsins (P0DMH7, P15647, P33742), on sensory rhodopsin II (P42196) and on proteorhodopsin (Q9F7P4). None of these is a channel; only the algal channelrhodopsins are. The correct activity is already captured by the IDA row for GO:0015454. Supporting Evidence: PMID:4517939 Starved or anaerobic cells containing purple membrane, in the absence of any apparent source of energy, generate and maintain a proton gradient across the cell membrane as long as they are exposed to light. PMID:10949309 is a light driven pump which transports protons across the cell membrane of the halophilic organism Halobacterium salinarum PMID:3288985 The Asp-85----Asn mutant showed not detectable proton pumping |
| GO:0005886 plasma membrane | EXP PMID:6706999 Bacteriorhodopsin precursor. Characterization and its integr... | ACCEPT | Summary: Seehra and Khorana showed that the bacteriorhodopsin precursor made in spheroplasts integrates, correctly folded and with retinal attached, into the purple membrane. The purple membrane is a differentiated region of the H. salinarum cell (plasma) membrane. Reason: The plasma membrane location is the correct, and the most specific available, GO cellular component for bacteriorhodopsin; GO has no purple membrane term. Many structures and the original physiology (a proton gradient across the cell membrane) also support it. The cited abstract describes integration into the purple membrane, which is part of the cell membrane. Supporting Evidence: PMID:6706999 it integrates into the purple membrane in the correctly folded conformation PMID:10949309 transports protons across the cell membrane of the halophilic organism Halobacterium salinarum |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt SubCell mapping from "Cell membrane; Multi-pass membrane protein", which UniProt supports experimentally (PMID:6706999 and many structure papers). Reason: Agrees with the EXP row for the same term. Bacteriorhodopsin is a seven-helix protein of the purple membrane, a patch of the cell membrane. Supporting Evidence: PMID:6706999 it integrates into the purple membrane in the correctly folded conformation |
| GO:0006811 monoatomic ion transport | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO process mapping from IPR018229. The statement is true but very broad: the transported ion is known to be the proton, and the transport is across the cell membrane. Reason: Bacteriorhodopsin itself carries out the transport step (it moves protons across the membrane), so a transport process term is appropriate. The evidence supports the specific is_a descendant GO:1902600 proton transmembrane transport, so the broad term should be refined to that. Proposed replacements: proton transmembrane transport Supporting Evidence: PMID:10949309 is a light driven pump which transports protons across the cell membrane of the halophilic organism Halobacterium salinarum PMID:4524635 These results indicate that the purple membrane functions as a lightdriven proton pump and the cells use the resulting chemiosmotic gradient for ATP synthesis. |
| GO:0007602 phototransduction | IDA PMID:4517939 Functions of a new photoreceptor membrane. | KEEP AS NON CORE | Summary: FlyBase IDA from Oesterhelt and Stoeckenius (1973). The abstract describes conversion of light into a proton gradient used for energy coupling, which is energy transduction rather than conversion of photons into a signal. Later work (Bibikov et al. 1993) showed that bacteriorhodopsin, expressed alone in a strain lacking the other three retinal proteins, does support phototactic responses, because the cell senses the light-driven change in proton motive force. Reason: The cached paper is abstract-only and the curator saw the full text, so I do not remove the row. The term is defensible on biological grounds: bacteriorhodopsin absorbs the photon and generates the change in proton motive force that the cell reads as a photosensory input. It is not the protein's main role, which is energy conversion, and in wild-type cells phototaxis is mediated mainly by sensory rhodopsins I and II and their transducers. It is therefore kept as non-core. GO:0007602 is also not a good container for the core energy role; that role is captured by GO:0015454 and the proton transport terms. Supporting Evidence: PMID:8415720 We conclude that the BR-mediated photoreception is due to the light-dependent generation of delta mu H+. PMID:8415720 The cells accumulated in a light spot, demonstrating the BR-mediated orientation in spatial light gradients. PMID:4517939 Preliminary results indicate that the gradient in H. halobium plays the central role in energy coupling attributed to such electrochemical gradients by Mitchell's chemiosmotic theory. |
| GO:0015454 light-driven active monoatomic ion transmembrane transporter activity | IDA PMID:4517939 Functions of a new photoreceptor membrane. | ACCEPT | Summary: The founding demonstration of light-driven proton pumping by bacteriorhodopsin: light-exposed cells containing purple membrane generate a proton gradient without any other energy source, and the pigment releases and takes up protons during its photocycle. Later work confirmed this with reconstituted vesicles, mutagenesis of the proton path (Asp85, Asp96) and atomic structures of photocycle intermediates. Reason: This is the core molecular function of bacteriorhodopsin and is directly demonstrated. GO:0015454 is a leaf term with no proton-specific child, so it is the most specific light-driven transporter term available; the ion specificity is added by the NEW GO:0015078 row and a new term is proposed below. In all of GOA bop is the only gene product annotated to GO:0015454. Supporting Evidence: PMID:4517939 We postulate that the light-generated proton gradient arises from a vectorial release and uptake of protons by bacteriorhodopsin PMID:4524635 These results indicate that the purple membrane functions as a lightdriven proton pump and the cells use the resulting chemiosmotic gradient for ATP synthesis. PMID:10949309 Here we present an atomic model for structural changes involved in the vectorial, light-driven transport of protons by bacteriorhodopsin. |
| GO:0016020 membrane | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the microbial rhodopsin family signatures. True, but the membrane is known: the cell (plasma) membrane, in its purple membrane domain. Reason: The term is correct but less specific than the evidence. The gene already carries the is_a descendant GO:0005886 plasma membrane by EXP and IEA, so the refinement is to that term. Proposed replacements: plasma membrane Supporting Evidence: PMID:6706999 it integrates into the purple membrane in the correctly folded conformation |
| GO:0034220 monoatomic ion transmembrane transport | IEA GO_REF:0000120 | MODIFY | Summary: Combined automated annotation inferred from the channel (GO:0005216) and light-driven transporter (GO:0015454) function annotations. The channel source is wrong, but the transporter source is correct, so the process claim is true. The ion is the proton. Reason: Bacteriorhodopsin does transport ions across the membrane, so the term is true, but the evidence supports the specific is_a descendant GO:1902600 proton transmembrane transport. Proposed replacements: proton transmembrane transport Supporting Evidence: PMID:10949309 The Schiff base then releases a proton to the extracellular medium, and is subsequently reprotonated from the cytoplasm. |
| GO:0015078 proton transmembrane transporter activity | IDA PMID:3288985 Aspartic acid substitutions affect proton translocation by b... | NEW | Summary: Proposed new function annotation that names the ion. Purified bacteriorhodopsin (expressed in E. coli and regenerated with retinal) pumps protons, and replacing single aspartates on the proton path abolishes or strongly reduces pumping. Reason: GO:0015454 says "light-driven" but not "proton", and it has no proton-specific child, so the ion specificity of the core activity is currently missing from GO. GO:0015078 is not an ancestor or descendant of GO:0015454, so this adds information rather than redundancy. Bacteriorhodopsin itself moves the proton, so participation is not in doubt. Other proton transporters carry GO:0015078 by experimental evidence in GOA, for example V-type ATPase subunits (Atp6v0a2, Atp6v1a) and the uncoupling proteins UCP1-3. Supporting Evidence: PMID:3288985 The Asp-85----Asn mutant showed not detectable proton pumping, the Asp-96----Asn and Asp-212----Glu mutants showed less than 10% and the Asp-115----Glu mutant showed approximately equal to 30% of the normal proton pumping. PMID:10949309 is a light driven pump which transports protons across the cell membrane of the halophilic organism Halobacterium salinarum |
| GO:0016918 retinal binding | IDA PMID:6794028 Attachment site(s) of retinal in bacteriorhodopsin. | NEW | Summary: Proposed new function annotation. Retinal is the chromophore of bacteriorhodopsin and is bound covalently as a Schiff base to Lys216; the binding site was mapped chemically and is seen in every crystal structure. Reason: Retinal binding is the structural basis of light absorption and of the pump mechanism (the photocycle starts with retinal isomerisation and the Schiff base is the first proton donor). Opsins do carry retinal-binding terms in GO: bovine rhodopsin has GO:0005502 11-cis retinal binding by IDA. The parent GO:0016918 is used rather than all-trans retinal binding because the bound retinal is all-trans in light-adapted and a 13-cis/all-trans mixture in dark-adapted bacteriorhodopsin. No archaeal protein currently has any retinal binding annotation in GOA. Supporting Evidence: PMID:6794028 After chemical reduction of the retinylidene-lysine Schiff base linkage in bacteriorhodopsin, the retinyl residue is covalently attached to Lys-216 PMID:10452895 Near Lys216 where the retinal binds PMID:3288985 The mutant proteins all regenerated bacteriorhodopsin-like chromophores when treated with a detergent-phospholipid mixture and retinal. |
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Download this section (compressed HTML)Q: Should the InterPro2GO mapping of IPR018229 (rhodopsin retinal-binding site) to GO:0005216 monoatomic ion channel activity be withdrawn? It places channel activity on bacteriorhodopsin, halorhodopsins, sensory rhodopsins and proteorhodopsin, none of which is a channel; only the eukaryotic channelrhodopsins are.
Q: Should GO have a cellular component term for the purple membrane, the crystalline bacteriorhodopsin-lipid domain of the haloarchaeal cell membrane, or is plasma membrane the intended level for such membrane domains?
Q: Should a light-driven proton pump that generates the proton motive force be annotated to GO:0042777 proton motive force-driven plasma membrane ATP synthesis? The term definition includes the proton transport that builds the gradient, but experimental annotations are on ATP synthase subunits (and Pyrococcus Mbh), so the convention appears to restrict the term to the synthase.
Experiment: Compare phototrophic growth and ATP levels of an in-frame bop deletion in H. salinarum NRC-1 with the parent strain under low oxygen and illumination, to give a genetic (IMP) basis for the physiological role that is so far supported mainly by biochemistry and by older strain comparisons.
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