Crystal structure of heliorhodopsin 48C12

Yang, Lu; Zhou, Xuemei; Gao, Xiang; Wang, Na; Xia, Ruixue; Xu, Zhenmei; Leng, Yu; Shi, Yanting; Wang, Guangfu; Melcher, Karsten; Xu, Hongxia; He, Yuanzheng

doi:10.1038/s41422-019-0266-0

“…Recently, a distinct and abundant group of microbial rhodopsins, HeRs, has been discovered [37][38][39] . Although HeRs share low sequence identity with the other rhodopsins and adopt the inverted membrane topology, the crystal structures revealed that HeR comprises seven TMs with the retinal chromophore, as in the other rhodopsins [40][41][42] . Unlike these rhodopsins, the enzyme rhodopsins have long N-termini, and are predicted to have 1-2 additional transmembrane helices 11,12,43 , while the existence of TM0 and its function still have remained to be elucidated.…”

Section: Discussionmentioning

confidence: 95%

Structural insights into the mechanism of rhodopsin phosphodiesterase

Ikuta

¹

,

Shihoya

²

,

Sugiura

³

et al. 2020

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Rhodopsin phosphodiesterase (Rh-PDE) is an enzyme rhodopsin belonging to a recently discovered class of microbial rhodopsins with light-dependent enzymatic activity. Rh-PDE consists of the N-terminal rhodopsin domain and C-terminal phosphodiesterase (PDE) domain, connected by 76-residue linker, and hydrolyzes both cAMP and cGMP in a light-dependent manner. Thus, Rh-PDE has potential for the optogenetic manipulation of cyclic nucleotide concentrations, as a complementary tool to rhodopsin guanylyl cyclase and photosensitive adenylyl cyclase. Here we present structural and functional analyses of the Rh-PDE derived from Salpingoeca rosetta. The crystal structure of the rhodopsin domain at 2.6 Å resolution revealed a new topology of rhodopsins, with 8 TMs including the N-terminal extra TM, TM0. Mutational analyses demonstrated that TM0 plays a crucial role in the enzymatic photoactivity. We further solved the crystal structures of the rhodopsin domain (3.5 Å) and PDE domain (2.1 Å) with their connecting linkers, which showed a rough sketch of the full-length Rh-PDE. Integrating these structures, we proposed a model of full-length Rh-PDE, based on the HS-AFM observations and computational modeling of the linker region. These findings provide insight into the photoactivation mechanisms of other 8-TM enzyme rhodopsins and expand the definition of rhodopsins.

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“…BLASTp (Camacho et al 2009) was used to identify 452 homologous type 1 rhodopsin sequences from the National Center for Biotechnology Information (NCBI) non-redundant and UniProt protein databases. We additionally identified 116 homologs belonging to heliorhodopsins, a recently discovered rhodopsin class that exhibits an inverted membrane topology relative to type 1 rhodopsins and constitutes a distinct outgroup (Pushkarev 2018; Lu et al 2019; Rozenberg et al 2021). Animal, or type 2, rhodopsins, though exhibiting a similar seven transmembrane architecture, possess little sequence homology with microbial type 1 rhodopsins and were thus excluded from the dataset (Sharma 2006; Rozenberg et al 2021).…”

Section: Resultsmentioning

confidence: 99%

“…BLASTp 32 was used to identify 452 homologous type I rhodopsin sequences from the National Center for Biotechnology Information (NCBI) non-redundant and UniProt protein databases. We additionally identified 116 homologs belonging to heliorhodopsins, a recently discovered rhodopsin class that exhibits an inverted membrane topology relative to type I rhodopsins and constitutes a distinct outgroup [33][34][35] .…”

Section: Conservation and Statistical Support For Ancestral Rhodopsin Residues Important For Function And Spectral Tuningmentioning

confidence: 99%

Earliest photic zone niches probed by ancestral microbial rhodopsins

Cd

¹

,

Fer

²

,

Ak

³

et al. 2021

Preprint

0

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For billions of years, life has continuously adapted to dynamic physical conditions near the Earth’s surface. Fossils and other preserved biosignatures in the paleontological record are the most direct evidence for reconstructing the broad historical contours of this adaptive interplay. However, biosignatures dating to Earth’s earliest history are exceedingly rare. Here, we combine phylogenetic inference of primordial rhodopsin proteins with modeled spectral features of the Precambrian Earth environment to reconstruct the paleobiological history of this essential family of photoactive transmembrane proteins. Our results suggest that ancestral microbial rhodopsins likely acted as light-driven proton pumps and were spectrally tuned toward the absorption of green light, which would have enabled their hosts to occupy depths in a water column or biofilm where UV wavelengths were attenuated. Subsequent diversification of rhodopsin functions and peak absorption frequencies track the diversification of surface ecological niches induced by the accumulation of atmospheric oxygen. Inferred ancestors retain distinct associations between extant functions and peak absorption frequencies. Our findings suggest that novel information encoded by biomolecules can be used as paleosensors for conditions of ancient, inhabited niches of host organisms not represented elsewhere in the paleontological record. The coupling of functional diversification and spectral tuning of this pervasive protein family underscores the utility of rhodopsins as universal testbeds for inferring remotely detectable biosignatures on inhabited planetary bodies.

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“…TMs with the retinal chromophore, as in the other rhodopsins [39][40][41] . Unlike these rhodopsins, the enzyme rhodopsins have long N-termini, and are predicted to have 1-2 additional transmembrane helices 11,12,42 , while the existence of TM0 and its function still have remained to be elucidated.…”

Section: Discussionmentioning

confidence: 99%

“…Recently, a distinct and abundant group of microbial rhodopsins, the heliorhodopsins (HeRs) has been discovered [36][37][38] . Although HeRs share low sequence identity with the other rhodopsins and adopt the inverted membrane topology, the crystal structures revealed that HeR comprises 7TMs with the retinal chromophore, as in the other rhodopsins [39][40][41] . Unlike these rhodopsins, the enzyme rhodopsins have long N-termini, and are predicted to have 1-2 additional transmembrane helices 11,12,42 , while the existence of TM0 and its function still have remained to be elucidated.…”

mentioning

confidence: 94%

Structural insights into the mechanism of rhodopsin phosphodiesterase

Ikuta

¹

,

Shihoya

²

,

Sugiura

³

et al. 2020

Preprint

View full text Add to dashboard Cite

Rhodopsin phosphodiesterase (Rh-PDE) is an enzyme rhodopsin belonging to a recently discovered class of microbial rhodopsins with light-dependent enzymatic activity. Rh-PDE consists of the N-terminal rhodopsin domain and C-terminal phosphodiesterase (PDE) domain, connected by 76-residue linker, and hydrolyzes both cAMP and cGMP in a light-dependent manner. Thus, Rh-PDE has potential for the optogenetic manipulation of cyclic nucleotide concentrations, as a complementary tool to rhodopsin guanylyl cyclase (Rh-GC) and photosensitive adenylyl cyclase (PAC). Here we present structural and functional analyses of the Rh-PDE derived from Salpingoeca rosetta. The 2.6 Å resolution crystal structure of the transmembrane domain revealed a new topology of rhodopsin, with 8 TMs including the N-terminal extra TM, TM0. Mutational analyses demonstrated that TM0 plays a crucial role in the enzymatic photoactivity. We further solved the crystal structures of the transmembrane and PDE domain (2.1 Å) with their connecting linkers. Integrating these structures, we proposed a model of full-length Rh-PDE, based on the HS-AFM observations and computational modeling of the linker region. These findings provide insight into the photoactivation mechanisms of other 8-TM enzyme rhodopsins and expand the definition of rhodopsins. -3 - Main text IntroductionMicrobial rhodopsins are photoreceptive membrane proteins with an all-trans retinylidene chromophore 1,2 (all-trans retinal). All microbial rhodopsins share a seven transmembrane topology, in which all-trans retinal chromophore is bound to a conserved lysine residue via Schiff base in the transmembrane helix (TM) 7. Most microbial rhodopsins function as light-driven ion pumps that actively transport various ions 1 (H + , Na + , Cl -, etc.). Some microbial rhodopsins function as light-gated ion channels (channelrhodopsins 3,4 ), which are used as optogenetic tools in neuroscience 5,6 . Enzyme rhodopsins are a group of newly discovered microbial rhodopsins 7 , found in eukaryotes such as fungi and green algae, and choanoflagellates. Enzyme rhodopsins comprise the N-terminal rhodopsin domain and C-terminal enzyme domain, connected by a linker, and function as light-activated enzymes. Two types of enzyme rhodopsins were initially discovered, the histidine kinase rhodopsins 8 (HKRs) and rhodopsin guanylyl cyclase 9 (Rh-GC). While HKRs function as ATP-dependent light-inhibited guanylyl cyclase 10 , Rh-GC from Blastocladiella emersonii (BeGC1) induces a rapid light-triggered cGMP increase in heterologous cells (~5,000-fold) and could be utilized as an optogenetic tool to rapidly manipulate cGMP levels in cells and animals 11,12 .In 2017, rhodopsin phosphodiesterase 13 (Rh-PDE), a novel type of enzyme rhodopsin, was discovered. Rh-PDE derived from Salpingoeca rosetta (SrRh-PDE) was first identified and exhibits light-dependent hydrolytic activity for both of cAMP and cGMP, whereas it lacks pump or channel activity. Moreover, four Rh-PDE homologs were recently discovered in Choanoeca flexa 14 . Thes...

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Crystal structure of heliorhodopsin 48C12

Cited by 26 publications

References 8 publications

Structural insights into the mechanism of rhodopsin phosphodiesterase

Structural insights into the mechanism of rhodopsin phosphodiesterase

Earliest photic zone niches probed by ancestral microbial rhodopsins

Structural insights into the mechanism of rhodopsin phosphodiesterase

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