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Aci Actinobacteria Assemble a Functional Actinorhodopsin With bioRxiv preprint doi: https://doi.org/10.1101/367102; this version posted July 11, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 acI Actinobacteria Assemble a Functional Actinorhodopsin with 2 Natively-synthesized Retinal 3 4 Running Title: (54 characters and spaces) Actinorhodopsin and Carotenoid Synthesis in acI 5 6 Jeffrey R. Dwulit-Smitha,b, Joshua J. Hamiltona, David M. Stevensona, Shaomei Hea,c, Ben O. 7 Oysermand, Francisco Moya-Floresd, Daniel Amador-Nogueza, Katherine D. McMahona,d, Katrina T. 8 Foresta,b# 9 10 aDepartment of Bacteriology; bProgram in Biophysics; cDepartment of Geoscience, and dDepartment of Civil 11 and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA. 12 # Address correspondence to Katrina T. Forest, 1550 Linden Drive, Madison, WI 53706, tel. 608 265-3566, 13 email [email protected]. 14 15 KEYWORDS 16 Freshwater, photoheterotrophy, opsin, rhodopsin, xanthorhodopsin, proton pump, carotenoid, blh 17 bioRxiv preprint doi: https://doi.org/10.1101/367102; this version posted July 11, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Dwulit-Smith et al. Actinorhodopsin and Carotenoid Synthesis in acI 18 ABSTRACT 19 Freshwater lakes harbor complex microbial communities, but these ecosystems are often dominated by acI 20 Actinobacteria from three clades (acI-A, acI-B, acI-C). Members of this cosmopolitan lineage are proposed 21 to bolster heterotrophic growth using phototrophy because their genomes encode actino-opsins (actR). 22 This model has been difficult to experimentally validate because acI are not consistently culturable. In this 23 study, using genomes from single cells and metagenomes, we provide a detailed biosynthetic route for 24 many acI-A and -B members to synthesize retinal and its carotenoid precursors. Accordingly, these acI 25 should be able to natively assemble light-driven actinorhodopsins (holo-ActR) to pump protons, in contrast 26 to acI-C members and other bacteria that encode opsins but lack retinal-production machinery. Moreover, 27 we show that all acI clades contain genes for a complex carotenoid pathway that starts with retinal 28 precursors. Transcription analysis of acI in a eutrophic lake shows that all retinal and carotenoid pathway 29 operons are transcribed and that actR is among the most highly-transcribed of all acI genes. Furthermore, 30 heterologous expression of retinal pathway genes shows that lycopene, retinal, and ActR can be made. 31 Model cells producing ActR and the key acI retinal-producing β-carotene oxygenase formed acI-holo-ActR 32 and acidified solution during illumination. Our results prove that acI containing both ActR and retinal- 33 production enzymes have the capacity to natively synthesize a green light-dependent outward proton- 34 pumping rhodopsin. 35 36 IMPORTANCE 37 Microbes play critical roles in determining the quality of freshwater ecosystems that are vital to human 38 civilization. Because acI Actinobacteria are ubiquitous and abundant in freshwater lakes, clarifying their 39 ecophysiology is a major step in determining the contributions that they make to nitrogen and carbon 40 cycling. Without accurate knowledge of these cycles, freshwater systems cannot be incorporated into 41 climate change models, ecosystem imbalances cannot be predicted, and policy for service disruption 42 cannot be planned. Our work fills major gaps in microbial light utilization, secondary metabolite production, 43 and energy cycling in freshwater habitats. 44 2 bioRxiv preprint doi: https://doi.org/10.1101/367102; this version posted July 11, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Dwulit-Smith et al. Actinorhodopsin and Carotenoid Synthesis in acI 45 INTRODUCTION 46 Fresh water lakes contain complex and dynamic microbial communities that influence water quality 47 by mediating biogeochemical cycling. These ecosystems are often numerically dominated by three clades 48 of acI Actinobacteria (acI-A, acI-B, acI-C), ultra-microbacteria with low GC genomes that are streamlined 49 to approximately 1.2-1.5 MBp (1–5). The ubiquity and abundance of acI raise the question, what are the 50 factors that enable their success? Major proposed advantages include scavenging resources with 51 membrane transporters (3, 6), evading protist feeding by virtue of their small size (7, 8), and supplementing 52 energy needs via photoheterotrophy. Light utilization is feasible because each clade encodes actino-opsin 53 (ActR), the putative platform protein for actinorhodopsin (holo-ActR) (3, 9–11). Validating this hypothesis 54 not only requires a demonstration that acI can synthesize or acquire sufficient retinal, the chromophore 55 needed to complete holo-ActR, but also biochemical evidence that the holo-ActR is functional. Additionally, 56 the relevant genes must be shown to be expressed in the native freshwater environments where acI is 57 dominant. That these requirements are satisfied by acI is not guaranteed; Rhodoluna lacicola holo-ActR 58 was shown to be active if, and only if, exogenous retinal was added (12). Without an encoded, retinal- 59 producing enzyme or a solution for obtaining dilute environmental chromophores, it is unclear what the 60 physiological role and ecosystem implications of ActR in such organisms are. On the other hand, the Luna1 61 bacterium Candidatus Rhodoluna planktonica encodes a putative retinal-synthesizing enzyme (13). This 62 family of Actinobacteria is radically different from acI and much less abundant and prevalent in freshwater 63 lakes (2), but this organism provides motivation to determine if acI truly use rhodopsins for 64 photoheterotrophy. 65 Rhodopsins are seven-transmembrane-helix bundles that bind retinal at an internal lysine via a 66 Schiff base (14). The retinal pocket amino acid sidechains, specifically a tuning residue (15), determine the 67 maximal absorption wavelength of the holo-protein. The captured photon energy triggers the geometric 68 isomerization of retinal, which completes a transfer pathway through the interior of the bundle and thus 69 across the membrane. Most commonly, protons are shuttled out of the cytoplasm to form a gradient that 70 can be harnessed for activities like ATP synthesis (16). The retinal that ultimately enables the gradient is 71 derived from carotenoids, colorful molecules that act as photoprotectants, cofactors, pigments, and 72 membrane stabilizers throughout nature (17, 18). The initial building blocks of carotenoids are the five- 3 bioRxiv preprint doi: https://doi.org/10.1101/367102; this version posted July 11, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Dwulit-Smith et al. Actinorhodopsin and Carotenoid Synthesis in acI 73 carbon monomers isopentenyl diphosphate and dimethylallyl diphosphate. These units can be polymerized 74 and modified to form lycopene, β-carotene, and various intermediates (19). Moreover, more complex keto- 75 carotenoid chromophores like salinixanthin and echinenone boost rhodopsin activity by resonance energy 76 transfer to retinal in rare xanthorhodopsin-like systems (20–22). Microorganisms with the machinery to 77 produce functional, chromophore-loaded rhodopsins may have a competitive advantage in their native 78 ecosystems (23, 24). 79 Here we provide experimental evidence that acI has photoheterotrophic potential. A significant 80 challenge when these studies were initiated was the inability to purely culture acI (5, 25), although it appears 81 this hurdle may soon be overcome (26). Consequently, we pursued a multidisciplinary approach that did 82 not rely on large amounts of acI biomass, but instead focused on bioinformatic, transcriptomic, and 83 biochemical data. Specifically, we characterize a biosynthetic pathway for retinal and its carotenoid 84 precursors using heterologous expression. We then demonstrate that acI-actR is highly transcribed in the 85 freshwater acI biome, Lake Mendota, and acI-ActR can function as a retinylidene holoprotein to produce a 86 light-driven proton gradient. Most importantly, the nanomachine is active in cells that produce retinal using 87 the native acI β-carotene oxygenase. Finally, we provide evidence for a complex carotenoid that may 88 screen cells from oxidative damage and/or boost the light harvesting ability of actinorhodopsin. 89 RESULTS 90 All acI-ActR contain key amino acids for function. We first determined whether acI-ActR 91 sequences were consistent with acI-holo-ActR formation. Indeed, all contain the features for proper 92 rhodopsin structure and function (Fig. 1A). Seven predicted helices (a1-7) match those found in xantho- 93 opsin, a close homolog of acI-ActR from Salinibacter ruber (20). A conserved lysine for Schiff base 94 formation and acidic residues for proton-shuttling across the retinylidene gate are present (27), and a 95 leucine is predicted to tune the absorbance of all acI-holo-ActRs to the green region (28). We also found 96 novel features. A proline in the middle of a4 differentiates ActRs from xantho-opsins, and the residue may 97 serve as a means for better phylogenetic classification (Fig. S1). Additionally, 3D structure predictions 98 suggest cysteines on a1 and a7 in acI clades A and B form a disulfide staple (Fig. 1B). acI-ActRs also 99 contain glycine near the top of a5, a required feature for binding the ketolated antenna carotenoids (21, 4 bioRxiv preprint doi: https://doi.org/10.1101/367102; this version posted July 11, 2018.
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