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AffiliationsDepartment of Earth and Environmental Sciences, Macquarie University, Sydney, New South Wales, AustraliaErnest F. Asamoah & Joseph M. MainaDepartment of Biological Sciences, Macquarie University, Sydney, New South Wales, AustraliaLinda J. BeaumontAuthorsErnest F. AsamoahLinda J. BeaumontJoseph M. MainaCorresponding authorCorrespondence to
Ernest F. Asamoah. More

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Fatty acid profilePlukenetia volubilisThe fatty acid composition of P. volubilis is the most well studied in the genus, and the results from the two P. volubilis accessions from Ecuador and Peru in the current study are similar to previous results. The most abundant fatty acid in the seed oil of P. volubilis from Ecuador and Peru, respectively, is α-linolenic acid (C18:3 n-3, ω-3, ALA; 51.5 ± 3.3 and 46.6 ± 1.2%), followed by linoleic acid (C18:2 n-6, ω-6, LA; 32.5 ± 3.9 and 36.5 ± 0.8%), oleic acid (C18:1, OA; 8.5 ± 1,2 and 8.3 ± 0,4%) and smaller amounts ( More

Phylogenetic placement of Saccharibacteria rhodopsins (SacRs) shows that these sequences form a sibling clade to characterized light-driven inward and outward H+ pumps (Fig. 1a). We selected three phylogenetically diverse SacRs from freshwater lakes (Table S1) and two related, previously uncharacterized sequences from the Gammaproteobacteria (Kushneria aurantia and Halomonas sp.) for synthesis and functional characterization (highlighted in Fig. 1a). All sequences have Asp–Thr–Ser (DTS) residues at the positions of D85–T96–D96 of bacteriorhodopsin (BR) in the third transmembrane helix (Fig. S1). These residues are known as the triplet DTD motif and represent key residues for proton pumping function in BR [6].Fig. 1: Characteristics of Saccharibacteria rhodopsins (SacRs).a Rhodopsin protein tree indicating that SacRs from freshwater lakes form a broad clade of proton pumps. b The ion-pumping activity of SacRs. Blue and green lines indicate the pH change with and without 10 μM CCCP, respectively. Yellow bars indicate the period of light illumination. c Time evolution of transient absorption changes of SacRNC335 in 100 mM NaCl, 20 mM HEPES–NaOH, pH 7.0, and POPE/POPG (molar ratio 3:1) vesicles with a lipid to protein molar ratio = 50. Time evolution at 406 nm (blue, representing the M accumulation), 561 nm (green, representing the bleaching of the initial state and the L accumulation), and 638 nm (red, representing the K and O accumulations). Yellow lines indicate fitting curves by a multi-exponential function. Inset: The photocycle of SacRNC335 based on the fitting in (c) and a kinetic model assuming a sequential photocycle. The lifetime (τ) of each intermediate is indicated by numbers as follow (mean ± S.D., fraction of the intermediate decayed with each lifetime in its double exponential decay is indicated in parentheses): I: τ = 1.7 ± 0.3 μs (42%), τ = 13 ± 1.8 μs (58%), II: τ = 118 ± 2 μs, III: τ = 1.6 ± 0.1 ms, IV: τ = 23.5 ± 1.0 ms, V: τ = 98.4 ± 6.4 ms (56%), τ = 384 ± 18 ms (44%). d Genomic context of SacRNC335. Neighboring genes with above-threshold KEGG annotations are indicated in gray with the highest-scoring HMM model. Genes without KEGG annotations are indicated in white.Full size imageProton transport assays for the SacRs and Gammaproteobacteria proteins expressed in Escherichia coli showed marked decrease of external pH upon light illumination (Fig. 1b and Fig. S2), indicating that these proteins are light-driven outward H+ pumps. The pH decrease was almost eliminated after adding the protonophore carbonyl cyanide m-chlorophenyl hydrazone (CCCP), which dissipates the H+ gradient, confirming that it was indeed formed upon illumination (Fig. 1b and Fig. S2). We also characterized the absorption spectra and the photocycle of the SacRs, showing that the three rhodopsins have an absorption peak around 550 nm (Fig. S3). The photocycle of the SacRs, determined by measuring the transient absorption change after nanosecond laser pulse illumination (Fig. 1c and Fig. S4), displays a blue-shifted M intermediate that represents the deprotonated state of the retinal chromophore. This has been observed for other H+ pumping rhodopsins [7, 8] and indicates that the proton bound to retinal is translocated during pumping.Given that SacRs function as outward proton pumps, we searched Saccharibacteria genomes for the F1Fo ATP synthase that would be required to harness the generated proton motive force for ATP synthesis. HMM searches showed that all genomes encoded the complete ATP synthase gene cluster and, furthermore, had c subunits with motifs consistent with H+ binding, instead of Na+ binding (Table S1 and Fig. S5). Together, our experimental and genomic analyses strongly suggest that some Saccharibacteria utilize rhodopsins for auxiliary energy generation in addition to their core fermentative capacities [6].Retinal is the rhodopsin chromophore that enables function of the complex upon illumination [9]. We found no evidence for the presence of β-carotene 15,15’-dioxygenase (blh), which produces all-trans-retinal (ATR) from β-carotene, in Saccharibacteria genomes encoding rhodopsin. This absence was likely not due to genome incompleteness, as genomic bins were generally of high quality (79–98% completeness, Table S1) and rhodopsin genomic loci were well-sampled. Additionally, no conserved hypothetical proteins were present in these regions, where blh is often found [10] (Fig. 1d, Fig. S6 and Table S2). As SacRs do contain the conserved lysine for retinal binding [4], we instead hypothesized that Saccharibacteria may uptake retinal from the environment, as has been previously observed for other microorganisms encoding rhodopsin but also lacking blh [11, 12].We tested the ability of SacR proteins to bind ATR from an external source by performing a retinal reconstitution assay. In contrast to the proton transport assays, where rhodopsin was expressed in the presence of ATR, here ATR was dissociated from the purified complex and the visible absorbance of rhodopsin was measured upon re-addition of ATR [13]. Both Gloeobacter rhodopsin (GR), a typical Type-1 outward H+ pump, and SacRs showed an increase in absorption in the visible region with time after the addition of ATR (Fig. 2a and Fig. S7). For all SacRs, the binding of ATR by their apoprotein was saturated within 30 sec after retinal addition (Fig. 2b), indicating that SacR is able to be efficiently functionalized using externally derived ATR. The observed reconstitution rate is substantially faster than that of GR (  > 20 min) and comparable to that of heliorhodopsin, which is used by other microorganisms also lacking a retinal synthetic pathway and rapidly binds ATR through a small opening in the apoprotein [12]. In the structure of SacRNC335 modeled by Alphafold2 [14, 15], a similar hole is visible in the protein moiety constructing the retinal binding pocket (Fig. S8). Hence, SacRs may also bind retinal through this hole in a similar manner to TaHeR (heliorhodopsin).Fig. 2: Binding of retinal by Saccharibacteria rhodopsins and context for biosynthesis.a UV-visible absorption spectra showing the regeneration of retinal binding to SacRNC335 and GR in 20 mM HEPES–NaOH, pH 7.0, 100 mM NaCl and 0.05% n-dodecyl-β-D-maltoside (DDM). In SacRNC335, a peak around 470 nm was transiently observed in the spectrum 30 s after the addition of ATR, suggesting that an intermediate species appears during the retinal incorporation process that involves formation of the Schiff base linkage. b Time evolution of visible absorption representing retinal binding to apo-protein. Numbers in parentheses in the legend indicate the absorption maxima of each rhodopsin. c Genetic potential for β-carotene 15,15’-dioxygenase (blh) production in freshwater lake metagenomes where SacRs are found. Fractions indicate the number of blh-encoding scaffolds taxonomically affiliated with the Actinobacteria in each sample. d Conceptual diagram illustrating potential retinal exchange between Saccharibacteria and host cells. ATR all-trans-retinal, GR Gloeobacter rhodopsin, AM Alinen Mustajärvi, Ki Kiruna, rhod. rhodopsin.Full size imageSaccharibacteria with rhodopsin must obtain retinal from other organisms. To evaluate possible sources of ATR, we investigated the genetic potential for retinal biosynthesis in 15 subarctic and boreal lakes [16] where Saccharibacteria with rhodopsin were present (Fig. S9). Blh-encoding scaffolds were found in 14 of the 15 metagenomes profiled (~93%) and, in nearly all cases, these scaffolds derived from Actinobacteria (Fig. 2c and Table S3). This is intriguing because Actinobacteria are known to be hosts of Saccharibacteria in the human microbiome [17, 18] and potentially more generally [4, 19]. 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Here at the Germplasm Bank of Wild Species of China at the Kunming Institute of Botany, we want to preserve the seeds of as many wild plants as possible from across China’s vast land area. I work on developing the best techniques to freeze plant seeds and tissues at ultracold temperatures, to maintain their viability for years. The idea is that if we plant these seeds again in hundreds of years, a plant will grow.The picture shows me taking a sample of embryos from the seeds of a magnolia tree out of a liquid-nitrogen cryopreservation tank to test whether they’ll regrow when thawed. I dress in protective equipment from head to toe to protect me from the nitrogen, which has a temperature of −196 °C.When I came to the institute in 2009 as a PhD student, it had just purchased its first liquid-nitrogen cryopreservation system, but no one knew how to operate it. I was the one to work it out.Over the years, human activities and climate change have had a negative impact on plant biodiversity. The ultimate goal of the plant seed bank is to collect and preserve all wild plant species in China that are endangered, rare or valuable. We want to save these species before they go extinct. We’ve collected seeds from nearly 11,000 plant species, but that’s only one-third of what grows in China.Many wild plants have genes that help them to survive in harsh environments and make them disease- or drought-resistant. In the future, we might need these genetic materials to breed new crops that can better adapt to the changing climate.I am constantly amazed by how diverse and beautiful seeds are. Some of them are brightly coloured and others are star-shaped. I feel proud when I see the unfrozen seeds germinate in test tubes and gradually grow into large plants. We have three plants in the seed-bank lobby that we cultivated from preserved tissues, and they are all now taller than me. More