ORCID Profile
0000-0002-6335-1815
Current Organisations
Helmholtz Centre Potsdam - GFZ German Research Centre for Geosciences
,
Georgia State University
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Publisher: Springer Science and Business Media LLC
Date: 15-01-2021
DOI: 10.1038/S41467-020-20630-1
Abstract: Glycosidases are phylogenetically widely distributed enzymes that are crucial for the cleavage of glycosidic bonds. Here, we present the exceptional properties of a putative ancestor of bacterial and eukaryotic family-1 glycosidases. The ancestral protein shares the TIM-barrel fold with its modern descendants but displays large regions with greatly enhanced conformational flexibility. Yet, the barrel core remains comparatively rigid and the ancestral glycosidase activity is stable, with an optimum temperature within the experimental range for thermophilic family-1 glycosidases. None of the ∼5500 reported crystallographic structures of ∼1400 modern glycosidases show a bound porphyrin. Remarkably, the ancestral glycosidase binds heme tightly and stoichiometrically at a well-defined buried site. Heme binding rigidifies this TIM-barrel and allosterically enhances catalysis. Our work demonstrates the capability of ancestral protein reconstructions to reveal valuable but unexpected biomolecular features when s ling distant sequence space. The potential of the ancestral glycosidase as a scaffold for custom catalysis and biosensor engineering is discussed.
Publisher: Cold Spring Harbor Laboratory
Date: 28-05-2020
DOI: 10.1101/2020.05.27.118968
Abstract: Glycosidases are phylogenetically widely distributed enzymes that are crucial for the cleavage of glycosidic bonds. Here, we present the exceptional properties of a putative ancestor of bacterial and eukaryotic family-1 glycosidases. The ancestral protein shares the TIM-barrel fold with its modern descendants but displays large regions with greatly enhanced conformational flexibility. Yet, the barrel core remains comparatively rigid and the ancestral glycosidase activity is stable, with an optimum temperature within the experimental range for thermophilic family-1 glycosidases. None of the ~5500 reported crystallographic structures of ~1400 modern glycosidases show a bound porphyrin. Remarkably, the ancestral glycosidase binds heme tightly and stoichiometrically at a well-defined buried site. Heme binding rigidifies this TIM-barrel and allosterically enhances catalysis. Our work demonstrates the capability of ancestral protein reconstructions to reveal valuable but unexpected biomolecular features when s ling distant sequence space. The potential of the ancestral glycosidase as a scaffold for custom catalysis and biosensor engineering is discussed.
Publisher: Springer Science and Business Media LLC
Date: 29-01-2019
DOI: 10.1038/S41467-019-08306-X
Abstract: Eukaryotic algae rose to ecological relevance after the Neoproterozoic Snowball Earth glaciations, but the causes for this consequential evolutionary transition remain enigmatic. Cap carbonates were globally deposited directly after these glaciations, but they are usually organic barren or thermally overprinted. Here we show that uniquely-preserved cap dolostones of the Araras Group contain exceptional abundances of a newly identified biomarker: 25,28-bisnorgammacerane. Its secular occurrence, carbon isotope systematics and co-occurrence with other demethylated terpenoids suggest a mechanistic connection to extensive microbial degradation of ciliate-derived biomass in bacterially dominated ecosystems. Declining 25,28-bisnorgammacerane concentrations, and a parallel rise of steranes over hopanes, indicate the transition from a bacterial to eukaryotic dominated ecosystem after the Marinoan deglaciation. Nutrient levels already increased during the Cryogenian and were a prerequisite, but not the ultimate driver for the algal rise. Intense predatory pressure by bacterivorous protists may have irrevocably cleared self-sustaining cyanobacterial ecosystems, thereby creating the ecological opportunity that allowed for the persistent rise of eukaryotic algae to global importance.
Publisher: Oxford University Press (OUP)
Date: 28-10-2021
Abstract: The role of uric acid during primate evolution has remained elusive ever since it was discovered over 100 years ago that humans have unusually high levels of the small molecule in our serum. It has been difficult to generate a neutral or adaptive explanation in part because the uricase enzyme evolved to become a pseudogene in apes thus masking typical signals of sequence evolution. Adding to the difficulty is a lack of clarity on the functional role of uric acid in apes. One popular hypothesis proposes that uric acid is a potent antioxidant that increased in concentration to compensate for the lack of vitamin C synthesis in primate species ∼65 Ma. Here, we have expanded on our previous work with resurrected ancient uricase proteins to better resolve the reshaping of uricase enzymatic activity prior to ape evolution. Our results suggest that the pivotal death-knell to uricase activity occurred between 20 and 30 Ma despite small sequential modifications to its catalytic efficiency for the tens of millions of years since primates lost their ability to synthesize vitamin C, and thus the two appear uncorrelated. We also use this opportunity to demonstrate how molecular evolution can contribute to biomedicine by presenting ancient uricases to human immune cells that assay for innate reactivity against foreign antigens. A highly stable and highly catalytic ancient uricase is shown to elicit a lower immune response in more human haplotypes than other uricases currently in therapeutic development.
Publisher: Oxford University Press (OUP)
Date: 14-06-2018
Publisher: Research Square Platform LLC
Date: 07-11-2022
DOI: 10.21203/RS.3.RS-2202848/V1
Abstract: Fossilized lipids offer one of only few windows into ancient ecosystems. The utility of such biomarkers is determined by the phylogenetic distribution of lipid biosynthetic capabilities in extant organisms and extrapolation of this information into the past. 2-Methylhopanes in sedimentary rocks were once used to infer the importance of Cyanobacteria as primary producers in the geological past. However, the discovery of the hopanoid C-2 methyltransferase (HpnP) in Alphaproteobacteria led to the downfall of this molecular proxy. In the present study, we re-examined the distribution of HpnP in a new phylogenetic framework including novel candidate phyla, and re-interpreted a revised geological record of 2-methylhopanes based on contamination-free s les. We show that HpnP was likely present in the last common ancestor of Cyanobacteria, while the gene appeared in Alphaproteobacteria only around 750 million years ago. A subsequent rise of sedimentary 2-methylhopanes around 600 Ma likely reflects the expansion of Alphaproteobacteria that coincided with the rise of eukaryotic algae — possibly connected by algal dependency on microbially-produced vitamin B12. Our findings re-establish 2-methylhopanes as cyanobacterial biomarkers prior to 750 Ma and thus as a potential tool to measure the importance of oxygenic Cyanobacteria as primary producers on the early Earth. Our study illustrates how genetics can improve the diagnostic value of biomarkers and refine the reconstruction of early ecosystems.
Publisher: Springer Science and Business Media LLC
Date: 26-10-2023
Publisher: Springer Science and Business Media LLC
Date: 08-2017
DOI: 10.1038/NATURE23457
Abstract: The transition from dominant bacterial to eukaryotic marine primary productivity was one of the most profound ecological revolutions in the Earth's history, reorganizing the distribution of carbon and nutrients in the water column and increasing energy flow to higher trophic levels. But the causes and geological timing of this transition, as well as possible links with rising atmospheric oxygen levels and the evolution of animals, remain obscure. Here we present a molecular fossil record of eukaryotic steroids demonstrating that bacteria were the only notable primary producers in the oceans before the Cryogenian period (720-635 million years ago). Increasing steroid ersity and abundance marks the rapid rise of marine planktonic algae (Archaeplastida) in the narrow time interval between the Sturtian and Marinoan 'snowball Earth' glaciations, 659-645 million years ago. We propose that the incumbency of cyanobacteria was broken by a surge of nutrients supplied by the Sturtian deglaciation. The 'Rise of Algae' created food webs with more efficient nutrient and energy transfers, driving ecosystems towards larger and increasingly complex organisms. This effect is recorded by the concomitant appearance of biomarkers for sponges and predatory rhizarians, and the subsequent radiation of eumetazoans in the Ediacaran period.
Publisher: Proceedings of the National Academy of Sciences
Date: 15-06-2021
Abstract: Steroids are one of three major lipid components of the eukaryotic cellular membrane, along with glycerophospolipids and sphingolipids. Steroids have critical roles in eukaryotic endocytosis and thus may have been structural prerequisites for the endocytic acquisition of mitochondria during eukaryogenesis. The evolutionary history of the eukaryotic cellular membrane is poorly understood and, as such, has limited our understanding of eukaryogenesis. We address the evolution of steroid biosynthesis by combining ancestral sequence reconstruction and phylogenetic analyses of steroid biosynthesis genes. Our results indicate that steroid biosynthesis evolved within bacteria in response to the rise of oxygen and was later horizontally transferred to eukaryotes. Membrane properties of early eukaryotes are inferred to have been different than that of modern eukaryotes.
Publisher: Wiley
Date: 13-11-2015
DOI: 10.1111/GBI.12117
Abstract: The hydrocarbons preserved in an Archean rock were extracted, and their composition and distribution in consecutive slices from the outside to the inside of the rock were examined. The 2.7 Ga rock was collected from the Fortescue Group in the Pilbara region, Western Australia. The bitumen I (solvent-extracted rock) and bitumen II (solvent-extracted hydrochloric acid-treated rock) fractions have different hydrocarbon compositions. Bitumen I contains only trace amounts of aliphatic hydrocarbons and virtually no aromatic hydrocarbons. In contrast, bitumen II contains abundant aliphatic and aromatic hydrocarbons. The difference seems to reflect the weathering history and preservational environment of the investigated rock. Aliphatic hydrocarbons in bitumen I are considered to be mainly from later hydrocarbon inputs, after initial deposition and burial, and are therefore not indigenous. The lack of aromatic hydrocarbons in bitumen I suggests a severe weathering environment since uplift and exposure of the rock at the Earth's surface in the Cenozoic. On the other hand, the high abundance of aromatic hydrocarbons in bitumen II suggests that bitumen II hydrocarbons have been physically isolated from removal by their encapsulation within carbonate minerals. The richness of aromatic hydrocarbons and the relative scarcity of aliphatic hydrocarbons may reflect the original compositions of organic materials biosynthesised in ancient organisms in the Archean era, or the high thermal maturity of the rock. Cyanobacterial biomarkers were observed in the surficial slices of the rock, which may indicate that endolithic cyanobacteria inhabited the surface outcrop. The distribution of aliphatic and aromatic hydrocarbons implies a high thermal maturity, which is consistent with the lack of any specific biomarkers, such as hopanes and steranes, and the prehnite-pumpellyite facies metamorphic grade.
Publisher: Proceedings of the National Academy of Sciences
Date: 27-04-2015
Abstract: The advent of oxygenic photosynthesis set the stage for the evolution of complex life on an oxygenated planet, but it is unknown when this transformative biochemistry emerged. The existing hydrocarbon biomarker record requires that oxygenic photosynthesis and eukaryotes emerged more than 300 million years before the Great Oxidation Event [∼2.4 billion years ago (Ga)]. We report that hopane and sterane concentrations measured in new ultraclean Archean drill cores from Australia are comparable to blank concentrations, yet their concentrations in the exteriors of conventionally collected cores of stratigraphic equivalence exceed blank concentrations by more than an order of magnitude due to surficial contamination. Consequently, previous hydrocarbon biomarker reports no longer provide valid evidence for the advent of oxygenic photosynthesis and eukaryotes by ∼2.7 Ga.
Publisher: Mary Ann Liebert Inc
Date: 07-2015
Abstract: High abundances of 7- and 6-monomethylalkanes as well as C17 n-alkane, indicative of cyanobacteria, have been discovered near the surfaces of Archean carbonate rocks of the Fortescue Group in the Pilbara region, Western Australia. The presence of cyanobacterial biomarkers is mostly limited to the surface layer (<1 cm thickness) of the rocks, indicating that the cyanobacteria are an endolithic species. Biomarkers are found in bitumen I (solvent-extracted rock) and also in bitumen II (solvent-extracted decarbonated rock). The abundance of biomarkers is generally the same between both bitumen fractions in the surface layer, which suggests that the cyanobacteria penetrated into the carbonate minerals. Trace amounts of the biomarkers have also diffused into a deeper part of the rocks, but this influence is only seen in bitumen I. This implies that hydrocarbons moved toward the inside of the rock through pores and fissures in the rock fabric. In contrast, hydrocarbons in bitumen II, which mainly come from within the carbonate minerals, are isolated from the hydrocarbon migration from the outside of the rock and may be ancient indigenous organic matter. To the best of our knowledge, this is the first report of the past or modern inhabitation of cyanobacteria on Archean rocks in the Pilbara region for which hydrocarbon biomarker analyses was used.
Publisher: Oxford University Press (OUP)
Date: 03-2023
Abstract: Terpenoids, also known as isoprenoids, are the largest and most erse class of organic compounds in nature and are involved in many membrane-associated cellular processes, including membrane organization, electron transport chain, cell signaling, and phototrophy. Terpenoids are ancient compounds with their origin presumably before the last universal common ancestor. However, Bacteria and Archaea are known to possess two distinct terpenoid repertoires and utilize terpenoids differently. Most notably, archaea constitute their cellular membrane solely made of terpenoid-based phospholipids, contrary to the bacterial membrane that consists of fatty acid-based phospholipids. Thus, the composition of ancestral membranes at the beginning of cellular life and the ersification of terpenoids in early life remain enigmatic. This review addresses these key issues through comprehensive phylogenomic analyses of extant terpenoid biosynthesis enzymes in Bacteria and Archaea. We aim to infer the basal components of terpenoid biosynthesis machinery that have an ancient origin before the ergence of the two domains and shed light on the deep evolutionary connection between terpenoid biochemistry and early life.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 09-2017
Abstract: Biosynthesis of C 29 sterols, enhancing eukaryotic temperature resistance, evolved during the global Neoproterozoic glaciations.
Location: Germany
No related grants have been discovered for Yosuke Hoshino.