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Kudo F, Eguchi T. Biosynthesis of cyclitols. Nat Prod Rep 2022; 39:1622-1642. [PMID: 35726901 DOI: 10.1039/d2np00024e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Review covering up to 2021Cyclitols derived from carbohydrates are naturally stable hydrophilic substances under ordinary physiological conditions, increasing the water solubility of whole molecules in cells. The stability of cyclitols is derived from their carbocyclic structures bearing no acetal groups, in contrast to sugar molecules. Therefore, carbocycle-forming reactions are critical for the biosynthesis of cyclitols. Herein, we review naturally occurring cyclitols that have been identified to date and categorize them according to the type of carbocycle-forming enzymatic reaction. Furthermore, the cyclitol-forming enzymatic reaction mechanisms and modification pathways of the initially generated cyclitols are reviewed.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-Okayama, Meguro-ku, Tokyo, Japan.
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-Okayama, Meguro-ku, Tokyo, Japan.
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Tsunoda T, Tanoeyadi S, Proteau PJ, Mahmud T. The chemistry and biology of natural ribomimetics and related compounds. RSC Chem Biol 2022; 3:519-538. [PMID: 35656477 PMCID: PMC9092360 DOI: 10.1039/d2cb00019a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/06/2022] [Indexed: 11/21/2022] Open
Abstract
Natural ribomimetics represent an important group of specialized metabolites with significant biological activities. Many of the activities, e.g., inhibition of seryl-tRNA synthetases, glycosidases, or ribosomes, are manifestations of their structural resemblance to ribose or related sugars, which play roles in the structural, physiological, and/or reproductive functions of living organisms. Recent studies on the biosynthesis and biological activities of some natural ribomimetics have expanded our understanding on how they are made in nature and why they have great potential as pharmaceutically relevant products. This review article highlights the discovery, biological activities, biosynthesis, and development of this intriguing class of natural products.
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Affiliation(s)
- Takeshi Tsunoda
- Department of Pharmaceutical Sciences, Oregon State University Corvallis OR 97331 USA
| | - Samuel Tanoeyadi
- Department of Pharmaceutical Sciences, Oregon State University Corvallis OR 97331 USA
| | - Philip J Proteau
- Department of Pharmaceutical Sciences, Oregon State University Corvallis OR 97331 USA
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University Corvallis OR 97331 USA
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Calditol-linked membrane lipids are required for acid tolerance in Sulfolobus acidocaldarius. Proc Natl Acad Sci U S A 2018; 115:12932-12937. [PMID: 30518563 DOI: 10.1073/pnas.1814048115] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Archaea have many unique physiological features of which the lipid composition of their cellular membranes is the most striking. Archaeal ether-linked isoprenoidal membranes can occur as bilayers or monolayers, possess diverse polar head groups, and a multiplicity of ring structures in the isoprenoidal cores. These lipid structures are proposed to provide protection from the extreme temperature, pH, salinity, and nutrient-starved conditions that many archaea inhabit. However, many questions remain regarding the synthesis and physiological role of some of the more complex archaeal lipids. In this study, we identify a radical S-adenosylmethionine (SAM) protein in Sulfolobus acidocaldarius required for the synthesis of a unique cyclopentyl head group, known as calditol. Calditol-linked glycerol dibiphytanyl glycerol tetraethers (GDGTs) are membrane spanning lipids in which calditol is ether bonded to the glycerol backbone and whose production is restricted to a subset of thermoacidophilic archaea of the Sulfolobales order within the Crenarchaeota phylum. Several studies have focused on the enzymatic mechanism for the synthesis of the calditol moiety, but to date no protein that catalyzes this reaction has been discovered. Phylogenetic analyses of this putative calditol synthase (Cds) reveal the genetic potential for calditol-GDGT synthesis in phyla other than the Crenarchaeota, including the Korarchaeota and Marsarchaeota. In addition, we identify Cds homologs in metagenomes predominantly from acidic ecosystems. Finally, we demonstrate that deletion of calditol synthesis renders S. acidocaldarius sensitive to extremely low pH, indicating that calditol plays a critical role in protecting archaeal cells from acidic stress.
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Wolf J, Stark H, Fafenrot K, Albersmeier A, Pham TK, Müller KB, Meyer BH, Hoffmann L, Shen L, Albaum SP, Kouril T, Schmidt-Hohagen K, Neumann-Schaal M, Bräsen C, Kalinowski J, Wright PC, Albers SV, Schomburg D, Siebers B. A systems biology approach reveals major metabolic changes in the thermoacidophilic archaeon Sulfolobus solfataricus in response to the carbon source L-fucose versus D-glucose. Mol Microbiol 2016; 102:882-908. [PMID: 27611014 DOI: 10.1111/mmi.13498] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2016] [Indexed: 12/01/2022]
Abstract
Archaea are characterised by a complex metabolism with many unique enzymes that differ from their bacterial and eukaryotic counterparts. The thermoacidophilic archaeon Sulfolobus solfataricus is known for its metabolic versatility and is able to utilize a great variety of different carbon sources. However, the underlying degradation pathways and their regulation are often unknown. In this work, the growth on different carbon sources was analysed, using an integrated systems biology approach. The comparison of growth on L-fucose and D-glucose allows first insights into the genome-wide changes in response to the two carbon sources and revealed a new pathway for L-fucose degradation in S. solfataricus. During growth on L-fucose major changes in the central carbon metabolic network, as well as an increased activity of the glyoxylate bypass and the 3-hydroxypropionate/4-hydroxybutyrate cycle were observed. Within the newly discovered pathway for L-fucose degradation the following key reactions were identified: (i) L-fucose oxidation to L-fuconate via a dehydrogenase, (ii) dehydration to 2-keto-3-deoxy-L-fuconate via dehydratase, (iii) 2-keto-3-deoxy-L-fuconate cleavage to pyruvate and L-lactaldehyde via aldolase and (iv) L-lactaldehyde conversion to L-lactate via aldehyde dehydrogenase. This pathway as well as L-fucose transport shows interesting overlaps to the D-arabinose pathway, representing another example for pathway promiscuity in Sulfolobus species.
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Affiliation(s)
- Jacqueline Wolf
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Helge Stark
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Katharina Fafenrot
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
| | - Andreas Albersmeier
- Center for Biotechnology - CeBiTec, Universität Bielefeld, Bielefeld, 33615, Germany
| | - Trong K Pham
- Departement of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, S1 3JD, UK
| | - Katrin B Müller
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Benjamin H Meyer
- Molecular Biology of Archaea, Institute for Biology II - Microbiology, Universität Freiburg, Freiburg, 79104, Germany
| | - Lena Hoffmann
- Molecular Biology of Archaea, Institute for Biology II - Microbiology, Universität Freiburg, Freiburg, 79104, Germany
| | - Lu Shen
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
| | - Stefan P Albaum
- Center for Biotechnology - CeBiTec, Universität Bielefeld, Bielefeld, 33615, Germany
| | - Theresa Kouril
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
| | - Kerstin Schmidt-Hohagen
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Meina Neumann-Schaal
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
| | - Jörn Kalinowski
- Center for Biotechnology - CeBiTec, Universität Bielefeld, Bielefeld, 33615, Germany
| | - Phillip C Wright
- Departement of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, S1 3JD, UK
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute for Biology II - Microbiology, Universität Freiburg, Freiburg, 79104, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
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Abstract
The first synthesis of carbasugars, compounds in which the ring oxygen of a monosaccharide had been replaced by a methylene moiety, was described in 1966 by Professor G. E. McCasland’s group. Seven years later, the first true natural carbasugar (5a-carba-R-D-galactopyranose) was isolated from a fermentation broth of Streptomyces sp. MA-4145. In the following decades, the chemistry and biology of carbasugars have been extensively studied. Most of these compounds show interesting biological properties, especially enzymatic inhibitory activities, and, in consequence, an important number of analogues have also been prepared in the search for improved biological activities. The aim of this review is to give coverage on the progress made in two important aspects of these compounds: the elucidation of their biosynthesis and the consideration of their biological properties, including the extensively studied carbapyranoses as well as the much less studied carbafuranoses.
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On physical properties of tetraether lipid membranes: effects of cyclopentane rings. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2012; 2012:138439. [PMID: 23028246 PMCID: PMC3458407 DOI: 10.1155/2012/138439] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 08/08/2012] [Indexed: 01/25/2023]
Abstract
This paper reviews the recent findings related to the physical properties of tetraether lipid membranes, with special attention to the effects of the number, position, and configuration of cyclopentane rings on membrane properties. We discuss the findings obtained from liposomes and monolayers, composed of naturally occurring archaeal tetraether lipids and synthetic tetraethers as well as the results from computer simulations. It appears that the number, position, and stereochemistry of cyclopentane rings in the dibiphytanyl chains of tetraether lipids have significant influence on packing tightness, lipid conformation, membrane thickness and organization, and headgroup hydration/orientation.
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