scholarly journals 'Lose-to-gain' adaptation to genome decay in the structure of the smallest eukaryotic ribosomes

2021 ◽  
Author(s):  
David Nicholson ◽  
Marco Salamina ◽  
Johan Panek ◽  
Karla Helena-Bueno ◽  
Charlotte R Brown ◽  
...  
Keyword(s):  
Evolutionary Process ◽  
Building Blocks ◽  
Structural Features ◽  
Molecular Structures ◽  
Evolutionary Pattern ◽  
Gain Adaptation ◽  
Intracellular Parasites ◽  
Genome Decay ◽  
The One ◽  
Genetic Drifts

The evolution of microbial parasites involves the interplay of two opposing forces. On the one hand, the pressure to survive drives parasites to improve through Darwinian natural selection. On the other, frequent genetic drifts result in genome decay, an evolutionary process in which an ever-increasing burden of deleterious mutations leads to gene loss and gradual genome reduction. Here, seeking to understand how this interplay occurs at the scale of individual macromolecules, we describe cryo-EM and evolutionary analyses of ribosomes from Encephalitozoon cuniculi, a eukaryote with one of the most reduced genomes in nature. We show that E. cuniculi ribosomes, the smallest eukaryotic cytoplasmic ribosomes to be structurally characterized, employ unparalleled structural innovations that allow extreme rRNA reduction without loss of ribosome integrity. These innovations include the evolution of previously unknown rRNA features such as molten rRNA linkers and bulgeless rRNA. Furthermore, we show that E. cuniculi ribosomes withstand the loss of rRNA and protein segments by evolving a unique ability to effectively trap small molecules and use them as ribosomal building-blocks and structural mimics of degenerated rRNA and protein segments. Overall, our work reveals a recurrent evolutionary pattern, which we term 'lose-to-gain' evolution, where it is only through the loss of rRNA and protein segments that E. cuniculi ribosomes evolve their major innovations. Our study shows that the molecular structures of intracellular parasites long viewed as reduced, degenerated, and suffering from various debilitating mutations instead possess an array of systematically overlooked and extraordinary structural features. These features allow them to not only adapt to molecular reduction but evolve new activities that parasites can possibly use to their advantage.

scholarly journals Muller’s Ratchet and Ribosome Degeneration in the Obligate Intracellular Parasites Microsporidia

2018 ◽  
Vol 19 (12) ◽  
pp. 4125 ◽  
Author(s):  
Sergey Melnikov ◽  
Kasidet Manakongtreecheep ◽  
Keith Rivera ◽  
Arthur Makarenko ◽  
Darryl Pappin ◽  
...  
Keyword(s):  
Ribosomal Proteins ◽  
Evolutionary Process ◽  
Obligate Intracellular ◽  
Muller's Ratchet ◽  
Automated Annotation ◽  
Intracellular Parasites ◽  
Genome Decay ◽  
Muller’S Ratchet ◽  
Forms Of Life ◽  
Cellular Components

Microsporidia are fungi-like parasites that have the smallest known eukaryotic genome, and for that reason they are used as a model to study the phenomenon of genome decay in parasitic forms of life. Similar to other intracellular parasites that reproduce asexually in an environment with alleviated natural selection, Microsporidia experience continuous genome decay that is driven by Muller’s ratchet—an evolutionary process of irreversible accumulation of deleterious mutations that lead to gene loss and the miniaturization of cellular components. Particularly, Microsporidia have remarkably small ribosomes in which the rRNA is reduced to the minimal enzymatic core. In this study, we analyzed microsporidian ribosomes to study an apparent impact of Muller’s ratchet on structure of RNA and protein molecules in parasitic forms of life. Through mass spectrometry of microsporidian proteome and analysis of microsporidian genomes, we found that massive rRNA reduction in microsporidian ribosomes appears to annihilate the binding sites for ribosomal proteins eL8, eL27, and eS31, suggesting that these proteins are no longer bound to the ribosome in microsporidian species. We then provided an evidence that protein eS31 is retained in Microsporidia due to its non-ribosomal function in ubiquitin biogenesis. Our study illustrates that, while Microsporidia carry the same set of ribosomal proteins as non-parasitic eukaryotes, some ribosomal proteins are no longer participating in protein synthesis in Microsporidia and they are preserved from genome decay by having extra-ribosomal functions. More generally, our study shows that many components of parasitic cells, which are identified by automated annotation of pathogenic genomes, may lack part of their biological functions due to continuous genome decay.

scholarly journals Muller’s Ratchet and Ribosome Degeneration in the Obligate Intracellular Parasites Microsporidia

2018 ◽  
Author(s):  
Sergey Melnikov ◽  
Kasidet Manakongtreecheep ◽  
Keith Rivera ◽  
Arthur Makarenko ◽  
Darryl Pappin ◽  
...  
Keyword(s):  
Ribosomal Proteins ◽  
Evolutionary Process ◽  
Mass Spectrometry Analysis ◽  
Spectrometry Analysis ◽  
Muller's Ratchet ◽  
Ribosome Structure ◽  
Intracellular Parasites ◽  
Genome Decay ◽  
Muller’S Ratchet ◽  
The Impact

Microsporidia are fungi-like parasites that have the smallest known eukaryotic genome, and for that reason they are used as a model to study the phenomenon of genome decay in parasitic forms of life. Similar to other intracellular parasites that reproduce asexually in an environment with alleviated natural selection, Microsporidia experience continuous genome decay driven by Muller's ratchet - an evolutionary process of irreversible accumulation of deleterious mutations, which leads to gene loss and miniaturization of cellular components. Particularly, Microsporidia have remarkably small ribosomes in which the rRNA is reduced to the minimal enzymatic core. To better understand the impact of Muller's ratchet on RNA and protein molecules in parasitic organisms, particularly regarding their ribosome structure, we have explored an apparent effect of Muller's ratchet on microsporidian ribosomal proteins. Through mass spectrometry, analysis of microsporidian genome sequences and analysis of ribosome structure from non-parasitic eukaryotes, we found that massive rRNA reduction in microsporidian ribosomes appears to annihilate binding sites for ribosomal proteins eL8, eL27, and eS31, suggesting that these proteins are no longer bound to the ribosome in microsporidian species. We then provided an evidence that protein eS31 is retained in Microsporidia due to its non-ribosomal function in ubiquitin biogenesis. To sum up, our study illustrates that while Microsporidia carry the same set of ribosomal proteins as non-parasitic eukaryotes, some of ribosomal proteins are no longer participating in protein synthesis in Microsporidia and they are preserved from genome decay by having extra-ribosomal functions.

Factors Affecting Molecular Self-Assembly and Its Mechanism

2012 ◽  
Vol 9 (1) ◽  
pp. 43 ◽  
Author(s):  
Hueyling Tan
Keyword(s):  
Self Assembly ◽  
Building Blocks ◽  
Molecular Engineering ◽  
Molecular Structures ◽  
Polymer Science ◽  
New Approach ◽  
Factors Affecting ◽  
Dna Structures ◽  
Self Assembling ◽  
Wide Range

Molecular self-assembly is ubiquitous in nature and has emerged as a new approach to produce new materials in chemistry, engineering, nanotechnology, polymer science and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use ofpeptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. The study ofbiological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries ofexisting disciplines. Many self-assembling systems are rangefrom bi- andtri-block copolymers to DNA structures as well as simple and complex proteins andpeptides. The ultimate goal is to harness molecular self-assembly such that design andcontrol ofbottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes oflife and non-life science applications. Such aspirations can be achievedthrough understanding thefundamental principles behind the selforganisation and self-synthesis processes exhibited by biological systems.

A Pseudo Five-Fold Symmetrical Ligand Drives Geometric Frustration in Porous Metal-Organic and Hydrogen Bonded Frameworks

2020 ◽  
Author(s):  
Frederik Haase ◽  
Gavin Craig ◽  
Mickaele Bonneau ◽  
kunihisa sugimoto ◽  
Shuhei Furukawa
Keyword(s):  
Topological Defects ◽  
Porous Metal ◽  
Building Blocks ◽  
Structural Features ◽  
Equilibrium Structure ◽  
Sorption Behavior ◽  
Building Unit ◽  
Geometric Frustration ◽  
Secondary Building Units ◽  
Hydrogen Bonded

Reticular framework materials thrive on designability, but unexpected reaction outcomes are crucial in exploring new structures and functionalities. By combining “incompatible” building blocks, we employed geometric frustration in reticular materials leading to emergent structural features. The combination of a pseudo C<sub>5</sub> symmetrical organic building unit based on a pyrrole core, with a C<sub>4</sub> symmetrical copper paddlewheel synthon led to three distinct frameworks by tuning the synthetic conditions. The frameworks show structural features typical for geometric frustration: self-limiting assembly, internally stressed equilibrium structures and topological defects in the equilibrium structure, which manifested in the formation of a hydrogen bonded framework, distorted and broken secondary building units and dangling functional groups, respectively. The influence of geometric frustration on the CO<sub>2</sub> sorption behavior and the discovery of a new secondary building unit shows geometric frustration can serve as a strategy to obtain highly complex porous frameworks.

A Pseudo Five-Fold Symmetrical Ligand Drives Geometric Frustration in Porous Metal-Organic and Hydrogen Bonded Frameworks

2020 ◽  
Author(s):  
Frederik Haase ◽  
Gavin Craig ◽  
Mickaele Bonneau ◽  
kunihisa sugimoto ◽  
Shuhei Furukawa
Keyword(s):  
Topological Defects ◽  
Porous Metal ◽  
Building Blocks ◽  
Structural Features ◽  
Equilibrium Structure ◽  
Sorption Behavior ◽  
Building Unit ◽  
Geometric Frustration ◽  
Secondary Building Units ◽  
Hydrogen Bonded

Reticular framework materials thrive on designability, but unexpected reaction outcomes are crucial in exploring new structures and functionalities. By combining “incompatible” building blocks, we employed geometric frustration in reticular materials leading to emergent structural features. The combination of a pseudo C<sub>5</sub> symmetrical organic building unit based on a pyrrole core, with a C<sub>4</sub> symmetrical copper paddlewheel synthon led to three distinct frameworks by tuning the synthetic conditions. The frameworks show structural features typical for geometric frustration: self-limiting assembly, internally stressed equilibrium structures and topological defects in the equilibrium structure, which manifested in the formation of a hydrogen bonded framework, distorted and broken secondary building units and dangling functional groups, respectively. The influence of geometric frustration on the CO<sub>2</sub> sorption behavior and the discovery of a new secondary building unit shows geometric frustration can serve as a strategy to obtain highly complex porous frameworks.

Application of Nitrogen Heterocyclic Carbenes in Organocatalysis

2020 ◽  
Vol 09 ◽  
Author(s):  
Minita Ojha ◽  
R. K. Bansal
Keyword(s):  
Asymmetric Catalysis ◽  
Building Blocks ◽  
Structural Features ◽  
Heterocyclic Carbenes ◽  
Stetter Reaction ◽  
Metal Pollutants ◽  
Synthetic Strategy ◽  
Wide Range ◽  
Benzoin Condensation ◽  
Nitrogen Heterocyclic

Background: During the last two decades, horizon of research in the field of Nitrogen Heterocyclic Carbenes (NHC) has widened remarkably. NHCs have emerged as ubiquitous species having applications in a broad range of fields, including organocatalysis and organometallic chemistry. The NHC-induced non-asymmetric catalysis has turned out to be a really fruitful area of research in recent years. Methods: By manipulating structural features and selecting appropriate substituent groups, it has been possible to control the kinetic and thermodynamic stability of a wide range of NHCs, which can be tolerant to a variety of functional groups and can be used under mild conditions. NHCs are produced by different methods, such as deprotonation of Nalkylhetrocyclic salt, transmetallation, decarboxylation and electrochemical reduction. Results: The NHCs have been used successfully as catalysts for a wide range of reactions making a large number of building blocks and other useful compounds accessible. Some of these reactions are: benzoin condensation, Stetter reaction, Michael reaction, esterification, activation of esters, activation of isocyanides, polymerization, different cycloaddition reactions, isomerization, etc. The present review includes all these examples published during the last 10 years, i.e. from 2010 till date. Conclusion: The NHCs have emerged as versatile and powerful organocatalysts in synthetic organic chemistry. They provide the synthetic strategy which does not burden the environment with metal pollutants and thus fit in the Green Chemistry.

scholarly journals A novel approach to the computation of one-loop three- and four-point functions: I. The real mass case

2019 ◽  
Vol 2019 (11) ◽  
Author(s):  
J Ph Guillet ◽  
E Pilon ◽  
Y Shimizu ◽  
M S Zidi
Keyword(s):  
Building Blocks ◽  
The Real ◽  
Alternative Method ◽  
Novel Approach ◽  
Reduction Methods ◽  
Real Mass ◽  
Novel Method ◽  
Algebraic Reduction ◽  
The One ◽  
Mass Case

Abstract This article is the first of a series of three presenting an alternative method of computing the one-loop scalar integrals. This novel method enjoys a couple of interesting features as compared with the method closely following ’t Hooft and Veltman adopted previously. It directly proceeds in terms of the quantities driving algebraic reduction methods. It applies to the three-point functions and, in a similar way, to the four-point functions. It also extends to complex masses without much complication. Lastly, it extends to kinematics more general than that of the physical, e.g., collider processes relevant at one loop. This last feature may be useful when considering the application of this method beyond one loop using generalized one-loop integrals as building blocks.

scholarly journals 1,3-Diketone Calix[4]arene Derivatives—A New Type of Versatile Ligands for Metal Complexes and Nanoparticles

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1214
Author(s):  
Sergey N. Podyachev ◽  
Rustem R. Zairov ◽  
Asiya R. Mustafina
Keyword(s):  
Structural Diversity ◽  
Building Blocks ◽  
Structural Features ◽  
Structure Property ◽  
One Pot ◽  
Arene Ligands ◽  
Structure Property Relationships ◽  
New Type ◽  
Synthetic Routes ◽  
Magnetic Resonance Imaging Mri

The present review is aimed at highlighting outlooks for cyclophanic 1,3-diketones as a new type of versatile ligands and building blocks of the nanomaterial for sensing and bioimaging. Thus, the main synthetic routes for achieving the structural diversity of cyclophanic 1,3-diketones are discussed. The structural diversity is demonstrated by variation of both cyclophanic backbones (calix[4]arene, calix[4]resorcinarene and thiacalix[4]arene) and embedding of different substituents onto lower or upper macrocyclic rims. The structural features of the cyclophanic 1,3-diketones are correlated with their ability to form lanthanide complexes exhibiting both lanthanide-centered luminescence and magnetic relaxivity parameters convenient for contrast effect in magnetic resonance imaging (MRI). The revealed structure–property relationships and the applicability of facile one-pot transformation of the complexes to hydrophilic nanoparticles demonstrates the advantages of 1,3-diketone calix[4]arene ligands and their complexes in developing of nanomaterials for sensing and bioimaging.

Zeolates: A Coordination Chemistry View of Metal-Ligand Bonding in Intrazeolite MOCVD Type Precursors and Semiconductor Nanoclusters

1992 ◽  
Vol 277 ◽  
Author(s):  
Geoffrey A. Ozin ◽  
Carol L. Bowes ◽  
Mark R. Steele
Keyword(s):  
Self Assembly ◽  
Materials Science ◽  
Zeolite Y ◽  
Chemical Vapour ◽  
Internal Surface ◽  
Building Blocks ◽  
Structural Features ◽  
Organic Chemical ◽  
Wide Range ◽  
Shape Selective

ABSTRACTVarious MOCVD (metal-organic chemical vapour deposition) type precursors and their self-assembled semiconductor nanocluster products [1] have been investigated in zeolite Y hosts. From analysis of in situ observations (FTIR, UV-vis reflectance, Mössbauer, MAS-NMR) of the reaction sequences and structural features of the precursors and products (EXAFS and Rietveld refinement of powder XRD data) the zeolite is viewed as providing a macrospheroidal, multidendate coordination environment towards encapsulated guests. By thinking about the α- and β-cages of the zeolite Y host effectively as a zeolate ligand composed of interconnected aluminosilicate “crown ether-like” building blocks, the materials chemist is able to better understand and exploit the reactivity and coordination properties of the zeolite internal surface for the anchoring and self-assembly of a wide range of encapsulated guests. This approach helps with the design of synthetic strategies for creating novel guest-host inclusion compounds having possible applications in areas of materials science such as nonlinear optics, quantum electronics, and size/shape selective catalysis.

scholarly journals Steric control of supramolecular association in structures of Zn(S2COR)2 with N,N′-bis(pyridin-4-ylmethyl)oxalamide

2019 ◽  
Vol 234 (3) ◽  
pp. 165-175 ◽  
Author(s):  
Yee Seng Tan ◽  
Hao Zhe Chun ◽  
Mukesh M. Jotani ◽  
Edward R.T. Tiekink
Keyword(s):  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Molecular Structures ◽  
Coordination Geometry ◽  
Hirshfeld Surfaces ◽  
Binuclear Molecule ◽  
Supramolecular Chain ◽  
The One ◽  
Distorted Tetrahedral Coordination ◽  
Cyclohexyl Group

Abstract The crystal and molecular structures of the one-dimensional coordination polymer [Zn(S2COEt)2(4LH2)]n (1) and binuclear [Zn(S2COCy)2]2(4LH2) (2) are described, where 4LH2 is N,N′-bis(pyridin-4-ylmethyl)ethanediamide. In 1, the Zn(S2COEt)2 entities are linked by bidentate bridging 4LH2 ligands through the pyridyl-N atoms to generate a twisted supramolecular chain. As a result of monodentate xanthate ligands, the N2S4 donor set defines a distorted tetrahedral coordination geometry and, crucially, allows the participation of the non-coordinating sulfur atoms in supramolecular association. Thus, in the crystal amide-N–H···O(amide) and amide-N–H···S(thione) hydrogen bonds link chains into a three-dimensional architecture. The substitution of the ethyl group in the xanthate ligand with a cyclohexyl group results in very different structural outcomes. In 2, a binuclear molecule is observed with the coordination geometry for zinc being defined by chelating xanthate ligands and a pyridyl-N atom with the NS4 donor set defining a highly distorted geometry. In the molecular packing, amide-N–H···S(thione) hydrogen bonds stabilise a supramolecular chain along the a-axis and these are connected into a three-dimensional arrangement by methylene-C–H···O and methylene-C–H···π(pyridyl) interactions. The relative importance of the specified intermolecular interactions and weaker, contributing contacts has been revealed by an analysis of the calculated Hirshfeld surfaces of 1 and 2.

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