Ancient dynamin segments capture early stages of host–mitochondrial integration

Eukaryotic cells use dynamins—mechano-chemical GTPases—to drive the division of endosymbiotic organelles. Here we probe early steps of mitochondrial and chloroplast endosymbiosis by tracing the evolution of dynamins. We develop a parsimony-based phylogenetic method for protein sequence reconstruction, with deep time resolution. Using this, we demonstrate that dynamins diversify through the punctuated transformation of sequence segments on the scale of secondary-structural elements. We find examples of segments that have remained essentially unchanged from the 1.8-billion-y-old last eukaryotic common ancestor to the present day. Stitching these together, we reconstruct three ancestral dynamins: The first is nearly identical to the ubiquitous mitochondrial division dynamins of extant eukaryotes, the second is partially preserved in the myxovirus-resistance-like dynamins of metazoans, and the third gives rise to the cytokinetic dynamins of amoebozoans and plants and to chloroplast division dynamins. The reconstructed sequences, combined with evolutionary models and published functional data, suggest that the ancestral mitochondrial division dynamin also mediated vesicle scission. This bifunctional protein duplicated into specialized mitochondrial and vesicle variants at least three independent times—in alveolates, green algae, and the ancestor of fungi and metazoans—accompanied by the loss of the ancient prokaryotic mitochondrial division protein FtsZ. Remarkably, many extant species that retain FtsZ also retain the predicted ancestral bifunctional dynamin. The mitochondrial division apparatus of such organisms, including amoebozoans, red algae, and stramenopiles, seems preserved in a near-primordial form.

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Parametric Analysis of the Shear Lag Effect in Tube Structural Systems of Tall Buildings

Applied Sciences ◽

10.3390/app11010278 ◽

2020 ◽

Vol 11 (1) ◽

pp. 278

Author(s):

Ivan Hafner ◽

Anđelko Vlašić ◽

Tomislav Kišiček ◽

Tvrtko Renić

Keyword(s):

Parametric Analysis ◽

Numerical Models ◽

Tall Buildings ◽

Structural Systems ◽

Structural Elements ◽

Structural System ◽

Shear Lag ◽

Shear Lag Effect ◽

Lag Effect ◽

Secondary Structural Elements

Horizontal loads such as earthquake and wind are considered dominant loads for the design of tall buildings. One of the most efficient structural systems in this regard is the tube structural system. Even though such systems have a high resistance when it comes to horizontal loads, the shear lag effect that is characterized by an incomplete and uneven activation of vertical elements may cause a series of problems such as the deformation of internal panels and secondary structural elements, which cumulatively grow with the height of the building. In this paper, the shear lag effect in a typical tube structure will be observed and analyzed on a series of different numerical models. A parametric analysis will be conducted with a great number of variations in the structural elements and building layout, for the purpose of giving recommendations for an optimal design of a tube structural system.

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In Silico Genetic Robustness Analysis of Secondary Structural Elements in the miRNA Gene

Journal of Molecular Evolution ◽

10.1007/s00239-008-9174-5 ◽

2008 ◽

Vol 67 (5) ◽

pp. 560-569 ◽

Cited By ~ 5

Author(s):

Wenjie Shu ◽

Ming Ni ◽

Xiaochen Bo ◽

Zhiqiang Zheng ◽

Shengqi Wang

Keyword(s):

In Silico ◽

Mirna Gene ◽

Robustness Analysis ◽

Structural Elements ◽

Genetic Robustness ◽

Secondary Structural Elements

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In silico identification and characterization of sensory motifs in the transcriptional regulators of the ArsR-SmtB family

Metallomics ◽

10.1039/c8mt00082d ◽

2018 ◽

Vol 10 (10) ◽

pp. 1476-1500 ◽

Cited By ~ 4

Author(s):

Rima Roy ◽

Saikat Samanta ◽

Surajit Patra ◽

Nav Kumar Mahato ◽

Rudra P. Saha

Keyword(s):

In Silico ◽

Transcriptional Regulators ◽

Transcriptional Repressors ◽

Structural Elements ◽

In Silico Identification ◽

Metal Efflux ◽

Identification And Characterization ◽

Secondary Structural Elements ◽

Efflux Proteins

The ArsR-SmtB family of transcriptional repressors regulates the transcription of metal-efflux proteins by binding specific metals at a variety of secondary structural elements, called motifs, on the surface of the proteins.

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Spider crabs of the Western Atlantic with special reference to fossil and some modern Mithracidae

PeerJ ◽

10.7717/peerj.1301 ◽

2015 ◽

Vol 3 ◽

pp. e1301 ◽

Cited By ~ 12

Author(s):

Adiël A. Klompmaker ◽

Roger W. Portell ◽

Aaron T. Klier ◽

Vanessa Prueter ◽

Alyssa L. Tucker

Keyword(s):

Fossil Record ◽

Early Pleistocene ◽

Caribbean Region ◽

Deep Time ◽

Western Atlantic ◽

Extant Species ◽

Length Width ◽

The Caribbean ◽

Abundance And Diversity ◽

First Time

Spider crabs (Majoidea) are well-known from modern oceans and are also common in the western part of the Atlantic Ocean. When spider crabs appeared in the Western Atlantic in deep time, and when they became diverse, hinges on their fossil record. By reviewing their fossil record, we show that (1) spider crabs first appeared in the Western Atlantic in the Late Cretaceous, (2) they became common since the Miocene, and (3) most species and genera are found in the Caribbean region from the Miocene onwards. Furthermore, taxonomic work on some modern and fossil Mithracidae, a family that might have originated in the Western Atlantic, was conducted. Specifically,Maguimithraxgen. nov. is erected to accommodate the extant speciesDamithrax spinosissimus, whileDamithraxcf.pleuracanthusis recognized for the first time from the fossil record (late Pliocene–early Pleistocene, Florida, USA). Furthermore, two new species are described from the lower Miocene coral-associated limestones of Jamaica (Mithrax arawakumsp. nov. andNemausa windsoraesp. nov.). Spurred by a recent revision of the subfamily, two known species from the same deposits are refigured and transferred to new genera:Mithrax donovanitoNemausa, andMithrax unguistoDamithrax. The diverse assemblage of decapods from these coral-associated limestones underlines the importance of reefs for the abundance and diversity of decapods in deep time. Finally, we quantitatively show that these crabs possess allometric growth in that length/width ratios drop as specimens grow, a factor that is not always taken into account while describing and comparing among taxa.

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Structural characterization of a Thorarchaeota profilin indicates eukaryotic-like features but with an extended N-terminus

10.1101/2021.08.06.455371 ◽

2021 ◽

Author(s):

Celestine N Chi ◽

Ravi Teja Inturi ◽

Sandra Martinez Lara ◽

Mahmoud Darweesh

Keyword(s):

Common Ancestor ◽

Three Dimensional ◽

Eukaryotic Cell ◽

Dimensional Structure ◽

Resonance Spectroscopy ◽

Last Eukaryotic Common Ancestor ◽

Rigid Core ◽

N Terminus ◽

Metagenomics Analysis

The emergence of the first eukaryotic cell was preceded by evolutionary events which are still highly debatable. Recently, comprehensive metagenomics analysis has uncovered that the Asgard super-phylum is the closest yet known archaea host of eukaryotes. However, it remains to be established if a large number of eukaryotic signature proteins predicated to be encoded by the Asgard super-phylum are functional at least, in the context of a eukaryotic cell. Here, we determined the three-dimensional structure of profilin from Thorarchaeota by nuclear magnetic resonance spectroscopy and show that this profilin has a rigid core with a flexible N-terminus which was previously implicated in polyproline binding. In addition, we also show that thorProfilin co-localizes with eukaryotic actin in cultured HeLa cells. This finding reaffirm the notion that Asgardean encoded proteins possess eukaryotic-like characteristics and strengthen likely existence of a complex cytoskeleton already in a last eukaryotic common ancestor

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Selecting Folded Proteins from a Library of Secondary Structural Elements

Journal of the American Chemical Society ◽

10.1021/ja074405w ◽

2008 ◽

Vol 130 (1) ◽

pp. 176-185 ◽

Cited By ~ 14

Author(s):

James J. Graziano ◽

Wenshe Liu ◽

Roshan Perera ◽

Bernhard H. Geierstanger ◽

Scott A. Lesley ◽

...

Keyword(s):

Structural Elements ◽

Folded Proteins ◽

Secondary Structural Elements

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Targeting G-quadruplexes in the rhinovirus genome by Pyridostatin inhibits uncoating 3 and highlights a critical role for sodium ions.

10.21203/rs.3.rs-646190/v2 ◽

2021 ◽

Author(s):

Antonio Real-Hohn ◽

Martin Groznica ◽

Georg Kontaxis ◽

Rong Zhu ◽

Otávio Chaves ◽

...

Keyword(s):

Common Cold ◽

Critical Role ◽

Sodium Ions ◽

Structural Elements ◽

Temperature Dependent ◽

Physiological Conditions ◽

Metastable Structures ◽

G Quadruplex ◽

The Common ◽

Secondary Structural Elements

Abstract The ~ 2.4 µm long rhinovirus ss(+)RNA genome consists of roughly 7,200 nucleotides. It is tightly folded to fit into the ~ 22 nm diameter void in the protein capsid. In addition to previously predicted secondary structural elements in the RNA, using the QGRS mapper, we revealed the presence of multiple quadruplex forming G-rich sequences (QGRS) in the RV-A, B, and C clades, with four of them being exquisitely conserved. The biophysical analyses of ribooligonucleotides corresponding to selected QGRS demonstrate G-quadruplex (GQ) formation in each instance and resulted in discovering another example of an unconventional, two-layer zero-nucleotide loop RNA GQ stable at physiological conditions. By exploiting the temperature-dependent viral breathing to allow diffusion of small compounds into the virion, we demonstrate that the GQ-binding compounds PhenDC3 and pyridostatin (PDS) uniquely interfere with viral uncoating. Remarkably, this inhibition was entirely prevented in the presence of K+ but not Na+, despite the higher GQ stabilising effect of K+. Based on virus thermostability studies combined with ultrastructural imaging of isolated viral RNA, we propose a mechanism where Na+ keeps the encapsidated genome loose, allowing its penetration by PDS to promote the transition of QGRS sequestered in alternative metastable structures into GQs. The resulting conformational change then materialises in a severely compromised RNA release from the proteinaceous shell. Targeting extracellularly circulating RVs with GQ-stabilisers might thus become a novel way of combating the common cold.

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NMR resonance assignment and dynamics of profilin from Heimdallarchaeota

Scientific Reports ◽

10.1038/s41598-020-72550-1 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Syed Razaul Haq ◽

Sabeen Survery ◽

Fredrik Hurtig ◽

Ann-Christin Lindås ◽

Celestine N. Chi

Keyword(s):

Structural Analysis ◽

Structural Properties ◽

Resonance Assignment ◽

Eukaryotic Cell ◽

Nmr Resonance Assignment ◽

Metagenomic Data ◽

Divergent Evolution ◽

Structural Elements ◽

Scientific Question ◽

Secondary Structural Elements

Abstract The origin of the eukaryotic cell is an unsettled scientific question. The Asgard superphylum has emerged as a compelling target for studying eukaryogenesis due to the previously unseen diversity of eukaryotic signature proteins. However, our knowledge about these proteins is still relegated to metagenomic data and very little is known about their structural properties. Additionally, it is still unclear if these proteins are functionally homologous to their eukaryotic counterparts. Here, we expressed, purified and structurally characterized profilin from Heimdallarchaeota in the Asgard superphylum. The structural analysis shows that while this profilin possesses similar secondary structural elements as eukaryotic profilin, it contains additional secondary structural elements that could be critical for its function and an indication of divergent evolution.

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