scholarly journals Evolution of Archaellum Rotation Involved Invention of a Stator Complex by Duplicating and Modifying a Core Component

2021 ◽  
Vol 12 ◽  
Author(s):  
Trishant R. Umrekar ◽  
Yvonne B. Winterborn ◽  
Shamphavi Sivabalasarma ◽  
Julian Brantl ◽  
Sonja-Verena Albers ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Quaternary Structure ◽  
Atp Hydrolysis ◽  
Molecular Motor ◽  
Gene Duplications ◽  
Bacterial Flagellum ◽  
Rotary Motors ◽  
Prediction Techniques ◽  
Evolutionary Emergence ◽  
Work Supports

Novelty in biology can arise from opportunistic repurposing of nascent characteristics of existing features. Understanding how this process happens at the molecular scale, however, suffers from a lack of case studies. The evolutionary emergence of rotary motors is a particularly clear example of evolution of a new function. The simplest of rotary motors is the archaellum, a molecular motor that spins a helical propeller for archaeal motility analogous to the bacterial flagellum. Curiously, emergence of archaellar rotation may have pivoted on the simple duplication and repurposing of a pre-existing component to produce a stator complex that anchors to the cell superstructure to enable productive rotation of the rotor component. This putative stator complex is composed of ArlF and ArlG, gene duplications of the filament component ArlB, providing an opportunity to study how gene duplication and neofunctionalization contributed to the radical innovation of rotary function. Toward understanding how this happened, we used electron cryomicroscopy to determine the structure of isolated ArlG filaments, the major component of the stator complex. Using a hybrid modeling approach incorporating structure prediction and validation, we show that ArlG filaments are open helices distinct to the closed helical filaments of ArlB. Curiously, further analysis reveals that ArlG retains a subset of the inter-protomer interactions of homologous ArlB, resulting in a superficially different assembly that nevertheless reflects the common ancestry of the two structures. This relatively simple mechanism to change quaternary structure was likely associated with the evolutionary neofunctionalization of the archaellar stator complex, and we speculate that the relative deformable elasticity of an open helix may facilitate elastic energy storage during the transmission of the discrete bursts of energy released by ATP hydrolysis to continuous archaellar rotation, allowing the inherent properties of a duplicated ArlB to be co-opted to fulfill a new role. Furthermore, agreement of diverse experimental evidence in our work supports recent claims to the power of new structure prediction techniques.

scholarly journals A FRET-Based Sensor Reveals Large ATP Hydrolysis–Induced Conformational Changes and Three Distinct States of the Molecular Motor Myosin

Cell ◽  
2000 ◽  
Vol 102 (5) ◽  
pp. 683-694 ◽  
Author(s):  
William M Shih ◽  
Zygmunt Gryczynski ◽  
Joseph R Lakowicz ◽  
James A Spudich
Keyword(s):  
Conformational Changes ◽  
Atp Hydrolysis ◽  
Molecular Motor

scholarly journals Evolution of the C-Type Lectin-Like Receptor Genes of the DECTIN-1 Cluster in the NK Gene Complex

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Susanne Sattler ◽  
Hormas Ghadially ◽  
Erhard Hofer
Keyword(s):  
Pattern Recognition ◽  
Sequence Data ◽  
Gene Duplications ◽  
Gene Complex ◽  
Adaptive Immune ◽  
Recognition Function ◽  
Recent Developments ◽  
Evolutionary Emergence ◽  
Related Proteins ◽  
Nk Gene Complex

Pattern recognition receptors are crucial in initiating and shaping innate and adaptive immune responses and often belong to families of structurally and evolutionarily related proteins. The human C-type lectin-like receptors encoded in the DECTIN-1 cluster within the NK gene complex contain prominent receptors with pattern recognition function, such as DECTIN-1 and LOX-1. All members of this cluster share significant homology and are considered to have arisen from subsequent gene duplications. Recent developments in sequencing and the availability of comprehensive sequence data comprising many species showed that the receptors of the DECTIN-1 cluster are not only homologous to each other but also highly conserved between species. Even inCaenorhabditis elegans, genes displaying homology to the mammalian C-type lectin-like receptors have been detected. In this paper, we conduct a comprehensive phylogenetic survey and give an up-to-date overview of the currently available data on the evolutionary emergence of the DECTIN-1 cluster genes.

scholarly journals The cryo-EM structure of the bacterial flagellum cap complex suggests a molecular mechanism for filament elongation

2019 ◽  
Author(s):  
Natalie S. Al-Otaibi ◽  
Aidan J. Taylor ◽  
Daniel P. Farrell ◽  
Svetomir B. Tzokov ◽  
Frank DiMaio ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Campylobacter Jejuni ◽  
Bacterial Cell ◽  
Molecular Basis ◽  
Molecular Model ◽  
Molecular Motor ◽  
Terminal Region ◽  
Bacterial Flagellum ◽  
Filament Assembly ◽  
Oligomeric Assembly

AbstractThe bacterial flagellum is a remarkable molecular motor, present at the surface of many bacteria, whose primary function is to allow motility through the rotation of a long filament protruding from the bacterial cell. A cap complex, consisting of an oligomeric assembly of the protein FliD, is localized at the tip of the flagellum, and is essential for filament assembly, as well as adherence to surfaces in some bacteria. However, the structure of the intact cap complex, and the molecular basis for its interaction with the filament, remains elusive. Here we report the cryo-EM structure of the Campylobacter jejuni cap complex. This structure reveals that FliD is pentameric, with the N-terminal region of the protomer forming an unexpected extensive set of contacts across several subunits, that contribute to FliD oligomerization. We also demonstrate that the native C. jejuni flagellum filament is 11-stranded and propose a molecular model for the filament-cap interaction.

scholarly journals High-Resolution pH Imaging of Living Bacterial Cells To Detect Local pH Differences

mBio ◽  
2016 ◽  
Vol 7 (6) ◽  
Author(s):  
Yusuke V. Morimoto ◽  
Nobunori Kami-ike ◽  
Tomoko Miyata ◽  
Akihiro Kawamoto ◽  
Takayuki Kato ◽  
...  
Keyword(s):  
High Resolution ◽  
Atp Hydrolysis ◽  
Imaging System ◽  
Proton Motive Force ◽  
Energy Transduction ◽  
Protein Export ◽  
Motive Force ◽  
Bacterial Flagellum ◽  
Ph Imaging ◽  
Local Ph

ABSTRACTProtons are utilized for various biological activities such as energy transduction and cell signaling. For construction of the bacterial flagellum, a type III export apparatus utilizes ATP and proton motive force to drive flagellar protein export, but the energy transduction mechanism remains unclear. Here, we have developed a high-resolution pH imaging system to measure local pH differences within livingSalmonella entericacells, especially in close proximity to the cytoplasmic membrane and the export apparatus. The local pH near the membrane was ca. 0.2 pH unit higher than the bulk cytoplasmic pH. However, the local pH near the export apparatus was ca. 0.1 pH unit lower than that near the membrane. This drop of local pH depended on the activities of both transmembrane export components and FliI ATPase. We propose that the export apparatus acts as an H+/protein antiporter to couple ATP hydrolysis with H+flow to drive protein export.IMPORTANCEThe flagellar type III export apparatus is required for construction of the bacterial flagellum beyond the cellular membranes. The export apparatus consists of a transmembrane export gate and a cytoplasmic ATPase complex. The export apparatus utilizes ATP and proton motive force as the energy source for efficient and rapid protein export during flagellar assembly, but it remains unknown how. In this study, we have developed anin vivopH imaging system with high spatial and pH resolutions with a pH indicator probe to measure local pH near the export apparatus. We provide direct evidence suggesting that ATP hydrolysis by the ATPase complex and the following rapid protein translocation by the export gate are both linked to efficient proton translocation through the gate.

scholarly journals 3P-164 Molecular mechanism of ATP hydrolysis reaction in F_1-ATPase molecular motor(The 46th Annual Meeting of the Biophysical Society of Japan)

2008 ◽  
Vol 48 (supplement) ◽  
pp. S152
Author(s):  
Abdul Rajjak Shaikh ◽  
Yuko Ito ◽  
Mitsunori Ikeguchi ◽  
Hiroshi Ueno ◽  
Hiroyuki Noji ◽  
...  
Keyword(s):  
Annual Meeting ◽  
Molecular Mechanism ◽  
Atp Hydrolysis ◽  
Molecular Motor ◽  
Hydrolysis Reaction ◽  
Biophysical Society

scholarly journals Hexagonal Ti2B2 monolayer: a promising anode material offering high rate capability for Li-ion and Na-ion batteries

2018 ◽  
Vol 20 (34) ◽  
pp. 22168-22178 ◽  
Author(s):  
Tao Bo ◽  
Peng-Fei Liu ◽  
Juping Xu ◽  
Junrong Zhang ◽  
Yuanbo Chen ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Density Functional ◽  
Density Functional Method ◽  
Rate Capability ◽  
Functional Method ◽  
High Rate ◽  
Crystal Structure Prediction ◽  
Metal Borides ◽  
Li Ion ◽  
Prediction Techniques

Combining the first-principles density functional method and crystal structure prediction techniques, we report a series of hexagonal two-dimensional transition metal borides including Sc2B2, Ti2B2, V2B2, Cr2B2, Y2B2, Zr2B2, and Mo2B2.

scholarly journals RNA Packaging Motor: From Structure to Quantum Mechanical Modelling and Sequential-Stochastic Mechanism

2008 ◽  
Vol 9 (3-4) ◽  
pp. 351-369 ◽  
Author(s):  
Jelena Telenius ◽  
Anders E. Wallin ◽  
Michal Straka ◽  
Hongbo Zhang ◽  
Erika J. Mancini ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Atp Hydrolysis ◽  
Structural Information ◽  
Molecular Motor ◽  
Structural Similarity ◽  
Binding Pocket ◽  
Reaction Coordinate ◽  
Rna Packaging ◽  
Cooperative Action ◽  
Empty Capsid

The bacteriophages of theCystoviridaefamily package their single stranded RNA genomic precursors into empty capsid (procapsids) using a hexameric packaging ATPase motor (P4). This molecular motor shares sequence and structural similarity with RecA-like hexameric helicases. A concerted structural, mutational and kinetic analysis helped to define the mechanical reaction coordinate,i.e.the conformational changes associated with RNA translocation. The results also allowed us to propose a possible scheme of coupling between ATP hydrolysis and translocation which requires the cooperative action of three consecutive subunits. Here, we first test this model by preparing hexamers with defined proportions of wild type and mutant subunits and measuring their activity. Then, we develop a stochastic kinetic model which accounts for the catalytic cooperativity of the P4 hexamer. Finally, we use the available structural information to construct a quantum-chemical model of the chemical reaction coordinate and obtain a detailed description of the electron density changes during ATP hydrolysis. The model explains the results of the mutational analyses and yields new insights into the role of several conserved residues within the ATP binding pocket. These hypotheses will guide future experimental work.

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