scholarly journals Quantitative mining of compositional heterogeneity in cryo-EM datasets of ribosome assembly intermediates

Structure ◽  
2022 ◽  
Author(s):  
Jessica N. Rabuck-Gibbons ◽  
Dmitry Lyumkis ◽  
James R. Williamson
Keyword(s):  
Ribosome Assembly ◽  
Compositional Heterogeneity

scholarly journals Quantitative Mining of Compositional Heterogeneity in Cryo-EM Datasets of Ribosome Assembly Intermediates

2021 ◽  
Author(s):  
Jessica N Rabuck-Gibbons ◽  
Dmitry Lyumkis ◽  
James R Williamson
Keyword(s):  
Structural Heterogeneity ◽  
Ribosome Assembly ◽  
Compositional Heterogeneity ◽  
Assembly Process ◽  
Branch Points ◽  
Macromolecular Complexes ◽  
E Coli ◽  
Cryo Electron Microscopy ◽  
Assembly Factor ◽  
Structural Configurations

Macromolecular complexes are dynamic entities whose function is often intertwined with their many structural configurations. Single particle cryo-electron microscopy (cryo-EM) offers a unique opportunity to characterize macromolecular structural heterogeneity by virtue of its ability to place distinct populations into different groups through computational classification. However, current workflows are limited, and there is a dearth of tools for surveying the heterogeneity landscape, quantitatively analyzing heterogeneous particle populations after classification, deciding how many unique classes are represented by the data, and accurately cross-comparing reconstructions. Here, we develop a workflow that contains discovery and analysis modules to quantitatively mine cryo-EM data for a set of structures with maximal diversity. This workflow was applied to a dataset of E. coli 50S ribosome assembly intermediates, which is characterized by significant structural heterogeneity. We identified new branch points in the assembly process and characterized the interactions of an assembly factor with immature intermediates. While the tools described here were developed for ribosome assembly, they should be broadly applicable to the analysis of other heterogeneous cryo-EM datasets.

COMPOSITIONAL HETEROGENEITY OF THE JOSEPHINE MOUNTAIN INTRUSION

2020 ◽  
Author(s):  
Patrick B. Oliver ◽  
◽  
Zachary Levenson ◽  
Roger L. Putnam
Keyword(s):  
Compositional Heterogeneity

scholarly journals Unraveling the compositional heterogeneity and carrier dynamics of alkali cation doped 3D/2D perovskites with improved stability

2021 ◽  
Author(s):  
Ming-Chun Tang ◽  
Siyuan Zhang ◽  
Timothy J. Magnanelli ◽  
Nhan V. Nguyen ◽  
Edwin J. Heilweil ◽  
...  
Keyword(s):  
Relative Humidity ◽  
Comprehensive Analysis ◽  
Carrier Dynamics ◽  
Alkali Cation ◽  
Compositional Heterogeneity ◽  
Improved Stability

A comprehensive analysis of the compositional heterogeneity and carrier dynamics in novel rubidium-doped 3D/2D perovskites is investigated, showing a PCE over 20% and improved stability at ≈50% relative humidity without encapsulation.

scholarly journals HectD1 controls hematopoietic stem cell regeneration by coordinating ribosome assembly and protein synthesis

2021 ◽  
Author(s):  
Kaosheng Lv ◽  
Chujie Gong ◽  
Charles Antony ◽  
Xu Han ◽  
Jian-Gang Ren ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Stem Cell ◽  
Hematopoietic Stem Cell ◽  
Ribosome Assembly ◽  
Cell Regeneration ◽  
Hematopoietic Stem

scholarly journals Ubiquitin and Ubiquitin-Like Proteins and Domains in Ribosome Production and Function: Chance or Necessity?

2021 ◽  
Vol 22 (9) ◽  
pp. 4359
Author(s):  
Sara Martín-Villanueva ◽  
Gabriel Gutiérrez ◽  
Dieter Kressler ◽  
Jesús de la Cruz
Keyword(s):  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Ribosome Assembly ◽  
Cellular Processes ◽  
Substrate Protein ◽  
Precursor Proteins ◽  
Assembly Factors ◽  
Ubiquitin Moiety ◽  
And Function

Ubiquitin is a small protein that is highly conserved throughout eukaryotes. It operates as a reversible post-translational modifier through a process known as ubiquitination, which involves the addition of one or several ubiquitin moieties to a substrate protein. These modifications mark proteins for proteasome-dependent degradation or alter their localization or activity in a variety of cellular processes. In most eukaryotes, ubiquitin is generated by the proteolytic cleavage of precursor proteins in which it is fused either to itself, constituting a polyubiquitin precursor, or as a single N-terminal moiety to ribosomal proteins, which are practically invariably eL40 and eS31. Herein, we summarize the contribution of the ubiquitin moiety within precursors of ribosomal proteins to ribosome biogenesis and function and discuss the biological relevance of having maintained the explicit fusion to eL40 and eS31 during evolution. There are other ubiquitin-like proteins, which also work as post-translational modifiers, among them the small ubiquitin-like modifier (SUMO). Both ubiquitin and SUMO are able to modify ribosome assembly factors and ribosomal proteins to regulate ribosome biogenesis and function. Strikingly, ubiquitin-like domains are also found within two ribosome assembly factors; hence, the functional role of these proteins will also be highlighted.

scholarly journals Effects of Iodoamphenicol on Ribosome Assembly in Two Strains of Escherichia coli

Microbiology ◽  
1982 ◽  
Vol 128 (5) ◽  
pp. 997-1001
Author(s):  
P. D. Butler ◽  
P. F. G. Sims ◽  
D. G. Wild
Keyword(s):  
Escherichia Coli ◽  
Ribosome Assembly
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