scholarly journals Structural Analysis Reveals Features of Ribosome Assembly Factor Nsa1/WDR74 Important for Localization and Interaction with Rix7/NVL2

Structure ◽  
2017 ◽  
Vol 25 (5) ◽  
pp. 762-772.e4 ◽  
Author(s):  
Yu-Hua Lo ◽  
Erin M. Romes ◽  
Monica C. Pillon ◽  
Mack Sobhany ◽  
Robin E. Stanley
Keyword(s):  
Structural Analysis ◽  
Ribosome Assembly ◽  
Assembly Factor

scholarly journals Ribosome assembly factor URB1 contributes to colorectal cancer proliferation through transcriptional activation of ATF4

2020 ◽  
Vol 112 (1) ◽  
pp. 101-116
Author(s):  
Tao Wang ◽  
Lai‐Yuan Li ◽  
Yi‐Feng Chen ◽  
Si‐Wu Fu ◽  
Zhi‐Wei Wu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Transcriptional Activation ◽  
Ribosome Assembly ◽  
Cancer Proliferation ◽  
Assembly Factor

scholarly journals Efficient Assembly of Ribosomes Is Inhibited by Deletion ofbipAin Escherichia coli

2015 ◽  
Vol 197 (10) ◽  
pp. 1819-1827 ◽  
Author(s):  
Promisree Choudhury ◽  
Ann M. Flower
Keyword(s):  
Low Temperature ◽  
Modified Nucleosides ◽  
Cold Sensitivity ◽  
23S Rrna ◽  
Ribosome Assembly ◽  
Rrna Processing ◽  
Pseudouridine Synthase ◽  
Assembly Factor ◽  
Cold Sensitive ◽  
And Function

ABSTRACTThe bacterial BipA protein belongs to the EF-G family of translational GTPases and has been postulated to be either a regulatory translation factor or a ribosome assembly factor. To distinguish between these hypotheses, we analyzed the effect ofbipAdeletion on three phenotypes associated with ribosome assembly factors: cold sensitivity, ribosome subunit distribution, and rRNA processing. We demonstrated that a ΔbipAstrain exhibits a cold-sensitive phenotype that is similar to, and synergistic with, that of a strain with a known ribosome assembly factor,deaD. Additionally, thebipAdeletion strain displayed a perturbed ribosome subunit distribution when grown at low temperature, similar to that of adeaDmutant, and again, the double mutant showed additive effects. The primary ribosomal deficiency noted was a decreased level of the 50S subunit and the appearance of a presumed pre-50S particle. Finally, deletion ofbipAresulted in accumulation of pre23S rRNA, as did deletion ofdeaD. We further found that deletion ofrluC, which encodes a pseudouridine synthase that modifies the 23S rRNA at three sites, suppressed all three phenotypes of thebipAmutant, supporting and extending previous findings. Together, these results suggest that BipA is important for the correct and efficient assembly of the 50S subunit of the ribosome at low temperature but when unmodified by RluC, the ribosomes become BipA independent for assembly.IMPORTANCEThe ribosome is the complex ribonucleoprotein machine responsible for protein synthesis in all cells. Although much has been learned about the structure and function of the ribosome, we do not fully understand how it is assembled or the accessory proteins that increase efficiency of biogenesis and function. This study examined one such protein, BipA. Our results indicate that BipA either directly or indirectly enhances the formation of the 50S subunit of the ribosome, particularly at low temperature. In addition, ribosomes contain a large number of modified nucleosides, including pseudouridines. This work demonstrates that the function of BipA is tied to the modification status of the ribosome and may help us understand why these modifications have been retained.

Assembling the archaeal ribosome: roles for translation-factor-related GTPases

2011 ◽  
Vol 39 (1) ◽  
pp. 45-50 ◽  
Author(s):  
Fabian Blombach ◽  
Stan J.J. Brouns ◽  
John van der Oost
Keyword(s):  
Conformational Changes ◽  
Ribosomal Proteins ◽  
Major Type ◽  
Ribosome Assembly ◽  
Ribosomal Subunits ◽  
Translation Factor ◽  
Associated Functions ◽  
Assembly Factor ◽  
Switch Mechanism ◽  
Stepwise Assembly

The assembly of ribosomal subunits from their individual components (rRNA and ribosomal proteins) requires the assistance of a multitude of factors in order to control and increase the efficiency of the assembly process. GTPases of the TRAFAC (translation-factor-related) class constitute a major type of ribosome-assembly factor in Eukaryota and Bacteria. They are thought to aid the stepwise assembly of ribosomal subunits through a ‘molecular switch’ mechanism that involves conformational changes in response to GTP hydrolysis. Most conserved TRAFAC GTPases are involved in ribosome assembly or other translation-associated processes. They typically interact with ribosomal subunits, but in many cases, the exact role that these GTPases play remains unclear. Previous studies almost exclusively focused on the systems of Bacteria and Eukaryota. Archaea possess several conserved TRAFAC GTPases as well, with some GTPase families being present only in the archaeo–eukaryotic lineage. In the present paper, we review the occurrence of TRAFAC GTPases with translation-associated functions in Archaea.

scholarly journals Structure and RNA recognition of ribosome assembly factor Utp30

RNA ◽  
2017 ◽  
Vol 23 (12) ◽  
pp. 1936-1945
Author(s):  
Jianfei Hu ◽  
Xing Zhu ◽  
Keqiong Ye
Keyword(s):  
Ribosome Assembly ◽  
Rna Recognition ◽  
Assembly Factor

scholarly journals Structural Analysis of Mycobacterium tuberculosis Homologues of the Eukaryotic Proteasome Assembly Chaperone 2 (PAC2)

2017 ◽  
Vol 199 (9) ◽  
Author(s):  
Lin Bai ◽  
Jordan B. Jastrab ◽  
Marta Isasa ◽  
Kuan Hu ◽  
Hongjun Yu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Mycobacterium Tuberculosis ◽  
Structural Analysis ◽  
Posttranslational Modification ◽  
Bioinformatics Analysis ◽  
Genetic Studies ◽  
Modification System ◽  
Content Type ◽  
Assembly Factor ◽  
Substrate Proteins

ABSTRACT A previous bioinformatics analysis identified the Mycobacterium tuberculosis proteins Rv2125 and Rv2714 as orthologs of the eukaryotic proteasome assembly chaperone 2 (PAC2). We set out to investigate whether Rv2125 or Rv2714 can function in proteasome assembly. We solved the crystal structure of Rv2125 at a resolution of 3.0 Å, which showed an overall fold similar to that of the PAC2 family proteins that include the archaeal PbaB and the yeast Pba1. However, Rv2125 and Rv2714 formed trimers, whereas PbaB forms tetramers and Pba1 dimerizes with Pba2. We also found that purified Rv2125 and Rv2714 could not bind to M. tuberculosis 20S core particles. Finally, proteomic analysis showed that the levels of known proteasome components and substrate proteins were not affected by disruption of Rv2125 in M. tuberculosis. Our work suggests that Rv2125 does not participate in bacterial proteasome assembly or function. IMPORTANCE Although many bacteria do not encode proteasomes, M. tuberculosis not only uses proteasomes but also has evolved a posttranslational modification system called pupylation to deliver proteins to the proteasome. Proteasomes are essential for M. tuberculosis to cause lethal infections in animals; thus, determining how proteasomes are assembled may help identify new ways to combat tuberculosis. We solved the structure of a predicted proteasome assembly factor, Rv2125, and isolated a genetic Rv2125 mutant of M. tuberculosis. Our structural, biochemical, and genetic studies indicate that Rv2125 and Rv2714 do not function as proteasome assembly chaperones and are unlikely to have roles in proteasome biology in mycobacteria.

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.

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