scholarly journals Shaping the Nascent Ribosome: AAA-ATPases in Eukaryotic Ribosome Biogenesis

Biomolecules ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 715 ◽  
Author(s):  
Prattes ◽  
Lo ◽  
Bergler ◽  
Stanley
Keyword(s):  
Molecular Mechanism ◽  
Ribosome Biogenesis ◽  
Current Knowledge ◽  
Target Recognition ◽  
Efficient Removal ◽  
Ribonucleoprotein Complex ◽  
Eukaryotic Ribosome ◽  
Macromolecular Assemblies ◽  
Chemical Complex ◽  
Aaa Atpases

AAA-ATPases are molecular engines evolutionarily optimized for the remodeling of proteins and macromolecular assemblies. Three AAA-ATPases are currently known to be involved in the remodeling of the eukaryotic ribosome, a megadalton range ribonucleoprotein complex responsible for the translation of mRNAs into proteins. The correct assembly of the ribosome is performed by a plethora of additional and transiently acting pre-ribosome maturation factors that act in a timely and spatially orchestrated manner. Minimal disorder of the assembly cascade prohibits the formation of functional ribosomes and results in defects in proliferation and growth. Rix7, Rea1, and Drg1, which are well conserved across eukaryotes, are involved in different maturation steps of pre-60S ribosomal particles. These AAA-ATPases provide energy for the efficient removal of specific assembly factors from pre-60S particles after they have fulfilled their function in the maturation cascade. Recent structural and functional insights have provided the first glimpse into the molecular mechanism of target recognition and remodeling by Rix7, Rea1, and Drg1. Here we summarize current knowledge on the AAA-ATPases involved in eukaryotic ribosome biogenesis. We highlight the latest insights into their mechanism of mechano-chemical complex remodeling driven by advanced cryo-EM structures and the use of highly specific AAA inhibitors.

scholarly journals Phylogenetic Utility of rRNA ITS2 Sequence-Structure under Functional Constraint

2020 ◽  
Vol 21 (17) ◽  
pp. 6395
Author(s):  
Wei Zhang ◽  
Wen Tian ◽  
Zhipeng Gao ◽  
Guoli Wang ◽  
Hong Zhao
Keyword(s):  
Base Pair ◽  
Ribosome Biogenesis ◽  
Current Knowledge ◽  
Its2 Sequence ◽  
Its2 Region ◽  
Function Structure ◽  
Sequence Structure ◽  
Structure Information ◽  
Tree Construction ◽  
Phylogenetic Implications

The crucial function of the internal transcribed spacer 2 (ITS2) region in ribosome biogenesis depends on its secondary and tertiary structures. Despite rapidly evolving, ITS2 is under evolutionary constraints to maintain the specific secondary structures that provide functionality. A link between function, structure and evolution could contribute an understanding to each other and recently has created a growing point of sequence-structure phylogeny of ITS2. Here we briefly review the current knowledge of ITS2 processing in ribosome biogenesis, focusing on the conservative characteristics of ITS2 secondary structure, including structure form, structural motifs, cleavage sites, and base-pair interactions. We then review the phylogenetic implications and applications of this structure information, including structure-guiding sequence alignment, base-pair mutation model, and species distinguishing. We give the rationale for why incorporating structure information into tree construction could improve reliability and accuracy, and some perspectives of bioinformatics coding that allow for a meaningful evolutionary character to be extracted. In sum, this review of the integration of function, structure and evolution of ITS2 will expand the traditional sequence-based ITS2 phylogeny and thus contributes to the tree of life. The generality of ITS2 characteristics may also inspire phylogenetic use of other similar structural regions.

scholarly journals Proteasomes: unfoldase-assisted protein degradation machines

2019 ◽  
Vol 401 (1) ◽  
pp. 183-199 ◽  
Author(s):  
Parijat Majumder ◽  
Wolfgang Baumeister
Keyword(s):  
Stress Response ◽  
Molecular Machines ◽  
Molecular Architecture ◽  
Core Particle ◽  
Protein Substrates ◽  
Macromolecular Assemblies ◽  
Current State ◽  
Intracellular Proteins ◽  
Domains Of Life ◽  
Aaa Atpases

Abstract Proteasomes are the principal molecular machines for the regulated degradation of intracellular proteins. These self-compartmentalized macromolecular assemblies selectively degrade misfolded, mistranslated, damaged or otherwise unwanted proteins, and play a pivotal role in the maintenance of cellular proteostasis, in stress response, and numerous other processes of vital importance. Whereas the molecular architecture of the proteasome core particle (CP) is universally conserved, the unfoldase modules vary in overall structure, subunit complexity, and regulatory principles. Proteasomal unfoldases are AAA+ ATPases (ATPases associated with a variety of cellular activities) that unfold protein substrates, and translocate them into the CP for degradation. In this review, we summarize the current state of knowledge about proteasome – unfoldase systems in bacteria, archaea, and eukaryotes, the three domains of life.

scholarly journals Molecular mechanism of the RNA helicase DHX37 and its activation by UTP14A in ribosome biogenesis

RNA ◽  
2019 ◽  
Vol 25 (6) ◽  
pp. 685-701 ◽  
Author(s):  
Franziska M. Boneberg ◽  
Tobias Brandmann ◽  
Lena Kobel ◽  
Jasmin van den Heuvel ◽  
Katja Bargsten ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Ribosome Biogenesis ◽  
Rna Helicase

Pathway Analysis of the Restrictedly Expressed Genes in Oryza Sativa Implanted by the Low-Energy Nitrogen Ion

2011 ◽  
Vol 108 ◽  
pp. 176-182
Author(s):  
Hui Yuan Ya ◽  
Wei Dong Wang ◽  
Qiu Fang Chen ◽  
Guang Yong Qin ◽  
Zhen Jiao ◽  
...  
Keyword(s):  
Ion Implantation ◽  
Molecular Mechanism ◽  
Current Knowledge ◽  
Biological Effects ◽  
Ion Beam ◽  
Low Energy ◽  
P Value ◽  
Rice Seedlings ◽  
Vigor Index ◽  
Nitrogen Ion

The current knowledge of the transcriptome is limited to understand the exact molecular mechanism of the ion-implantation biological effects on cereals. In order to investigating the overall characteristics of the transcript profiles associated with these puzzling biological effects. We used the Agilent Rice Oligo Microarray （4×44K）Genome Array to learn the molecular mechanism in rice responding to ion-implantation. Rice seeds were implanted by the Nitrogen ion beam and their vigor index was investigated at ten days after germination. Total RNAs was extracted from the rice seedlings at 96 hour after germination and hybridized by the genome genechip. The results of measuring of the vigor index showed that lower-dose implantation of the nitrogen ion beam (6×1017 N+/cm2) promoted the vigor index of the rice seedlings and the higher-dose implantation (9×1017 N+/cm2) damaged the rice seedlings because of the smaller vigor index than the control. The analysis of the genechip array showed that there were 982 transcripts expressed differentially (fold change＞2 and P value＜0.05) including 429 up-regulated transcripts and 553 down-regulated transcripts under the dose3 6×1017 N+/cm2. 30 out of the 553 down-regulated transcripts were involved in 48 pathways. 14 out of these 30 transcripts were associated with more than two interrelated pathways. Os04g0518400 (Phenylalanine ammonia-lyase 2 (PAL; EC 4.3.1.5; down-regulated 3.3 folds; p value=0.005) were involved in 7 pathways, Os07g0446800 (Hexokinase; dwon-regulated 2.8 folds; p value =0.006) were involved in 12 pathways, and Os02g0730000 (Mitochondrial aldehyde dehydrogenase ALDH2a; down-regulated 2.2 folds; p value=0.019) were involved in 13 pathways. These results revealed that down-regulated genes involving important pathways were compatible with the distinct cellular events in response to implantation of low-energy ion beam and supplied the first comprehensive and comparative molecular information for further understanding the mechanism underlying implantation of the low-energy nitrogen ion beam.

scholarly journals Integrin and GPCR Crosstalk in the Regulation of ASM Contraction Signaling in Asthma

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Chun Ming Teoh ◽  
John Kit Chung Tam ◽  
Thai Tran
Keyword(s):  
Smooth Muscle ◽  
G Protein ◽  
Molecular Mechanism ◽  
Airway Smooth Muscle ◽  
Airway Hyperresponsiveness ◽  
Current Knowledge ◽  
Symptom Relief ◽  
Airway Wall ◽  
G Protein Coupled ◽  
Review Current

Airway hyperresponsiveness (AHR) is one of the cardinal features of asthma. Contraction of airway smooth muscle (ASM) cells that line the airway wall is thought to influence aspects of AHR, resulting in excessive narrowing or occlusion of the airway. ASM contraction is primarily controlled by agonists that bind G protein-coupled receptor (GPCR), which are expressed on ASM. Integrins also play a role in regulating ASM contraction signaling. As therapies for asthma are based on symptom relief, better understanding of the crosstalk between GPCRs and integrins holds good promise for the design of more effective therapies that target the underlying cellular and molecular mechanism that governs AHR. In this paper, we will review current knowledge about integrins and GPCRs in their regulation of ASM contraction signaling and discuss the emerging concept of crosstalk between the two and the implication of this crosstalk on the development of agents that target AHR.

Assessing the function of the Ro ribonucleoprotein complex using Caenorhabditis elegans as a biological tool

1999 ◽  
Vol 77 (4) ◽  
pp. 349-354 ◽  
Author(s):  
Jean-Claude Labbé ◽  
Siegfried Hekimi ◽  
Luis A Rokeach
Keyword(s):  
Caenorhabditis Elegans ◽  
Lupus Erythematosus ◽  
Ribosome Biogenesis ◽  
General Structure ◽  
Major Protein ◽  
Phenotypic Analysis ◽  
Gene Encoding ◽  
Ribonucleoprotein Complex ◽  
Biological Tool ◽  
Ro Ribonucleoprotein

The Ro ribonucleoprotein complex (Ro RNP) was initially described as an autoimmune target in human diseases such as systemic lupus erythematosus and Sjögren's syndrome. In Xenopus and human cells, its general structure is composed of one major protein of 60 kDa, Ro60, that binds to one of four small RNA molecules, designated Y RNAs. Although no function has been assigned to the Ro RNP, Ro60 has been shown to bind mutant 5S ribosomal RNA (rRNA) molecules in Xenopus oocytes, suggesting a role for Ro60 in 5S rRNA biogenesis. Ro60 has also been shown to participate in the regulation of the translational fate of the L4 ribosomal protein mRNA by interacting with the 5prime untranslated region, again suggesting its possible implication in ribosome biogenesis. To identify the function of Ro RNP, we have taken a genetic approach in the nematode Caenorhabditis elegans. As such, we characterized the gene encoding the protein ROP-1, the homologue of the human Ro60 protein. Here, we review the phenotypic analysis of C. elegans rop-1(-) mutants and integrate these results into a model for the function of the Ro RNP particle.Key words: Caenorhabditis elegans, Ro ribonucleoprotein complex, ROP-1, small RNAs, quality control.

scholarly journals Nitrogen Deficiency in Culture Affects the Metabolic Pathways in Amphora Coffeaeformis for Biodiesel Production

2021 ◽  
Author(s):  
Kang Wang ◽  
Yulin Cui ◽  
Chunxiao Meng ◽  
Zhengquan Gao ◽  
Song Qin
Keyword(s):  
Molecular Mechanism ◽  
Lipid Accumulation ◽  
Ribosome Biogenesis ◽  
Carbon Fixation ◽  
Nitrogen Deficiency ◽  
Raw Material ◽  
Biodiesel Production ◽  
Microalgal Biodiesel ◽  
Amphora Coffeaeformis ◽  
Tag Accumulation

Abstract Background: Amphora coffeaeformis, a unicellular diatom, can accumulate large amounts of lipids under nitrogen (N) limitation, because of which it can act as a promising raw material for biodiesel production. However, the molecular mechanism underlying lipid accumulation in A. coffeaeformis remains unknown. Results: In this study, we investigated the mechanism underlying lipid accumulation under N deprivation conditions in A. coffeaeformis using RNA-seq. The results showed that the total lipid (TL) content of A. coffeaeformis in normal f/2 medium was 28.22% (TL/DW), which increased to 44.05% after 5 days of N deprivation, while the neutral lipid triacylglycerol (TAG) content increased from 10.41% (TAG/DW) to 25.21%. The transcriptional profile showed that 591 genes were up-regulated, with false discovery rate cutoff of 0.1%, and 1,021 genes were down-regulated, indicating that N deprivation induced wide-ranging reprogramming of regulation, and that most physiological activities were repressed. In addition, ribosome biogenesis, carbon fixation, and photosynthesis in A. coffeaeformis were considerably affected by N deprivation. Conclusions: In summary, the findings initially clarified the molecular mechanism of TAG accumulation and revealed the key genes involved in lipid metabolism in A. coffeaeformis, which will be useful in designing strategies for improving microalgal biodiesel production.

scholarly journals snR30/U17 Small Nucleolar Ribonucleoprotein: A Critical Player during Ribosome Biogenesis

Cells ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 2195
Author(s):  
Timothy John Vos ◽  
Ute Kothe
Keyword(s):  
Ribosome Biogenesis ◽  
Current Knowledge ◽  
Small Subunit ◽  
Future Research ◽  
Unique Role ◽  
Ribosome Synthesis ◽  
Guide Rna ◽  
Guide Rnas ◽  
Ssu Processome ◽  
Nucleolar Rna

The small nucleolar RNA snR30 (U17 in humans) plays a unique role during ribosome synthesis. Unlike most members of the H/ACA class of guide RNAs, the small nucleolar ribonucleoprotein (snoRNP) complex assembled on snR30 does not direct pseudouridylation of ribosomal RNA (rRNA), but instead snR30 is critical for 18S rRNA processing during formation of the small subunit (SSU) of the ribosome. Specifically, snR30 is essential for three pre-rRNA cleavages at the A0/01, A1/1, and A2/2a sites in yeast and humans, respectively. Accordingly, snR30 is the only essential H/ACA guide RNA in yeast. Here, we summarize our current knowledge about the interactions and functions of snR30, discuss what remains to be elucidated, and present two non-exclusive hypotheses on the possible molecular function of snR30 during ribosome biogenesis. First, snR30 might be responsible for recruiting other proteins including endonucleases to the SSU processome. Second, snR30 may contribute to the refolding of pre-rRNA into a required conformation that serves as a checkpoint during ribosome biogenesis facilitating pre-rRNA cleavage. In both scenarios, the snR30 snoRNP may have scaffolding and RNA chaperoning activity. In conclusion, the snR30 snoRNP is a crucial player with an unknown molecular mechanism during ribosome synthesis, posing many interesting future research questions.

Renin release: role of SNAREs

2014 ◽  
Vol 307 (5) ◽  
pp. R484-R486 ◽  
Author(s):  
Mariela Mendez
Keyword(s):  
Molecular Mechanism ◽  
Current Knowledge ◽  
Renin Release ◽  
Juxtaglomerular Cells ◽  
Attachment Protein ◽  
Granule Exocytosis ◽  
Protein Receptor ◽  
Sensitive Factor ◽  
Factor Attachment Protein Receptor

Little is known about the molecular mechanism mediating renin granule exocytosis and the identity of proteins involved. We previously showed that soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNAREs), a family of proteins required for exocytosis, mediate the stimulated release of renin from juxtaglomerular cells. This minireview focuses on the current knowledge of the proteins that facilitate renin-granule exocytosis. We discuss the identity of potential candidates that mediate the signaling and final steps of exocytosis of the renin granule.

Sign in / Sign up

Export Citation Format

Share Document