scholarly journals Pre-rRNA processing and its response to temperature stress in maize

2019 ◽  
Author(s):  
Guoqin Liu ◽  
Pengshuai Yan ◽  
Qingguo Du ◽  
Yafei Wang ◽  
Yu Guo ◽  
...  
Keyword(s):  
Ribosome Biogenesis ◽  
Higher Plants ◽  
Future Research ◽  
Cleavage Sites ◽  
Rrna Processing ◽  
Detailed Model ◽  
Reverse Transcription Pcr ◽  
Endonucleolytic Cleavage ◽  
Response To Temperature ◽  
Staple Crop

Abstract Ribosome biogenesis is a fundamental process in all eukaryotic cells and is coupled with the processing and maturation of pre-rRNAs. Maize is the primary staple crop across the world. However, little is known about the exact pre-rRNA processing sites and pathways in maize. In this study, we identified the critical endonucleolytic cleavage sites and detected the pre-rRNA intermediates by circular reverse transcription PCR (cRT-PCR) and northern blot, presenting a detailed model of the pre-rRNA processing pathway in maize. We demonstrated that two pathways coexist in maize to promote the processing of 35S pre-rRNA and that the processing of 27SA pre-rRNA could proceed via two different pathways, which were distinguished based on the order of ITS1 removal and ITS2 cleavage. Compared with yeast and mammals, this new 27SA pre-rRNA processing mechanism is unique to maize and other higher plants. Moreover, we discovered that maize could modulate pre-rRNA processing levels in response to chilling and heat stress, as indicated by the significant reduction of P-A3. Our study should facilitate future research on ribosome biogenesis and pre-rRNA processing in maize.

scholarly journals Arabidopsis small nucleolar RNA monitors the efficient pre-rRNA processing during ribosome biogenesis

2016 ◽  
Vol 113 (42) ◽  
pp. 11967-11972 ◽  
Author(s):  
Pan Zhu ◽  
Yuqiu Wang ◽  
Nanxun Qin ◽  
Feng Wang ◽  
Jia Wang ◽  
...  
Keyword(s):  
Ribosome Biogenesis ◽  
Higher Plants ◽  
Ribosomal Subunit ◽  
Rrna Processing ◽  
Developmental Defects ◽  
Protein Mutants ◽  
5.8S Rrna ◽  
Important Regulator ◽  
Nucleolar Rna

Ribosome production in eukaryotes requires the complex and precise coordination of several hundred assembly factors, including many small nucleolar RNAs (snoRNAs). However, at present, the distinct role of key snoRNAs in ribosome biogenesis remains poorly understood in higher plants. Here we report that a previously uncharacterized C (RUGAUGA)/D (CUGA) type snoRNA, HIDDEN TREASURE 2 (HID2), acts as an important regulator of ribosome biogenesis through a snoRNA–rRNA interaction. Nucleolus-localized HID2 is actively expressed in Arabidopsis proliferative tissues, whereas defects in HID2 cause a series of developmental defects reminiscent of ribosomal protein mutants. HID2 associates with the precursor 45S rRNA and promotes the efficiency and accuracy of pre-rRNA processing. Intriguingly, disrupting HID2 in Arabidopsis appears to impair the integrity of 27SB, a key pre-rRNA intermediate that generates 25S and 5.8S rRNA and is known to be vital for the synthesis of the 60S large ribosomal subunit and also produces an imbalanced ribosome profile. Finally, we demonstrate that the antisense-box of HID2 is both functionally essential and highly conserved in eukaryotes. Overall, our study reveals the vital and possibly conserved role of a snoRNA in monitoring the efficiency of pre-rRNA processing during ribosome biogenesis.

scholarly journals Hierarchical recruitment of ribosomal proteins and assembly factors remodels nucleolar pre-60S ribosomes

2018 ◽  
Vol 217 (7) ◽  
pp. 2503-2518 ◽  
Author(s):  
Stephanie Biedka ◽  
Jelena Micic ◽  
Daniel Wilson ◽  
Hailey Brown ◽  
Luke Diorio-Toth ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Large Subunit ◽  
Ribosome Assembly ◽  
Rrna Processing ◽  
Endonucleolytic Cleavage ◽  
Cryo Electron Microscopy ◽  
External Transcribed Spacer ◽  
Assembly Factors

Ribosome biogenesis involves numerous preribosomal RNA (pre-rRNA) processing events to remove internal and external transcribed spacer sequences, ultimately yielding three mature rRNAs. Removal of the internal transcribed spacer 2 spacer RNA is the final step in large subunit pre-rRNA processing and begins with endonucleolytic cleavage at the C2 site of 27SB pre-rRNA. C2 cleavage requires the hierarchical recruitment of 11 ribosomal proteins and 14 ribosome assembly factors. However, the function of these proteins in C2 cleavage remained unclear. In this study, we have performed a detailed analysis of the effects of depleting proteins required for C2 cleavage and interpreted these results using cryo–electron microscopy structures of assembling 60S subunits. This work revealed that these proteins are required for remodeling of several neighborhoods, including two major functional centers of the 60S subunit, suggesting that these remodeling events form a checkpoint leading to C2 cleavage. Interestingly, when C2 cleavage is directly blocked by depleting or inactivating the C2 endonuclease, assembly progresses through all other subsequent steps.

scholarly journals The Complexity of Human Ribosome Biogenesis Revealed by Systematic Nucleolar Screening of Pre-rRNA Processing Factors

2013 ◽  
Vol 51 (4) ◽  
pp. 539-551 ◽  
Author(s):  
Lionel Tafforeau ◽  
Christiane Zorbas ◽  
Jean-Louis Langhendries ◽  
Sahra-Taylor Mullineux ◽  
Vassiliki Stamatopoulou ◽  
...  
Keyword(s):  
Ribosome Biogenesis ◽  
Rrna Processing ◽  
Processing Factors

scholarly journals Bop1 Is a Mouse WD40 Repeat Nucleolar Protein Involved in 28S and 5.8S rRNA Processing and 60S Ribosome Biogenesis

2000 ◽  
Vol 20 (15) ◽  
pp. 5516-5528 ◽  
Author(s):  
Žaklina Strezoska ◽  
Dimitri G. Pestov ◽  
Lester F. Lau
Keyword(s):  
Ribosome Biogenesis ◽  
Ribosomal Subunit ◽  
Weight Fraction ◽  
Rnase A ◽  
Mutant Form ◽  
Rrna Processing ◽  
Ribonucleoprotein Complexes ◽  
Nuclear Extracts ◽  
Mouse Tissues ◽  
Mouse Cells

ABSTRACT We have identified and characterized a novel mouse protein, Bop1, which contains WD40 repeats and is highly conserved through evolution. bop1 is ubiquitously expressed in all mouse tissues examined and is upregulated during mid-G1 in serum-stimulated fibroblasts. Immunofluorescence analysis shows that Bop1 is localized predominantly to the nucleolus. In sucrose density gradients, Bop1 from nuclear extracts cosediments with the 50S-80S ribonucleoprotein particles that contain the 32S rRNA precursor. RNase A treatment disrupts these particles and releases Bop1 into a low-molecular-weight fraction. A mutant form of Bop1, Bop1Δ, which lacks 231 amino acids in the N- terminus, is colocalized with wild-type Bop1 in the nucleolus and in ribonucleoprotein complexes. Expression of Bop1Δ leads to cell growth arrest in the G1phase and results in a specific inhibition of the synthesis of the 28S and 5.8S rRNAs without affecting 18S rRNA formation. Pulse-chase analyses show that Bop1Δ expression results in a partial inhibition in the conversion of the 36S to the 32S pre-rRNA and a complete inhibition of the processing of the 32S pre-rRNA to form the mature 28S and 5.8S rRNAs. Concomitant with these defects in rRNA processing, expression of Bop1Δ in mouse cells leads to a deficit in the cytosolic 60S ribosomal subunits. These studies thus identify Bop1 as a novel, nonribosomal mammalian protein that plays a key role in the formation of the mature 28S and 5.8S rRNAs and in the biogenesis of the 60S ribosomal subunit.

scholarly journals Ribonucleoproteins in Archaeal Pre-rRNA Processing and Modification

Archaea ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-14 ◽  
Author(s):  
W. S. Vincent Yip ◽  
Nicholas G. Vincent ◽  
Susan J. Baserga
Keyword(s):  
Ribosome Biogenesis ◽  
Gene Organization ◽  
Rrna Gene ◽  
Rrna Processing ◽  
Ribosomal Rnas ◽  
Intensive Research ◽  
Complex Process ◽  
Nucleotide Modification

Given that ribosomes are one of the most important cellular macromolecular machines, it is not surprising that there is intensive research in ribosome biogenesis. Ribosome biogenesis is a complex process. The maturation of ribosomal RNAs (rRNAs) requires not only the precise cleaving and folding of the pre-rRNA but also extensive nucleotide modifications. At the heart of the processing and modifications of pre-rRNAs in Archaea and Eukarya are ribonucleoprotein (RNP) machines. They are called small RNPs (sRNPs), in Archaea, and small nucleolar RNPs (snoRNPs), in Eukarya. Studies on ribosome biogenesis originally focused on eukaryotic systems. However, recent studies on archaeal sRNPs have provided important insights into the functions of these RNPs. This paper will introduce archaeal rRNA gene organization and pre-rRNA processing, with a particular focus on the discovery of the archaeal sRNP components, their functions in nucleotide modification, and their structures.

scholarly journals Skeletal Muscle Ribosome and Mitochondrial Biogenesis in Response to Different Exercise Training Modalities

2021 ◽  
Vol 12 ◽  
Author(s):  
Paulo H. C. Mesquita ◽  
Christopher G. Vann ◽  
Stuart M. Phillips ◽  
James McKendry ◽  
Kaelin C. Young ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Endurance Training ◽  
Mitochondrial Biogenesis ◽  
Ribosome Biogenesis ◽  
Exercise Physiology ◽  
Future Research ◽  
Mitochondrial Dna Copy Number ◽  
Mtorc1 Signaling ◽  
Amp Activated Protein Kinase ◽  
Training Modalities

Skeletal muscle adaptations to resistance and endurance training include increased ribosome and mitochondrial biogenesis, respectively. Such adaptations are believed to contribute to the notable increases in hypertrophy and aerobic capacity observed with each exercise mode. Data from multiple studies suggest the existence of a competition between ribosome and mitochondrial biogenesis, in which the first adaptation is prioritized with resistance training while the latter is prioritized with endurance training. In addition, reports have shown an interference effect when both exercise modes are performed concurrently. This prioritization/interference may be due to the interplay between the 5’ AMP-activated protein kinase (AMPK) and mechanistic target of rapamycin complex 1 (mTORC1) signaling cascades and/or the high skeletal muscle energy requirements for the synthesis and maintenance of cellular organelles. Negative associations between ribosomal DNA and mitochondrial DNA copy number in human blood cells also provide evidence of potential competition in skeletal muscle. However, several lines of evidence suggest that ribosome and mitochondrial biogenesis can occur simultaneously in response to different types of exercise and that the AMPK-mTORC1 interaction is more complex than initially thought. The purpose of this review is to provide in-depth discussions of these topics. We discuss whether a curious competition between mitochondrial and ribosome biogenesis exists and show the available evidence both in favor and against it. Finally, we provide future research avenues in this area of exercise physiology.

scholarly journals Post-transcriptional regulation of ribosome formation in the nucleus of regenerating rat liver

1983 ◽  
Vol 210 (1) ◽  
pp. 183-192 ◽  
Author(s):  
K P Dudov ◽  
M D Dabeva
Keyword(s):  
Rat Liver ◽  
Ribosome Biogenesis ◽  
Rrna Processing ◽  
Regenerating Liver ◽  
Regenerating Rat Liver ◽  
Rrna Species ◽  
Rrna Maturation ◽  
The Individual ◽  
Post Transcriptional Regulation

Kinetic experiments on RNA labelling in vivo with [14C]orotate were performed with normal and 12h-regenerating rat liver. The specific radioactivities of nucleolar, nucleoplasmic and cytoplasmic rRNA species were analysed by computer according to the models of rRNA processing and nucleo-cytoplasmic migration given previously [Dudov, Dabeva, Hadjiolov & Todorov, Biochem. J. (1978) 171, 375-383]. The rates of formation and the half-lives of the individual pre-rRNA and rRNA species were determined in both normal and regenerating liver. The results show clearly that the formation of ribosomes in regenerating rat liver is post-transcriptionally activated: (a) the half-lives of all the nucleolar pre-rRNA and rRNA species are decreased by 30% on average; (b) the pre-rRNA processing is directed through the shortest maturation pathway: 45 S leads to 32 S + 18 S leads to 28 S; (c) the nucleo-cytoplasmic transfer of ribosomes is accelerated. As a consequence, the time for formation and appearance of ribosomes in the cytoplasm is shortened 1.5-fold for the large and 2-fold for the small subparticle. A new scheme for endonuclease cleavage of 45 S pre-rRNA is proposed, which explains the alterations in pre-rRNA processing in regenerating liver. Its validity for pre-rRNA processing in other eukaryotes is discussed. It is concluded that: (i) the control sites in the intranucleolar formation of 28 S and 18 S rRNA are the immediate precursor of 28 S rRNA, 32 S pre-rRNA, and the primary pre-rRNA, 45 S pre-rRNA, respectively; (ii) the limiting step in the post-transcriptional stages of ribosome biogenesis is the pre-rRNA maturation.

scholarly journals Translational control during cellular senescence

2020 ◽  
Author(s):  
Matthew J. Payea ◽  
Carlos Anerillas ◽  
Ravi Tharakan ◽  
Myriam Gorospe
Keyword(s):  
Translational Control ◽  
Ribosome Biogenesis ◽  
Rrna Processing ◽  
Proliferating Cells ◽  
Cycle Arrest ◽  
Nucleolar Stress ◽  
Specific Proteins ◽  
Inflammatory Proteins ◽  
Secretory Phenotype

Senescence is a state of long-term cell-cycle arrest that arises in cells that have incurred sub-lethal damage. While senescent cells no longer replicate, they remain metabolically active and further develop unique and stable phenotypes that are not present in proliferating cells. On one hand, senescent cells increase in size, maintain an active mTORC1 complex, and produce and secrete a substantial amount of inflammatory proteins as part of the senescence associated secretory phenotype (SASP). On the other hand, these pro-growth phenotypes contrast with the p53-mediated growth arrest typical of senescent cells that is associated with nucleolar stress and an inhibition of rRNA processing and ribosome biogenesis. In sum, translation in senescent cells paradoxically comprises both a global repression of translation triggered by DNA damage and a select increase in the translation of specific proteins, including SASP factors.

scholarly journals Controlling the material properties and rRNA processing function of the nucleolus using light

2019 ◽  
Vol 116 (35) ◽  
pp. 17330-17335 ◽  
Author(s):  
Lian Zhu ◽  
Tiffany M. Richardson ◽  
Ludivine Wacheul ◽  
Ming-Tzo Wei ◽  
Marina Feric ◽  
...  
Keyword(s):  
Phase Behavior ◽  
Ribosomal Rna ◽  
Material Properties ◽  
Viscoelastic Properties ◽  
Ribosome Biogenesis ◽  
Threshold Concentration ◽  
Rrna Processing ◽  
Small Proteins ◽  
Nucleolar Material ◽  
Processing Steps

The nucleolus is a prominent nuclear condensate that plays a central role in ribosome biogenesis by facilitating the transcription and processing of nascent ribosomal RNA (rRNA). A number of studies have highlighted the active viscoelastic nature of the nucleolus, whose material properties and phase behavior are a consequence of underlying molecular interactions. However, the ways in which the material properties of the nucleolus impact its function in rRNA biogenesis are not understood. Here we utilize the Cry2olig optogenetic system to modulate the viscoelastic properties of the nucleolus. We show that above a threshold concentration of Cry2olig protein, the nucleolus can be gelled into a tightly linked, low mobility meshwork. Gelled nucleoli no longer coalesce and relax into spheres but nonetheless permit continued internal molecular mobility of small proteins. These changes in nucleolar material properties manifest in specific alterations in rRNA processing steps, including a buildup of larger rRNA precursors and a depletion of smaller rRNA precursors. We propose that the flux of processed rRNA may be actively tuned by the cell through modulating nucleolar material properties, which suggests the potential of materials-based approaches for therapeutic intervention in ribosomopathies.

scholarly journals Complexity of diatom response to Lateglacial and Holocene climate and environmental change in ancient, deep and oligotrophic Lake Ohrid (Macedonia and Albania)

2016 ◽  
Vol 13 (4) ◽  
pp. 1351-1365 ◽  
Author(s):  
X. S. Zhang ◽  
J. M. Reed ◽  
J. H. Lacey ◽  
A. Francke ◽  
M. J. Leng ◽  
...  
Keyword(s):  
Environmental Change ◽  
Water Temperature ◽  
Nutrient Availability ◽  
Future Research ◽  
Lake Ohrid ◽  
Nutrient Input ◽  
Holocene Climate ◽  
Lake Productivity ◽  
Climate And Environmental Change ◽  
Response To Temperature

Abstract. Lake Ohrid (Macedonia and Albania) is a rare example of a deep, ancient Mediterranean lake and is a key site for palaeoclimate research in the northeastern Mediterranean region. This study conducts the analysis of diatoms as a proxy for Lateglacial and Holocene climate and environmental change in Lake Ohrid at a higher resolution than in previous studies. While Lake Ohrid has the potential to be sensitive to water temperature change, the data demonstrate a highly complex diatom response, probably comprising a direct response to temperature-induced lake productivity in some phases and an indirect response to temperature-related lake stratification or mixing and epilimnetic nutrient availability in others. The data also demonstrate the possible influence of physical limnological (e.g. the influence of wind stress on stratification or mixing) and chemical processes (e.g. the influence of catchment dynamics on nutrient input) in mediating the complex response of diatoms. During the Lateglacial (ca. 12 300–11 800 cal yr BP), the low-diversity dominance of hypolimnetic Cyclotella fottii indicates low lake productivity, linked to low water temperature. Although the subsequent slight increase in small, epilimnetic C. minuscula during the earliest Holocene (ca. 11 800–10 600 cal yr BP) suggests climate warming and enhanced stratification, diatom concentration remains as low as during the Lateglacial, suggesting that water temperature increase was muted across this major transition. The early Holocene (ca. 10 600–8200 cal yr BP) is characterised by a sustained increase in epilimnetic taxa, with mesotrophic C. ocellata indicating high water-temperature-induced productivity between ca. 10 600–10 200 cal yr BP and between ca. 9500–8200 cal yr BP and with C. minuscula in response to low nutrient availability in the epilimnion between ca. 10 200–9500 cal yr BP. During the middle Holocene (ca. 8200–2600 cal yr BP), when sedimentological and geochemical proxies provide evidence for maximum Holocene water temperature, anomalously low C. ocellata abundance is probably a response to epilimnetic nutrient limitation, almost mimicking the Lateglacial flora apart from the occurrence of mesotrophic Stephanodiscus transylvanicus in the hypolimnion. During the late Holocene (ca. 2600 cal yr BP–present), high abundance and fluctuating composition of epilimnetic taxa are probably a response more to enhanced anthropogenic nutrient input, particularly nitrogen enrichment, than to climate. Overall, the data indicate that previous assumptions concerning the linearity of diatom response in this deep, ancient lake are invalid, and multi-proxy analysis is essential to improve understanding of palaeolimnological dynamics in future research on the long, Quaternary sequence.

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