scholarly journals The composition and turnover of the Arabidopsis thaliana 80S cytosolic ribosome

2020 ◽  
Vol 477 (16) ◽  
pp. 3019-3032 ◽  
Author(s):  
Karzan Jalal Salih ◽  
Owen Duncan ◽  
Lei Li ◽  
Josua Trösch ◽  
A. Harvey Millar
Keyword(s):  
Arabidopsis Thaliana ◽  
Ribosome Biogenesis ◽  
Cell Function ◽  
Protein A ◽  
Protein Composition ◽  
Turnover Rates ◽  
The Core ◽  
Peptide Mass ◽  
Peptide Mass Spectrometry

Cytosolic 80S ribosomes contain proteins of the mature cytosolic ribosome (r-proteins) as well as proteins with roles in ribosome biogenesis, protein folding or modification. Here, we refined the core r-protein composition in Arabidopsis thaliana by determining the abundance of different proteins during enrichment of ribosomes from cell cultures using peptide mass spectrometry. The turnover rates of 26 40S subunit r-proteins and 29 60S subunit r-proteins were also determined, showing that half of the ribosome population is replaced every 3–4 days. Three enriched proteins showed significantly shorter half-lives; a protein annotated as a ribosomal protein uL10 (RPP0D, At1g25260) with a half-life of 0.5 days and RACK1b and c with half-lives of 1–1.4 days. The At1g25260 protein is a homologue of the human Mrt4 protein, a trans-acting factor in the assembly of the pre-60S particle, while RACK1 has known regulatory roles in cell function beyond its role in the 40S subunit. Our experiments also identified 58 proteins that are not from r-protein families but co-purify with ribosomes and co-express with r-proteins; 26 were enriched more than 10-fold during ribosome enrichment. Some of these enriched proteins have known roles in translation, while others are newly proposed ribosome-associated factors in plants. This analysis provides an improved understanding of A. thaliana ribosome protein content, shows that most r-proteins turnover in unison in vivo, identifies a novel set of potential plant translatome components, and how protein turnover can help identify r-proteins involved in ribosome biogenesis or regulation in plants.

scholarly journals Refining the composition of the Arabidopsis thaliana 80S cytosolic ribosome

2019 ◽  
Author(s):  
Karzan Jalal Salih ◽  
Owen Duncan ◽  
Lei Li ◽  
Josua Troesch ◽  
A. Harvey Millar
Keyword(s):  
Arabidopsis Thaliana ◽  
Ribosome Biogenesis ◽  
Cell Function ◽  
Protein A ◽  
Mass Spectrometry Analysis ◽  
Turnover Rates ◽  
80S Ribosome ◽  
Spectrometry Analysis ◽  
Peptide Mass

AbstractThe cytosolic 80S ribosome is composed of protein and RNA molecules and its function in protein synthesis is modulated through interaction with other cytosolic components. Defining the role of each of the proteins associated with ribosomes in plants is a major challenge which is hampered by difficulties in attribution of different proteins to roles in ribosome biogenesis, the mature cytosolic ribosome (r-proteins) or to the broader translatome associated with functioning ribosomes. Here we refined the core r-protein composition in plants by determining the abundance of proteins in low, partially and highly purified ribosomal samples from Arabidopsis thaliana cell cultures. To characterise this list of proteins further we determined their degradation (KD) and synthesis (KS) rate by progressive labelling with 15N combined with peptide mass spectrometry analysis. The turnover rates of 55 r-proteins, including 26 r-proteins from the 40S subunit and 29 r-proteins from the 60S subunit could be determined. Overall, ribosome proteins showed very similar KD and KS rates suggesting that half of the ribosome population is replaced every 3-4 days. Three proteins showed significantly shorter half-lives; ribosomal protein P0D (RPP0D) with a half-life of 0.5 days and RACK1b and c with half-lives of 1-1.4 days. The ribosomal RPP0D protein is a homolog of the human Mrt4 protein, a trans-acting factor in the assembly of the pre-60S particle, while RACK1 has known regulatory roles in cell function beyond its role as a 40S subunit. Our experiments also identified 58 proteins that are not from r-protein families but co-purify with ribosomes and co-express with r-proteins in Arabidopsis. Of this set, 26 were enriched more than 10-fold during ribosome purification. A number have known roles in translation or ribosome-association while others are newly proposed ribosome-associated factors in plants. This analysis provides a more robust understanding of Arabidopsis ribosome content, shows that most r-proteins turnover in unison in vivo, identifies a novel set of potential plant translatome components, and reveals how protein turnover can identify r-proteins involved in ribosome biogenesis or regulation in plants. Data are available via ProteomeXchange with identifier PXD012839.

scholarly journals Molecular Characterization of Dendritic Cell-Derived Exosomes

1999 ◽  
Vol 147 (3) ◽  
pp. 599-610 ◽  
Author(s):  
Clotilde Théry ◽  
Armelle Regnault ◽  
Jérôme Garin ◽  
Joseph Wolfers ◽  
Laurence Zitvogel ◽  
...  
Keyword(s):  
Dendritic Cell ◽  
Heat Shock ◽  
Immune Responses ◽  
Milk Fat ◽  
Protein Composition ◽  
Antitumor Effects ◽  
Peripheral Tissues ◽  
Peptide Mass ◽  
Dc Maturation

Exosomes are membrane vesicles secreted by hematopoietic cells upon fusion of late multivesicular endosomes with the plasma membrane. Dendritic cell (DC)-derived exosomes induce potent antitumor immune responses in mice, resulting in the regression of established tumors (Zitvogel, L., A. Regnault, A. Lozier, J. Wolfers, C. Flament, D. Tenza, P. Ricciardi-Castagnoli, G. Raposo, and S. Amigorena. 1998. Nat. Med. 4:594–600). To unravel the molecular basis of exosome-induced immune stimulation, we now analyze the regulation of their production during DC maturation and characterize extensively their protein composition by peptide mass mapping. Exosomes contain several cytosolic proteins (including annexin II, heat shock cognate protein hsc73, and heteromeric G protein Gi2α), as well as different integral or peripherally associated membrane proteins (major histocompatiblity complex class II, Mac-1 integrin, CD9, milk fat globule-EGF-factor VIII [MFG-E8]). MFG-E8, the major exosomal component, binds integrins expressed by DCs and macrophages, suggesting that it may be involved in exosome targeting to these professional antigen-presenting cells. Another exosome component is hsc73, a cytosolic heat shock protein (hsp) also present in DC endocytic compartments. hsc73 was shown to induce antitumor immune responses in vivo, and therefore could be involved in the exosome's potent antitumor effects. Finally, exosome production is downregulated upon DC maturation, indicating that in vivo, exosomes are produced by immature DCs in peripheral tissues. Thus, DC-derived exosomes accumulate a defined subset of cellular proteins reflecting their endosomal biogenesis and accounting for their biological function.

scholarly journals Formation of a Complex between Nucleolin and Replication Protein a after Cell Stress Prevents Initiation of DNA Replication

2000 ◽  
Vol 149 (4) ◽  
pp. 799-810 ◽  
Author(s):  
Yaron Daniely ◽  
James A. Borowiec
Keyword(s):  
Dna Replication ◽  
Ribosome Biogenesis ◽  
Protein A ◽  
Simian Virus 40 ◽  
Replication Protein A ◽  
Cell Stress ◽  
Replication Protein ◽  
Binding Studies

We used a biochemical screen to identify nucleolin, a key factor in ribosome biogenesis, as a high-affinity binding partner for the heterotrimeric human replication protein A (hRPA). Binding studies in vitro demonstrated that the two proteins physically interact, with nucleolin using an unusual contact with the small hRPA subunit. Nucleolin significantly inhibited both simian virus 40 (SV-40) origin unwinding and SV-40 DNA replication in vitro, likely by nucleolin preventing hRPA from productive interaction with the SV-40 initiation complex. In vivo, use of epifluorescence and confocal microscopy showed that heat shock caused a dramatic redistribution of nucleolin from the nucleolus to the nucleoplasm. Nucleolin relocalization was concomitant with a tenfold increase in nucleolin–hRPA complex formation. The relocalized nucleolin significantly overlapped with the position of hRPA, but only poorly with sites of ongoing DNA synthesis. We suggest that the induced nucleolin–hRPA interaction signifies a novel mechanism that represses chromosomal replication after cell stress.

scholarly journals The Existence and Localization of Nuclear snoRNAs in Arabidopsis thaliana Revisited

Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1016 ◽  
Author(s):  
Deniz Streit ◽  
Thiruvenkadam Shanmugam ◽  
Asen Garbelyanski ◽  
Stefan Simm ◽  
Enrico Schleiff
Keyword(s):  
Single Molecule ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Cell Function ◽  
Model Systems ◽  
Rna Deep Sequencing ◽  
Nucleolar Rnas ◽  
Different Tissues

Ribosome biogenesis is one cell function-defining process. It depends on efficient transcription of rDNAs in the nucleolus as well as on the cytosolic synthesis of ribosomal proteins. For newly transcribed rRNA modification and ribosomal protein assembly, so-called small nucleolar RNAs (snoRNAs) and ribosome biogenesis factors (RBFs) are required. For both, an inventory was established for model systems like yeast and humans. For plants, many assignments are based on predictions. Here, RNA deep sequencing after nuclei enrichment was combined with single molecule species detection by northern blot and in vivo fluorescence in situ hybridization (FISH)-based localization studies. In addition, the occurrence and abundance of selected snoRNAs in different tissues were determined. These approaches confirm the presence of most of the database-deposited snoRNAs in cell cultures, but some of them are localized in the cytosol rather than in the nucleus. Further, for the explored snoRNA examples, differences in their abundance in different tissues were observed, suggesting a tissue-specific function of some snoRNAs. Thus, based on prediction and experimental confirmation, many plant snoRNAs can be proposed, while it cannot be excluded that some of the proposed snoRNAs perform alternative functions than are involved in rRNA modification.

scholarly journals Nucleolus-like morphology produced during the in vitro reassociation of nucleolar components

1993 ◽  
Vol 122 (4) ◽  
pp. 753-766 ◽  
Author(s):  
GM Trimbur ◽  
CJ Walsh
Keyword(s):  
Ribosome Biogenesis ◽  
Rrna Synthesis ◽  
Protein Distribution ◽  
The Core ◽  
Nucleolar Proteins ◽  
Fibrillar Component ◽  
20 Nm ◽  
The Relationship

Nucleoli, the sites of rRNA synthesis, rRNA processing, and the assembly of ribosomes, are dynamic organelles that, in most cells, disperse and reform during mitosis. The mechanisms that regulate nucleolar formation are unknown as is the relationship between nucleolar morphology and the pathway of ribosome biogenesis. In this report we describe the in vitro formation of nucleolus-like particles (NLPs) from soluble extracts of nucleoli. NLPs, which reached sizes comparable to nucleoli (1-3 microns), were found to contain 40% of the nucleolar DNA, RNA, and protein. The ultrastructure of NLPs resembled that of a number of in vivo structures including compact nucleoli, prenucleolar bodies, and pseudonucleoli. The particles were composed of two morphologically distinct regions. The core resembled the dense fibrillar component (DFC) of nucleoli while the cortex resembled the granular component (GC) of nucleoli. The cortex of NLPs contained numerous 15-20 nm osmophilic granules that resembled the preribosomes found in the GC of nucleoli. The distribution of nucleolar proteins in NLPs also resembled that in nucleoli. BN46/51, a component of the GC of nucleoli, was restricted to the GC-like cortex of NLPs. A mAb that bound to the DFC of nucleoli, bound only to the DFC-like core of NLPs while a second mAb that bound to both the DFC and GC of nucleoli, bound to both the core and cortex of NLPs. Thus solubilized components of nucleoli can reassociate in vitro to produce particles that resemble nucleoli in their size, ultrastructure, and protein distribution.

scholarly journals In vivo homopropargylglycine incorporation enables nascent protein tagging, isolation and characterisation from Arabidopsis thaliana

2021 ◽  
Author(s):  
Nathan Tivendale ◽  
Ricarda Fenske ◽  
Owen Duncan ◽  
A. Harvey Millar
Keyword(s):  
Plant Responses ◽  
Plant Proteins ◽  
Peptide Mass ◽  
Age Related ◽  
Protein Pool ◽  
Whole Plant ◽  
Canonical Amino Acid ◽  
Peptide Mass Spectrometry ◽  
Protein Tagging

Determining which proteins are actively synthesised at a given point in time and extracting them for analysis is important to understand plant responses. Here we show that the methionine (Met) analogue homopropargylglycine (HPG) enables BONCAT (Bio-Orthogonal Non-Canonical Amino acid Tagging) of proteins being synthesised in Arabidopsis plants or cell cultures, facilitating their click-chemistry enrichment for analysis. The sites of HPG incorporation could be confirmed by peptide mass spectrometry at Met-sites throughout protein AA sequences and correlation with independent studies of protein labelling with 15N verified the data. We provide evidence that HPG-based BONCAT tags nascent plant proteins more efficiently than azidohomoalanine (AHA)-based BONCAT in Arabidopsis and show that AHA's induction of Met metabolism and greater inhibition of cell growth rate than HPG likely limits AHA incorporation at Met sites in Arabidopsis. We show HPG-based BONCAT provides a verifiable method for determining which plant proteins are being synthesised at a given time point and enriches new protein molecules from the bulk protein pool for identification, quantitation and subsequent biochemical analysis. Enriched nascent polypeptides were found to contain significantly fewer common post-translationally modified residues than the same proteins from whole plant extracts, providing evidence for age-related accumulation of PTMs in plants.

scholarly journals Protein turnover and growth in the whole body, liver and kidney of the rat from the foetus to senility

1984 ◽  
Vol 217 (2) ◽  
pp. 507-516 ◽  
Author(s):  
D F Goldspink ◽  
F J Kelly
Keyword(s):  
Protein Synthesis ◽  
Protein Turnover ◽  
Post Partum ◽  
Protein Composition ◽  
Whole Body ◽  
Turnover Rates ◽  
Tissue Mass ◽  
Age Related ◽  
Foetal Life

Changes in the growth and protein turnover (measured in vivo) of the rat liver, kidney and whole body were studied between 16 days of life in utero and 105 weeks post partum. Tissue and whole-body growth were related to changes in both cellular hyperplasia (i.e. changes in DNA) and hypertrophy (protein/DNA values) and to the protein composition within the enlarging tissue mass. The suitability of using a single large dose of phenylalanine for measuring the rates of protein synthesis during both pre- and post-natal life was established. The declining growth rates in the whole animal and the two visceral tissues were then explained by developmental changes in the fractional rates of protein synthesis and breakdown, turnover rates being age-for-age higher in the liver than in the kidney, which in turn were higher than those measured in the whole animal. The declining fractional rates of synthesis in both tissues and the whole body with increasing age were related to changes in the tissues' ribosomal capacity and activity. The fall in the hepatic rate between 18 and 20 days of foetal life (from 134 to 98% per day) corresponded to a decrease in both the ribosomal capacity and the rate of synthesis per ribosome. No significant changes in any of these parameters were, however, found in the liver between weaning (3 weeks) and senility (105 weeks). In contrast, the fractional synthetic (and degradative) rates progressively declined in the kidney (from 95 to 24% per day) and whole body (from 70 to 11% per day) throughout both pre- and post-natal life, mainly as a consequence of a progressive decline in the ribosomal capacity, but with some fall in the ribosomal activity also during foetal life. The age-related contributions of these visceral tissues to the total amount of protein synthesized per day by the whole animal were determined. The renal contribution remained fairly constant at 1.6-2.9%, whereas the hepatic contribution declined from 56 to 11%, with increasing age. Approximate-steady-state conditions were reached at, and between, 44 and 105 weeks post partum, the half-life values of mixed whole-body, kidney and liver proteins being 6.4, 3.0 and 1.5 days, respectively, at 105 weeks.

scholarly journals Fractional Synthesis Rates of Individual Proteins in Rat Soleus and Plantaris Muscles

Proteomes ◽  
2020 ◽  
Vol 8 (2) ◽  
pp. 10
Author(s):  
Connor A. Stead ◽  
Stuart J. Hesketh ◽  
Samuel Bennett ◽  
Hazel Sutherland ◽  
Jonathan C. Jarvis ◽  
...  
Keyword(s):  
Body Weight ◽  
Protein Turnover ◽  
Deuterium Oxide ◽  
Protein Composition ◽  
Synthesis Rate ◽  
Control Group ◽  
Turnover Rates ◽  
Peptide Mass ◽  
Fractional Synthesis ◽  
Slow Twitch

Differences in the protein composition of fast- and slow-twitch muscle may be maintained by different rates of protein turnover. We investigated protein turnover rates in slow-twitch soleus and fast-twitch plantaris of male Wistar rats (body weight 412 ± 69 g). Animals were assigned to four groups (n = 3, in each), including a control group (0 d) and three groups that received deuterium oxide (D2O) for either 10 days, 20 days or 30 days. D2O administration was initiated by an intraperitoneal injection of 20 μL of 99% D2O-saline per g body weight, and maintained by provision of 4% (v/v) D2O in the drinking water available ad libitum. Soluble proteins from harvested muscles were analysed by liquid chromatography–tandem mass spectrometry and identified against the SwissProt database. The enrichment of D2O and rate constant (k) of protein synthesis was calculated from the abundance of peptide mass isotopomers. The fractional synthesis rate (FSR) of 44 proteins in soleus and 34 proteins in plantaris spanned from 0.58%/day (CO1A1: Collagen alpha-1 chain) to 5.40%/day NDRG2 (N-myc downstream-regulated gene 2 protein). Eight out of 18 proteins identified in both muscles had a different FSR in soleus than in plantaris (p < 0.05).

Tele-Substitution Reactions in the Synthesis of a Promising Class of Antimalarials

2020 ◽  
Author(s):  
Marat Korsik ◽  
Edwin Tse ◽  
David Smith ◽  
William Lewis ◽  
Peter J. Rutledge ◽  
...  
Keyword(s):  
Heterocyclic Ring ◽  
Ring System ◽  
Substitution Reactions ◽  
Laboratory Notebook ◽  
Polar Solvents ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Core ◽  
Nmr Data

<p></p><p>We have discovered and studied a <i>tele</i>substitution reaction in a biologically important heterocyclic ring system. Conditions that favour the <i>tele</i>-substitution pathway were identified: the use of increased equivalents of the nucleophile or decreased equivalents of base, or the use of softer nucleophiles, less polar solvents and larger halogens on the electrophile. Using results from X-ray crystallography and isotope labelling experiments a mechanism for this unusual transformation is proposed. We focused on this triazolopyrazine as it is the core structure of the <i>in vivo </i>active anti-plasmodium compounds of Series 4 of the Open Source Malaria consortium.</p> <p> </p> <p>Archive of the electronic laboratory notebook with the description of all conducted experiments and raw NMR data could be accessed via following link <a href="https://ses.library.usyd.edu.au/handle/2123/21890">https://ses.library.usyd.edu.au/handle/2123/21890</a> . For navigation between entries of laboratory notebook please use file "Strings for compounds in the article.pdf" that works as a reference between article codes and notebook codes, also this file contain SMILES for these compounds. </p><br><p></p>

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