scholarly journals Simplification of ribosomes in bacteria with tiny genomes

2019 ◽  
Author(s):  
Daria D. Nikolaeva ◽  
Mikhail S. Gelfand ◽  
Sofya K. Garushyants
Keyword(s):  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Protein Biosynthesis ◽  
Large Subunit ◽  
Protein Composition ◽  
Small Subunit ◽  
Genome Reduction ◽  
Bacterial Genomes ◽  
Shine Dalgarno Sequence

AbstractThe ribosome is an essential cellular machine performing protein biosynthesis. Its structure and composition are highly conserved in all species. However, some bacteria have been reported to have an incomplete set of ribosomal proteins. We have analyzed ribosomal protein composition in 214 small bacterial genomes (< 1 Mb) and found that although the ribosome composition is fairly stable, some ribosomal proteins may be absent, especially in bacteria with dramatically reduced genomes. The protein composition of the large subunit is less conserved than that of the small subunit. We have identified the set of frequently lost ribosomal proteins and demonstrated that they tend to be situated on the ribosome surface and have fewer contacts to other ribosome components. Moreover, some proteins are lost in an evolutionary correlated manner. The reduction of rRNA is also common in bacteria with tiny genomes with deletions mostly occurring in free loops. Finally, the loss of the anti-Shine-Dalgarno sequence is associated with the genome reduction, the number of lost ribosomal proteins, and with the loss of bL9 and TF.

scholarly journals Simplification of Ribosomes in Bacteria with Tiny Genomes

2020 ◽  
Vol 38 (1) ◽  
pp. 58-66 ◽  
Author(s):  
Daria D Nikolaeva ◽  
Mikhail S Gelfand ◽  
Sofya K Garushyants
Keyword(s):  
Ribosomal Protein ◽  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Protein Biosynthesis ◽  
Large Subunit ◽  
Protein Composition ◽  
Small Subunit ◽  
Bacterial Genomes ◽  
Shine Dalgarno Sequence

Abstract The ribosome is an essential cellular machine performing protein biosynthesis. Its structure and composition are highly conserved in all species. However, some bacteria have been reported to have an incomplete set of ribosomal proteins. We have analyzed ribosomal protein composition in 214 small bacterial genomes (&lt;1 Mb) and found that although the ribosome composition is fairly stable, some ribosomal proteins may be absent, especially in bacteria with dramatically reduced genomes. The protein composition of the large subunit is less conserved than that of the small subunit. We have identified the set of frequently lost ribosomal proteins and demonstrated that they tend to be positioned on the ribosome surface and have fewer contacts to other ribosome components. Moreover, some proteins are lost in an evolutionary correlated manner. The reduction of ribosomal RNA is also common, with deletions mostly occurring in free loops. Finally, the loss of the anti-Shine–Dalgarno sequence is associated with the loss of a higher number of ribosomal proteins.

scholarly journals Ribosome Biogenesis in African Trypanosomes Requires Conserved and Trypanosome-Specific Factors

2014 ◽  
Vol 13 (6) ◽  
pp. 727-737 ◽  
Author(s):  
Khan Umaer ◽  
Martin Ciganda ◽  
Noreen Williams
Keyword(s):  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Large Subunit ◽  
Ribosomal Subunit ◽  
Small Subunit ◽  
5S Rrna ◽  
Content Type ◽  
African Trypanosomes ◽  
Ribosomal Protein L5

ABSTRACTLarge ribosomal subunit protein L5 is responsible for the stability and trafficking of 5S rRNA to the site of eukaryotic ribosomal assembly. InTrypanosoma brucei, in addition to L5, trypanosome-specific proteins P34 and P37 also participate in this process. These two essential proteins form a novel preribosomal particle through interactions with both the ribosomal protein L5 and 5S rRNA. We have generated a procyclic L5 RNA interference cell line and found that L5 itself is a protein essential for trypanosome growth, despite the presence of other 5S rRNA binding proteins. Loss of L5 decreases the levels of all large-subunit rRNAs, 25/28S, 5.8S, and 5S rRNAs, but does not alter small-subunit 18S rRNA. Depletion of L5 specifically reduced the levels of the other large ribosomal proteins, L3 and L11, whereas the steady-state levels of the mRNA for these proteins were increased. L5-knockdown cells showed an increase in the 40S ribosomal subunit and a loss of the 60S ribosomal subunits, 80S monosomes, and polysomes. In addition, L5 was involved in the processing and maturation of precursor rRNAs. Analysis of polysomal fractions revealed that unprocessed rRNA intermediates accumulate in the ribosome when L5 is depleted. Although we previously found that the loss of P34 and P37 does not result in a change in the levels of L5, the loss of L5 resulted in an increase of P34 and P37 proteins, suggesting the presence of a compensatory feedback loop. This study demonstrates that ribosomal protein L5 has conserved functions, in addition to nonconserved trypanosome-specific features, which could be targeted for drug intervention.

Depletion and Reconstitution of Active E. Coli Ribosomes

1975 ◽  
Vol 33 ◽  
pp. 640-641
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Protein Biosynthesis ◽  
Large Subunit ◽  
High Resolution Electron Microscopy ◽  
Small Subunit ◽  
Structure And Function ◽  
Biologically Active ◽  
Biological Macromolecules ◽  
E Coli ◽  
Resolution Electron ◽  
And Function

Correlations between structure and function of biological macromolecules have been studied intensively for many years, mostly by indirect methods. High resolution electron microscopy is a unique tool which can provide such information directly by comparing the conformation of biopolymers in their biologically active and inactive state. We have correlated the structure and function of ribosomes, ribonucleoprotein particles which are the site of protein biosynthesis. 70S E. coli ribosomes, used in this experiment, are composed of two subunits - large (50S) and small (30S). The large subunit consists of 34 proteins and two different ribonucleic acid molecules. The small subunit contains 21 proteins and one RNA molecule. All proteins (with the exception of L7 and L12) are present in one copy per ribosome.This study deals with the changes in the fine structure of E. coli ribosomes depleted of proteins L7 and L12. These proteins are unique in many aspects.

scholarly journals The proteins of Xenopus ovary ribosomes

1971 ◽  
Vol 125 (4) ◽  
pp. 1091-1107 ◽  
Author(s):  
P J Ford
Keyword(s):  
Potassium Chloride ◽  
Ribosomal Proteins ◽  
Large Subunit ◽  
Buoyant Density ◽  
Small Subunit ◽  
Chemical Methods ◽  
Ribosomal Subunits ◽  
Molecular Weights ◽  
Caesium Chloride ◽  
Chloride Treatment

1. The preparation of ribosomes and ribosomal subunits from Xenopus ovary is described. 2. The yield of once-washed ribosomes (buoyant density in caesium chloride 1.601g·cm-3; 44% RNA, 56% protein by chemical methods) was 10.1mg/g wet wt. of tissue. 3. Buoyant density in caesium chloride and RNA/protein ratios by chemical methods have been determined for ribosome subunits produced by 1.0mm-EDTA or 0.5m-potassium chloride treatment and also for EDTA subunits extracted with 0.5m-, 1.0m- or 1.5m-potassium chloride, 4. Analysis of ribosomal protein on acrylamide gels at pH4.5 in 6m-urea reveals 24 and 26 bands from small and large EDTA subunits respectively. The actual numbers of proteins are greater than this, as many bands are obviously doublets. 5. Analysis of the proteins in the potassium chloride extract and particle fractions showed that some bands are completely and some partially extracted. Taking partial extraction as an indication of possible doublet bands it was found that there were 12 and 20 such bands in the small and large subunits respectively, making totals of 36 and 46 proteins. 6. From the measured protein contents and assuming weight-average molecular weights for the proteins of large and small subunits close to those observed for eukaryote ribosomal proteins it is possible to compute the total numbers of protein molecules per particle. It appears that too few protein bands have been identified on acrylamide gels to account for all the protein in the large subunit, but probably enough for the small subunit.

Comparison of the Effect of Various Methods of Dissociation on the Protein Composition of Rat Liver Ribosomal Subunits

1975 ◽  
Vol 53 (9) ◽  
pp. 935-942 ◽  
Author(s):  
Nabil Hanna ◽  
Claude Godin
Keyword(s):  
Rat Liver ◽  
Ribosomal Proteins ◽  
Gradient Centrifugation ◽  
Polyacrylamide Gel Electrophoresis ◽  
Protein Composition ◽  
Small Subunit ◽  
Protein Patterns ◽  
Major Loss ◽  
Centrifugation Technique ◽  
High Concentrations

Rat liver ribosomes were dissociated into subunits using EDTA, sodium pyrophosphate, high concentrations of KCl, as well as by incubation with puromycin in presence of 0.5 M KCl. The subunits obtained were analyzed using the density gradient centrifugation technique and their ribosomal proteins were separated by means of two-dimensional polyacrylamide gel electrophoresis. The ribosomal protein patterns of the two subunits isolated using each of the dissociating method were compared to the protein patterns of monosomes prepared by puromycin treatment alone. Our results revealed that the use of chelating agents to dissociate the ribosomes resulted in the loss of some ribosomal proteins from the small subunit. On the other hand, the use of KCl in high concentrations to dissociate the ribsosomes did not appear to cause any major loss of proteins from the ribosomes except for some acidic proteins.

Subcellular distribution of ribosomal proteins in Dictyostelium discoideum

1990 ◽  
Vol 68 (5) ◽  
pp. 839-845
Author(s):  
S. Ramagopal
Keyword(s):  
Ribosomal Proteins ◽  
Large Subunit ◽  
Small Subunit ◽  
Cellular Slime Mold ◽  
Developmentally Regulated ◽  
Two Dimensional Gel Electrophoresis ◽  
Coomassie Blue ◽  
Cellular Slime ◽  
State Growth

The distribution of ribosomal proteins in monosomes, polysomes, the postribosomal cytosol, and the nucleus was determined during steady-state growth in vegetative amoebae. A partitioning of previously reported cell-specific ribosomal proteins between monosomes and polysomes was observed. L18, one of the two unique proteins in amoeba ribosomes, was distributed equally among monosomes and polysomes. However S5, the other unique protein, was abundant in monosomes but barely visible in polysomes. Of the developmentally regulated proteins, D and S6 were detectable only in polysomes and S14 was more abundant in monosomes. The cystosol revealed no ribosomal proteins. On staining of the nuclear proteins with Coomassie blue, about 18, 7 from 40S subunit and 11 from 60S subunit, were identified as ribosomal proteins. By in vivo labeling of the proteins with [35S]methionine, 24 of the 34 small subunit proteins and 33 of the 42 large subunit proteins were localized in the nucleus. For the majority of the ribosomal proteins, the apparent relative stoichiometry was similar in nuclear preribosomal particles and in cytoplasmic ribosomes. However, in preribosomal particles the relative amount of four proteins (S11, S30, L7, and L10) was two- to four-fold higher and of eight proteins (S14, S15, S20, S34, L12, L27, L34, and L42) was two- to four-fold lower than that of cytoplasmic ribosomes.Key words: cellular slime mold, cell-specific ribosomal proteins, nucleus, cytoplasm, two-dimensional gel electrophoresis.

scholarly journals A novel small-subunit ribosomal protein of yeast mitochondria that interacts functionally with an mRNA-specific translational activator.

1990 ◽  
Vol 10 (9) ◽  
pp. 4590-4595 ◽  
Author(s):  
T W McMullin ◽  
P Haffter ◽  
T D Fox
Keyword(s):  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Mitochondrial Gene ◽  
Ribosomal Subunit ◽  
Nuclear Gene ◽  
Small Subunit ◽  
Rrna Gene ◽  
Mitochondrial Translation ◽  
Activator Proteins ◽  
Translational Activator

Mitochondrial translation of the mRNA encoding cytochrome c oxidase subunit III (coxIII) specifically requires the action of three position activator proteins encoded in the nucleus of Saccharomyces cerevisiae. Some mutations affecting one of these activators, PET122, can be suppressed by mutations in an unlinked nuclear gene termed PET123. PET123 function was previously demonstrated to be required for translation of all mitochondrial gene products. We have now generated an antibody against the PET123 protein and have used it to demonstrate that PET123 is a mitochondrial ribosomal protein of the small subunit. PET123 appears to be present at levels comparable to those of other mitochondrial ribosomal proteins, and its accumulation is dependent on the presence of the 15S rRNA gene in mitochondria. Taken together with the previous genetic data, these results strongly support a model in which the mRNA-specific translational activator PET122 works by directly interacting with the small ribosomal subunit to promote translation initiation on the coxIII mRNA.

scholarly journals Ribosomal protein gene deletions in Diamond-Blackfan anemia

Blood ◽  
2011 ◽  
Vol 118 (26) ◽  
pp. 6943-6951 ◽  
Author(s):  
Jason E. Farrar ◽  
Adrianna Vlachos ◽  
Eva Atsidaftos ◽  
Hannah Carlson-Donohoe ◽  
Thomas C. Markello ◽  
...  
Keyword(s):  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Protein Gene ◽  
Single Nucleotide Polymorphism Array ◽  
Ribosomal Protein Gene ◽  
Small Subunit ◽  
Ribosomal Protein Genes ◽  
Gene Deletions ◽  
Diamond Blackfan Anemia ◽  
Genome Wide

Abstract Diamond-Blackfan anemia (DBA) is a congenital BM failure syndrome characterized by hypoproliferative anemia, associated physical abnormalities, and a predisposition to cancer. Perturbations of the ribosome appear to be critically important in DBA; alterations in 9 different ribosomal protein genes have been identified in multiple unrelated families, along with rarer abnormalities of additional ribosomal proteins. However, at present, only 50% to 60% of patients have an identifiable genetic lesion by ribosomal protein gene sequencing. Using genome-wide single-nucleotide polymorphism array to evaluate for regions of recurrent copy variation, we identified deletions at known DBA-related ribosomal protein gene loci in 17% (9 of 51) of patients without an identifiable mutation, including RPS19, RPS17, RPS26, and RPL35A. No recurrent regions of copy variation at novel loci were identified. Because RPS17 is a duplicated gene with 4 copies in a diploid genome, we demonstrate haploinsufficient RPS17 expression and a small subunit ribosomal RNA processing abnormality in patients harboring RPS17 deletions. Finally, we report the novel identification of variable mosaic loss involving known DBA gene regions in 3 patients from 2 kindreds. These data suggest that ribosomal protein gene deletion is more common than previously suspected and should be considered a component of the initial genetic evaluation in cases of suspected DBA.

scholarly journals Decoding regulatory specificity of human ribosomal proteins on global gene expression

2021 ◽  
Author(s):  
Yizhao Luan ◽  
Nan Tang ◽  
Jiaqi Yang ◽  
Shuting Liu ◽  
Chichi Cheng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Ribosomal Proteins ◽  
Translational Regulation ◽  
Large Subunit ◽  
Global Gene Expression ◽  
Small Subunit ◽  
Sequencing Analysis ◽  
Retina Development ◽  
P53 Signaling

Human ribosomes, made of around 80 ribosomal proteins (RPs) and four ribosomal RNAs, have long been thought as uniform passive protein-making factories with few regulatory functions. Recently, accumulating evidence showed heterogeneity of RP composition in ribosomes responsible for regulating gene expression in development and tumorigenesis. However, a comprehensive understanding of regulatory spectrum of RPs is unclear. In this study, we conducted a systematic survey of regulatory specificity of human RPs on global gene expression. We assessed deficiency of 75 RP, including 44 from the large subunit (60S) and 31 from the small subunit (40S), on gene translation and transcription via ribosomal profiling and RNA sequencing analysis. We showed that RP deficiency induced diverse expression changes, particularly at the translational level. RPs were subjected to co-translational regulation under ribosomal stress where deficiency of the 60S or the 40S RPs had distinguished effects on the two subunits. The gene ontology analysis revealed that RP deficiency perturbed expression of genes related to cell cycle, cellular metabolism, signal transduction and development. Deficiency of RPs from the 60S led to a greater repression effect on cell growth than that from the 40S by affecting P53 signaling and cell cycle pathways. To demonstrate functional specificity of RPs, we showed that RPS8 deficiency stimulated cellular apoptosis but RPL13 or RPL18 deficiency promoted cellular senescence. We also showed that RPL11 and RPL15 played important roles in retina development and angiogenesis, respectively. Overall, our study demonstrated a widespread regulatory role of RPs in controlling cellular activity and provided an important resource which offered novel insights into ribosome regulation in human diseases and cancer.

scholarly journals Theoretical ribosomal protein mass distribution of Pseudomonas aeruginosa PAO1

2018 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Small Subunit ◽  
Structure And Function ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
And Function ◽  
Unique Mass ◽  
Tof Ms

Ribosomes are the protein synthesis factories of a cell and thus are evolutionary conserved in structure and function. Comprising a large and small subunit, the ribosome is further made up of ribosomal proteins that give structure and function to different parts of the macromolecular complex. Current methods for isolating the ribosome include density gradient ultracentrifugation that separates the ribosome into the large and small subunit. Separation of the various ribosomal proteins that comprise each of the subunit would require a solubilization step followed by the use of sodium dodecyl sulphate and polyacrylamide gel electrophoresis (SDS-PAGE). However, possibility exists for the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to profile the set of ribosomal proteins that could be solubilized from each ribosome subunit. Using ribosomal protein amino acid sequence information from Kyoto Encyclopaedia of Genes and Genomes (KEGG), the molecular weight of each ribosomal protein from Pseudomonas aeruginosa PAO1 was calculated in this report. Obtained results revealed that each ribosomal protein had a unique mass that could be detected by mid-range MALDI-TOF MS instruments. More importantly, the mass of ribosomal proteins constitutes a unique mass fingerprint of each ribosome subunit, which accounts for the different structure and functions of the large and small ribosome subunit. Overall, current mass resolution of MALDI-TOF MS instruments could resolve ribosomal proteins and thus provides a tool for profiling the set of ribosomal proteins that constitute the large and small subunit of the ribosome.

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