scholarly journals Ribosome heterogeneity in Drosophila melanogaster gonads through paralog-switching

2020 ◽  
Author(s):  
Tayah Hopes ◽  
Michaela Agapiou ◽  
Karl Norris ◽  
Charley G.P. McCarthy ◽  
Mary J O’Connell ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Amino Acid ◽  
Ribosomal Protein ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Mrna Translation

ABSTRACTRibosomes have long been thought of as homogeneous, macromolecular machines but recent evidence suggests they are heterogeneous and could be specialised to regulate translation. Here, we have characterised ribosomal protein heterogeneity across 5 tissues of Drosophila melanogaster. We find that testes and ovaries contain the most heterogeneous ribosome populations, which occurs through paralog-switching. We have solved structures of ribosomes purified from in vivo tissues by cryo-EM, revealing differences in precise ribosomal arrangement for testis and ovary 80S ribosomes. Differences in the amino acid composition of paralog pairs and their localisation on the ribosome exterior indicate paralog-switching could alter the ribosome surface, enabling different proteins to regulate translation. One testis-specific paralog-switching pair is also found in humans, suggesting this is a conserved site of ribosome heterogeneity. Overall, this work allows us to propose that mRNA translation might be regulated in the gonads through ribosome heterogeneity, providing a potential means of ribosome specialisation.

scholarly journals Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates

2018 ◽  
Author(s):  
Andrea Riba ◽  
Noemi Di Nanni ◽  
Nitish Mittal ◽  
Erik Arhné ◽  
Alexander Schmidt ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Translation Initiation ◽  
Mrna Translation ◽  
Elongation Rate ◽  
Translation Elongation ◽  
Lower Protein ◽  
Protein Output

AbstractAlthough protein synthesis dynamics has been studied both with theoretical models and by profiling ribosome footprints, the determinants of ribosome flux along open reading frames (ORFs) are not fully understood. Combining measurements of protein synthesis rate with ribosome footprinting data, we here inferred translation initiation and elongation rates for over a thousand ORFs in exponentially-growing wildtype yeast cells. We found that the amino acid composition of synthesized proteins is as important a determinant of translation elongation rate as parameters related to codon and tRNA adaptation. We did not find evidence of ribosome collisions curbing the protein output of yeast transcripts, either in high translation conditions associated with exponential growth, or in strains in which deletion of individual ribosomal protein genes leads to globally increased or decreased translation. Slow translation elongation is characteristic of RP-encoding transcripts, which have markedly lower protein output than other transcripts with equally high ribosome densities.Significance StatementAlthough sequencing of ribosome footprints has uncovered new aspects of mRNA translation, the determinants of ribosome flux remain incompletely understood. Combining ribosome footprint data with measurements of protein synthesis rates, we here inferred translation initiation and elongation rates for over a thousand ORFs in yeast strains with varying translation capacity. We found that the translation elongation rate varies up to ~20-fold among yeast transcripts, and is significantly correlated with the rate of translation initiation. Furthermore, the amino acid composition of synthesized proteins impacts the rate of translation elongation to the same extent as measures of codon and tRNA adaptation. Transcripts encoding ribosomal proteins are translated especially slow, having markedly lower protein output than other transcripts with equally high ribosome densities.

Predicting Interactions Between Pathogen and Human Proteins Based on the Relation Between Sequence Length and Amino Acid Composition

2021 ◽  
Vol 16 ◽  
Author(s):  
Saud Alguwaizani ◽  
Shulei Ren ◽  
De-Shuang Huang ◽  
Kyungsook Han
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Yersinia Pestis ◽  
Acid Composition ◽  
Sequence Length ◽  
Support Vector ◽  
Human Ppis ◽  
Svm Model

Aim: Both bacterial infection and viral infection involve a large number of protein-protein interactions (PPIs) between a pathogen and its target host. Background: So far, many computational methods have focused on predicting PPIs within the same species rather than PPIs across different species. Methods: From the extensive analysis of PPIs between Yersinia pestis bacteria and humans, we recently discovered an interesting relation; a linear relation between amino acid composition and sequence length was observed in many proteins involved in PPIs. We have built a support vector machine (SVM) model, which predicts PPIs between human and bacteria using two feature types derived from the relation. The two feature types used in the SVM are the amino acid composition group (AACG) and the difference in amino acid composition between host and pathogen proteins. Result: The SVM model achieved high performance in predicting bacteria-human PPIs. The model showed an accuracy of 96%, sensitivity of 94%, and specificity of 98% in predicting PPIs between humans and Yersinia pestis, in which there is a strong relation between amino acid composition and sequence length. The SVM model was also tested in predicting PPIs between human and viruses, which include Ebola, HCV, and SARSCoV-2, and showed a good performance. Conclusion: The feature types identified in our study are simple yet powerful in predicting pathogen-human PPIs. Although preliminary, our method will be useful for finding unknown target host proteins or pathogen proteins and designing in vitro or in vivo experiments.

Ribosomal proteins from goose reticulocytes are not histones

1968 ◽  
Vol 46 (12) ◽  
pp. 1507-1514 ◽  
Author(s):  
J. M. Neelin ◽  
G. Vidali
Keyword(s):  
Amino Acid ◽  
Ribosomal Protein ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Ribosomal Proteins ◽  
Cross Contamination ◽  
Guanidinium Chloride ◽  
Electrophoretic Patterns ◽  
Starch Gel ◽  
Cell Fractions

Ribosomes were isolated from goose reticulocytes after lysis with saponin in 50 mM KCl, 1.5 mM MgCl2, 1 mM Tris, pH 7.5. Maximum yields of ribosomes were obtained about 4 days after injection of the birds with Phenylhydrazine, but ribosomal proteins did not vary with the stage of recovery.Ribosomal proteins (extracted with either HCl–urea or LiCl–urea) differed generally from histones (extracted with either HCl or HCl–urea) according to amino acid composition and to electrophoretic patterns in starch gel and in Polyacrylamide gel, but a few zones of ribosomal protein appeared to coincide electrophoretically with the main histone components. Since all of the former proteins were eluted unretarded from Amberlite CG-50 in 9% guanidinium chloride, in which all histones are adsorbed, we conclude that histones and ribosomal proteins are different classes of protein.The hazards of assuming chemical identities of proteins on the basis of limited electrophoretic evidence and the risks of misleading cross-contamination of cell fractions were demonstrated.

scholarly journals Sequence determinants of in cell condensate assembly morphology, dynamics, and oligomerization as measured by number and brightness analysis

2021 ◽  
Author(s):  
Ryan J Emenecker ◽  
Alex S Holehouse ◽  
Lucia Strader
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Material Properties ◽  
Oligomeric State ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Brightness Analysis ◽  
Oligomerization Domain

Background: Biomolecular condensates are non-stoichiometric assemblies that are characterized by their capacity to spatially concentrate biomolecules and play a key role in cellular organization. Proteins that drive the formation of biomolecular condensates frequently contain oligomerization domains and intrinsically disordered regions (IDRs), both of which can contribute multivalent interactions that drive higher-order assembly. Our understanding of the relative and temporal contribution of oligomerization domains and IDRs to the material properties of in vivo biomolecular condensates is limited. Similarly, the spatial and temporal dependence of protein oligomeric state inside condensates has been largely unexplored in vivo. Methods: In this study, we combined quantitative microscopy with number and brightness analysis to investigate the aging, material properties, and protein oligomeric state of biomolecular condensates in vivo. Our work is focused on condensates formed by AUXIN RESPONSE FACTOR 19 (ARF19), which is a transcription factor integral to the signaling pathway for the plant hormone auxin. ARF19 contains a large central glutamine-rich IDR and a C-terminal Phox Bem1 (PB1) oligomerization domain and forms cytoplasmic condensates. Results: Our results reveal that the IDR amino acid composition can influence the morphology and material properties of ARF19 condensates. In contrast the distribution of oligomeric species within condensates appears insensitive to the IDR composition. In addition, we identified a relationship between the abundance of higher- and lower-order oligomers within individual condensates and their apparent fluidity. Conclusions: IDR amino acid composition affects condensate morphology and material properties. In ARF condensates, altering the amino acid composition of the IDR did not greatly affect the oligomeric state of proteins within the condensate.

scholarly journals Scrambled Prion Domains Form Prions and Amyloid

2004 ◽  
Vol 24 (16) ◽  
pp. 7206-7213 ◽  
Author(s):  
Eric D. Ross ◽  
Ulrich Baxa ◽  
Reed B. Wickner
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Sequence Composition ◽  
Amino Terminal ◽  
Rich Domain ◽  
The Many ◽  
Necessary And Sufficient

ABSTRACT The [URE3] prion of Saccharomyces cerevisiae is a self-propagating amyloid form of Ure2p. The amino-terminal prion domain of Ure2p is necessary and sufficient for prion formation and has a high glutamine (Q) and asparagine (N) content. Such Q/N-rich domains are found in two other yeast prion proteins, Sup35p and Rnq1p, although none of the many other yeast Q/N-rich domain proteins have yet been found to be prions. To examine the role of amino acid sequence composition in prion formation, we used Ure2p as a model system and generated five Ure2p variants in which the order of the amino acids in the prion domain was randomly shuffled while keeping the amino acid composition and C-terminal domain unchanged. Surprisingly, all five formed prions in vivo, with a range of frequencies and stabilities, and the prion domains of all five readily formed amyloid fibers in vitro. Although it is unclear whether other amyloid-forming proteins would be equally resistant to scrambling, this result demonstrates that [URE3] formation is driven primarily by amino acid composition, largely independent of primary sequence.

scholarly journals Sequence determinants of in cell condensate morphology, dynamics, and oligomerization as measured by number and brightness analysis

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Ryan J. Emenecker ◽  
Alex S. Holehouse ◽  
Lucia C. Strader
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Material Properties ◽  
Auxin Signaling ◽  
Oligomeric State ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Brightness Analysis

Abstract Background Biomolecular condensates are non-stoichiometric assemblies that are characterized by their capacity to spatially concentrate biomolecules and play a key role in cellular organization. Proteins that drive the formation of biomolecular condensates frequently contain oligomerization domains and intrinsically disordered regions (IDRs), both of which can contribute multivalent interactions that drive higher-order assembly. Our understanding of the relative and temporal contribution of oligomerization domains and IDRs to the material properties of in vivo biomolecular condensates is limited. Similarly, the spatial and temporal dependence of protein oligomeric state inside condensates has been largely unexplored in vivo. Methods In this study, we combined quantitative microscopy with number and brightness analysis to investigate the aging, material properties, and protein oligomeric state of biomolecular condensates in vivo. Our work is focused on condensates formed by AUXIN RESPONSE FACTOR 19 (ARF19), a transcription factor integral to the auxin signaling pathway in plants. ARF19 contains a large central glutamine-rich IDR and a C-terminal Phox Bem1 (PB1) oligomerization domain and forms cytoplasmic condensates. Results Our results reveal that the IDR amino acid composition can influence the morphology and material properties of ARF19 condensates. In contrast the distribution of oligomeric species within condensates appears insensitive to the IDR composition. In addition, we identified a relationship between the abundance of higher- and lower-order oligomers within individual condensates and their apparent fluidity. Conclusions IDR amino acid composition affects condensate morphology and material properties. In ARF condensates, altering the amino acid composition of the IDR did not greatly affect the oligomeric state of proteins within the condensate.

scholarly journals Selective translational regulation of ribosomal protein gene expression during early development of Drosophila melanogaster.

1985 ◽  
Vol 5 (12) ◽  
pp. 3583-3592 ◽  
Author(s):  
M A Kay ◽  
M Jacobs-Lorena
Keyword(s):  
Drosophila Melanogaster ◽  
Ribosomal Protein ◽  
Translational Regulation ◽  
Mrna Translation ◽  
Ribosomal Protein Gene ◽  
Rrna Synthesis ◽  
Developmentally Regulated ◽  
Free Translation ◽  
Cloned Cdna

We have previously characterized a cloned cDNA coding for a developmentally regulated mRNA in Drosophila melanogaster whose expression is selectively regulated at the translational level during oogenesis and embryogenesis. In this report we show that this translationally regulated mRNA (rpA1) codes for an acidic ribosomal protein. Furthermore, our results indicate that most ribosomal protein mRNAs are regulated similarly to rpA1 mRNA. This conclusion is based on cell-free translation of mRNAs derived from polysomes and postpolysomal supernatants as well as in vivo labeling experiments. Thus, the translation of many ribosomal protein mRNAs appears to be temporally related to the synthesis of rRNA during D. melanogaster development. The relationship between rRNA transcription and ribosomal protein mRNA translation was further investigated by genetically reducing rRNA synthesis with the use of bobbed mutants. Unexpectedly, neither ribosomal protein mRNA abundance nor translation was altered in these mutants.

scholarly journals A Promiscuous Prion: Efficient Induction of [URE3] Prion Formation by Heterologous Prion Domains

Genetics ◽  
2009 ◽  
Vol 183 (3) ◽  
pp. 929-940 ◽  
Author(s):  
Carley D. Ross ◽  
Blake R. McCarty ◽  
Michael Hamilton ◽  
Asa Ben-Hur ◽  
Eric D. Ross
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
De Novo ◽  
Amyloid Formation ◽  
Wild Type ◽  
Amyloid Aggregates ◽  
Efficient Induction

The [URE3] and [PSI+] prions are the infections amyloid forms of the Saccharomyces cerevisiae proteins Ure2p and Sup35p, respectively. Randomizing the order of the amino acids in the Ure2 and Sup35 prion domains while retaining amino acid composition does not block prion formation, indicating that amino acid composition, not primary sequence, is the predominant feature driving [URE3] and [PSI+] formation. Here we show that Ure2p promiscuously interacts with various compositionally similar proteins to influence [URE3] levels. Overexpression of scrambled Ure2p prion domains efficiently increases de novo formation of wild-type [URE3] in vivo. In vitro, amyloid aggregates of the scrambled prion domains efficiently seed wild-type Ure2p amyloid formation, suggesting that the wild-type and scrambled prion domains can directly interact to seed prion formation. To test whether interactions between Ure2p and naturally occurring yeast proteins could similarly affect [URE3] formation, we identified yeast proteins with domains that are compositionally similar to the Ure2p prion domain. Remarkably, all but one of these domains were also able to efficiently increase [URE3] formation. These results suggest that a wide variety of proteins could potentially affect [URE3] formation.

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