Hsp90 dictates viral sequence space by balancing the evolutionary tradeoffs between protein stability, aggregation and translation rate

Mapping Intimacies ◽

10.1101/208462 ◽

2017 ◽

Author(s):

Ron Geller ◽

Sebastian Pechmann ◽

Ashley Acevedo ◽

Raul Andino ◽

Judith Frydman

Keyword(s):

Protein Stability ◽

Stability Limit ◽

Translation Rate ◽

Aggregation Propensity ◽

Synonymous Mutations ◽

Protein Biogenesis ◽

Domain Boundaries ◽

Polypeptide Folding ◽

Hsp90 Activity ◽

Population Sequence

AbstractAcquisition of mutations is central to evolution but the detrimental effects of most mutations on protein folding and stability limit protein evolvability. Molecular chaperones, which suppress aggregation and facilitate polypeptide folding, are proposed to promote sequence diversification by buffering destabilizing mutations. However, whether and how chaperones directly control protein evolution remains poorly understood. Here, we examine the effect of reducing the activity of the key eukaryotic chaperone Hsp90 on poliovirus evolution. Contrary to predictions of a buffering model, inhibiting Hsp90 increases population sequence diversity and promotes accumulation of mutations reducing protein stability. Explaining this counterintuitive observation, we find that Hsp90 offsets the evolutionary tradeoff between protein stability and aggregation. Lower chaperone levels favor sequence variants of reduced hydrophobicity, thus decreasing protein aggregation propensity but at a cost to protein stability. Notably, reducing Hsp90 activity also promotes clusters of codon-deoptimized synonymous mutations at inter-domain boundaries, likely to promote local ribosomal slowdown to facilitate cotranslational domain folding. Our results reveal how a chaperone can shape the sequence landscape at both the protein and RNA levels to harmonize the competing constraints posed by protein stability, aggregation propensity and translation rate on successful protein biogenesis.

Download Full-text

Convergent evolution and structural adaptation to the deep ocean in the protein folding chaperonin CCTα

10.1101/775585 ◽

2019 ◽

Author(s):

Alexandra A.-T. Weber ◽

Andrew F. Hugall ◽

Timothy D. O’Hara

Keyword(s):

Protein Folding ◽

Protein Stability ◽

Deep Sea ◽

In Silico ◽

Molecular Mechanisms ◽

Amino Acid Level ◽

Deep Ocean ◽

Cold Shock Protein ◽

Protein Biogenesis ◽

Molecular Convergence

AbstractThe deep ocean is the largest biome on Earth and yet it is among the least studied environments of our planet. Life at great depths requires several specific adaptations, however their molecular mechanisms remain understudied. We examined patterns of positive selection in 416 genes from four brittle star (Ophiuroidea) families displaying replicated events of deep-sea colonization (288 individuals from 216 species). We found consistent signatures of molecular convergence in functions related to protein biogenesis, including protein folding and translation. Five genes were recurrently positively selected, including CCTα (Chaperonin Containing TCP-1 subunit α), which is essential for protein folding. Molecular convergence was detected at the functional and gene levels but not at the amino-acid level. Pressure-adapted proteins are expected to display higher stability to counteract the effects of denaturation. We thus examined in silico local protein stability of CCTα across the ophiuroid tree of life (967 individuals from 725 species) in a phylogenetically-corrected context and found that deep sea-adapted proteins display higher stability within and next to the substrate-binding region, which was confirmed by in silico global protein stability analyses. This suggests that CCTα not only displays structural but also functional adaptations to deep water conditions. The CCT complex is involved in the folding of ∼10% of newly synthesized proteins and has previously been categorized as ‘cold-shock’ protein in numerous eukaryotes. We thus propose that adaptation mechanisms to cold and deep-sea environments may be linked and highlight that efficient protein biogenesis, including protein folding and translation, are key metabolic deep-sea adaptations.

Download Full-text

Forms of Iron in Beer

Journal of AOAC INTERNATIONAL ◽

10.1093/jaoac/59.6.1380 ◽

1976 ◽

Vol 59 (6) ◽

pp. 1380-1386

Author(s):

Shela Gorinstein

Keyword(s):

Protein Stability ◽

Emission Spectroscopy ◽

Stability Limit ◽

Protein Composition ◽

Hydrogen Ion ◽

Ion Concentration ◽

Ferric Ions ◽

Agar Gel ◽

Hydrogen Ion Concentration ◽

Forms Of Iron

Abstract Different forms of iron (total, ionic, and complexed) were investigated by colorimetry, emission spectroscopy, spectrophotometry, and electrophoresis on agar gel with the following results: The lowest concentration of complexed iron occurs in the sample of highest colloid-protein stability (limit of precipitation) ; the colloid protein stability is directly dependent on the content of complexed iron in hordein-globulin fractions ; a decrease in hydrogen ion concentration leads to an increase in the content of complexed iron; a low redox potential corresponds to high protein stability ; the change in fractional protein composition depends on the amount of complexed iron; the content of proteins in salt and in alcoholic fractions increases with added ferric ions, resulting in decreased colloid protein stability.

Download Full-text

Whole-Genome Sequences of the Severe Acute Respiratory Syndrome Coronavirus-2 obtained from Romanian patients between March and June of 2020

10.1101/2020.06.28.175802 ◽

2020 ◽

Author(s):

Mihaela Lazar ◽

Odette Popovici ◽

Barbara Mühlemann ◽

Tim Durfee ◽

Razvan Stan

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Protein Stability ◽

Treatment Options ◽

Protein Structures ◽

Spike Glycoprotein ◽

Effective Prevention ◽

Angiotensin Converting Enzyme 2 ◽

Viral Genomes ◽

Synonymous Mutations

AbstractImpact of mutations on the evolution of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) are needed for ongoing global efforts to track and trace the current pandemic, in order to enact effective prevention and treatment options. SARS-Co-V-2 viral genomes were detected and sequenced from 18 Romanian patients suffering from coronavirus disease-2019. Viral Spike S glycoprotein sequences were used to generate model structures and assess the role of mutations on protein stability. We integrated the phylogenetic tree within the available European SARS-Co-V-2 genomic sequences. We further provide an epidemiological overview of the pre-existing conditions that are lethal in relevant Romanian patients. Non-synonymous mutations in the viral Spike glycoprotein relating to infectivity are constructed in models of protein structures. Continuing search to limit and treat SARS-CoV-2 benefit from our contribution in delineating the viral Spike glycoprotein mutations, as well as from assessment of their role on protein stability or complex formation with human receptor angiotensin-converting enzyme 2. Our results help implement and extend worldwide genomic surveillance of coronavirus disease-2019.

Download Full-text

Efficient Manipulations of Synonymous Mutations for Controlling Translation Rate: An Analytical Approach

Journal of Computational Biology ◽

10.1089/cmb.2011.0275 ◽

2012 ◽

Vol 19 (2) ◽

pp. 200-231 ◽

Cited By ~ 18

Author(s):

Alexandra Dana ◽

Tamir Tuller

Keyword(s):

Analytical Approach ◽

Translation Rate ◽

Synonymous Mutations

Download Full-text

Differential proteostatic regulation of insoluble and abundant proteins

Bioinformatics ◽

10.1093/bioinformatics/btz214 ◽

2019 ◽

Vol 35 (20) ◽

pp. 4098-4107 ◽

Cited By ~ 2

Author(s):

Reshmi Ramakrishnan ◽

Bert Houben ◽

Frederic Rousseau ◽

Joost Schymkowitz

Keyword(s):

Fluorescent Protein ◽

Meta Analysis ◽

Trigger Factor ◽

Supplementary Information ◽

Translational Efficiency ◽

Translation Rate ◽

Synonymous Mutations ◽

Metabolic Functions ◽

Client Proteins ◽

Green Fluorescent

Abstract Motivation Despite intense effort, it has been difficult to explain chaperone dependencies of proteins from sequence or structural properties. Results We constructed a database collecting all publicly available data of experimental chaperone interaction and dependency data for the Escherichia coli proteome, and enriched it with an extensive set of protein-specific as well as cell-context-dependent proteostatic parameters. Employing this new resource, we performed a comprehensive meta-analysis of the key determinants of chaperone interaction. Our study confirms that GroEL client proteins are biased toward insoluble proteins of low abundance, but for client proteins of the Trigger Factor/DnaK axis, we instead find that cellular parameters such as high protein abundance, translational efficiency and mRNA turnover are key determinants. We experimentally confirmed the finding that chaperone dependence is a function of translation rate and not protein-intrinsic parameters by tuning chaperone dependence of Green Fluorescent Protein (GFP) in E.coli by synonymous mutations only. The juxtaposition of both protein-intrinsic and cell-contextual chaperone triage mechanisms explains how the E.coli proteome achieves combining reliable production of abundant and conserved proteins, while also enabling the evolution of diverging metabolic functions. Availability and implementation The database will be made available via http://phdb.switchlab.org. Supplementary information Supplementary data are available at Bioinformatics online.

Download Full-text

Yeast Tripartite Biosensors Sensitive to Protein Stability and Aggregation Propensity

ACS Chemical Biology ◽

10.1021/acschembio.0c00083 ◽

2020 ◽

Vol 15 (4) ◽

pp. 1078-1088

Author(s):

Veronika Sachsenhauser ◽

Xiexiong Deng ◽

Hyun-hee Kim ◽

Maja Jankovic ◽

James C.A. Bardwell

Keyword(s):

Protein Stability ◽

Aggregation Propensity

Download Full-text

Ribosomal stalk proteins RPLP1 and RPLP2 promote biogenesis of flaviviral and cellular multi-pass transmembrane proteins

Nucleic Acids Research ◽

10.1093/nar/gkaa717 ◽

2020 ◽

Vol 48 (17) ◽

pp. 9872-9885

Author(s):

Rafael K Campos ◽

H R Sagara Wijeratne ◽

Premal Shah ◽

Mariano A Garcia-Blanco ◽

Shelton S Bradrick

Keyword(s):

Protein Stability ◽

Transmembrane Protein ◽

Ribosome Profiling ◽

Small Subset ◽

Ribosome Density ◽

Protein Biogenesis ◽

Cellular Translation ◽

Cellular Mrnas ◽

Ribosomal Stalk ◽

Ribosome Pausing

Abstract The ribosomal stalk proteins, RPLP1 and RPLP2 (RPLP1/2), which form the ancient ribosomal stalk, were discovered decades ago but their functions remain mysterious. We had previously shown that RPLP1/2 are exquisitely required for replication of dengue virus (DENV) and other mosquito-borne flaviviruses. Here, we show that RPLP1/2 function to relieve ribosome pausing within the DENV envelope coding sequence, leading to enhanced protein stability. We evaluated viral and cellular translation in RPLP1/2-depleted cells using ribosome profiling and found that ribosomes pause in the sequence coding for the N-terminus of the envelope protein, immediately downstream of sequences encoding two adjacent transmembrane domains (TMDs). We also find that RPLP1/2 depletion impacts a ribosome density for a small subset of cellular mRNAs. Importantly, the polarity of ribosomes on mRNAs encoding multiple TMDs was disproportionately affected by RPLP1/2 knockdown, implying a role for RPLP1/2 in multi-pass transmembrane protein biogenesis. These analyses of viral and host RNAs converge to implicate RPLP1/2 as functionally important for ribosomes to elongate through ORFs encoding multiple TMDs. We suggest that the effect of RPLP1/2 at TMD associated pauses is mediated by improving the efficiency of co-translational folding and subsequent protein stability.

Download Full-text

Prediction of the Effects of Synonymous Variants on SARS-CoV-2 Genome

F1000Research ◽

10.12688/f1000research.72896.1 ◽

2021 ◽

Vol 10 ◽

pp. 1053

Author(s):

Wan Xin Boon ◽

Boon Zhan Sia ◽

Chong Han Ng

Keyword(s):

Codon Usage ◽

Rna Structure ◽

Rna Virus ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Viral Fitness ◽

Translation Rate ◽

Synonymous Mutations ◽

Global Initiative ◽

The Stability

Background: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had led to a global pandemic since December 2019. SARS-CoV-2 is a single-stranded RNA virus, which mutates at a higher rate. Multiple studies had been done to identify and study nonsynonymous mutations, which change amino acid residues of SARS-CoV-2 proteins. On the other hand, there is little study on the effects of SARS-CoV-2 synonymous mutations. Although these mutations do not alter amino acids, some studies suggest that they may affect viral fitness. This study aims to predict the effect of synonymous mutations on the SARS-CoV-2 genome. Methods: A total of 30,229 SARS-CoV-2 genomic sequences were retrieved from Global Initiative on Sharing all Influenza Data (GISAID) database and aligned using MAFFT. Then, the mutations and their respective frequency were identified. A prediction of RNA secondary structures and their base pair probabilities was performed to study the effect of synonymous mutations on RNA structure and stability. Relative synonymous codon usage (RSCU) analysis was also performed to measure the codon usage bias (CUB) of SARS-CoV-2. Results: A total of 150 synonymous mutations were identified. The synonymous mutation identified with the highest frequency is C3037U mutation in the nsp3 of ORF1a, followed by C313U and C9286U mutation in nsp1 and nsp4 of ORF1a, respectively. Conclusion: Among the synonymous mutations identified, C913U mutation in ORF1a and C26735U in membrane (M) protein may affect RNA secondary structure, reducing the stability of RNA folding and possibly resulting in a higher translation rate. However, lab experiments are required to validate the results obtained from prediction analysis.

Download Full-text

Convergent Evolution and Structural Adaptation to the Deep Ocean in the Protein-Folding Chaperonin CCTα

Genome Biology and Evolution ◽

10.1093/gbe/evaa167 ◽

2020 ◽

Vol 12 (11) ◽

pp. 1929-1942

Author(s):

Alexandra A -T Weber ◽

Andrew F Hugall ◽

Timothy D O’Hara

Keyword(s):

Protein Folding ◽

Protein Stability ◽

Deep Sea ◽

In Silico ◽

Molecular Mechanisms ◽

Amino Acid Level ◽

Deep Ocean ◽

Cold Shock Protein ◽

Protein Biogenesis ◽

Molecular Convergence

Abstract The deep ocean is the largest biome on Earth and yet it is among the least studied environments of our planet. Life at great depths requires several specific adaptations; however, their molecular mechanisms remain understudied. We examined patterns of positive selection in 416 genes from four brittle star (Ophiuroidea) families displaying replicated events of deep-sea colonization (288 individuals from 216 species). We found consistent signatures of molecular convergence in functions related to protein biogenesis, including protein folding and translation. Five genes were recurrently positively selected, including chaperonin-containing TCP-1 subunit α (CCTα), which is essential for protein folding. Molecular convergence was detected at the functional and gene levels but not at the amino-acid level. Pressure-adapted proteins are expected to display higher stability to counteract the effects of denaturation. We thus examined in silico local protein stability of CCTα across the ophiuroid tree of life (967 individuals from 725 species) in a phylogenetically corrected context and found that deep-sea-adapted proteins display higher stability within and next to the substrate-binding region, which was confirmed by in silico global protein stability analyses. This suggests that CCTα displays not only structural but also functional adaptations to deep-water conditions. The CCT complex is involved in the folding of ∼10% of newly synthesized proteins and has previously been categorized as a “cold-shock” protein in numerous eukaryotes. We thus propose that adaptation mechanisms to cold and deep-sea environments may be linked and highlight that efficient protein biogenesis, including protein folding and translation, is a key metabolic deep-sea adaptation.

Download Full-text