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Figure S1 in Natural selection on various sites of ribosomal proteins: a cladistic view

Figure S1. Conserved sites of ribosomal protein 40S subunit labeling on crystal structure. The ribbons colored in red represent the synapomorphic s. str. sites of Eukaryota, the green ones represent the synapomorphic s. lat. sites of Eukaryota, and the blue ones represent the potential autapomorphic sites of clades lower than Eukaryota. The magenta ribbons represent the sites related to DBA, and the sites presented by sticks and balls are also synapomorphic sites. Because there are too many synapomorphic sites according to clades lower than Eukaryota in the RP, only the synapomorphic sites related to DBA are colored in this figure (shown in orange).

Figure S2 in Natural selection on various sites of ribosomal proteins: a cladistic view

Figure S2. Conserved sites of ribosomal protein 60S subunit labeling on crystal structure. The ribbons colored in red represent the synapomorphic s. str. sites of Eukaryota, the green ones represent the synapomorphic s. lat. sites of Eukaryota and the blue ones represent the potential autapomorphic sites of clades lower than Eukaryota. The magenta ribbons represent the sites related to DBA, and the sites shown by sticks and balls are also synapomorphic sites. Because there are too many synapomorphic sites according to clades lower than Eukaryota in the RP, only the synapomorphic sites related to DBA are colored in this figure (shown in orange).

Figure 1 in Natural selection on various sites of ribosomal proteins: a cladistic view

Figure 1. Summarized distribution of group-specific sites in the cladogram of eukaryotic diversification. The numerals shown above the line correspond to RPL, and the numerals shown below correspond to RPS. The Ecdysozoa-Neoptera and Chordata-Mammalia lineages are highlighted with blue and yellow, respectively. The amino acids with equivalent biochemical properties were not taken into account.

Figure 2 in Natural selection on various sites of ribosomal proteins: a cladistic view

Figure 2. Conserved sites in the tertiary structures of RPL11 (A) and RPS19 (B). The red ribbons represent the synapomorphic s. str. sites of Eukaryota, the green ones represent the synapomorphic sites s. lat. of Eukaryota, and the blue ones represent the potential autapomorphic sites of clades lower than Eukaryota. The ribbons with sticks and balls represent sites related to DBA. The synapomorphic sites related to DBA are shown in orange. The magenta ones represent the sites for which it is difficult to deduce the synapomorphy but appear to be related to DBA.

opencc-by-4.0Jan 2022View details →

zenodo36/100

An in vivo stable isotope labeling method to investigate individual matrix protein synthesis, ribosomal biogenesis, and chondrocyte proliferation in murine articular cartilage

These experiments have used a stable-isotope method using in vivo deuterium oxide labeling and mass spectrometry to measure protein concentration, protein half-life, cell proliferation, and ribosomal biogenesis in a single sample of murine articular cartilage. We hypothesized that a 60-day labeling period would capture age-related declines in cartilage matrix protein content, protein synthesis rates, and chondrocyte proliferation. Knee cartilage was isolated from 25- and 90-week-old female C57BL/6J mice treated with deuterium oxide for 15, 30, 45 and 60 days. We measured protein abundance and half-lives using high resolution accurate mass spectrometry (HRAM) and d2ome data processing software.

dryad36/100

Ribosome demand links transcriptional bursts to protein expression noise

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publicNov 2025View details →

dryad32/100

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

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 multipass 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.

opencc-zeroNov 2020View details →

dryad32/100

The ribosome-inactivating proteins MAP30 and Momordin inhibit SARS-CoV-2

These data are related to a manuscript submitted to PLOS ONE. The recombinant proteins MAP30 and Momordin, prepared at the National Institute of Arthritis and Musculoskeletal and Skin Diseases, were analyzed for SARS-CoV-2 inhibition using A549-NLRV human lung cell assays performed at Southern Research during the Covid-19 pandemic. All viral inhibition and cell viability values reported can be derived from the raw data provided here. Some data are replicates. File dates correspond to those originally provided by and preserved at Southern Research, Birmingham AL.

opencc-zeroMay 2023View details →

opencc-by-4.0Jun 2023View details →

Adaptive preservation of orphan ribosomal proteins in chaperone-stirred condensates

Python and Fiji code used for the study "Adaptive preservation of orphan ribosomal proteins in chaperone-stirred condensates"

Fig. 4 in Phylogeny and domain architecture of plant ribosome inactivating proteins

Fig. 4. - Circular gene tree of RIPs. Our dataset comprised a curated selection from all the proteins available within NCBI's Conserved Domain Database containing a RIP domain. The phylogenetic tree was constructed using the maximum-likelihood method with the amino acid substitution model WAG + R9, ultrafast bootstrapping approximation (UFBoot) with 1000 iterations and the SH-like approximate likelihood ratio test with 1000 iterations. The legend titled 'Order (outer ring)' outlines the coloured dots around the perimeter of the tree and represents the phylogenetic order from which each protein sequence originated. Proteins without a coloured dot belong to orders with less than ten proteins. The legend titled 'RIP domains (inner lines)' defines colours in the branches of the tree, each representing a RIP group, based on presence/absence of a signal peptide and domains listed in both NCBI's Conserved Domain and Protein databases. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in Phylogeny and domain architecture of plant ribosome inactivating proteins

Fig. 2. - The number and type of RIPs within each plant order. Our dataset comprised a curated selection from all the proteins available within NCBI's Conserved Domain Database containing a RIP domain. The groups were sorted based on presence/absence of a signal peptide and domains listed in both NCBI's Conserved Domain and Protein databases. Colours represent different RIP groups. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 6 in Phylogeny and domain architecture of plant ribosome inactivating proteins

Fig. 6. Tile plot of the most conserved amino acids within RIP domains of each protein group. The Y axis depicts the amino acid and corresponding position within the pokeweed antiviral protein (protein databank: 1QCI), the X axis depicts the proteins groups. For the two pink-highlighted amino acids on the Y axis, different amino acids were present in 70% of sequences at that position but were not present in the amino acid sequence of the crystal structure. The solid blue cells represent amino acids conserved at least 70% within each RIP group and with shared identity to the reference sequence 1QCI. Patterned blue cells represent amino acids conserved at least 70% within RIP groups but without identity to 1QCI. Any amino acid positions with 70% consensus in less than three protein groups were collapsed and shaded black.

Fig. 3 in Phylogeny and domain architecture of plant ribosome inactivating proteins

Fig. 3. - The number of RIPs within each plant species. Our dataset comprised a curated selection from all the proteins available within NCBI's Conserved Domain Database containing a RIP domain. The groups were sorted based on presence/absence of a signal peptide and domains listed in both NCBI's Conserved Domain and Protein databases. Colours represent different RIP groups. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1 in Phylogeny and domain architecture of plant ribosome inactivating proteins

Fig. 1. - Physicochemical characteristics of different RIP groups. Values were calculated from the amino acid coding sequence of each protein in our dataset with the R package 'peptides' and presented on boxplot format. Our dataset comprised a curated selection from all the proteins available within NCBI's Conserved Domain Database containing a RIP domain. The groups were sorted based on presence/absence of a signal peptide and domains listed in both NCBI's Conserved Domain and Protein databases. (A) molecular weight prediction; (B) theoretical net charge prediction; (C) Boman potential protein interaction index prediction; (D) aliphatic index prediction.

Fig. 5. - The most highly conserved RIP amino acids. Our dataset comprised a in Phylogeny and domain architecture of plant ribosome inactivating proteins

Fig. 5. - The most highly conserved RIP amino acids. Our dataset comprised a curated selection from all the proteins available within NCBI's Conserved Domain Database containing a RIP domain. Colours indicate amino acids conserved in at least 70% of sequences. For the two pink-highlighted proteins, the black bolded amino acids were present in 70% of sequences at that position but were not present in the amino acid sequence of the crystal structure. (A) Sequence alignment. RIP domain consensus: the consensus sequence generated from the multiple sequence alignment in Jalview excluding gaps; 1QCI: the amino acid sequence of pokeweed antiviral protein (protein databank: 1QCI). The third line denotes the similarity in the two sequences as determined by Clustal Omega. (B) The crystal structure of 1QCI visualized in UCSF ChimeraX in surface representation; (C) mesh representation; and (D) cartoon representation. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3 in Involvement of OsRIP1, a ribosome-inactivating protein from rice, in plant defense against Nilaparvata lugens

Fig. 3. Average biomass per surviving insect. Every day of the feeding experiment, the average weight per surviving insect was determined by weighing separate feeding cages with and without the surviving insects and dividing the difference in mass by the number of insects in that cage. This was done for the three repeats per treatment and the averages and standard errors are represented. Statistical differences on day 3 are represented by asterisks (*: p ≤ 0.05, **: p ≤ 0.01, ***: p ≤ 0.001).

Fig. 2 in Involvement of OsRIP1, a ribosome-inactivating protein from rice, in plant defense against Nilaparvata lugens

Fig. 2. Effect of different concentrations of OsRIP1 compared on N. lugens survival and development. 30 insects (three cages with each 10 insects) were fed with artificial diet, supplemented with either different concentrations of OsRIP1 (0.75 μM, 1.5 μM or 3 μM), BSA (3 μM) or buffer only, for 3 days. Every day the artificial diet was refreshed, the surviving insects were counted and the developmental stage of each insect was assessed. Letters (a, b, c) denote statistical differences observed between treatments. (Jonckheere-Terpstra test with pairwise multiple comparisons, p <0.05).

Fig. 4 in Involvement of OsRIP1, a ribosome-inactivating protein from rice, in plant defense against Nilaparvata lugens

Fig. 4. Effect of OsRIP1 on translation in a cell-free transcription/translation system based on insect cell extract. The dose dependent effect of recombinant OsRIP1 on the translation of luciferase was assessed using a luminometer. Percentage of translation (= percentage of luciferase activity) is shown as a function of OsRIP1 concentration. BSA was used as a control. Data of two independent replicates are shown.

Fig. 1. Transcript levels for OsRIP1 in Involvement of OsRIP1, a ribosome-inactivating protein from rice, in plant defense against Nilaparvata lugens

Fig. 1. Transcript levels for OsRIP1 in rice shoots after high (A) or low (B) infestation with N. lugens. Expression of OsRIP1 in BPH infested seedlings was determined at different timepoints (3, 5, 6, 9 or 13 days post infestation (dpi)), relative to the transcript levels in mock treated plants. Bars represent mean expression values from three independent biological replicates (normalized to three reference genes), error bars indicate standard errors. Asterisks indicate statistically significant differences compared to expression levels in mock treated plants (*p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001).