Ribosomal stalk proteins RPLP1 and RPLP2 promote biogenesis of flaviviral and cellular multi-pass transmembrane proteins
Authors/Creators
- 1. Rutgers University
- 2. The University of Texas Medical Branch at Galveston
Description
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.
Notes
The datasets from this Dryad repository should be used in conjunction with dengue_rplp1p2.Rmd in the associated GitHub repository - Dengue_RPLP1-P2
This repository contains *bam files (generated using HISAT2 mapping to human transcriptome), *h5 files generated using RiboViz, and several *tsv files.
The final directory structure should be:
| - scripts
| - data
| | - *bam
| | - *h5
| | - *tsv
| | - *csv
| | - *pos
| | - *txt
| | - *xls
| | - *gz
| - plots
File types:
Input files for the dengue_rplp1p2.Rmd script in Dengue_RPLP1-P2
- *bam files - RNA-seq and ribosome-footprinting files HISAT2 aligned to principal transcripts (human_appris_data.principal.tsv) in the transcriptome (human_dengue.gff3).
- *bai files - Index files for each of the bam files. above.
- *h5 files - Processed data from RiboViz package providing position and length specific read counts for each transcript. See more about this file format here - https://github.com/riboviz/riboviz/blob/master/docs/reference/hdf5-data.md).
- *xls file - An excel file with information about transmembrane domain regions of human proteins.
- dengue.gene_pos - Nucleotide positions of Dengue genes on the Dengue genome
- human_dengue.gff3 - Transcript annotation file with information about 5' UTR length, CDS length, and 3' UTR length. This was generated using the RiboViz package.
- human.ribo.csv - List of ribosomal proteins in the human genome
- human_appris_data.principal.txt - Principal transcript annotations for the APPRIS database
- dengue_rplp1p2.Rmd - A single R markdown notebook with all the codes for analysis and visualization of data associated with ribosome-profiling in Dengue. This file is available in the associated GitHub repository - Dengue_RPLP1-P2
- human_features.tsv - Sequence-based features of human transcripts
Output files from the dengue_rplp1p2.Rmd script in Dengue_RPLP1-P2
- all_counts.tsv - Transcript specific read counts for each condition
- all_tpms.tsv - Transcript specific TPM for each condition
- periodicity_3n.tsv - Periodicity data for ribosome profiling datasets
- polarity_data.tsv - Polarity data for ribosome footprints on human transcripts
- TPM.w.foldchange.tsv - DESeq2 and riborex fold-changes
- codon_id.tsv.gz - Position-specific codon identities for each human transcript
- codon_sp_ribodens.tsv.gz - Codon-specific ribosome densities for each human transcript
Funding provided by: National Institute of General Medical Sciences
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000057
Award Number: GM124976
Funding provided by: Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100015691
Award Number: AI089526
Funding provided by: Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100015691
Award Number: AI101431
Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: 1936046
Funding provided by: National Institute of Diabetes and Digestive and Kidney Diseases
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000062
Award Number: DK056645
Funding provided by: National Institute of Diabetes and Digestive and Kidney Diseases
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000062
Award Number: DK109714
Funding provided by: National Institute of Diabetes and Digestive and Kidney Diseases
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000062
Award Number: DK124369
Files
human.ribo.csv
Files
(7.1 GB)
| Name | Size | |
|---|---|---|
|
md5:af445535263eaaaa4ad68223465474a0
|
1.3 MB | Download |
|
md5:28ded73dd4669c389e399460ed6dccff
|
4.1 MB | Download |
|
md5:f86419abfb2d78bc8e254c8d0cdce7d1
|
40.7 MB | Download |
|
md5:1a7a96f5e89cf3356a764459714391a4
|
307.9 MB | Download |
|
md5:00f7a558ee68adc5da4d2a2546287836
|
179 Bytes | Download |
|
md5:db75004add7b2da60542db5a232ae1f5
|
3.0 MB | Download |
|
md5:118c7b7a3e200230156926cd40431e1b
|
13.5 kB | Preview Download |
|
md5:fbf572c97623ebdf500e370fcd690778
|
2.2 MB | Preview Download |
|
md5:9e5ab77f6db4028f1681a726d5737126
|
3.9 MB | Download |
|
md5:1a4ed186e653759cf64faf81231b328b
|
2.5 MB | Download |
|
md5:209b272c794e5904e2e9d62050763aa8
|
35.8 kB | Download |
|
md5:0c1010a5d85feb17d3d6948635316e8a
|
4.3 MB | Download |
|
md5:8fb460c06dbdb084692f1879e47e54b3
|
447.9 MB | Download |
|
md5:f0aedf522522ea799161d1359ebcf1b5
|
1.2 MB | Download |
|
md5:35584e1b34f68319271a69ef98a9bd00
|
180.7 MB | Download |
|
md5:c05f44d5a714925b3bfbf067b3656378
|
586.2 MB | Download |
|
md5:e0783ebea3e1b70cdacb278e393b4bbd
|
1.3 MB | Download |
|
md5:3a32cac1f53d33e50ab16a00e8bd55a0
|
183.5 MB | Download |
|
md5:acf74eb76f30f0fa8993e32aabbbc648
|
524.9 MB | Download |
|
md5:7fbfbc9593f595565a72b5304b1dc9ec
|
1.3 MB | Download |
|
md5:8fc15cb3407899852e0dffd3f294644a
|
183.0 MB | Download |
|
md5:12715ff0e423d6cf554fe28820f76d6d
|
387.9 MB | Download |
|
md5:e92fdcc6859f6b3f69f076822fe5dfdb
|
1.2 MB | Download |
|
md5:a25602252375bd3fc3e19f45ae4590d2
|
179.6 MB | Download |
|
md5:40a803a70071e325e096497737608f7f
|
523.0 MB | Download |
|
md5:3bb59dcc0369dd26789c717f48f765e1
|
1.2 MB | Download |
|
md5:0aec3338fbe033878457a3758ac8a9e8
|
182.4 MB | Download |
|
md5:4f7921ed66a22c570db395cee924eba1
|
529.7 MB | Download |
|
md5:7c9b9267253fd828955f7f0a6f28ae4c
|
1.2 MB | Download |
|
md5:b39e1cdfec30bcda67f81570d288e529
|
182.5 MB | Download |
|
md5:c23a1fbffc7c37f5d50c7860062bcbc9
|
270.9 MB | Download |
|
md5:f804c02dcf0a741adaf2497759aa4c28
|
1.3 MB | Download |
|
md5:b642366a11f6e51dd33a5b32564aa016
|
182.4 MB | Download |
|
md5:a42f811b4ea220300c3a25e8b13265dc
|
313.2 MB | Download |
|
md5:5927f63fd5ea20000a6fad14cc1681c6
|
1.3 MB | Download |
|
md5:6f0e4d1095750b3e0b559d6f82819835
|
182.3 MB | Download |
|
md5:30266ad1a9e7640eeeeb83cb75648354
|
229.2 MB | Download |
|
md5:89af69899eecc4fa9c3249deb63a479e
|
1.3 MB | Download |
|
md5:86f5985ecd0e32fdfd4ffdad1f2ef6b3
|
181.2 MB | Download |
|
md5:b36be3fa0f9d83f84d63ab2278576e08
|
145.5 MB | Download |
|
md5:83f002e49f78a66847edde2327e0f50d
|
1.3 MB | Download |
|
md5:710a18f0db95cc253ca5f5251763067c
|
177.9 MB | Download |
|
md5:17989113c69f27de0af3c32ca279fa85
|
288.0 MB | Download |
|
md5:18064dcb5577360e5d5325f2123ab051
|
1.3 MB | Download |
|
md5:a4fd139d125d17bf479ac3be534ec186
|
183.0 MB | Download |
|
md5:9f0a80c5258bbcd02a5cfe20eaab9f23
|
241.5 MB | Download |
|
md5:0c352333c7bbf89a0ab12c8d0f865b90
|
1.3 MB | Download |
|
md5:2d77ecbf98b5acbd134dc02a94328618
|
181.5 MB | Download |
|
md5:15c86900f38bc3b07c96769256f70870
|
5.0 MB | Download |
Additional details
Related works
- Is cited by
- 10.1093/nar/gkaa717 (DOI)