On 2017 Oct 26, Duke RNA Biology Journal Club commented:

We were excited to see another paper on ribosome heterogeneity from Maria Barna’s lab since their 2011 paper linking loss of a ribosomal protein (RP) with developmental phenotypes in mice PMCID: PMC4445650. In comparison, we found this paper less of a complete story but still powerful in the questions it reveals. To summarize, Shi and co-workers used a combination of selected reaction monitoring based proteomics and tandem mass tagging to identify and orthogonally validate 4 RPs as substoichiometric in tissue culture polysomes. We viewed this result as the major breakthrough in the field. The remainder of the paper looked more closely at two RPs, RPS25 and RPL10A, and their associated transcriptome. Interestingly, they found divergent enrichments within the Ribo-seq datasets associated with these proteins. We speculated, from the distinct transcriptome of these RPs, that cellular environment could play a large role in RP composition. However, instead of following up on these observations, the authors instread probe RPL10A’s function in IRES mediated translation. After performing multiple rounds of experiments with bicistronic constructs, they found this protein had the ability to interact with some - such as HCV, host-mRNAs - but not every IRES type. We discussed previous publications linking ribosomal proteins PMCID: PMC4243054 and RP PTMs PMCID: PMC2253395 to proper translation of HCV. Therefore, we found the observations in Fig 6 interesting but unsurprising and wondered how each observation pieced together in the larger picture of viral translation. This conversation brought us to the conclusion of the paper, with a noticeably short discussion section. We were left with two main unanswered questions: are these substochiometric differences ever combined or limited to one RP at a time; and does RP composition change with cell environment and location? This publication makes a big step towards answering these questions, especially with the quantitative lengths used to determine stoichiometric ratios of RPs, but we found the paper lacking in proposing a distinct in vivo role for these substoichiometric ribosomes and will look forward to follow-up publications leading to these answers.

On 2017 Oct 26, Duke RNA Biology Journal Club commented:

We were excited to see another paper on ribosome heterogeneity from Maria Barna’s lab since their 2011 paper linking loss of a ribosomal protein (RP) with developmental phenotypes in mice PMCID: PMC4445650. In comparison, we found this paper less of a complete story but still powerful in the questions it reveals. To summarize, Shi and co-workers used a combination of selected reaction monitoring based proteomics and tandem mass tagging to identify and orthogonally validate 4 RPs as substoichiometric in tissue culture polysomes. We viewed this result as the major breakthrough in the field. The remainder of the paper looked more closely at two RPs, RPS25 and RPL10A, and their associated transcriptome. Interestingly, they found divergent enrichments within the Ribo-seq datasets associated with these proteins. We speculated, from the distinct transcriptome of these RPs, that cellular environment could play a large role in RP composition. However, instead of following up on these observations, the authors instread probe RPL10A’s function in IRES mediated translation. After performing multiple rounds of experiments with bicistronic constructs, they found this protein had the ability to interact with some - such as HCV, host-mRNAs - but not every IRES type. We discussed previous publications linking ribosomal proteins PMCID: PMC4243054 and RP PTMs PMCID: PMC2253395 to proper translation of HCV. Therefore, we found the observations in Fig 6 interesting but unsurprising and wondered how each observation pieced together in the larger picture of viral translation. This conversation brought us to the conclusion of the paper, with a noticeably short discussion section. We were left with two main unanswered questions: are these substochiometric differences ever combined or limited to one RP at a time; and does RP composition change with cell environment and location? This publication makes a big step towards answering these questions, especially with the quantitative lengths used to determine stoichiometric ratios of RPs, but we found the paper lacking in proposing a distinct in vivo role for these substoichiometric ribosomes and will look forward to follow-up publications leading to these answers.