bims-micpro 2021-11-07 papers

Front Genet. 2021 ;12 713400

Small Protein Enrichment Improves Proteomics Detection of sORF Encoded Polypeptides.

Igor Fijalkowski, Marlies K R Peeters, Petra Van Damme.

With the rapid growth in the number of sequenced genomes, genome annotation efforts became almost exclusively reliant on automated pipelines. Despite their unquestionable utility, these methods have been shown to underestimate the true complexity of the studied genomes, with small open reading frames (sORFs; ORFs typically considered shorter than 300 nucleotides) and, in consequence, their protein products (sORF encoded polypeptides or SEPs) being the primary example of a poorly annotated and highly underexplored class of genomic elements. With the advent of advanced translatomics such as ribosome profiling, reannotation efforts have progressed a great deal in providing translation evidence for numerous, previously unannotated sORFs. However, proteomics validation of these riboproteogenomics discoveries remains challenging due to their short length and often highly variable physiochemical properties. In this work we evaluate and compare tailored, yet easily adaptable, protein extraction methodologies for their efficacy in the extraction and concomitantly proteomics detection of SEPs expressed in the prokaryotic model pathogen Salmonella typhimurium (S. typhimurium). Further, an optimized protocol for the enrichment and efficient detection of SEPs making use of the of amphipathic polymer amphipol A8-35 and relying on differential peptide vs. protein solubility was developed and compared with global extraction methods making use of chaotropic agents. Given the versatile biological functions SEPs have been shown to exert, this work provides an accessible protocol for proteomics exploration of this fascinating class of small proteins.

Keywords: SEPs; amphipathic polymers; peptidomics; proteomics; riboproteogenomics; sORFs

DOI: https://doi.org/10.3389/fgene.2021.713400

Math Med Biol. 2021 Oct 29. pii: dqab015. [Epub ahead of print]

A deterministic model for non-monotone relationship between translation of upstream and downstream open reading frames.

D E Andreev, P V Baranov, A Milogorodskii, D Rachinskii.

Totally asymmetric simple exclusion process (TASEP) modelling was shown to offer a parsimonious explanation for the experimentally confirmed ability of a single upstream open reading frames (uORFs) to upregulate downstream translation during the integrated stress response. As revealed by numerical simulations, the model predicts that reducing the density of scanning ribosomes upstream of certain uORFs increases the flow of ribosomes downstream. To gain a better insight into the mechanism which ensures the non-monotone relation between the upstream and downstream flows, in this work, we propose a phenomenological deterministic model approximating the TASEP model of the translation process. We establish the existence of a stationary solution featuring the decreasing density along the uORF for the deterministic model. Further, we find an explicit non-monotone relation between the upstream ribosome density and the downstream flow for the stationary solution in the limit of increasing uORF length and increasingly leaky initiation. The stationary distribution of the TASEP model, the stationary solution of the deterministic model and the explicit limit are compared numerically.

Keywords: asymptotics of stationary solution; mRNA translation regulation; modified TASEP model; ordinary differential equation model; stress resistance

DOI: https://doi.org/10.1093/imammb/dqab015

Commun Biol. 2021 Nov 02. 4(1): 1248

Proteogenomic discovery of sORF-encoded peptides associated with bacterial virulence in Yersinia pestis.

Shiyang Cao, Xinyue Liu, Yin Huang, Yanfeng Yan, Congli Zhou, Chen Shao, Ruifu Yang, Weimin Zhu, Zongmin Du, Chenxi Jia.

Plague caused by Yersinia pestis is one of the deadliest diseases. However, many molecular mechanisms of bacterial virulence remain unclear. This study engaged in the discovery of small open reading frame (sORF)-encoded peptides (SEPs) in Y. pestis. An integrated proteogenomic pipeline was established, and an atlas containing 76 SEPs was described. Bioinformatic analysis indicated that 20% of these SEPs were secreted or localized to the transmembrane and that 33% contained functional domains. Two SEPs, named SEPs-yp1 and -yp2 and encoded in noncoding regions, were selected by comparative peptidomics analysis under host-specific environments and high-salinity stress. They displayed important roles in the regulation of antiphagocytic capability in a thorough functional assay. Remarkable attenuation of virulence in mice was observed in the SEP-deleted mutants. Further global proteomic analysis indicated that SEPs-yp1 and -yp2 affected the bacterial metabolic pathways, and SEP-yp1 was associated with the bacterial virulence by modulating the expression of key virulence factors of the Yersinia type III secretion system. Our study provides a rich resource for research on Y. pestis and plague, and the findings on SEP-yp1 and SEP-yp2 shed light on the molecular mechanism of bacterial virulence.

DOI: https://doi.org/10.1038/s42003-021-02759-x

Mol Cell. 2021 Nov 04. pii: S1097-2765(21)00841-8. [Epub ahead of print]81(21): 4349-4351

APPLE and translation: When a small peptideproduced from a "non-coding RNA" matters!

Swati Mohapatra, George A Calin.

Sun et al. (2021) identified a novel translation initiation mechanism mediated through a new type of regulator named APPLE, a small peptide produced from a non-coding RNA transcript in acute myeloid leukemia, providing unforeseen opportunities for targeting the translation machinery in cancer cells.

DOI: https://doi.org/10.1016/j.molcel.2021.10.012