bims-micpro 2025-01-05 papers

Sci Rep. 2024 12 28. 14(1): 31186

Large-scale proteogenomics characterization of microproteins in Mycobacterium tuberculosis.

Eduardo V de Souza, Pedro F Dalberto, Adriana C Miranda, Alan Saghatelian, Antonio M Pinto, Luiz A Basso, Pablo Machado, Cristiano V Bizarro.

Tuberculosis remains a burden to this day, due to the rise of multi and extensively drug-resistant bacterial strains. The genome of Mycobacterium tuberculosis (Mtb) strain H37Rv underwent an annotation process that excluded small Open Reading Frames (smORFs), which encode a class of peptides and small proteins collectively known as microproteins. As a result, there is an overlooked part of its proteome that is a rich source of potentially essential, druggable molecular targets. Here, we employed our recently developed proteogenomics pipeline to identify novel microproteins encoded by non-canonical smORFs in the genome of Mtb using hundreds of mass spectrometry experiments in a large-scale approach. We found protein evidence for hundreds of unannotated microproteins and identified smORFs essential for bacterial survival and involved in bacterial growth and virulence. Moreover, many smORFs are co-expressed and share operons with a myriad of biologically relevant genes and play a role in antibiotic response. Together, our data presents a resource of unknown genes that play a role in the success of Mtb as a widespread pathogen.

DOI: https://doi.org/10.1038/s41598-024-82465-w

Imeta. 2024 Dec;3(6): e244

Bioprospecting of culturable marine biofilm bacteria for novel antimicrobial peptides.

Shen Fan, Peng Qin, Jie Lu, Shuaitao Wang, Jie Zhang, Yan Wang, Aifang Cheng, Yan Cao, Wei Ding, Weipeng Zhang.

Antimicrobial peptides (AMPs) have become a viable source of novel antibiotics that are effective against human pathogenic bacteria. In this study, we construct a bank of culturable marine biofilm bacteria constituting 713 strains and their nearly complete genomes and predict AMPs using ribosome profiling and deep learning. Compared with previous approaches, ribosome profiling has improved the identification and validation of small open reading frames (sORFs) for AMP prediction. Among the 80,430 expressed sORFs, 341 are identified as candidate AMPs with high probability. Most potential AMPs have less than 40% similarity in their amino acid sequence compared to those listed in public databases. Furthermore, these AMPs are associated with bacterial groups that are not previously known to produce AMPs. Therefore, our deep learning model has acquired characteristics of unfamiliar AMPs. Chemical synthesis of 60 potential AMP sequences yields 54 compounds with antimicrobial activity, including potent inhibitory effects on various drug-resistant human pathogens. This study extends the range of AMP compounds by investigating marine biofilm microbiomes using a novel approach, accelerating AMP discovery.

Keywords: Ribo‐seq; antimicrobial peptide; deep learning; marine biofilm; marine resource

DOI: https://doi.org/10.1002/imt2.244

EMBO J. 2025 Jan 02.

MCTS2 and distinct eIF2D roles in uORF-dependent translation regulation revealed by in vitro re-initiation assays.

Romane Meurs, Mara De Matos, Adrian Bothe, Nicolas Guex, Tobias Weber, Aurelio A Teleman, Nenad Ban, David Gatfield.

Ribosomes scanning from the mRNA 5' cap to the start codon may initiate at upstream open reading frames (uORFs), decreasing protein biosynthesis. Termination at a uORF can lead to re-initiation, where 40S subunits resume scanning and initiate another translation event downstream. The noncanonical translation factors MCTS1-DENR participate in re-initiation at specific uORFs, but knowledge of other trans-acting factors or uORF features influencing re-initiation is limited. Here, we establish a cell-free re-initiation assay using HeLa lysates to address this question. Comparing in vivo and in vitro re-initiation on uORF-containing reporters, we validate MCTS1-DENR-dependent re-initiation in vitro. Using this system and ribosome profiling in cells, we found that knockdown of the MCTS1-DENR homolog eIF2D causes widespread gene deregulation unrelated to uORF translation, and thus distinct to MCTS1-DENR-dependent re-initiation regulation. Additionally, we identified MCTS2, encoded by an Mcts1 retrogene, as a DENR partner promoting re-initiation in vitro, providing a plausible explanation for clinical differences associated with DENR vs. MCTS1 mutations in humans.

Keywords: DENR-MCTS1; In Vitro Translation; Re-Initiation; eIF2D; uORF

DOI: https://doi.org/10.1038/s44318-024-00347-3