bims-micpro 2025-03-02 papers

Proc Natl Acad Sci U S A. 2025 Mar 04. 122(9): e2417695122

Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae.

Marco A Dueñas, Rory J Craig, Sean D Gallaher, Jeffrey L Moseley, Sabeeha S Merchant.

Advances in sequencing technology have unveiled examples of nucleus-encoded polycistrons, once considered rare. Exclusively polycistronic transcripts are prevalent in green algae, although the mechanism by which multiple polypeptides are translated from a single transcript is unknown. Here, we used bioinformatic and in vivo mutational analyses to evaluate competing mechanistic models for translation of bicistronic mRNAs in green algae. High-confidence manually curated datasets of bicistronic loci from two divergent green algae, Chlamydomonas reinhardtii and Auxenochlorella protothecoides, revealed a preference for weak Kozak-like sequences for ORF 1 and an underrepresentation of potential initiation codons before the ORF 2 start codon, which are suitable conditions for leaky ribosome scanning to allow ORF 2 translation. We used mutational analysis in A. protothecoides to test the mechanism. In vivo manipulation of the ORF 1 Kozak-like sequence and start codon altered reporter expression at ORF 2, with a weaker Kozak-like sequence enhancing expression and a stronger one diminishing it. A synthetic bicistronic dual reporter demonstrated inversely adjustable activity of green fluorescent protein expressed from ORF 1 and luciferase from ORF 2, depending on the strength of the ORF 1 Kozak-like sequence. Our findings demonstrate that translation of multiple ORFs in green algal bicistronic transcripts is consistent with episodic leaky scanning of ORF 1 to allow translation at ORF 2. This work has implications for the potential functionality of upstream open reading frames (uORFs) found across eukaryotic genomes and for transgene expression in synthetic biology applications.

Keywords: Iso-Seq; dicistronic; ribosome profiling; transgene expression; uORFs

DOI: https://doi.org/10.1073/pnas.2417695122

New Phytol. 2025 Feb 25.

A novel peptide encoded by a rice circular RNA confers broad-spectrum disease resistance in rice plants.

Xin Pan, Sipei Xu, Gehui Cao, Siping Chen, Tong Zhang, Burton B Yang, Guohui Zhou, Xin Yang.

Circular RNAs (circRNAs) are a significant class of endogenous RNAs that exert crucial biological functions in human and animal systems, but little is currently understood regarding their roles in plants. Here, we identified a circRNA originating from the back-splicing of exon 4 and exon 5 of a rice gene, OsWRKY9, and named it circ-WRKY9. It is upregulated in rice stripe mosaic virus (RSMV)-infected rice plants. Notably, circ-WRKY9 contains two open reading frames with an internal ribosome entry site. We found that circ-WRKY9 encoded a peptide of 88 amino acids (aa) and named it WRKY9-88aa. Overexpression of WRKY9-88aa suppresses RSMV infection in rice plants, with increased reactive oxygen species production. Furthermore, WRKY9-88aa enhances resistance to blast disease and bacterial leaf blight, suggesting its potential to provide broad-spectrum disease resistance. Our findings provide the first evidence of a peptide encoded by a circRNA in planta and highlight its potential application to control a wide spectrum of plant diseases.

Keywords: cell death; circular RNAs; reactive oxygen species; rice stripe mosaic virus; translation

DOI: https://doi.org/10.1111/nph.70018

Curr Gene Ther. 2025 Feb 26.

The Antimicrobial Peptide Pipeline: A Bacteria-Centric AMP Predictor.

Werner Pieter Veldsman, Qi Zhang, Qian Zhao, Lu Zhang, Zou Yuanjie.

INTRODUCTION: Antimicrobial peptides (AMPs), unlike antibiotics, are encoded in genomes. AMPs are exported from the cell after expression and translation. In the case of bacteria, the exported peptides target other microbes to give the producing bacterium a competitive edge. While AMPs are sought after for their similar antimicrobial activity to traditional antibiotics, it is difficult to predict which combinations of amino acids will confer antimicrobial activity. Many computer algorithms have been designed to predict whether a sequence of amino acids will exhibit antimicrobial activity, but the vast majority of validated AMPs in databases are still of eukaryotic origin. This defies common sense since the vast majority of life on Earth is prokaryotic.
METHODS: The antimicrobial peptide pipeline, presented here, is a bacteria-centric AMP predictor that predicts AMPs by taking design inspiration from the sequence properties of bacterial genomes with the intention to improve the detection of naturally occurring bacterial AMPs. The pipeline integrates multiple concepts of comparative biology to search for candidate AMPs at the primary, secondary, and tertiary peptide structure levels.
RESULTS: Results showed that the antimicrobial peptide pipeline identifies known AMPs that are missed by state-of-the-art AMP predictors and that the pipeline yields more AMP candidates from real bacterial genomes than from fake genomes, with the rate of AMP detection being significantly higher in the genomes of six nosocomial pathogens than in the fake genomes.
CONCLUSION: This bacteria-centric AMP pipeline enhances the detection of bacterial AMPs by incorporating sequence properties unique to bacterial genomes. It complements existing tools, addressing gaps in AMP detection and providing a promising avenue for discovering novel antimicrobial peptides.

Keywords: AMPs; antibiotics; antimicrobial peptides; bacterial peptides; functional proteomics; small open reading frames.

DOI: https://doi.org/10.2174/0115665232343790250120071445