Shabalina, S. A. | Search bioRxiv

bioRxiv2024

The Cryptic Bacterial Microproteome

Microproteins encoded by small open reading frames (smORFs) comprise the "dark matter" of proteomes. Although functional microproteins were identified in diverse organisms from all three domains of life, bacterial smORFs remain poorly characterized. In this comprehensive study of intergenic smORFs (ismORFs, 15-70 codons) in 5,668 bacterial genomes of the family Enterobacteriaceae, we identified 67,297 clusters of ismORFs subject to purifying selection. The ismORFs mainly code for hydrophobic, potentially transmembrane, unstructured, or minimally structured microproteins. Using AlphaFold Multimer, we predicted interactions of some of the predicted microproteins encoded by transcribed ismORFs with proteins encoded by neighboring genes, revealing the potential of microproteins to regulate the activity of various proteins, particularly, under stress. We compiled a catalog of predicted microprotein families with different levels of evidence from synteny analysis, structure prediction, and transcription and translation data. This study offers a resource for investigation of biological functions of microproteins. HighlightsO_LIThousands of previously unknown bacterial microproteins predicted C_LIO_LIMost microproteins belong to lineage-specific families, revealing unexplored diversity of bacterial proteomes C_LIO_LIComparative genome analysis suggests de novo emergence of numerous microproteins C_LIO_LIInteractions between stress-induced microproteins and known functional proteins predicted C_LIO_LIThis study provides a resource to investigate cryptic bacterial microproteomes C_LI

genomics↗

bioRxiv2022

A 3' UTR-derived small RNA connecting nitrogen and carbon metabolism in enteric bacteria

Increasing numbers of small, regulatory RNAs (sRNAs) corresponding to 3 untranslated regions (UTR) are being discovered in bacteria. One such sRNA, denoted GlnZ, corresponds to the 3 UTR of the Escherichia coli glnA mRNA encoding glutamine synthetase. Several forms of GlnZ, processed from the glnA mRNA, are detected in cells growing with limiting ammonium. GlnZ levels are regulated transcriptionally by the NtrC transcription factor and post-transcriptionally by RNase III. Consistent with the expression, E. coli cells lacking glnZ show delayed outgrowth from nitrogen starvation compared to wild type cells. Transcriptome-wide RNA-RNA interactome datasets indicated that GlnZ binds to multiple target RNAs. Immunoblot and assays of fusions confirmed GlnZ-mediated repression of glnP and sucA, encoding proteins that contribute to glutamine transport and the citric acid cycle, respectively. Although the overall sequences of GlnZ from E. coli K-12, Enterohemorrhagic E. coli and Salmonella enterica have significant differences due to various sequence insertions, all forms of the sRNA were able to regulate the two targets characterized. Together our data show that GlnZ promotes survival of E. coli under low nitrogen conditions by modulating genes that affect carbon and nitrogen flux.

microbiology↗