Metabolic remodeling in Escherichia coli MG1655. A prophage e14‐encoded small RNA, co293, post‐transcriptionally regulates transcription factors HcaR and FadR

• Published in: The FEBS journal Vol. 287; no. 21; pp. 4767 - 4782
• Main Authors: Madikonda, Ashok Kumar, Shaikh, Akbarpasha, Khanra, Sonali, Yakkala, Harshita, Yellaboina, Sailu, Lin‐Chao, Sue, Siddavattam, Dayananda
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.11.2020
• Subjects: bacteriophage; E coli; Escherichia coli; Esterase; genomic islands; lateral gene transfer; Lipase; Metabolism; Operons; post‐transcriptional regulation; Propionic acid; Ribonucleic acid; RNA; small RNAs; Transcription factors; genomic islands; bacteriophage; post-transcriptional regulation; lateral gene transfer; small RNAs
• ISSN: 1742-464X; 1742-4658
• DOI: 10.1111/febs.15247

In previous studies, we have shown the existence of metabolic remodeling in glucose‐grown Escherichia coli MG1655 cells expressing the esterase Orf306 from the opd island of Sphingobium fuliginis. We now show that Orf306‐dependent metabolic remodeling is due to regulation of a novel small RNA (sRNA). Endogenous propionate, produced due to the esterase/lipase activity of Orf306, repressed expression of a novel E. coli sRNA, co293. This sRNA post‐transcriptionally regulates expression of the transcription factors HcaR and FadR either by inhibiting translation or by destabilizing their transcripts. Hence, repression of co293 expression elevates the levels of HcaR and FadR with consequent activation of alternative carbon catabolic pathways. HcaR activates the hca and MHP operons leading to upregulation of the phenyl propionate and hydroxy phenyl propionate (HPP) degradation pathways. Similarly, FadR stimulates the expression of the transcription factor IclR which negatively regulates the glyoxylate bypass pathway genes, aceBAK. Propionate, generated in Escherichia coli from a genomic island encoded lipase, represses the expression of phage e14 encoded small RNA, co293. Repression of co293 generated HcaR‐ and FadR‐positive background which contributed to the activation of phenyl propionate and glyoxylate pathways in E. coli.