Mining RNA‐seq data reveals the massive regulon of GcvB small RNA and its physiological significance in maintaining amino acid homeostasis in Escherichia coli
Abstract
Bacterial small RNAs regulate the expression of multiple genes through imperfect base‐pairing with target mRNAs mediated by RNA chaperone proteins such as Hfq. GcvB is the master sRNA regulator of amino acid metabolism and transport in a wide range of Gram‐negative bacteria. Recently, independent RNA‐seq approaches identified a plethora of transcripts interacting with GcvB in Escherichia coli . In this study, the compilation of RIL‐seq, CLASH, and MAPS data sets allowed us to identify GcvB targets with high accuracy. We validated 21 new GcvB targets repressed at the posttranscriptional level, raising the number of direct targets to >50 genes in E. coli . Among its multiple seed sequences, GcvB utilizes either R1 or R3 to regulate most of these targets. Furthermore, we demonstrated that both R1 and R3 seed sequences are required to fully repress the expression of gdhA, cstA , and sucC genes. In contrast, the ilvLXGMEDA polycistronic mRNA is targeted by GcvB through at least four individual binding sites in the mRNA. Finally, we revealed that GcvB is involved in the susceptibility of peptidase‐deficient E. coli strain (Δpeps) to Ala‐Gln dipeptide by regulating both Dpp dipeptide importer and YdeE dipeptide exporter via R1 and R3 seed sequences, respectively.
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BibTeX
@article{miyakoshi2026mining,
title = {{Mining RNA‐seq data reveals the massive regulon of GcvB small RNA and its physiological significance in maintaining amino acid homeostasis in Escherichia coli}},
author = {Masatoshi Miyakoshi and Haruna Okayama and Maxence Lejars and Takeshi Kanda and Yuki Tanaka and Kaori Itaya and Miki Okuno and Takehiko Itoh and Noritaka Iwai and Masaaki Wachi},
journal = {Molecular Microbiology},
year = {2026},
month = aug,
doi = {10.1111/mmi.14814},
url = {https://hal.science/hal-05732287v1},
note = {CC BY-SA 4.0},
}
RIS
TY - JOUR
TI - Mining RNA‐seq data reveals the massive regulon of GcvB small RNA and its physiological significance in maintaining amino acid homeostasis in Escherichia coli
AU - Masatoshi Miyakoshi
AU - Haruna Okayama
AU - Maxence Lejars
AU - Takeshi Kanda
AU - Yuki Tanaka
AU - Kaori Itaya
AU - Miki Okuno
AU - Takehiko Itoh
AU - Noritaka Iwai
AU - Masaaki Wachi
PY - 2026
DA - 2026/08/31
JO - Molecular Microbiology
DO - 10.1111/mmi.14814
UR - https://hal.science/hal-05732287v1
AB - Bacterial small RNAs regulate the expression of multiple genes through imperfect base‐pairing with target mRNAs mediated by RNA chaperone proteins such as Hfq. GcvB is the master sRNA regulator of amino acid metabolism and transport in a wide range of Gram‐negative bacteria. Recently, independent RNA‐seq approaches identified a plethora of transcripts interacting with GcvB in Escherichia coli . In this study, the compilation of RIL‐seq, CLASH, and MAPS data sets allowed us to identify GcvB targets with high accuracy. We validated 21 new GcvB targets repressed at the posttranscriptional level, raising the number of direct targets to >50 genes in E. coli . Among its multiple seed sequences, GcvB utilizes either R1 or R3 to regulate most of these targets. Furthermore, we demonstrated that both R1 and R3 seed sequences are required to fully repress the expression of gdhA, cstA , and sucC genes. In contrast, the ilvLXGMEDA polycistronic mRNA is targeted by GcvB through at least four individual binding sites in the mRNA. Finally, we revealed that GcvB is involved in the susceptibility of peptidase‐deficient E. coli strain (Δpeps) to Ala‐Gln dipeptide by regulating both Dpp dipeptide importer and YdeE dipeptide exporter via R1 and R3 seed sequences, respectively.
SN - 0950-382X
SN - 1365-2958
ER -