The Serine Biosynthesis of Paenibacillus polymyxa WLY78 Is Regulated by the T-Box Riboswitch

Haowei Zhang,Yongbin Li,Qin Li,Sanfeng Chen

doi:10.3390/ijms22063033

Haowei Zhang, Yongbin Li + Show 2 more

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https://doi.org/10.3390/ijms22063033

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Abstract

Serine is important for nearly all microorganisms in protein and downstream amino acids synthesis, however, the effect of serine on growth and nitrogen fixation was not completely clear in many bacteria, besides, the regulatory mode of serine remains to be fully established. In this study, we demonstrated that L-serine is essential for growth and nitrogen fixation of Paenibacillus polymyxa WLY78, but high concentrations of L-serine inhibit growth, nitrogenase activity, and nifH expression. Then, we revealed that expression of the serA whose gene product catalyzes the first reaction in the serine biosynthetic pathway is regulated by the T-box riboswitch regulatory system. The 508 bp mRNA leader region upstream of the serA coding region contains a 280 bp T-box riboswitch. The secondary structure of the T-box riboswitch with several conserved features: three stem-loop structures, a 14-bp T-box sequence, and an intrinsic transcriptional terminator, is predicted. Mutation and the transcriptional leader-lacZ fusions experiments revealed that the specifier codon of serine is AGC (complementary to the anticodon sequence of tRNAser). qRT-PCR showed that transcription of serA is induced by serine starvation, whereas deletion of the specifier codon resulted in nearly no expression of serA. Deletion of the terminator sequence or mutation of the continuous seven T following the terminator led to constitutive expression of serA. The data indicated that the T-box riboswitch, a noncoding RNA segment in the leader region, regulates expression of serA by a transcription antitermination mechanism.

Highlights

Riboswitches, one type of non-coding RNAs, are genetic regulation elements commonly located in the 5 -untranslated regions (5 -UTRs) of mRNAs [1,2,3]
To test whether L-serine could be used as the sole nitrogen source for the growth of P. polymyxa WLY78, 0–10 mM L-serine was supplemented in medium lacking nitrogen source
We found that L-serine can be used as the sole nitrogen source for the growth of P. polymyxa WLY78

Summary

Introduction

Riboswitches, one type of non-coding RNAs, are genetic regulation elements commonly located in the 5 -untranslated regions (5 -UTRs) of mRNAs [1,2,3]. Many bacteria use riboswitches to detect a variety of metabolites and ions to regulate gene expression. Riboswitches consist of two functional domains, the ligand-binding aptamer domain and the downstream adjoining expression platform [4,5]. The binding of a ligand to the aptamer domain will cause conformation changes that are transduced into the expression platform domain which results in expression regulation of downstream genes [4]. The expression of methionine and cysteine biosynthesis genes is controlled by the S-box riboswitch in which S-adenosylmethionine (SAM) is the molecular effector sensed by the S-box leader RNAs during transcription [13,14]

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