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Dynamics of transcription–translation coordination tune bacterial indole signaling

Nature Chemical Biology volume 16, pages 440–449 (2020)Cite this article

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Abstract

Indole signaling is an important cross-species communication pathway in the mammalian gut. In bacteria, upon induction by tryptophan, the molecular sensor (tnaC) controls indole biosynthesis by precisely coordinating dynamics of the corresponding macromolecular machineries during its transcription and translation. Our understanding of this regulatory program is still limited owing to its rapid dynamic nature. To address this shortcoming, we adopted a massively parallel profiling method to quantify the responses of 1,450 synthetic tnaC variants in the presence of three concentrations of tryptophan in living bacterial cells. The resultant dataset enabled us to comprehensively probe the key intermediate states of macromolecular machineries during the transcription and translation of tnaC. We also used modeling to provide a systems-level understanding of how these critical states collectively shape the output of this regulatory program quantitatively. A similar methodology will likely apply to other poorly understood dynamics-dependent cis-regulatory elements.

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Fig. 1: FACS–seq produces a high-quality dataset.
Fig. 2: Overview of residues regulating ligand induction and the basal response of the tnaC sensor.
Fig. 3: RNAP–ribosome synchronization during transcription–translation of tnaC.
Fig. 4: Key intermediate states during transcription–translation of tnaC and dynamic modeling of macromolecule coordination.
Fig. 5: Dynamic modeling provides insight about the molecular mechanism of tnaC.
Fig. 6: The two subsections of tnaC are functionally independent and face divergent selection pressures.

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Data availability

NGS raw data from FACS–seq have been deposited in the NCBI Sequence Read Archive under BioProject PRJNA503322. Any other data or materials related to this work are available from the corresponding author upon request.

Code availability

The Python script used to process raw FACS–seq data and perform reliability test simulation can be accessed at https://github.com/wtmbiohacker/FACS_NGS.git. The custom Python script used to perform the modeling of macromolecular coordination during the tnaC sensor response can be accessed at https://github.com/wtmbiohacker/tnaC_kinetics_modeling. We also provide a comprehensive user guide to enable reuse of this code.

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Acknowledgements

We would like to thank C. Pan for support in FACS experiment. We thank C. Guan and H. Feng from the C. Zhang and H. Xing laboratories for their assistance in treatment of raw NGS data and phylogenetic analysis. We also would like to thank J. Zhang for critical discussion about the dynamic process, Q. Hu for critical discussion of structural biology and J. Liu for comments on the manuscript. This work was supported by the National Natural Science Foundation of China (NSFC21676156, to C.Z.), Tsinghua University Initiative Scientific Research Program (20161080108, to C.Z.), the National Natural Science Foundation of China (NSFC21627812, to X.-H.X.), a postdoctoral innovation support plan from the China Postdoctoral Science Foundation (to T.W.) and a postdoctoral fellowship from the Tsinghua–Peking Joint Center for Life Sciences (to T.W.).

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Author notes

  1. These authors contributed equally: Tianmin Wang, Xiang Zheng.

Authors and Affiliations

  1. Key Laboratory of Industrial Biocatalysis, Ministry of Education; Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, China

    Tianmin Wang, Xiang Zheng, Haonan Ji, Xin-Hui Xing & Chong Zhang

  2. Tsinghua–Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China

    Tianmin Wang

  3. School of Medicine, Tsinghua University, Beijing, China

    Ting-Liang Wang

  4. Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China

    Xin-Hui Xing & Chong Zhang

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Contributions

T.W. conceived the project and contributed to all computational analysis, validation experiments, data analysis, model design and preparation of the manuscript. X.Z. conceived the project, performed FACS–seq, validation experiments and data analysis, and helped write the manuscript. H.J. helped in performing validation experiments. T.L.W. helped in analysis of the TnaC–nascent peptide structure. C.Z. conceived and supervised the project, and edited the manuscript. X.-H.X. supervised the project.

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Correspondence to Tianmin Wang or Chong Zhang.

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Supplementary information

Supplementary Information

Supplementary Tables 1–9, Supplementary Figs. 1–29, Supplementary Note

Reporting Summary

Supplementary Dataset 1

The result of FACS-seq about the response of each sensor variant (mean value, u)

Supplementary Dataset 2

The result of FACS-seq about the response of each sensor variant (noise, σ)

Supplementary Dataset 3

The nucleotide sequences of the 1,450 synthetic tnaC variants used in this work

Supplementary Dataset 4

The nucleotide sequences of all collected tnaC genes from gut bacteria

Supplementary Dataset 5

The mRNA folding energy values of tnaC variants with mutations covering codon 2~9 (n = 444)

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Wang, T., Zheng, X., Ji, H. et al. Dynamics of transcription–translation coordination tune bacterial indole signaling. Nat Chem Biol 16, 440–449 (2020). https://doi.org/10.1038/s41589-019-0430-3

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