Structures and mechanism of transcription initiation by bacterial ECF factors

Chengli Fang; Lingting Li; Liqiang Shen; Jing Shi; sheng wang; Yu Feng; Yu Zhang

doi:10.1093/nar/gkz470

Structures and mechanism of transcription initiation by bacterial ECF factors

Chengli Fang, Lingting Li, Liqiang Shen, Jing Shi, sheng wang, Yu Feng, Yu Zhang

Computer, Electrical and Mathematical Sciences and Engineering

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Abstract

Bacterial RNA polymerase (RNAP) forms distinct holoenzymes with extra-cytoplasmic function (ECF) σ factors to initiate specific gene expression programs. In this study, we report a cryo-EM structure at 4.0 Å of Escherichia coli transcription initiation complex comprising σE—the most-studied bacterial ECF σ factor (Ec σE-RPo), and a crystal structure at 3.1 Å of Mycobacterium tuberculosis transcription initiation complex with a chimeric σH/E (Mtb σH/E-RPo). The structure of Ec σE-RPo reveals key interactions essential for assembly of E. coli σE-RNAP holoenzyme and for promoter recognition and unwinding by E. coli σE. Moreover, both structures show that the non-conserved linkers (σ2/σ4 linker) of the two ECF σ factors are inserted into the active-center cleft and exit through the RNA-exit channel. We performed secondary-structure prediction of 27,670 ECF σ factors and find that their non-conserved linkers probably reach into and exit from RNAP active-center cleft in a similar manner. Further biochemical results suggest that such σ2/σ4 linker plays an important role in RPo formation, abortive production and promoter escape during ECF σ factors-mediated transcription initiation.

Original language	English (US)
Pages (from-to)	7094-7104
Number of pages	11
Journal	Nucleic Acids Research
Volume	47
Issue number	13
DOIs	https://doi.org/10.1093/nar/gkz470
State	Published - May 27 2019

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: We thank Prof. Richard Ebright for generous gifts of pACYC-duet-Mtb-rpoA-rpoD, pETDuet-Mtb-rpoB-rpoC, Prof. Bryce Nickels for generous gift of pET28c-Ecσ70, Prof. Xiaoming Zhang for generous gift of M. tuberculosis genomic DNA and Tolo Biotechnology for generous gift of pTolo-EX vectors. We thank the staff at beamline BL18U1/BL19U1 of National Center for Protein Science Shanghai (NCPSS), and at beamline BL17U1 of Shanghai Synchrotron Radiation Facility for assistance during data collection. We thank Shenghai Chang at center of cryo Electron Microscopy for help with cryo-EM sample preparation and data collection. We thank the state key laboratory of bio-organic and natural products chemistry at Shanghai institute of organic chemistry at CAS for sharing the stopped-flow fluorescence spectrometer

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https://repository.kaust.edu.sa/bitstream/10754/656303/1/gkz470.pdf

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@article{d3e7b99260cd4ff5b56d60a5ca1d90c2,

title = "Structures and mechanism of transcription initiation by bacterial ECF factors",

abstract = "Bacterial RNA polymerase (RNAP) forms distinct holoenzymes with extra-cytoplasmic function (ECF) σ factors to initiate specific gene expression programs. In this study, we report a cryo-EM structure at 4.0 {\AA} of Escherichia coli transcription initiation complex comprising σE—the most-studied bacterial ECF σ factor (Ec σE-RPo), and a crystal structure at 3.1 {\AA} of Mycobacterium tuberculosis transcription initiation complex with a chimeric σH/E (Mtb σH/E-RPo). The structure of Ec σE-RPo reveals key interactions essential for assembly of E. coli σE-RNAP holoenzyme and for promoter recognition and unwinding by E. coli σE. Moreover, both structures show that the non-conserved linkers (σ2/σ4 linker) of the two ECF σ factors are inserted into the active-center cleft and exit through the RNA-exit channel. We performed secondary-structure prediction of 27,670 ECF σ factors and find that their non-conserved linkers probably reach into and exit from RNAP active-center cleft in a similar manner. Further biochemical results suggest that such σ2/σ4 linker plays an important role in RPo formation, abortive production and promoter escape during ECF σ factors-mediated transcription initiation.",

author = "Chengli Fang and Lingting Li and Liqiang Shen and Jing Shi and sheng wang and Yu Feng and Yu Zhang",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: We thank Prof. Richard Ebright for generous gifts of pACYC-duet-Mtb-rpoA-rpoD, pETDuet-Mtb-rpoB-rpoC, Prof. Bryce Nickels for generous gift of pET28c-Ecσ70, Prof. Xiaoming Zhang for generous gift of M. tuberculosis genomic DNA and Tolo Biotechnology for generous gift of pTolo-EX vectors. We thank the staff at beamline BL18U1/BL19U1 of National Center for Protein Science Shanghai (NCPSS), and at beamline BL17U1 of Shanghai Synchrotron Radiation Facility for assistance during data collection. We thank Shenghai Chang at center of cryo Electron Microscopy for help with cryo-EM sample preparation and data collection. We thank the state key laboratory of bio-organic and natural products chemistry at Shanghai institute of organic chemistry at CAS for sharing the stopped-flow fluorescence spectrometer",

year = "2019",

month = may,

day = "27",

doi = "10.1093/nar/gkz470",

language = "English (US)",

volume = "47",

pages = "7094--7104",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "OXFORD UNIV PRESS",

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T1 - Structures and mechanism of transcription initiation by bacterial ECF factors

AU - Fang, Chengli

AU - Li, Lingting

AU - Shen, Liqiang

AU - Shi, Jing

AU - wang, sheng

AU - Feng, Yu

AU - Zhang, Yu

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: We thank Prof. Richard Ebright for generous gifts of pACYC-duet-Mtb-rpoA-rpoD, pETDuet-Mtb-rpoB-rpoC, Prof. Bryce Nickels for generous gift of pET28c-Ecσ70, Prof. Xiaoming Zhang for generous gift of M. tuberculosis genomic DNA and Tolo Biotechnology for generous gift of pTolo-EX vectors. We thank the staff at beamline BL18U1/BL19U1 of National Center for Protein Science Shanghai (NCPSS), and at beamline BL17U1 of Shanghai Synchrotron Radiation Facility for assistance during data collection. We thank Shenghai Chang at center of cryo Electron Microscopy for help with cryo-EM sample preparation and data collection. We thank the state key laboratory of bio-organic and natural products chemistry at Shanghai institute of organic chemistry at CAS for sharing the stopped-flow fluorescence spectrometer

PY - 2019/5/27

Y1 - 2019/5/27

N2 - Bacterial RNA polymerase (RNAP) forms distinct holoenzymes with extra-cytoplasmic function (ECF) σ factors to initiate specific gene expression programs. In this study, we report a cryo-EM structure at 4.0 Å of Escherichia coli transcription initiation complex comprising σE—the most-studied bacterial ECF σ factor (Ec σE-RPo), and a crystal structure at 3.1 Å of Mycobacterium tuberculosis transcription initiation complex with a chimeric σH/E (Mtb σH/E-RPo). The structure of Ec σE-RPo reveals key interactions essential for assembly of E. coli σE-RNAP holoenzyme and for promoter recognition and unwinding by E. coli σE. Moreover, both structures show that the non-conserved linkers (σ2/σ4 linker) of the two ECF σ factors are inserted into the active-center cleft and exit through the RNA-exit channel. We performed secondary-structure prediction of 27,670 ECF σ factors and find that their non-conserved linkers probably reach into and exit from RNAP active-center cleft in a similar manner. Further biochemical results suggest that such σ2/σ4 linker plays an important role in RPo formation, abortive production and promoter escape during ECF σ factors-mediated transcription initiation.

AB - Bacterial RNA polymerase (RNAP) forms distinct holoenzymes with extra-cytoplasmic function (ECF) σ factors to initiate specific gene expression programs. In this study, we report a cryo-EM structure at 4.0 Å of Escherichia coli transcription initiation complex comprising σE—the most-studied bacterial ECF σ factor (Ec σE-RPo), and a crystal structure at 3.1 Å of Mycobacterium tuberculosis transcription initiation complex with a chimeric σH/E (Mtb σH/E-RPo). The structure of Ec σE-RPo reveals key interactions essential for assembly of E. coli σE-RNAP holoenzyme and for promoter recognition and unwinding by E. coli σE. Moreover, both structures show that the non-conserved linkers (σ2/σ4 linker) of the two ECF σ factors are inserted into the active-center cleft and exit through the RNA-exit channel. We performed secondary-structure prediction of 27,670 ECF σ factors and find that their non-conserved linkers probably reach into and exit from RNAP active-center cleft in a similar manner. Further biochemical results suggest that such σ2/σ4 linker plays an important role in RPo formation, abortive production and promoter escape during ECF σ factors-mediated transcription initiation.

UR - http://hdl.handle.net/10754/656303

UR - https://academic.oup.com/nar/article/47/13/7094/5498757

UR - http://www.scopus.com/inward/record.url?scp=85070183151&partnerID=8YFLogxK

U2 - 10.1093/nar/gkz470

DO - 10.1093/nar/gkz470

M3 - Article

C2 - 31131408

SN - 0305-1048

VL - 47

SP - 7094

EP - 7104

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 13

ER -

Structures and mechanism of transcription initiation by bacterial ECF factors

Abstract

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