Gas sensing in cells

314 Pages·2018·16.667 MB·English

by  Aono, Shigetoshi

Gas Sensing in Cells
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Metallobiology Series
Editor-in-chief:
C. David Garner, University of Nottingham, UK
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P Series editors:
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36- Stefano L. Ciurli, University of Bologna, Italy
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12 Hongzhe Sun, University of Hong Kong, China
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88 Anthony Wedd, University of Melbourne, Australia
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81 Julie Kovacs, University of Washington, USA
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0 Titles in the Series:
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10. 1: Mechanisms and Metal Involvement in Neurodegenerative Diseases
doi: 2: Binding, Transport and Storage of Metal Ions in Biological Cells
g | 3: 2-Oxoglutarate-Dependent Oxygenases
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c. 4: Heme Peroxidases
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bs.r 5: Molybdenum and Tungsten Enzymes: Biochemistry
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http://p 67:: M Moollyybbddeennuumm aanndd T uTunngsgtsetnen E nEznyzmymese: sB: ioSipneocrtgraonscico pCihce manisdt rTyheoretical
n Investigations
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17 8: Metal Chelation in Medicine
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er 2 9: Metalloenzymes in Denitrification: Applications and Environmental
ob Impacts
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3 11: Gas Sensing in Cells
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Gas Sensing in Cells
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6- Edited by
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80 Shigetoshi Aono
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1 Okazaki Institute for Integrative Bioscience, Institute for Molecular Science,
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6-
3 Preface
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0. Gas molecules are well known as substrates/products of enzymes in a variety
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oi: of biological reactions including respiration, denitrification, photosynthe-
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g | sis, methanogenesis, and several other metabolism/catabolism systems. It
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c. has become apparent that they also act as signalling molecules to regulate
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s.r their biological activities in all living organisms. In the late 1980s, nitric
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p oxide (NO) was shown to act as the mediator of endothelium-derived relax-
p:// ing factor via the activation of an NO receptor (soluble guanylate cyclase) by
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n a nitrosyl–haem complex. The Nobel Prize in Physiology or Medicine 1998
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7 was awarded jointly to Robert F. Furchgott, Louis J. Ignarro and Ferid Murad
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2 “for their discoveries concerning nitric oxide as a signalling molecule in the
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b cardiovascular system”.
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Oct In the late 1990s carbon monoxide (CO) was confirmed to act as a physio-
31 logical effector of a bacterial transcriptional regulator CooA employing haem
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o to sense CO and before that it was reported that haem acts as a molecular
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he oxygen (O ) sensor in FixL, a histidine kinase in the FixL/FixJ two-component
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bli system responsible for the regulation of O -dependent gene expression. In
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2000, haem-based O -sensors HemATs were identified in aerotaxis regulatory
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systems, which are chemotaxis signal transducer proteins directly sensing
O . Though it had been well known that molecular oxygen controls the met-
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abolic switch between respiration and fermentation in facultative anaerobes
such as Escherichia coli, the molecular mechanism of the metabolic switch
was unknown. In the 1990s and later, FNR was identified as a master switch
whose function is regulated by O . A protein-bound iron–sulfur cluster acts
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as the O sensor. Recently, it was verified that iron–sulfur clusters act as NO
2
sensors as well.

Metallobiology Series No. 11
Gas Sensing in Cells
Edited by Shigetoshi Aono
© The Royal Society of Chemistry 2018
Published by the Royal Society of Chemistry, www.rsc.org
v
View Online
vi Preface
Though the first report suggesting that ethylene functions as a plant hor-
mone dates back to 1896, developments of research on ethylene signalling
had to wait for the introduction of molecular biology techniques and the
model plant, Arabidopsis thaliana. An ethylene receptor was cloned in 1988
5 for the first time and 16 genes related to ethylene signalling have been iden-
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P0 tified in Arabidopsis thaliana. Cu(i) is proposed as the active site for sensing
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6- ethylene in ethylene receptors.
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28 The numbers of gas-sensor proteins identified and characterized are
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80 increasing partly because of the expansion of genomic data and develop-
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17 ment of experimental techniques including X-ray crystallography and cer-
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97 tain spectroscopies. Metal-containing prosthetic groups are good probes
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0. and functional relationships of active sites in gas-sensor proteins at atomic/
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oi: molecular levels. This book focuses on recent developments in research on
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g | gas sensor systems. Haem-, iron–sulfur cluster- and nonhaem iron-based
c.or gas-sensor proteins are surveyed in Chapters 2–6 and mammalian O2 and
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s.r plant ethylene signalling systems in Chapters 7 and 8, respectively.
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pu I would like to thank the authors of each of the chapters in this book for
p:// their efforts in preparing the comprehensive and up-to-date chapters. Finally,
n htt I would like to express my gratitude to Anthony G. Wedd for his encourage-
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0. Chapter 1 Overview of Gas-sensing Systems 1
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c. 1.1 Introduction 1
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p:// 1.2.1 Single-component Systems 2
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2 1.3 Prosthetic Groups Utilized to Sense Gas Molecules 7
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31 1.3.3 Nonhaem Iron Centres 9
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bli Chapter 2 Haem-based Sensors of Nitric Oxide 15
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D. E. Williams, J. T. Fischer, I. Heckler and E. M. Boon
2.1 Introduction 15
2.2 The Mammalian NO Sensor: Soluble Guanylyl
Cyclase (sGC) 17
2.3 Bacterial NO-sensing H-NOX Proteins 19
2.3.1 Discovery of the H-NOX Family 19
2.3.2 Operon Organization of H-NOX Proteins 20
2.3.3 Ligand-binding Properties of H-NOX
Proteins 21
2.3.4 Structural Characterization of H-NOX
Proteins 22

Metallobiology Series No. 11
Gas Sensing in Cells
Edited by Shigetoshi Aono
© The Royal Society of Chemistry 2018
Published by the Royal Society of Chemistry, www.rsc.org
vii
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viii Contents
2.3.5 Hydrogen Bonding Through a Tyrosine
Residue in the Distal Pocket Facilitates
Ligand Discrimination 23
2.3.6 H-NOX Haem Distortion and Its Role in
7 Signal Transduction 24
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6- Binding Leads to Haem Relaxation 26
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80 Tunnel System 29
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17 2.4 The YybT Family of Haem–PAS Domains 29
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97 2.4.1 Discovery That YybT is a Haemoprotein
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3 Family 30
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c.or 2.5.1 Characterization of E75 in Drosophila
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p:// 2.6 Haem and NO Signalling in Regulating Biofilm
n htt Formation in Pseudomonas aeruginosa 35
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ber 2.6.2 The Discovery of a Novel Bacterial
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ct NO-sensing Protein (NosP) 36
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1 2.7 DNR: Transcriptional Regulator of Denitrification 36
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on 2.7.1 Protein Structure of Inactive and Active DNR 37
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References 41
Chapter 3 Haem-based Sensors of Dioxygen 47
Hitomi Sawai and Yoshitsugu Shiro
3.1 Introduction 47
3.2 Variations in the Sensor Domain of Haem-based
O -sensor Proteins 49
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3.2.1 PAS Domain 49
3.2.2 GAF Domain 50
3.2.3 GCS Domain 50
3.3 Two-component Signal Transduction Regulated
by O Sensing 51
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3.3.1 FixL 52
3.3.2 DevS (DosS) and DosT 57
3.3.3 Af GcHK 59
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Contents ix
3.4 Aerotaxis Control for the Regulation of
Bacterial Flagellar Rotation 61
3.4.1 HemAT 62
3.4.2 Aer2 63
7 3.5 Synthesis and Hydrolysis of Nucleotide Second
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p:// 4.1 Introduction 84
n htt 4.2 Biological Production of CO 85
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20 of the Metal Clusters in Hydrogenases 85
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4.4.2 Allosteric Control of CRP as a Model
of CooA 95
4.4.3 Allosteric Control of CooA by CO 99
4.4.4 Coordination Structures of the Haem
in CooA 102
4.4.5 Redox Properties of the Haem in CooA 104
4.4.6 Spectroscopic Properties of the Haem
in CooA 105
4.4.7 Ligand Discrimination of CooA 106
4.4.8 CO-binding Kinetics of CooA 107
4.4.9 DNA Binding and Transcriptional
Activation of CooA 108
4.5 Bacterial CO-sensor Protein RcoM 110
4.5.1 PAS Domain in RcoM 110
4.5.2 Spectroscopic Properties of the PAS
Domain in RcoM 111
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x Contents
4.5.3 Coordination Structure of the Haem
in RcoM 111
4.5.4 CO-binding Kinetics of RcoM 113
4.5.5 LytTR Domain as a DNA-binding Motif 113
7 4.5.6 DNA Binding of LytTR Domain 114
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6- CLOCK 115
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28 4.6.1 Structure of CLOCK/BMAL1 bHLH-PAS
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c.or 4.7.1 Structural and Spectroscopic Properties
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n htt 4.8 Concluding Remarks 125
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1 Jason C. Crack and Nick E. Le Brun
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5.2.2 NreB 149
5.2.3 AirS 150
5.3 Iron–Sulfur Cluster Proteins that Sense Reduced
O (Reactive Oxygen Species) 150
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5.3.1 SoxR 151
5.3.2 IscR 154
5.3.3 RsrR 155
5.4 Iron–Sulfur Cluster Proteins that Sense Nitric
Oxide (NO) 156
5.4.1 NsrR 157
5.4.2 WhiB-like (Wbl) [4Fe–4S] Cluster-
containing Regulatory Protein Family
in Actinobacteria 163
5.4.3 FNR and FnrP 165
5.4.4 SoxR 166
5.4.5 Iron Regulatory Protein 1 (IRP1) 166
5.4.6 Corynebacterium glutamicum ArnR 168