Abstract
Sensory domain-containing proteins that modulate levels of the intracellular second messenger cyclic diguanylate (cyclic di-GMP) have the potential to form direct regulatory links between local conditions and bacterial behaviors. Coupling the detection of external stimuli (e.g. O2, small molecule signals, or light) to the control of cyclic di-GMP-regulated activities such as swimming and matrix production allows bacteria to adapt immediately to environmental changes. Much of this coupling is mediated by Per-Arnt-Sim (PAS) domains, which are found throughout the tree of life and can bind diverse cofactors and ligands. Here, we describe selected proteins with both sensory domains and those involved in cyclic di-GMP synthesis or degradation that has been studied in diverse bacteria, focusing on PAS domains and highlighting the stimulus perception mechanisms that enable their physiological roles. We also provide an overview of the sets of proteins with both PAS and cyclic di-GMP-modulating domains in Escherichia coli and Pseudomonas aeruginosa and use structure-based modeling to predict the sensory capabilities of those that have not been characterized. More detailed models of environmental sensing and intracellular signaling will facilitate efforts to control bacterial activities in various contexts.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Römling U, Galperin MY, Gomelsky M (2013) Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev 77:1–52
Ryjenkov DA, Tarutina M, Moskvin OV, Gomelsky M (2005) Cyclic diguanylate is a ubiquitous signaling molecule in bacteria: insights into biochemistry of the GGDEF protein domain. J Bacteriol 187:1792–1798
Schmidt AJ, Ryjenkov DA, Gomelsky M (2005) The ubiquitous protein domain EAL is a cyclic diguanylate-specific phosphodiesterase: enzymatically active and inactive EAL domains. J Bacteriol 187:4774–4781
Flemming H-C, Wingender J, Szewzyk U et al (2016) Biofilms: an emergent form of bacterial life. Nat Rev Microbiol 14:563–575
Hengge R (2009) Principles of c-di-GMP signalling in bacteria. Nat Rev Microbiol 7:263–273
Ha D-G, O’Toole GA (2015) c-di-GMP and its effects on biofilm formation and dispersion: a Pseudomonas aeruginosa review. Microbiol Spectr 3:MB-0003-2014
Römling U, Galperin MY (2017) Discovery of the second messenger cyclic di-GMP. Methods Mol Biol 1657:1–8
Mulder NJ, Apweiler R, Attwood TK et al (2002) InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform 3:225–235
Möglich A, Ayers RA, Moffat K (2009) Structure and signaling mechanism of Per-ARNT-Sim domains. Structure 17:1282–1294
Galperin MY (2004) Bacterial signal transduction network in a genomic perspective. Environ Microbiol 6:552–567
Freitas TAK, Saito JA, Wan X et al (2008) Chapter 7 – Protoglobin and globin-coupled sensors. In: Ghosh A (ed) The smallest biomolecules: diatomics and their interactions with heme proteins. Elsevier, Amsterdam, pp 175–202
Anantharaman V, Aravind L (2001) The CHASE domain: a predicted ligand-binding module in plant cytokinin receptors and other eukaryotic and bacterial receptors. Trends Biochem Sci 26:579–582
Herbst S, Lorkowski M, Sarenko O et al (2018) Transmembrane redox control and proteolysis of PdeC, a novel type of c-di-GMP phosphodiesterase. EMBO J 37:e97825. https://doi.org/10.15252/embj.201797825
Henry JT, Crosson S (2011) Ligand-binding PAS domains in a genomic, cellular, and structural context. Annu Rev Microbiol 65:261–286
Finn RD, Mistry J, Schuster-Böckler B et al (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34:D247–D251
Letunic I, Bork P (2018) 20 years of the SMART protein domain annotation resource. Nucleic Acids Res 46:D493–D496
Römling U, Balsalobre C (2012) Biofilm infections, their resilience to therapy and innovative treatment strategies. J Intern Med 272:541–561
Ross P, Weinhouse H, Aloni Y et al (1987) Regulation of cellulose synthesis in Acetobacter xylinum by cyclic diguanylic acid. Nature 325:279–281
Tal R, Wong HC, Calhoon R et al (1998) Three cdg operons control cellular turnover of cyclic di-GMP in Acetobacter xylinum: genetic organization and occurrence of conserved domains in isoenzymes. J Bacteriol 180:4416–4425
Chang AL, Tuckerman JR, Gonzalez G et al (2001) Phosphodiesterase A1, a regulator of cellulose synthesis in Acetobacter xylinum, is a heme-based sensor. Biochemistry 40:3420–3426
Qi Y, Rao F, Luo Z, Liang Z-X (2009) A flavin cofactor-binding PAS domain regulates c-di-GMP synthesis in AxDGC2 from Acetobacter xylinum. Biochemistry 48:10275–10285
Delgado-Nixon VM, Gonzalez G, Gilles-Gonzalez MA (2000) Dos, a heme-binding PAS protein from Escherichia coli, is a direct oxygen sensor. Biochemistry 39:2685–2691
Tuckerman JR, Gonzalez G, Sousa EHS et al (2009) An oxygen-sensing diguanylate cyclase and phosphodiesterase couple for c-di-GMP control. Biochemistry 48:9764–9774
Sarenko O, Klauck G, Wilke FM et al (2017) More than enzymes that make or break cyclic di-GMP-local signaling in the interactome of GGDEF/EAL domain proteins of Escherichia coli. MBio 8:e01639-17. https://doi.org/10.1128/mBio.01639-17
Tagliabue A, Bopp L, Dutay J-C et al (2010) Hydrothermal contribution to the oceanic dissolved iron inventory. Nat Geosci 3:252
Donné J, Van Kerckhoven M, Maes L et al (2016) The role of the globin-coupled sensor YddV in a mature E. coli biofilm population. Biochim Biophys Acta 1864:835–839
Tuckerman JR, Gonzalez G, Gilles-Gonzalez M-A (2011) Cyclic di-GMP activation of polynucleotide phosphorylase signal-dependent RNA processing. J Mol Biol 407:633–639
Kwan BW, Osbourne DO, Hu Y et al (2015) Phosphodiesterase DosP increases persistence by reducing cAMP which reduces the signal indole. Biotechnol Bioeng 112:588–600
Friedman L, Kolter R (2004) Genes involved in matrix formation in Pseudomonas aeruginosa PA14 biofilms. Mol Microbiol 51:675–690
Jo J, Cortez KL, Cornell WC et al (2017) An orphan cbb3-type cytochrome oxidase subunit supports Pseudomonas aeruginosa biofilm growth and virulence. eLife 6:e30205
Xu KD, Stewart PS, Xia F et al (1998) Spatial physiological heterogeneity in Pseudomonas aeruginosa biofilm is determined by oxygen availability. Appl Environ Microbiol 64:4035–4039
Dietrich LEP, Okegbe C, Price-Whelan A et al (2013) Bacterial community morphogenesis is intimately linked to the intracellular redox state. J Bacteriol 195:1371–1380
Wang Y, Kern SE, Newman DK (2010) Endogenous phenazine antibiotics promote anaerobic survival of Pseudomonas aeruginosa via extracellular electron transfer. J Bacteriol 192:365–369
Dietrich LEP, Teal TK, Price-Whelan A, Newman DK (2008) Redox-active antibiotics control gene expression and community behavior in divergent bacteria. Science 321:1203–1206
Lin Y-C, Sekedat MD, Cornell WC et al (2018) Phenazines regulate Nap-dependent denitrification in Pseudomonas aeruginosa biofilms. J Bacteriol 200(9):e00031-18. https://doi.org/10.1128/JB.00031-18
Madsen JS, Lin Y-C, Squyres GR et al (2015) Facultative control of matrix production optimizes competitive fitness in Pseudomonas aeruginosa PA14 biofilm models. Appl Environ Microbiol 81:8414–8426
Okegbe C, Fields BL, Cole SJ et al (2017) Electron-shuttling antibiotics structure bacterial communities by modulating cellular levels of c-di-GMP. Proc Natl Acad Sci USA 114:E5236–E5245
Li Y, Xia H, Bai F et al (2007) Identification of a new gene PA5017 involved in flagella-mediated motility, chemotaxis and biofilm formation in Pseudomonas aeruginosa. FEMS Microbiol Lett 272:188–195
Laventie B-J, Sangermani M, Estermann F et al (2019) A surface-induced asymmetric program promotes tissue colonization by Pseudomonas aeruginosa. Cell Host Microbe 25:140–152.e6
Roy AB, Petrova OE, Sauer K (2012) The phosphodiesterase DipA (PA5017) is essential for Pseudomonas aeruginosa biofilm dispersion. J Bacteriol 194:2904–2915
Kulasekara BR, Kamischke C, Kulasekara HD et al (2013) c-di-GMP heterogeneity is generated by the chemotaxis machinery to regulate flagellar motility. eLife 2:e01402
Almblad H, Randall TE, Rich JD, et al (2019, submitted) Bacterial cyclic diguanylate signaling networks sense temperature
Elias M, Wieczorek G, Rosenne S, Tawfik DS (2014) The universality of enzymatic rate-temperature dependency. Trends Biochem Sci 39:1–7
Dhaka A, Viswanath V, Patapoutian A (2006) Trp ion channels and temperature sensation. Annu Rev Neurosci 29:135–161
Vriens J, Nilius B, Voets T (2014) Peripheral thermosensation in mammals. Nat Rev Neurosci 15:573–589
Kang K, Panzano VC, Chang EC et al (2011) Modulation of TRPA1 thermal sensitivity enables sensory discrimination in Drosophila. Nature 481:76–80
Deng Y, Schmid N, Wang C et al (2012) Cis-2-dodecenoic acid receptor RpfR links quorum-sensing signal perception with regulation of virulence through cyclic dimeric guanosine monophosphate turnover. Proc Natl Acad Sci USA 109:15479–15484
Fazli M, Almblad H, Rybtke ML et al (2014) Regulation of biofilm formation in Pseudomonas and Burkholderia species. Environ Microbiol 16:1961–1981
Schmid N, Suppiger A, Steiner E et al (2017) High intracellular c-di-GMP levels antagonize quorum sensing and virulence gene expression in Burkholderia cenocepacia H111. Microbiology 163:754–764
Waldron EJ, Snyder D, Fernandez NL et al (2019) Structural basis of DSF recognition by its receptor RpfR and its regulatory interaction with the DSF synthase RpfF. PLoS Biol 17:e3000123
Enomoto G, Nomura R, Shimada T et al (2014) Cyanobacteriochrome SesA is a diguanylate cyclase that induces cell aggregation in Thermosynechococcus. J Biol Chem 289:24801–24809
Enomoto G, Ni-Ni-Win, Narikawa R, Ikeuchi M (2015) Three cyanobacteriochromes work together to form a light color-sensitive input system for c-di-GMP signaling of cell aggregation. Proc Natl Acad Sci USA 112(26):8082–8087
Zavafer A, Cheah MH, Hillier W et al (2015) Photodamage to the oxygen evolving complex of photosystem II by visible light. Sci Rep 5:16363
Schirmer T, Jenal U (2009) Structural and mechanistic determinants of c-di-GMP signalling. Nat Rev Microbiol 7:724–735
Al-Bassam MM, Haist J, Neumann SA et al (2018) Expression patterns, genomic conservation and input into developmental regulation of the GGDEF/EAL/HD-GYP domain proteins in Streptomyces. Front Microbiol 9:2524
Dahlstrom KM, Collins AJ, Doing G et al (2018) A multimodal strategy used by a large c-di-GMP network. J Bacteriol 200:e00703-17. https://doi.org/10.1128/JB.00703-17
Gilles-Gonzalez MA, Gonzalez G, Perutz MF et al (1994) Heme-based sensors, exemplified by the kinase FixL, are a new class of heme protein with distinctive ligand binding and autoxidation. Biochemistry 33:8067–8073
Purcell EB, McDonald CA, Palfey BA, Crosson S (2010) An analysis of the solution structure and signaling mechanism of LovK, a sensor histidine kinase integrating light and redox signals. Biochemistry 49:6761–6770
Ukaegbu UE, Henery S, Rosenzweig AC (2006) Biochemical characterization of MmoS, a sensor protein involved in copper-dependent regulation of soluble methane monooxygenase. Biochemistry 45:10191–10198
Purcell EB, Siegal-Gaskins D, Rawling DC et al (2007) A photosensory two-component system regulates bacterial cell attachment. Proc Natl Acad Sci USA 104:18241–18246
Swartz TE, Tseng T-S, Frederickson MA et al (2007) Blue-light-activated histidine kinases: two-component sensors in bacteria. Science 317:1090–1093
Christie JM, Salomon M, Nozue K et al (1999) LOV (light, oxygen, or voltage) domains of the blue-light photoreceptor phototropin (nph1): binding sites for the chromophore flavin mononucleotide. Proc Natl Acad Sci USA 96:8779–8783
Liu C, Liew CW, Wong YH et al (2018) Insights into biofilm dispersal regulation from the crystal structure of the PAS-GGDEF-EAL region of RbdA from Pseudomonas aeruginosa. J Bacteriol 200:e00515-17. https://doi.org/10.1128/JB.00515-17
Kelley LA, Mezulis S, Yates CM et al (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10:845–858
Yang J, Yan R, Roy A et al (2015) The I-TASSER Suite: protein structure and function prediction. Nat Methods 12:7–8
Brunger AT (2013) CNS (Crystallography and NMR System). In: Roberts GCK (ed) Encyclopedia of biophysics. Springer, Berlin, pp 326–327
Adams PD, Afonine PV, Bunkóczi G et al (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66:213–221
McRee DE (1999) XtalView/Xfit – a versatile program for manipulating atomic coordinates and electron density. J Struct Biol 125:156–165
Schrodinger LLC (2015) The PyMOL molecular graphics system Version 1.8.0
Key J, Hefti M, Purcell EB, Moffat K (2007) Structure of the redox sensor domain of Azotobacter vinelandii NifL at atomic resolution: signaling, dimerization, and mechanism. Biochemistry 46:3614–3623
Park H, Suquet C, Satterlee JD, Kang C (2004) Insights into signal transduction involving PAS domain oxygen-sensing heme proteins from the X-ray crystal structure of Escherichia coli Dos heme domain (Ec DosH). Biochemistry 43:2738–2746
Airola MV, Huh D, Sukomon N et al (2013) Architecture of the soluble receptor Aer2 indicates an in-line mechanism for PAS and HAMP domain signaling. J Mol Biol 425:886–901
Miyatake H, Mukai M, Park SY et al (2000) Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies. J Mol Biol 301:415–431
Hengge R, Galperin MY, Ghigo J-M et al (2016) Systematic nomenclature for GGDEF and EAL domain-containing cyclic di-GMP turnover proteins of Escherichia coli. J Bacteriol 198:7–11
Pesavento C, Becker G, Sommerfeldt N et al (2008) Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli. Genes Dev 22:2434–2446
Lindenberg S, Klauck G, Pesavento C et al (2013) The EAL domain protein YciR acts as a trigger enzyme in a c-di-GMP signalling cascade in E. coli biofilm control. EMBO J 32:2001–2014
Kulasakara H, Lee V, Brencic A et al (2006) Analysis of Pseudomonas aeruginosa diguanylate cyclases and phosphodiesterases reveals a role for bis-(3′-5′)-cyclic-GMP in virulence. Proc Natl Acad Sci USA 103:2839–2844
Ha D-G, Richman ME, O’Toole GA (2014) Deletion mutant library for investigation of functional outputs of cyclic diguanylate metabolism in Pseudomonas aeruginosa PA14. Appl Environ Microbiol 80:3384–3393
Christen M, Kulasekara HD, Christen B et al (2010) Asymmetrical distribution of the second messenger c-di-GMP upon bacterial cell division. Science 328:1295–1297
Moura-Alves P, Faé K, Houthuys E et al (2014) AhR sensing of bacterial pigments regulates antibacterial defence. Nature 512:387–392
Xu N, Ahuja EG, Janning P et al (2013) Trapped intermediates in crystals of the FMN-dependent oxidase PhzG provide insight into the final steps of phenazine biosynthesis. Acta Crystallogr D Biol Crystallogr 69:1403–1413
Schulte KW, Green E, Wilz A et al (2017) Structural basis for aryl hydrocarbon receptor-mediated gene activation. Structure 25:1025–1033.e3
An S, Wu J, Zhang L-H (2010) Modulation of Pseudomonas aeruginosa biofilm dispersal by a cyclic-di-GMP phosphodiesterase with a putative hypoxia-sensing domain. Appl Environ Microbiol 76:8160–8173
Paiardini A, Mantoni F, Giardina G et al (2018) A novel bacterial l-arginine sensor controlling c-di-GMP levels in Pseudomonas aeruginosa. Proteins Struct Funct Bioinf 86:1088–1096
Sakhtah H, Koyama L, Zhang Y et al (2016) The Pseudomonas aeruginosa efflux pump MexGHI-OpmD transports a natural phenazine that controls gene expression and biofilm development. Proc Natl Acad Sci USA 113:E3538–E3547
Zhou L, Zhang L-H, Cámara M, He Y-W (2017) The DSF family of quorum sensing signals: diversity, biosynthesis, and turnover. Trends Microbiol 25:293–303
Mantoni F, Paiardini A, Brunotti P et al (2018) Insights into the GTP-dependent allosteric control of c-di-GMP hydrolysis from the crystal structure of PA0575 protein from Pseudomonas aeruginosa. FEBS J 285:3815–3834
Römling U, Galperin MY (2015) Bacterial cellulose biosynthesis: diversity of operons, subunits, products, and functions. Trends Microbiol 23:545–557
Acknowledgments
Research in the Dietrich laboratory is supported by NIH/NIAID grant R01AI103369 and an NSF CAREER award. Dr. Forouhar’s research is supported by NCI grant UR007972. Dr. Harrison’s research is supported by a Canada Research Chair and a Project Scheme Grant from the Canadian Institutes for Health Research (CIHR).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Dayton, H., Smiley, M.K., Forouhar, F., Harrison, J.J., Price-Whelan, A., Dietrich, L.E.P. (2020). Sensory Domains That Control Cyclic di-GMP-Modulating Proteins: A Critical Frontier in Bacterial Signal Transduction. In: Chou, SH., Guiliani, N., Lee, V., Römling, U. (eds) Microbial Cyclic Di-Nucleotide Signaling. Springer, Cham. https://doi.org/10.1007/978-3-030-33308-9_9
Download citation
DOI: https://doi.org/10.1007/978-3-030-33308-9_9
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-33307-2
Online ISBN: 978-3-030-33308-9
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)