Overview of Gas-sensing Systems

SHIGETOSHI AONO

1.1 Introduction

Gas molecules such as O2, NO, CO and ethylene are present in the environment and are endogenously (enzymatically) produced to act as signalling molecules in biological systems. Sensing these gas molecules is the first step in their acting as signalling molecules. Sensor proteins are usually required. Input signals generated by gas sensing have to transduce to output signals that regulate biological functions. This is achieved by biological signal-transduction systems, as described in Section 1.2.

Recognition of the cognate gas molecules is a general mechanism of functional regulation for gas-sensor proteins. This induces conformational changes in proteins that controls their activities for following signal transductions. Interaction between gas molecules and sensor proteins is essential for recognition of gas molecules. Metal-containing prosthetic groups are widely used. It is known that O2, NO, and reactive oxygen/nitrogen species react with thiol groups and nucleotides to induce biological signal transductions. However, this book will focus on metal-containing gas-sensor proteins and the signalling systems working with them. The sensor proteins discussed here are summarized in Table 1.1. The basic properties of typical prosthetic groups used by these proteins are summarized in Section 1.3. Chapters 2, 3, and 4 will cover the haem-based NO, O2, and CO sensors, respectively. Iron–sulfur cluster-based sensors will be addressed in Chapter 5, followed by Chapter 6 describing nonhaem iron-based sensors. The book also will cover mammalian O2 signalling systems and plants ethylene signalling systems in Chapters 7 and 8, respectively.

1.2 Biological Signal-transduction Systems Including Gas Sensing

1.2.1 Single-component Systems

Both the sensing and regulatory modules are required to respond to external signals including gas molecules in biological signal-transduction systems. In a single-component system, these two modules are present as separate domains in a single protein molecule. When the sensor domain senses an external signal, an intramolecular signal transduction takes place to regulate the biological function of a regulatory domain such as DNA binding, enzymatic activity, or protein–protein interaction. Transcriptional regulators whose activity is regulated by a cognate gas molecule belong to this category, where a DNA-binding domain is adopted as the regulatory domain. NO-, O2-, and CO-dependent transcriptional regulators are described in Chapters 2, 4, 5, and 6, respectively.

Proteins consisting of an enzymatic domain connected to a sensor domain are also members of the single-component systems. The enzymatic activity is regulated by external signals sensed by the sensor domains. The NO- or O2-dependent phosphodiesterases, adenylate cyclases, guanylate cyclases, or diguanylate cyclases are characterized in detail as members of single component systems that are responsible for production/degradation of nucleotide second messengers. These are discussed in Chapters 2 and 3, respectively.

1.2.2 Two-component Systems

Two-component signal-transduction systems (TCS) are widely distributed in bacteria and archaea. They are also found in reduced numbers in some eukaryotic organisms but not in the animal kingdom. The canonical TCS consists of two proteins, a sensor histidine kinase (HK) and a response regulator (RR). HKs are multidomain molecules consisting of the sensor and kinase domains. The sensor domain senses a cognate external signal, which is followed by an intramolecular signal transduction to regulate its autokinase activity. Once the kinase activity is activated upon signal sensing, a conserved histidine residue in the kinase domain of HK is phosphorylated and a phosphor-transfer reaction proceeds to phosphorylate a cognate RR. As the latter regulates their biological functions such as DNA binding, RNA binding, enzymatic activity and protein–protein interactions, the response to the cognate signals can be achieved. In Chapters 2, 3, and 5, the NO-sensing and O2-sensing HKs are described: most of them adopt the cognate RRs acting as transcriptional regulators and are responsible for this transcriptional regulation in response to NO or O2.

1.2.3 Multicomponent Systems

Chemotaxis regulatory systems consist of a network system of multiple proteins, in which a signal-transducer protein (MCP: methyl-accepting chemotaxis protein) senses a cognate external signal and Che proteins (CheA, CheB, CheR, CheW, and CheY) are responsible for signal transduction, adaptation, and control of flagellar rotation. Most MCPs are membrane-bound proteins, which consist of a ligand-binding domain (sensor domain) plus a signalling domain; these domains are connected by transmembrane helices. The MCP forms a complex with CheA and CheW at the C-terminal signalling domain; autokinase activity of CheA is activated upon ligand binding to the sensor domain in the MCP. Ligand binding will cause conformational changes in the MCP/CheA/CheW complex to activate CheA, but the detailed mechanism remains to be elucidated. Once phosphorylated CheA is formed, the phosphor-transfer reaction proceeds to phosphorylate CheY, as is the case of the canonical TCS. Then, phosphorylated CheY interacts with the motors that control the rotation of the flagella. The MCPs that sense NO or O2 are described in Chapters 2 and 3, respectively. These are located in the cytoplasm as soluble proteins as these gas molecules are freely permeable to cell membranes. Though a candidate of CO-sensing MCP, which adopts a c-type haem as a sensor module, was reported, it is not clear whether CO acts as a physiological effector.

In mammalian O2-sensing systems mediated by the hypoxia inducible factors (HIFs), a-ketoglutarate-dependent oxygenases (a-KG oxygenases) act as HIF hydroxylases to sense O2 levels. These O2-sensing and regulatory pathways consist of multiple components, as described in Chapter 7. Hydroxylation of the specific Pro and/or Asn residues in HIFa proteins are catalysed by different HIF hydroxylases for different residues and plays a crucial role for the control of the stability and activity of the HIFa. In the absence of O2 (hypoxia condition), hydroxylation of these residues does not occur, which results in the formation of an active transcriptional complex consisting of HIFa, HIFß, and p300/CBP to enhance HIF-mediated gene expression. Once the Pro residue(s) in HIFa is hydroxylated in the presence of O2 (normoxia condition), the...