LEHNINGER PRINCIPLES OF BIOCHEMISTRY - VOL. 1. THE FOUNDATIONS OF BIOCHEMISTRY: STRUCTURE AND CATALYSIS - 2011

PART I. STRUCTURE AND CATALYSIS

12. BIOSIGNALING

12.9. Signaling in Microorganisms and Plants

Much of what we have discussed regarding signaling thus far pertains to mammalian Tissues or Cell cultures derived from them. Bacteria, archaea, eukaryotic microorganisms, and vascular plants must also respond to a multitude of external signals, such as oxygen, nutrients, light, toxic chemicals, and others. We now turn to a Brief Overview of the types of signaling systems utilized by microorganisms and plants.

Bacterial Signaling Involves Two-Component Phosphorylation Systems

The bacterium Escherichia coli responds to numerous nutrients in its environment, including sugars and Amino Acids, by moving toward them—a process propelled by one or more flagella. Membrane Proteins feature binding domains on the outer surface of The Plasma Membrane that bind specific attractants (sugars or amino acids; Fig. 12-30). Ligand binding prompts another domain on the inner surface of the plasma membrane to autophosphorylate at a His residue. This initial component of the two-component system—a receptor Histidine kinase—then catalyzes The transfer of the phosphoryl group from the His residue to an Asp residue on a second, soluble protein, the response regulator; this phosphoprotein migrates to the Base of the flagellum, relaying the signal from the membrane receptor. The flagellum is driven by a rotary motor that can propel The Cell through its environment or cause it to pause, depending on the direction of motor rotation. Information received from the receptor allows the cell to determine whether it is moving toward or away from the source of the attractant. If movement is directed toward the attractant, the response regulator instructs the cell to continue moving in a straight line; if movement is away from the attractant source, the cell abruptly tumbles to reorient itself. The repetition of this behavior results in a random walk directed toward increasing concentrations of the attractant.

Class="center">Fig. 12-30. Two-component signaling mechanism in bacterial chemotaxis. When an attractant ligand A binds to the receptor domain of a membrane-associated receptor, the protein histidine kinase in the cytosolic domain (component 1) is activated and autophosphorylates at a His residue. This phosphoryl group is subsequently transferred to an Asp residue on component 2 (either a separate protein or another domain of the receptor protein). Upon phosphorylation at Asp, component 2 migrates to the base of the flagellum, where it determines the direction of flagellar motor rotation.

Utilizing this fundamental two-component system, E. coli responds not only to sugars and amino acids but also to oxygen, Temperature fluctuations, and other environmental factors. Two-component systems are found in numerous bacteria—both Gram-positive and Gram-negative—as well as in archaea, Protozoa, and Fungi. Clearly, this signaling mechanism evolved early in cellular evolution and has been conserved ever since.

Various signaling systems utilized by animal Cells have counterparts in prokaryotes as well. As the complete genome sequences of an increasing number of diverse bacteria have become available, researchers have discovered genes encoding proteins analogous to Serine or Tyrosine Kinases, GTP-binding Ras-like proteins, and proteins containing SH3 domains. Receptor Tyr kinases have not been found in bacteria, but R-Tyr residues do occur in certain bacterial proteins, implying the existence of an enzyme capable of phosphorylating Tyr residues.

Plant Signaling Systems Contain Components Shared by Microorganisms and Mammals

Like animals, vascular plants require mechanisms for communication between tissues to coordinate and regulate GROWTH AND DEVELOPMENT; to adapt to oxygen levels, nutrients, light, and temperature; and to warn against the presence of toxic chemicals and damaging pathogens (Fig. 12-31). At least a billion years of evolution have passed since the PLANT AND ANIMAL lineages of eukaryotes diverged, and this is reflected in their signaling mechanisms: some plant signaling pathways are conserved—that is, similar to those found in animals (protein kinases, adaptor proteins, Cyclic NUCLEOTIDES, electrogenic ion pumps, and regulated Ion Channels); some resemble bacterial two-component systems; and others are unique to plants (such as light-sensing mechanisms) (Table 12-7). The Genome of the extensively studied plant Arabidopsis thaliana, for example, encodes about 1,000 protein Ser/Thr kinases, including roughly 60 MAPKs and about 400 membrane-associated receptor kinases that phosphorylate Ser or Thr residues; numerous protein Phosphatases; adaptor proteins that assemble other proteins into signaling complexes; Enzymes for the Synthesis and degradation of cyclic nucleotides; and 100 or more ion channels, including approximately 20 cyclic nucleotide-gated channels. Inositol Phospholipids and kinases that interconvert them via phosphorylation of inositol polar HEAD groups are also present.

Table 12-7. Signaling Components in Mammals, Plants, or Bacteria

Fig. 12-31. Selected stimuli that elicit responses in plants.

However, certain types of signaling proteins prevalent in animal tissues are absent in plants or represented by only a small number of genes; for example, cyclic nucleotide-dependent protein kinases (PKA and PKG) appear to be lacking. Genes for heterotrimeric G proteins and protein tyrosine kinases are far less prominent in plant genomes, and GPCR genes (the largest family in The Human Genome, ~1,000 genes) are sparsely represented. DNA-associated nuclear steroid receptors have not been detected and are likely entirely absent in plants. Although plants lack most of the widespread, common light-sensing mechanisms found in animals (such as rhodopsin with retinal as its pigment), they possess a diverse array of alternative light-perceiving systems absent in animal tissues, such as phytochromes and cryptochromes (Chapter 19).

The classes of compounds that generate signals in plants resemble certain signaling molecules found in mammals (Fig. 12-32). In place of Prostaglandins, plants synthesize jasmonates; in place of Steroid Hormones, they produce brassinosteroids. Approximately 100 diverse low-molecular-weight Peptides serve as signaling substances in plants. Both plants and animals utilize derivatives of aromatic Amino acids as signaling agents.

Fig. 12-32. Structural similarities between plant and animal signaling molecules. The plant signaling molecules jasmonate, indole-3-acetate, and brassinolide resemble the mammalian signaling molecules prostaglandin E1, serotonin, and estradiol, respectively.

Plants Detect Ethylene via a Two-Component System and a MAPK Cascade

Receptors for the gaseous plant hormone ethylene (CH₂=CH₂) show Primary Structure similarity to receptor His kinases of bacterial two-component systems and likely evolved from them. In A. thaliana, this two-component signaling system consists of a single integral protein localized in The Endoplasmic reticulum (rather than the plasma membrane). Ethylene diffuses into the cell through the plasma membrane and enters the ER. The first downstream component engaged in ethylene signaling is a protein Ser/Thr kinase (CTR1; Fig. 12-33) with a sequence homologous to Raf, a protein kinase that initiates the MAPK cascade in mammals in response to Insulin (cf. Fig. 12-15). In plants, in the absence of ethylene, the CTR kinase is active and inhibits the MAPK cascade, thereby preventing the METABOLISM/31.html">Transcription of ethylene-responsive genes. The binding of ethylene inactivates CTR1, consequently turning on the MAPK cascade, which leads to the activation of the EIN3 transcription factor. Active EIN3 stimulates the synthesis of a second transcription factor (ERF1), which in turn activates the transcription of a battery of ethylene-responsive genes; the products of these genes influence processes ranging from seed development to fruit ripening.

Fig. 12-33. Signal Transduction mechanism in plant ethylene perception. The ethylene receptor in the endoplasmic reticulum (pink) is a single-protein two-component system comprising a receptor domain (component 1) and a response regulator domain (component 2). The receptor regulates—by a mechanism not yet fully understood—The activity of CTR1, a protein kinase similar to MAPKK kinases and presumably part of a MAPK cascade. CTR1 acts as a negative regulator of the ethylene response; when CTR1 is inactive, the ethylene signal is relayed through the product of the EIN2 Gene (believed to be a nuclear envelope protein), which somehow prompts an increase in the Synthesis of the transcription factor ERF1; ERF1, in turn, stimulates the expression of genes specific to the ethylene response.

Obviously, the ethylene-signaling system in Arabidopsis species, which presumably evolved from a bacterial two-component signaling system, differs in that the His-kinase activity—which serves as component 1 in bacteria—is not essential for signal transduction in Arabidopsis.

Receptor-like protein kinases mediate signal transduction for peptides and brassinosteroids

A common motif in plant signal transduction is the involvement of receptor-like protein kinases (RLKs), which contain a single transmembrane helical segment linking an extracellular receptor domain to a cytoplasmic Ser/Thr protein kinase domain. This type of receptor plays a key role in the defense mechanism against bacterial pathogen infection (Fig. 12-34a). The signal for genes required for infection defense is the peptide flg22, which is released during The breakdown of flagellin, the major protein of the bacterial flagellum. Binding of flg22 to the ELS2 receptor in Arabidopsis triggers receptor dimerization and autophosphorylation at specific Ser and Thr residues, with the downstream effect of activating a MAPK cascade, much like the insulin signaling pathway described earlier (Fig. 12-15). The terminal kinase in this cascade activates a specific transcription factor that initiates the synthesis of defense proteins against bacterial infection. The intermediate steps between receptor phosphorylation and the MAPK cascade remain largely unknown. To terminate the response to the stimulus, a phosphoprotein phosphatase (KAPP) binds to the active receptor protein and inactivates it via dephosphorylation.

Fig. 12-34. Similarities between the signaling pathways that trigger immune responses in plants and animals, (a) In the plant Arabidopsis thaliana, the flg22 peptide—derived from the flagella of a bacterial pathogen—binds to a plasma membrane receptor, inducing receptor dimerization and triggering autophosphorylation of the cytosolic protein kinase domain at Ser and Thr residues (not Tyr). Autophosphorylation activates the receptor protein kinase, which subsequently phosphorylates downstream proteins in the pathway. The activated receptor also stimulates (via an unknown mechanism) a MAPKKK. The resulting kinase cascade leads to the phosphorylation of a nuclear protein that normally inhibits the WRKY22 and WRKY29 transcription factors; this results in inhibitor degradation, enabling the transcription factors to stimulate the expression of immune-response genes, (b) In mammals, toxic bacterial lipopolysaccharide (LPS; see Fig. 7-30) is detected by Plasma Membrane Receptors that bind to and activate a soluble protein kinase (IRAK). The principal flagellar protein of a pathogenic bacterium acts through a similar receptor to activate IRAK. IRAK then initiates two distinct MAPK cascades that terminate in The Nucleus, inducing the synthesis of proteins essential for the Immune Response. Jun, Fos, and NFkB are transcription factors.

The MAPK cascade involved in plant defense against bacterial pathogens bears a striking resemblance to the genetically determined immune response in mammals (Fig. 12-34b), which is triggered by bacterial lipopolysaccharide and mediated by Toll-like receptors (TLRs, named after the Drosophila mutant "Toll" from the German word for "mad"; TLRs were subsequently discovered in many organisms and shown to participate in Embryogenesis). Other membrane receptors employ similar mechanisms to activate the MAPK cascade, ultimately switching on transcription factors and engaging the genes required for the defense response.

It is believed that most of the several hundred RLKs in plants function in a similar manner: ligand binding induces dimerization and autophosphorylation, and the activated receptor kinases trigger subsequent reactions by phosphorylating key proteins at Ser and Thr residues.

Summary of Section 12.9 Signaling in Microorganisms and Plants

■ Bacteria and eukaryotic microorganisms possess A wide variety of Sensory systems that allow them to "sample" their environment and respond to environmental stimuli. In a two-component system, a sensor His-kinase perceives the signal and autophosphorylates a His residue, which then transfers the phosphate to an Asp residue on a response regulator protein.

■ Plants respond to numerous environmental stimuli and utilize hormones and growth factors to coordinate the development and METABOLIC ACTIVITY OF their tissues. The plant genome encodes hundreds of signaling proteins, including several that closely resemble those used for signal transduction in mammalian cells.

■ Two-component signaling mechanisms, widespread in bacteria, are found in modified forms in plants, where they serve to detect chemical signals and light.

■ Plant receptor-like kinases (RLKs) participate in the perception of diverse stimuli, including brassinosteroids, pathogen-derived peptides, and developmental signals. RLKs autophosphorylate Ser/Thr residues and subsequently activate downstream proteins, which in some cases form a MAPK cascade. The ultimate outcome of many such signals is the enhanced transcription of specific genes.