Modular evolution of phosphorylation-based signalling systems

Phosphorylation sites are formed by protein kinases ('writers'), frequently exert their effects following recognition by phospho-binding proteins ('readers') and are removed by protein phosphatases ('erasers'). This writer-reader-eraser toolkit allows phosphorylation events to control a broad range of regulatory processes, and has been pivotal in the evolution of new functions required for the development of multi-cellular animals. The proteins that comprise this system of protein kinases, phospho-binding targets and phosphatases are typically modular in organization, in the sense that they are composed of multiple globular domains and smaller peptide motifs with binding or catalytic properties. The linkage of these binding and catalytic modules in new ways through genetic recombination, and the selection of particular domain combinations, has promoted the evolution of novel, biologically useful processes. Conversely, the joining of domains in aberrant combinations can subvert cell signalling and be causative in diseases such as cancer. Major inventions such as phosphotyrosine (pTyr)-mediated signalling that flourished in the first multi-cellular animals and their immediate predecessors resulted from stepwise evolutionary progression. This involved changes in the binding properties of interaction domains such as SH2 and their linkage to new domain types, and alterations in the catalytic specificities of kinases and phosphatases. This review will focus on the modular aspects of signalling networks and the mechanism by which they may have evolved.     

Cytokinin effects on protein synthesis of in vitro systems of higher plants

Cytokinin, N₆-(₂-isopentenyl) adenine, stimulates the proteinsynthesis of in vitro systems prepared from tobacco pith and/orone-day-old corn shoots. The maximal stimulation was found ata cytokinin concentration of 10^–7 to 10^–6 M andwas 20 to 30% higher than the control level. ¹Herrn Prof. Dr. K. Mothes fur Vollendung seines 75. Lebensjahresgewidmet. (Received September 19, 1975; )     

Cytokinin signaling

Although cytokinin plays a central role in plant development, our knowledge of the biosynthesis, distribution, perception and signal transduction of cytokinin is limited. Recent molecular-genetic studies have, however, implicated involvement of a two-component system in cytokinin signal transduction. Furthermore, new mutants with altered cytokinin responses and genes involved in cytokinin signaling have been identified.     

Cytokinin signaling

Cytokinins influence many aspects of plant growth and development. The current model for cytokinin signaling is a multi-step phosphorelay similar to the prokaryotic two-component systems that are used in responses to environmental stimuli. Recently, progress has been made in improving our understanding of the molecular mechanism that underlies cytokinin signaling. Molecular and genetic analyses of loss-of-function mutants indicate that the two-component elements that are involved in cytokinin signaling have redundant and overlapping functions. These elements regulate both the shoot and root meristems, are required for the development of fertile flowers, and modulate the response to varying nutrient levels.     

The evolution of hormonal signalling systems.

1. A comparative analysis was made of chemosignalling systems responsible for the action of hormones, hormone-like substances, pheromones, etc. in vertebrates--multicellular invertebrates--unicellular eukaryotes. Many common features revealed in structural-functional organization of the above systems give evidence of their evolutionary conservatism. 2. It was shown that some molecular components as well as signal transduction mechanisms similar to those of higher eukaryote hormonal signalling systems are present in such early organisms as bacteria. This allowed a suggestion that the roots of chemosignalling systems are likely to be found in prokaryotes. 3. The evolution of hormonal signalling systems is discussed in terms of current theories of the origin of eukaryotic cell, its organelles and components. A hypothesis is put forward about endosymbiotic genesis of these signal transduction systems in eukaryotes. 4. A possible evolutionary scenario of the formation of hormonocompetent systems is proposed with hormone-sensitive adenylate cyclase complex taken as an example.     

Predicting inter-species cross-talk in two-component signalling systems

Phosphosignalling pathways are an attractive option for the synthetic biologist looking for a wide repertoire of modular components from which to build. We demonstrate that two-component systems can be used in synthetic biology. However, their potential is limited by the fact that host cells contain many of their own phosphosignalling pathways and these may interact with, and cross-talk to, the introduced synthetic components. In this paper we also demonstrate a simple bioinformatic tool that can help predict whether interspecies cross-talk between introduced and native two-component signalling pathways will occur and show both in vitro and in vivo that the predicted interactions do take place. The ability to predict potential cross-talk prior to designing and constructing novel pathways or choosing a host organism is essential for the promise that phosphosignalling components hold for synthetic biology to be realised.     

EGF-ERBB signalling: towards the systems level

Signalling through the ERBB/HER receptors is intricately involved in human cancer and already serves as a target for several cancer drugs. Because of its inherent complexity, it is useful to envision ERBB signalling as a bow-tie-configured, evolvable network, which shares modularity, redundancy and control circuits with robust biological and engineered systems. Because network fragility is an inevitable trade-off of robustness, systems-level understanding is expected to generate therapeutic opportunities to intercept aberrant network activation.     

Volume signalling in real and robot nervous systems

Summary This paper presents recent work in computational modelling of diffusing gaseous neuromodulators in biological nervous systems. A variety of interesting and significant properties of such four dimensional neural signalling systems are demonstrated. It is shown that the morphology of the neuromodulator source plays a highly significant role in the diffusion patterns observed. The paper goes on to describe work in adaptive autonomous systems directly inspired by this: an exploration of the use of virtual diffusing modulators in robot nervous systems built from non-standard artificial neural networks. These virtual chemicals act over space and time modulating a variety of node and connection properties in the networks. A wide variety of rich dynamics are possible in such systems; in the work described here, evolutionary robotics techniques have been used to harness the dynamics to produce autonomous behaviour in mobile robots. Detailed comparative analyses of evolutionary searches, and search spaces, for robot controllers with and without the virtual gases are introduced. The virtual diffusing modulators are found to provide significant advantages.     

Cytokinin biosynthesis and interconversion

To maintain hormone homeostasis, the rate of cytokinin biosynthesis, interconversion, and degradation is regulated by enzymes in plant cells. Cytokinins can be synthesized via direct (de novo) or indirect (tRNA) pathways. In the de novo pathway, a cytokinin nucleotide is synthesized from 5'-AMP and isopentenyl pyrophosphate; a key enzyme which catalyzes this synthesis has been isolated from plant tissues, slime mold, and some microorganisms. Studies on the in vitro synthesis of the isopentenyl side chain of cytokinin in tRNA demonstrated that the isopentenyl group was derived from mevalonate, and turnover of the cytokinin-containing tRNA may serve as a minor source of free cytokinins in plant cells. The interconversion of cytokinin bases, nucleosides and nucleotides is a major feature of cytokinin metabolism; and enzymes that regulate the interconversion have been identified. The N⁶-side chain and purine moiety of cytokinins are often modified and some of the enzymes involved in the modifications have been isolated. Most of the cytokinin metabolites have been characterized but very few enzymes regulating their metabolism have been purified to homogeneity. It remains a significant challenge to isolate plant genes involved in the regulation of cytokinin biosynthesis, interconversion and degradation.     

Cytokinin biosynthesis and perception

Cytokinin has been considered to be a master regulator of plant growth and development, but only in the past several years has substantial progress been made uncovering the roles of cytokinins at various developmental stages. Recent studies on key metabolic enzymes and signaling components have contributed to understanding the basic mechanism of biosynthesis and perception of cytokinin within a whole plant body. The initial products of de novo cytokinin biosynthesis in higher plants and Agrobacterium are different, and the regulatory systems in biosynthesis and homeostasis are finely controlled and appear to be important in communicating nutrient signals to morphogenetic responses. The cytokinin receptors have largely overlapping, but still specific, functions in diverse cytokinin responses. In this review, we will specifically emphasize the biosynthesis of isoprenoid cytokinins and perception of cytokinin signals in Arabidopsis.     

Root-shoot signalling in sunflower plants with confined root systems

Sunflower plants were grown hydroponically under controlled conditions with the root systems confined in small containers. Root confinement inhibited the growth of sunflower plants as indicated by reduction in both leaf and cotyledon area and root and shoot fresh weight. This effect was more pronounced in shoots. Root confinement favored the accumulation of potassium in the roots and shoots, and the exudation of potassium and water in excised roots. Xylem sap from root confined plants inhibited cotyledon expansion as revealed by bioassay with decapited sunflower seedlings. In addition decapited control plants incubated in ABA solution also showed cotyledon growth reduction. Xylem sap ABA analysis indicated a 7-times higher concentration in root confined than control plants. Our results suggest the synthesis of a chemical signal in the roots of plants subjected to mechanical stress which can be responsible for the inhibition of plant growth.     

Evolution of signalling systems with multiple senders and receivers

Sender–receiver games are simple, tractable models of information transmission. They provide a basic setting for the study the evolution of meaning. It is possible to investigate not only the equilibrium structure of these games but also the dynamics of evolution and learning—with sometimes surprising results. Generalizations of the usual binary game to interactions with multiple senders, multiple receivers or both provide the elements of signalling networks. These can be seen as the loci of information processing, group decisions, and teamwork.     

Characterization of five novel Pseudomonas aeruginosa cell-surface signalling systems

Cell-surface signalling is a sophisticated regulatory mechanism used by Gram-negative bacteria to sense signals from outside the cell and transmit them into the cytoplasm. This regulatory system consists of an outer membrane-localized TonB-dependent receptor (TonB-dependent transducer), a cytoplasmic membrane-localized antisigma factor and an extracytoplasmic function (ECF) sigma factor. Pseudomonas aeruginosa contains 13 potential surface signalling systems of which only six have been studied in detail. In this work we have identified the regulons of five novel P. aeruginosa signalling systems. For that, the ECF sigmas PA0149, PA1912, PA2050, PA2093 and PA4896 have been overexpressed and their target gene candidates have been identified using DNA microarray, proteomic analysis, and/or lacZ reporter construct. All five ECF sigma factors control the production of one TonB-dependent transducer. Interestingly, two sigma factors, PA2050 and PA2093, regulate the synthesis of a second transducer. Furthermore, we show that although all these sigma factors seem to control putative (metal) transport systems, one of them also regulates the expression of P. aeruginosa pyocins. Finally, we also show that the PA1912-PA1911-PA1910 (designated FemI-FemR-FemA in this work) signalling system responds to the presence of the Mycobacterium siderophores mycobactin and carboxymycobactin and is involved in the utilization of these heterologous siderophores.     

Cytokinin modification of mitochondrial function

6-Benzylaminopurine, 6-(Δ²-isopentenylamino)purine, 6-furfurylaminopurine, rotenone, and antimycin A inhibited oxidation of NADH by mitochondrial sonicates or submitochondrial particles (but not by intact mitochondria) from pea (Pisum sativum L., cult. Alaska) stems and mung bean (Vigna radiata L. Wilczak) hypocotyls. The above purine cytokinins can interfere with electron transport from NADH to the cytochrome system in the inner mitochondrial membrane. Adenine did not inhibit oxidation by sonicated mitochondria, and zeatin was almost ineffective. Zeatin scarcely inhibited state 3 malate respiration by intact mitochondria, but the O-formyl and O-n-propionyl esters of zeatin and the O-acetyl ester of 2-chlorozeatin were more active. Perhaps zeatin is ineffective because it does not get into the inner membranes of the isolated mitochondria, whereas the esters and other cytokinins mentioned above do. N-4-(2-chloropyridyl)-N′-Phenylurea, which has cytokinin-like effects on plant growth and development, inhibited NADH oxidation by sonicated mitochondria. It also inhibited malate, succinate, and NADH oxidation by intact mitochondria; in contrast, the latter two oxidations were not decreased by purine cytokinins.