Genome-wide comparison of the His-to-Asp phosphorelay signaling components of three symbiotic genera of Rhizobia.

Histidine-to-aspartate (His-Asp) phosphorelay (or two-component) systems are very common signal transduction mechanisms that are implicated in a wide variety of cellular responses to environmental stimuli. The His-Asp phosphorelay components include "sensor histidine kinase (HK)", "phosphotransfer intermediate (HPt)", and "response regulator (RR)". With special reference to three bacterial species (Mesorhizobium loti, Bradyrhizobium japonicum, Sinorhizobium meliloti), each of which belongs to a different genera of Rhizobia, here we attempted to compile all of the His-Asp phosphorelay components in order to reveal a comparative genome-wide overview as to the His-Asp phosphorelay. It was revealed that M. loti has 47 HKs, 1 HPts, and 58 RRs; B. japonicum has 80 HKs, 3 HPts, and 91 RRs; whereas S. meliloti has 40 HKs, 1 HPt, and 58 RRs. These His-Asp phosphorelay components were extensively compiled and characterized. The resulting overview as to the His-Asp phosphorelay of Rhizobia will provide us with a basis for understanding of the fundamental mechanisms underlying interactions between plants and microorganisms (including symbiosis), as well as nitrogen fixation.     

Comparative studies of the AHP histidine-containing phosphotransmitters implicated in His-to-Asp phosphorelay in Arabidopsis thaliana

The evolutionarily-conserved histidine to aspartate (His-to-Asp) phosphorelay signal transduction is common in both prokaryotes and eukaryotes. Such a phosphorelay system is generally made up of 'a histidine (His)-kinase', 'a histidine-containing phosphotransmitter (HPt)', and 'a phospho-accepting response regulator (RR)'. In general, an HPt factor acts as an intermediate in a given multistep His-to-Asp phosphorelay. In Arabidopsis thaliana, this model higher plant has five genes (named AHP1 to AHP5), each of which seems to encode an HPt factor. Recent studies suggested that the His-to-Asp phosphorelay involving the AHP factors is at least partly implicated in signal transduction in response to cytokinin (a plant hormone). Nevertheless, the properties of AHPs have not yet been fully clarified. Here we did comparative studies of all the AHP factors, in terms of (i) expression profiles in plants, (ii) intracellular localization, (iii) ability to acquire a phosphoryl group in vitro, and (iv) ability to interact with the downstream components, ARRs (Arabidopsis response regulators). The results of this study provided us with a comprehensive view at the molecular level for understanding the functions of the AHP phosphotransmitters in the His-to-Asp phosphorelay.     

Histidine-containing phosphotransfer (HPt) signal transducers implicated in His-to-Asp phosphorelay in Arabidopsis

His to Asp phosphorelay signal transduction mechanisms involve three types of widespread signaling components: a sensor His-kinase, a response regulator, and a histidine-containing phosphotransfer (HPt) domain. In Arabidopsis, several sensor His-kinases have recently been discovered (e.g., ETR1 and CKI1) through extensive genetic studies. Furthermore, a recent search for response regulators in this higher plant revealed that it possesses a group of response regulators (ARR-series), each of which exhibits the phospho-accepting receiver function. However, no signal transducer containing the HPt domain has been reported. Here we identify three distinct Arabidopsis genes (AHP1 to AHP3), each encoding a signal transducer containing a HPt domain. Both in vivo and in vitro evidence that each AHP can function as a phospho-transmitting HPt domain with an active histidine site was obtained by employing both the Escherichia coli and yeast His-Asp phosphorelay systems. It was demonstrated that AHP1 exhibits in vivo ability to complement a mutational lesion of the yeast YPD1 gene, encoding a typical HPt domain involved in an osmosensing signal transduction. It was also demonstrated that AHPs can interact in vitro with ARRs through the His-Asp phosphotransfer reaction. It was thus suggested that the uncovered sensors-AHPs-ARRs lineups may play important roles in propagating environmental stimuli through the multistep His-Asp phosphorelay in Arabidopsis.     

Compilation and characterization of histidine-containing phosphotransmitters implicated in His-to-Asp phosphorelay in plants: AHP signal transducers of Arabidopsis thaliana

Histidine (His)-to-Aspartate (Asp) phosphorelay signal transduction systems are generally made up of a "sensor histidine (His)-kinase", a "response regulator", and a "histidine-containing phosphotransmitter (HPt)". In the higher plant, Arabidopsis thaliana, results from recent intensive studies suggested that the His-to-Asp phosphorelay mechanism is at least partly responsible for propagation of environmental stimuli, such as phytohormones (e.g. ethylene and cytokinin). Here we compiled the members of the HPt family of phosphotransmitters in Arabidopsis thaliana (AHP-series, Arabidopsis HPt phosphotransmitters), based on both database and experimental analyses, in order to provide a comprehensive basis at the molecular level for understanding the function of the AHP phosphotransmitters that are implicated in the His-to-Asp phosphorelay of higher plants.     

Two types of putative nuclear factors that physically interact with histidine-containing phosphotransfer (Hpt) domains, signaling mediators in His-to-Asp phosphorelay, in Arabidopsis thaliana

The higher plant, Arabidopsis thaliana, has a large number of genes, each of which encodes a component of His-to-Asp phosphorelay signal transduction systems. One type of such signal transducers are the histidine-containing phosphotransmitters (termed AHPs), which presumably mediate His-to-Asp phosphorelay. Here we attempted to isolate a factor or factors that interact with AHP1, AHP2 and AHP3 by means of a yeast two-hybrid system. This allowed us to identify two types of nuclear-localizing proteins. They are the members of the type-B family of response regulators (specifically, ARR1, APP2 and ARR10), and a novel protein named TCP10. The binding of ARR1 to AHP2 was also confirmed by in vitro binding assays. Moreover, dephosphorylation of AHP2 was observed in a manner dependent on ARR in vitro. A subset of AHPs appeared to also interact with a protein that contains a TCP domain, a recently proposed basic helix-loop-helix motif. Because several factors carrying the TCP domain have been implicated in the regulation of growth and development in lateral organs, the binding of TCP10 to this subset of AHPs suggests a possible linkage between the His-to-Asp phosphorelay systems and plant growth regulation.     

Possible His to Asp phosphorelay signaling in an Arabidopsis two-component system

We have so far cloned a cDNA encoding a hybrid-type histidine kinase (ATHK1), three cDNAs encoding phosphorelay intermediates (ATHP1-3), and four cDNAs encoding response regulators (ATRR1-4) from Arabidopsis thaliana. To determine which molecules constitute a His to Asp phosphorelay pathway, we examined protein-protein interactions between them using a pairwise yeast two-hybrid analysis, as an initial step. We detected a specific interaction between ATHK1 and ATHP1. We further examined protein-protein interactions between ATHP1-3 and other histidine kinases. We detected interactions between ETR1 and all ATHPs, and between CKI1 and ATHP1 or ATHP2. Interestingly, ERS1 could not interact with any ATHPs. We also examined protein-protein interactions between ATHP1-3 and ATRR1-4. The results indicated that ATHP2 could interact with ATRR4, and that ATHP3 could interact with ATRR1 or ATRR4. However, ATHP1 could not interact with any ATRRs. On the basis of these results, we discuss the possible phosphorelay networks in an Arabidopsis two-component system.     

Genetic analysis of the His-to-Asp phosphorelay implicated in mitotic cell cycle control: involvement of histidine-kinase genes of Schizosaccharomyces pombe.

Common histidine-to-aspartate (His-to-Asp) phosphorelay signaling systems involve three types of signaling components: a sensor His-kinase, a response regulator, and a histidine-containing phosphotransfer (HPt) protein. In the fission yeast Schizosaccharomyces pombe, two response regulators, Mcs4 and Prr1, have been identified, and it was shown that they are involved in signal transduction in stress responses. Furthermore, Mcs4 and Prr1 appear to be involved in mitotic cell-cycle control and meiosis, respectively. Recently we have identified Spy1 (also known as Mpr1), which encodes an HPt phosphotransmitter, and reported that Spy1, together with Mcs4, plays a role in cell cycle regulation. In this study, we identified and characterized three genes encoding histidine kinase, named Phk1, Phk2, and Phk3 (S. pombe histidine kinase) (also referred as Mak2, Mak3, and Mak1, respectively). Deletion of individual kinase genes has no apparent phenotypes but multiple deletion of these kinases showed the same phenotype of Spyl (Mpr1)-deficient cells, indicating precocious entry into M phase. These results indicated that three histidine kinases that work upstream of the HPt-transmitter, Spy1 (Mpr1), have a redundant function in cell cycle control.     

Cellular stoichiometry of the components of the chemotaxis signaling complex

The chemotactic sensory system of Escherichia coli comprises membrane-embedded chemoreceptors and six soluble chemotaxis (Che) proteins. These components form signaling complexes that mediate sensory excitation and adaptation. Previous determinations of cellular content of individual components provided differing and apparently conflicting values. We used quantitative immunoblotting to perform comprehensive determinations of cellular amounts of all components in two E. coli strains considered wild type for chemotaxis, grown in rich and minimal media. Cellular amounts varied up to 10-fold, but ratios between proteins varied no more than 30%. Thus, cellular stoichiometries were almost constant as amounts varied substantially. Calculations using those cellular stoichiometries and values for in vivo proportions of core components in complexes yielded an in vivo stoichiometry for core complexes of 3.4 receptor dimers and 1.6 CheW monomers for each CheA dimer and 2.4 CheY, 0.5 CheZ dimers, 0.08 CheB, and 0.05 CheR per complex. The values suggest a core unit of a trimer of chemoreceptor dimers, a dimer (or two monomers) of kinase CheA, and two CheW. These components may interact in extended arrays and, thus, stoichiometries could be nonintegral. In any case, cellular stoichiometries indicate that CheY could be bound to all signaling complexes and this binding would recruit essentially the entire cellular complement of unphosphorylated CheY, and also that phosphatase CheZ, methylesterase CheB, and methyltransferase CheR would be present at 1 per 2, per 14, and per 20 core complexes, respectively. These characteristic ratios will be important in quantitative treatments of chemotaxis, both experimental and theoretical.     

Cellular metabolites modulate in vivo signaling of Arabidopsis cryptochrome-1

Cryptochromes are blue-light absorbing flavoproteins with multiple signaling roles. In plants, cryptochrome (cry1, cry2) biological activity has been linked to flavin photoreduction via an electron transport chain to the protein surface comprising 3 evolutionarily conserved tryptophan residues known as the ‘Trp triad.’ Mutation of any of the Trp triad residues abolishes photoreduction in isolated cryptochrome protein in vitro and therefore had been suggested as essential for electron transfer to the flavin. However, photoreduction of the flavin in Arabidopsis cry2 proteins occurs in vivo even with mutations in the Trp triad, indicating the existence of alternative electron transfer pathways to the flavin. These pathways are potentiated by metabolites in the intracellular environment including ATP, ADP, AMP, and NADH. In the present work we extend these observations to Arabidopsis cryptochrome 1 and demonstrate that Trp triad substitution mutants at W400F and W324F positions which are not photoreduced in vitro can be photoreduced in whole cell extracts, albeit with reduced efficiency. We further show that the flavin signaling state (FADH°) is stabilized in an in vivo context. These data illustrate that in vivo modulation by metabolites in the cellular environment may play an important role in cryptochrome signaling, and are discussed with respect to possible effects on the conformation of the C-terminal domain to generate the biologically active conformational state.     

Cellular localization of Arabidopsis xyloglucan endotransglycosylase-related proteins during development and after wind stimulation.

A gene family encoding xyloglucan endotransglycosylase (XET)-related proteins exists in Arabidopsis. TCH4, a member of this family, is strongly up-regulated by environmental stimuli and encodes an XET capable of modifying cell wall xyloglucans. To investigate XET localization we generated antibodies against the TCH4 carboxyl terminus. The antibodies recognized TCH4 and possibly other XET-related proteins. These data indicate that XETs accumulate in expanding cell, at the sites of intercellular airspace formation, and at the bases of leaves, cotyledons, and hypocotyls. XETs also accumulated in vascular tissue, where cell wall modifications lead to the formation of tracheary elements and sieve tubes. Thus, XETs may function in modifying cell walls to allow growth, airspace formation, the development of vasculature, and reinforcement of regions under mechanical strain. Following wind stimulation, overall XET levels appeared to decrease in the leaves of wind-stimulated plants. However, consistent with an increase in TCH4 mRNA levels following wind, there were regions that showed increased immunoreaction, including sites around cells of the pith parenchyma, between the vascular elements, and within the epidermis. These results indicate that TCH4 may contribute to the adaptive changes in morphogenesis that occur in Arabidopsis following exposure to mechanical stimuli.     

Mutations of Arabidopsis in potential transduction and response components of the phototropic signaling pathway.

Four genetic loci were recently identified by mutations that affect phototropism in Arabidopsis thaliana (L.) Heyhn. seedlings. It was hypothesized that one of these loci, NPH1, encodes the apoprotein for a phototropic photoreceptor. All of the alleles at the other three mutant loci (nph2, nph3, and nph4) contained wild-type levels of the putative NPH1 protein and exhibited normal blue-light-dependent phosphorylation of the NPH1 protein. This indicated that the NPH2, NPH3, and NPH4 proteins likely function downstream of NPH1 photoactivation. We show here that, although the nph2, nph3, and nph4 mutants are all altered with respect to their phototropic responses, only the nph4 mutants are also altered in their gravitropic responsiveness. Thus, NPH2 and NPH3 appear to act as signal carriers in a phototropism-specific pathway, whereas NPH4 is required for both phototropism and gravitropism and thus may function directly in the differential growth response. Despite their altered phototropic responses in blue and green light as etiolated seedlings, the nph2 and nph4 mutants exhibited less dramatic mutant phenotypes as de-etiolated seedlings and when etiolated seedlings were irradiated with unilateral ultraviolet-A (UV-A) light. Examination of the phototropic responses of a mutant deficient in biologically active phytochromes, hy1-100, indicated that phytochrome transformation by UV-A light mediates an increase in phototropic responsiveness, accounting for the greater phototropic curvature of the nph2 and nph4 mutants to UV-A light than to blue light.     

Comparative Studies of the AHP Histidine-containing Phosphotransmitters Implicated in His-to-Asp Phosphorelay in Arabidopsis thaliana

The evolutionarily-conserved histidine to aspartate (His-to-Asp) phosphorelay signal transduction is common in both prokaryotes and eukaryotes. Such a phosphorelay system is generally made up of ‘a histidine (His)-kinase’, ‘a histidine-containing phosphotransmitter (HPt)’, and ‘a phospho-accepting response regulator (RR)’. In general, an HPt factor acts as an intermediate in a given multistep His-to-Asp phosphorelay. In Arabidopsis thaliana, this model higher plant has five genes (named AHP1 to AHP5), each of which seems to encode an HPt factor. Recent studies suggested that the His-to-Asp phosphorelay involving the AHP factors is at least partly implicated in signal transduction in response to cytokinin (a plant hormone). Nevertheless, the properties of AHPs have not yet been fully clarified. Here we did comparative studies of all the AHP factors, in terms of (i) expression profiles in plants, (ii) intracellular localization, (iii) ability to acquire a phosphoryl group in vitro, and (iv) ability to interact with the downstream components, ARRs (Arabidopsis response regulators). The results of this study provided us with a comprehensive view at the molecular level for understanding the functions of the AHP phosphotransmitters in the His-to-Asp phosphorelay.     

Cellular localization of Arabidopsis EARLY FLOWERING3 is responsive to light quality

Circadian clocks facilitate the coordination of physiological and developmental processes to changing daily and seasonal cycles. A hub for environmental signaling pathways in the Arabidopsis (Arabidopsis thaliana) circadian clock is the evening complex (EC), a protein complex composed of EARLY FLOWERING3 (ELF3), ELF4, and LUX ARRYTHMO (LUX). Formation of the EC depends on ELF3, a scaffold protein that recruits the other components of the EC and chromatin remodeling enzymes to repress gene expression. Regulating the cellular distribution of ELF3 is thus an important mechanism in controlling its activity. Here, we determined that the cellular and sub-nuclear localization of ELF3 is responsive to red (RL) and blue light and that these two wavelengths have apparently competitive effects on where in the cell ELF3 localizes. We further characterized the RL response, revealing that at least two RL pathways influence the cellular localization of ELF3. One of these depends on the RL photoreceptor phytochrome B (phyB), while the second is at least partially independent of phyB activity. Finally, we investigated how changes in the cellular localization of ELF3 are associated with repression of EC target-gene expression. Our analyses revealed a complex effect whereby ELF3 is required for controlling RL sensitivity of morning-phased genes, but not evening-phased genes. Together, our findings establish a previously unknown mechanism through which light signaling influences ELF3 activity.

Light signaling pathways converge on the evening complex scaffold protein EARLY FLOWERING3 by controlling its cellular and sub-cellular localization and regulating circadian clock gene expression.