Physcomitrium patens pentatricopeptide repeat protein PpPPR_32 is involved in the accumulation of psaC mRNA encoding the iron sulfur protein of photosystem I.

Pentatricopeptide repeat (PPR) proteins are involved in RNA metabolism and also play a role in posttranscriptional regulation during plant organellar gene expression. Although a hundred of PPR proteins exist in the moss Physcomitrium patens, their functions are not fully understood. Here, we report the function of P-class PPR protein PpPPR_32 in P. patens. A transient expression assay using green fluorescent protein demonstrated that the N-terminal region of PpPPR_32 functions as a chloroplast-targeting transit peptide, indicating that PpPPR_32 is localized in chloroplasts. PpPPR_32 knockout mutants grew autotrophically but with reduced protonema growth and the poor formation of photosystem I (PSI) complexes. Quantitative real-time reverse transcription-polymerase chain reaction and RNA gel blot hybridization analyses revealed a significant reduction in the transcript level of the psaC gene encoding the iron sulfur protein of PSI but no alteration to the transcript levels of other PSI genes. This suggests that PpPPR_32 is specifically involved in the expression level of the psaC gene. Our results indicate that PpPPR_32 is essential for the accumulation of psaC transcript and PSI complexes.

Diurnal control of intracellular distributions of PAS-Histidine kinase 1 and its interactions with partner proteins in the moss Physcomitrium patens.

In multi-step phosphorelay (MSP) signaling, upon reception of various environmental signals, histidine kinases (HKs) induce autophosphorylation and subsequent phosphotransfer to partner histidine-containing phosphotransfer proteins (HPts). Recently, we reported that (i) two Per-Arnt-Sim (PAS) domain-containing HKs (PHK1 and PHK2) of the moss Physcomitrium (Physcomitrella) patens suppressed red light-induced branching of protonema tissue, and (ii) they interacted with partner HPts (HPt1 and HPt2) in the nucleus in the dark while cytoplasmic interactions also occurred under red light. Here we demonstrate that PHK1 is diurnally regulated, i.e., it is localized and interacts with HPt1 and HPt2 in the nucleus at night whereas these activities reversibly expand and become nucleocytoplasmic in the day. In the dark, PHK1 interacts with HPts only in the nucleus, even in subjective daytime, indicating that endogenous regulation by the circadian clock is not involved. These results suggest that PHK1 is a regulator of moss' adaptation to a light environment on a daily timescale. We discuss a possible regulatory mechanism for the branching of protonema.

Red light-regulated interaction of Per-Arnt-Sim histidine kinases with partner histidine-containing phosphotransfer proteins in Physcomitrium patens.

Multi-step phosphorelay (MSP) is a broadly distributed signaling system in organisms. In MSP, histidine kinases (HKs) receive various environmental signals and transmit them by autophosphorylation followed by phosphotransfer to partner histidine-containing phosphotransfer proteins (HPts). Previously, we reported that Per-Arnt-Sim (PAS) domain-containing HK1 (PHK1) and PHK2 of the moss Physcomitrium (Physcomitrella) patens repressed red light-induced protonema branching, a critical step in the moss life cycle. In plants, PHK homolog-encoding genes are conserved only in early-diverging lineages such as bryophytes and lycophytes. PHKs-mediated signaling machineries attract attention especially from an evolutionary viewpoint, but they remain uninvestigated. Here, we studied the P. patens PHKs focusing on their subcellular patterns of localization and interaction with HPts. Yeast two-hybrid analysis, a localization assay with a green fluorescent protein, and a bimolecular fluorescence complementation analysis together showed that PHKs are localized and interact with partner HPts mostly in the nucleus, as unprecedented features for plant HKs. Additionally, red light triggered the interactions between PHKs and HPts in the cytoplasm, and light co-repressed the expression of PHK1 and PHK2 as well as genes encoding their partner HPts. Our results emphasize the uniqueness of PHKs-mediated signaling machineries, and functional implications of this uniqueness are discussed.

Bioluminescence burst caused by a process in carbohydrate metabolism in a luciferase reporter strain of Escherichia coli.

We previously reported that Escherichia coli strains carrying a firefly luciferase reporter gene (luc+) showed a posttranslationally-generated bioluminescence burst upon entry into the stationary phase. In this paper, we studied the mechanism underpinning this burst by using a series of "Keio" gene deletion strains. When luc+ driven by the lac gene promoter (lacp::luc+) was introduced into a group of Keio strains, the resulting reporter strains showed significantly altered timing and/or sizes of the burst. Remarkably, a reporter strain that lacked phosphoglucose isomerase (PGI), which catalyzes the second step of glycolysis, showed no burst, while the onset of the stationary phase of this strain was the same as that of the wild-type (WT) reporter strain. Consistently, the WT reporter strain showed no burst, when grown on arabinose or xylose instead of glucose as the carbon source. These results suggest that a process in carbohydrate metabolism is involved in the mechanism of generation of the burst. We measured temporal changes in intracellular NADPH concentrations but could not detect a significant increase or decrease relative to the occurrence of the burst. Functional implications and possible applications of the burst are discussed.

PAS-histidine kinases PHK1 and PHK2 exert oxygen-dependent dual and opposite effects on gametophore formation in the moss Physcomitrella patens.

Two-component systems, versatile signaling mechanisms based on phosphate transfer between component proteins, must have played important roles in adaptation and diversification processes in land plant evolution. We previously demonstrated that two Per-Arnt-Sim (PAS)-histidine kinases, PHK1 and PHK2, repress gametophore formation in the moss Physcomitrella patens under aerobic conditions, and that, in eukaryotes, the presence of their homologs is restricted to early-diverging streptophyte linages. We assessed here whether or not PHKs play a role in oxygen signaling. When submerged under water, the double disruption line for PHK1 and PHK2 formed fewer gametophores than the wild-type line (WT) both under light-dark cycles or continuous light, indicating that PHKs promote gametophore formation under an aquatic environment, in contrast to aerobic conditions. Similarly, in an artificial low-oxygen condition, the double disruption line formed fewer gametophores than WT. These results indicate that PHKs exert dual and opposite effects on gametophore formation depending on oxygen status. This study adds important insight into functional versatility and evolutionary significance of two-component systems in land plants.

Light-regulated PAS-containing histidine kinases delay gametophore formation in the moss Physcomitrella patens.

Two-component systems (TCSs) are signal transduction mechanisms for responding to various environmental stimuli. In angiosperms, TCSs involved in phytohormone signaling have been intensively studied, whereas there are only a few reports on TCSs in basal land plants. The moss Physcomitrella patens possesses several histidine kinases (HKs) that are lacking in seed plant genomes. Here, we studied two of these unique HKs, PAS-histidine kinase 1 (PHK1) and its paralog PHK2, both of which have PAS (Per-Arnt-Sim) domains, which are known to show versatile functions such as sensing light or molecular oxygen. We found homologs of PHK1 and PHK2 only in early diverged clades such as bryophytes and lycophytes, but not in seed plants. The PAS sequences of PHK1 and PHK2 are more similar to a subset of bacterial PAS sequences than to any angiosperm PAS sequences. Gene disruption lines that lack either PHK1 or PHK2 or both formed gametophores earlier than the wild-type, and consistently, more caulonema side branches were induced in response to light in the disruption lines. Therefore, PHK1 and PHK2 delay the timing of gametophore development, probably by suppressing light-induced caulonema branching. This study provides new insights into the evolution of TCSs in plants.

Posttranslationally caused bioluminescence burst of the Escherichia coli luciferase reporter strain.

We continuously monitored bioluminescence from a wild-type reporter strain of Escherichia coli (lacp::luc+/WT), which carries the promoter of the lac operon (lacp) fused with the firefly luciferase gene (luc+). This strain showed a bioluminescence burst when shifted into the stationary growth phase. Bioluminescence profiles of other wild-type reporter strains (rpsPp::luc+ and argAp::luc+) and gene-deletion reporter strains (lacp::luc+/crp- and lacp::luc+/lacI-) indicate that transcriptional regulation is not responsible for generation of the burst. Consistently, changes in the luciferase protein levels did not recapitulate the profile of the burst. On the other hand, dissolved oxygen levels increased over the period across the burst, suggesting that the burst is, at least partially, caused by an increase in intracellular oxygen levels. We discuss limits of the firefly luciferase when used as a reporter for gene expression and its potential utility for monitoring metabolic changes in cells.

Firefly luciferase as the reporter for transcriptional response to the environment in Escherichia coli.

We demonstrate that firefly luciferase is a good reporter in Escherichia coli for transcription dynamics in response to the environment. E. coli strains, carrying a fusion of the promoter of the ycgZ gene and the coding region of the luciferase gene, showed transient bioluminescence on receiving blue light. This response was compromised in mutants lacking known regulators in manners consistent with each regulator's function. We also show that relA, a gene encoding a (p)ppGpp synthetase, affects ycgZ dynamics when nullified. Moreover, two unstable luciferase variants showed improved response dynamics and should be useful to study quick changes of gene expression.

Quantification of cyanobacterial cyclic di-guanosine monophosphate (c-di-GMP) by liquid chromatography electrospray ionization tandem mass spectrometry.

Cyclic di-guanosine monophosphate (c-di-GMP) is a second messenger found ubiquitously in bacteria. This signaling molecule regulates a variety of physiological activities such as phototaxis and flocculation in cyanobacteria and is critical for their environmental adaptation. Although genes encoding the enzymes for synthesis and/or degradation of c-di-GMP are found in the genomes of both multicellular and unicellular cyanobacteria, little is known about the biological functions of these enzymes in cyanobacterial cells. Here we have established a robust and highly sensitive liquid chromatography tandem mass spectrometry (LC-MS/MS)-based method for c-di-GMP quantification using a cost-effective solvent, methanol. Quantification methods were validated by measuring c-di-GMP in the cyanobacterium Synechococcus elongatus PCC 7942 through spiking and recovery assays after which the method was applied to examine short-term changes in cellular levels of c-di-GMP in response to a transition from light to dark or from dark to light in S. elongatus. Results showed that a transient increase in c-di-GMP upon transitioning from light to dark was occurring which resembled responses involving cyclic adenosine monophosphate and other second messengers in cyanobacteria. These findings demonstrated that our method enabled relatively specific and sensitive quantification of c-di-GMP in cyanobacteria at lower cost.

Heterologous expression and functional characterization of a Physcomitrella Pseudo response regulator homolog, PpPRR2, in Arabidopsis.

Physcomitrella patens has four homologs of the pseudo-response regulator involved in the circadian clock mechanism in seed plants. To gain insight into their function, Arabidopsis transgenic lines misexpressing PpPRR2 were constructed. Phenotypic analysis of the transformants with reference to clock-related gene expression and photoperiodic responses revealed that heterologous expression of the moss PpPRR2 gene modifies the intrinsic mechanism underlying the circadian clock in Arabidopsis, suggesting that PpPRR2 serves as a clock component in P. patens.

Functional characterization of CCA1/LHY homolog genes, PpCCA1a and PpCCA1b, in the moss Physcomitrella patens.

The evolution of circadian clocks in land plants is not understood, because circadian rhythms have received little attention in plants other than angiosperms. We have characterized two genes, PpCCA1a and PpCCA1b, homologs of the Arabidopsis thaliana clock genes CCA1/LHY, from the moss Physcomitrella patens. PpCCA1a and PpCCA1b, together with angiosperm CCA1/LHY homologs, belong to the clock-associated single-myb gene family of green plants (including green algae and land plants). The accumulation of PpCCA1a and PpCCA1b mRNA showed rhythms with a period of approximately 1 day, phased as are those of angiosperm homologs, under 24 h light/dark cycles or in continuous dark. However, in marked contrast to angiosperm homologs, both genes showed arrhythmic profiles in continuous light. The timing of the PpCCA1b peak is determined by the time of the last light to dark transition, suggesting that the arrhythmicity in continuous light is due to dysfunction of the core clock. We generated single and double disruptants for PpCCA1a and PpCCA1b, and found that the double disruptants showed: (i) short periodicity and damped amplitude in the PpCCA1b rhythm, (ii) similar changes in the rhythmically expressed genes PpSIG5 and PpPRRa, and (iii) de-repression of PpCCA1b transcription levels, indicating negative feedback regulation. These observations indicate that the two genes are not merely structural homologs but also functional counterparts of CCA1/LHY. Together, our results illustrate similarities as well as divergence of the clock machineries between P. patens and A. thaliana, two distantly placed species in land plant phylogeny.

Photoperiod-dependent regulation of cell growth by PpCCA1a and PpCCA1b genes encoding single-myb clock proteins in the moss Physcomitrella patens.

The PpCCA1a and PpCCA1b genes of the moss Physcomitrella patens are functional homologs of the Arabidopsis thaliana circadian clock genes CCA1/LHY. We made use of disruptant lines for PpCCA1a and/or PpCCA1b to elucidate the physiological significance of these genes in the growth of moss protonemal tissue under alternating day/night cycles. Protonemal cells of the double disruptant line, carrying neither of the two genes, grew faster than those of the wild-type plant (WT) in long days (LD), whereas no difference in the growth rate was detected between them in short days (SD). The double disruptant line also showed day length-dependent phenotypic changes in the PpCCA1b promoter activity: the diurnal profile of bioluminescence from the P(CCA1b)::LUC+ reporter strain was more significantly affected in LD than in SD. These observations are the first demonstration of a physiological function of the circadian clock in non-angiosperm land plants, and are consistent with recent findings that the clock controls hypocotyl elongation of A. thaliana in a photoperiod-dependent manner.

The plastid sigma factor SIG5 is involved in the diurnal regulation of the chloroplast gene psbD in the moss Physcomitrella patens.

We analyzed the function of a plastid sigma factor, SIG5, by targeted gene disruption in the moss Physcomitrella patens. High-intensity light induced the chloroplast gene psbD in the wild-type strain (WT), whereas this induction was nullified in the PpSig5-disrupted strains (DeltaSig5). Moreover, diurnally regulated changes of psbD transcription showed lowered amplitude in DeltaSig5 than in WT. We concluded that the moss SIG5 mediates multiple layers of signals to intricately regulate psbD transcription.

A compact multi-channel apparatus for automated real-time monitoring of bioluminescence.

We have developed a multi-channel apparatus for automated monitoring of bioluminescence in real time. We designed this apparatus to be compact (230 mm wide, 600 mm deep, and 227.5 mm high) so that it can be operated in a relatively small commercially-available incubator. The apparatus can process 20 samples at maximum in a single run, providing enough processibility in small-scale experiments. We verified the reliability and sensitivity of the apparatus by observing circadian bioluminescence rhythms over one week from a bioluminescent reporter strain (E9) of the cyanobacterium Synechococcus sp. strain PCC 7942 [Ishiura, M., Kutsuna, S., Aoki, S., Iwasaki, H., Andersson, C.R., Tanabe, A., Golden, S.S., Johnson, C.H., Kondo, T., Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria, Science, 281 (1998) 1519-1523]. Our apparatus allows flexible experimental designs and will be effectively used for the studies of gene expression in various purposes.

Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus.

The complete chloroplast DNA sequence (122 890 bp) of the moss Physcomitrella patens has been determined. The genome contains 83 protein, 31 tRNA and four rRNA genes, and a pseudogene. Four protein genes (rpoA, cysA, cysT and ccsA) found in the liverwort Marchantia polymorpha and the hornwort Anthoceros formosae are absent from P.patens. The overall structure of P.patens chloroplast DNA (cpDNA) differs substantially from that of liverwort and hornwort. Compared with its close relatives, a 71 kb region from petD to rpoB of P.patens is inverted. To investigate whether this large inversion and the loss of rpoA usually occur in moss plants, we analyzed amplified cpDNA fragments from four moss species. Our data indicate that the large inversion occurs only in P.patens, whereas the loss of the rpoA gene occurs in all mosses. Moreover, we have isolated and characterized the nuclear rpoA gene encoding the alpha subunit of RNA polymerase (RNAP) from P.patens and examined its subcellular localization. When fused to green fluorescent protein, RpoA was observed in the chloroplasts of live moss protonemata cells. This indicates that chloroplast RNAP is encoded separately by chloroplast and nuclear genomes in the moss. These data provide new insights into the regulation and evolution of chloroplast transcription.

Diversity of plant circadian clocks: Insights from studies of Chlamydomonas reinhardtii and Physcomitrella patens.

Arabidopsis thaliana has long been the model plant of choice for elucidating the mechanisms of the circadian clock. Recently, relevant results have accumulated in other species of green plant lineages, including green algae. This mini-review describes a comparison of the mechanism of the A. thaliana clock to those of the green alga Chlamydomonas reinhardtii and the moss Physcomitrella patens, focusing on commonalities and divergences of subsystems of the clock. The potential of such an approach from an evolutionary viewpoint is discussed.

A promoter-trap vector for clock-controlled genes in the cyanobacterium Synechocystis sp. PCC 6803.

We constructed a promoter-trap vector pPT6803-1 to isolate circadian clock-controlled promoters in the cyanobacterium Synechocystis sp. strain PCC 6803. The vector contains a promoterless luciferase gene set (luxAB) from Vibrio harveyi that is targeted to a specific site of the Synechocystis genome as a reporter for gene expression. A library was constructed in pPT6803-1 by introducing the genomic DNA fragments upstream of luxAB to transform Synechocystis cells. Of approximately 10,000 Synechocystis transformants, at least 55 (#1-55) showed circadian rhythms of bioluminescence under continuous illumination. Clones #19, #22, and #26 exhibited obviously different waveforms of bioluminescence from each other. Deletion analysis and primer extension experiments mapped the promoters for the clpP, slr1634, and rbpP genes that are responsible for bioluminescence from #19, #22, and #26, respectively.

Transformation and measurement of bioluminescence rhythms in the moss Physcomitrella patens.

Gene targeting is a highly effective and straightforward technique for the functional analysis of a gene of interest. However, its efficiency is not satisfactorily high in many model plants including Arabidopsis thaliana. In the moss Physcomitrella patens, a model species of basal plants, the efficiency of gene targeting is as high as in yeasts, and this moss is becoming widely recognized as an experimental model of choice in various areas of plant biology. Here we focus on the transformation of protoplast cells and on the measurement of bioluminescence rhythms from protonema tissues of luciferase reporter strains in P. patens, both of which are important for mechanistic studies of the circadian clock.

Pseudo-response regulator (PRR) homologues of the moss Physcomitrella patens: insights into the evolution of the PRR family in land plants.

The pseudo-response regulators (PRRs) are the circadian clock component proteins in the model dicot Arabidopsis thaliana. They contain a receiver-like domain (RLD) similar to the receiver domains of the RRs in the His-Asp phosphorelay system, but the RLDs lack the phosphoacceptor aspartic acid residue invariably conserved in the receiver domains. To study the evolution of PRR genes in plants, here we characterize their homologue genes, PpPRR1, PpPRR2, PpPRR3 and PpPRR4, from the moss Physcomitrella patens. In the phylogenetic analysis, PpPRRs cluster together, sister to an angiosperm PRR gene subfamily, illustrating their close relationships with the angiosperm PRRs. However, distinct from the angiosperm sequences, the RLDs of PpPRR2/3/4 exhibit a potential phosphoacceptor aspartic acid-aspartic acid-lysine (DDK) motif. Consistently, the PpPRR2 RLD had phosphotransfer ability in vitro, suggesting that PpPRR2 functions as an RR. The PpPRR1 RLD, on the other hand, shows a partially diverged DDK motif, and it did not show phosphotransfer ability. All PpPRRs were expressed in a circadian and light-dependent manner, with differential regulation between PpPRR2/4 and PpPRR1/3. Altogether, our results illustrate that PRRs originated from an RR(s) and that there are intraspecific divergences among PpPRRs. Finally, we offer scenarios for the evolution of the PRR family in land plants.

The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.

We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.