Control by phytochrome of the appearance of ribulose-1,5-bisphosphate carboxylase and the mRNA for its small subunit

Integrative analysis of transcript and metabolite profiling data sets to evaluate the regulation of biochemical pathways during photomorphogenesis

One of the key developmental processes during photomorphogenesis is the differentiation of prolamellar bodies of proplastids into thylakoid membranes containing the photosynthetic pigment-protein complexes of chloroplasts. To study the regulatory events controlling pigment-protein complex assembly, including the biosynthesis of metabolic precursors and pigment end products, etiolated Arabidopsis thaliana seedlings were irradiated with continuous red light (Rc), which led to rapid greening, or continuous far-red light (FRc), which did not result in visible greening, and subjected to analysis by oligonucleotide microarrays and targeted metabolite profiling. An analysis using BioPathAt, a bioinformatic tool that allows the visualization of post-genomic data sets directly on biochemical pathway maps, indicated that in Rc-treated seedlings mRNA expression and metabolite patterns were tightly correlated (e.g., Calvin cycle, biosynthesis of chlorophylls, carotenoids, isoprenoid quinones, thylakoid lipids, sterols, and amino acids). K-means clustering revealed that gene expression patterns across various biochemical pathways were very similar in Rc- and FRc-treated seedlings (despite the visible phenotypic differences), whereas a principal component analysis of metabolite pools allowed a clear distinction between both treatments (in accordance with the visible phenotype). Our results illustrate the general importance of integrative approaches to correlate post-genomic data sets with phenotypic outcomes.

Post-transcriptional and post-translational regulatory steps are crucial in controlling the appearance and stability of thylakoid polypeptides during the transition of etiolated tobacco seedlings to white light

We have investigated the expression of nuclear-encoded chloroplast proteins that are not associated with chlorophyll (the lumenal 33-kDa and 23-kDa polypeptides of the oxygen-evolving system of photosystem II, plastocyanin and the Rieske Fe/S protein) by comparing mRNA-accumulation rates with those of the corresponding proteins during illumination of etiolated tobacco seedlings. Using subcellular fractionation, pulse/chase, Northern and Western techniques, we found that the biogenesis and stability of these proteins are regulated both translationally, as well as post-translationally, including the efficiency of mRNA uptake into polysomes, processes that operate between translation and assembly or monitor the status (soluble and membrane-attached) of a terminally processed polypeptide. Polypeptide synthesis is generally not limited by mRNA amounts. For instance, steady-state transcript levels may increase 10-fold during illumination, while those associated with polysomes increase only 2-3-fold without measurable influence on the rate of protein synthesis. The 23-kDa and Rieske polypeptides are predominantly membrane associated, but plastocyanin and the 33-kDa polypeptide are distributed among both soluble and membrane-associated protein fractions. Plastocyanin appears to be comparably stable in both forms. However, for the 33-kDa polypeptide, only the membrane-attached form is stable (> 8 h) and only this pool increases upon illumination. Its soluble form is rapidly degraded with a half-life of approximately 1 h under the chosen conditions. Our findings probably reflect part of a more general regulatory principle operating in the differentiation and maintenance of subcellular structure.

Regulation of the appearance of glutamine synthetase in mustard (Sinapis alba L.) cotyledons by light, nitrate and ammonium

During transformation of mustard seedlings cotyledons from storage organs to photosynthetically competent leaves, a process which occurs during the first 4 d after sowing, total glutamine-synthetase (GS, EC 6.3.1.2) activity increases from zero to the high level usually observed in green leaves. In the present study we have used ion-exchange chromatography to separate possible isoforms of GS during the development of the cotyledons. The approach failed since we could only detect a single form of GS, presumably plastidic GS, under all circumstances tested. The technique of selective photooxidative destruction of plastids in situ was applied to solve the problem of GS localization. It was inferred from the data that the GS as detected by ion-exchange chromatography is plastidic GS.The regulatory role, if any, of light, nitrate and ammonium in the process of the appearance of GS in the developing cotyledons was investigated. The results show that nitrate and ammonium play only minor roles. Light, operating via phytochrome, is the major regulatory factor.

Temporal control of phytochrome-dependent gene expression during radish seedling development

The level of two nuclear-encoded transcripts (the small subunit of ribulose-1,5-bisphosphate carboxylase and the chlorophyll a/b-binding protein of photosystem II) and two chloroplastencoded mRNAs (the large subunit of ribulose-1,5-bisphosphate carboxylase and the chloroplast 32-kDa polypeptide) were analysed during the first 4 d of radish (Raphanus sativus L.) seedling development. A single 5-min red-light pulse increased the concentrations of all transcripts by various orders of magnitude, depending on the particular mRNA. For all transcripts the maximal effect of the red light was observed when the irradiation was applied 48 h following sowing. The red-light treatment did not lead to changes in the total RNA level or to alterations in the levels of nuclear and chloroplastic DNAs; the level of β-actin mRNA was also unaffected by the light treatment. It is concluded that during the first days of development, cells of radish cotyledons undergo light-independent molecular changes, occurring at the transcriptional level, conferring on them a transient competence towards the photoreceptor phytochrome.

Effect of nitrate, ammonium, light and a plastidic factor on the appearance of multiple forms of nitrate reductase in mustard (Sinapis alba L.) cotyledons

In mustard (Sinapis alba L.) cotyledons, four different forms of nitrate reductase (NR) can be separated by anion-exchange chromatography. Two of these forms (NR1 and NR2) appear in the presence of NO 3 (-) while the other two (NR3 and NR4) appear as a response to the application of NH 4 (+) as the sole nitrogen source. In the presence of NH4NO3, NR3 appears to be superimposed on nitrate-induced NR1 and NR2 while the NH 4 (+) -induced appearance of NR4 is totally abolished in the presence of equimolar amounts of NO 3 (-) . The appearance of NR1, NR2 and NR3 is strongly stimulated by red light pulses which operate via the far-red-absorbing form of phytochrome (Pfr), whereas the appearance of NR4 requires continuous light (likewise operating through pytochrome). Continuous red light is more effective in this case than continuous far-red light. Analysis of the data shows that the mode of action of phytochrome (Pfr) is the same in the case of the appearances of NR1 and NR2, whereas it is quantitatively different in the case of NR3 and totally different in that of NR4. A 'plastidic factor' has previously been postulated to be obligatorily involved in the transcriptional control of nuclear genes encoding for proteins destined for the chloroplast. Photooxidative damage of the plastid is postulated to destroy the ability of the organelle to produce this signal. If the plastids are damaged by photooxidation, the action of nitrate and phytochrome on the appearance of NR is abolished. The plant cell regulates the appearance of nitrate-induced NR, which is cytosolic, as if it were a plastidic protein. The appearance of NR3 depends on the plastidic factor in principally the same way as that of NR1 and NR2 whereas NR4 is totally independent of the plastidic factor. The data document particular kinds of interaction between controlling factors (light, nitrate, ammonium, plastidic factor) which affect gene expression in plants. These intricacies of regulation have so far not been considered in molecular studies on NR-gene expression.

Time courses for phytochrome-induced enzyme levels in phenylpropanoid metabolism (phenylalanine ammonia-lyase, naringenin-chalcone synthase) compared with time courses for phytochrome-mediated end-product accumulation (anthocyanin, quercetin)

Time course for changes in the levels of enzymes characteristic of general phenylpropanoid metabolism (phenylalanine ammonia-lyase, PAL; EC 4.3.1.5) and of the flavonoid-glycoside branch pathway (naringenin-chalcone synthase, CHS; EC 2.3.1.74) were measured in the cotyledons of mustard (Sinapis alba L.) seedlings and compared with the rates of accumulation of related end products (anthocyanin and quercetin). Induction of enzyme levels and of end-product accumulation was carried out with red and far-red (FR) light, operating via phytochrome. The data are compatible with the concept that the phytochrome-mediated appearance of enzymes such as PAL and CHS is indeed a prerequisite for the appearance of anthocyanins and flavonols. However, there is no close correlation between enzyme levels and the rates of synthesis of end products which could justify the identification of specific rate-limiting enzymes. Rather, the data indicate that there is a second phytochrome-dependent step, beyond enzyme induction, where the actual rate of flavonoid accumulation is determined. Anthocyanin and quercetin accumulation respond differently to light. However, the relative action of continuous FR, red light pulses and 'stored phytochrome signal' is the same in both cases. This indicates that the mode of operation of phytochrome is the same in both cases. The two syntheses differ only in the degree of responsiveness towards phytochrome. The time course for changes in CHS levels in continuous FR, i.e. under conditions of phytochrome photosteady state, is similar to the time course for PAL levels whereas the time courses in darkness, following transfer from FR to darkness, are totally different. In the case of CHS, a transient rise is observed whereas, with PAL, an instantaneous drop in enzyme level occurs after transfer from FR to darkness. It is concluded that the 'stored phytochrome signal' operates in darkness in the case of CHS but not in the case of PAL.

Action of light, nitrate and ammonium on the levels of NADH- and ferredoxin-dependent glutamate synthases in the cotyledons of mustard seedlings

In mustard (Sinapis alba L.) cotyledons, NADH-dependent glutamate synthase (NADH-GOGAT, EC 1.4.1.14) is only detectable during early seedling development with a peak of enzyme activity occurring between 2 and 2.5 d after sowing. With the beginning of plastidogenesis at approximately 2 d after sowing, ferredoxindependent glutamate synthase (Fd-GOGAT, EC 1.4.7.1) appears while NADH-GOGAT drops to a very low level. The enzymes were separated by anion exchange chromatography. Both enzymes are stimulated by light operating through phytochrome. However, the extent of induction is much higher in the case of Fd-GOGAT than in the case of NADH-GOGAT. Moreover, NADH-GOGAT is inducible predominantly by red light pulses, while the light induction of Fd-GOGAT operates predominantly via the high irradiance response of phytochrome. The NADH-GOGAT level is strongly increased if mustard seedlings are grown in the presence of nitrate (15 mM KNO3,15 mM NH4NO3) while the Fd-GOGAT level is only slightly affected by these treatments. No effect on NADH-GOGAT level was observed by growing the seedlings in the presence of ammonium (15 mM NH4Cl) instead of water, whereas the level of Fd-GOGAT was considerably reduced when seedlings were grown in the presence of NH4Cl. Inducibility of NADH-GOGAT by treatment with red light pulses or by transferring water-grown seedlings to NO 3 (-) -containing medium follows a temporal pattern of competence. The very low Fd-GOGAT level in mustard seedlings grown under red light in the presence of the herbicide Norflurazon, which leads to photooxidative destruction of the plastids, indicates that the enzyme is located in the plastids. The NADH-GOGAT level is, in contrast, completely independent of plastid integrity which indicates that its location is cytosolic. It is concluded that NADH-GOGAT in the early seedling development is mainly concerned with metabolizing stored glutamine whereas Fd-GOGAT is involved in ammonium assimilation.