Cell-free synthesis of phytochrome apoprotein

Phytochrome: molecular properties and biogenesis

Native Avena phytochrome, recently shown to have a monomeric molecular mass of 124 kDa, has molecular properties that differ significantly from those of the extensively characterized ‘ 120’ kDa or ‘large’ phytochrome preparations now known to contain a mixture of proteolytically degraded 118 and 114 kDa polypeptides. For example, 124 kDa phytochrome has a blocked N-terminus, a P fr λ max of 730 nm, a higher photostationary state in red light (86% P fr ), exhibits no dark reversion and shows no differential reactivity of P r and P fr toward a chemical probe of hydrophobic domains. The data indicate that the proteolytically removed 6-10 kDa polypeptide segment (s) is critical to the spectral and structural integrity of the photoreceptor; that at least part of the cleaved domain is located at the N-terminus of the molecule; that this domain influences the chemical reactivity of the chromophore with the external medium; and that a current hypothesis that P r —P fr photoconversion results in the exposure of a hydrophobic domain on the molecule is inconsistent with the properties of native phytochrome. Phytochrome has been found to exert rapid negative feedback control over the level of its own translatable mRNA. P fr formation in etiolated tissue causes a decline in translatable phytochrome mRNA that is detectable within 15—30 min and that results in more than a 95 % reduction within 2 h. Less than 1 % P fr is sufficient to induce 60 % of the maximum response, which is saturated at 20 % P fr or less. The rapidity of this autoregulatory control makes phytochrome itself an attractive system for investigating phytochrome-regulated gene expression. A project to clone phytochrome complementary DNA (cDNA) has been initiated. A major obstacle in this work has been the unexpectedly low abundance of phytochrome mRNA, less than 0.005 % of the poly (A) RNA in etiolated tissue. cDNA made from poly (A) RNA enriched ca. 200-fold in phytochrome mRNA has been cloned and bacterial colonies have been screened with a synthetic oligodeoxynucleotide hybridization probe. The sequence of this probe was derived from a known partial amino acid sequence of the phytochrome protein. Difficulties encountered with this approach are discussed.

Down-regulation of phytochrome mRNA abundance by red light and benzyladenine in etiolated cucumber cotyledons

Northern blot analysis revealed that a single 4.2 kb phytochrome mRNA species was detectable in cotyledons excised from five-day-old etiolated cucumber seedlings. Intact etiolated five-day-old cucumber seedlings were given a red light or benzyladenine treatment, and cotyledons were harvested at various times following treatment. The abundance of phytochrome mRNA in the cotyledons was quantitated using 32P-labeled RNA probes and slot blot analysis. By 2 h after irradiation the phytochrome mRNA level was reduced to 40% of the initial abundance and reaccumulation began by 3 h after irradiation. Reaccumulation of phytochrome mRNA to the time-zero dark control level was achieved by 10 h after treatment. A decrease in phytochrome mRNA abundance was evident by 2 h after benzyladenine treatment, and a maximal reduction to 45% of the time-zero dark control was attained by 4 h after treatment. No recovery of the phytochrome mRNA level was evident by 8 h after benzyladenine treatment. The abundance of actin mRNA was unaffected by benzyladenine treatment.

The levels of two distinct species of phytochrome are regulated differently during germination in Avena sativa L

The abundance and molecular mass of phytochrome in germinating embryos of A. sativa (oat) grown in light or darkness have been monitored using immunoblot and spectrophotometric assays. Immunoblot analysis shows that imbibed but quiescent embryos have two immunochemically distinct species of phytochrome with monomeric molecular masses of 124 and 118 kDa (kdalton). The 118-kDa species has the properties of the 118-kDa phytochrome extracted from fully green oat tissue (J.G. Tokuhisa, S.M. Daniels, P.H. Quail, 1985, Planta 164, 321-332), whereas the 124-kDa polypeptide appears similar to the well-characterized photoreceptor of etiolated tissue. The capacity of antibodies directed against etiolated-oat phytochrome to immunoprecipitate the 124-kDa species but not the 118-kDa species has been exploited to quantitate the levels of each separately over a 72-h time course of germination and seedling development. The abundance of the 124-kDa molecule increases at least 200-fold in etiolated seedlings over 72 h whereas in light-grown seedlings the level of this molecule is relatively constant. In contrast, the amount of the 118-kDa species increases only twofold in both dark- and light-grown seedlings over the same period of time. These data indicate that whereas the abundance of 124-kDa phytochrome is regulated at the protein level by the well-documented, differential stability of the red- and far-red-absorbing forms in vivo, the 118-kDa molecule is present at a low constitutive level, presumably reflecting no such difference in the stability of the two spectral forms.

Cloning of cDNA for phytochrome from etiolated Cucurbita and coordinate photoregulation of the abundance of two distinct phytochrome transcripts

We have isolated several cDNA clones for phytochrome from a dicot, Cucurbita pepo L. cv. Black Beauty (zucchini), and have used them to study the regulation of Cucurbita phytochrome mRNA levels. A cDNA library was constructed from poly(A)(+) RNA isolated from etiolated Cucurbita hypocotyl hooks and enriched for phytochrome mRNA by size fractionation. This library was screened with a (32)P-labeled fragment isolated from an Avena phytochrome cDNA clone. Several putative phytochrome clones were isolated and mapped by restriction endonuclease analysis. On the basis of this analysis there is no evidence for the expression of multiple phytochrome genes in Cucurbita. Recent sequence analysis has confirmed that the largest of these clones, pFMD1 (∼3.6 kb), does indeed encode phytochrome and that it contains the entire amino acid coding sequence for Cucurbita phytochrome (33). RNA blot analysis has revealed that two polyadenylated phytochrome transcripts (∼5.6 kb and ∼4.2 kb) are present in both cotyledons and hypocotyl hooks of Cucurbita. In etiolated Cucurbita seedlings given a saturating pulse of red light, the abundance of both transcripts coordinately declines to 50-60% of the dark levels within 3 h and reaccumulates to dark levels within 24 h. Reversal of induction of this response by a far-red light pulse immediately following red light treatment is not observed, which is in contrast to the far-red reversibility of the red light promoted decrease in phytochrome mRNA abundance observed in Avena (6). Etiolated seedlings transferred to continuous white light also show a coordinate decrease in the levels of the two RNAs to ∼40% of the dark levels within 3 h. The magnitude of the light-induced decline in phytochrome mRNA abundance in Cucurbita is substantially less than the decrease previously reported for Avena (6).

Regulation of synthesis of nitrite reductase in pea leaves: in-vivo and in-vitro studies

Crude protein extracts from leaves of pea (Pisum sativum L.) labeled with an L-(14)C-amino-acid mixture or [(35)S]methionine, were treated with antibodies prepared against nitrite reductase (NiR; EC 1.6.6.4). When the immunoprecipitates were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) a polypeptide with the same mobility as that of the native NiR was detected. By using darkened or illuminated leaves in the absence or presence of nitrate, it has been confirmed that nitrate is required in the in-vivo synthesis of NiR and that this synthesis is stimulated by light. Cell-free translation with a wheat-germ extract primed with polysomes from illuminated leaves treated with nitrate yielded polypeptides of a wide range of molecular weights (Mrs). Two polypeptides were immunoprecipitated from the translational products by anti-NiR serum. The mobility of one of them on SDS-PAGE corresponded to that of NiR while the other had a slightly higher Mr. It is concluded that NiR is synthesized as a heavy-molecular-weight precursor. Nitrate appears to regulate NiR synthesis by triggering transcription whereas the light may control the level of transcription or translation.

The role of separate molecular domains in the structure of phytochrome from etiolated Avena sativa L

The spectral properties of peptides generated from etiolated-Avana, 124-kDa (kilodalton) phytochrome by endogenous protease(s) have been studied to assess the role of the amino-terminal and the carboxyl-terminal domains in maintaining the proper interaction between protein and chromophore. The amino-terminal, 74-kDa chromopeptide, a degradation product of the far-red absorbing form of the pigment (Pfr), is shown to be spectrally similar to the 124-kDa, undegraded molecule. The minimum and maximum of the difference spectrum (Pr-Pfr) are 730 and 665 nm, respectively, and the spectral-change ratio is unity. Also, like undegraded, 124-kDa phytochrome, the 74-kDa peptide exhibits minimal dark reversion. These data indicate that the 55-kDa, carboxyl-terminal half of the polypeptide does not interact with the chromophore and may not have a role in the structureal integrity of the amino-terminal domain. The 64-kDa chromopeptide can be generated directly from the 74-kDa species by cleavage of 10 kDa from the amino terminus upon incubation of this species as Pr. Accompanying this conversion are changes in the spectral properties, namely, a shift in the difference spectrum minimum to 722-724 nm and a tenfold increase in the capacity for dark reversion. These data indicate that the 6-10 kDa, amino-terminal segment continues to function in its role of maintaining proper chromophore-protein interactions in the 74-kDa peptide as it does in the undegraded molecule. Conversely, removal of this segment upon proteolysis to the 63-kDa species leads to aberrant spectral properties analogous to those observed when this domain is lost from the full-length, 124-kDa molecule, resulting in the 118/114-kDa degradation products. The data also show that photoconversion of the 74-kDa chromopeptide from Pfr to Pr exposes proteolytically susceptible sites in the same way as in the 124-kDa molecule. Thus, the separated, 74-kDa amino-terminal domain undergoes a photoinducible conformational change comparable to that in the intact molecule.

Phytochrome in green tissue: Spectral and immunochemical evidence for two distinct molecular species of phytochrome in light-grown Avena sativa L

A method is described for the extraction of phytochrome from chlorophyllous shoots of Avena sativa L. Poly(ethyleneimine) and salt fractionation are used to reduce chlorophyll and to increase the phytochrome concentration sufficiently to permit spectral and immunochemical analyses. The phototransformation difference spectrum of this phytochrome is distinct from that of phytochrome from etiolated shoots in that the maximum in the red region of the difference spectrum is shifted about 15 nm to a shorter wavelength. Immunochemical probing of electroblotted proteins (Western blotting), using a method sensitive to 50 pg, demonstrates the presence of two polypeptides in green tissue that bind antiphytochrome antibodies: a predominant species with a relative molecular mass (Mr) of 118000 and a lesser-abundant 124000-Mr polypeptide. Under nondenaturing conditions all of the 124000-Mr species is immunoprecipitable, but the 118000-Mr species remains in the supernatant. Peptide mapping and immunochemical analysis with monoclonal antibodies show that the 118000-Mr species has structural features that differ from etiolated-oat phytochrome. Mixing experiments show that these structural differences are intrinsic to the molecular species from these two tissues rather than being the result of post-homogenization modifications or interfering substances in the green-tissue extracts. Together the data indicate that the phytochrome that predominates in green-tissue has a polypeptide distinct from the well-characterized molecule from etiolated tissue.

Phytochrome regulation of phytochrome mRNA abundance

Pure phytochrome RNA sequence synthesized in an SP6-derived in vitro transcription system has been used as a standard to quantitate phytochrome mRNA abundance in Avena seedlings using a filter hybridization assay. In 4-day-old etiolated Avena seedlings phytochrome mRNA represents ∼0.1% of the total poly(A)(+) RNA. Irradiation of such seedlings with a saturating red-light pulse or continuous white light induces a decline in this mRNA that is detectable within 30 min and results in a 50% reduction by ∼60 min and >90% reduction within 5 h. The effect of the red-light pulse is reversed, approximately to the level of the far-red control, by an immediately subsequent far-red pulse. In seedlings maintained in extended darkness after the red-light pulse, the initial rapid decline in phytochrome mRNA level is followed by a slower reaccumulation such that 50-60% of the initial abundance is reached by 48 h. White-light grown seedlings transferred to darkness exhibit a similar accumulation of phytochrome mRNA that is accelerated by removal of residual Pfr with a far-red light pulse at the start of the dark period. The data establish that previously reported phytochrome-regulated changes in translatable phytochrome mRNA levels result from changes in the physical abundance of this mRNA rather than from altered translatability.

Native phytochrome: immunoblot analysis of relative molecular mass and in-vitro proteolytic degradation for several plant species

The relative molecular mass (Mr) of the native phytochrome monomer from etiolated Cucurbita pepo L., Pisum sativum L., Secale cereale L. and Zea mays L. seedlings has been determined using immunoblotting to visualize the chromoprotein in crude extracts subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis. A single phytochrome band is observed for each plant species when the molecule is extracted under conditions previously demonstrated to inhibit the proteolysis of native Avena sativa L. phytochrome. A comparison among plant species indicates that the Mr of native phytochrome is variable: Zea mays=127000; Secale=Avena=124000; Pisum=121000; Cucurbita=120000. The in-vitro phototransformation difference spectrum for native phytochrome from each species is similar to that observed in vivo in each case and is indistinguishable from that described for native Avena phytochrome. The difference minima between the red- and far-red-absorbing forms of the pigment (Pr-Pfr) are all at 730 nm and the spectral change ratios (ΔAr/ΔAfr) are near unity. When incubated in crude extracts, phytochrome from all four species is susceptible to Pr-specific limited proteolysis in a manner qualitatively similar to that observed for Avena phytochrome, albeit with slower rates and with the production of different Mr degradation products. Further examination of the in-vitro proteolysis of Avena phytochrome by endogeneous proteases has identified several additional phytochrome degradation products and permitted construction of a peptide map of the molecule. The results indicate that both the 6000- and 4000-Mr polypeptide segments cleaved by Pr-specific proteolysis are located at the NH2-terminus of the chromoprotein and are adjacent to a 64000-Mr polypeptide that contains the chromophore.

Proteolysis alters the spectral properties of 124 kdalton phytochrome from Avena

Native phytochrome from Avena sativa L. is homogeneous with a monomeric molecular weight of 124 kdalton; 6-10 kdalton larger than the heterogeneous "120" kdalton preparations previously considered to be undegraded (Vierstra and Quail, 1982, Proc. Natl. Acad. Sci. USA, 79: 5272-5276). The phototransformation difference spectrum (Pr-Pfr) of 124 kdalton phytochrome measured in crude extracts has a minimum in the farred region at 730 nm, the same as that observed in vivo. These spectral properties contrast with those of "120" kdalton phytochrome purified by column immunoaffinity chromatography where the difference minimum is at 724 nm. When 124 kdalton phytochrome is incubated as Pr in crude extracts, the difference minimum shifts progressively to shorter wavelengths (from 730 to 722 nm) concomitant with the proteolytic degradation of the chromoprotein to the mixture of 118 and 114 kdalton species that comprise "120" kdalton phytochrome preparations. These two effects are inhibited in concert by the serine protease inhibitor, phenylmethylsulfonylfluoride, and or maintenance of the phytochrome in the Pfr form. These results provide further evidence that 124 kdalton phytochrome is the native molecule in Avena and indicate that the peptide segments removed by proteolysis of the Pr form are important to the pigment's spectral integrity. The present data thus resolve the previously unsettled question of why the Pfr form of "120" kdalton phytochrome isolated by various procedures from Avena has been found to absorb at shorter wavelengths than that observed in vivo. Previous spectral studies with "120" kdalton phytochrome preparations are open to reexamination.