Hybrid Indicators for Fast and Sensitive Voltage Imaging.

Membrane voltage is an important biophysical signal that underlies intercellular electrical communications. A fluorescent voltage indicator is presented that enables the investigation of electrical signaling at high spatial resolution. The method is built upon the site-specific modification of microbial rhodopsin proteins with organic fluorophores, resulting in a hybrid indicator scaffold that is one of the most sensitive and fastest orange-colored voltage indicators developed to date. We applied this technique to optically map electrical connectivity in cultured cells, which revealed gap junction-mediated long-range coupling that spanned over hundreds of micrometers.

Interaction with plant transcription factors can mediate nuclear import of phytochrome B.

Phytochromes (phy) are red/far-red-absorbing photoreceptors that regulate the adaption of plant growth and development to changes in ambient light conditions. The nuclear transport of the phytochromes upon light activation is regarded as a key step in phytochrome signaling. Although nuclear import of phyA is regulated by the transport facilitators far red elongated hypocotyl 1 (FHY1) and fhy1-like, an intrinsic nuclear localization signal was proposed to be involved in the nuclear accumulation of phyB. We recently showed that nuclear import of phytochromes can be analyzed in a cell-free system consisting of isolated nuclei of the unicellular green algae Acetabularia acetabulum. We now show that this system is also versatile to elucidate the mechanism of the nuclear transport of phyB. We tested the nuclear transport characteristics of full-length phyB as well as N- and C-terminal phyB fragments in vitro and showed that the nuclear import of phyB can be facilitated by phytochrome-interacting factor 3 (PIF3). In vivo measurements of phyB nuclear accumulation in the absence of PIF1, -3, -4, and -5 indicate that these PIFs are the major transport facilitators during the first hours of deetiolation. Under prolonged irradiations additional factors might be responsible for phyB nuclear transport in the plant.

Photochemistry of Acetabularia rhodopsin II from a marine plant, Acetabularia acetabulum.

Acetabularia rhodopsins are the first microbial rhodopsins discovered in a marine plant organism, Acetabularia acetabulum. Previously, we expressed Acetabularia rhodopsin II (ARII) by a cell-free system from one of two opsin genes in A. acetabulum cDNA and showed that ARII is a light-driven proton pump [Wada, T., et al. (2011) J. Mol. Biol. 411, 986-998]. In this study, the photochemistry of ARII was examined using the flash-photolysis technique, and data were analyzed using a sequential irreversible model. Five photochemically defined intermediates (P(i)) were sufficient to simulate the data. Noticeably, both P(3) and P(4) contain an equilibrium mixture of M, N, and O. Using a transparent indium tin oxide electrode, the photoinduced proton transfer was measured over a wide pH range. Analysis of the pH-dependent proton transfer allowed estimation of the pK(a) values of some amino acid residues. The estimated values were 2.6, 5.9 (or 6.3), 8.4, 9.3, 10.5, and 11.3. These values were assigned as the pK(a) of Asp81 (Asp85(BR)) in the dark, Asp92 (Asp96(BR)) at N, Glu199 (Glu204(BR)) at M, Glu199 in the dark, an undetermined proton-releasing residue at the release, and the pH to start denaturation, respectively. Following this analysis, the proton transfer of ARII is discussed.

Biosynthesis in isolated Acetabularia chloroplasts. I. Protein amino acids.

The ability of chloroplasts isolated from Acetabulana mediterranea to synthesize the protein amino acids has been investigated. When this chloroplast isolate was presented with (14)CO(2) for periods of 6-8 hr, tracer was found in essentially all amino acid species of their hydrolyzed protein Phenylalanine labeling was not detected, probably due to technical problems, and hydroxyproline labeling was not tested for The incorporation of (14)CO(2) into the amino acids is driven by light and, as indicated by the amount of radioactivity lost during ninhydrin decarboxylation on the chromatograms, the amino acids appear to be uniformly labeled. The amino acid labeling pattern of the isolate is similar to that found in plastids labeled with (14)CO(2) in vivo. The chloroplast isolate did not utilize detectable amounts of externally supplied amino acids in light or, with added adenosine triphosphate (ATP), in darkness. It is concluded that these chloroplasts are a tight cytoplasmic compartment that is independent in supplying the amino acids used for its own protein synthesis. These results are discussed in terms of the role of contaminants in the observed synthesis, the "normalcy" of Acetabularia chloroplasts, the synthetic pathways for amino acids in plastids, and the implications of these observations for cell compartmentation and chloroplast autonomy.

Growth of the nuclear envelope in the vegetative phase of the green alga Acetabularia. Evidence for assembly from membrane components synthesized in the cytoplasm.

The primary nucleus of the green alga Acetabularia grows about 25,000-fold in volume while it is separated from the endoplasmic reticulum and the whole cytoplasm by a special paranuclear cisterna of a vacuolar labyrinthum system which shows only very few (two to six per square micrometer) and small (ca. 40-120 nm in diamter) fenestrations. The nuclear envelope does not bear polyribosomes, nor do they occur in the entire zone intermediate between the nuclear envelope and the paranuclear cisterna. It is suggested that this special form of nuclear envelope growth takes place by assembly from cytoplasmically synthesized proteins that are translocated across the paranuclear cisterna in a nonmembrane-structured form.

Dynamics of voltage profile in enzymatic ion transporters, demonstrated in electrokinetics of proton pumping rhodopsin.

H(+)-pumping rhodopsins mediate a primordial conversion of light to metabolic energy. Bacteriorhodopsin from Halobacterium salinarium is the first identified and (biochemically) best-studied H(+)-pumping rhodopsin. The electrical properties of H(+)-pumping rhodopsins, however, are known in more detail for the homolog Acetabularia rhodopsin, isolated from the eukaryotic green alga Acetabularia acetabulum. Based on data from Acetabularia rhodopsin we present a general reaction kinetic model of H(+)-pumping rhodopsins with only seven independent parameters, which fits the kinetic properties of photocurrents as functions of light, transmembrane voltage, internal and external pH, and time. The model describes fast photoisomerization of retinal with simultaneous H(+) transfer to an H(+) acceptor, reprotonation of retinal from the intracellular face via an H(+) donor, and proton release to the extracellular space via an H(+) release complex. The voltage sensitivities of the individual reaction steps and their temporal changes are treated here by a novel approach, whereby--as in an Ohmic voltage divider--the effective portions of the total transmembrane voltage decrease with the relative velocities of the individual reaction steps. This analysis quantitatively infers dynamic changes of the voltage profile and of the pK values of the H(+)-binding sites involved.

Interhelical interactions between D92 and C218 in the cytoplasmic domain regulate proton uptake upon N-decay in the proton transport of Acetabularia rhodopsin II.

Acetabularia rhodopsin II (ARII or Ace2), an outward light-driven algal proton pump found in the giant unicellular marine alga Acetabularia acetabulum, has a unique property in the cytoplasmic (CP) side of its channel. The X-ray crystal structure of ARII in a dark state suggested the formation of an interhelical hydrogen bond between C218ARII and D92ARII, an internal proton donor to the Schiff base (Wada et al., 2011). In this report, we investigated the photocycles of two mutants at position C218ARII: C218AARII which disrupts the interaction with D92ARII, and C218SARII which potentially forms a stronger hydrogen bond. Both mutants exhibited slower photocycles compared to the wild-type pump. Together with several kinetic changes of the photoproducts in the first half of the photocycle, these replacements led to specific retardation of the N-to-O transition in the second half of the photocycle. In addition, measurements of the flash-induced proton uptake and release using a pH-sensitive indium-tin oxide electrode revealed a concomitant delay in the proton uptake. These observations strongly suggest the importance of a native weak hydrogen bond between C218ARII and D92ARII for proper proton translocation in the CP channel during N-decay. A putative role for the D92ARII-C218ARII interhelical hydrogen bond in the function of ARII is discussed.

Transcriptional feedback oscillators: maybe, maybe not...

The molecular mechanism of circadian rhythmicity is usually modeled by a transcription/translation feedback oscillator in which clock proteins negatively feed back on their own transcription to produce rhythmic levels of clock protein mRNAs, which in turn cause the production of rhythmic levels of clock proteins. This mechanism has been applied to all model organisms for which molecular data are available. This review summarizes the increasing number of anomalous observations that do not fit the standard molecular mechanism for the model organisms Acetabularia, Synechococcus, Drosophila, Neurospora, and mouse. The anomalies fall into 2 classes: observations of rhythmicity in the organism when transcription of clock genes is held constant, and rhythmicity in the organism when clock gene function is missing in knockout mutants. It is concluded that the weight of anomalies is now so large that the standard transcription/translation mechanism is no longer an adequate model for circadian oscillators. Rhythmic transcription may have other functions in the circadian system, such as participating in input and output pathways and providing robustness to the oscillations. It may be most useful to think in terms of a circadian system that uses a noncircadian oscillator consisting of metabolic feedback loops, which acquires its circadian properties from additional regulatory molecules such as the products of canonical clock genes.

Covalently closed minicircular DNA associated with Acetabularia chloroplasts.

When Acetabularia cliftonii chloroplast DNA (p = 1.706 g/cm3) is centrifuged in an ethidium bromide-CsCl gradient, the lower band is enriched for DNA with a buoyant density of 1.712 g/cm3 containing small covalently closed circular molecules. The minicircles measure 4.15 +/- 0.30 mum in the closed conformation and 4.35 +/- 0.20 mum in the open conformation. They are not of nuclear or bacterial origin, and appear to exist as independent entities within the chloroplast, although a mitochondrial origin cannot be completely ruled out. No 40-45 mum circles, as found in other chloroplasts, were found in either ethidium bromide-CsCl fraction. None were found in total chloroplast DNA by any of a number of methods tried. Linear molecules up to 200 mum were measured in chloroplast lysates. The main chloroplast genome may consist of very large circular molecules which are broken by even small shear forces.

Exchangeability of the b subunit of the Cl(-)-translocating ATPase of Acetabularia acetabulum with the beta subunit of E. coli F1-ATPase: construction of the chimeric beta subunits and complementation studies.

The gene encoding the b subunit of the Cl(-)-translocating ATPase (aclB) was isolated from total RNA and poly(A)+ RNA of Acetabularia acetabulum and sequenced (total nucleotides of 3038 bp and an open reading frame with 478 amino acids). The deduced amino acid sequence showed high similarity to the beta subunit of the F type ATPases, but was different in the N-terminal 120 amino acids. The role of the N-terminal region was investigated using an F -ATPase beta-less mutant of E. coli, JP17. The JP17 strain expressing the aclB could not grow under conditions permitting oxidative phosphorylation, although ACLB was detected in the membrane fraction. The beta subunit was divided into three portions: amino acid position from 1 to 95 (portion A), 96 to 161 (portion B) and 162 to the C-terminus (portion C). The corresponding regions of ACLB were designated as portions A' (from 1 to 106), B' (from 107 to 172) and C' (from 173 to 478). Chimeric proteins with combinations of A-B'-C', A-B-C' and A'-B-C restored the function as the beta subunit in E. coli F0F1-complex, but those with combinations of A'-B'-C and A-B'-C had no function as the beta subunit. These findings suggested that portion B plays an important role in the assembly and function of the beta subunit in the F0F1-complex, while portion B' of ACLB exhibited inhibitory effects on assembly and function. In addition, portion A was also important for interaction of the beta subunit with the alpha subunit in E. coli F0F1-complex. These findings also suggested that the b subunit of the Cl(-)-translocating ATPase of A. acetabulum has a different function in the Cl(-)-translocating ATPase complex, although the primary structure resembled to the beta subunit of the F1-ATPase.

Prokaryotic and eukaryotic unicellular chronomics.

An impeccable time series, published in 1930, consisting of hourly observations on colony advance in a fluid culture of E. coli, was analyzed by a periodogram and power spectrum in 1961. While the original senior author had emphasized specifically periodicity with no estimate of period length, he welcomed further analyses. After consulting his technician, he knew of no environmental periodicity related to human schedules other than an hourly photography. A periodogram analysis in 1961 showed a 20.75-h period. It was emphasized that "... the circadian period disclosed is not of exactly 24-h length." Confirmations notwithstanding, a committee ruled out microbial circadian rhythms based on grounds that could have led to a different conclusion, namely first, the inability of some committee members to see (presumably by eyeballing) the rhythms in their own data, and second, what hardly follows, that there were "too many analyses" in the published papers. Our point in dealing with microbes and humans is that analyses are indispensable for quantification and for discovering a biologically novel spectrum of cyclicities, matching physical ones. The scope of circadian organization estimated in 1961 has become broader, including about 7-day, about half-yearly, about-yearly and ex-yearly and decadal periodisms, among others. Microbial circadians have become a field of their own with eyeballing, yet time-microscopy can quantify characteristics with their uncertainties and can assess broad chronomes (time structures) with features beyond circadians. As yet only suggestive differences between eukaryotes and prokaryotes further broaden the perspective and may lead to life's sites of origin and to new temporal aspects of life's development as a chronomic tree by eventual rhythm dating in ontogeny and phylogeny.

Decreasing period-length of the endogenous circadian rhythm of oxygen evolution in Acetabularia and its possible relation to aging.

Endogenous circadian rhythms observed under constant conditions normally show period length variations. However, a general trend is difficult to identify when cells or organisms are entrained with the usual 24-h-period light/dark cycles. Therefore, these variations in time have been considered as fluctuations. In order to gain more insight into this phenomenon, individual Acetabularia cells were exposed to light/dark cycles of 16 h (LD 8:8) and 33.6 h (LD 16.8:16.8), respectively, i.e., periods which lie distinctly outside the range of the normal circadian entrainment. Employing a high-resolution procedure for data analysis, decreasing period lengths could consistently be detected when cells were kept under constant conditions for several weeks. Possible causes of this decrease are discussed.

Model for the positional differentiation of the cap in Acetabularia.

A late stage during the biological cycle of the unicellular alga Acetabularia is the differentiation of a cap at the apical end of the stalk. A minimal model of the spatio-temporal regulation of this event is proposed on the basis of biological data available and current hypotheses. This involves the interaction between a diffusing inhibitor specific to the translation of cap mRNAs and a graded distribution of these messengers. The model accounts for delayed protein synthesis which occurs preferably at the apex and is likely to initiate the formation of the cap. The biological and theoretical implications are discussed.

[Synthesis of virus-specific products following introduction of tobacco mosaic virus RNA pereparations and the native virus into acetabularia]. / Izuchenie sinteza virusspetsificheskikh produktov posle vvedeniia v atsetabuliariiu preparatov RNK virusa tabachnoi mozaiki i nativnogo virusa.

The possibility to synthesize the viral-specific products after microinjection of Tobacco mosaic virus (TMV) preparations and the TMV RNA into the single-celled seaweed Acetabularia was studied. The accumulation of the newly synthesized protein and double-stranded RNA 24 hours after injection of TMV RNA and native virus preparations was demonstrated by immunological and immunofluorescent methods. The virus titer sharply dropped 3--4 hours after introduction into Acetabularia and in 48 hours it reached a maximum level. The presented data showed the possibility of TMW RNA replication and translation involving formation of viral-specific proteins and the production of a virus of full value in the Acetabularia cell.

[Intracellular transport of nuclear ribosomal RNA in Acetabularia mediterranea]. / Vnutrikletochnyi transport ribosomnoi RNK iadernogo proiskhozhdeniia u Acetabularia mediterranea.

The ribosomal RNA transport from a nucleus to a perinuclear cytoplasm and its following distribution in the cytoplasm of Acetabularia mediterranea cells were studied using transplantation of RNA-labeled rhizoid into unlabeled stalk. In addition rifamycin treatment was used for inhibition of cytoplasmic RNA synthesis. Acetabularia nuclei contain the stable RNA fractions similar to those present in some other eukaryotes. Nuclear 25S and 17S ribosomal RNA rapidly enter the rhizoid cytoplasm whereas the following trasfer of them to other regions of the cell is a very slow process. Within two days only an insignificant part of 25S and 17S ribosomal RNA is transferred from the rhizoid to the stalk and is distributed there over the base-apical gradient. No preferential transfer of the nuclear ribosomal RNA to the apical region was observed.

[Intracellular distribution of RNA in Acetabularia mediterranea]. / Izuchenie vnutrikletochnogo raspredeleniia RNK u Acetabularia mediterranea

RNA synthesis and distribution in cytoplasm of Acetabularia mediterranea cell were studied by radiochemical and ultramicrobiochemical methods. Existance of an apico-basal gradient of RNA concentration in the cytoplasm was shown. Variations in the rate of the RNA synthesis in different regions of the cytoplasm are of great importance for the formation of this gradient whereas a contribution of nuclear RNA transport is insignificant. Sedimentation coefficients of about 23S and 16S were detected for the most part of the synthesized cytoplasmic RNAs. Evidently these RNAs represent rRNA of chloroplast ribosomes. Basal region of cytoplasm contains a relatively large amount of low molecular weight RNA. The differences in stability of newly-synthesized RNA were found in cytoplasmic regions under examination.

[RNA synthesis gradients in the nucleus-free fragments of Acetabularia mediterranea under conditions of local illumination]. / Gradienty sinteza RNK u bez'iadernykh fragmentov Acetabularia meditarranea v usloviiakh lokal'nogo osveshcheniia.

The intensity of RNA synthesis was studied in different regions of anuclear fragments of the Acetabularia mediterranea stem under their local illumination. The local illumination was shown to activate RNA synthesis and formation of distal-medial gradients of this synthesis in the illuminated regions of the fragments to a much greater extent than in their darkened regions. The formation of the gradient in the illuminated region took place even if the growth in this region was insignificant and was not accompanied by the cap formation. The results obtained suggests the absence of obligatory correspondence between the ability of morphogenesis and the gradient of RNA synthesis.

[Rna transport from the nucleus to the cytoplasm in Acetabularia mediterranea]. / Issledovanie transporta RNK iz iadra v tsitoplazmu u Acetabularia mediterranea

The biosynthesis of nuclear RNA, its transport from the nucleus to the cytoplasm and distribution in the cytoplasm were studied in Acetabularia mediterranea under different light conditions. It was shown that the nuclear RNA incorportate 3H-uracil more rapidly in the darkness and the transport of labeled RNA from the nucleus slowed down after the transfer of plants in the cold medium in the darkness. To study the distribution of nuclear RNA in the cytoplasm, the 3H-uracil labeled nuclei were transplanted in the rhizoids of unlabeled plants, the dikaryons obtained were kept for different time in the light and in the darkness and the content of 3H-RNA was determined in different stem regions. It was shown that the transport of 3H-RNA in the cytoplasm is slowed down in the darkness and it is distributed by the basal-apical gradient. RNA is rapidly accumulated in the apical stem zone in the light and redistributed afterwards in the basal stem zones. The problem of relationship between the polarity and nuclear RNA distribution in Acetabularia is discussed.

[Mammalian protein synthesis in the cytoplasm of a plant cell]. / Sintez belkov mlekopitaiushchikh v tsitoplazme rastitel'noi kletki.

Using immunochemical and, subsequently, autoradiographic methods, the authors have shown that after the injection of the total fraction of polyribosomes isolated from the rat liver in the Acetabularia cytoplasm a protein interacting with the antiserum against rat thyrosine aminotransferase is synthesized. Prospects of using Acetabularia as a test-system for the translation of heterogenous mRNA and mRNP are discussed.

Crystal structure of the eukaryotic light-driven proton-pumping rhodopsin, Acetabularia rhodopsin II, from marine alga.

Acetabularia rhodopsin (AR) is a rhodopsin from the marine plant Acetabularia acetabulum. The opsin-encoding gene from A. acetabulum, ARII, was cloned and found to be novel but homologous to that reported previously. ARII is a light-driven proton pump, as demonstrated by the existence of a photo-induced current through Xenopus oocytes expressing ARII. The photochemical reaction of ARII prepared by cell-free protein synthesis was similar to that of bacteriorhodopsin (BR), except for the lack of light-dark adaptation and the different proton release and uptake sequence. The crystal structure determined at 3.2 Å resolution is the first structure of a eukaryotic member of the microbial rhodopsin family. The structure of ARII is similar to that of BR. From the cytoplasmic side to the extracellular side of the proton transfer pathway in ARII, Asp92, a Schiff base, Asp207, Asp81, Arg78, Glu199, and Ser189 are arranged in positions similar to those of the corresponding residues directly involved in proton transfer by BR. The side-chain carboxyl group of Asp92 appears to interact with the sulfhydryl group of Cys218, which is unique to ARII and corresponds to Leu223 of BR and to Asp217 of Anabaena sensory rhodopsin. The orientation of the Arg78 side chain is opposite to the corresponding Arg82 of BR. The putative absence of water molecules around Glu199 and Arg78 may disrupt the formation of the low-barrier hydrogen bond at Glu199, resulting in the "late proton release".