The photoreceptor protein of Euglena gracilis

Advanced Microscopy Techniques for Molecular Biophysics

Though microscopy is most often intended as a technique for providing qualitative assessment of cellular and subcellular properties, when coupled with other instruments such as wavelength selectors, lasers, photoelectric devices and computers, it can perform a wide variety of quantitative measurements, which are demanding in establishing relationships between the properties and structures of biological material in all their spatial and temporal complexities. These combinations of instruments are a powerful approach to improve non-destructive investigations of cellular and subcellular properties (both physical and chemical) at a macromolecular scale resolution. Since many subcellular compartments in living cells are characterized by structurally organized molecules, this review deals with three advanced microscopy techniques well-suited for these kind of investigations, i.e., microspectrophotometry (MSP), super-resolution localization microscopy (SRLM) and holotomographic microscopy (HTM). These techniques can achieve an insight view into the role intracellular molecular organizations such as photoreceptive and photosynthetic structures and lipid bodies play in many cellular processes as well as their biophysical properties. Microspectrophotometry uses a set-up based on the combination of a wide-field microscope and a polychromator, which allows the measurement of spectroscopic features such as absorption spectra. Super resolution localization microscopy combines dedicated optics and sophisticated software algorithms to overcome the diffraction limit of light and allow the visualization of subcellular structures and dynamics in greater detail with respect to conventional optical microscopy. Holotomographic microscopy combines holography and tomography techniques into a single microscopy set-up, and allows 3D reconstruction by means of the phase separation of biomolecule condensates. This review is organized in sections, which for each technique describe some general aspects, a peculiar theoretical aspect, a specific experimental configuration and examples of applications (fish and algae photoreceptors, single labeled proteins and endocellular aggregates of lipids).

Transcriptome, proteome and draft genome of Euglena gracilis

BACKGROUND

Photosynthetic euglenids are major contributors to fresh water ecosystems. Euglena gracilis in particular has noted metabolic flexibility, reflected by an ability to thrive in a range of harsh environments. E. gracilis has been a popular model organism and of considerable biotechnological interest, but the absence of a gene catalogue has hampered both basic research and translational efforts.

RESULTS

We report a detailed transcriptome and partial genome for E. gracilis Z1. The nuclear genome is estimated to be around 500 Mb in size, and the transcriptome encodes over 36,000 proteins and the genome possesses less than 1% coding sequence. Annotation of coding sequences indicates a highly sophisticated endomembrane system, RNA processing mechanisms and nuclear genome contributions from several photosynthetic lineages. Multiple gene families, including likely signal transduction components, have been massively expanded. Alterations in protein abundance are controlled post-transcriptionally between light and dark conditions, surprisingly similar to trypanosomatids.

CONCLUSIONS

Our data provide evidence that a range of photosynthetic eukaryotes contributed to the Euglena nuclear genome, evidence in support of the 'shopping bag' hypothesis for plastid acquisition. We also suggest that euglenids possess unique regulatory mechanisms for achieving extreme adaptability, through mechanisms of paralog expansion and gene acquisition.

Light and the evolution of vision

It might seem a little ridiculous to cover the period over which vision evolved, perhaps 1.5 billion years, in only 3000 words. Yet, if we examine the photoreceptor molecules of the most basic eukaryote protists and even before that, in those of prokaryote bacteria and cyanobacteria, we see how similar they are to those of mammalian rod and cone photoreceptor opsins and the photoreceptive molecules of light sensitive ganglion cells. This shows us much with regard the development of vision once these proteins existed, but there is much more to discover about the evolution of even more primitive vision systems.

Photoactivated cyclases: In memoriam Masakatsu Watanabe

In memoriamMasakatsu Watanabe.

A genetic dissection of the photophobic response of Paramecium tetraurelia

Paramecium tetraurelia displayed two behavioral responses upon the initiation of a light stimulus at 7 x 10(4) lux. The cells exhibited a photophobic response in the form of behavioral avoiding reactions, followed by an increase in forward swimming velocity that was significantly higher than prior to the light stimulus activation. It was determined that an intensity of approximately 6.5 x 10(3) lux was required to initiate a moderate avoidance behavioral response. Following the avoiding response, a gradual increase in speed occurred as the intensity increased, indicating that increased swimming speeds are dependent on the light intensity. Two mutants, pawnA and Dancer, were utilized since they affect known Ca(2+)-currents of the cell. The use of pawnA cells, which lack voltage-dependent Ca(2+) channel activity, showed that the two responses to light could be genetically separated, in that the cells showed no avoiding reactions, but did increase their swimming speed. The Dancer cells, which display exaggerated Ca(2+) channel activity, exhibited similar initial avoiding responses as the wild type cells, however did not increase their swimming speed as the intensity of the light was increased. This phenotype as replicated in wildtype cells that had been placed in 25 μM 8-Br-cGMP. These data demonstrate that the photophobic light response of Paramecium tetraurelia can be genetically dissected as a means of elucidating the molecular mechanisms of the light response.

Fundamental questions and concepts about photoreception and the case of Euglena gracilis

The ability to sense light can be considered the most fundamental and presumably the most ancient property of visual systems. This ability is the basis of phototaxis, one of the most striking behavioral responses of motile photosynthetic microorganisms (i.e. microalgae) to light stimuli, which allows them to move toward or away directional light. In order to fully exploit the information content of light (intensity, direction, distribution) microorganisms need proper perceiving devices, termed photoreceptors, which must act as sensors, to perceive wavelength and direction of light, as transducers, to convert the light signal into chemical and/or electrical information, but also as amplifiers and eventually as transmitters. This review describes the universal structural, behavioral and physiological features necessary for the proper functioning of these devices in algae, and how these features have been investigated by means of different analytical techniques such as for example microspectroscopy, digital fluorescence microscopy, two photons FLIM. The insight of the photoreceptive response mechanism is explained using the unicellular alga Euglena gracilis, in which the different structural, behavioral and physiological features combine to achieve a concerted, efficient response to light stimuli.

A rhodopsin-like protein in Cyanophora paradoxa: gene sequence and protein immunolocalization

Here, we report the DNA sequence of the rhodopsin gene in the alga Cyanophora paradoxa (Glaucophyta). The primers were designed according to the conserved regions of prokaryotic and eukaryotic rhodopsin-like proteins deposited in the GenBank. The sequence consists of 1,272 bp comprised of 5 introns. The correspondent protein, named Cyanophopsin, showed high identity to rhodopsin-like proteins of Archea, Bacteria, Fungi, and Algae. At the N-terminal, the protein is characterized by a region with no transmembrane alpha-helices (80 aa), followed by a region with 7alpha-helices (219 aa) and a shorter 35-aa C-terminal region. The DNA sequence of the N-terminal region was expressed in E. coli and the recombinant purified peptide was used as antigen in hens to obtain polyclonal antibodies. Indirect immunofluorescence in C. paradoxa cells showed a marked labeling of the muroplast (aka cyanelle) membrane.

A polychromator-based microspectrophotometer

A microspectrophotometer is a digital microscope used to measure absorption and fluorescence spectra. In this paper we describe a polychromator-based microspectrophotometer that performs in vivo absorption or emission measurements at the same time on different subcellular compartments such as photoreceptive and photosynthetic structures of algal cells. In this system, a flat field imaging concave grating polychromator is connected to the slit-shaped exit pupil of a light-guide probe mounted onto a microscope equipped with an epifluorescence module. The subcellular components, on which the spectra will be measured, are placed in the microscope field and finely adjusted. The outer bundle of the probe is used for centering the objects, while the central bundle of the probe, containing 19 light guides, is used for acquiring either transmitted or emitted light (i.e. fluorescence). The light transmitted or emitted by the subcellular components is collected by the probe mounted in the back focal plane of the ocular. The exit pupil of this probe, connected to a flat field imaging concave grating polychromator, produces a dispersion image that in turn is focused onto a digital slow scan cooled CCD camera. Absorption and emission spectra of algal subcellular compartments are presented.

Photoactivated adenylyl cyclase (PAC) genes in the flagellate Euglena gracilis mutant strains

The unicellular, green flagellate wild-type Euglena gracilis(strain Z) and its colorless phototaxis-mutant strains as well as the non-photosynthetic close relative, Astasia longa, possess several genes of the photoactivated adenylyl cyclase (PAC) family. The corresponding gene products were found to be responsible for step-up (but not step-down) photophobic responses as well as both positive and negative phototaxis. The proteins consist of two PACalpha(M(r) 105 kDa) and two PACbeta(90 kDa) subunits. While the proteins were first believed all to be located in the paraxonemal body (PAB), confocal microscopy revealed that Astasia longa as well as some of the mutant strains do not contain a PAB. Immunofluorescence using PAC antibodies showed that the PAC proteins are also located along the total length of the flagellum at least in some of the strains. In order to determine if the genes responsible for the PAC proteins in the PAB and flagella are identical, sequences of all PAC proteins were analyzed in the Euglena and Astasia strains studied for PAC protein location. Full sequence analysis using PCR and 3' and 5' RACE indicated a substantial divergence between strains with a homology between strains of between 45 and 100%. Sequence alignment and sequence tree construction for the main functional groups (BLUF domain, which binds FAD, and adenylyl cyclase) showed that the pacalpha and the pacbeta gene products form clusters each with some of the mutants being closely related while others show a substantial degree of genetic diversity. The conclusion of these results is that there is a family of very dissimilar PAC proteins located in the PAB and the flagellum where they serve different functions in phototaxis and step-up photophobic reactions.

Photoactivated adenylyl cyclase controls phototaxis in the flagellate Euglena gracilis

Euglena gracilis, a unicellular freshwater protist exhibits different photomovement responses, such as phototaxis (oriented movement toward or away from the light source) and photophobic (abrupt turn in response to a rapid increase [step-up] or decrease [step-down] in the light fluence rate) responses. Photoactivated adenylyl cyclase (PAC) has been isolated from whole-cell preparations and identified by RNA interference (RNAi) to be the photoreceptor for step-up photophobic responses but not for step-down photophobic responses (M. Iseki, S. Matsunaga, A. Murakami, K. Ohno, K. Shiga, C. Yoshida, M. Sugai, T. Takahashi, T. Hori, M. Watanabe [2002] Nature 415: 1047-1051). The present study shows that knockdown of PAC by RNAi also effectively suppresses both positive and negative phototaxis, indicating for the first time that PAC or a PAC homolog is also the photoreceptor for photoorientation of wild-type E. gracilis. Recovery from RNAi occurred earlier for step-up photophobic responses than for positive and negative phototaxis. In addition, we investigated several phototaxis mutant strains of E. gracilis with different cytological features regarding the stigma and paraxonemal body (PAB; believed to be the location for the phototaxis photoreceptor) as well as Astasia longa, a close relative of E. gracilis. All of the E. gracilis mutant strains had PAC mRNAs, whereas in A. longa, a different but similar mRNA was found and designated AlPAC. Consistently, all of these strains showed no phototaxis but performed step-up photophobic responses, which were suppressed by RNAi of the PAC mRNA. The fact that some of these strains possess a cytologically altered or no PAB demonstrates that at least in these strains, the PAC photoreceptor responsible for the step-up photophobic responses is not located in the PAB.

Fluorescence behavior of Euglena photoreceptor

To provide new information on the series of structural changes that Euglena photoreceptive proteins undergo inside the photoreceptor in response to light, we measured in vivo emission fluorescence spectra in the stable intermediates of its photocycle. Our emission spectra give a certain indication that fluorescent proteins are present in the Euglena photoreceptor and that they undergo a photocycle. On the basis of our data, we suggested that at least two stable intermediates, one of which is fluorescent, can be discriminated at room temperature and with our time resolution.

Photoreception and photomovements of microorganisms

Many freely motile microorganisms can perceive and transduce external photic stimuli to the motor apparatus, eventually moving, by means of various behavioural strategies, into environments in which the illumination conditions are the most favourable for their life. In different microorganisms, a wide range of chromophores operate as light detectors, each of them set in a special molecular pocket that, in its turn, can be linked to another component of the transduction chain. The diverse photosensors are organized in special (and in many cases dedicated) photoreceptor units or subcellular organelles. The main molecular mechanisms connecting the early event of photon absorption to the formation of the signalling state down to the dark steps of the transduction chain are discussed in a selected number of case examples. The possible importance of an intensive multidisciplinary approach to these problems in an evolutionary perspective is finally briefly outlined.

A rhodopsin-like protein in the plasma membrane of Silvetia compressa eggs

Unidirectional blue light directs the rhizoid-thallus axis in the apolar zygote of the brown alga, Silvetia compressa. This effect is mediated by an increase in the intracellular concentration of guanosine 3', 5'-cyclic monophosphate. In this study we show the identification of a rhodopsin-like protein, by means of antibody reaction, in the plasma membrane of Silvetia eggs. This new result suggests a role for opsins in Silvetia photopolarity.