Construction of a Chlamydomonas reinhardtii mutant with an intronless psbA gene

An All-Green Photo-Electrochemical Biosensor Using Microalgae Immobilized on Eco-Designed Lignin-Based Screen-Printed Electrodes to Detect Sustainable Nanoherbicides

Herein, a novel completely green biosensor was designed exploiting both the biological and instrumental components made of eco-friendly materials for the detection of herbicides encapsulated into biodegradable nanoparticles for a sustainable agriculture. Similar nanocarriers, indeed, can deliver herbicides to the correct location, reducing the amount of active chemicals deposited in the plant, impacting the agricultural and food industries less. However, handling measurements of nanoherbicides is crucial to provide comprehensive information about their status in the agricultural fields to support farmers in decision-making. In detail, whole cells of the unicellular green photosynthetic alga Chlamydomonas reinhardtii UV180 mutant were immobilized by a green protocol on carbonized lignin screen-printed electrodes and integrated into a photo-electrochemical transductor for the detection of nanoformulated atrazine. Specifically, atrazine encapsulated into zein and chitosan doped poly-ε-caprolactone nanoparticles (atrazine-zein and atrazine-PCL-Ch) were analyzed following the current signals at a fixed applied potential of 0.8 V, in a range between 0.1 and 5 µM, indicating a linear relationship in the measured dose-response curves and a detection limit of 0.9 and 1.1 nM, respectively. Interference studies resulted in no interference from 10 ppb bisphenol A, 1 ppb paraoxon, 100 ppb arsenic, 20 ppb copper, 5 ppb cadmium, and 10 ppb lead at safety limits. Finally, no matrix effect was observed on the biosensor response from wastewater samples and satisfactory recovery values of 106 ± 8% and 93 ± 7% were obtained for atrazine-zein and atrazine-PCL-Ch, respectively. A working stability of 10 h was achieved.

A dual electro-optical biosensor based on Chlamydomonas reinhardtii immobilised on paper-based nanomodified screen-printed electrodes for herbicide monitoring

The indiscriminate use of herbicides in agriculture contributes to soil and water pollution, with important endangering consequences on the ecosystems. Among the available analytical systems, algal biosensors have demonstrated to be valid tools thanks to their high sensitivity, cost-effectiveness, and eco-design. Herein, we report the development of a dual electro-optical biosensor for herbicide monitoring, based on Chlamydomonas reinhardtii whole cells immobilised on paper-based screen-printed electrodes modified with carbon black nanomaterials. To this aim, a systematic study was performed for the selection and characterisation of a collection among 28 different genetic variants of the alga with difference response behaviour towards diverse herbicide classes. Thus, CC125 strain was exploited as case study for the study of the analytical parameters. The biosensor was tested in standard solutions and real samples, providing high sensitivity (detection limit in the pico/nanomolar), high repeatability (RSD of 5% with n = 100), long lasting working (10 h) and storage stability (3 weeks), any interference in the presence of heavy metals and insecticides, and low matrix effect in drinking water and moderate effect in surface one.

An eco-designed paper-based algal biosensor for nanoformulated herbicide optical detection

In this study we reported the development of a paper-based algal biosensor for the optical detection of nanoencapsulated-atrazine, a forefront nanoformulated herbicide with a high effective post-emergence herbicidal activity. In particular, the unicellular green photosynthetic algae Chlamydomonas reinhardtii was immobilised on a paper substrate soaked with an agar thin film and placed in a glass optical measurement cell, obtaining a totally environmental-friendly device. Nanoencapsulated-atrazine was detected by following the variable fluorescence (1-V_J) parameter, which decreased inversely proportional to the herbicide concentrations, in a range between 0.5 and 200 nM, indicating a linear relationship in the measured dose-response curves and a detection limit of 4 pM. Interference studies resulted in a very slight interference in presence of 2 ppm copper and 10 ppb arsenic at safety limits, as well as a slight matrix effect and a satisfactory recovery value of 96 ± 5% for 75 nM nanoencapsulated-atrazine in tap water. Stability studies were also performed obtaining a good storage stability up to 3 weeks. Results demonstrated the suitability of the proposed paper-based optical biosensor as a valid support in smart agriculture for on site, environmental friendly, cost effective and sensitive nanoencapsulated-atrazine analysis.

Targeting mutations to the plastidial psbA gene of Chlamydomonas reinhardtii without direct positive selection

Targeting mutations to specific genomic loci is invaluable for assessing in vivo the effect of these changes on the biological role of the gene in study. Here, we attempted to introduce a mutation that was previously implicated in an increased heat stability of the mesophilic cyanobacterium Synechocystis sp. PCC6803 via homologous recombination to the psbA gene of Chlamydomonas reinhardtii. For that, we established a strategy for targeted mutagenesis that was derived from the efficient genome-wide homologous-recombination-based methodology that was used to target individual genes of Saccharomyces cerevisiae. While the isolated mutants did not show any benefit under elevated temperature conditions, the new strategy proved to be efficient for C. reinhardtii even in the absence of direct positive selection.

Dynamics Properties of Photosynthetic Microorganisms Probed by Incoherent Neutron Scattering

Studies on the dynamical properties of photosynthetic membranes of land plants and purple bacteria have been previously performed by neutron spectroscopy, revealing a tight coupling between specific photochemical reactions and macromolecular dynamics. Here, we probed the intrinsic dynamics of biotechnologically useful mutants of the green alga Chlamydomonas reinhardtii by incoherent neutron scattering coupled with prompt chlorophyll fluorescence experiments. We brought to light that single amino acid replacements in the plastoquinone (PQ)-binding niche of the photosystem II D1 protein impair electron transport (ET) efficiency between quinones and confer increased flexibility to the host membranes, expanding to the entire cells. Hence, a more flexible environment in the PQ-binding niche has been associated to a less efficient ET. A similar function/dynamics relationship was also demonstrated in Rhodobacter sphaeroides reaction centers having inhibited ET, indicating that flexibility at the quinones region plays a crucial role in evolutionarily distant organisms. Instead, a different functional/dynamical correlation was observed in algal mutants hosting a single amino acid replacement residing in a D1 domain far from the PQ-binding niche. Noteworthy, this mutant displayed the highest degree of flexibility, and besides having a nativelike ET efficiency in physiological conditions, it acquired novel, to our knowledge, phenotypic traits enabling it to preserve a high maximal quantum yield of photosystem II photochemistry in extreme habitats. Overall, in the nanosecond timescale, the degree of the observed flexibility is related to the mutation site; in the picosecond timescale, we highlighted the presence of a more pronounced dynamic heterogeneity in all mutants compared to the native cells, which could be related to a marked chemically heterogeneous environment.

Photosystem-II D1 protein mutants of Chlamydomonas reinhardtii in relation to metabolic rewiring and remodelling of H-bond network at QB site

Photosystem II (PSII) reaction centre D1 protein of oxygenic phototrophs is pivotal for sustaining photosynthesis. Also, it is targeted by herbicides and herbicide-resistant weeds harbour single amino acid substitutions in D1. Conservation of D1 primary structure is seminal in the photosynthetic performance in many diverse species. In this study, we analysed built-in and environmentally-induced (high temperature and high photon fluency – HT/HL) phenotypes of two D1 mutants of Chlamydomonas reinhardtii with Ala250Arg (A250R) and Ser264Lys (S264K) substitutions. Both mutations differentially affected efficiency of electron transport and oxygen production. In addition, targeted metabolomics revealed that the mutants undergo specific differences in primary and secondary metabolism, namely, amino acids, organic acids, pigments, NAD, xanthophylls and carotenes. Levels of lutein, β-carotene and zeaxanthin were in sync with their corresponding gene transcripts in response to HT/HL stress treatment in the parental (IL) and A250R strains. D1 structure analysis indicated that, among other effects, remodelling of H-bond network at the Q_B site might underpin the observed phenotypes. Thus, the D1 protein, in addition to being pivotal for efficient photosynthesis, may have a moonlighting role in rewiring of specific metabolic pathways, possibly involving retrograde signalling.

Fast pesticide pre-screening in marine environment using a green microalgae-based optical bioassay

The present study evaluates an optical bioassay based on green photosynthetic microalgae as a promising alternative for monitoring of relevant seawater pollutants. Photosystem II fluorescence parameters from several microalgae species were examined in the presence of three common marine pesticides that act as photosynthesis inhibitors. The three pollutants were detected within 10 min in concentrations between ng/L-μg/L. The different algae species showed slightly diverse pesticide sensitivities, being Chlorella mirabilis the most sensitive one. Potential interferences due to oil-spill pollutants were discarded. The lipid content was characterized to identify microorganisms with suitable mechanisms that could facilitate stress acclimatization. C. mirabilis presented elevated content of unsaturated lipids, showing a promising potential for biosensing in saline stress conditions. The optimized microalgae-based bioassay was preliminarily incorporated into a marine buoy for autonomous pre-screening of pesticides in coastal areas, demonstrating its suitability for real-time monitoring of marine water and quantitative evaluation of total biotoxicity.

A nucleus-encoded chloroplast protein regulated by iron availability governs expression of the photosystem I subunit PsaA in Chlamydomonas reinhardtii

The biogenesis of the photosynthetic electron transfer chain in the thylakoid membranes requires the concerted expression of genes in the chloroplast and the nucleus. Chloroplast gene expression is subjected to anterograde control by a battery of nucleus-encoded proteins that are imported in the chloroplast, where they mostly intervene at posttranscriptional steps. Using a new genetic screen, we identify a nuclear mutant that is required for expression of the PsaA subunit of photosystem I (PSI) in the chloroplast of Chlamydomonas reinhardtii. This mutant is affected in the stability and translation of psaA messenger RNA. The corresponding gene, TRANSLATION OF psaA1 (TAA1), encodes a large protein with two domains that are thought to mediate RNA binding: an array of octatricopeptide repeats (OPR) and an RNA-binding domain abundant in apicomplexans (RAP) domain. We show that as expected for its function, TAA1 is localized in the chloroplast. It was previously shown that when mixotrophic cultures of C. reinhardtii (which use both photosynthesis and mitochondrial respiration for growth) are shifted to conditions of iron limitation, there is a strong decrease in the accumulation of PSI and that this is rapidly reversed when iron is resupplied. Under these conditions, TAA1 protein is also down-regulated through a posttranscriptional mechanism and rapidly reaccumulates when iron is restored. These observations reveal a concerted regulation of PSI and of TAA1 in response to iron availability.

A rapid, modular and marker-free chloroplast expression system for the green alga Chlamydomonas reinhardtii

In search of alternative expression platforms heterologous protein production in microalgae has gained increasing importance in the last years. Particularly, the chloroplast of the green alga Chlamydomonas reinhardtii has been adopted to successfully express foreign proteins like vaccines and antibodies. However, when compared with other expression systems, the development of the algal chloroplast to a powerful production platform for recombinant proteins is still in its early stages. In an effort to further improve methods for a reliable and rapid generation of transplastomic Chlamydomonas strains we constructed the key plasmid pMM2 containing the psbA gene and a multiple cloning site for foreign gene insertion. The psbA gene allows a marker-free selection procedure using as a recipient the Fud7 strain of Chlamydomonas, which grows on media containing acetate as a carbon source, but is unable to grow photoautotrophically due to the lack of an intact psbA gene. Biolistic transformation of Fud7 with vectors containing this gene restores photoautotrophic growth and thus permits selection in the light on media without carbon sources and antibiotics. The multiple cloning site with a BsaI recognition sequence allows type IIs restriction enzyme-based modular cloning which rapidly generates new gene constructs without sequences, which could influence the expression and characteristics of the foreign protein. In order to demonstrate the feasibility of this approach, a codon optimized version of the gene for the bacterial protein MPT64 has been integrated into the plastome. Several strains with different promoter/UTR combinations show a stable expression of the HA tagged MPT64 protein in Chlamydomonas chloroplasts.

Acclimation to hypoxia in Chlamydomonas reinhardtii: can biophotolysis be the major trigger for long-term H2 production?

In anaerobiosis, the microalga Chlamydomonas reinhardtii is able to produce H2 gas. Electrons mainly derive from mobilization of internal reserves or from water through biophotolysis. However, the exact mechanisms triggering this process are still unclear. Our hypothesis was that, once a proper redox state has been achieved, H2 production is eventually observed. To avoid nutrient depletion, which would result in enhanced fermentative pathways, we aimed to induce long-lasting H2 production solely through a photosynthesis : respiration equilibrium. Thus, growing cells were incubated in Tris Acetate Phosphate (TAP) medium under low light and high chlorophyll content. After a 250-h acclimation phase, a 350-h H2 production phase was observed. The light-to-H2 conversion efficiency was comparable to that given in some reports operating under sulphur starvation. Electron sources were found to be water, through biophotolysis, and proteins, particularly through photofermentation. Nonetheless, a substantial contribution from acetate could not be ruled out. In addition, photosystem II (PSII) inhibition by 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) showed that it actively contributed to maintaining a redox balance during cell acclimation. In appropriate conditions, PSII may represent the major source of reducing power to feed the H2 evolution process, by inducing and maintaining an ideal excess of reducing power.

Mutations of photosystem II D1 protein that empower efficient phenotypes of Chlamydomonas reinhardtii under extreme environment in space

Space missions have enabled testing how microorganisms, animals and plants respond to extra-terrestrial, complex and hazardous environment in space. Photosynthetic organisms are thought to be relatively more prone to microgravity, weak magnetic field and cosmic radiation because oxygenic photosynthesis is intimately associated with capture and conversion of light energy into chemical energy, a process that has adapted to relatively less complex and contained environment on Earth. To study the direct effect of the space environment on the fundamental process of photosynthesis, we sent into low Earth orbit space engineered and mutated strains of the unicellular green alga, Chlamydomonas reinhardtii, which has been widely used as a model of photosynthetic organisms. The algal mutants contained specific amino acid substitutions in the functionally important regions of the pivotal Photosystem II (PSII) reaction centre D1 protein near the Q_B binding pocket and in the environment surrounding Tyr-161 (Y_Z) electron acceptor of the oxygen-evolving complex. Using real-time measurements of PSII photochemistry, here we show that during the space flight while the control strain and two D1 mutants (A250L and V160A) were inefficient in carrying out PSII activity, two other D1 mutants, I163N and A251C, performed efficient photosynthesis, and actively re-grew upon return to Earth. Mimicking the neutron irradiation component of cosmic rays on Earth yielded similar results. Experiments with I163N and A251C D1 mutants performed on ground showed that they are better able to modulate PSII excitation pressure and have higher capacity to reoxidize the Q_A⁻ state of the primary electron acceptor. These results highlight the contribution of D1 conformation in relation to photosynthesis and oxygen production in space.

A powerful molecular engineering tool provided efficient Chlamydomonas mutants as bio-sensing elements for herbicides detection

This study was prompted by increasing concerns about ecological damage and human health threats derived by persistent contamination of water and soil with herbicides, and emerging of bio-sensing technology as powerful, fast and efficient tool for the identification of such hazards. This work is aimed at overcoming principal limitations negatively affecting the whole-cell-based biosensors performance due to inadequate stability and sensitivity of the bio-recognition element. The novel bio-sensing elements for the detection of herbicides were generated exploiting the power of molecular engineering in order to improve the performance of photosynthetic complexes. The new phenotypes were produced by an in vitro directed evolution strategy targeted at the photosystem II (PSII) D1 protein of Chlamydomonas reinhardtii, using exposures to radical-generating ionizing radiation as selection pressure. These tools proved successful to identify D1 mutations conferring enhanced stability, tolerance to free-radical-associated stress and competence for herbicide perception. Long-term stability tests of PSII performance revealed the mutants capability to deal with oxidative stress-related conditions. Furthermore, dose-response experiments indicated the strains having increased sensitivity or resistance to triazine and urea type herbicides with I(50) values ranging from 6 × 10(-8) M to 2 × 10(-6) M. Besides stressing the relevance of several amino acids for PSII photochemistry and herbicide sensing, the possibility to improve the specificity of whole-cell-based biosensors, via coupling herbicide-sensitive with herbicide-resistant strains, was verified.

Analysis of heterologous regulatory and coding regions in algal chloroplasts

The basic photosynthetic apparatus is highly conserved across all photosynthetic organisms, and this conservation can be seen in both protein composition and amino acid sequence. Conservation of regulatory elements also seems possible in chloroplast genes, as many mRNA untranslated regions (UTRs) appear to have similar structural elements. The D1 protein of Photosystem II (psbA gene) is a highly conserved core reaction center protein that shows very similar regulation from cyanobacteria through higher plants. We engineered full and partial psbA genes from a diverse set of photosynthetic organisms into a psbA deficient strain of Chlamydomonas reinhardtii. Analysis of D1 protein accumulation and photosynthetic growth revealed that coding sequences and promoters are interchangeable even between anciently diverged species. On the other hand functional recognition of 5' UTRs is limited to closely related organisms. Furthermore transformation of heterologous promoters and 5' UTRs from the atpA, tufA and psbD genes conferred psbA mRNA accumulation but not translation. Overall, our results show that heterologous D1 proteins can be expressed and complement Photosystem II function in green algae, while RNA regulatory elements appear to be very specific and function only from closely related species. Nonetheless, there is great potential for the expression of heterologous photosynthetic coding sequences for studying and modifying photosynthesis in C. reinhardtii chloroplasts.

Effects of rare codon clusters on the expression of a high-turnover chloroplast protein in Chlamydomonas reinhardtii

Expression of foreign proteins in chloroplasts has become an important field of plant genetic engineering. Optimized codon usage is generally thought to increase translational efficiency, but high speed translation of codon bias-adjusted mRNAs can also result in protein misfolding due to a lack of rare codons. In order to analyze the effect of rare codons on a native chloroplast protein in vivo, we modified the D1 subunit of photosystem II by fusing small peptides with different codons into a loop region which tolerates insertions without loss of function. Because of its high-turnover properties, the D1 protein represents an excellent test object to investigate the impact of rare codons on its translation. We choose codons for amino acids Arg, Leu, Ser, Ala and Gly which are rarely used and compared translation of the modified D1 proteins with the respective mutant proteins containing insertions with frequently used codons. Our data indicate that only rare Arg codons drastically affect synthesis of the D1 protein and cluster of rare Ser-codon can induce strategic ribosomal pausing sites.

Preliminary investigation on the production of fuels and bio-char from Chlamydomonas reinhardtii biomass residue after bio-hydrogen production

The aim of this work was to investigate the potential conversion of Chlamydomonas reinhardtii biomass harvested after hydrogen production. The spent algal biomass was converted into nitrogen-rich bio-char, biodiesel and pyrolysis oil (bio-oil). The yield of lipids (algal oil), obtained by solvent extraction, was 15 ± 2% w/w(dry-biomass). This oil was converted into biodiesel with a 8.7 ± 1% w/w(dry-biomass) yield. The extraction residue was pyrolysed in a fixed bed reactor at 350 °C obtaining bio-char as the principal fraction (44 ± 1% w/w(dry-biomass)) and 28 ± 2% w/w(dry-biomass) of bio-oil. Pyrolysis fractions were characterized by elemental analysis, while the chemical composition of bio-oil was fully characterized by GC-MS, using various derivatization techniques. Energy outputs resulting from this approach were distributed in hydrogen (40%), biodiesel (12%) and pyrolysis fractions (48%), whereas bio-char was the largest fraction in terms of mass.

Directed evolution and in silico analysis of reaction centre proteins reveal molecular signatures of photosynthesis adaptation to radiation pressure

Evolutionary mechanisms adopted by the photosynthetic apparatus to modifications in the Earth's atmosphere on a geological time-scale remain a focus of intense research. The photosynthetic machinery has had to cope with continuously changing environmental conditions and particularly with the complex ionizing radiation emitted by solar flares. The photosynthetic D1 protein, being the site of electron tunneling-mediated charge separation and solar energy transduction, is a hot spot for the generation of radiation-induced radical injuries. We explored the possibility to produce D1 variants tolerant to ionizing radiation in Chlamydomonas reinhardtii and clarified the effect of radiation-induced oxidative damage on the photosynthetic proteins evolution. In vitro directed evolution strategies targeted at the D1 protein were adopted to create libraries of chlamydomonas random mutants, subsequently selected by exposures to radical-generating proton or neutron sources. The common trend observed in the D1 aminoacidic substitutions was the replacement of less polar by more polar amino acids. The applied selection pressure forced replacement of residues more sensitive to oxidative damage with less sensitive ones, suggesting that ionizing radiation may have been one of the driving forces in the evolution of the eukaryotic photosynthetic apparatus. A set of the identified aminoacidic substitutions, close to the secondary plastoquinone binding niche and oxygen evolving complex, were introduced by site-directed mutagenesis in un-transformed strains, and their sensitivity to free radicals attack analyzed. Mutants displayed reduced electron transport efficiency in physiological conditions, and increased photosynthetic performance stability and oxygen evolution capacity in stressful high-light conditions. Finally, comparative in silico analyses of D1 aminoacidic sequences of organisms differently located in the evolution chain, revealed a higher ratio of residues more sensitive to oxidative damage in the eukaryotic/cyanobacterial proteins compared to their bacterial orthologs. These results led us to hypothesize an archaean atmosphere less challenging in terms of ionizing radiation than the present one.

Chloroplast RNA metabolism

The chloroplast genome encodes proteins required for photosynthesis, gene expression, and other essential organellar functions. Derived from a cyanobacterial ancestor, the chloroplast combines prokaryotic and eukaryotic features of gene expression and is regulated by many nucleus-encoded proteins. This review covers four major chloroplast posttranscriptional processes: RNA processing, editing, splicing, and turnover. RNA processing includes the generation of transcript 5' and 3' termini, as well as the cleavage of polycistronic transcripts. Editing converts specific C residues to U and often changes the amino acid that is specified by the edited codon. Chloroplasts feature introns of groups I and II, which undergo protein-facilitated cis- or trans-splicing in vivo. Each of these RNA-based processes involves proteins of the pentatricopeptide motif-containing family, which does not occur in prokaryotes. Plant-specific RNA-binding proteins may underpin the adaptation of the chloroplast to the eukaryotic context.

Structure-based design of novel Chlamydomonas reinhardtii D1-D2 photosynthetic proteins for herbicide monitoring

The D1-D2 heterodimer in the reaction center core of phototrophs binds the redox plastoquinone cofactors, Q(A) and Q(B), the terminal acceptors of the photosynthetic electron transfer chain in the photosystem II (PSII). This complex is the target of the herbicide atrazine, an environmental pollutant competitive inhibitor of Q(B) binding, and consequently it represents an excellent biomediator to develop biosensors for pollutant monitoring in ecosystems. In this context, we have undertaken a study of the Chlamydomonas reinhardtii D1-D2 proteins aimed at designing site directed mutants with increased affinity for atrazine. The three-dimensional structure of the D1 and D2 proteins from C. reinhardtii has been homology modeled using the crystal structure of the highly homologous Thermosynechococcus elongatus proteins as templates. Mutants of D1 and D2 were then generated in silico and the atrazine binding affinity of the mutant proteins has been calculated to predict mutations able to increase PSII affinity for atrazine. The computational approach has been validated through comparison with available experimental data and production and characterization of one of the predicted mutants. The latter analyses indicated an increase of one order of magnitude of the mutant sensitivity and affinity for atrazine as compared to the control strain. Finally, D1-D2 heterodimer mutants were designed and selected which, according to our model, increase atrazine binding affinity by up to 20 kcal/mol, representing useful starting points for the development of high affinity biosensors for atrazine.

Optical biosensors for environmental monitoring based on computational and biotechnological tools for engineering the photosynthetic D1 protein of Chlamydomonas reinhardtii

Homology-based protein modelling and computational screening followed by virtual mutagenesis analyses were used to identify functional amino acids in the D1 protein of the photosynthetic electron transfer chain interacting with herbicides. A library of functional mutations in the unicellular green alga Chlamydomonas reinhardtii for preparing biomediators was built and their interactions with herbicides were calculated. D1 proteins giving the lowest and highest binding energy with herbicides were considered as suitable for preparing the environmental biosensors for detecting specific herbicide classes. Arising from the results of theoretical calculations, three mutants were prepared by site-directed mutagenesis and characterized by fluorescence analysis. Their adsorption and selective recognition ability were studied by an equilibrium-adsorption method. The S268C and S264K biomediators showed high sensitivity and resistance, respectively, to both triazine and urea classes of herbicides. When immobilized on a silicon septum, the biomediators were found to be highly stable, remaining so for at least 1-month at room temperature. The fluorescence properties were exploited and a reusable and portable multiarray optical biosensor for environmental monitoring was developed with limits of detection between 0.8 x 10(-11) and 3.0 x 10(-9), depending on the target analyte. In addition, biomediator regeneration without obvious deterioration in performance was demonstrated.

Chlamydomonas reinhardtii genetic variants as probes for fluorescence sensing system in detection of pollutants

The unicellular green alga Chlamydomonas reinhardtii is employed here for the setup of a biosensor demonstrator based on multibiomediators for the detection of herbicides. The detection is based on the activity of photosystem II, the multienzymatic chlorophyll-protein complex located in the thylakoid membrane that catalyzes the light-dependent photosynthetic primary charge separation and the electron transfer chain in cyanobacteria, algae, and higher plants. Several C. reinhardtii mutants modified on the D1 photosystem II protein are generated by site-directed mutagenesis and experimentally tested for the development of a biosensor revealing the modification of the fluorescence parameter (1 - V (J)) in the presence of herbicides. The A250R, A250L, A251C, and I163N mutants are highly sensitive to the urea and triazine herbicide classes; the newly generated F255N mutant is shown to be especially resistant to the class of urea. It follows that the response of the multibiomediators is associated to a particular herbicide subclass and can be useful to monitor several species of pollutants.

Chlamydomonas chloroplasts can use short dispersed repeats and multiple pathways to repair a double-strand break in the genome

Certain group I introns insert into intronless DNA via an endonuclease that creates a double-strand break (DSB). There are two models for intron homing in phage: synthesis-dependent strand annealing (SDSA) and double-strand break repair (DSBR). The Cr.psbA4 intron homes efficiently from a plasmid into the chloroplast psbA gene in Chlamydomonas, but little is known about the mechanism. Analysis of co-transformants selected using a spectinomycin-resistant 16S gene (16S(spec)) provided evidence for both pathways. We also examined the consequences of the donor DNA having only one-sided or no homology with the psbA gene. When there was no homology with the donor DNA, deletions of up to 5 kb involving direct repeats that flank the psbA gene were obtained. Remarkably, repeats as short as 15 bp were used for this repair, which is consistent with the single-strand annealing (SSA) pathway. When the donor had one-sided homology, the DSB in most co-transformants was repaired using two DNAs, the donor and the 16S(spec) plasmid, which, coincidentally, contained a region that is repeated upstream of psbA. DSB repair using two separate DNAs provides further evidence for the SDSA pathway. These data show that the chloroplast can repair a DSB using short dispersed repeats located proximally, distally, or even on separate molecules relative to the DSB. They also provide a rationale for the extensive repertoire of repeated sequences in this genome.

Expression, purification, and biochemical characterization of the intron-encoded endonuclease, I-CreII

The ORF of the Cr.psbA4 intron of Chlamydomonas reinhardtii mediates efficient intron homing, and contains an H-N-H and possibly a GIY-YIG motif. The ORF was over-expressed in Escherichia coli without non-native amino acids, but was mostly insoluble. However, co-over-expression of E. coli chaperonins GroEL/GroES solubilized approximately 50% of the protein, which was purified by ion-exchange and heparin-affinity chromatography. Biochemical characterization showed that the protein is a double-strand-specific endonuclease that cleaves fused psbA exon 4-exon 5 DNA, and was named I-CreII. I-CreII has a relatively relaxed divalent metal ion requirement (Mg(2+), Mn(2+), Ca(2+), and Fe(2+) supported cleavage), is insensitive to salt <350 mM, and is stabilized by DNA. Cleavage of target DNA occurs close (4 nt on the top strand) to the intron-insertion site, and leaves 2-nt 3'-OH overhangs, similar to GIY-YIG endonucleases. The boundaries of the recognition sequence span approximately 30 bp, and encompass the cleavage and intron-insertion sites. Cleavage of heterologous psbA DNAs indicates the enzyme can tolerate multiple, but not all, substitutions in the recognition site. This work will facilitate further study of this novel endonuclease, which may also find use in site-specific manipulation of chloroplast DNA.

Phylogenetic analyses suggest reverse splicing spread of group I introns in fungal ribosomal DNA

BACKGROUND

Group I introns have spread into over 90 different sites in nuclear ribosomal DNA (rDNA) with greater than 1700 introns reported in these genes. These ribozymes generally spread through endonuclease-mediated intron homing. Another putative pathway is reverse splicing whereby a free group I intron inserts into a homologous or heterologous RNA through complementary base-pairing between the intron and exon RNA. Reverse-transcription of the RNA followed by general recombination results in intron spread. Here we used phylogenetics to test for reverse splicing spread in a taxonomically broadly sampled data set of fungal group I introns including 9 putatively ancient group I introns in the rDNA of the yeast-like symbiont Symbiotaphrina buchneri.

RESULTS

Our analyses reveal a complex evolutionary history of the fungal introns with many cases of vertical inheritance (putatively for the 9 introns in S. buchneri) and intron lateral transfer. There are several examples in which introns, many of which are still present in S. buchneri, may have spread through reverse splicing into heterologous rDNA sites. If the S. buchneri introns are ancient as we postulate, then group I intron loss was widespread in fungal rDNA evolution.

CONCLUSION

On the basis of these results, we suggest that the extensive distribution of fungal group I introns is at least partially explained by the reverse splicing movement of existing introns into ectopic rDNA sites.

Rapid, ATP-dependent degradation of a truncated D1 protein in the chloroplast

The D1 protein constitutes one of the reaction center subunits of photosystem II and turns over rapidly due to photooxidative damage. Here, we studied the degradation of a truncated D1 protein. A plasmid with a precise deletion in the reading frame of the psbA gene encoding D1 was introduced into the chloroplast of Chlamydomonas reinhardtii. A homoplasmic mutant containing the desired gene was able to synthesize the truncated form of the polypeptide, but could not accumulate significant levels of it. As a consequence, other central photosystem II subunits did not assemble within the thylakoid membrane. In vivo pulse-chase experiments showed that the abnormal D1 protein is rapidly degraded in the light. Degradation was delayed in the light in the presence of an uncoupler, or when cells were incubated in the dark. Pulse-chase experiments performed in vitro indicate that an ATP and metal-dependent protease is responsible for the breakdown process. The paper describes the first in vivo and in vitro functional test for ATP-dependent degradation of a defect polypeptide in chloroplasts. The possible involvement of proteases similar to those removing abnormal proteins in prokaryotic organisms is discussed on the basis of proteases recently identified in chloroplasts.

Mobile self-splicing group I introns from the psbA gene of Chlamydomonas reinhardtii: highly efficient homing of an exogenous intron containing its own promoter

Introns 2 and 4 of the psbA gene of Chlamydomonas reinhardtii chloroplasts (Cr.psbA2 and Cr.psbA4, respectively) contain large free-standing open reading frames (ORFs). We used transformation of an intronless-psbA strain (IL) to test whether these introns undergo homing. Each intron, plus short exon sequences, was cloned into a chloroplast expression vector in both orientations and then cotransformed into IL along with a spectinomycin resistance marker (16S rrn). For Cr.psbA2, the sense construct gave nearly 100% cointegration of the intron whereas the antisense construct gave 0%, consistent with homing. For Cr.psbA4, however, both orientations produced highly efficient cointegration of the intron. Efficient cointegration of Cr.psbA4 also occurred when the intron was introduced as a restriction fragment lacking any known promoter. Deletion of most of the ORF, however, abolished cointegration of the intron, consistent with homing. The Cr.psbA4 constructs also contained a 3-(3,4-dichlorophenyl)-1,1-dimethylurea resistance marker in exon 5, which was always present when the intron integrated, thus demonstrating exon coconversion. Remarkably, primary selection for this marker gave >100-fold more transformants (>10,000/microgram of DNA) than did the spectinomycin resistance marker. A trans homing assay was developed for Cr.psbA4; the ORF-minus intron integrated when the ORF was cotransformed on a separate plasmid. This assay was used to identify an intronic region between bp -88 and -194 (relative to the ORF) that stimulated homing and contained a possible bacterial (-10, -35)-type promoter. Primer extension analysis detected a transcript that could originate from this promoter. Thus, this mobile, self-splicing intron also contains its own promoter for ORF expression. The implications of these results for horizontal intron transfer and organelle transformation are discussed.

Preparation protocols for high-activity photosystem II membrane particles of green algae and higher plants, pH dependence of oxygen evolution and comparison of the S2-state multiline signal by X-band EPR spectroscopy

Photosystem II (PS II) membrane particles are particularly well suited for various types of spectroscopic investigations on the PS II manganese complex. Here we present: (1) a preparation protocol for PS II membrane particles of higher plants, which yields exceptionally high oxygen-evolution activity due to the use of glycinebetaine as a PS II-stabilizing agent; (2) preparation protocols for highly active PS II membrane particles for the green algae Scenedesmus obliquus and Chlamydomonas reinhardtii; (3) a determination of pH dependence of oxygen evolution for spinach and Scenedesmus; (4) a comparison of the EPR multiline signal observed in the S2-state of green algae and higher plants of PS II membrane particles. A clearly broader type of multiline EPR signal is observed in green algae.

Structure and orientation of the oxygen-evolving manganese complex of green algae and higher plants investigated by X-ray absorption linear dichroism spectroscopy on oriented photosystem II membrane particles

X-ray absorption spectroscopy at the Mn K-edge has been performed on multilayers of photosystem II-enriched fragments of the native thylakoid membrane prepared from a higher plant (spinach) and a unicellular green alga (Scenedesmus obliquus). Spectra collected for various angles between the prevailing orientation of the thylakoid membrane normal and the X-ray electric field vector contain information on the atomic structure of the tetranuclear manganese complex of photosystem II (PS II) and its orientation with respect to the membrane normal. The previously used approach for evaluation of the dichroism of extended X-ray absorption fine structure (EXAFS) spectra [George, G. N., et al. (1989) Science 243, 789-791] is modified, and the following results are obtained for PS II in its dark-stable state (S1-state): (1) structure and orientation of the PS II manganese complexes of green algae and higher plants are highly similiar or fully identical; (2) two 2.7-A vectors, which, most likely, connect the Mn nuclei of a planar Mn2(mu-O2) structure, are at an average angle of 80 degrees +/- 10 degrees with respect to the thylakoid normal; (3) the plane of the Mn2(mu-O2) structures is rather in parallel with the thylakoid plane than perpendicular. Structural models for the oxygen-evolving manganese complex and its orientation in the thylakoid membrane are discussed within the context of the presented results.

Genetic engineering of thylakoid protein complexes by chloroplast transformation in Chlamydomonas reinhardtii

Chloroplast transformation of Chlamydomonas reinhardtii has developed into a powerful tool for studying the structure, function and assembly of thylakoid protein complexes in a eukaryotic organism. In this article we review the progress that is being made in the development of procedures for efficient chloroplast transformation. This focuses on the development of selectable markers and the use of Chlamydomonas mutants, individually lacking thylakoid protein complexes, as recipients. Chloroplast transformation has now been used to engineer all four major thylakoid protein complexes, photosystem II, photosystem I, cytochrome b 6/f and ATP synthase. These results are discussed with an emphasis on new insights into assembly and function of these complexes in chloroplasts as compared with their prokaryotic counterparts.

A robust protocol for site-directed mutagenesis of the D1 protein inChlamydomonas reinhardtii: A PCR-splicedpsbA gene in a plasmid conferring spectinomycin resistance was introduced into apsbA deletion strain

In this paper, we describe a protocol to obtain a site-directed mutants in thepsbA gene ofChlamydomonas reinhardtii, which overcomes several drawbacks of previous protocols, and makes it possible to generate a mutant within a month. Since the large size of the gene, and the presence of four large introns has made molecular genetics of thepsbA gene rather unwieldy, we have spliced all of the exons of thepsbA gene by PCR to facilitate genetic manipulation and sequencing of the gene. The resultant construct (plasmid pBA153, with several unique restriction sites introduced at exon boundaries) carried 1.2 and 1.8 kb intact sequences from the 5'- and 3'-flanking regions, respectively. The plasmid was used to transform a D1-deletion mutant and was found to complement the deletion and restore photosynthetic activity. In addition, a bacterialaadA gene conferring spectinomycin resistance (spe (r)) was inserted downstream of the intron-freepsbA gene, to give construct pBA155. This allowed selection of mutant strains deficient in photosynthesis by using spectinomycin resistance, and eliminated the possibility of selection for revertant strains which is a consequence of having to use photosynthetic activity as a selection pressure. Finally, pBA155 was used to construct pBA157, in which additional restriction sites were inserted to facilitate cassette mutagenesis for generation of mutations in spans thought to be involved in donor-side interactions. AllpsbA deletion strains transformed with intron-freepsbA-aadA constructs encoding the wild-type D1 sequence, and screened on spectinomycin plates for thespe (r) phenotype, were able to grow photosynthetically, and all showed identical kinetics for electron transfer from primary (QA) to secondary quinone (QB) in Photosystem II, as assayed by the decay of the high fluorescence yield on oxidation of the reduced primary acceptor (QA (-)).

Correct in vivo RNA splicing of a mitochondrial intron in algal chloroplasts

The self-splicing group II intron (rl1) from Scenedesmus obliquus mitochondria together with its 6 bp intron binding site (IBS1) were inserted in the correct and inverse orientation into the chloroplast tscA gene from C.reinhardtii. Precursor RNA derived from the chimeric tscA-rl1 gene can be used to demonstrate in vitro self-splicing of the rl1 intron RNA. Using the particle bombardment technique, the tscA-rl1 construct was transferred into the chloroplast of the unicellular alga Chlamydomonas reinhardtii. We recovered transformants which contain the chimeric tscA-rl1 gene as shown by Southern analysis. Hybridization and PCR analysis of transcripts confirmed that the heterologous intron is correctly spliced in vivo. From sequencing of cDNA clones we conclude that the IBS1 sequence is sufficient for correct splicing of the mitochondrial intron in C. reinhardtii chloroplasts. Using specific probes, we demonstrate by Northern hybridization that the mature RNA, as well as an intron-3' exon intermediate, accumulate in transformants containing the rl1 intron, correctly inserted into the tscA gene. As expected, no RNA splicing at all was observed when the intron had an inverted orientation within the tscA gene. In addition, a mutated intron RNA with an altered 3' terminal nucleotide was tested in vivo. In contrast to similar mutants examined in vitro, this mutated RNA shows accumulated intron and intron-3' exon intermediates, but no ligated exons at all. Our approach should prove useful for elucidating nucleotide residues involved in splicing of organelle introns in vivo.

Particle bombardment: a universal approach for gene transfer to cells and tissues

In the past year, significant progress in the field of gene transfer has been made possible by refinement of the technique of particle bombardment. The process has been utilized for the study of gene expression in plastids and mitochondria, the production of transgenic crop plants and gene transfer into live animals. Bombarding tissues of live animals with genes that code for antigenic proteins may provide an effective means of vaccination.