The two genes for the small subunit of RuBP Carboxylase/oxygenase are closely linked in Chlamydomonas reinhardtii

Transcriptomic analysis reveals the mechanism on the response of Chlorococcum sp. GD to glucose concentration in mixotrophic cultivation

In this study, the performance of Chlorococcum sp. GD in synthetic medium with different glucose concentrations (ranging from 1 to10 g/L) was investigated. Moreover, transcriptome sequencing was conducted to clarify the response of the microalga to glucose concentrations. High concentration of glucose (6-10 g/L) not only did not provide a higher yield of biomass but also inhibited photosynthesis. Transcriptomic analysis revealed that the glucose metabolism mainly depended on the glycolysis and the pentose phosphate pathway (PPP) as the microalga was cultivated with 10 g/L glucose. Meanwhile the tricarboxylic acid (TCA) cycle, oxidative phosphorylation and photosynthesis were significantly inhibited. The significant change on carbon metabolic flux caused by the increase in glucose concentration affected the synthesis of reducing power and ATP, which ultimately influenced the growth of the microalga. Appropriate supplement of organic carbon not only enhances the biomass accumulation but also increases the utilization efficiency of organic carbon.

Effects of paraquat on photosynthetic pigments, antioxidant enzymes, and gene expression in Chlorella pyrenoidosa under mixotrophic compared with autotrophic conditions

Only limited information is available on herbicide toxicity to algae under mixotrophic conditions. In the present study, we studied the effects of the herbicide paraquat on growth, photosynthetic pigments, antioxidant enzymes, and gene expression in Chlorella pyrenoidosa under mixotrophic compared with autotrophic conditions. The mean measured exposure concentrations of paraquat under mixotrophic and autotrophic conditions were in the range of 0.3-3.4 and 0.6-3.6 μM, respectively. Exposure to paraquat for 72 h under both autotrophic and mixotrophic conditions induced decreased growth and chlorophyll (Chl) content, increased superoxide dismutase and peroxidase activities, and decreased transcript abundances of three photosynthesis-related genes (light-independent protochlorophyllide reductase subunit, photosystem II protein D1, and ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit [rbcL]). Compared with autotrophic conditions, the inhibition percentage of growth rate under mixotrophic conditions was lower at 0.8 μM paraquat, whereas it was greater at 1.8 and 3.4 μM paraquat. With exposure to 0.8-3.4 μM paraquat, the inhibition rates of Chl a and b content under mixotrophic conditions (43.1-52.4% and 54.6-59.7%, respectively) were greater compared with autotrophic conditions, whereas the inhibition rate of rbcL gene transcription under mixotrophic conditions (35.7-44.0%) was lower. These data showed that similar to autotrophic conditions, paraquat affected the activities of antioxidant enzymes and decreased Chl synthesis and transcription of photosynthesis-related genes in C. pyrenoidosa under mixotrophic conditions, but a differential susceptibility to paraquat toxicity occurred between autotrophically versus mixotrophically grown cells.

Modeling the dependence of respiration and photosynthesis upon light, acetate, carbon dioxide, nitrate and ammonium in Chlamydomonas reinhardtii using design of experiments and multiple regression

BACKGROUND

In photosynthetic organisms, the influence of light, carbon and inorganic nitrogen sources on the cellular bioenergetics has extensively been studied independently, but little information is available on the cumulative effects of these factors. Here, sequential statistical analyses based on design of experiments (DOE) coupled to standard least squares multiple regression have been undertaken to model the dependence of respiratory and photosynthetic responses (assessed by oxymetric and chlorophyll fluorescence measurements) upon the concomitant modulation of light intensity as well as acetate, CO₂, nitrate and ammonium concentrations in the culture medium of Chlamydomonas reinhardtii. The main goals of these analyses were to explain response variability (i.e. bioenergetic plasticity) and to characterize quantitatively the influence of the major explanatory factor(s).

RESULTS

For each response, 2 successive rounds of multiple regression coupled to one-way ANOVA F-tests have been undertaken to select the major explanatory factor(s) (1st-round) and mathematically simulate their influence (2nd-round). These analyses reveal that a maximal number of 3 environmental factors over 5 is sufficient to explain most of the response variability, and interestingly highlight quadratic effects and second-order interactions in some cases. In parallel, the predictive ability of the 2nd-round models has also been investigated by k-fold cross-validation and experimental validation tests on new random combinations of factors. These validation procedures tend to indicate that the 2nd-round models can also be used to predict the responses with an inherent deviation quantified by the analytical error of the models.

CONCLUSIONS

Altogether, the results of the 2 rounds of modeling provide an overview of the bioenergetic adaptations of C. reinhardtii to changing environmental conditions and point out promising tracks for future in-depth investigations of the molecular mechanisms underlying the present observations.

SHORT-TERM EFFECTS OF ACETATE AND MICROAEROBIC CONDITIONS ON PHOTOSYNTHESIS AND RESPIRATION IN CHLORELLA SOROKINIANA GXNN 01 (CHLOROPHYTA)(1)

The culture of microalgae using organic carbon sources decreases the cost of operation in closed systems. The effect of carbon sources on microalgae is thus an interesting problem in not only theoretical research but also practical production. The short-term effects of acetate and microaerobic conditions on the growth, photosynthesis, and respiration of the green microalga Chlorella sorokiniana I. Shihira & R.W. Krauss GXNN 01 were described after acetate addition to autotrophic cultures. As the acetate concentration increased, cells needed a longer lag phase to grow, and 243.8 mM acetate completely inhibited growth. Acetate addition induced an immediate response in photosynthesis and respiration. The activity of PS II and PS I were impaired and declined with different rates, and then recovered compared with autotrophic cells. Carbonic anhydrase and Rubisco activities were also inhibited at the beginning, and respiration was increased. We propose that ATP consumption for acetate assimilation results in surplus NADPH, and then accumulated reducing power over-reduces inter-photosystem components and raises the transthylakoid proton gradient, which redistributes energy between PS I and PS II, and leads to a decrease in the PS II/PS I ratio and O2 evolution. An apparent cyclic electron flow was also observed, which may be mainly mediated by NAD(P)H dehydrogenase-dependent pathway since NADPH was in excess. These observations pointed to an acclimation process after acetate addition, and suggested the interaction between photosynthesis and respiration involving ATP and reducing power.

Sugar-mediated transcriptional regulation of the Gap gene system and concerted photosystem II functional modulation in the microalga Scenedesmus vacuolatus

Partial cDNAs corresponding to the GapA, GapC and GapN genes that encode the three different glyceraldehyde-3-phosphate dehydrogenases (GAPDHs) of the green microalga Scenedesmus vacuolatus SAG 211-8b have been cloned and characterized. Northern blot experiments, as well as immunoblots and activity measurements, demonstrate a differential regulation by sugars of the components of the algal Gap gene system. Addition of glucose or other metabolizable sugars to photoautotrophic cultures promoted a drastic repression of the GapA gene and depletion to negligible levels of the corresponding GAPDHA, a chloroplastic protein involved in photosynthetic CO2 assimilation. By contrast, expression of the GapC and GapN genes encoding their cytosolic counterparts involved in glycolysis was enhanced. However, no down-regulation of the GapA gene by glucose took place in the dark, indicating that the observed effect is associated with sugar assimilation in the light. Likewise, glucose promoted in illuminated algal cultures a severe decrease of photosystem II functionality, estimated by O2 evolution activity, thermoluminescence emission and D1 protein level, while again, no effect was observed in the dark. On the basis of the correlation found between photosystem II performance and sugar transcriptional regulation of the GapA gene, a scenario of sugar-mediated regulation of photosynthetic metabolism in microalgae is proposed that will help to explain the so-called glucose bleaching effect in photosynthetic eukaryotes.

Chlamydomonas DIP13 and human NA14: a new class of proteins associated with microtubule structures is involved in cell division

We have cloned and characterized a single copy C. reinhardtii gene containing an open reading frame of 333 nucleotides encoding a 12.7 kDa protein. The novel protein, DIP13, exhibits 60% identity with two mammalian proteins, human NA14 and an unnamed mouse protein. Homologous sequences are also present in several protozoan, trematode and fish genomes, but no homologs have been found in the completed genomes of yeast, Drosophila, C. elegans and A. thaliana. By using a specific antibody we have localized DIP13 to microtubule structures, namely basal bodies, flagellar axonemes and cytoplasmic microtubules. Anti-DIP13 antibody also specifically recognized human NA14 by immunofluorescence and stained basal bodies and flagella of human sperm cells as well as the centrosome of HeLa cells. Expression of the DIP13 open reading frame in antisense orientation in Chlamydomonas resulted in multinucleate, multiflagellate cells, which suggests a role for this protein in ensuring proper cell division. Thus, DIP13/NA14 could represent the founding members of a new class of highly conserved proteins that are associated with microtubule structures.

Knock-out of a putative transporter results in altered blue-light signalling in Chlamydomonas

Nitrogen starvation and blue light are the two environmental cues that control sexual differentiation in Chlamydomonas reinhardtii. Insertional mutagenesis was applied to generate mutants that still require nitrogen starvation as the initiating signal for gametogenesis but were no longer dependent on irradiation. In one mutant analysed, sequences adjacent to the site of insertion were cloned and used for the isolation of a genomic clone that, upon transformation, could complement the mutant phenotype. The gene identified (LRG6) encodes two mRNAs that appear to be the products of differential splicing. The two putative gene products derived from these mRNAs differ in their C-terminal ends. Both predicted gene products exhibit multiple hydrophobic domains with alpha-helical secondary structure typical for integral membrane proteins. These proteins may form pores, and may function as transporters of as-yet unknown substrates. Since rendering the LRG6 gene non-functional resulted in light-independence of gamete formation, it is suggested that this transporter may inhibit signal flux from the photoreceptor to target genes - either directly by its activity or indirectly by serving as a scaffold for signalling proteins. Shutting off this transporter may be required for the activation of signal flux in this pathway. This concept is supported by the observed reduction in LRG6 mRNA levels during the first phase of gametic differentiation.

Characterization of Mbb1, a nucleus-encoded tetratricopeptide-like repeat protein required for expression of the chloroplast psbB/psbT/psbH gene cluster in Chlamydomonas reinhardtii

Genetic analysis has revealed that the accumulation of several chloroplast mRNAs of the green alga Chlamydomonas reinhardtii requires specific nucleus-encoded functions. To gain insight into this process, we have cloned the nuclear gene encoding the Mbb1 factor by genomic rescue of a mutant specifically deficient in the accumulation of the mRNAs of the psbB/psbT/psbH chloroplast transcription unit. Mbb1 is a soluble protein in the stromal phase of the chloroplast. It consists of 662 amino acids with a putative chloroplast-transit peptide at its N-terminal end. A striking feature is the presence of 10 tandemly arranged tetratricopeptide-like repeats that account for half of the protein sequence and are thought to be involved in protein-protein interactions. The Mbb1 protein seems to have a homologue in higher plants and is part of a 300-kDa complex that is associated with RNA. This complex is most likely involved in psbB mRNA processing, stability, and/or translation.

Chloroplast signalling in the light induction of nuclear HSP70 genes requires the accumulation of chlorophyll precursors and their accessibility to cytoplasm/nucleus

Chlorophyll precursors Mg-protoporphyrin IX and its monomethylester are candidates for plastid-derived molecules involved in light signalling from the chloroplast to the nucleus. The pool sizes of these two Mg2+-containing porphyrins and of protoporphyrin IX transiently increased upon a shift of Chlamydomonas cultures from dark to light. This increase coincided with the accumulation of mRNAs encoded by the nuclear genes HSP70A and HSP70B. Analysis of a mutant (brs-1), previously shown to be defective in the light induction of these genes, revealed high levels of protoporphyrin IX but no light-induced increase in the levels of Mg2+-containing porphyrins. Inhibitors of cytoplasmic protein synthesis prevented both the light-induced rise in pool levels and induction of the HSP70 genes. Similarly, pre-gametes, intermediates of sexual differentiation, lacked both responses to light. The block in light induction of the HSP70 genes in inhibitor-treated cells and in pre-gametes could be circumvented by the exogenous addition of Mg-protoporphyrin IX in the dark. This suggests an essential role for light-induced Mg-protoporphyrin IX accumulation in this chloroplast-to-nucleus signalling pathway. However, accumulation of this porphyrin in the dark - presumably in the chloroplast - did not result in induction. A second crucial role for light in this signalling pathway is postulated which makes this plastidic compound accessible to the cytoplasm/nucleus where the downstream signalling pathway may be activated.

The cytochrome c gene from the green alga Chlamydomonas reinhardtii. Structure and expression in wild-type cells and in obligate photoautotrophic (dk) mutants

The expression of the Chlamydomonas reinhardtii cytochrome c gene was studied at the steady-state mRNA level. The inclusion of acetate under illumination produced a marked increase in cytochrome c transcripts. This effect was not affected by two inhibitors of mitochondrial energy metabolism. Three different obligate photoautotrophic mutants with defective mitochondria showed normal levels of induction, suggesting that utilization of acetate for respiration is not required for this process. Light, in the presence or absence of acetate, also promoted an increase in cytochrome c transcript levels. This effect could be abolished by treatment of the cells with an inhibitor of the photosynthetic electron transport chain, suggesting that light acts through photosynthesis to promote the induction. In addition, a genomic clone encompassing the Chlamydomonas cytochrome c gene has been isolated and analyzed. The gene contains three introns, two of which are located at positions similar to those in the rice and Arabidopsis cytochrome c genes, indicating the existence of an evolutionary link. It is concluded that the cytochrome c gene from C. reinhardtii is subject to metabolic regulation through a mechanism that responds to the intracellular level of either acetate or a compound derived from its metabolization through a pathway different from mitochondrial respiration.

Genetic engineering of the chloroplast

Transformation of the plastid genome has a number of inherent advantages for the engineering of gene expression in plants. These advantages include: 10-50 times higher transgene expression levels; the absence of gene silencing and position effect variation; the ability to express polycistronic messages from a single promoter; uniparental plastid gene inheritance in most crop plants that prevents pollen transmission of foreign DNA; integration via a homologous recombination process that facilitates targeted gene replacement and precise transgene control; and sequestration of foreign proteins in the organelle which prevents adverse interactions with the cytoplasmic environment. It is now 12 years since the first conclusive demonstration of stable introduction of cloned DNA into the Chlamydomonas chloroplast by the Boynton and Gillham laboratory, and 10 years since the laboratory of Pal Maliga successfully extended these approaches to tobacco. Since then, technical developments in plastid transformation and advances in our understanding of the rules of plastid gene expression have facilitated tremendous progress towards the goal of establishing the chloroplast as a feasible platform for genetic modification of plants.

Effects of acetate on facultative autotrophy in Chlamydomonas reinhardtii assessed by photosynthetic measurements and stable isotope analyses

The green alga Chlamydomonas reinhardtii can grow photoautotrophically utilizing CO(2), heterotrophically utilizing acetate, and mixotrophically utilizing both carbon sources. Growth of cells in increasing concentrations of acetate plus 5% CO(2) in liquid culture progressively reduced photosynthetic CO(2) fixation and net O(2) evolution without effects on respiration, photosystem II efficiency (as measured by chlorophyll fluorescence), or growth. Using the technique of on-line oxygen isotope ratio mass spectrometry, we found that mixotrophic growth in acetate is not associated with activation of the cyanide-insensitive alternative oxidase pathway. The fraction of carbon biomass resulting from photosynthesis, determined by stable carbon isotope ratio mass spectrometry, declined dramatically (about 50%) in cells grown in acetate with saturating light and CO(2). Under these conditions, photosynthetic CO(2) fixation and O(2) evolution were also reduced by about 50%. Some growth conditions (e.g. limiting light, high acetate, solid medium in air) virtually abolished photosynthetic carbon gain. These effects of acetate were exacerbated in mutants with slowed electron transfer through the D1 reaction center protein of photosystem II or impaired chloroplast protein synthesis. Therefore, in mixotrophically grown cells of C. reinhardtii, interpretations of the effects of environmental or genetic manipulations of photosynthesis are likely to be confounded by acetate in the medium.

Stability determinants in the chloroplast psbB/T/H mRNAs of Chlamydomonas reinhardtii

The chloroplast gene psbB encodes the chlorophyll-a binding protein P5 (CP47), one of the core subunits of photosystem II (PSII). The psbB mRNA and the downstream psbT and psbH transcripts fail to accumulate in the Chlamydomonas reinhardtii nuclear mutant 222E affected in the Mbb1 gene (Monod et al. 1992, Mol. Gen. Genet. 231, 449-459). By introducing chimeric genes consisting of sequences from psbB and the reporter gene aadA into the chloroplast, the target site of Mbb1 was mapped in the psbB 5' untranslated region (UTR). Primer extension analysis indicates that the psbB RNA exists in a less abundant long form and a more abundant short form, with 5' ends at positions -147 and -35 relative to the AUG initiation codon, respectively. The longer transcript is present both in the wild type (WT) and 222E mutant, but the shorter one accumulates only in the WT. Two putative stem-loop structures in the longer 5' UTR can be deleted individually without affecting psbB mRNA accumulation. Insertion of a poly G cassette in the long leader stabilizes a chimeric psbB transcript in the 222E mutant, suggesting the involvement of a 5'-3' exonuclease. We also show that psbH and psbT are transcribed from the upstream psbB gene promoter, and that the psbH mRNA has its own target sequence for Mbb1 function. We discuss the role of this nucleus-encoded factor, required for specific chloroplast gene expression, in the assembly of the multi-protein PSII complex.

Induction of coproporphyrinogen oxidase in Chlamydomonas chloroplasts occurs via transcriptional regulation of Cpx1 mediated by copper response elements and increased translation from a copper deficiency-specific form of the transcript

Coproporphyrinogen III oxidase, encoded by a single nuclear gene in Chlamydomonas reinhardtii, produces three distinct transcripts. One of these transcripts is greatly induced in copper-deficient cells by transcriptional activation, whereas the other forms are copper-insensitive. The induced form of the transcript was expressed coordinately with the cytochrome c6-encoding (Cyc6) gene, which is known to be transcriptionally regulated in copper-deficient cells. The sequence GTAC, which forms the core of a copper response element associated with the Cyc6 gene, is also essential for induction of the Cpx1 gene, suggesting that both are targets of the same signal transduction pathway. The constitutive and induced Cpx1 transcripts have the same half-lives in vivo, and all encode the same polypeptide with a chloroplast-targeting transit sequence, but the shortest one representing the induced form is a 2-4-fold better template for translation than are either of the constitutive forms. The enzyme remains localized to a soluble compartment in the chloroplast even in induced cells, and its abundance is not affected when the tetrapyrrole pathway is manipulated either genetically or by gabaculine treatment.

Elimination of the Chlamydomonas gene family that encodes the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase

Ribulose-1,5-bisphosphate carboxylase/ oxygenase (EC 4.1.1.39) is the key photosynthetic enzyme that catalyzes the first step of CO2 fixation. The chloroplast-localized holoenzyme of plants and green algae contains eight nuclear-encoded small subunits and eight chloroplast-encoded large subunits. Although much has been learned about the enzyme active site that resides within each large subunit, it has been difficult to assess the role of eukaryotic small subunits in holoenzyme function and expression. Small subunits are coded by a family of genes, precluding genetic screening or nuclear transformation approaches for the recovery of small-subunit mutants. In this study, the two small-subunit mutants. In this study, the two small-subunit genes of the green alga Chlamydomonas reinhardtii were eliminated during random insertional mutagenesis. The photosynthesis-deficient deletion mutant can be complemented with either of the two wild-type small-subunit genes or with a chimeric gene that contains features of both. Thus, either small subunit is sufficient for holoenzyme assembly and function. In the absence of small subunits, expression of chloroplast-encoded large subunits appears to be inhibited at the level of translation.

Translational regulation of chloroplast genes. Proteins binding to the 5'-untranslated regions of chloroplast mRNAs in Chlamydomonas reinhardtii

We have examined the effects of illumination, carbon source, and levels of chloroplast protein synthesis on trans-acting proteins that bind to the leaders of five representative chloroplast mRNAs. The accumulation of these five chloroplast mRNAs and the proteins they encode were measured in cells grown under identical conditions. Extracts from all cell types examined contain a minimum set of six chloroplast 5'-untranslated region (UTR)-binding proteins (81, 62, 56, 47, 38, and 15 kDa). Fractionation results suggest that multiple forms of the 81-, 62-, and 47-kDa proteins may exist. A 36-kDa protein was found in all cells except those deficient in chloroplast protein synthesis. Binding of the 81-, 47-, and 38-kDa proteins to the rps12 leader is effectively competed by the atpB or rbcL 5'-UTRs, indicating that the same proteins bind to all three leaders. In contrast, these three proteins do not bind to the nuclear-encoded alpha-1 tubulin leader, which bound novel proteins of 110, 70, and 43 kDa. Cis-acting sequences within the 5'-UTRs of two chloroplast mRNAs (rps7 and atpB) have been identified which are protected from digestion by RNase T1 by extracts enriched for the 81-, 47-, and 38-kDa proteins.

The pc-1 phenotype of Chlamydomonas reinhardtii results from a deletion mutation in the nuclear gene for NADPH:protochlorophyllide oxidoreductase

The pc-1 mutant of Chlamydomonas reinhardtii has been shown to be incapable of protochlorophyllide photoconversion in vivo and is thought to be defective in light-dependent NADPH:protochlorophyllide oxidoreductase activity. We have isolated and characterized the nuclear genes encoding this enzyme from wild-type and pc-1 mutant Chlamydomonas cells. The wild-type CRlpcr-1 gene encodes a 397 amino acid polypeptide of which the N-terminal 57 residues comprise the chloroplast transit sequence. The Chlamydomonas protochlorophyllide reductase has 66-70% identity (79-82% similarity) to the higher plant enzymes. Transcripts encoding protochlorophyllide reductase are abundant in dark-grown wild-type cells, but absent or at very low levels in cells grown in the light. Similarly, immunoreactive protochlorophyllide reductase protein is also present to a greater extent in dark- versus light-grown wild-type cells. Both pc-1 and pc-1 y-7 cells lack CRlpcr-1 mRNA and the major (36 kDa) immunodetectable form of protochlorophyllide reductase consistent with their inability to photoreduce protochlorophyllide. DNA sequence analysis revealed that the lpcr gene in pc-1 y-7 cells contains a two-nucleotide deletion within the fourth and fifth codons of the protochlorophyllide reductase precursor that causes a shift in the reading frame and results in premature termination of translation. The absence of protochlorophyllide reductase message in pc-1 and pc-1 y-7 cells is likely the consequence of this frameshift mutation in the lpcr gene. Introduction of the CRlpcr-1 gene into pc-1 y-7 cells by nuclear transformation was sufficient to restore the wild-type phenotype. Transformants contained both protochlorophyllide reductase mRNA and immunodetectable enzyme protein. These studies demonstrate that pc-1 was in fact a defect in protochlorophyllide reductase activity and provide the first in vivo molecular evidence that the lpcr gene product is essential for light-dependent protochlorophyllide reduction.

The organization structure and regulatory elements of Chlamydomonas histone genes reveal features linking plant and animal genes

The genome of the green alga Chlamydomonas reinhardtii contains approximately 15 gene clusters of the nucleosomal (or core) histone H2A, H2B, H3 and H4 genes and at least one histone H1 gene. Seven non-allelic histone gene loci were isolated from a genomic library, physically mapped, and the nucleotide sequences of three isotypes of each core histone gene species and one linked H1 gene determined. The core histone genes are organized in clusters of H2A-H2B and H3-H4 pairs, in which each gene pair shows outwardly divergent transcription from a short (< 300 bp) intercistronic region. These intercistronic regions contain typically conserved promoter elements, namely a TATA-box and the three motifs TGGCCAG-G(G/C)-CGAG, CGTTGACC and CGGTTG. Different from the genes of higher plants, but like those of animals and the related alga Volvox, the 3' untranslated regions contain no poly A signal, but a palindromic sequence (3' palindrome) essential for mRNA processing is present. One single H1 gene was found in close linkage to a H2A-H2B pair. The H1 upstream region contains the octameric promoter element GGTTGACC (also found upstream of the core histone genes) and two specific sequence motifs that are shared only with the Volvox H1 promoters. This suggests differential transcription of the H1 and the core histone genes. The H1 gene is interrupted by two introns. Unlike Volvox H3 genes, the three sequenced H3 isoforms are intron-free. Primer-directed PCR of genomic DNA demonstrated, however, that at least 8 of the about 15 H3 genes do contain one intron at a conserved position. In synchronized C. reinhardtii cells, H4 mRNA levels (representative of all core histone mRNAs) peak during cell division, suggesting strict replication-dependent gene control. The derived peptide sequences place C. reinhardtii core histones closer to plants than to animals, except that the H2A histones are more animal-like. The peptide sequence of histone H1 is closely related to the V. carteri VH1-II (66% identity). Organization of the core histone gene in pairs, and non-polyadenylation of mRNAs are features shared with animals, whereas peptide sequences and enhancer elements are shared with higher plants, assigning the volvocalean histone genes a position intermediate between animals and plants.

The plastid aldolase gene from Chlamydomonas reinhardtii: intron/exon organization, evolution, and promoter structure

Genomic clones encoding the plastidic fructose-1,6-bisphosphate aldolase of Chlamydomonas reinhardtii were isolated and sequenced. The gene contains three introns which are located within the coding sequence for the mature protein. No introns are located within or near the sequence encoding the transit-peptide, in contrast to the genes for plastidic aldolases of higher plants. Neither the number nor the positions of the three introns of the C. reinhardtii aldolase gene are conserved in the plastidic or cytosolic aldolase genes of higher plants and animals. The 5' border sequences of introns in the aldolase gene of C. reinhardtii exhibit the conserved plant consensus sequence. The 3' acceptor splice sites for introns 1 and 3 show much less similarity to the eukaryotic consensus sequences than do those of intron 2. The plastidic aldolase gene has two tandemly repeated CAAT box motifs in the promoter region. Genomic Southern blots indicate that the gene is encoded by a single locus in the C. reinhardtii genome.

Analysis of a family of ypt genes and their products from Chlamydomonas reinhardtii

Small G-proteins encoded by the ras-like ypt genes are ubiquitous in eukaryotic cells. They have been shown to play an essential role in membrane vesicle transport. We have isolated four ypt genes, yptC1, yptC4, yptC5 and yptC6, from Chlamydomonas reinhardtii (Cr) genomic and cDNA libraries. Three of them, yptC1, yptC4 and yptC5, are close homologues of ypt genes previously found in the multicellular alga Volvox carteri (Vc), the fourth, yptC6, is new. Each yptC gene is present as a single copy in the genome. Comparisons of genomic and cDNA sequences revealed that the coding regions are interrupted by five (yptC5), six (yptC6), seven (yptC4) and eight (yptC1) introns, respectively. Cr ypt genes and the closely related Vc ypt genes have identical exon-intron structures, but the corresponding intron sequences are completely different. Polyadenylation is signalled by UAUAA, UGUAG and UGUAA. The deduced amino acid (aa) sequence of YptC6 exhibited 79% identity with HRab2; YptC1, YptC4 and YptC5 exhibited over 90% identity with their Vc homologues. Primary structures of the 9-aa 'effector domain' and the contiguous 'helix3-loop7' motif (approx. 30 aa) are 'diagnostic' features for functional assignment. Recombinant YptC proteins, overproduced in Escherichia coli and purified to near homogeneity, displayed strong and specific binding of GTP, but not of GMP or ATP. The four Cr Ypt proteins showed immunochemical cross reactions to their Vc counterparts. Moreover, Western blots demonstrated at least six types of Ypt in both Cr and Vc, suggesting that these Ypt are used for household functions responsible for vesicle transport rather than for cellular differentiation.

Genes expressed during sexual differentiation of Chlamydomonas reinhardtii

Four genes specifically expressed during gametogenesis of Chlamydomonas reinhardtii have been cloned and their expression patterns analyzed. mRNAs encoded by these gamete-specific genes (gas) were absent or present only at very low levels in vegetative cells and mature zygotes. In young zygotes 2 h after gamete fusion, the mRNAs of three gas genes still persisted. The gas mRNAs accumulated during gametic differentiation. The temporal patterns of accumulation of individual mRNAs differed; some started to increase early during gametogenesis, others accumulated in the late phase. The accumulation of one of the late mRNAs (gas28) was strictly light-dependent. To illustrate the utility of the genes cloned in the analysis of sexual differentiation in Chlamydomonas reinhardtii we show that in a gametogenesis-defective mutant, the expression of late genes is prevented while that of early genes is normal.

Complementation of a Chlamydomonas reinhardtii mutant defective in the nuclear gene encoding the chloroplast coupling factor 1 (CF1) gamma-subunit (atpC)

Chlamydomonas reinhardtii strain atpC1 is a mutant defective in the nuclear gene that encodes the CF1 ATP synthase gamma-subunit polypeptide. Photoautotrophic growth was restored to atpC1 after it was transformed with wild-type DNA. Transformed strains were acetate-independent and arsenate-sensitive, similar in phenotype to the progenitor wild-type strain from which atpC1 was generated. Three transformed strains were examined in detail. Southern blot analyses demonstrated that the transformants were complements and not revertants. The transforming DNA integrated into the nuclear genome in a nonhomologous manner and at a low copy number. Northern blot analyses showed that the gamma-subunit mRNA in the complemented strains was expressed at the same relative level as that of wild-type. Western blots of total protein showed that whereas atpC1 was unable to synthesize any CF1 gamma-subunit, all three complemented strains could. Furthermore, the Western blot analyses demonstrated that the mutation in atpC1 had a pleiotropic effect on the accumulation of the CF1 beta-subunit which was relieved upon complementation. Cell extracts from atpC1 did not have any CF1-dependent catalytic activity, whereas extracts from all of the complemented strains and the wild-type strain had identical activities.

High level expression of nonacetylatable alpha-tubulin in Chlamydomonas reinhardtii

Following the discovery of acetylated alpha-tubulin in the flagella of Chlamydomonas, many studies have documented the presence of acetylated alpha-tubulin in a variety of evolutionarily divergent organisms. While this posttranslational modification may define an isoform with a unique function, the primary effect of alpha-tubulin acetylation remains unknown. To study the function of alpha-tubulin acetylation, we have transformed Chlamydomonas, an organism in which almost all of the flagellar tubulin and a subset of the cytoplasmic microtubules are acetylated, with an alpha 1-tubulin gene whose product cannot be acetylated. Specifically, the codon for lysine 40, the lysine that is acetylated, has been replaced with the codon of nonacetylatable amino acids. To distinguish mutagenized alpha-tubulin from that produced by the two endogenous alpha-tubulin genes, mutant alpha-tubulin was tagged with an epitope from influenza virus hemagglutinin. Utilizing the constitutive Chlamydomonas rubisco small subunit S2 promoter, we have obtained in selected clones high levels of nonacetylatable alpha-tubulin expression approximating 50-70% of the total flagellar alpha-tubulin. Immunofluorescence and immunoblot analysis of transformed cells indicated that nonacetylatable alpha-tubulin could assemble, along with endogenous alpha-tubulin, into both cytoplasmic and flagellar microtubules. However, no gross phenotypic effects were observed, suggesting that the effect of alpha-tubulin acetylation is subtle.

Accumulation of chloroplast psbB RNA requires a nuclear factor in Chlamydomonas reinhardtii

We have isolated and characterized a nuclear mutant, 222E, in Chlamydomonas reinhardtii, which is defective in photosystem II (PSII). Polypeptide P5, the product of psbB, is not produced in this mutant, leading to a destabilization of other PSII components. The mutant specifically fails to accumulate psbB transcripts and displays an altered transcription pattern downstream of psbB. Pulse-labelling experiments suggest that mRNA stability and/or processing are affected by the alteration of a nuclear gene product in this mutant. We show that the C. reinhardtii psbB gene is co-transcribed with a small open reading frame that is highly conserved in location and amino acid sequence in land plants. The 5' and 3' termini of the psbB transcript have been mapped to 35 bases upstream of the initiation codon and approximately 600 bases downstream of the stop codon. The 3' flanking region contains two potential stem-loops, of which the larger (with an estimated free energy of -46 kcal) is near the 3' terminus of the transcript.

A gene/pseudogene tandem duplication encodes a cysteine-rich protein expressed during zygote development in Chlamydomonas reinhardtii

The Class V zygote-specific gene from Chlamydomonas reinhardtii has been cloned and sequenced. This gene encodes a polypeptide of 86 amino acids, which contains a signal peptide and 6 cysteine residues arranged in an inverted symmetrical repeat. The Class V gene product is postulated to be a component of the zygote cell wall. Southern analysis revealed two tandemly oriented and closely linked copies of the Class V gene, designated A and B. The A gene appears to be a pseudogene, based on analysis of Class V cDNAs, primer extension with gene-specific primers, and Northern analysis which failed to detect an A gene transcript. Genetic analysis using a related Chlamydomonas species that lacks the A gene, but which produces normal zygotic progeny, further indicates that the A gene is not required for zygote development.

Identification of novel genes specifically expressed in Chlamydomonas reinhardtii zygotes

The maturation of zygotes formed by the fusion of two gametes is the essential part of the diploid phase of the Chlamydomonas reinhardtii sexual life cycle and results in mature zygotes competent to germinate. To understand the molecular mechanisms underlying zygote maturation and the attainment of competence for germination we isolated genomic clones representing three different genes that are specifically expressed in Chlamydomonas reinhardtii zygotes. Accumulation of the RNAs started more than 24 h after mating, setting these genes apart from genes expressed in young zygotes. Upon light-induced germination of zygotes, the mRNAs disappeared. The patterns of RNA accumulation and disappearance were gene-specific and suggested a function of these genes in maturation and/or in initial steps of germination.

Ribulose bisphosphate carboxylase in algae: synthesis, enzymology and evolution

Studies demonstrating differences in chloroplast structure and biochemistry have been used to formulate hypotheses concerning the origin of algal plastids. Genetic and biochemical experiments indicate that significant variation occurs in ribulose-1,5-bisphosphate carboxylase (Rubisco) when supertaxa of eukaryotic algae are compared. These differences include variations in the organelle location of the genes and their arrangement, mechanism of Rubisco synthesis, polypeptide immunological reactivity and sequence, as well as efficacy of substrate (ribulose bisphosphate and CO2) binding and inhibitor (6-phosphogluconate) action. The structure-function relationships observed among chromophytic, rhodophytic, chlorophytic and prokaryotic Rubisco demonstrate that: (a) similarities among chromophytic and rhodophytic Rubisco exist in substrate/inhibitor binding and polypeptide sequence, (b) characteristic differences in enzyme kinetics and subunit polypeptide structure occur among chlorophytes, prokaryotes and chromophytes/rhodophytes, and (c) there is structural variability among chlorophytic plant small subunit polypeptides, in contrast to the conservation of this polypeptide in chromophytes and rhodophytes. Taxa-specific differences among algal Rubisco enzymes most likely reflect the evolutionary history of the plastid, the functional requirements of each polypeptide, and the consequences of encoding the large and small subunit genes in the same or different organelles.

Trans-splicing mutants of Chlamydomonas reinhardtii

In Chlamydomonas reinhardtii the three exons of the psaA gene are widely scattered on the chloroplast genome: exons 1 and 2 are in opposite orientations and distant from each other and from exon 3. The mature mRNA, encoding a core polypeptide of photosystem I, is thus probably assembled from separate precursors by splicing in trans. We have isolated and characterized a set of mutants that are deficient in the maturation of psaA mRNA. The mutants belong to 14 nuclear complementation groups and one chloroplast locus that are required for the assembly of psaA mRNA. The chloroplast locus, tscA, is remote from any of the exons and must encode a factor required in trans. The mutants all show one of only three phenotypes that correspond to defects in one or other or both of the joining reactions. These phenotypes, and those of double mutants, are consistent with the existence of two alternative splicing pathways.

Isolation and characterization of cDNA clones encoding photosystem I subunits with molecular masses 11.0, 10.0 and 8.4 kDa from Chlamydomonas reinhardtii

cDNA clones encoding three photosystem I subunits of Chlamydomonas reinhardtii with apparent molecular masses 13, 5 and 3 kDa (thylakoid polypeptides 28, 35 and 37; P28, P35 and P37, respectively) were isolated using gene specific oligonucleotides as probes. The sequences of these oligonucleotides were deduced from the N-terminal amino acid sequences of the proteins. The cDNAs were sequenced and used to probe Southern and Northern blots. The Southern blot analysis indicates that the proteins are encoded by single-copy genes. The mRNA sizes of the three components are 960 (P28), 1120 (P35) and 790 (P37) nucleotides. Comparison between the open reading frames of the cDNAs and the N-terminal amino acid sequences of the proteins indicates that the nascent polypeptides possess N-terminal transit sequences that are removed to give mature proteins of 11.0 (P28), 10.0 (P35) and 8.4 (P37) kDa. Analysis of the deduced protein sequences suggests that P28 and P35 are extrinsic membrane proteins and that P37 spans the thylakoid membrane. All three proteins have short transit peptides that probably route them to the stromal side of the thylakoid membrane.

Mutation at the Chlamydomonas nuclear NAC2 locus specifically affects stability of the chloroplast psbD transcript encoding polypeptide D2 of PS II

The nuclear NAC2 locus of C. reinhardtii encodes a trans-acting factor that confers stability on the chloroplast message for the D2 protein of photosystem II (PS II). A mutant that carries a lesion in the NAC2 gene is unable to accumulate the psbD transcript encoding D2, but synthesizes all other PS II proteins normally. However, the PS II complex is completely unstable in the nac2-26 mutant, and all major PS II polypeptides, including the three oxygen-evolving enhancing proteins, are absent or greatly reduced in this strain because of posttranslational degradation. In C. reinhardtii the second exon of the trans-spliced psaA mRNA is cotranscribed with psbD (Choquet et al., 1988), but the nac2-26 mutation normally has no effect on psaA message maturation or stability. However, in double mutants carrying the nac2-26 mutation, as well as a mutation that prevents psaA splicing, splicing intermediates carrying psbD sequences are degraded. These results suggest that the NAC2 gene product acts in a very specific manner to control the half-life of psbD transcripts.

Strong homology between the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase of two species of Acetabularia and the occurrence of unusual codon usage

Amino acid sequences of the small subunit of ribulose-1,5-bisphosphate carboxylase (SSU) of Acetabularia cliftonii and A. mediterranea were derived from five cDNA sequences of each of the two species of algae and by direct amino acid sequence determination of the isolated protein. An homology of more than 96% between the proteins indicates the close relationship between the two algae. All ten cDNAs in the reading frame display the termination codons TAA and/or TAG at various positions, which seem to code for the amino acid glutamine when compared with the amino acid sequence from the mature protein. This is reminiscent of proteins from ciliates where TAA and TAG also code for glutamine.

Analysis of the genes of the OEE1 and OEE3 proteins of the photosystem II complex from Chlamydomonas reinhardtii

The sequences of the nuclear genes of the 33 kDa (OEE1) and the 16 kDa (OEE3) polypeptides of the oxygen evolving complex of Chlamydomonas reinhardtii have been established. Comparison between the OEE1 protein sequences of C. reinhardtii and higher plants and cyanobacteria reveals 67 and 47% homology. In contrast, C. reinhardtii and higher plants have only 28% overall homology for OEE3 which is mostly limited to the central portion of the protein. The transit peptides of the C. reinhardtii proteins consist of 52 (OEE1) and, most likely, 51 (OEE1) amino acids. They have a basic amino terminal region and, at least in the case of OEE1, a hydrophobic segment at their carboxy terminal end typical of thylakoid lumen proteins. Comparison of the genomic and cDNA clones indicates that the OEE1 and OEE3 genes contain five and four introns, respectively, some of which are located within the coding sequences of the transit peptides.

Isolation and characterization of cDNA clones encoding the 17.9 and 8.1 kDa subunits of Photosystem I from Chlamydomonas reinhardtii

cDNA clones encoding two Photosystem I subunits of Chlamydomonas reinhardtii with apparent molecular masses of 18 and 11 kDa (thylakoid polypeptides 21 and 30; P21 and P30 respectively) were isolated using oligonucleotides, the sequences of which were deduced from the N-terminal amino acid sequences of the proteins. The cDNAs were sequenced and used to probe Southern and Northern blots. The Southern blot analysis indicates that both proteins are encoded by single-copy genes. The mRNA sizes of the two components are 1400 and 740 nucleotides, respectively. Comparison between the open reading frames of the cDNAs and the N-terminal amino acid sequences of the proteins indicates that the molecular masses of the mature proteins are 17.9 (P21) and 8.1 kDa (P30). Analysis of the deduced protein sequences predicts that both subunits are extrinsic membrane proteins with net positive charges. The amino acid sequences of the transit peptides suggest that P21 and P30 are routed towards the lumenal and stromal sides of the thylakoid membranes, respectively.

cDNA and deduced amino acid sequences of cytochrome c from Chlamydomonas reinhardtii: unexpected functional and phylogenetic implications

We have isolated complementary DNA (cDNA) clones for apocytochrome c from the green alga Chlamydomonas reinhardtii and shown that they are encoded by a single nuclear gene termed cyc. Cyc mRNA levels are found to depend primarily on the presence of acetate as a reduced carbon source in the culture medium. The deduced amino acid sequence shows that, apart from the probable removal of the initiating methionine, C. reinhardtii apocytochrome c is synthesized in its mature form. Its structure is generally similar to that of cytochromes c from higher plants. Several punctual deviations from the general pattern of cytochrome c sequences that is found in other organisms have interesting structural and functional implications. These include, in particular, valines 19 and 39, asparagine 78, and alanine 83. A phylogenetic tree was constructed by the matrix method from cytochrome c data for a representative range of species. The results suggest that C. reinhardtii diverged from higher plants approximately 700-750 million years ago; they also are not easy to reconcile with the current attribution of Chlamydomonas reinhardtii and Enteromorpha intestinalis to a unique phylum, because these two species probably diverged from one another at about the same time as they diverged from the line leading to higher plants.

Structure and biogenesis of Chlamydomonas reinhardtii photosystem I

The photosystem I complex of the green alga Chlamydomonas reinhardtii was isolated and fractionated into its two subcomplex components: the core complex (CC I), which contained the reaction center (P-700) and had four polypeptide subunits, and the light-harvesting complex (LHC I) which contained four polypeptides of about 22, 25, 26 and 27 kDa. The 22-kDa apoprotein was isolated as a chlorophyll a and b binding protein. In the isolated photosystem I holocomplex, about ten copies of the 22-kDa LHC I apoprotein are present for each CC I unit. The 22-kDa polypeptide as well as the other three polypeptides of this complex and the subunit II of CC I are translated on 80S cytoplasmic ribosomes, and therefore are coded in the nucleus. During the greening process of the Chlamydomonas reinhardtii y-1 mutant the 22-kDa LHC I polypeptide, which cross-reacts with polyclonal antibodies raised against the Lemna gibba 20-kDa LHC I apoprotein, accumulates in thylakoids at a late stage of their development, and about 2-3 h after the LHC II and CC I subunit II polypeptides have accumulated. Accumulation of the 22-kDa protein during greening is inhibited by cycloheximide but not by chloramphenicol.

Synthesis of active Olisthodiscus luteus ribulose-1,5-bisphosphate carboxylase in Escherichia coli

The ribulose-1,5-bisphosphate carboxylase (Rubisco) large- and small-subunit genes are encoded on the chloroplast genome of the eukaryotic chromophytic alga Olisthodiscus luteus. Northern blot experiments indicate that both genes are co-transcribed into a single (>6 kb) mRNA molecule. Clones from the O. luteus rbc gene region were constructed with deleted 5' non-coding regions and placed under control of the lac promoter, resulting in the expression of high levels of O. luteus Rubisco large and small subunits in Escherichia coli. Sucrose gradient centrifugation of soluble extracts fractionated a minute amount of carboxylase activity that cosedimented with native hexadecameric O. luteus Rubisco. Most of the large subunit synthesized in E. coli appeared insoluble or formed an aggregate with the small subunit possessing an altered charge: mass ratio compared to the native holoenzyme. The presence in O. luteus of a polypeptide that has an identical molecular mass and cross reacts with antiserum generated against pea large-subunit binding protein may indicate that a protein of similar function is required for Rubisco assembly in O. luteus.

Mutant phenotypes support a trans-splicing mechanism for the expression of the tripartite psaA gene in the C. reinhardtii chloroplast

The chloroplast psaA gene of the green unicellular alga Chlamydomonas reinhardtii consists of three exons that are transcribed from different strands. Analysis of numerous nuclear and chloroplast mutants that are deficient in photosystem I activity reveals that roughly one-quarter of them are specifically affected in psaA mRNA maturation. These mutants can be grouped into three phenotypic classes, based on their inability to perform either one or both splicing reactions. The data indicate that the three exons are transcribed independently as precursors which are normally assembled in trans and that the splicing reactions can occur in either order. While some chloroplast mutations could act in cis, the nuclear mutations that fall into several complementation groups probably affect factors specifically required for assembling psaA mRNA.

Expression of a gene for a light-harvesting chlorophyll a/b-binding protein in Chlamydomonas reinhardtii: effect of light and acetate

In Chlamydomonas reinhardtii, the chlorophyll a/b-binding proteins of photosystem II are encoded in the nucleus by a small family of genes. We have studied the expression of one gene, which we call cabII-1, in a green-in-the-dark strain, which can synthesize chlorophyll in the dark or light, and in a yellow-in-the-dark mutant strain, which is able to make chlorophyll only in the light. In light/dark synchronized cultures of both strains, cabII-1 mRNA abundance increases during the first 6 h of a 12-h light phase, remains high for several hours, then declines. A variety of illumination conditions have been used to analyze the cabII-1 mRNA increase: continuous or intermittent red, blue, or white light, with or without 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), an inhibitor of photosystem II. Our results suggest that light induces increased cabII-1 transcript abundance in two ways: 1) by virtue of its role in the light reactions of photosynthesis and 2) by a blue lightstimulated mechanism which is independent of photosynthesis.We have also examined the role of acetate in regulating cabII-1 mRNA levels in the dark. In both green- and yellow-in-the-dark strains, 15 mM Na-acetate, added to synchronized cells in the dark, induces an increase in cabII-1 mRNA abundance with a temporal accumulation pattern very similar to that induced by continuous white light. We suggest that by providing an energy source, acetate stimulates cellular growth, cell cycle progression, and increased cabII-1 mRNA abundance. Interestingly, in cells exposed to light, acetate inhibits the light-induced increase in cabII-1 mRNA abundance by a mechanism which is not yet understood.

Sequence, evolution and differential expression of the two genes encoding variant small subunits of ribulose bisphosphate carboxylase/oxygenase in Chlamydomonas reinhardtii

We have sequenced the two genes for the small subunit of ribulose bisphosphate carboxylase/oxygenase (Rubisco) in Chlamydomonas reinhardtii and analyzed their expression. The two genes encode variant small subunits that differ by four amino acid residues. Both genes are expressed and each is transcribed into an RNA of distinct size. The accumulation of the two RNAs changes depending on the growth conditions, so the small subunit composition of Rubisco may be expected to differ in response to the environment. The C. reinhardtii small subunit sequence is homologous to those of vascular plants or cyanobacteria, but is longer at the amino terminus and in internal positions. The number and location of the intervening sequences in the genes from C. reinhardtii and from other plants differ. In several cases, internal length differences in the polypeptide coincide with the positions of introns in the coding sequence. Thus, changes in the exon structure of the genes during evolution may have been accompanied by substantial changes in the encoded protein. The translation and splicing signals in C. reinhardtii are similar to those of other eukaryotes, but the transcription signals are less conserved and the highly biased codon usage is very unusual.