Cloning and characterization of the nuclear gene encoding plastid glyceraldehyde-3-phosphate dehydrogenase from the marine red alga Gracilaria verrucosa

Redox regulation of chloroplast enzymes in Galdieria sulphuraria in view of eukaryotic evolution

Redox modulation is a general mechanism for enzyme regulation, particularly for the post-translational regulation of the Calvin cycle in chloroplasts of green plants. Although red algae and photosynthetic protists that harbor plastids of red algal origin contribute greatly to global carbon fixation, relatively little is known about post-translational regulation of chloroplast enzymes in this important group of photosynthetic eukaryotes. To address this question, we used biochemistry, phylogenetics and analysis of recently completed genome sequences. We studied the functionality of the chloroplast enzymes phosphoribulokinase (PRK, EC 2.7.1.19), NADP-dependent glyceraldehyde 3-phosphate dehydrogenase (NADP-GAPDH, GapA, EC 1.2.1.13), fructose 1,6-bisphosphatase (FBPase, EC 3.1.3.11) and glucose 6-phosphate dehydrogenase (G6PDH, EC 1.1.1.49), as well as NADP-malate dehydrogenase (NADP-MDH, EC 1.1.1.37) in the unicellular red alga Galdieria sulphuraria (Galdieri) Merola. Despite high sequence similarity of G. sulphuraria proteins to those of other photosynthetic organisms, we found a number of distinct differences. Both PRK and GAPDH co-eluted with CP12 in a high molecular weight complex in the presence of oxidized glutathione, although Galdieria CP12 lacks the two cysteines essential for the formation of the N-terminal peptide loop present in higher plants. However, PRK inactivation upon complex formation turned out to be incomplete. G6PDH was redox modulated, but remained in its tetrameric form; FBPase was poorly redox regulated, despite conservation of the two redox-active cysteines. No indication for the presence of plastidic NADP-MDH (and other components of the malate valve) was found.

Corynebacterium glutamicum glyceraldehyde-3-phosphate dehydrogenase isoforms with opposite, ATP-dependent regulation

Corynebacterium glutamicum gapA and gapB encode glyceraldehyde-3-phosphate dehydrogenases (GAPDHs) that differ in molecular weight and activity in the presence of ATP. Comparative genome analysis revealed that GapA, the product of gapA, represented the canonical GAPDH that is highly conserved across the three major life forms. GapB, with an additional 110-residue-long sequence upstream of its GAPDH-specific domain, was homologous only to select microbial putative GAPDHs. Upon gene disruption, the initial growth rates of the wild-type, DeltagapA and DeltagapB strains on glucose (0.77, 0.00 and 0.76 h(-1), respectively), lactate (0.20, 0.18 and 0.15 h(-1), respectively), pyruvate (0.39, 0.29 and 0.20 h(-1), respectively), and acetate (0.06, 0.06 and 0.04 h(-1), respectively), implied that GapA was indispensable for growth on glucose, that GapB, but not GapA, affected early growth on acetate, and that GapB had a greater influence on growth under gluconeogenic conditions than GapA. The disruption of either gapA or gapB showed no significant effect on the transcription of any of the other gap cluster genes although it led to reduced triosephosphate isomerase (TPI) activities. Glycolytic GAPDH activity at low in vitro ATP concentrations was solely attributed to the 35.9-kDa GapA. At higher ATP concentrations, the same activity was attributed to the 51.2-kDa GapB. Both enzymes, however, exhibited similar NADP-dependent GAPDH activities at the higher ATP concentrations. In effect therefore, the GAPDH-catalyzed reaction at low ATP concentrations was irreversible, with all the glycolytic activity strictly NAD-dependent and attributed to GapA. At higher ATP concentrations, the reaction was reversible, with glycolytic activity NAD- or NADP-dependent and attributed to GapB, while gluconeogenic activity was attributable to both GapA and GapB.

SC3 and SC4 hydrophobins have distinct roles in formation of aerial structures in dikaryons of Schizophyllum commune

Two monokaryons of Schizophyllum commune can form a fertile dikaryon when the mating-type genes differ. Monokaryons form sterile aerial hyphae, while dikaryons also form fruiting bodies that function in sexual reproduction. The SC3 hydrophobin gene is expressed both in monokaryons and in dikaryons. The SC4 hydrophobin is dikaryon specific. In the monokaryon, SC3 lowers the water surface tension, coats aerial hyphae with a hydrophobic layer and mediates attachment of hyphae to hydrophobic surfaces. The SC4 protein lines gas channels within fruiting bodies with a hydrophobic membrane. Using gene disruptions, in this study, we show that in dikaryons SC3 fulfils the same roles as in monokaryons. SC4, on the other hand, has a role within fruiting bodies. In contrast to gas channels in fruiting bodies of the wild type, those of a DeltaSC4 strain easily filled with water. Thus, SC4 prevents gas channels filling with water under wet conditions, probably serving uninterrupted gas exchange. Other dikaryon-specific hydrophobin genes, SC1 and SC6, apparently do not substitute for the SC4 gene. In addition, by expressing the SC4 gene behind the SC3 promoter in a DeltaSC3 monokaryon, it was shown that SC4 cannot fully substitute for SC3, indicating that both hydrophobins evolved to fulfil specific functions.

alpha-1,4-glucan lyases producing 1,5-anhydro-D-fructose from starch and glycogen have sequence similarity to alpha-glucosidases

In the past few years a novel enzyme alpha-1,4-glucan lyase (EC 4.2. 2.13), which releases 1,5-anhydrofructose from starch and glycogen, has been cloned and characterized from red algae and fungi. Accumulated evidence indicates that the lytic degradation of starch and glycogen also occurs in other organisms. The present review focuses on the biochemical and molecular aspects of eight known alpha-1,4-glucan lyases and their genes from red algae and fungi. While the amino acid sequence identity is 75-80% among the alpha-1, 4-glucan lyases from each of the taxonomic groups, the identity between the algal and fungal alpha-1,4-glucan lyases is only 25-28%. Notably database searches disclosed that the alpha-1,4-glucan lyases have a clear identity of 23-28% with alpha-glucosidases of glycoside hydrolase family 31, thus for the first time linking enzymes from the class of hydrolases with that of lyases. The alignment of lyases and alpha-glucosidases revealed seven well-conserved regions, three of which have been reported to be involved in catalysis and substrate binding in alpha-glucosidases. The shared substrate and inhibitor specificity and sequence similarity of alpha-1,4-glucan lyases with alpha-glucosidases suggest that related structural elements are involved in the two different catalytic mechanisms.

Evolutionary origin of cryptomonad microalgae: two novel chloroplast/cytosol-specific GAPDH genes as potential markers of ancestral endosymbiont and host cell components

Cryptomonads are complex microalgae which share characteristics of chromophytes (chlorophyll c, extra pair of membranes surrounding the plastids) and rhodophytes (phycobiliproteins). Unlike chromophytes, however, they contain a small nucleus-like organelle, the nucleomorph, in the periplastidial space between the inner and outer plastid membrane pairs. These cellular characteristics led to the suggestion that cryptomonads may have originated via a eukaryote-eukaryote endosymbiosis between a phagotrophic host cell and a unicellular red alga, a hypothesis supported by rRNA phylogenies. Here we characterized cDNAs of the nuclear genes encoding chloroplast and cytosolic glyceraldehyde-3-phosphate dehydrogenases (GAPDH) from the two cryptomonads Pyrenomonas salina and Guillardia theta. Our results suggest that in cryptomonads the classic Calvin cycle GAPDH enzyme of cyanobacterial origin, GapAB, is absent and functionally replaced by a photosynthetic GapC enzyme of proteobacterial descent, GapC1. The derived GapC1 precursor contains a typical signal/transit peptide of complex structure and sequence signatures diagnostic for dual cosubstrate specificity with NADP and NAD. In addition to this novel GapC1 gene a cytosol-specific GapC2 gene of glycolytic function has been found in both cryptomonads showing conspicuous sequence similarities to animal GAPDH. The present findings support the hypothesis that the host cell component of cryptomonads may be derived from a phototrophic rather than a organotrophic cell which lost its primary plastid after receiving a secondary one. Hence, cellular compartments of endosymbiotic origin may have been lost or replaced several times in eukaryote cell evolution, while the corresponding endosymbiotic genes (e.g., GapC1) were retained, thereby increasing the chimeric potential of the nuclear genome.

Functional studies of chloroplast glyceraldehyde-3-phosphate dehydrogenase subunits A and B expressed in Escherichia coli: formation of highly active A4 and B4 homotetramers and evidence that aggregation of the B4 complex is mediated by the B subunit carboxy terminus

Chloroplast glyceraldehyde-3-phosphate dehydrogenase (phosphorylating, E.C. 1.2.1.13) (GAPDH) of higher plants exists as an A2B2 heterotetramer that catalyses the reductive step of the Calvin cycle. In dark chloroplasts the enzyme exhibits a molecular mass of 600 kDa, whereas in illuminated chloroplasts the molecular mass is altered in favor of the more active 150 kDa form. We have expressed in Escherichia coli proteins corresponding to the mature A and B subunits of spinach chloroplast GAPDH (GapA and GapB, respectively) in addition to a derivative of the B subunit lacking the GapB-specific C-terminal extension (CTE). One mg of each of the three proteins so expressed was purified to electrophoretic homogeneity with conventional methods. Spinach GapA purified from E. coli is shown to be a highly active homotetramer (50-70 U/mg) which does not associate under aggregating conditions in vitro to high-molecular-mass (HMM) forms of ca. 600 kDa. Since B4 forms of the enzyme have not been described from any source, we were surprised to find that spinach GapB purified from E. coli was active (15-35 U/mg). Spinach GapB lacking the CTE purified from E. coli is more highly active (130 U/mg) than GapB with the CTE. Under aggregating conditions, GapB lacking the CTE is a tetramer that does not associate to HMM forms whereas GapB with the CTE occurs exclusively as an aggregated HMM form. The data indicate that intertetramer association of chloroplast GAPDH in vitro occurs through GapB-mediated protein-protein interaction.

Cloning and characterization of the nuclear gene and cDNAs for triosephosphate isomerase of the marine red alga Gracilaria verrucosa

cDNAs and an intronless single-copy nuclear gene (TPI1) encoding triosephosphate isomerase have been cloned and sequenced from the marine red alga Gracilaria verrucosa. The predicted amino-acid sequence of TPI1 is readily alignable with those of other known TPIs; 26 of 27 active-site residues and 19 of 26 intersubunit-contact residues are identical between TPIs of G. verrucosa and/or animals and green plants. A partial cDNA sequence of a second TPI gene (TPI2), presumably encoding plastid-localized TPI, was recovered by PCR and demonstrated by phylogenetic analysis to be red algal; no TP12 cDNA or genomic clones could be recovered. Genomic Southern analysis demonstrated that at least two TPI-like genes are present in the nuclear DNA of G. verrucosa.

The nuclear gene and cDNAs encoding cytosolic glyceraldehyde-3-phosphate dehydrogenase from the marine red alga Gracilaria verrucosa: cloning, characterization and phylogenetic analysis

We have cloned and sequenced the single-copy nuclear gene (GapC) encoding the complete 335-amino acid cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPC) from the red alga Gracilaria verrucosa. The proline residue which contributes to the specificity of NAD+ binding in other GAPC-like proteins is present. Putative regulatory regions, including GC-rich regions, a GATA element, and 11-base T- and T/G-clusters, but excluding TATA- and CCAAT-boxes, were identified upstream. Two types of GapC cDNAs differing in polyadenylation site were characterized. An 80-bp phase-two spliceosomal intron was identified in a novel position interrupting the highly conserved cofactor-coding region I. The G. verrucosa GAPC was easily aligned with other known GAPC-type sequences. Inferred phylogenetic trees place red algae among the eukaryote crown taxa, although with modest bootstrap support and without stable resolution among related GAPC lineages.

Structural features and phylogeny of the actin gene of Chondrus crispus (Gigartinales, Rhodophyta)

We have characterized the cDNA and genomic sequences that encode actin from the multicellular red alga Chondrus crispus. Southern-blot analysis indicates that the C. crispus actin gene (ChAc) is present as a single copy. Northern analysis shows that, like the GapA gene, the actin gene is well expressed in gametophytes but weakly in protoplasts. Compared to actin genes of animals, fungi, green plants and oomycetes, that of C. crispus displays a higher evolutionary rate and does not show any of the amino-acid signatures characteristic of the other lineages. As previously described for GapA, ChAc is interrupted by a single intron at the beginning of the coding region. The site of initiation of transcription was characterized by RNAse protection. The promoter region displays a CAAT box but lacks a canonical TATA motif. Other noticeable features, such as a high content of pyrimidines as well as a 14-nt motif found in both the 5'-untranslated region and the intron, were observed.

Characterization of the nuclear gene encoding mitochondrial aconitase in the marine red alga Gracilaria verrucosa

We have cloned a nuclear gene from the marine red alga Gracilaria verrucosa that encodes the complete 779 amino-acid mitochondrial aconitase (m-ACN), the first characterized from a photosynthetic organism. The N-terminal 28 deduced amino acids are predicted to constitute the mitochondrial transit peptide, the first described from a red alga. Putative transcriptional cis-acting elements were identified in the upstream untranslated region. The G. verrucosa m-ACN gene (m-ACN) is present in a single copy and is located ca. 1.5 kb upstream from the single-copy polyubiquitin gene. The single spliceosomal intron is located near the 5' end of the region encoding the mature m-ACN in precisely the same location and phase as intron 2 in Caenorhabditis elegans m-ACN; sequences at its 3' and 5' splice junctions and at the predicted lariat branch point conform well to the eukaryote consensus sequences. Multiple protein-sequence alignment of m-ACN, bacterial aconitase (b-ACN) and iron-responsive element-binding protein (IRE-BP), and phylogenetic analyses, revealed that m-ACN does not share a recent common ancestry with either b-ACN or IRE-BP.

The marine red alga Chondrus crispus has a highly divergent beta-tubulin gene with a characteristic 5' intron: functional and evolutionary implications

We characterized a nuclear gene and its corresponding cDNA encoding beta-tubulin (gene TubB1) of the marine red alga Chondrus crispus. The deduced TubB1 protein is the most divergent beta-tubulin so far reported with only 64 to 69% amino acid identity relative to other beta-tubulins from higher and lower eukaryotes. Our analysis reveals that TubB1 has an accelerated evolutionary rate probably due to a release of functional constraints in connexion with a specialization of microtubular structures in rhodophytes. It further indicates that isoform diversity and functional differentiation of tubulins in eukaryotic cells may be controlled by independent selective constraints. TubB1 has a short spliceosomal intron at its 5' end which seems to be a characteristic feature of nuclear protein-coding genes from rhodophytes. The splice junctions of the four known rhodophyte introns comply well with the corresponding consensus sequences of higher plants in agreement with previous suggestions from phylogenetic inference that red algae and green plants may be sister groups. The paucity and asymmetrical location of introns in rhodophyte genes can be explained by differential intron loss due to conversion of genes by homologous recombination with cDNAs corresponding to reverse transcribed mRNAs or partially spliced pre-mRNAs, respectively. The identification of an intron containing TubB1 cDNA in C. crispus confirms that pre-mRNAs can escape both splicing and degradation in the nucleus prior to transport into the cytoplasm. Differential Southern hybridizations under non-stringent conditions with homologous and heterologous probes suggest that C. crispus contains a second degenerate beta-tubulin gene (or pseudogene?) which, however, is only distantly related to TubB1 as it is to the more conserved homologues of other organisms.

Characterization of the polyubiquitin gene in the marine red alga Gracilaria verrucosa

We have cloned a nuclear gene (UBI6R) and corresponding cDNAs that encode polyubiquitin in the florideophycidean red alga Gracilaria verrucosa. The gene encodes a polyubiquitin composed of six tandem ubiquitin units, followed by a single glutamine residue. The deduced amino acid sequences are identical among all six units, and identical to the ubiquitin of the florideophyte Aglaothamnion neglectum. There is high sequence similarity among the red algal ubiquitins and those of animals, green plants, fungi and several protists. Only one polyubiquitin gene was found by Southern hybridization analysis of G. verrucosa nuclear DNA. The upstream region of the gene is rich in putative cis-acting transcription-regulatory elements, including a putative heat-responsive element. Poly(A) addition to UBI6R mRNA was observed in cDNAs at four different sites, implicating the sequences AATAAA and (or) AGTAAA as poly(A) addition signals. The polyubiquitin genes of red algae show features of concerted evolution, but appear to be subject to less sequence homogenization than those of animals.