Expression of C4-like photosynthesis in several species of Flaveria

Abstract Photosynthetic metabolism was investigated in leaves of five species of Flaveria (Asteraceac), all previously considered to be C₄ plants. Leaves were exposed to ¹⁴CO₂ for different intervals up to 16s. Extrapolation of ¹⁴C-product curves to zero time indicated that only F. trinervia and F.bidentis assimilated atmospheric CO₂ exclusively through phosphoenolpyruvate carboxylase. The proportion of direct fixation of ¹⁴CO₂ by ribulose-I, 5-bisphosphate carboxylase/oxygenase (Rubisco) ranged from 5 to 10% in leaves of F. australasica. F. palmeri and F. vaginata. Protoplasts of leaf mesophyll and bundle sheath cells were utilized to examine the intercellular compartmentation of principal photosynthetic enzymes. Leaves of F. australasica, F. palmeri and F. vaginata contained 5 to 7% of the leaf's Rubisco activity in the mesophyll cells, while leaves of F. trinervia and F. bidentis contained at most 0.2 to 0.8% of such activity in their mesophyll cells. Thus, F. trinervia and F. bidentis have the complete C₄ syndrome, while F. australasica, F. palmeri and F. vaginata are less advanced, C₄-like species.     

On the significance of C3—C4 intermediate photosynthesis to the evolution of C4 photosynthesis

Abstract Evidence is drawn from previous studies to argue that C₃—C₄ intermediate plants are evolutionary intermediates, evolving from fully-expressed C₃ plants towards fully-expressed C₄ plants. On the basis of this conclusion, C₃—C₄ intermediates are examined to elucidate possible patterns that have been followed during the evolution of C₄ photosynthesis. An hypothesis is proposed that the initial step in C₄-evolution was the development of bundle-sheath metabolism that reduced apparent photorespiration by an efficient recycling of CO₂ using RuBP carboxylase. The CO₂-recycling mechanism appears to involve the differential compartmentation of glycine decarboxylase between mesophyll and bundle-sheath cells, such that most of the activity is in the bundlesheath cells. Subsequently, elevated phosphoenolpyruvate (PEP) carboxylase activities are proposed to have evolved as a means of enhancing the recycling of photorespired CO₂. As the activity of PEP carboxylase increased to higher values, other enzymes in the C₄-pathway are proposed to have increased in activity to facilitate the processing of the products of C₄-assimilation and provide PEP substrate to PEP carboxylase with greater efficiency. Initially, such a ‘C₄-cycle’ would not have been differentially compartmentalized between mesophyll and bundlesheath cells as is typical of fully-expressed C₄ plants. Such metabolism would have limited benefit in terms of concentrating CO₂ at RuBP carboxylase and, therefore, also be of little benefit for improving water- and nitrogen-use efficiencies. However, the development of such a limited C₄-cycle would have represented a preadaptation capable of evolving into the leaf biochemistry typical of fully-expressed C₄ plants. Thus, during the initial stages of C₄-evolution it is proposed that improvements in photorespiratory CO₂-loss and their influence on increasing the rate of net CO₂ assimilation per unit leaf area represented the evolutionary ‘driving-force’. Improved resourceuse efficiency resulting from an efficient CO₂-concentrating mechanism is proposed as the driving force during the later stages.     

Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia

The crystal structure of the P-protein of the glycine cleavage system from Thermus thermophilus HB8 has been determined. This is the first reported crystal structure of a P-protein, and it reveals that P-proteins do not involve the alpha(2)-type active dimer universally observed in the evolutionarily related pyridoxal 5'-phosphate (PLP)-dependent enzymes. Instead, novel alphabeta-type dimers associate to form an alpha(2)beta(2) tetramer, where the alpha- and beta-subunits are structurally similar and appear to have arisen by gene duplication and subsequent divergence with a loss of one active site. The binding of PLP to the apoenzyme induces large open-closed conformational changes, with residues moving up to 13.5 A. The structure of the complex formed by the holoenzyme bound to an inhibitor, (aminooxy)acetate, suggests residues that may be responsible for substrate recognition. The molecular surface around the lipoamide-binding channel shows conservation of positively charged residues, which are possibly involved in complex formation with the H-protein. These results provide insights into the molecular basis of nonketotic hyperglycinemia.     

Molecular phylogeny of theChironomus genus deduced from nucleotide sequences of two nuclear genes,ssp 160 and the globin 2b gene

Two genes were employed to study phylogenetic relatedness of theChironomus species: the protein-coding, salivary gland-specificssp160 gene, and the globin 2b (gb2b) gene. By using PCR, it was demonstrated that all the 38Chironomus species analyzed possess thegb2b gene, while only 13 have thessp160 gene. Partial nucleotide sequences of the genes of 22 species were determined. The data obtained were employed to construct phylogenetic trees which appeared to be topologically similar and revealed five groups of phylogenetically closely related species. Combining the data obtained in the studies of nuclear and mitochondrial genes, a molecular-data-based scenario could be suggested for theChironomus genus evolution.     

Dead-end evolution of the Cnidaria as deduced from 5S ribosomal RNA sequences

Using nucleotide sequences of 5S ribosomal RNAs from 2 hydrozoan jellyfishes, 3 scyphozoan jellyfishes and 2 sea anemones, a phylogenetic tree of Cnidaria has been constructed to elucidate the evolutionary relationships of radial and bilateral symmetries. The 3 classes of Cnidaria examined herein belong to one branch, which does not include other metazoan phyla such as the Platyhelminthes. The Hydrozoa (having radial symmetry without septa) and the Scyphozoa (having radial symmetry with septa) are more closely related to each other than to the Anthozoa (having bilateral symmetry with septa). In classical taxonomy, multicellular animals are considered to have evolved through organisms with radial symmetry (e.g., Cnidaria) to bilateral symmetry. Our results, however, indicate that the emergence of the Bilateria was earlier than that of the Radiata, suggesting (in opposition to Haeckel's view) that the radial symmetry of Cnidaria is an evolutionary dead end.     

Molecular phylogeny of the Chinese ranids inferred from nuclear and mitochondrial DNA sequences

The phylogeny of representative species of Chinese ranids was reconstructed using two nuclear (tyrosinase and rhodopsin) and two mitochondrial (12S rRNA, 16S rRNA) DNA fragments. Maximum parsimony, Bayesian, and maximum likelihood analyses were employed. In comparison with the results from nuclear and mitochondrial data, we used nuclear gene data as our preferred phylogenetic hypothesis. We proposed two families (Ranidae, Dicroglossidae) for Chinese ranids, with the exception of genus Ingerana. Within Dicroglossidae, four tribes were supported including Dicroglossini, Paini, Limnonectini, and Occidozygini. A broader sampling strategy and evidence from additional molecular markers are required to decisively evaluate the evolutionary history of Chinese ranids.     

Molecular phylogeny of the Heterotrichea (Ciliophora, Postciliodesmatophora) based on small subunit rRNA gene sequences

A comprehensive molecular analysis of the phylogenetic relationships within the Heterotrichea including all described families is still lacking. For this reason, the complete nuclear small subunit (SSU) rDNA was sequenced from further representatives of the Blepharismidae and the Stentoridae. In addition, the SSU rDNA of a new, undescribed species of the genus Condylostomides (Condylostomatidae) was sequenced. The detailed phylogenetic analyses revealed a consistent branching pattern: while the terminal branches are generally well resolved, the basal relationships remain unsolved. Moreover, the data allow some conclusions about the macronuclear evolution within the genera Blepharisma, Stentor, and Spirostomum suggesting that a single, compact macronucleus represents the ancestral state.     

Crystal structure of human T-protein of glycine cleavage system at 2.0 A resolution and its implication for understanding non-ketotic hyperglycinemia

T-protein, a component of the glycine cleavage system, catalyzes the formation of ammonia and 5,10-methylenetetrahydrofolate from the aminomethyl moiety of glycine attached to the lipoate cofactor of H-protein. Several mutations in the human T-protein gene cause non-ketotic hyperglycinemia. To gain insights into the effect of disease-causing mutations and the catalytic mechanism at the molecular level, crystal structures of human T-protein in free form and that bound to 5-methyltetrahydrofolate (5-CH3-H4folate) have been determined at 2.0 A and 2.6 A resolution, respectively. The overall structure consists of three domains arranged in a cloverleaf-like structure with the central cavity, where 5-CH3-H4folate is bound in a kinked shape with the pteridine group deeply buried into the hydrophobic pocket and the glutamyl group pointed to the C-terminal side surface. Most of the disease-related residues cluster around the cavity, forming extensive hydrogen bonding networks. These hydrogen bonding networks are employed in holding not only the folate-binding space but also the positions and the orientations of alpha-helix G and the following loop in the middle region, which seems to play a pivotal role in the T-protein catalysis. Structural and mutational analyses demonstrated that Arg292 interacts through water molecules with the folate polyglutamate tail, and that the invariant Asp101, located close to the N10 group of 5-CH3-H4folate, might play a key role in the initiation of the catalysis by increasing the nucleophilic character of the N10 atom of the folate substrate for the nucleophilic attack on the aminomethyl lipoate intermediate. A clever mechanism of recruiting the aminomethyl lipoate arm to the reaction site seems to function as a way of avoiding the release of toxic formaldehyde.     

Hyperglycinemia due to folate deficiency in rats: evidence for the lack of involvement of the hepatic glycine cleavage system

In addition to a well-recognized hyperhomocysteinemic state, folate deficiency also leads to profound hyperglycinemia. To further characterize the latter observation, two trials were conducted using a folate-deficient rat model to (1) determine the sensitivity of plasma glycine to folate repletion and (2) test the hypothesis that hyperglycinemia results from a reduced flux through the folate-dependent glycine cleavage system (GCS). Weanling male Sprague–Dawley rats were used, and they consumed an amino acid-defined diet with either 0 (FD) or 1 (FA) mg/kg of crystalline folic acid. In Trial 1, 30 rats consumed the FD diet for 28 days. Rats then consumed diets containing 0.1, 0.2, 0.3 or 0.4 mg/kg of folic acid for 14 days before termination. In Trial 2, 16 rats were allocated to receive either the FA (n=8) or FD (n=8) diet for 30 days before termination. Liver mitochondria were isolated and flux through the GCS (measured as ¹⁴CO₂ production from 1-¹⁴C-glycine) was determined. Plasma from blood collected at termination was analyzed for folate, homocysteine and glycine. In Trial 1, both homocysteine and glycine responded linearly to increased dietary folic acid (milligrams per kilogram) levels (P<.05). In Trial 2, plasma folate (FA=25.85 vs. FD=0.66; S.E.M.=1.4 μM), homocysteine (FA=11.1 vs. FD=55.3; S.E.M.=1.7 μM) and glycine (FA=564 vs. FD=1983; S.E.M.=114 μM) were significantly affected by folate deficiency (P<.0001). However, glycine flux through hepatic GCS was not affected by folate deficiency (P>.05). These results provide evidence that in a folate-deficient rat model, both homocysteine and glycine are sensitive to dietary folic acid levels; however, the observed hyperglycinemia does not appear to be related to a reduced flux through the hepatic GCS.     

An examination of the advantages of C3-C4 intermediate photosynthesis in warm environments

Abstract. The photosynthetic responses to temperature in C₃, C₃-C₄ intermediate, and C₄ species in the genus Flaveria were examined in an effort to identify whether the reduced photorespiration rates characteristic of C₃-C₄ intermediate photosynthesis result in adaptive advantages at warm leaf temperatures. Reduced photorespiration rates were reflected in lower CO₂ compensation points at all temperatures examined in the C₃-C₄ intermediate, Flaveria floridana, compared to the C₃ species, F. cronquistii. The C₃-C₄ intermediate, F. floridana, exhibited a C₃-like photosynthetic temperature dependence, except for relatively higher photosynthesis rates at warm leaf temperatures compared to the C₃ species, F. cronquistii. Using models of C₃ and C₃-C₄ intermediate photosynthesis, it was predicted that by recycling photorespired CO₂ in bundle-sheath cells, as occurs in many C₃-C₄ intermediates, photosynthesis rates at 35°C could be increased by 28%, compared to a C₃ plant. Without recycling photorespired CO₂, it was calculated that in order to improve photosynthesis rates at 35°C by this amount in C₃ plants, (1) intercellular CO₂ partial pressures would have to be increased from 25 to 31 Pa, resulting in a 57% decrease in water-use efficiency, or (2) the activity of RuBP carboxylase would have to be increased by 32%, resulting in a 22% decrease in nitrogen-use efficiency. In addition to the recycling of photorespired CO₂, leaves of F. floridana appear to effectively concentrate CO₂ at the active site of RuBP carboxylase, increasing the apparent carboxylation efficiency per unit of in vitro RuBP carboxylase activity. The CO₂-concentrating activity also appears to reduce the temperature sensitivity of the carboxylation efficiency in F. floridana compared to F. cronquistii. The carboxylation efficiency per unit of RuBP carboxylase activity decreased by only 38% in F. floridana, compared to 50% in F. cronquistii, as leaf temperature was raised from 25 to 35°C. The C₃-C₄ intermediate, F. ramosissima, exhibited a photosynthetic temperature temperature response curve that was more similar to the C₄ species, F. trinervia, than the C₃ species, F. cronquistii. The C₄-like pattern is probably related to the advanced nature of C₄-like biochemical traits in F. ramosissima The results demonstrate that reductions in photorespiration rates in C₃-C₄ intermediate plants create photosynthetic advantages at warm leaf temperatures that in C₃ plants could only be achieved through substantial costs to water-use efficiency and/or nitrogen-use efficiency.     

Molecular phylogeny of early vertebrates: monophyly of the agnathans as revealed by sequences of 35 genes

Extant vertebrates are divided into three major groups: hagfishes (Hyperotreti, myxinoids), lampreys (Hyperoartia, petromyzontids), and jawed vertebrates (Gnathostomata). The phylogenetic relationships among the groups and within the jawed vertebrates are controversial, for both morphological and molecular studies have rendered themselves to conflicting interpretations. Here, we use the sequences of 35 nuclear protein-encoding genes to provide definitive evidence for the monophyly of the Agnatha (jawless vertebrates, a group encompassing the hagfishes and lampreys). Our analyses also give a strong support for the separation of Chondrichthyes (cartilaginous fishes) before the divergence of Osteichthyes (bony fishes) from the other gnathostomes.     

New light on bacterial carbonic anhydrases phylogeny based on the analysis of signal peptide sequences

Among protein families, carbonic anhydrases (CAs, EC 4.2.1.1) are metalloenzymes characterized by a common reaction mechanism in all life domains: the carbon dioxide hydration to bicarbonate and protons (CO₂+H₂O ? HCO₃^?+H⁺). Six genetically distinct CA families are known to date, the α-, β-, γ-, δ-, ζ- and η-CAs. The last CA class was recently discovered analyzing the amino acid sequences of CAs from Plasmodia. Bacteria encode for enzymes belonging to the α-, β-, and γ-CA classes and recently, phylogenetic analysis revealed an interesting relationship regarding the evolution of bacterial CA classes. This result evidenced that the three bacterial CA classes, in spite of the high level of the structural similarity, are evolutionarily distinct, but we noted that the primary structure of some β-CAs identified in the genome of Gram-negative bacteria present a pre-sequence of 18 or more amino acid residues at the N-terminal part. These observations and subsequent phylogenetic data presented here prompted us to propose that the β-CAs found in Gram-negative bacteria with a periplasmic space and characterized by the presence of a signal peptide might have a periplasmic localization and a role similar to that described previously for the α-CAs.     

A mtDNA phylogeny of sea eagles (genus Haliaeetus) based on nucleotide sequences of the cytochrome b-gene

The mitochondrial cytochrome b gene of seven species of sea eagles H. albicilla, H. leucocephalus, H. leucoryphus, H. leucogaster, H. sanfordi, H. pelagicus and H. vocifer was amplified by PCR and sequenced (1026 bp). Phylogeny reconstructions by the Maximum Parsimony and Neighbour-Joining methods produced similar trees in which sea eagles represent a monophyletic group. In addition, the clade H. albicilla/H. leucocephalus groups with the clade H. pelagicus/H. leucoryphus in a monophyletic boreal group while H. vocifer clusters with the H. leucogaster/H. sanfordi clade in a monophyletic tropical clade. The nearest relatives of sea eagles are the kites (genus Milvus) and buzzards (genus Buteo), whereas ‘booted’ eagles (genus Aquila) and vultures (genera Gyps and Aegypius) have diverged earlier from the accipitrid branch. Honey bussards (genus Pernis) and vultures of the genera Gypaetus and Neophron represent basal taxa of the accipitrid lineage. Falcons, New World vultures and the secretary bird (Sagittarius) appear in separate clades outside the Accipitridae.     

Molecular phylogeny of Lactarius volemus and its allies inferred from the nucleotide sequences of nuclear large subunit rDNA

The phylogenetic relationships of Lactarius volemus and its relatives were investigated using the nucleotide sequences of the nuclear-encoded large subunit ribosomal DNA (LSU rDNA). Thirty-six sequences from L. volemus, L. corrugis, and L. hygrophoroides, including three sequences obtained from the GenBank database, were used in this study. Samples studied were divided into four major subclades (A–D) in both neighbor-joining (NJ) and maximum-parsimony (MP) trees. Lactarius volemus and L. corrugis formed one large clade in both NJ and MP trees (bootstrap value, 100%), which was divided into three subclades (A–C). Subclade A included three clusters of L. volemus strains, i.e., velvet, red, and Chinese types. Subclade B included the common and red types of L. corrugis. Subclade C included the common and yellow types of L. volemus. Subclade D included only one type of L. hygrophoroides. An analysis of the fatty acid composition supported the divisions found in the molecular analysis. Analyses of nucleotide sequence, fatty acid composition, morphological characteristics, and the taste of the fruiting bodies all led us to conclude that the common, velvet, red, and Chinese types of L. volemus, and the common and red types of L. corrugis, may each belong to different species, subspecies, or varieties. Further studies with more material from a wide range of regions are required to conduct taxonomic revision of these types. The LSU rDNA region may be a useful tool to investigate phylogenetic relationships within the section Dulces of the genus Lactarius.     

Molecular phylogeny and phylogeography ofLupinus (Leguminosae) inferred from nucleotide sequences of therbcL gene and ITS 1 + 2 regions of rDNA

Total DNA was extracted from 55 species of theLeguminosae (including 29 species ofLupinus). The chloroplast generbcL and the ITS 1 + 2 regions of nuclear RNA genes were amplified by polymerase chain reaction (PCR) and sequenced directly. The sequences obtained were evaluated with character state (Maximum Parsimony) and distance methods (Neighbour Joining). Phylogenetic trees obtained with both data sets and methods are mostly congruent.Genisteae andCrotalarieae are sister groups and share ancestry with theThermopsideae/Podalyrieae. The genusLupinus, which forms a monophyletic clade within theGenisteae, shows a distinct Old-New World disjunction and appears to be divided into several more or less distinct groups: (1) The species from the eastern part of South America. (2) The homogeneous rough-seeded group (Scabrispermae) of the Old World species which is well distinguished from the smooth-seeded group (Malacospermae). (3) Within the rather heterogeneous smooth-seeded lupins a smaller subgroup withL. angustifolius, L. hispanicus andL. luteus is recognized. (4) Also separated are North American lupins and South American species with a western distribution. Genetic distances imply that the genusLupinus evolved during the last 12–14 million years, ruling out the hypothesis that the present Old-New World disjunction can be interpreted as a result of the continental drift. The genetic data suggest an origin in the Old World and an independant colonisation of the Eastern parts of South America as opposed to North America and the Western parts of South America.     

Stomatal mechanism as the basis of the evolution of CAM and C4 photosynthesis

Abstract. The similarities between the component reactions of the presently known variants of photosynthetic carbon metabolism (crassulacean acid metabolism, the acid metabolism of Tillandsia usneoides , aquatic acid metabolism, and C₄ photosynthesis) when considered along with their widely scattered taxonomic distribution strongly suggest polyphyletic origins resulting from evolutionary modification of a common, universally distributed metabolic sequence. The synthesis and consumption of four-carbon acids in the cation-balancing reactions involved in the regulation of stomatal aperture appear to exhibit all of the characteristics likely to be displayed by such a metabolic progenitor.
The present status of the proposal that the expression of aspects of stomatal metabolism in photosynthetic mesophyll cells represents the basis for the evolution of the variant of photosynthetic carbon metabolism is discussed. The prospects of experimental approaches which may yield information relevant to the proposal are also explored.