Codon usage in higher plants, green algae, and cyanobacteria

Codon usage is the selective and nonrandom use of synonymous codons by an organism to encode the amino acids in the genes for its proteins. During the last few years, a large number of plant genes have been cloned and sequenced, which now permits a meaningful comparison of codon usage in higher plants, algae, and cyanobacteria. For the nuclear and organellar genes of these organisms, a small set of preferred codons are used for encoding proteins. Codon usage is different for each genome type with the variation mainly occurring in choices between codons ending in cytidine (C) or guanosine (G) versus those ending in adenosine (A) or uridine (U). For organellar genomes, chloroplastic and mitochrondrial proteins are encoded mainly with codons ending in A or U. In most cyanobacteria and the nuclei of green algae, proteins are encoded preferentially with codons ending in C or G. Although only a few nuclear genes of higher plants have been sequenced, a clear distinction between Magnoliopsida (dicot) and Liliopsida (monocot) codon usage is evident. Dicot genes use a set of 44 preferred codons with a slight preference for codons ending in A or U. Monocot codon usage is more restricted with an average of 38 codons preferred, which are predominantly those ending in C or G. But two classes of genes can be recognized in monocots. One set of monocot genes uses codons similar to those in dicots, while the other genes are highly biased toward codons ending in C or G with a pattern similar to nuclear genes of green algae. Codon usage is discussed in relation to evolution of plants and prospects for intergenic transfer of particular genes.     

Cyanobacterial metabolites with bioactivity against photosynthesis in cyanobacteria, algae and higher plants

Cyanobacteria produce a large number and variety of bioactive allelochemical substances, with a diverse range of biological activities and chemical structures, and with effects on many biochemical processes within cells. An increasing number of such metabolites is being found to be directed against oxygenic photosynthetic processes, which, in the microbial world, are unique to algae and cyanobacteria. Such chemicals are likely to be involved in regulating natural populations, and are potentially useful as biochemical tools, and as herbicidal or biocontrol agents. This revised version was published online in June 2006 with corrections to the Cover Date.     

Electron microscopic structural analysis of Photosystem I,Photosystem II,and the cytochromeb6/f complex from green plants and cyanobacteria

Electron microscopy (EM) in combination with image analysis is a powerful technique to study protein structure at low- and high resolution. Since electron micrographs of biological objects are very noisy, substantial improvement of image quality can be obtained by averaging individual projections. Crystallographic and noncrystallographic averaging methods are available and have been applied to study projections of the large protein complexes embedded in photosynthetic membranes from cyanobacteria and higher plants. Results of EM on monomeric and trimeric Photosystem I complexes, on monomeric and dimeric Photosystem II complexes, and on the monomeric cytochromeb6/f complex are discussed.     

Electron transfer from cytochrome f to photosystem I in green algae

The time course of P700⁺ reduction and cytochrome f oxidation following a single-turnover flash excitation of photosystem I was measured under various conditions in different strains of green algae. P700⁺ was reduced with a half-time of 4 s. The rate of cytochrome f oxidation was found to depend widely on physiological factors. Reversible transitions are described from a slow-oxidation state (t _1/2=500 s) to a fast-oxidation state (t _1/2=80 s). The addition of ionophore strongly favours and stabilizes the fast-oxidation state. We suggest that these transitions reflect either reversible association between the cytochrome bf complex and the reaction center of photosystem I or changes in the mobility of oxidized plastocyanin. The transitions might be under the control of the membrane potential or the intracellular ATP content. The relation of these reversible transitions with the light state transitions, and their possible involvement in a switch from linear to cyclic electron transfer, are discussed.Abbreviations cyt cytochrome - DCHC dicyclohexyl-18-crown-6 - DCMU 3-(3,4-dichlorophenyl)-1,1-dimethylurea - DNP-INT dinitrophenylether of iodonitrothymol - FCCP carbonylcyanide-p-trifluoromethoxyphenylhydrazone - LHC light harvesting complex - PC plastocyanin - PS I photosystem I     

Cross-reconstitution of various extrinsic proteins and photosystem II complexes from cyanobacteria, red algae and higher plants

Photosystem II (PSII) contains different extrinsic proteins required for oxygen evolution among different organisms. Cyanobacterial PSII contains the 33 kDa, 12 kDa proteins and cytochrome (cyt) c-550; red algal PSII contains a 20 kDa protein in addition to the three homologous cyanobacterial proteins; whereas higher plant PSII contains the 33 kDa, 23 kDa and 17 kDa proteins. In order to understand the binding and functional properties of these proteins, we performed cross-reconstitution experiments with combinations of PSII and extrinsic proteins from three different sources: higher plant (spinach), red alga (Cyanidium caldarium) and cyanobacterium (Synechococcus vulcanus). Among all of the extrinsic proteins, the 33 kDa protein is common to all of the organisms and is totally exchangeable in binding to PSII from any of the three organisms. Oxygen evolution of higher plant and red algal PSII was restored to a more or less similar level by binding of any one of the three 33 kDa proteins, whereas oxygen evolution of cyanobacterial PSII was restored to a larger extent with its own 33 kDa protein than with the 33 kDa protein from other sources. In addition to the 33 kDa protein, the red algal 20 kDa, 12 kDa proteins and cyt c-550 were able to bind to cyanobacterial and higher plant PSII, leading to a partial restoration of oxygen evolution in both organisms. The cyanobacterial 12 kDa protein and cyt c-550 partially bound to the red algal PSII, but this binding did not restore oxygen evolution. The higher plant 23 kDa and 17 kDa proteins bound to the cyanobacterial and red algal PSII only through non-specific interactions. Thus, only the red algal extrinsic proteins are partially functional in both the cyanobacterial and higher plant PSII, which implies a possible intermediate position of the red algal PSII during its evolution from cyanobacteria to higher plants.     

Post-translational control of tetrapyrrole biosynthesis in plants, algae, and cyanobacteria

The tetrapyrrole biosynthetic pathway provides the vital cofactors and pigments for photoautotrophic growth (chlorophyll), several essential redox reactions in electron transport chains (haem), N- and S-assimilation (sirohaem), and photomorphogenic processes (phytochromobilin). While the biochemistry of the pathway is well understood and almost all genes encoding enzymes of tetrapyrrole biosynthesis have been identified in plants, the post-translational control and organization of the pathway remains to be clarified. Post-translational mechanisms controlling metabolic activities are of particular interest since tetrapyrrole biosynthesis needs adaptation to environmental challenges. This review surveys post-translational mechanisms that have been reported to modulate metabolic activities and organization of the tetrapyrrole biosynthesis pathway.     

Blue light photoreactivation of nitrate reductase from green algae and higher plants

The inactive form of NADH-nitrate reductase from spinach and $\text{Chlorella fusca}$ is fully reactivated in short periods of time when the enzyme-complex is illuminated with white or blue light but not with red light. Flavin nucleotides greatly accelerate the photoreactivation process. The results suggest that blue light might act as a modulating agent in the assimilation of nitrate in green algae and higher plants.     

Serpins in plants and green algae

Control of proteolysis is important for plant growth, development, responses to stress, and defence against insects and pathogens. Members of the serpin protein family are likely to play a critical role in this control through irreversible inhibition of endogenous and exogenous target proteinases. Serpins have been found in diverse species of the plant kingdom and represent a distinct clade among serpins in multicellular organisms. Serpins are also found in green algae, but the evolutionary relationship between these serpins and those of plants remains unknown. Plant serpins are potent inhibitors of mammalian serine proteinases of the chymotrypsin family in vitro but, intriguingly, plants and green algae lack endogenous members of this proteinase family, the most common targets for animal serpins. An Arabidopsis serpin with a conserved reactive centre is now known to be capable of inhibiting an endogenous cysteine proteinase. Here, knowledge of plant serpins in terms of sequence diversity, inhibitory specificity, gene expression and function is reviewed. This was advanced through a phylogenetic analysis of amino acid sequences of expressed plant serpins, delineation of plant serpin gene structures and prediction of inhibitory specificities based on identification of reactive centres. The review is intended to encourage elucidation of plant serpin functions.     

Microscopic green algae and cyanobacteria in high-frequency intermittent light

The effects of fluctuations in the irradiance onScenedesmus quadricauda, Chlorella vulgaris andSynechococcus elongatus were studied in dilute cultures using arrays of red light emitting diodes. The growth rate and the rate of photoinhibition were compared using intermittent and equivalent continuous light regimes in small-size (30 ml) bioreactors. The CO₂ dependent photosynthetic oxygen evolution rates in the intermittent and continuous light regimes were compared for different light/dark ratios and different mean irradiances. The kinetics of the electron transfer reactions were investigated using a double-modulation fluorometer. The rates of photosynthetic oxygen evolution normalized to equal mean irradiance were lower or equal in the intermittent light compared to the maximum rate found in the equivalent optimal continuous light regime. In contrast, the growth rates in the intermittent light can be higher than the growth rate in the equivalent continuous light. Photoinhibition is presented as an example of a physiological process affecting the growth rate that occurs at different rates in the intermittent and equivalent continuous lights. The difference in the dynamics of the redox state of the plastoquinone pool is proposed to be responsible for the low photoinhibition rates observed in the intermittent light.     

Competition between the photosynthetic and the (chloro)respiratory electron transport chains in cyanobacteria, green algae and higher plants. Effect of heat stress

By measuring the effect of cyanide on the flash-induced redox reactions of the cytochrome (cyt) b ₆/f complex we carried out a comparative study in order to characterize the interaction between the photosynthetic and the respiratory electron transport systems in cyanobacterial (Synechococcus sp. PCC 6301) and green algal (Chlamydomonas reinhardtii) cells, and in tobacco (Nicotiana tabacum L. cv. Petit Havana SR1) protoplasts. We found that the addition of 1 mM KCN resulted in a significant acceleration of the rereduction-rate of cyt f ⁺. This enhancement of the activity of the cyt b ₆/f complex apparently occurred with the same mechanism in prokaryotes and eukaryotes, and its dependence on the concentration of KCN in eukaryotes ruled out an origin in mitorespiration, superoxide dismutase and plastocyanin, strongly suggesting that a cyanide-sensitive terminal oxidase, a putative component of chlororespiration, competes with photosystem 1 (PS1) for electrons from the plastoquionone (PQ) pool. Concerning the physiological role of the competition between the (chloro)respiratory and the photosynthetic electron transport systems, our data obtained with cyanobacterial and algal cells incubated at elevated temperatures (30–50 °C) showed that the respiratory control over photosynthesis became significant in cells exposed to heat-stress. This revised version was published online in August 2006 with corrections to the Cover Date.     

Synthesis and assembly of the cytochrome b-f complex in higher plants

The cytochrome b-f complex is composed of four polypeptide subunits, three of which, cytochrome f, cytochrome b-563 and subunit IV, are encoded in chloroplast DNA and synthesised within the chloroplast, and the fourth, the Rieske FeS protein, is encoded in nuclear DNA and synthesised in the cytoplasm. The assembly of the cytochrome b-f complex therefore requires the interaction of subunits encoded by different genomes. A key role for the nuclear-encoded Rieske FeS protein in the assembly of the complex is suggested by a study of cytochrome b-f complex mutants. The assembly of individual subunits of the complex may be regulated by the availability of prosthetic groups. The genes for the chloroplast-encoded subunits and cDNA clones for the Rieske FeS protein have been isolated and characterised. Cytochrome f and the Rieske FeS protein are synthesised initially with N-terminal presequences required for their correct assembly within the chloroplast. The deduced amino acid sequences of the four subunits have been used to suggest models for the arrangement of the polypeptides in the thylakoid membrane.     

The low-potential cytochrome c of cyanobacteria and algae.

A water-soluble, low-potential cytochrome c-550 is found in some cyanobacteria and eukaryotic algae and has regions of sequence similarity to cytochrome c6. This cytochrome appears to be involved in a fermentation that sustains the organisms during prolonged periods of dark, anaerobic conditions.     

Biodegradation of dyes by some green algae and cyanobacteria

The ability of Chlorella vulgaris, Lyngbya lagerlerimi, Nostoc lincki, Oscillatoria rubescens, Elkatothrix viridis and Volvox aureus to decolorize and remove methyl red, orange II, G-Red (FN-3G), basic cationic, and basic fuchsin was investigated. These algae showed different efficiency for colour removal; varied from 4 to 95% according to the algal species, its growth state and the dye molecular structure. Basic cationic and basic fuchsin were the most susceptible dyes for decolorisation and removal by all algae being tested, and up to 82% of methyl red was also removed by N. lincki and O. rubescens. However, the algal activity to decolorize orange II and G-Red was markedly fluctuated and lower. C. vulgaris displayed activity to remove 43.7 and 59.12% while as V. aureus removed 5.02 and 3.25% of the added dyes respectively. The results also showed that treatment of either C. vulgaris or N. Linckia with G-Red or methyl red, respectively, induced the algal azo dye reductase enzyme by 72 and 71% at the same order.     

Measurement of cytochrome f in thylakoids of higher plants using quantitative gel electrophoresis

A quantitative method was developed to estimate the concentration of cytochrome (cyt) f in isolated thylakoids, using sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by staining with a heme-specific reagent containing 3,3',5,5'-tetramethylbenzidine and hydrogen peroxide. This densitometric technique was at least as sensitive as difference spectroscopy. Analysis of thylakoid preparations by densitometry of stained bands using cyt c as standard gave molar ratios of cyt/chlorophyll which were identical to ratios obtained by difference spectroscopy. Densitometric assays demonstrated that the molar ratio of cyt f/chlorophyll decreased during leaf aging in seven higher plants; however, there was a marked difference in the rate at which cyt f was lost from the leaves of different species.     

In vitro formation of chromium complex from higher plants

Chromium as either chromate or chromic ion reacts with expressed alfalfa liquid to form two complexes. The larger complex may be assembled from the smaller complex and the formation of the larger complex requires a heat labile factor.     

Growth ofLegionella pneumophila in two-membered cultures with green algae and cyanobacteria

Environmental and clinical isolates ofLegionella pneumophila were grown in minimal-salts media (no organic compounds added) in associated with various green algae and cyanobacteria. Growth was observed to level off after a period of hours to days with no subsequent significant loss in the numbers of viableL. pneumophila even several days after growth had ceased. Transfer to new algal or cyanobacterial cultures resulted in a new burst of growty by theL. pneumophila.     

Scavenging of superoxide and hydrogen peroxide in blue‐green algae (cyanobacteria)

Blue‐green algae (cyanobacteria) have evolved as the most primitive, oxygenic, plant‐type photosynthetic organisms. Within a single prokaryotic cell, they have uniquely accommodated both oxygenic photosynthesis and aerobic respiration, which are known to produce superoxide and hydrogen peroxide as inevitable byproducts. Two types of superoxide dismutase have been characterized in both N₂‐fixing and non‐N₂‐fixing cyanobacteria, namely cytosolic iron‐containing superoxide dismutase and thylakoid‐bound manganese‐containing superoxide dismutase. No qualitative differences between various cell types (vegetative cells, heterocysts) were found. In contrast to chloroplasts, most of the cyanobacterial species show catalatic activity. From two species the corresponding enzymes have been characterized as typical prokaryotic (bifunctional) catalase‐peroxidases with homologies to cytochrome c peroxidases and ascorbate peroxidases. In addition to catalatic activity, some strains exhibit ascorbate peroxidase activity, but to date there are no reports detailing purification and characterization.
Cyanobacteria were found to contain low intracellular ascorbate concentrations (30‐100 µ M ) and 2‐5 m M glutathione. Both monodehydroascorbate and glutathione reductase activities were detected in most species examined, whereas dehydroascorbate reductase activity was absent. The question as to whether a glutathione‐ascorbate cycle exists in cyanobacteria cannot be answered at present.