The family of Deg/HtrA proteases in plants

ABSTRACT: BACKGROUND: The Deg/HtrA family of ATP-independent serine endopeptidases is present in nearly all organisms from bacteria to human and vascular plants. In recent years, multiple deg/htrA protease genes were identified in various plant genomes. During genome annotations most proteases were named according to the order of discovery, hence the same names were sometimes given to different types of Deg/HtrA enzymes in different plant species. This can easily lead to false inference of individual protease functions based solely on a shared name. Therefore, the existing names and classification of these proteolytic enzymes does not meet our current needs and a phylogeny-based standardized nomenclature is required. RESULTS: Using phylogenetic and domain arrangement analysis, we improved the nomenclature of the Deg/HtrA protease family, standardized protease names based on their well-established nomenclature in Arabidopsis thaliana, and clarified the evolutionary relationship between orthologous enzymes from various photosynthetic organisms across several divergent systematic groups, including dicots, a monocot, a moss and a green alga. Furthermore, we identified a "core set" of eight proteases shared by all organisms examined here that might provide all the proteolytic potential of Deg/HtrA proteases necessary for a hypothetical plant cell. CONCLUSIONS: In our proposed nomenclature, the evolutionarily closest orthologs have the same protease name, simplifying scientific communication when comparing different plant species and allowing for more reliable inference of protease functions. Further, we proposed that the high number of Deg/HtrA proteases in plants is mainly due to gene duplications unique to the respective organism.     

FtsH proteases in chloroplasts and cyanobacteria

FtsH is a membrane-bound ATP-dependent metalloprotease complex found in prokaryotes and organelles of eukaryotic cells. It consists of one or two trans -membrane helices at its amino-terminus, a highly conserved ATPase domain, which relates it to the AAA protein family, and a zinc-binding domain towards its carboxy-terminus that serves as the proteolytic site. Most bacteria contain a single FtsH gene, but the cyanobacterium Synechocystis has four. The Arabidopsis thaliana genome contains 12 genes encoding FtsH proteins, nine of them can be targeted to chloroplasts, whereas the other three are mitochondrial. Chloroplast FtsH protease is located in the thylakoid membrane, where it forms complexes, most likely hexamers, whose ATPase and proteolytic domains are exposed to the stroma. It is involved in the degradation of the D1 protein of photosystem II reaction centre during its repair from photoinhibition, as well as in the degradation of unassembled proteins in the thylakoid and the stroma. In Arabidopsis , FtsH2 is the most abundant isomer, followed by FtsH5, 8 and 1. This hierarchy is well reflected in the severity of the variegated phenotype of mutants in these genes.     

The family of Deg/HtrA proteases: from Escherichia coli to Arabidopsis

In the genomic era, an increasing number of protease genes have been identified in various organisms. During the last few years, many of these proteases have been characterized using biochemical as well as molecular biological techniques. However, neither the precise location nor the physiological substrates of these enzymes has been identified in many cases, including the Deg/HtrA proteases, a family of serine-type ATP-independent proteases. This family has become especially interesting for many researchers following the determination of the crystal structures of an Escherichia coli and a human Deg/HtrA protease. A breakthrough in photosynthesis research has revealed that a Deg/HtrA protease of Arabidopsis thaliana is involved in the degradation of the D1 protein of photosystem II following photoinhibition. In this review, the available data on Deg/HtrAs of different organisms are compared with those from the photoautotroph cyanobacterium Synechocystis sp. PCC 6803 and the plant Arabidopsis thaliana .     

The ATP-dependent Clp protease in chloroplasts of higher plants

The best-known proteases in plastids are those that belong to families common to eubacteria. One of the first identified was the ATP-dependent caseinolytic protease (Clp), whose structure and function have been well characterized in Escherichia coli . Plastid Clp proteins in higher plants are surprisingly numerous and diverse, with at least 16 distinct Clp proteins in the model plant Arabidopsis thaliana . Multiple paralogues exist for several of the different types of plastid Clp protein, with the most extreme being five for the proteolytic subunit ClpP. Both biochemical and genetic studies have recently begun to reveal the intricate structural interactions between the various Clp proteins, and their importance for chloroplast function and plant development. Much of the recent data suggests that the function of many of the Clp proteins probably affects more specific processes within chloroplasts, in addition to the more general 'housekeeping' role previously assumed.     

The NADPH-dependent electron flow in chloroplasts of the higher plants

The NADPH-dependent reduction of some photosynthetic electron carriers in the dark, and the reduction of NADP+ associated with the glycolytic sequence and the oxidative pentose phosphate pathway in chloroplasts are reviewed. The postulated pathways of electron transports sensitive and insensitive to antimycin A are also evaluated. It is proposed that the electron flow, predominantly through cytochrome bf complex, may be also involved in the pathway of NADPH-dependent and antimycin A-insensitive back electron transport. An information on the chlororespiration in higher plants is also included.     

The NADPH-dependent electron flow in chloroplasts of the higher plants

The NADPH-dependent reduction of some photosynthetic electron carriers in the dark, and the reduction of NADP+ associated with the glycolytic sequence and the oxidative pentose phosphate pathway in chloroplasts are reviewed. The postulated pathways of electron transports sensitive and insensitive to antimycin A are also evaluated. It is proposed that the electron flow, predominantly through cytochrome bf complex, may be also involved in the pathway of NADPH-dependent and antimycin A-insensitive back electron transport. An information on the chlororespiration in higher plants is also included. This revised version was published online in June 2006 with corrections to the Cover Date.     

The role of a glyoxylate-glycolate system in chloroplasts of higher plants

Photoreduction of glyoxylate and oxidation of glycolate wereinvestigated using unwashed chloroplasts from spinach leaves.A glyoxylateglycolate system operated in light and under aerobicconditions. Accompanying the photoreduction of glyoxylate andthe oxidation of glycolate, was the disappearance of inorganicphosphate. Photoreduction of oxalate was also observed in illuminatedchloroplasts. The reaction rate was, however, much lower thanthat for the photoreduction of glyoxylate. (Received August 4, 1969; )     

Minor carotenoid components in the chloroplasts of higher plants

One-dimensional thin layer chromatography with microcrystallinecellulose was used for the separation of minor carotenoid componentsin spinach, parsley and Brassicachloroplasts. It was revealedthat chloroplasts of these plants contain two minor xanthophyllcomponents besides carotenes, lutein, violaxanthin and neoxanthin.These minor components, designated as xanthophyll–443and –439, were different in spectral properties from antheraxanthinand zeaxanthin which are known to be present in the chloroplastsof some higher plants, and evidence was obtained showing thatxanthophyll–439 has an epoxy group. Spectral propertiesof these xanthophylls in benzene, ethanol, H-hexane and carbondisulfide, as well as their contents relative to other carotenoids,are presented in this paper. ¹Postal address     

Lipids in oxygen-evolving photosystem II complexes of cyanobacteria and higher plants

Lipids in dimeric photosystem II complexes prepared from two species of cyanobacteria, Thermosynechococcus vulcanus and Synechocystis sp. PCC6803, and two higher plants, spinach and rice, were analyzed to determine how many lipid molecules and what class of lipids are present in the photosystem II complexes. It was estimated that 27, 20, 8, and 7 lipid molecules per monomer are bound to the dimeric photosystem II complexes of T. vulcanus, Synechocystis, spinach, and rice, respectively. In each of the organisms, the lipid composition of the photosystem II complexes was quite different from that of the thylakoid membranes used for preparation of the complexes. The content of phosphatidylglycerol in the photosystem II complexes of each organism was much higher than that in the thylakoid membranes. Phospholipase A2 treatment of the photosystem II complexes of Synechocystis that degraded phosphatidylglycerol resulted in impairment of QB-mediated but not QA-mediated electron transport. These findings suggest that phosphatidylglycerol plays important roles in the electron transport at the QB-binding site in photosystem II complexes.     

Ent-kaurene synthesis in chloroplasts from higher plants

Lysed chloroplasts from several higher plants synthesized ent-kaurene from copalyl pyrophosphate but not from geranylgeranyl pyrophosphate. The copalyl pyrophosphate transforming activity (so-called B activity of kaurene synthetase) was relatively stable in plastid lysates from Pisum sativum but remarkably unstable in similar preparations of Hordeum vulgare. The bulk of the B activity of kaurene synthetase appeared to reside in the stroma of plastids from P. sativum but required the presence of plastid membranes for maximum activity.     

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.     

Manipulating ribulose bisphosphate carboxylase/oxygenase in the chloroplasts of higher plants

Transgenic manipulation of the photosynthetic CO2-fixing enzyme, ribulose bisphosphate carboxylase/oxygenase (Rubisco) in higher plants provides a very specific means of testing theories about photosynthesis and its regulation. It also encourages prospects for radically improving the efficiencies with which photosynthesis and plants use the basic resources of light, water, and nutrients. Manipulation was once limited to variation of the leaf's total content of Rubisco by transforming the nucleus with antisense genes directed at the small subunit. More recently, technology for transforming the small genome of the plastid of tobacco has enabled much more precise manipulation and replacement of the plastome-encoded large subunit. Engineered changes in Rubisco's properties in vivo are reflected as profound changes in the photosynthetic gas-exchange properties of the leaves and the growth requirements of the plants. Unpredictable expression of plastid transgenes and assembly requirements of some foreign Rubiscos that are not satisfied in higher-plant plastids provide challenges for future research.     

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.