An ORF323 with homology to crtE, specifying prephytoene pyrophosphate dehydrogenase, is encoded by cyanelle DNA in the eukaryotic alga Cyanophora paradoxa

Conversion from archaeal geranylgeranyl diphosphate synthase to farnesyl diphosphate synthase. Two amino acids before the first aspartate-rich motif solely determine eukaryotic farnesyl diphosphate synthase activity

Farnesyl diphosphate (FPP) and geranylgeranyl diphosphate (GGPP) are precursors for a variety of important natural products, such as sterols, carotenoids, and prenyl quinones. Although FPP synthase and GGPP synthase catalyze similar consecutive condensations of isopentenyl diphosphate with allylic diphosphates and have several homologous regions in their amino acid sequences, nothing is known about how these enzymes form the specific products. To locate the region that causes the difference of final products between GGPP synthase and FPP synthase, we constructed six mutated archaeal GGPP synthases whose regions around the first aspartate-rich motif were replaced with the corresponding regions of FPP synthases from human, rat, Arabidopsis thaliana, Saccharomyces cerevisiae, Escherichia coli, Bacillus stearothermophilus, and from some other related mutated enzymes. From the analysis of these mutated enzymes, we revealed that the region around the first aspartate-rich motif is essential for the product specificity of all FPP synthases and that the mechanism of the chain termination in eukaryotic FPP synthases (type I) is different from those of prokaryotic FPP synthases (type II). In FPP synthases of type I, two amino acids situated at the fourth and the fifth positions before the motif solely determine their product chain length, while the product specificity of the type II enzymes is determined by one aromatic amino acid at the fifth position before the motif, two amino acids inserted in the motif, and other modifications. These data indicate that FPP synthases have evolved from the progenitor corresponding to the archaeal GGPP synthase in two ways.

Complete DNA sequence, specific Tn5 insertion map, and gene assignment of the carotenoid biosynthesis pathway of Rhodobacter sphaeroides

The carotenoid biosynthesis genes form a cluster within the genome of Rhodobacter sphaeroides, lying in the middle of a larger cluster and 45 kb in length, which contains genes for bacteriochlorophyll biosynthesis and for the reaction center and light-harvesting apoproteins. The positions and approximate limits of the carotenoid genes were determined previously by localized transposon Tn5 mutagenesis and by comparison with the closely related Rhodobacter capsulatus carotenoid gene cluster. In this report, analysis of the DNA and deduced amino acid sequences of the carotenoid genes in R. sphaeroides are presented. Twenty-five Tn5 insertion mutants were used to produce a base-specific Tn5 insertion map of this region, and carotenoid gene assignment was supported by spectroscopic, ultrastructural, and high-pressure liquid chromatography analyses of these mutants. A region in the 3' end of crtD which affects bacteriochlorophyll biosynthesis was discovered, and CrtA was found to possess a proline-rich C-terminal region containing a repeated (Ala-Pro)n motif. CrtF also showed a high degree of sequence conservation with eukaryotic O-methyltransferases. This study provides gene sequences and assignments based upon a comprehensive structural, spectroscopic, and biochemical analysis of a range of carotenoid biosynthetic mutants; in each mutation, the point of Tn5 insertion is determined accurate to 1 bp on the gene cluster.

Microbial carotenoids

Carotenoids occur universally in photosynthetic organisms but sporadically in nonphotosynthetic bacteria and eukaryotes. The primordial carotenogenic organisms were cyanobacteria and eubacteria that carried out anoxygenic photosynthesis. The phylogeny of carotenogenic organisms is evaluated to describe groups of organisms which could serve as sources of carotenoids. Terrestrial plants, green algae, and red algae acquired stable endosymbionts (probably cyanobacteria) and have a predictable complement of carotenoids compared to prokaryotes, other algae, and higher fungi which have a more diverse array of pigments. Although carotenoids are not synthesized by animals, they are becoming known for their important role in protecting against damage by singlet oxygen and preventing chronic diseases in humans. The growth of aquaculture during the past decade as well as the biological roles of carotenoids in human disease will increase the demand for carotenoids. Microbial synthesis offers a promising method for production of carotenoids.

Eubacteria show their true colors: genetics of carotenoid pigment biosynthesis from microbes to plants

The opportunities to understand eubacterial carotenoid biosynthesis and apply the lessons learned in this field to eukaryotes have improved dramatically in the last several years. On the other hand, many questions remain. Although the pigments illustrated in Fig. 2 represent only a small fraction of the carotenoids found in nature, the characterization of eubacterial genes required for their biosynthesis has not yet been completed. Identifying those eukaryotic carotenoid biosynthetic mutants, genes, and enzymes that have no eubacterial counterparts will also prove essential for a full description of the biochemical pathways (81). Eubacterial crt gene regulation has not been studied in detail, with the notable exceptions of M. xanthus and R. capsulatus (5, 33, 39, 45, 46, 84). Determination of the rate-limiting reaction(s) in carotenoid biosynthesis has thus far yielded species-specific results (12, 27, 47, 69), and the mechanisms of many of the biochemical conversions remain obscure. Predicted characteristics of some carotenoid biosynthesis gene products await confirmation by studying the purified proteins. Despite these challenges, (over)expression of eubacterial or eukaryotic carotenoid genes in heterologous hosts has already created exciting possibilities for the directed manipulation of carotenoid levels and content. Such efforts could, for example, enhance the nutritional value of crop plants or yield microbial production of novel and desirable pigments. In the future, the functional compatibility of enzymes from different organisms will form a central theme in the genetic engineering of carotenoid pigment biosynthetic pathways.

The gene for ribosomal protein L27 is located on the plastid rather than the nuclear genome of the chlorophyll c-containing alga Pleurochrysis carterae

The gene for ribosomal protein L27 (rpl27) has not been found in plastid genomes. We report here that the rpl27 gene is located in the plastid genome of the prymnesiophyte Pleurochrysis carterae. The deduced amino acid sequence showed 59% identity with E. coli L27. 1.0 kb transcript of the gene was detected by Northern blot analysis. Nucleotide sequence analysis of PCR products suggested that rpl27 is widespread in the genomes of Prymesiophyta and Rhodophyta. In all species of Prymnesiophyta examined in this study, the gene is located at the 3' downstream region of Rubisco operon.

Two amino-acid biosynthetic genes are encoded on the plastid genome of the red alga Porphyra umbilicalis

To isolate the gene encoding the amino-acid biosynthetic enzyme acetolactate synthase (ALS) from the red alga Porphyra umbilicalis, PCR experiments were carried out using P. umbilicalis DNA as the template and degenerate oligonucleotides representing conserved regions of ALS amino-acid sequences. Interestingly, the PCR product (0.9 kb) hybridized exclusively to the plastid DNA of this red alga. DNA sequencing of two contiguous EcoRI plastid DNA clones revealed a 590 amino-acid open reading frame with 55 to 61% identity to cyanobacterial ALS sequences. A second gene (argB) encoding another amino-acid biosynthetic enzyme, N-acetylglutamate kinase, was identified upstream of, and on the opposite strand to the gene encoding ALS (ilvB). This is the first molecular characterization of a gene for an arginine biosynthetic enzyme from any plant. In addition, two tRNA genes, trnT(GGU) and trnY(GUA), were detected downstream from ilvB while four tRNA genes, trnfM(CAU), trnA(GGC), trnA(GGC), trnS(-GCU) and trnD(GUC), were found downstream from argB. trnA(GGC) is not found in the chloroplast genomes of land plants.

Cloning and nucleotide sequencing of the genes, rpIU and rpmA, for ribosomal proteins L21 and L27 of Escherichia coli

The rpIU and rpmA genes that encode ribosomal proteins (r-proteins) L21 and L27 of Escherichia coli K-12 have been isolated from the ordered clone bank of this bacterium. They were found to be located at coordinates 3,351.7-3,352.3 kb on the physical map of E. coli. The nucleotide sequence of the cloned genes and their flanking regions indicated that the two r-protein genes compose an operon. Upstream of the two genes there is an open reading frame (ORF) in the opposite direction. The deduced polypeptide encoded by this ORF has a molecular weight of 35,215 and shows a significant degree of sequence similarity to the enzyme that is involved in the carotenoid biosynthesis and encoded by the crtE gene of carotenogenic bacteria and to prenyltransferases found in various organisms.

Ins and outs of plastid genome evolution

Recent findings have established cracks in the straight-laced image of the plastid genome as a molecule whose sole function is photosynthesis and whose gene content is highly conserved. Genes for numerous non-photosynthetic functions have been identified. Algal plastid genomes contain many genes with no homologs in angiosperms, and the recent transfer of genes from the plastid to the nuclear genome has been described. Wholesale abandonment of genes encoding photosynthetic and gene-expression functions has occurred in the plastid genomes of a non-green plant and alga. The origins of plastid DNA, its use in phylogenetic studies, and the origins of plastid introns are also reviewed.