The Structure and Gene Repertoire of an Ancient Red Algal Plastid Genome

Abstract

Abstract. Photosynthetic eukaryotes can, according to features of their chloroplasts, be divided into two major groups: the red and the green lineage of plastid evolution. To extend the knowledge about the evolution of the red lineage we have sequenced and analyzed the chloroplast genome (cp-genome) of Cyanidium caldarium RK1, a unicellular red alga (AF022186). The analysis revealed that this genome shows several unusual structural features, such as a hypothetical hairpin structure in a genefree region and absence of large repeat units. We provide evidence that this structural organization of the cpgenome of C. caldarium may be that of the most ancient cp-genome so far described. We also compared the cpgenome of C. caldarium to the other known cp-genomes of the red lineage. The cp-genome of C. caldarium cannot be readily aligned with that of Porphyra purpurea, a multicellular red alga, or Guillardia theta due to a displacement of a region of the cp-genome. The phylogenetic tree reveals that the secondary endosymbiosis, through which G. theta evolved, took place after the separation of the ancestors of C. caldarium and P. purpurea.We found several genes unique to the cp-genome of C. caldarium. Five of them seem to be involved in the building of bacterial cell envelopes and may be responsible for the thermotolerance of the chloroplast of this alga. Two additional genes may play a role in stabilizing the photosynthetic machinery against salt stress and detoxification of the chloroplast. Thus, these genes may be unique to the cp-genome of C. caldarium and may be required for the endurance of the extreme living conditions of this alga.

Biogenesis of Phycobiliproteins

“…S3). CpeS is also similar to the products of conserved hypothetical genes ycf58 (orf149) of the red algal chloroplast genomes of Porphyra purpurea (38) and Porphyra yezoensis, which synthesize PE, but a homolog is also found in the chloroplast genome of Cyanidium caldarium, which can only synthesize PC and AP (39). Using the sequence of the CpeS protein of the PE-containing cyanobacterium F. diplosiphon as the query (22), three unlinked open reading frames with 40 -51% sequence similarity to CpeS were identified in the genome of Synechococccus sp.…”

EST-analysis of the thermo-acidophilic red microalga Galdieriasulphuraria reveals potential for lipid A biosynthesis and unveils the pathway of carbon export from rhodoplasts

“…Here, we provide for the first time evidence for a complete lipid A biosynthetic pathway in plants. In Galdieria, the first two steps (LpxA, LpxC) in the pathway are likely to be encoded in the plastid genome by analogy with Cyanidioschyzon merolae (Ohta et al, 2003) and Cyanidium caldarium RK1 (Glo¨ckner et al, 2000). Later steps in the pathway (LpxD, LpxB, LpxK, WaaA) appear to be nuclear encoded and corresponding ESTs are present in our collection.…”

“…In addition, several ESTs representing glutamine synthetase were detected (A4_33A10, A4_33F03, HET_10AO, HET_24C05). Glutamate synthase (GOGAT) is encoded by the plastid genomes of the closely related species Cyanidium caldarium (Glo¨ckner et al, 2000) and Cyanidioschyzon merolae (Ohta et al, 2003); therefore the absence of GOGAT from the EST collection is not surprising. No ESTs with similarities to phosphoglycolate phosphatase or glycerate kinase were found, presumably because the expression of the respective genes is low in G. sulphuraria.…”

Reversed-phase HPLC Determination of Chlorophyll a′ and Naphthoquinones in Photosystem I of Red Algae: Existence of Two Menaquinone-4 Molecules in Photosystem I of Cyanidium caldarium

“…6 All of the key amino acid residues taking part in the hydrogen bond networks to Chl a′ in S. elongatus are conserved in the PsaA amino acid sequence of C. caldarium. 24 Though the PsaA amino acid sequence of P. purpureum has not yet been determined, that of another red alga, Porphyra purpurea, 25 also conserves these key amino acid residues. One of the reasons why the C13 2 stereoisomer of Chl a, Chl a′, is employed in P700 would, in part, be due to the geometrical requirements for properly binding to such a characteristic environment.…”

“…31 The condensation process is catalyzed by a menA gene product (DHNA phytyl transferase). 31,32 The deduced amino acid sequence of the menA of C. caldarium 24 possessed an identity of only 15%, between Syechocystis sp. PCC6803 33 and T. elongatus 34 containing PhQ, 6,27 while the identity was as high as 55% between S. PCC6803 and T. elongates.…”