The transcriptional activity of nucleoids changes during plastid development, presumably due to the morphological and molecular differences of the nucleoids. Pea chloroplast nucleoids have an abundant 70-kDa protein identified as sulfite reductase (SiR) that can compact DNA. Using an in vitro transcription assay, we show here that heparin increased the transcriptional activity of chloroplast nucleoids with concomitant release of SiR. Using a fluorometric method we developed for analyzing DNA compaction, we found that the fluorescence intensity of chloroplast DNA stained with 4,6-diamidino-2-phenylindole was decreased by the addition of SiR and increased by the subsequent addition of heparin. Addition of exogenous SiR increased the compaction of isolated nucleoids, and the addition of heparin relaxed it. SiR effectively repressed the in vitro transcription activity of nucleoids and counteracted the activation by heparin. These results suggest that SiR regulates the transcriptional activity of chloroplast nucleoids through changes in DNA compaction.

We determined the complete nucleotide sequence of the plastid genome of the unicellular marine red alga Porphyridium purpureum strain NIES 2140, belonging to the unsequenced class Porphyridiophyceae. The genome is a circular DNA composed of 217,694 bp with the GC content of 30.3%. Twenty-nine of the 224 protein-coding genes contain one or multiple intron(s). A group I intron was found in the rpl28 gene, whereas the other introns were group II introns. The P. purpureum plastid genome has one non-coding RNA (ncRNA) gene, 29 tRNA genes and two nonidentical ribosomal RNA operons. One rRNA operon has a tRNA(Ala)(UGC) gene between the rrs and the rrl genes, whereas another has a tRNA(Ile)(GAU) gene. Phylogenetic analyses suggest that the plastids of Heterokontophyta, Cryptophyta and Haptophyta originated from the subphylum Rhodophytina. The order of the genes in the ribosomal protein cluster of the P. purpureum plastid genome differs from that of other Rhodophyta and Chromalveolata. These results suggest that a large-scale rearrangement occurred in the plastid genome of P. purpureum after its separation from other Rhodophyta.

The assimilation of sulfur is an important process for the synthesis of various sulfur compounds such as amino acids, sulfolipids, and coenzymes. Sulfite reductase (SiR) is a central enzyme within the sulfur assimilation pathway. Sulfate ions taken up by the sulfate transporter are first activated with ATP by ATP sulfurylase, forming adenosine-5¢-phosphosulfate. Adenosine-5¢-phosphosulfate is further phosphorylated by adenosine-5¢-phosphosulfate kinase, forming 3¢-phosphoadenosine-5¢-phosphosulphate. 3¢-Phosphoadenosine-5¢-phosphosulfate is reduced to sulfite by 3¢-phosphoadenosine-5¢-phosphosulfate reductase, and sulfite is further reduced to sulfide by SiR. The resultant sulfide is fixed into cysteine by cysteine synthase using O-acetylserine as an acceptor. SiR is localized to chloroplasts in green leaves and to nongreen plastids in nonphotosynthetic tissues. SiR has been identified as one of the main constituents of plastid nucleoids in pea [1] and soybean [2]. Chloroplast DNA was previously thought to occur dissolved in the stroma, but recent studies have revealed that the functional form of chloroplast DNA is a DNA-protein complex called a nucleoid [3]. Plant SiR contains a siroheme and a [4Fe-4S] cluster and catalyzes the six-electron reduction of sulfite to sulfide, depending on ferredoxin as an electron donor [4]. Plant SiR was considered to be a