A 2,900 base pair DNA segment of the spinach plastid chromosome which encodes the genes for the 44 kd chlorophyll a apoprotein and a "32 kd"-like protein of the photosystem II reaction center has been subjected to sequence and Northern blot analysis. The genes are located almost centrally in the large single-copy segment of the chromosome adjacent to the two genes for the P700 chlorophyll a apoproteins of the photosystem I reaction center. The DNA sequence reveals two uninterrupted protein-coding regions of 473 (44 kd chlorophyll a apoprotein) and 353 triplets ("32 kd"-like protein). The latter gene is strikingly similar to the gene for the herbicide-binding "32 kd" protein which maps some 30 kbp distant on the plastid chromosome. The two genes overlap by 50 base pairs but are read in different phases. They may be contranscribed and the RNA modified to give several discrete species ranging in size from 1.6 to 4.6 kb. A presumptive promoter site was only identified for the "32 kd"-like protein, while potential ribosome binding and transcription termination sites are found preceding and following both genes, respectively. The polypeptides possess a high content of hydrophobic amino acids, most of which appear to be clustered in transmembrane spans. The molecular weights of 51,785 (44 kd chlorophyll a apoprotein) and 39,465 ("32 kd"-like protein) derived from the deduced amino acid sequences are higher than the experimentally determined protein sizes. Amino acid codon usage for both genes is highly selective. Comparison of the chlorophyll a apoproteins of spinach reveals regions of sequence homology.

Analysis of a 0.6 kb fragment of the spinach plastic chromosome adjacent to the 3' end of the apocytochrome f gene has disclosed two uninterrupted reading frames of 83 and 39 triplets, the product of the first one being apocytochrome b‐559. The first 27 predicted amino acid residues had been verified by protein sequence analysis and the molecular mass of 9390 Da derived from the amino acid sequence deduced here is close to that of the authentic protein. The two genes are transcribed by a bicistronic RNA in a direction opposite to that of cytochrome f, and their translation stop/potential ribosome binding sites overlap. Features of the two genes resembling those of bacterial genes include putative tetra‐ or pentanucleotide ShineDalgarno sequences, Pribnow boxes, ‘−35’ promotor consensus sequences and possibly a transcription termination region. Both gene structure and products of DNA‐ or RNA‐programmed cell‐free translation preclude that apocytochrome b‐559 is made as a precursor. The amino acid sequence includes only one histidine residue located in a predicted secondary structure of strong hydrophobicity which indicates the intriguing possibility that more than one protein chain must cooperate in heme binding of this cytochrome.

A photosystem I reaction center complex has been purified to homogeneity by a procedure involving partial solubilization of spinach thylakoid membranes, ion exchange chromatography and centrifugation in sucrose gradients. The complex contains 7 polypeptides: the P700 chlorophylla apoprotein with an apparent molecular weight of 67 kd, which at high resolution splits into two bands, and smaller polypeptides of 22 (subunit 2), 18.5, 18, 16, 12 and 10 kd.Stable transcripts for the P700 chlorophylla apojprotein and subunit 2 were found in plastid and cytosolic RNA, respectively. The apoprotein product obtained by translation in a mRNA-dependent cell-free rabbit reticulocyte lysate and also by DNA-programmed transcription-translation of cloned plastid DNA fragments inE. coli lysates was indistinguishable immunologically and electrophoretically from the authentic protein. However, the product immunologically related to subunit 2 was 4 kd larger than the mature compound indicating that this protein is encoded in the nucleus and synthesized as a precursor.The gene for the P700 chlorophylla apoprotein has been physically mapped on the spinach plastid chromosome by hybrid selection mapping and DNA-programmed cell-free transcription-translation using cloned restriction fragments of plastid DNA. There is one gene copy per chromosome and it is located centrally in the large single-copy region of the circular DNA molecule. This gene is uninterrupted and is transcribed in the same direction as that of the large subunit of ribulose bisphosphate carboxylase/oxygenase. Its transcript is approximately 4 kb longer than the 2 kbp structural gene.

A 2.4 kilobase-pair segment of the spinach plastid chromosome carrying the genes for apocytochrome b6 and subunit 4 of the thylakoid membrane cytochrome b/f complex has been analysed by DNA sequencing and Northern blot analysis. The nucleotide sequence reveals two uninterrupted open reading frames of 211 and 139 triplets coding for two hydrophobic proteins of 23.7 kd (cytochrome b6) and 15.2 kd (subunit 4). The genes are located on the same strand and are separated from each other by 1018 untranslated base pairs. They map adjacent to the gene for the P680 chlorophyll α apoprotein of the photosystem II reaction center. The three genes appear to be under common transcriptional control and the transcripts post-transcriptionally modified. The deduced amino acid sequences of cytochrome b6 and subunit 4 both exhibit significant homology with published sequences from mitochondrial b cytochromes (42 kd) suggesting that these functionally equivalent polypeptides in photosynthetic and respiratory electron transport chains arose monophyletically.

The nucleotide sequence of 2.5 kbp from the cloned SalI fragments 8 and 11 of spinach plastid DNA has been determined. This region was found to encode three open reading frames for hydrophilic polypeptides of 77, 138, and 335 amino acids. Using the computer search algorithm of Lipman and Pearson (Science 227, 1435, 1985), these genes were identified as coding for homologues of E. coli initiation factor IF-1 (inFA), 30S ribosomal protein S11 (rps11), and the alpha-subunit of DNA-dependent RNA polymerase (rpoA). The spinach plastid gene organization is inFA - 381 bp spacer - rps11 - 72 bp spacer - rpoA. The genes are transcribed in vivo and appear to encode functional proteins. These findings imply that plastid chromosomes code for components of the organelle transcription apparatus.