Location and nucleotide sequence of the gene for cytochrome f in wheat chloroplast DNA

Proteolytic removal of the C-terminal transmembrane region of cytochrome f during extraction from turnip and charlock leaves generates a water-soluble monomeric form of the protein

Water-soluble, monomeric cytochrome f purified from leaves of turnip (Brassica rapa) and charlock (Sinapis arvensis) is approximately 3 kDa smaller than the protein in chloroplast thylakoid membranes determined by SDS/PAGE. Sequencing the N-terminal and C-terminal regions of the monomeric protein, by automated Edman degradation and carboxypeptidase P digestion, suggested the loss of 33 amino acid residues at the C-terminus by comparison to sequences of cytochrome f from other higher plants. This was confirmed by the isolation and nucleotide sequencing of the turnip petA gene and by determination of the molecular mass of the monomeric turnip protein by electrospray mass spectrometry. The turnip petA gene encodes a protein of 320 amino acid residues consisting of a presequence of 35 amino acid residues and a mature protein of 285 amino acid residues. The molecular mass of the monomeric turnip protein was 28,160.2 +/- 5.4 Da, indicating cleavage after Gln252 of the mature protein. Electrospray mass spectrometry of the monomeric charlock protein indicated the presence of two main forms with molecular masses of 28,135.1 +/- 5.5 Da and 27,750.7 +/- 4.3 Da corresponding to cleavage after Gln252 and Leu249, respectively. Cleavage in this region of the cytochrome f polypeptide during extraction with butanone removes the single transmembrane span of the protein and liberates the water-soluble globular domain of cytochrome f.

Cytochrome f: Structure, function and biosynthesis

Cytochrome f is an intrinsic membrane component of the cytochrome bf complex, transferring electrons from the Rieske FeS protein to plastocyanin in the thylakoid lumen. The protein is held in the thylakoid membrane by a single transmembrane span located near its C-terminus with a globular hydrophilic domain extending into the lumen. The globular domain of the turnip protein has recently been crystallised, offering the prospect of a detailed three-dimensional structure. Reaction with plastocyanin involves localised positive charges on cytochrome f interacting with the acidic patch on plastocyanin and electron transfer via the surface-exposed tyrosine residue (Tyr83) of plastocyanin. Apocytochrome f is encoded in the chloroplast genome and is synthesised with an N-terminal presequence which targets the protein to the thylakoid membrane. The synthesis of cytochrome f is coordinated with the synthesis of the other subunits of the cytochrome bf complex.

The cloning and sequencing of Synechococcus sp. PCC 7002 petCA operon: Implications for the cytochrome c-553 binding domain of cytochrome f

The genes encoding the Rieske iron-sulfur protein and cytochrome f from a unicellular, naturally transformable, photoheterotrophic cyanobacterium, Synechococcus sp. PCC 7002, formerly Agmenellum quadruplicatum, have been isolated and sequenced. The two genes were found to be on a single operon, petCA.The Synechococcus sp. PCC 7002 iron-sulfur protein contains 181 amino acids, the conserved putative iron-binding domains CTHLGCV, residues 108-114, and CPCHGS, residues 128-133, no presequence and has a 73% sequence identity to the Nostoc PCC 7906 iron-sulfur protein. The 325 amino acid apocytochrome f sequence contains a 42 amino acid presequence, a CANCH heme binding domain, residues 20-24 from the presumed start of the mature protein, and a predicted hydrophobic membrane-spanning domain, residues 250-269. The mature cytochrome f sequence has a 71.5% sequence identity with Nostoc PCC 7906 cytochrome f and possesses a large (-14) negative charge and low calculated pI of 4.47 compared to higher plant chloroplast sequences. Nine separate domains showing differences in charged residues among cyanobacteria and plants have been identified and the possibility that these domains are involved in the ionic interactions with plastocyanin or cytochrome c-553 is discussed.

Cleavage of the precursor of pea chloroplast cytochrome f by leader peptidase from Escherichia coli

Leader peptidase from Escherichia coli was able to process the precursor of pea cytochrome f synthesised in vitro. N-Terminal sequencing established that cleavage by leader peptidase generated the same mature sequence as in pea chloroplasts. Processing by leader peptidase was much more efficient co-translationally rather than post-translationally, and the extent of post-translational processing declined with time suggesting that the cytochrome f precursor folded to an uncleavable conformation. Detergent extracts of pea thylakoid membranes were unable to process the cytochrome f precursor co- or post-translationally.

A plastome mutation affects processing of both chloroplast and nuclear DNA-encoded plastid proteins

Immunoblotting of a chloroplast mutant (pm7) of Oenothera showed that three proteins, cytochrome f and the 23 kDa and 16 kDa subunits of the oxygen-evolving subcomplex of photosystem II, were larger than the corresponding mature proteins of the wild type and, thus, appear to be improperly processed in pm7. The mutant is also chlorotic and has little or no internal membrane development in the plastids. The improperly processed proteins, and other proteins that are completely missing, represent products of both the plastid and nuclear genomes. To test for linkage of these defects, a green revertant of pm7 was isolated from cultures in which the mutant plastids were maintained in a nuclear background homozygous for the plastome mutator (pm) gene. In this revertant, all proteins analyzed co-reverted to the wild-type condition, indicating that a single mutation in a plastome gene is responsible for the complex phenotype of pm7. These results suggest that the defect in pm7 lies in a gene that affects a processing protease encoded in the chloroplast genome.

Structure and expression of cytochrome f in an Oenothera plastome mutant

The chloroplast mutant pm7 is one of a number of mutants derived from the plastome mutator (pm) line of Oenothera hookeri, strain Johansen. Immunoblotting showed that this mutant accumulates a protein that is cross-antigenic with cytochrome f, but five kilodaltons larger than the mature wild-type protein. Since cytochrome f is known to be translated on plastid ribosomes as a precursor with an amino-terminal extension, it is proposed that the unprocessed cytochrome f precursor accumulates in pm7. In addition to this precursor-sized cytochrome f protein, some mature-sized cytochrome f was also found in the mutant plastids. The pm7 mutation is inherited in a non-Mendelian fashion; but no alterations in chloroplast DNA restriction patterns, or differences in DNA sequence in the region encoding cytochrome f, were found in a comparison of the wild-type and pm7 chloroplast DNAs. Although the mutant was capable of synthesizing heme, no covalently-bound heme, normally found associated with mature, functional, cytochrome f was detected in the mutant at sizes expected for the presumed precursor, or for mature cytochrome f. These results indicate that the aberrant accumulation of a precursor-sized cytochrome f in pm7 is not due to a lesion directly in the plastid gene encoding cytochrome f, petA, or to a deficiency in the ability of the mutant plastids to synthesize or accumulate heme.

On the interaction between cytochrome f and plastocyanin

The interaction between cytochrome f and its electron acceptor plastocyanin (PC) was studied. To address the question of which specific regions and which of the positively charged residues of cytochrome f are important for the interaction with the negatively charged residues of PC we have used two different experimental approaches. Cytochrome f was proteolytically cleaved and fragments that could bind to a PC-affinity column were isolated. The smallest of these fragments was analysed to give information on the minimum structural requirement for binding to PC. By this procedure, we identified a peptide of approx. 11 kDa, containing the heme binding site, and having an N-terminal sequence identical to that of the mature cytochrome f. This finding suggests that the first 90 amino acids of cytochrome f contain at least some of the residues interacting with PC. The second approach involved modification of Arg residues of cytochrome f with the specific chemical modifier, hydroxyphenylglyoxal (HPG). Cytochrome f modification was performed in the absence of PC to enable identification of residues that are protected from modification when PC is bound to cytochrome f. Two peptides containing Arg residues which are modified in the absence of PC, but are not modified when PC is present, were isolated. Sequence analysis of these two peptides revealed that Arg residues no. 88 and 154 of cytochrome f are the residues that are protected from modification when cytochrome f is bound to PC, suggesting a role for these residues in the binding of cytochrome f to PC.

Resonance Raman spectroscopy indicates a lysine as the sixth iron ligand in cytochrome f

The resonance Raman spectrum of turnip cytochrome f is similar to that of other c-type cytochromes with the exception of a single band at 1532 cm-1 which is shifted to lower frequency relative to its position (1542-1545 cm-1) in other c-type cytochromes. Comparison of the frequency of this band with that in alkylated cytochrome c at high pH suggests that the sixth heme iron ligand in cytochrome f is a deprotonated lysine amino group rather than a methionine sulfur. Comparison of the amino-acid sequences of cytochromes f and c1 suggests lysine-145 as a likely candidate for the sixth heme iron ligand in cytochrome f.

Nicotiana chloroplast genes for components of the photosynthetic apparatus

In order to understand more fully chloroplast genetic systems, we have determined the complete nucleotide sequence (155, 844 bp) of tobacco (Nicotiana tabacum var. Bright Yellow 4) chloroplast DNA. It contains two copies of an identical 25,339 bp inverted repeat, which are separated by 86, 684 bp and 18,482 bp single-copy regions. The genes for 4 different rRNAs, 30 different tRNAs, 44 different proteins and 9 other predicted protein-coding genes have been located. Fifteen different genes contain introns.Twenty-two genes for components of the photosynthetic apparatus have so far been identified. Most of the genes (except the gene for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase) code for thylakoid membrane proteins. Twenty of them are located in the large single-copy region and one gene for a 9-kd polypeptide of photosystem I is located in the small single-copy region. The gene for the 32-kd protein of photosystem II as well as the gene for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase have strong promoters and are transcribed monocistronically while the other genes are transcribed polycistronically. We have found that the predicted amino acid sequences of six DNA sequences resemble those of components of the respiratory-chain NADH dehydrogenase from human mitochondria. As these six sequences are highly transcribed in tobacco chloroplasts, they are probably genes for components of a chloroplast NADH dehydrogenase. These observations suggest the existence of a respiratory-chain in the chloroplast of higher plants.

The chloroplast genes encoding subunits of the H(+)-ATP synthase

Three CF1 and three CF0 subunits of the chloroplast H(+)-ATP synthase are encoded on the chloroplast genome. The chloroplast atp genes are organized as two operons in plants but not in the green alga, Chlamydomonas reinhardtii. The atpBE or β operon shows a relatively simple organisation and transcription pattern, while the atpIHFA or α operon is transcribed into a large variety of mRNAs. The atp genes are related to those of cyanobacteria and, more distantly, to those of non-photosynthetic bacteria such as E. coli, suggesting a common origin of most F1F0 ATP synthase subunits. Both the chloroplast and cyanobacterial ATP synthases have four F0 subunits, not three as in the E. coli complex. The proton pore of the CF0 is proposed to be formed by the interaction of subunits III and IV.

Structure and organization of Marchantia polymorpha chloroplast genome. III. Gene organization of the large single copy region from rbcL to trnI(CAU)

The nucleotide sequence (25,320 base-pairs) of a part of the large single-copy region of chloroplast DNA from the liverwort Marchantia polymorpha was determined. This region encodes putative genes for four tRNAs, isoleucine tRNA(CAU), arginine tRNA(CCG), proline tRNA(UGG) and tryptophan tRNA(CCA); eight photosynthetic polypeptides, the large subunit of ribulose bisphosphate carboxylase/oxygenase (rbcL), 51,000 Mr photosystem II chlorophyll alpha apoprotein (psbB), apocytochrome b-559 polypeptides (psbE and psbF), 10,000 Mr phosphoprotein (psbH), cytochrome f preprotein (petA), cytochrome b6 polypeptide (petB), and cytochrome b6/f complex subunit 4 polypeptide (petD); 13 ribosomal proteins (L2, L14, L16, L20, L22, L23, L33, S3, S8, S11, S12, S18 and S19); initiation factor 1 (infA); ribosome-associating polypeptide (secX); and alpha subunit of RNA polymerase (rpoA). Functionally related genes were located in several clusters in this region of the genome. There were two ribosomal protein gene clusters: rpl23-rpl2-rps19-rpl22-rps3-rpl16-+ ++rpl14-rps8-infA-secX-rps11-rpoA, with a gene arrangement similar to that of the Escherichia coli S10-spc-alpha operons, and the rps12'-rpl20-rps18-rpl33 cluster. There were gene clusters encoding photosynthesis components such as the psbB-psbH-petB-petD and the psbE-psbF clusters. Thirteen open reading frames, ranging in length from 31 to 434 amino acid residues, remain to be identified.

Variation in copy number of a 24-base pair tandem repeat in the chloroplast DNA of Oenothera hookeri strain Johansen

A highly variable region of chloroplast DNA has been analyzed from three isolates of Oenothera hookeri strain Johansen. The variability results from the presence of two, four or seven copies of a discrete 24-base pair tandem repeat in a segment of the chloroplast DNA within the inverted repeat. Alignment of this DNA region with the published tobacco cpDNA sequence shows that in Oenothera, the repeats are insertions within a large unidentified reading frame, with each repeat unit specifying an eight amino acid in-frame addition. A model to explain the frequent alterations in the copy number of this 24-bp unit is proposed: imprecise alignment and recombination between the two large inverted repeats followed by copy correction could result in an amplification or deletion of the 24-bp segments.

Synthesis and assembly of the cytochrome b-f complex in higher plants

The cytochrome b-f complex is composed of four polypeptide subunits, three of which, cytochrome f, cytochrome b-563 and subunit IV, are encoded in chloroplast DNA and synthesised within the chloroplast, and the fourth, the Rieske FeS protein, is encoded in nuclear DNA and synthesised in the cytoplasm. The assembly of the cytochrome b-f complex therefore requires the interaction of subunits encoded by different genomes. A key role for the nuclear-encoded Rieske FeS protein in the assembly of the complex is suggested by a study of cytochrome b-f complex mutants. The assembly of individual subunits of the complex may be regulated by the availability of prosthetic groups. The genes for the chloroplast-encoded subunits and cDNA clones for the Rieske FeS protein have been isolated and characterised. Cytochrome f and the Rieske FeS protein are synthesised initially with N-terminal presequences required for their correct assembly within the chloroplast. The deduced amino acid sequences of the four subunits have been used to suggest models for the arrangement of the polypeptides in the thylakoid membrane.

Amino acid identities in the three redox center-carrying polypeptides of cytochrome bc1/b6f complexes

The comparison of primary structures is extended to 22 cytochromes b or b6, 12 cytochromes c1 or f, and 8 Rieske FeS proteins. Conclusions are drawn as to their phylogenetic relationship as well as on conserved, functionally important amino acids and secondary structures. The results are in favor of two independent quinone binding sites at opposite surfaces of the membrane, topping one of the two hemes of cytochrome b each.

Organization and structure of the genes for the cytochrome b/c1 complex in purple photosynthetic bacteria. A phylogenetic study describing the homology of the b/c1 subunits between prokaryotes, mitochondria, and chloroplasts

The cytochrome b/c1 complex is an ubiquitous energy transducing enzyme, part of the electron transport chain of prokaryotes, mitochondria, and chloroplasts (b6/f). In the ancient purple photosynthetic bacteria, the b/c1 complex occupies a central metabolic role, being part of their photosynthetic and respiratory electron transport chain. In Rhodobacter the three subunits of the b/c1 complex are FeS protein, cytochrome b, and cytochrome c1, and they are encoded by a constitutively expressed operon named fbc. The organization of the genes for the cytochrome b/c1 complex, the modality of transcription, and the biogenesis of the encoded polypeptides will be described. The Rhodobacter species used to isolate the fbc genes, previously reported as R. sphaeroides was identified as R. capsulatus. Further biochemical characterization of the prokaryotic b/c1 complex indicated that the three polypeptides encoded by the fbc operon comprise the entire catalytic structure: ubiquinol-cytochrome-c reductase. The amino acid sequences of the three b/c1 subunits from the photosynthetic bacterium Rhodobacter capsulatus were compared with the corresponding sequences from yeast mitochondria and spinach chloroplasts. The high homology found between the sequences of all three redox polypeptides from R. capsulatus and yeast mitochondria (cytochrome b 41%, FeS protein 46%, cytochrome c1 31%) provided further evidence that mitochondria arose from the phylogenetic line of purple bacteria. The structure of cytochrome b also exhibited considerable homology to chloroplast cytochrome b6 plus subunit IV (26%). The amino acid sequence of the Rieske FeS protein from R. capsulatus and chloroplasts were found to be conserved only in the C-terminal part (14% total identity), whereas the homology between cytochrome c1 and cytochrome f is very weak (12%), despite similar topology of the two polypeptides. Analysis of the homology suggested that the catalytic sites quinol oxidase (Q0) and quinone reductase (Qi) arose monophonetically, whereas cytochrome c and plastocyanin reductase sites are not homologous and could derive from diverse ancestral genes by convergent evolution.

Reconstitution of isolated Rieske Fe-S protein into a Rieske-depleted cytochrome b6-f complex

The Rieske Fe-S protein can be isolated from the cytochrome b6-f complex by means of chromatography on a hydroxyapatite column in the presence of detergent. Depletion of the cytochrome complex from the Rieske protein results in the loss of oxidoreductase activity, as well as the ability to reduce cytochrome b6. The Rieske Fe-S protein can be reconstituted into the Rieske-depleted complex by removal of the Triton X-100 molecules associated with the protein fractions, and their substitution by lipids. Upon reconstitution the complex is reactivated, and the role of the Rieske Fe-S protein in the reduction of both plastocyanin and cytochrome b6 can be demonstrated.

Isolation of the structural genes for the Rieske Fe-S protein, cytochrome b and cytochrome c1 all components of the ubiquinol: cytochrome c2 oxidoreductase complex of Rhodopseudomonas capsulata

The structural genes for the Rieske Fe-S protein (petA), cytochrome b (petB) and cytochrome c1 (petC) subunits of the ubiquinol:cytochrome c2 oxidoreductase (bc1 complex) of Rhodopseudomonas capsulata have been cloned by complementation, using a mutant defective in this complex. The location of these genes on the obtained plasmid, pR14A, was determined using synthetic mixed oligonucleotide probes corresponding to highly conserved amino acid sequences of these proteins from various organisms. Their correct identity was established by partial sequencing. The petA, petB and petC genes were found to lie close to each other in this order, spanning two adjacent EcoRI fragments of 2.7 X 10(3) and 1.3 X 10(3) base-pairs, respectively. An insertion-deletion mutation, covering most of petB and all of petC and an insertion mutation, located in petB were constructed in vitro and were introduced into the chromosome of an otherwise wild-type strain by gene transfer agent-mediated genetic crosses. The bc-1 mutants obtained were defective in photosynthesis but, as expected, they could grow by respiration because of a branched respiratory pathway. Therefore, in R. capsulata a functional bc1 complex is essential in vivo for photosynthesis but not for respiration. Further, in the respiratory pathway the branch point must be before the bc1 complex, most likely at the quinone pool. These mutants were also proficient in anaerobic growth in the presence of dimethylsulfoxide, indicating that a functional bc1 complex is not required for this pathway. Several other insertions and deletions, located outside of the pet gene cluster, were also constructed. The ability of these latter mutants to grow photosynthetically suggested that no other gene essential for photosynthesis is located in the proximity of the pet cluster. The plasmid pR14A was shown to complement in trans the bc-1 insertion or insertion-deletion mutants, indicating that the pet genes were expressed in R. capsulata. Cross-hybridization experiments showed that the pet cluster was quite distinct from other known genes involved in photosynthesis.

The gene for the Mr 10,000 phosphoprotein associated with photosystem II is part of the psbB operon of the spinach plastid chromosome

We present the nucleotide and derived amino acid sequence of the gene for the 10 kd phosphoprotein associated with photosystem II. This gene was identified by comparing the recently published first nine amino acid residues for the 10 kd phosphoprotein of spinach (Farchaus and Dilley 1986) with available sequence data from the spinach plastid chromosome. The gene, designated psbH, is part of an operon that encodes the 51 kd chlorophyll a apoprotein of the photosystem II reaction center (psbB), the phosphoprotein (73 codons), cytochrome b6 (petB) and subunit IV (petD) of the cytochrome b/f complex in the order given. Northern blot analysis revealed a complex in vivo RNA pattern for this DNA segment resulting from an extensive modification of a 5.6 kb long putative primary transcript which includes a monocistronic RNA species for the phosphoprotein of approximately 420 bases. The deduced amino acid sequence for the phosphoprotein indicates a polypeptide corresponding to a molecular weight of 7.8 kb. Secondary structure predictions place all potential phosphorylation sites on the stromal side of the membrane.

Location and nucleotide sequence of the pre-apocytochrome f gene on the Oenothera hookeri plastid chromosome (Euoenothera plastome I)

The gene for pre-apocytochrome f has been mapped by blot hybridization on a 2.4 kbp HindIII fragment of the circular plastid chromosome of Oenothera hookeri employing probes from the corresponding spinach gene. The gene is located distal to the gene for the ATP synthase subunit alpha, at the border of the 45 kbp inversion that distinguishes spinach and Oenothera plastid chromosomes. Both genes are transcribed in the same direction. Nucleotide sequence analysis reveals a single open reading frame encoding 318 amino acids of which 285 comprise the mature polypeptide and another 33 residues represent probably a N-terminal signal sequence. The putative pre-sequence is 2 residues shorter than those known from the spinach, wheat and pea protein. The deduced amino acid sequences of f cytochromes from the four plant species show over 80% conservation, maintaining the structural characteristics of the protein.

Nucleotide sequence of the rice cytochrome f gene and the presence of sequence variation near this gene

The rice (Oryza sativa L. var. Labelle) chloroplast (cp) gene encoding cytochrome f has been isolated and sequenced. The coding region of this rice gene displays 95.1%, 85.3% and 85.2% nucleotide sequence homology with that of wheat, pea and spinach, respectively. To examine the cpDNA sequence variation in rice, cpDNA from Labelle and its parents, Belle Patna and Dawn was compared. Using the cytochrome f gene as the probe for hybridization, we found several differences in the size and number of restriction fragments in the cp genome of three rice varieties. An additional restriction fragment found in the Belle Patna cp suggests that this cp genome is either heterogeneous or contains two copies of cytochrome f gene per cpDNA.

Chloroplast DNA deletions associated with wheat plants regenerated from pollen: possible basis for maternal inheritance of chloroplasts

Albinism in plants regenerated from pollen by anther culture may result from the same mechanisms as postulated to be responsible for maternal inheritance of chloroplasts. Consistent with this view, Southern blotting was used to show that large regions of the chloroplast genome (over 80% in one case) were deleted in the major ctDNA molecules present in eight albino wheat plants regenerated from separate pollen calluses. A wide variety of deleted ctDNA molecules was present in these plants. Most albino plants appeared to contain a heterogeneous population of ctDNA molecules. Albino plant 6 contained one major type of deleted ctDNA molecule that had a circular 39 kb restriction map. The retention of only two Pst l (unaltered in size) fragments in albino plant 7 may delimit a region of ctDNA that contains a replication origin.

Nicotiana chloroplast genome : 8. Localization of genes for subunits of ATP synthase, the cytochrome b-f complex and the 32 kD protein

Using the existing restriction map and probes from wheat and pea ct-DNA, seven protein genes have been localized in the chloroplast genome of N. tabacum. On the clock-like map, the location of each gene is indicated by its time zone: the 15.2 kD polypeptide of the cytochrome b/f complex at 3∶15, cytochrome f at 4∶30, LS of RuBPCase at 4∶50, both β and ɛ subunits of ATP synthase at or near 5∶00, proton-translocating subunit of ATP synthase at 8∶20, α subunit of ATP synthase at 8∶40 and the 32 kD protein at 9∶30. The genome organization of Nicotiana chloroplast DNA is similar to spinach.