A gene cluster in the spinach and pea chloroplast genomes encoding one CF1 and three CF0 subunits of the H+-ATP synthase complex and the ribosomal protein S2

The chloroplast CF0I subunit can replace the b-subunit of the F0F1-ATPase in a mutant strain of Escherichia coli K12

The amino acid sequence of the CF0I subunit from the chloroplast F0F1-ATPase has only a low similarity to the amino acid sequence of the b-subunit of the E. coli F0F1-ATPase. However, secondary and tertiary structure predictions plus the distribution of hydrophobic and hydrophilic amino acids have indicated that these two subunits serve a similar function. This proposition was investigated directly. A cDNA clone for the chloroplast atpF gene, encoding the CF0I subunit, was altered by site-directed mutagensis such that the translation start site corresponded to the N-terminus of the mature protein. An E. coli mutant strain carrying a chain-terminating mutation in the uncF gene, encoding the b-subunit, was transformed with the plasmid carrying the altered atpF gene. The resultant transformant was able to grow on succinate and gave a growth yield similar to that of a wild-type control. Assays on membrane preparations from the transformant also clearly indicated that the mature CF0I subunit from spinach chloroplasts was able to replace the E. coli b-subunit in the E. coli F0F1-ATPase.

Comparative and functional anatomy of group II catalytic introns--a review

The 70 published sequences of group II introns from fungal and plant mitochondria and plant chloroplasts are analyzed for conservation of primary sequence, secondary structure and three-dimensional base pairings. Emphasis is put on structural elements with known or suspected functional significance with respect to self-splicing: the exon-binding and intron-binding sites, the bulging A residue involved in lariat formation, structural domain V and two isolated base pairs, one of them involving the last intron nucleotide and the other one, the first nt of the 3' exon. Separate sections are devoted to the 29 group II-like introns from Euglena chloroplasts and to the possible relationship of catalytic group II introns to nuclear premessenger introns. Alignments of all available sequences of group II introns are provided in the APPENDIX.

Translation of chloroplast-encoded mRNA: potential initiation and termination signals

A survey of 196 protein-coding chloroplast DNA sequences demonstrated the preference for AUG and UAA codons for initiation and termination of translation, respectively. As in prokaryotes at every nucleotide position from -25 to +25 (AUG is +1 to +3) and for 25 nucleotides 5' and 3' to the termination codon an A or U is predominant, except for C at +5 and G at +22. A Shine-Dalgarno (SD) sequence (GGAGG or tri- or tetranucleotide variant) was found within 100 bp 5' to the AUG codon in 92% of the genes. In 40% of these cases, the location of the SD sequence was similar to that of the consensus for prokaryotes (-12 to -7 5' to AUG), presumed to be optimal for translation initiation. A SD sequence could not be located in 6% of the chloroplast sequences. We propose that mRNA secondary structures may be required for the relocation of a distal SD sequences to within the optimal region (-12 to -7) for initiation of translation. We further suggest that termination at UGA codons in chloroplast genes may occur by a mechanism, involving 16S rRNA secondary structure, which has been proposed for UGA termination in E. coli.

Mutational replacements of conserved amino acid residues in the alpha subunit change the catalytic properties of Escherichia coli F1-ATPase

Four Escherichia coli mutants with defects in the alpha subunit of H+-ATPase (F0F1) (strain KF154, Pro-281----Leu; KF101 and KF131, Ala-285----Val; KF114, Arg-376----Cys) were isolated, and the kinetic properties of their F1-ATPases were studied. All the mutations so far identified are clustered in the two defined regions of the alpha subunit. With F1 of strain KF114, as with F1 of uncA401 (Ser-373----Phe; T. Noumi, M. Futai, and H. Kanazawa (1984) J. Biol. Chem. 259, 10076-10079), the rate of multisite hydrolysis of ATP was 4 X 10(-3)-fold lower than that with wild-type F1, suggesting that residues Ser-373 and Arg-376 or the regions in their vicinities are essential for positive catalytic cooperativity. With F1 from strain KF101, multisite hydrolysis was higher (about 40% of that of the wild type), but the F1 was unstable and showed defective interaction with the membrane sector (F0). The F1 from KF154 had lower multisite hydrolysis (about 10% of that of the wild type) but could support slow growth by oxidative phosphorylation.

Chloroplast ATP synthase contains one single copy of subunit delta that is indispensable for photophosphorylation

F0F1 ATP synthases synthesize ATP in their F1 portion at the expense of free energy supplied by proton flow which enters the enzyme through their channel portion F0. The smaller subunits of F1, especially subunit delta, may act as energy transducers between these rather distant functional units. We have previously shown that chloroplast delta, when added to thylakoids partially depleted of the coupling factor CF1, can reconstitute photophosphorylation by inhibiting proton leakage through exposed coupling factor CF0. In view of controversies in the literature, we reinvestigated two further aspects related to subunit delta, namely (a) its stoichiometry in CF0CF1 and (b) whether or not delta is required for photophosphorylation. By rocket immunoelectrophoresis of thylakoid membranes and calibration against purified delta, we confirmed a stoichiometry of one delta per CF0CF1. In CF1-depleted thylakoids photophosphorylation could be reconstituted not only by adding CF1 and subunit delta but, surprisingly, also by CF1 (-delta). We found that the latter was attributable to a contamination of CF1 (-delta) preparations with integral CF1. To lesser extent CF1 (-delta) acted by complementary rebinding to CF0 channels that were closed because they contained delta [CF0(+delta)]. This added catalytic capacity to proton-tight thylakoid vesicles. The ability of subunit delta to control proton flow through CF0 and the absolute requirement for delta in restoration of photophosphorylation suggest an essential role of this small subunit at the interface between the large portions of ATP synthase: delta may be part of the coupling site between electrochemical, conformational and chemical events in this enzyme.

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.

Transcription of ten ribosomal protein genes from tobacco chloroplasts: a compilation of ribosomal protein genes found in the tobacco chloroplast genome

Transcription of rps2, rps4, rps7, rps11, rps14, rps15, rps18, rpl20, rpl33 and rpl36 from the tobacco chloroplast genome has been studied. Northern blot analysis has revealed that all these genes are transcribed in the chloroplast. Multiple transcripts were detected for all the genes and amounts of the transcripts were quite different among the ten genes. These ten ribosomal protein genes together with the ten other ribosomal protein genes published previously were complied and compared. Four out of the twenty genes contain introns, possible secondary structures of which are presented.

ATP synthases--structure of the F1-moiety and its relationship to function and mechanism

A great deal of progress has been made in understanding both the structure and the mechanism of F1-ATPase. The primary structure is now fully known for at least five species. Sequence comparison between chloroplast, photobacteria, aerobic bacteria, and mitochondrial representatives allow us to infer more general functional relationships and evolutionary trends. Although the F1 moiety is the most studied segment of the H+-ATPase complex, there is not a full understanding of the mechanism and regulation of its hydrolytic activity. The beta subunit is now known to contain one and probably two nucleotide binding domains, one of which is believed to be a catalytic site. Recently, two similar models have been proposed to attempt to describe the "active" part of the beta subunits. These models are mainly an attempt to use the structure of adenylate kinase to represent a more general working model for nucleotide binding phosphotransferases. Labelling experiments seem to indicate that several critical residues outside the region described by the "adenylate kinase" part of this model are also actively involved in the ATPase activity. New models will have to be introduced to include these regions. Finally, it seems that a consensus has been reached with regard to a broad acceptance of the asymmetric structure of the F1-moiety. In addition, recent experimental evidence points toward the presence of nonequivalent subunits to describe the functional activity of the F1-ATPase. A summary diagram of the conformational and binding states of the enzyme including the nonequivalent beta subunit is presented. Additional research is essential to establish the role of the minor subunits--and of the asymmetry they introduce in F1--on the physiological function of the enzyme.

Spinach chloroplast rpoBC genes encode three subunits of the chloroplast RNA polymerase

Sequence analysis of a 12,400 base-pair region of the spinach chloroplast genome indicates the presence of three genes encoding subunits of the chloroplast RNA polymerase. These genes are analogous to the rpoBC operon of Escherichia coli, with some significant differences. The first gene, termed rpoB, encodes a 121,000 Mr homologue of the bacterial beta subunit. The second and third genes, termed rpoC1 and rpoC2, encode 78,000 and 154,000 Mr proteins homologous to the N and C-terminal portions, respectively, of the bacterial beta' subunit. RNA mapping analysis indicates that the three genes are cotranscribed, and that a single intron occurs in the rpoC1 gene. No splicing occurs within the rpoC2 gene or between rpoC1 and rpoC2. Furthermore, the data indicate the possibility of an alternative splice acceptor site for the rpoC1 intron that would give rise to a 71,000 Mr gene product. Thus, with the inclusion of the alpha subunit encoded by rpoA at a separate locus, the chloroplast genome is predicted to encode four subunits (respectively called alpha, beta, beta', beta") equivalent to the three subunits of the core enzyme of the E. coli RNA polymerase.

Introns in chloroplast protein-coding genes of land plants

Several protein-coding genes from land plant chloroplasts have been shown to contain introns. The majority of these introns resemble the fungal mitochondrial group II introns due to considerable nucleotide sequence homology at their 5' and 3' ends and they can readily be folded to form six hairpins characteristic of the predicted secondary structure of the mitochondrial group II introns. Recently it has been demonstrated that some mitochondrial group II introns are capable of self-splicing in vitro in the absence of protein co-factors. However evidence presented in this overview suggests that this is probably not the case for chloroplast introns and that trans-acting factors are almost certainly involved in their processing reactions.

Physical map and protein gene map of cyanelle DNA from the second known isolate of Cyanophora paradoxa (Kies-strain)

A restriction map of the cyanelle DNA from a different isolate of Cyanophora paradoxa (Kies-strain) was established. The positions of 18 protein genes and the rRNA genes have been located and compared to the positions of these genes from the first isolate of C. paradoxa (Pringsheim-strain). The gene arrangement is absolutely conserved in both cyanelle DNAs. The differences in size (ca. 9 kb) and the unrelatedness in the restriction patterns could be explained by numerous small insertions into intergenic regions of the cyanelle chromosomes.

Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs

Comparison of plant mitochondrial (mt), chloroplast (cp) and nuclear (n) DNA sequences shows that the silent substitution rate in mtDNA is less than one-third that in cpDNA, which in turn evolves only half as fast as plant nDNA. The slower rate in mtDNA than in cpDNA is probably due to a lower mutation rate. Silent substitution rates in plant and mammalian mtDNAs differ by one or two orders of magnitude, whereas the rates in nDNAs may be similar. In cpDNA, the rate of substitution both at synonymous sites and in noncoding sequences in the inverted repeat is greatly reduced in comparison to single-copy sequences. The rate of cpDNA evolution appears to have slowed in some dicot lineages following the monocot/dicot split, and the slowdown is more conspicuous at nonsynonymous sites than at synonymous sites.