The nucleotide sequence of five ribosomal protein genes from the cyanelles of Cyanophora paradoxa: implications concerning the phylogenetic relationship between cyanelles and chloroplasts

Chloroplast ribosomes and protein synthesis

Consistent with their postulated origin from endosymbiotic cyanobacteria, chloroplasts of plants and algae have ribosomes whose component RNAs and proteins are strikingly similar to those of eubacteria. Comparison of the secondary structures of 16S rRNAs of chloroplasts and bacteria has been particularly useful in identifying highly conserved regions likely to have essential functions. Comparative analysis of ribosomal protein sequences may likewise prove valuable in determining their roles in protein synthesis. This review is concerned primarily with the RNAs and proteins that constitute the chloroplast ribosome, the genes that encode these components, and their expression. It begins with an overview of chloroplast genome structure in land plants and algae and then presents a brief comparison of chloroplast and prokaryotic protein-synthesizing systems and a more detailed analysis of chloroplast rRNAs and ribosomal proteins. A description of the synthesis and assembly of chloroplast ribosomes follows. The review concludes with discussion of whether chloroplast protein synthesis is essential for cell survival.

Phylogenetic depth of S10 and spc operons: cloning and sequencing of a ribosomal protein gene cluster from the extremely thermophilic bacterium Thermotoga maritima

A segment of Thermotoga maritima DNA spanning 6,613 bp downstream from the gene tuf for elongation factor Tu was sequenced by use of a chromosome walking strategy. The sequenced region comprised a string of 14 tightly linked open reading frames (ORFs) starting 50 bp downstream from tuf. The first 11 ORFs were identified as homologs of ribosomal protein genes rps10, rpl3, rpl4, rpl23, rpl2, rps19, rpl22, rps3, rpl16, rpl29, and rps17 (which in Escherichia coli constitute the S10 operon, in that order); the last three ORFs were homologous to genes rpl14, rpl24, and rpl5 (which in E. coli constitute the three promoter-proximal genes of the spectinomycin operon). The 14-gene string was preceded by putative -35 and -10 promoter sequences situated 5' to gene rps10, within the 50-bp spacing between genes tuf and rps10; the same region exhibited a potential transcription termination signal for the upstream gene cluster (having tuf as the last gene) but displayed also the potential for formation of a hairpin loop hindering the terminator; this suggests that transcription of rps10 and downstream genes may start farther upstream. The similar organization of the sequenced rp genes in the deepest-branching bacterial phyla (T. maritima) and among Archaea has been interpreted as indicating that the S10-spc gene arrangement existed in the (last) common ancestor. The phylogenetic depth of the Thermotoga lineage was probed by use of r proteins as marker molecules: in all except one case (S3), Proteobacteria or the gram-positive bacteria, and not the genus Thermotoga, were the deepest-branching lineage; in only two cases, however, was the inferred branching order substantiated by bootstrap analysis.

Purification and characterization of seven chloroplast ribosomal proteins: evidence that organelle ribosomal protein genes are functional and that NH2-terminal processing occurs via multiple pathways in chloroplasts

Putative genes for 21 ribosomal proteins (RPs) have been identified in the chloroplast DNA of four plants by nucleotide sequencing and homology comparison but few of the gene products have been characterized. Here we report the purification and N-terminal sequencing of seven proteins from the spinach chloroplast ribosome. The data show them to be the homologues of Escherichia coli RPs L20, L32, L33, L36, S12, S16 and S19, and thus support the view that their genes identified in the chloroplast DNA represent functional genes. The initiating methionine residue was not detected in the mature protein in most cases but it was present in S16, indicating that only the formyl group is removed in this case. This result and the previously reported finding of N-methyl alanine at the N-terminus of chloroplast L2 indicate the existence of multiple N-terminal processing pathways in the chloroplast.

Controversy on chloroplast origins

Controversy exists over the origins of photosynthetic organelles in that contradictory trees arise from different sequence, biochemical and ultrastructural data sets. We propose a testable hypothesis which explains this inconsistency as a result of the differing GC contents of sequences. We report that current methods of tree reconstruction tend to group sequences with similar GC contents irrespective of whether the similar GC content is due to common ancestry or is independently acquired. Nuclear encoded sequences (high GC) give different trees from chloroplast encoded sequences (low GC). We find that current data is consistent with the hypothesis of multiple origins for photosynthetic organelles and single origins for each type of light harvesting complex.

Characterization and primary structure of proteins L28, L33 and L34 from Bacillus stearothermophilus ribosomes

The complete amino acid sequences of 3 proteins from the 50S subunit of Bacillus stearothermophilus ribosomes were determined by N-terminal sequence analysis and by sequencing of overlapping fragments obtained from enzymatic digestions and chemical cleavages. The proteins BstL28, BstL33 and BstL34, named according to the equivalent proteins in Escherichia coli ribosomes, consist of 60, 49, and 44 amino acid residues and have calculated molecular masses of 6811.0, 5908.6, and 5253.9 Da, respectively. They are highly basic with a content of positively charged residues ranging between 29% for L33 and 45% for L34. The 3 proteins were positioned in the 2-dimensional map of B stearothermophilus 50S ribosomal proteins. The electrophoretic mobilities confirm sizes and net charges deduced from the sequences.

Ribosomal protein S19 is encoded by the mitochondrial genome in Petunia hybrida

The rps19 ribosomal protein gene, which has not been previously reported in any mitochondrial genome, was identified by sequence analysis in the mitochondrial DNA of the higher plant Petunia hybrida. According to the sequence of eight rps19 cDNAs, seven C to U conversions with respect to the genomic sequence are present in rps19 transcripts. Not all transcripts are fully edited at these seven sites. Six of the seven C to U conversions change the encoded amino acid sequence by altering four codons. The rps19 gene is located entirely within a repeat sequence which is present in three copies on the 443 kb genome. Due to intragenomic recombination across these repeats, Petunia rps19 is present in nine different genomic environments.

The chloroplast gene for ribosomal protein CL23 is functional in tobacco

Chloroplast rpl23 loci potentially coding for a polypeptide homologous to the E. coli L23 ribosomal protein are frame-shifted in spinach and several other plants, indicating that these loci are pseudogenes. In tobacco, rpl23 constitutes a continuous open reading frame of 93 codons and its transcript initiates at least 66 bp upstream from the initiation codon. The N-terminal amino acid sequence of a 13 kDa protein from the 50 S subunit of tobacco chloroplast ribosomes matches that derived from the tobacco rpl23 locus. This shows that rpl23 is a functional gene in tobacco.

Unusual organization of a ribosomal protein operon in the plastid genome of Cryptomonas phi: evolutionary considerations

The region of the plastid genome containing the genes for ribosomal proteins S12 and S7 and the elongation factor Tu (corresponding to three of the four str operon genes of Escherichia coli) was investigated in the unicellular marine alga Cryptomonas. Sequence analysis shows the gene organization to be rps12-60 bp spacer-rps7-68 bp spacer-tufA. No introns are present in any of the genes. Comparisons of the deduced amino acid sequence of these genes with homologues from other organisms show rps12 to be very highly conserved, except at the amino terminus, and rps7 and tufA to be less well-conserved. Transcript analysis suggests that these genes are co-transcribed along with several up and/or down-stream genes. The evolutionary significance of this unique gene organization is discussed.

rps10, unreported for plastid DNAs, is located on the cyanelle genome of Cyanophora paradoxa and is cotranscribed with the str operon genes

rps10, encoding the plastid ribosomal protein S10, is a nuclear gene in higher plants and green algae, and is missing from the large ribosomal protein gene cluster of chlorophyll b-type plastids that contains components of the prokaryotic S10, spc and alpha operons. The cyanelle genome of Cyanophora paradoxa is shown to harbor rps10 as another specific feature of its organization. However, this novel plastid gene is not contiguous with the genes of the "S10" operon, but is adjacent to, and cotranscribed with, the str operon, a trait also found in archaebacteria.

A heptapeptide repeat contributes to the unusual length of chloroplast ribosomal protein S18. Nucleotide sequence and map position of the rpl33-rps18 gene cluster in maize

The rpl33-rps18 gene cluster of the maize chloroplast genome has been mapped and sequenced. The derived amino acid sequence of the S18 protein shows a 7-fold repeat of a hydrophilic heptapeptide domain, S K Q P F R K, in the N-terminal region. Such a sequence is absent in the E. coli S18 and in the chloroplast S18 of the lower plant liverwort. In tobacco and rice chloroplast S18 it is present 2 and 6 times, respectively. Thus a long N-terminal repeat (resembling in composition the large C-terminal heptapeptide repeat in the eukaryotic pol II) appears to be characteristic of monocot cereal S18.

Ferredoxin and ribosomal protein S10 are encoded on the cyanelle genome of Cyanophora paradoxa

The petF and rsp10 genes of the cyanellar genome of the taxonomically ambiguous flagellate Cyanophora paradoxa have been cloned, mapped, and sequenced. In higher plants these genes are not encoded in the chloroplast DNA, but are encoded in the nucleus. The C. paradoxa petF gene predicts a protein of 99 amino acids (aa) which is more similar to type-I ferredoxins of diverse cyanobacteria than to those of green algae, dinoflagellates, and higher plants. The rsp10 gene (rspJ) predicts a protein of 105 aa which is about 50% identical and 71% homologous to the proteins of Escherichia coli and Mycoplasma capricolum. The results are discussed within the context of the endosymbiotic origins of chloroplasts from cyanobacteria.

The cyanelle S10 spc ribosomal protein gene operon from Cyanophora paradoxa

In Cyanophora paradoxa photosynthetic organelles termed cyanelles perform the functions of chloroplasts in higher plants, while the structural and biochemical characteristics of the cyanelle are essentially cyanobacterial. Our interest in studying the evolutionary relationship between cyanelles and chloroplasts led us to focus on cyanelle-encoded genes of the translational apparatus, specifically genes equivalent to those of the bacterial S10 and spc operons. The structure of a large ribosomal protein gene cluster from cyanelle DNA was characterized and compared with that from plastids and bacteria. Sequences of the following cyanelle genes encompassing 4.8 kb are reported here: 5'-rpl22-rps3-rpl16-rps17-rpl14-rpl5-rps8-rpl6-rpl18- rps5-3'. Cyanelles contain five more ribosomal protein genes than do higher plant chloroplasts and four more genes than Euglena gracilis plastids in the S10/spc region of this gene cluster. The gene encoding rpl36 is absent, in contrast to the case in other plastid DNAs. These genes, including the previously characterized genes rpl3, rpl2 and rps19, are transcribed as a primary transcript of approximately 7500 nucleotides. The occurrence of transcripts smaller than this presumptive primary transcript suggests that it is processed into defined segments. Transcription terminates 3' of rps5 where a 40 bp hairpin with one mismatch (-42.2 kcal) may be folded. Immediately downstream of rps5 an open reading frame, ORF492, is contained on a separate transcript. A comparison of gene content, operon structure and deduced amino acid sequence of the genes in the S10 and spc operons from different organisms supports the notion that cyanelles are intermediary between known plastids and cyanobacteria.

Nucleotide sequence of the gene for the large subunit of Rubisco from Cyanophora paradoxa--phylogenetic implications

The gene (rbcL) for the large subunit (LSU) of Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Cyanophora paradoxa was cloned and the nucleotide sequence determined. Sequence homologies to rbcL genes from other sources clearly indicated a close phylogenetic relationship between the photosynthetic organelles of Cyanophora (cyanelles), green chloroplasts and cyanobacteria. Our data support the hypothesis that the cyanelles of Cyanophora may represent a closely related, but independent, side line to chloroplast evolution. Cyanelles and rhodoplasts or phaeoplasts seem not to be related.

The petFI gene encoding ferredoxin I is located close to the str operon on the cyanelle genome of Cyanophora paradoxa

The petFI gene encoding ferredoxin I was localized in the large single copy region of cyanelle DNA by heterologous hybridization. Sequence analysis revealed an ORF of 99 amino acids (including the N-terminal processed methionine) at a position 477 bp from the 3' end of tufA but on the opposite strand. The 25 amino-terminal residues well corresponded to partial sequences obtained with purified cyanelle ferredoxin. The assignment of yet another gene that is not found on the genomes of chlorophyll b-type plastids to cyanelle DNA again corroborates the special position of cyanelles serving as a model for plastid evolution from endocytobiotic cyanobacteria.

The cyanelle genome of Cyanophora paradoxa, unlike the chloroplast genome, codes for the ribosomal L3 protein

We describe a 1132 bp sequence of the cyanelle genome of Cyanophora paradoxa containing the rpl3 gene. This gene, which is not chloroplast encoded in plants, is the first of a long cyanelle ribosomal operon whose organization resembles that of the S10 operon of E. coli. We have shown that the rpl3 gene is transcribed in cyanelles as a 7500 nucleotide precursor and that the 5'-end of the mRNA starts approximately 90 nucleotides upstream from the initiation codon. However, no typical procaryotic promoter could be found for this gene. We have detected, using anti E. coli L3 antibodies, the cyanelle L3 protein in cyanelle extracts and in E. coli cells transformed with the cyanelle rpl3 gene.