Nucleotide sequence, promoter analysis, and linkage mapping of the unusually organized operon encoding ribosomal proteins S7 and S12 in maize chloroplast

Structural and functional analysis of plastid genomes from parasitic plants: loss of an intron within the genus Cuscuta

The gene cluster rps12/rps7/psi ndhB of the plastome from the holoparasitic plant Cuscuta europaea has been analysed at the nucleotide level. A comparison with the homologous region of the plastome from the closely related parasite Cuscuta reflexa reveals a complete loss of the cis-spliced intron of the rps12 gene in addition to a drastic size reduction of the ndhB pseudogene. It is demonstrated by RT-PCR analysis that the entire gene cluster is transcribed in the form of a multicistronic transcript which also includes the sequences encoded by the ndhB pseudogene. A cDNA containing the correctly transpliced exon 1 of the rps12 transcript can also be amplified. This shows that trans-splicing of the rps12 transcript persists in the plastids of the holoparasite despite the loss of the cis-spliced intron and the loss of many other gene functions. The rps12 and rps7 genes, therefore, still appear to code for functional ribosomal proteins CS12 and CS7, respectively. The conservation of apparently intact ribosomal-protein genes from which correctly processed transcripts are produced is taken as evidence that the translational apparatus of the plastids is still functional and necessary for the expression of the genes remaining in the reduced plastome of a parasitic plant.

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.

Nucleotide sequence of maize chloroplast rpl32: completing the apparent set of plastid ribosomal protein genes and their tentative operon organization

By sequencing the rpl32 gene, we have characterized the apparent complete set of the RP genes in Zea mays plastid genome. Key data for these 21 genes (total of 26 gene copies) and the proteins encoded by them are presented, and the operon organization is discussed on the basis of available transcription data. A nomenclature for the inferred 13 operons is suggested.

Analysis of nuclear sequences homologous to the B4 plasmid-like DNA of rice mitochondria; evidence for sequence transfer from mitochondria to nuclei

Nuclear sequences homologous to the plasmid-like DNA, B4, were analyzed in the Japonica rice variety, Fujiminori. Homologous sequences existed at several positions in the nuclear genome, but each contained only a portion of the B4 sequence. It was impossible to reconstruct the entire sequence of B4 even by collating all the homologous sequences. Overlaps between some of the B4 sequences present in the nuclear genome resulted in parts of the sequence being represented more than once. These features indicate that nuclear sequences homologous to B4 are not the origin of B4 and that they have been transferred from mitochondria and integrated into the nuclear genome. Five other foreign sequences originating in the chloroplast or mitochondrial genome were found within 1 kb of the B4-homologous sequences. Structural analysis is consistent with the hypothesis that the DNA sequences were transferred via RNA.

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.

Nucleotide sequence analysis of the Leptospira biflexa serovar patoc rpsL and rpsG genes

The Leptospira biflexa rpsL and rpsG genes were sequenced. Although similar in many respects, proteins encoded by these L. biflexa genes had several unusual features when compared with homologous proteins of other organisms. Unlike the rpsL genes of other eubacteria, the L. biflexa rpsL gene is adjacent to a rpoC-like gene.

Cloning and characterization of the genes for ribosomal proteins L10 and L12 from Synechocystis Sp. PCC 6803: comparison of gene clustering pattern and protein sequence homology between cyanobacteria and chloroplasts

The endosymbiont theory proposes that chloroplasts have originated from ancestral cyanobacteria through a process of engulfment and subsequent symbiotic adaptation. The molecular data for testing this theory have mainly been the nucleotide sequence of rRNAs and of photosystem component genes. In order to provide additional data in this area, we have isolated genomic clones of Synechocystis DNA containing the ribosomal protein gene cluster rplJL. The nucleotide sequence of this cluster and flanking regions was determined and the derived amino acid sequences were compared to the available homologous sequences from other eubacteria and chloroplasts. In Escherichia coli these two genes are part of a larger cluster, i.e., rplKAJL-rpoBC. In Synechocystis, the genes for the RNA polymerase subunit (rpoBC) are shown to be widely separated from the r-protein genes. The Synechocystis gene arrangement is similar to that in the chloroplast system, where the rpoBC1C2 and rplKAJL clusters are separated and located in two cell compartments, the chloroplast and the nucleus, respectively.

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.

Ribosomal protein S12 as a site for streptomycin resistance in Nicotiana chloroplasts

A streptomycin resistant Nicotiana plastome mutant, X/strR6, was subjected to molecular analysis. In this mutant, a single nucleotide transition, C----T, in the chloroplast gene for ribosomal protein S12 alters codon 90 from proline to serine while the nucleotide sequence of the chloroplast 16 S rRNA gene is identical to that of the wild type. Mutant X/strR6 thus differs from several previously reported streptomycin resistant chloroplast mutants which are altered in the gene for 16 S rRNA.

Characterization of the str operon genes from Spirulina platensis and their evolutionary relationship to those of other prokaryotes

A 5.3 kb DNA segment containing the str operon (ca. 4.5 kb) of the cyanobacterium Spirulina platensis has been sequenced. The str operon includes the structural genes rpsL (ribosomal protein S12), rpsG (ribosomal protein S7), fus (translation elongation factor EF-G) and tuf (translation elongation factor EF-Tu). From the nucleotide sequence of this operon, the primary structures of the four gene products have been derived and compared with the available corresponding structures from eubacteria, archaebacteria and chloroplasts. Extensive homologies were found in almost all cases and in the order S12 greater than EF-Tu greater than EF-G greater than S7; the largest homologies were generally found between the cyanobacterial proteins and the corresponding chloroplast gene products. Overall codon usage in S. platensis was found to be rather unbiased.

A novel site for streptomycin resistance in the "530 loop" of chloroplast 16S ribosomal RNA

The chloroplast gene for 16S rRNA was cloned from two maternally inherited streptomycin-resistant mutants ofNicotiana differing in degree of resistance at the whole plant and isolated chloroplast level. A single-nucleotide change in the 16S rRNA gene was detected for each mutant: a C to T transition at nucleotide 860 (Escherichia coli coordinate C912) which is an often mutated site, and a novel transition of C to T at nucleotide 472 (E. coli coordinate C525). The novel mutation is located in the phylogenetically conserved "530 loop".

Chloroplast ribosomal protein L12 is encoded in the nucleus: construction and identification of its cDNA clones and nucleotide sequence including the transit peptide

An architectural feature found in all classes of ribosomes is a thin, 10-nm-long protuberance in the large subunit, generated by multiple copies of r-protein L12. The primary structure of spinach chloroplast r-protein L12 is known [Bartsch, M., Kimura, M., & Subramanian, A. R. (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 6871-6875], but the location of its gene, whether in the organelle or in the nucleus, has not been determined. Therefore, we synthesized four oligodeoxynucleotides based on the amino acid sequence data and used them to probe a spinach cDNA library we constructed in lambda gt11 vector. cDNA inserts from four of the hybridizing recombinant clones were characterized and sequenced. The data showed that they are reverse transcripts of varying length, all derived from a single poly(A+) RNA species. The longest cDNA molecule is 900 base pairs (bp) long and includes a 5' noncoding sequence followed by two neighboring AUG codons both in the consensus, eukaryotic initiator context, a 56-codon-long transit peptide sequence (starting from the first AUG codon), the amino acid sequence of mature L12 protein, and a 238 bp long 3' downstream noncoding sequence including a polyadenylation signal and the start of the poly(A) tail. The transit peptide sequence has an unusual amino acid composition similar to that of other known chloroplast transit peptides. Northern blot analysis of the poly(A+) RNA isolated from spinach seedlings and probed with the cDNA insert revealed the occurrence of a strong, broad, 950-nucleotide-long band of the corresponding poly(A+)-containing mRNA species.(ABSTRACT TRUNCATED AT 250 WORDS)

Structure and expression of a split chloroplast gene from mustard (Sinapis alba): ribosomal protein gene rps16 reveals unusual transcriptional features and complex RNA maturation

The mustard chloroplast gene rps16 is split by an 887 bp group II (or III) intron. Three RNA 5' ends upstream of the rps16 coding region define both the transcription start site and two RNA processing sites. The DNA region preceding the start site contains a procaryotic-type "-10" promoter element, but not a typical "-35" element. One single RNA 3' end has been detected downstream from the rps16 coding region, but it is not in close proximity to any inverted repeat that might serve as a termination signal. Northern analysis has revealed several rps16 transcripts ranging in size from 1.6 kb to 0.5 kb. During seedling development, transcript levels show an initial increase and then remain constant without much difference between seedlings grown under light or in the dark.

Location, identity, amount and serial entry of chloroplast DNA sequences in crucifer mitochondrial DNAs

Southern blot hybridization techniques were used to examine the chloroplast DNA (cpDNA) sequences present in the mitochondrial DNAs (mtDNAs) of two Brassica species (B. campestris and B. hirta), two closely related species belonging to the same tribe as Brassica (Raphanus sativa, Crambe abyssinica), and two more distantly related species of crucifers (Arabidopsis thaliana, Capsella bursa-pastoris). The two Brassica species and R. sativa contain roughly equal amounts (12-14 kb) of cpDNA sequences integrated within their 208-242 kb mtDNAs. Furthermore, the 11 identified regions of transferred DNA, which include the 5' end of the chloroplast psaA gene and the central segment of rpoB, have the same mtDNA locations in these three species. Crambe abyssinica mtDNA has the same complement of cpDNA sequences, plus an additional major region of cpDNA sequence similarity which includes the 16S rRNA gene. Therefore, except for the more recently arrived 16S rRNA gene, all of these cpDNA sequences appear to have entered the mitochondrial genome in the common ancestor of these three genera. The mitochondrial genomes of A. thaliana and Capsella bursa-pastoris contain significantly less cpDNA (5-7 kb) than the four other mtDNAs. However, certain cpDNA sequences, including the central portion of the rbcL gene and the 3' end of the psaA gene, are shared by all six crucifer mtDNAs and appear to have been transferred in a common ancestor of the crucifer family over 30 million years ago. In conclusion, DNA has been transferred sequentially from the chloroplast to the mitochondrion during crucifer evolution and there cpDNA sequences can persist in the mitochondrial genome over long periods of evolutionary time.