Sequence and transcriptional analysis of the barley ctDNA region upstream of psbD-psbC encoding trnK(UUU), rps16, trnQ(UUG), psbK, psbI, and trnS(GCU)

The P-class pentatricopeptide repeat protein PpPPR_21 is needed for accumulation of the psbI-ycf12 dicistronic mRNA in Physcomitrella chloroplasts

Chloroplast gene expression is controlled by numerous nuclear-encoded RNA-binding proteins. Among these, pentatricopeptide repeat (PPR) proteins are known to be key players in post-transcriptional regulation in chloroplasts. However, the functions of many PPR proteins remain unknown. In this study, we characterized the function of a chloroplast-localized P-class PPR protein PpPPR_21 in Physcomitrella patens. Knockout (KO) mutants of PpPPR_21 exhibited reduced protonemata growth and lower photosynthetic activity. Immunoblot analysis and blue-native gel analysis showed a remarkable reduction of the photosystem II (PSII) reaction center protein and poor formation of the PSII supercomplexes in the KO mutants. To assess whether PpPPR_21 is involved in chloroplast gene expression, chloroplast genome-wide microarray analysis and Northern blot hybridization were performed. These analyses indicated that the psbI-ycf12 transcript encoding the low molecular weight subunits of PSII did not accumulate in the KO mutants while other psb transcripts accumulated at similar levels in wild-type and KO mutants. A complemented PpPPR_21KO moss transformed with the cognate full-length PpPPR_21cDNA rescued the level of accumulation of psbI-ycf12 transcript. RNA-binding experiments showed that the recombinant PpPPR_21 bound efficiently to the 5' untranslated and translated regions of psbImRNA. The present study suggests that PpPPR_21 may be essential for the accumulation of a stable psbI-ycf12mRNA.

Identification of species and materia medica within Saussurea subg. Amphilaena based on DNA barcodes

Saussurea is one of the most species-rich genera in the family Asteraceae, where some have a complex evolutionary history, including radiation and convergent evolution, and the identification of these species is notoriously difficult. This genus contains many plants with medical uses, and thus an objective identification method is urgently needed. Saussurea subg. Amphilaena is one of the four subgenera of Saussurea and it is particularly rich in medical resources, where 15/39 species are used in medicine. To test the application of DNA barcodes in this subgenus, five candidates were sequenced and analyzed using 131 individuals representing 15 medical plants and four additional species from this subgenus. Our results suggested that internal transcribed spacer (ITS) + rbcL or ITS + rbcL + psbA-trnH could distinguish all of the species, while the ITS alone could identify all of the 15 medical plants. However, the species identification rates based on plastid barcodes were low, i.e., 0% to 36% when analyzed individually, and 63% when all four loci were combined. Thus, we recommend using ITS + rbcL as the DNA barcode for S. subg. Amphilaena or the ITS alone for medical plants. Possible taxonomic problems and substitutes for medicinal plant materials are also discussed.

New Saussurea (Asteraceae) species from Bogeda Mountain, eastern Tianshan, China, and inference of its evolutionary history and medical usage

In this study, Saussurea bogedaensis Yu-J. Wang & Jie Chen, a new species from Bogeda Mountain in the eastern part of the Tianshan Mountains, is described and discussed based on evidence in terms of both morphological and genetic data. S. bogedaensis is morphologically similar to S. involucrata, which is distributed in the western part of the Tianshan Mountains, and it is well known because of its beauty, rarity, and medicinal value. The new species is also similar to S. orgaadayi, which is distributed in the nearby Altai Mountains. Our genetic data support the close relationships among these three species. According to their allopathic distributions, we suggest that these three species are derived from the same ancestor but that they differentiated after reaching their current range. In addition, we propose that the new species might serve as an alternative to S. involucrata in medicine due to their very high similarity. However, this species appears to be rare because we only found six mature individuals in the field despite extensive investigations.

Genome-wide analysis of thylakoid-bound ribosomes in maize reveals principles of cotranslational targeting to the thylakoid membrane

Chloroplast genomes encode ∼ 37 proteins that integrate into the thylakoid membrane. The mechanisms that target these proteins to the membrane are largely unexplored. We used ribosome profiling to provide a comprehensive, high-resolution map of ribosome positions on chloroplast mRNAs in separated membrane and soluble fractions in maize seedlings. The results show that translation invariably initiates off the thylakoid membrane and that ribosomes synthesizing a subset of membrane proteins subsequently become attached to the membrane in a nuclease-resistant fashion. The transition from soluble to membrane-attached ribosomes occurs shortly after the first transmembrane segment in the nascent peptide has emerged from the ribosome. Membrane proteins whose translation terminates before emergence of a transmembrane segment are translated in the stroma and targeted to the membrane posttranslationally. These results indicate that the first transmembrane segment generally comprises the signal that links ribosomes to thylakoid membranes for cotranslational integration. The sole exception is cytochrome f, whose cleavable N-terminal cpSecA-dependent signal sequence engages the thylakoid membrane cotranslationally. The distinct behavior of ribosomes synthesizing the inner envelope protein CemA indicates that sorting signals for the thylakoid and envelope membranes are distinguished cotranslationally. In addition, the fractionation behavior of ribosomes in polycistronic transcription units encoding both membrane and soluble proteins adds to the evidence that the removal of upstream ORFs by RNA processing is not typically required for the translation of internal genes in polycistronic chloroplast mRNAs.

Plastid non-coding RNAs: emerging candidates for gene regulation

Recent advances in transcriptomics and bioinformatics, specifically strand-specific RNA sequencing, have allowed high-throughput, comprehensive detection of low-abundance transcripts typical of the non-coding RNAs studied in bacteria and eukaryotes. Before this, few plastid non-coding RNAs (pncRNAs) had been identified, and even fewer had been investigated for any functional role in gene regulation. Relaxed plastid transcription initiation and termination result in full transcription of both chloroplast DNA strands. Following this, post-transcriptional processing produces a pool of metastable RNA species, including distinct pncRNAs. Here we review pncRNA biogenesis and possible functionality, and speculate that this RNA class may have an underappreciated role in plastid gene regulation.

Motif analysis unveils the possible co-regulation of chloroplast genes and nuclear genes encoding chloroplast proteins

Chloroplasts play critical roles in land plant cells. Despite their importance and the availability of at least 200 sequenced chloroplast genomes, the number of known DNA regulatory sequences in chloroplast genomes are limited. In this paper, we designed computational methods to systematically study putative DNA regulatory sequences in intergenic regions near chloroplast genes in seven plant species and in promoter sequences of nuclear genes in Arabidopsis and rice. We found that -35/-10 elements alone cannot explain the transcriptional regulation of chloroplast genes. We also concluded that there are unlikely motifs shared by intergenic sequences of most of chloroplast genes, indicating that these genes are regulated differently. Finally and surprisingly, we found five conserved motifs, each of which occurs in no more than six chloroplast intergenic sequences, are significantly shared by promoters of nuclear-genes encoding chloroplast proteins. By integrating information from gene function annotation, protein subcellular localization analyses, protein-protein interaction data, and gene expression data, we further showed support of the functionality of these conserved motifs. Our study implies the existence of unknown nuclear-encoded transcription factors that regulate both chloroplast genes and nuclear genes encoding chloroplast protein, which sheds light on the understanding of the transcriptional regulation of chloroplast genes.

The primary transcriptome of barley chloroplasts: numerous noncoding RNAs and the dominating role of the plastid-encoded RNA polymerase

Gene expression in plastids of higher plants is dependent on two different transcription machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. The division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear due to a lack of comprehensive information on promoter usage. Here, we present a thorough investigation into the distribution of PEP and NEP promoters within the plastid genome of barley (Hordeum vulgare). Using a novel differential RNA sequencing approach, which discriminates between primary and processed transcripts, we obtained a genome-wide map of transcription start sites in plastids of mature first leaves. PEP-lacking plastids of the albostrians mutant allowed for the unambiguous identification of NEP promoters. We observed that the chloroplast genome contains many more promoters than genes. According to our data, most genes (including genes coding for photosynthesis proteins) have both PEP and NEP promoters. We also detected numerous transcription start sites within operons, indicating transcriptional uncoupling of genes in polycistronic gene clusters. Moreover, we mapped many transcription start sites in intergenic regions and opposite to annotated genes, demonstrating the existence of numerous noncoding RNA candidates.

Reverse protection assay: a tool to analyze transcriptional rates from individual promoters

Transcriptional activity of entire genes in chloroplasts is usually assayed by run-on analyses. To determine not only the overall intensity of transcription of a gene, but also the rate of transcription from a particular promoter, we created the Reverse RNase Protection Assay (RePro): in-organello run-on transcription coupled to RNase protection to define distinct transcript ends during transcription. We demonstrate successful application of RePro in plastid promoter analysis and transcript 3' end processing.

Unexpected Diversity of Chloroplast Noncoding RNAs as Revealed by Deep Sequencing of the Arabidopsis Transcriptome

Noncoding RNAs (ncRNA) are widely expressed in both prokaryotes and eukaryotes. Eukaryotic ncRNAs are commonly micro- and small-interfering RNAs (18-25 nt) involved in posttranscriptional gene silencing, whereas prokaryotic ncRNAs vary in size and are involved in various aspects of gene regulation. Given the prokaryotic origin of organelles, the presence of ncRNAs might be expected; however, the full spectrum of organellar ncRNAs has not been determined systematically. Here, strand-specific RNA-Seq analysis was used to identify 107 candidate ncRNAs from Arabidopsis thaliana chloroplasts, primarily encoded opposite protein-coding and tRNA genes. Forty-eight ncRNAs were shown to accumulate by RNA gel blot as discrete transcripts in wild-type (WT) plants and/or the pnp1-1 mutant, which lacks the chloroplast ribonuclease polynucleotide phosphorylase (cpPNPase). Ninety-eight percent of the ncRNAs detected by RNA gel blot had different transcript patterns between WT and pnp1-1, suggesting cpPNPase has a significant role in chloroplast ncRNA biogenesis and accumulation. Analysis of materials deficient for other major chloroplast ribonucleases, RNase R, RNase E, and RNase J, showed differential effects on ncRNA accumulation and/or form, suggesting specificity in RNase-ncRNA interactions. 5' end mapping demonstrates that some ncRNAs are transcribed from dedicated promoters, whereas others result from transcriptional read-through. Finally, correlations between accumulation of some ncRNAs and the symmetrically transcribed sense RNA are consistent with a role in RNA stability. Overall, our data suggest that this extensive population of ncRNAs has the potential to underpin a previously underappreciated regulatory mode in the chloroplast.

A molecular phylogenetic study of the subtribe Glycininae (Leguminosae) derived from the chloroplast DNA rps16 intron sequences

Phylogenetic relationships among 13 genera of the subtribe Glycininae, two genera of the allied subtribe Diocleinae that were included within Glycininae by Polhill, and two genera of the subtribe Erythrininae as outgroups were inferred from chloroplast DNA rps16 intron sequence variation. Pairwise sequence divergence values ranged from identity between Teramnus mollis and T. micans and between T. flexilis and T. labialis to 7.89% between Pueraria wallichii and Pseudeminia comosa across all accessions. Phylogenies estimated using parsimony and neighbor-joining methods revealed that (1) Glycininae is monophyletic if Pachyrhizus and Calopogonium (both Diocleinae) are included within Glycininae; (2) the genus Teramnus is closely related to Glycine, and Amphicarpaea showed a sister relationship to the clade comprising Teramnus and Glycine; (3) the expanded Glycininae including two genera of Diocleinae is divided into three branches, temporarily named I (comprising the rest of the examined taxa), II (Pueraria wallichii), and III (Mastersia), but their relationships are equivocal; and (4) the genus Pueraria, regarded as a closely related genus to Glycine, is not monophyletic and should be divided into at least four genera (a hypothesis supported previously by Lackey).

Molecular systematics of Old World Apioideae (Apiaceae): relationships among some members of tribe Peucedaneae sensu lato, the placement of several island-endemic species, and resolution within the apioid superclade

Comparative sequencing of the two internal transcribed spacer regions of nuclear ribosomal DNA was carried out to examine evolutionary relationships among representatives of Old World Apiaceae (Umbelliferae) subfamily Apioideae. Emphasis was placed on delimiting groups within the previously designated apioid superclade and clarifying relationships within and among the peucedanoid genera Angelica, Ferula, Heracleum, and Peucedanum. These spacer data, and those obtained from the chloroplast rps16 intron for a subset of the taxa, also enabled hypotheses on the phylogenetic placement of several narrowly distributed endemic species. The monophyly of Drude's tribe Echinophoreae is confirmed and it is sister to the Socotran endemic genera Nirarathamnos and Rughidia; the Balearic Islands endemic genus Naufraga allies with Apium graveolens; tribes Careae and Pyramidoptereae are recognized formally to be the previously designated clades "Aegopodium" and "Crithmum"; and tribes Oenantheae and Scandiceae are each expanded to include two species of Apium, previously attributable to Helosciadium, and four species of Ferula, respectively. Within the apioid superclade, five major lineages are recognized that are consistent with all available molecular evidence: tribe Echinophoreae, the clades "Pimpinella" and "Heracleum," and the more narrowly circumscribed clades "Angelica" and "Apium." Angelica and Ferula each comprise at least two lineages; Heracleum is polyphyletic if Heracleum candicans is retained in the genus; and Peucedanum is distributed in three well-separated clades with some species allied with those species of Angelica referred to Xanthogalum.Key words: Apiaceae subfamily Apioideae, nuclear rDNA ITS, chloroplast rps16 intron, Umbelliferae.

Phylogenetic analysis of chloroplast rps16 intron sequences reveals relationships within the woody southern African Apiaceae subfamily Apioideae

Evolutionary relationships among 48 genera of Apiaceae (Umbelliferae) were inferred using maximum parsimony, maximum-likelihood, and neighbor-joining analyses of chloroplast DNA rps16 intron and adjacent rps16 3prime exon sequences. Emphasis was placed on woody members of Apiaceae subfamily Apioideae endemic to southern Africa, a region hypothesized to be the place of origin of this largely herbaceous subfamily. The resultant phylogenies were highly concordant and indicate that the apioid genera Polemanniopsis and Steganotaenia form a clade sister to Apiaceae subfamily Saniculoideae. The African genera Anginon, Dracosciadium, Glia, Heteromorpha, and Polemannia also comprise a clade and likely represent the most basal elements within Apioideae. Heteromorpha, however, is not monophyletic, with Heteromorpha arborescens (Spreng.) Cham. & Schltdl. var. abyssinica (A. Rich.) H. Wolff and Heteromorpha arborescens (Spreng.) Cham. & Schltdl. var. arborescens arising in separate subclades. Progressing up the trees, Annesorhiza then Bupleurum fall as successive sister taxa to all remaining Apioideae. The major clades recognized within subfamily Apioideae are largely congruent with those inferred using other types of molecular evidence. Sequence divergence is similar to that of other chloroplast introns, including being generally low among congeners and woody taxa. While the rps16 intron has seen very little use in molecular systematic studies to date, this study demonstrates its ability to discern high-level relationships within Apiaceae.Key words: Apiaceae, Apioideae, chloroplast rps16 intron, phylogeny, southern Africa, Umbelliferae.

Organellar RNA polymerases of higher plants

The nuclear genome of the model plant Arabidopsis thaliana contains a small gene family consisting of three genes encoding RNA polymerases of the single-subunit bacteriophage type. There is evidence that similar gene families also exist in other plants. Two of these RNA polymerases are putative mitochondrial enzymes, whereas the third one may represent the nuclear-encoded RNA polymerase (NEP) active in plastids. In addition, plastid genes are transcribed from another, entirely different multisubunit eubacterial-type RNA polymerase, the core subunits of which are encoded by plastid genes [plastid-encoded RNA polymerase (PEP)]. This core enzyme is complemented by one of several nuclear-encoded sigma-like factors. The development of photosynthetically active chloroplasts requires both PEP and NEP. Most NEP promoters show certain similarities to mitochondrial promoters in that they include the sequence motif 5'-YRTA-3' near the transcription initiation site. PEP promoters are similar to bacterial promoters of the -10/-35 sigma 70 type.

Detailed architecture of the barley chloroplast psbD-psbC blue light-responsive promoter

The photosystem II reaction center chlorophyll protein D2, is encoded by the chloroplast gene psbD. PsbD is transcribed from at least three different promoters, one which is activated by high fluence blue light. Sequences within 130 base pairs (bp) of the psbD blue light-responsive promoter (BLRP) are highly conserved in higher plants. In this study, the structure of the psbD BLRP was analyzed in detail using deletion and site-directed mutagenesis and in vitro transcription. Deletion analysis showed that a 53-bp DNA region of the psbD BLRP, from -57 to -5, was sufficient for transcription in vitro. Mutation of a putative prokaryotic -10 element (TATTCT) located from -7 to -12 inhibited transcription from the psbD BLRP. In contrast, mutation of a putative prokaryotic -35 element, had no influence on transcription. Mutation of a TATATA sequence located between the barley psbA -10 and -35 elements significantly reduced transcription from this promoter. However, site-directed mutation of sequences located between -35 and -10 had no effect on transcription from the psbD BLRP. Transcription from the psbD BLRP was previously shown to require a 22-bp sequence, termed the AAG-box, located between -36 and -57. The AAG-box specifically binds the protein complex AGF. Site-directed mutagenesis identified two different sequence motifs in the AAG-box that are important for transcription in vitro. Based on these results, we propose that positive factors bind to the AAG-box and interact with the chloroplast-encoded RNA polymerase to promote transcription from the psbD BLRP. Transcription from the psbD BLRP is thus similar to type II bacterial promoters that use activating proteins to stimulate transcription. Transcription of the psbD BLRP was approximately 6. 5-fold greater in plastid extracts from illuminated versus dark-grown plants. This suggests that light-induced activation of this promoter in vivo involves factors interacting with the 53-bp psbD BLRP in vitro.

Splicing and intron-internal RNA editing of trnK-matK transcripts in barley plastids: support for MatK as an essential splice factor

Group II introns frequently require assistance by specific factors, maturases, for folding and effective splicing in vivo. The only putative maturase of higher plant chloroplasts is encoded by matK, located in the intron of trnK. We show that in barley matK transcripts are modified at a first codon base by C-to-U RNA editing. The resulting H --> Y substitution restores a sequence motif that is present in maturases of yeast and plant mitochondria and of Lactococcus ltrA and that is positioned within the X domain. Processing of trnK-matK transcripts was further investigated in plastids lacking functional ribosomes due to a mutation. Absence of the intron-encoded matK gene product in these plastids is correlated with the accumulation of precursor transcripts for tRNALys(UUU)-matK, processed to different degrees, and by the lack of mature and spliced tRNA molecules. These results suggest an essential role of MatK for splicing of its own transcript in vivo. Processing of the 5' end of trnK exon 1 was found to proceed efficiently also in the mutant plastids although the two tRNA exons were separated by the 2481 nt intron. Consequently, presence of the intron does not interfere with the formation of mature 5' termini.

Regulation of gene expression in chloroplasts of higher plants

Chloroplasts contain their own genetic system which has a number of prokaryotic as well as some eukaryotic features. Most chloroplast genes of higher plants are organized in clusters and are cotranscribed as polycistronic pre-RNAs which are generally processes into many shorter overlapping RNA species, each of which accumulates of steady-state RNA levels. This indicates that posttranscriptional RNA processing of primary transcripts is an important step in the control of chloroplast gene expression. Chloroplast RNA processing steps include RNA cleavage/trimming, RNA splicing, ENA editing and RNA stabilization. Several chloroplast genes are interrupted by introns and therefore require processing for gene function. In tobacco chloroplasts, 18 genes contain introns, six for tRNA genes and 12 for protein-encoding genes. A number of specific proteins and RNA factors are believed to be involved in splicing and maturation of pre-RNAs in chloroplasts. Processing enzymes and RNA-binding proteins which could be involved in posttranscriptional steps have been identified in the last several years. Our current knowledge of the regulation of gene expression in chloroplasts of higher plants is overviewed and further studies on this matter are also considered.

Leaf development and phytochrome modulate the activation ofpsbD-psbC transcription by high-fluence blue light in barley chloroplasts

Activation ofpsbD transcription by light assists in maintaining the synthesis of the PS II reaction center protein, D2, which is photodamaged in plants exposed to high light. In this study, the photosensory pathways and mechanisms that regulate the expression of thepsbD-psbC light-responsive promoter, LRP, were investigated during barley (Hordeum vulgare L.) seedling development. Accumulation ofpsbD-psbC mRNAs in response to light was observed in apical sections of primary leaves with little or no increase in mRNAs in basal sections. In both 4.5- and 7.5-day-old etiolated seedlings, blue light was most effective for activating mRNA accumulation from thepsbD-psbC LRP. However, the response of the LRP to red light increased 7-fold in 7.5-day relative to 4.5-day-old seedlings. Blue light preferentially activatedpsbD-psbC transcription, while red light was most effective for activating total plastid transcription and the expression of genes encoding the small (RbcS) and large (rbcL) subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase and Chl-a/b-binding protein (Lhcb). The stimulatory effects of red light onpsbD-psbC expression were partially reversed, and of blue light were not reversed, by subsequent pulses of far-red light. In contrast, continuous far-red light given together with blue light enhancedpsbD-psbC transcription in a synergistic manner. These observations indicate that phytochrome modulates the effects of high-fluence blue light onpsbD-psbC transcription by affecting total plastid transcription.

Impaired splicing of the rps12 transcript in ribosome-deficient plastids

Analysis of RNA maturation in ribosome-deficient plastids of four non-allelic barley mutants revealed an increased accumulation and altered processing of transcripts of the ribosomal protein gene CS12 (rps12) compared to normal chloroplasts. The three exons of rps12 are part of two different polycistronic transcription units. Generation of mature rps12-mRNA involves both cis- and trans-splicing. In ribosome-deficient plastids, the cis-intron separating exons 2 and 3 remains entirely unspliced whereas the splicing of the bipartite rps12 trans-intron between exon 1 and exon 2 occurs, but at a reduced level. A comparison of the 3' and 5' ends of the two RNAs that are generally assumed to interact during trans-splicing showed a difference in the processing pathways of 3' rps12 transcripts between mutated and normal chloroplasts. Nonetheless, the final products were identical.

Transcription, splicing and editing of plastid RNAs in the nonphotosynthetic plant Epifagus virginiana

Expression of the vestigial plastid genome of the nonphotosynthetic, parasitic flowering plant Epifagus virginiana was examined by northern analysis and by characterization of cDNAs. Probes for each of 12 plastid genes tested hybridized to all lanes of northern blots containing total RNA prepared from stems and fruits of Epifagus and from leaves of tobacco. Certain transcript patterns in Epifagus plastids are highly complex and similar to those of tobacco operons. In contrast, genes such as rps2, which have become orphaned in Epifagus as a result of evolutionary loss of formerly cotranscribed genes, show simpler transcript patterns in Epifagus than in tobacco. Sizing and sequencing of cDNAs generated by reverse transcriptase-PCR for three genes, rps12, rpl2, and clpP, show that their transcripts are properly cis- and/or trans-spliced at the same five group II intron insertion sites used in photosynthetic plants. A single, conventional C-->U edit in rps12 was found among the total of 1401 nucleotides of cDNA sequence that was determined for the three genes. An octanucleotide sequence identical to a putative guide RNA of plant organelles and perfectly complementary to the rps12 edit site itself was identified just 200 bp upstream of the edit site. These data, together with previous results from the complete sequencing of the Epifagus plastid genome, provide compelling evidence that this degenerate genome is nonetheless expressed and functional. Analysis of the putative maturase MatK, encoded by the group II intron of trnK in photosynthetic land plants but by a freestanding gene in Epifagus, leads us to hypothesize that it acts 'in trans' to assist the splicing of group II introns other than the one in which it is normally encoded.

Characterization and expression of rpoC2 in CMS and fertile lines of sorghum

A 165 bp deletion in the middle of rpoC2, the plastid gene which encodes the RNA polymerase beta" subunit, was identified in the small-anthered types of CMS sorghum, Sorghum bicolor (L.). Moench, containing A1, A2, A5, and A6 cytoplasms. It was previously shown that the amino acid sequence deleted in these CMS lines is in a monocot-specific region that contains several protein motifs that are characteristic of several transcription factors. Using primers flanking the deletion in PCR analyses, various types of CMS lines, some of which are used in hybrid sorghum production, were classified into two groups. CMS lines containing A1, A2, A5, A6 cytoplasms display the deletion in rpoC2. These lines have small anthers in which pollen development is arrested at an early stage and in which usually only empty exines are found. CMS lines containing A3, A4, and 9E cytoplasms do not possess the deletion. These lines have large anthers in which pollen degenerates at a later stage. Run-on transcription assays using 15 chloroplast genes showed that chloroplast gene transcription rates are similar in CMS and fertile (maintainer and restorer) lines and F1 in seedling leaves. Analyses of RNA blots indicated that rbcL, rpoB and rpoC2 transcripts are accumulated mainly in the leaves and low in the inflorescence tissues and pollen. These data document plastid gene expression in leaves and non-photosynthetic tissues from CMS and fertile lines of sorghum.

A mutant strain of Chlamydomonas reinhardtii lacking the chloroplast photosystem II psbI gene grows photoautotrophically

The product of the chloroplast psbI gene is associated with the photosystem II reaction center. To gain insights into the function of this polypeptide, we have disrupted its gene in Chlamydomonas reinhardtii with an aadA expression cassette that confers resistance to spectinomycin through biolistic transformation. The transformants are still able to grow photoautotrophically in dim light, but not in high light, and they remain photosensitive when grown on acetate containing medium. The amounts of photosystem II complex and oxygen evolving activity are both reduced to 10-20% of wild-type levels in these psbI-deficient mutants. It appears that the PsbI polypeptide plays a role in the stability of photosystem II and possibly also in modulating electron transport or energy transfer in this complex.

Structure and expression characteristics of the chloroplast DNA region containing the split gene for tRNA(Gly) (UCC) from mustard (Sinapis alba L.)

The mustard chloroplast gene trnG-UCC is split by a 717-bp group-II intron. Northern hybridization and RNase protection experiments suggest cotranscription with the upstream psbK-psbI operon, but not with the downstream trnR-UCU gene. The ends of most RNase-protected fragments between psbI and trnG correlate with the position of two potential stem-loop structures in this region, which could act as RNA processing elements. However, one RNA 5' end, approximately 75 bp upstream of the trnG 5' exon, does not so correlate and is preceded by prokaryotic-type '-10' and '-35' sequence elements. This suggests the possibility that a fraction of the trnG transcripts is initiated here. All precursor transcripts spanning the trnG region seem to have a common 3' end, which was located 117 bp downstream from the 3' exon, immediately after a stem-loop region. During seedling development, the major 0.8-0.9-kb trnG precursor transcripts show a transient maximum level at around 48 h after sowing, at a time when the mature tRNA begins to accumulate to constant levels. No significant differences in transcript patterns were observed either in the light or in darkness.

Chloroplastic genomes of Ginkgo biloba and Chlamydomonas moewusii contain a chlB gene encoding one subunit of a light-independent protochlorophyllide reductase

We have cloned and sequenced a Chlamydomonas moewusii chloroplastic DNA fragment that includes a 563 amino-acid open reading frame (ORF563, chlB) presenting 89% amino-acid homology with ORF513 from Marchantia polymorpha. It is also homologous to ORF510 from Pinus thunbergii but includes two insertions absent in both M. polymorphia and P. thunbergii. The derived polypeptide is 54% similar to the product of bchB from Rhodobacter capsulatus, identified as one subunit of a light-independent NADH-protochlorophyllide reductase. We also isolated and sequenced an homologous chloroplastic gene from the gymnosperm Ginkgo biloba. Northern hybridizations performed on RNA isolated from synchronized Chlamydomonas eugametos cells showed higher expression between the tenth hour of light and the eighth hour of darkness, peaking during the first 2 h of darkness.

Expression of intron-encoded maturase-like polypeptides in potato chloroplasts

The trnK gene has been identified on a cloned plastid DNA fragment of potato (Solanum tuberosum cv Désirée). This gene codes for a tRNA-Lys and is interrupted by a 2.5-kb intron belonging to the group II organellar introns. In addition, this intervening sequence contains a long open reading frame potentially coding for a 509 amino-acid polypeptide (ORF509) related to mitochondrial intron-encoded maturases from fungi. The translational capacity of the trnK intron was first demonstrated in vitro in a prokaryotic DNA-directed expression system. In order to examine the expression of the intron in the potato plant, a synthetic peptide corresponding to the last nine amino acids of the predicted ORF509 product was used to raise antibodies. Western-blot experiments on chloroplast protein extracts, using a sensitive chemiluminescent detection system, identified polypeptides similar to in-vitro products. These results suggest that the trnK intron is expressed at the protein level in the plant. This is the first report of the in-vivo expression of an intron-encoded polypeptide in higher plant plastids.

Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function

Many group II introns encode reverse transcriptase-like proteins that potentially function in intron mobility and RNA splicing. We compared 34 intron-encoded open reading frames and four related open reading frames that are not encoded in introns. Many of these open reading frames have a reverse transcriptase-like domain, followed by an additional conserved domain X, and a Zn(2+)-finger-like region. Some open reading frames have lost conserved sequence blocks or key amino acids characteristic of functional reverse transcriptases, and some lack the Zn(2+)-finger-like region. The open reading frames encoded by the chloroplast tRNA(Lys) genes and the related Epifagus virginiana matK open reading frame lack a Zn(2+)-finger-like region and have only remnants of a reverse transcriptase-like domain, but retain a readily identifiable domain X. Several findings lead us to speculate that domain X may function in binding of the intron RNA during reverse transcription and RNA splicing. Overall, our findings are consistent with the hypothesis that all of the known group II intron open reading frames evolved from an ancestral open reading frame, which contained reverse transcriptase, X, and Zn(2+)-finger-like domains, and that the reverse transcriptase and Zn(2+)-finger-like domains were lost in some cases. The retention of domain X in most proteins may reflect an essential function in RNA splicing, which is independent of the reverse transcriptase activity of these proteins.

Direct evidence for selective modulation of psbA, rpoA, rbcL and 16S RNA stability during barley chloroplast development

The turnover of RNAs encoded by seven different barley chloroplast genes was analyzed after treatment of barley shoots with tagetitoxin, a selective inhibitor of chloroplast transcription. Changes in RNA stability were examined during chloroplast development using basal and apical leaf sections of 4.5-day-old dark-grown seedlings and apical leaf sections of 4.0-day-old dark-grown seedlings which had been illuminated for 12 h. Of the RNAs examined, a 2.6 kb unspliced precursor of tRNA(lys) exhibited the shortest half-life, which was estimated to be 3 h. The 16S rRNA and psbA mRNA had the longest estimated half-lives, which were greater than 40 h. Among mRNAs, half-lives were estimated to range from 6 h for psaA mRNA, to over 40 h for psbA mRNA. Therefore, barley chloroplast mRNAs have long half-lives relative to bacterial mRNAs. The stability of atpB mRNA and the unspliced precursor of tRNA-lys was not altered during chloroplast development, while the stability of psaA mRNA decreased 2-fold. In contrast, the stability of the 16S rRNA and mRNAs for rpoA, psbA and rbcL increased during chloroplast development. The stability of 16S rRNA increased markedly during chloroplast development in the dark and this increase was maintained in illuminated seedlings. The stability of rbcL mRNA increased 2.5-fold during chloroplast development in the dark, and then decreased 2-fold in chloroplasts of light-grown plants. The initial increase in rpoA and psbA mRNA stability was also light-independent, with total increases in stability of at least 5-fold. In the case of rpoA, the stability of 2 of the 13 polycistronic rpoA transcripts that were detected in dark-grown plants was selectively increased during chloroplast development. In conclusion, the stability of some transcripts is selectively increased and further modulated during chloroplast development in barley. We propose that the selective stabilization of chloroplast mRNA, which occurred independent of light, is an indication that non-light regulated developmental signals are involved in barley chloroplast mRNA stability.

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.

Characterization of the psbK locus of Synechocystis sp. PCC 6803 in terms of Photosystem II function

The psbK gene encodes a small protein of Photosystem II. The gene has previously been cloned and sequenced in Synechocystis sp. PCC 6803. Our new results, presented here, confirm the conclusions of Ikeuchi et al. Based on Northern hybridization and primer extension analyses, we show that psbK is transcribed as a monocistronic message in this cyanobacterium. Analysis of DNA sequence immediately upstream of the transcription start site revealed an E. coli-like-10 consensus sequence. A deletion mutant was constructed where the psbK gene was replaced by a kanamycin resistant cartridge. In situ complementation experiments, as well as Southern and Northern hybridization analyses, confirmed that the mutant strain contains a lesion in psbK. The psbK-less mutant could grow photoautotrophically as well as photoheterotrophically both in liquid culture and on agar plates. The rate of growth was slightly less compared with the wild-type as clearly observed by in situ complementation experiments. Although the mutant showed correspondingly lower rates of electron transport, thermoluminescence, oxygen flash yield and chlorophyll a fluorescence measurements did not detect any significant modification of the reactions of PS II. Moreover, the mutant was no more susceptible to excess light than the wild-type. It is, therefore, concluded that the product of the psbK gene is not crucial for PS II activity and possibly plays some other role in the metabolism of Synechocystis.

Dynamical behavior of psb gene transcripts in greening wheat seedlings. I. Time course of accumulation of the pshA through psbN gene transcripts during light-induced greening

The time course of the accumulation of the transcripts from 13 psb genes encoding a major part of the proteins composing photosystem II during light-induced greening of dark-grown wheat seedlings was examined focusing on early stages of plastid development (0.5 h through 72 h). The 13 genes can be divided into three groups. (1) The psbA gene is transcribed as a single transcript of 1.3 kb in the dark-grown seedlings, but its level increases 5- to 7-fold in response to light due to selective increase in RNA stability as well as in transcription activity. (2) The psbE-F-L-J operon, psbM and psbN genes are transcribed as a single transcript of 1.1 kb, two transcripts of 0.5 and 0.7 kb and a single transcript of 0.3 kb, respectively, in the dark-grown seedlings. The levels of accumulation of every transcript remain unchanged or rather decrease during plastid development under illumination. (3) The psbK-I-D-C gene cluster and psbB-H operon exhibit fairly complicated northern hybridization patterns during the greening process. When a psbC or psbD gene probe was used for northern hybridization, five transcripts differing in length were detected in the etioplasts from 5-day old dark-grown seedlings. After 2 h illumination, two new transcripts of different length appeared. Light induction of new transcripts was also observed in the psbB-H operon.

Active transcription from a promoter positioned within the coding region of a divergently oriented gene: the tobacco chloroplast rpl32 gene

A new transcription unit has been identified and characterized in the small single-copy region of tobacco chloroplast DNA. A primary transcript (1550 nucleotides) spanning the entire transcription unit contains no significant open reading frames (ORFs), other than ORF55, recently identified as the gene encoding the ribosomal protein CL32 (rpl32). The leader sequence extends 1101 nucleotides from the rpl32 initiation codon. Primer extension and in vitro capping experiments in combination with ribonuclease protection assays, revealed a promoter situated more than 322 bp inside the coding region of ndhF, which is divergently oriented with respect to rpl32. A canonical Pribnow-box is found just upstream of the transcription start site, but a typical -35 motif was not detected. This is the first internal divergent promoter to be characterized in the chloroplast genome.

Chloroplast DNA of black pine retains a residual inverted repeat lacking rRNA genes: nucleotide sequences of trnQ, trnK, psbA, trnI and trnH and the absence of rps16

A physical map of black pine (Pinus thunbergii) chloroplast DNA (120 kb) was constructed and two separate portions of its nucleotide sequence were determined. One portion contains trnQ-UUG, ORF510, ORF83, trnK-UUU (ORF515 in the trnK intron), ORF22, psbA, trnI-CAU (on the opposing strand) and trnH-GUG, in that order. Sequence analysis of another portion revealed the presence of a 495 bp inverted repeat containing trnI-CAU and the 3' end of psbA but lacking rRNA genes. The position of trnI-CAU is unique because most chloroplast DNAs have no gene between psbA and trnH (trnI-CAU is usually located further downstream). Black pine chloroplast DNA lacks rps16, which has been found between trnQ and trnK in angiosperm chloroplast DNAs, but possesses ORF510 instead. This ORF is highly homologous to ORF513 found in the corresponding region of liverwort chloroplast DNA and ORF563 located downstream from trnT in Chlamydomonas moewusii chloroplast DNA. A possible pathway for the evolution of black pine chloroplast DNA is discussed.

Two promoters within the psbK-psbI-trnG gene cluster in tobacco chloroplast DNA

Transcription of the 2.6 kbp psbK-psbI-trnG cluster in tobacco chloroplasts has been studied. This cluster contains, in linear sequence, the genes encoding two low-molecular-mass polypeptides, K and I, of photosystem II (psbK and psbI, respectively), and tRNA(Gly) (UCC) (trnG). Northern blot hybridization revealed that the largest transcript (2.6 kb) hybridizes to psbK, psbI and trnG, but not to the following trnR-UCU. Ten other transcripts ranging from 0.1 to 1.3 kb were also detected. Three of these transcripts overlap the divergent transcript arising from trnS-GCU located on the opposite DNA strand. S1 mapping and primer extension experiments showed that these multiple transcripts comprise eight distinct 5' ends. By in vitro capping assays two of them were determined to be transcriptional initiation sites; one is located 163 bp upstream of psbK and the other is 6 bp upstream of trnG. The 3' ends of transcripts were determined by S1 mapping; one lies between psbI and trnG and the other is at the end of trnG. The presence of dual promoters of trnG is discussed.

The chloroplast psbK operon from mustard (Sinapis alba L.): multiple transcripts during seedling development and evidence for divergent overlapping transcription

The mustard chloroplasts genes psbK and psbI are co-transcribed, giving rise to precursor transcripts of several size classes, which are processed to the monocistronic mature RNAs. The psbK and psbI coding regions are flanked by the two tRNA genes trnS-GCU and trnQ-UUG on the opposite DNA strand. Transcript mapping indicates that the (primary) psbK-psbI transcript overlaps the complete trnS-GCU and trnQ-UUG transcripts. The transcription start site of the psbK operon appears to overlap that of the rps16 gene. During seedling development, the psbK and psbI precursors and mature transcripts all become detectable between 30 and 48 h after sowing and then remain at constant levels without much difference either in light or in darkness.