A long antisense RNA in plant chloroplasts.

Based on computational prediction of RNA secondary structures, a long antisense RNA (asRNA) was found in chloroplasts of Arabidopsis, Nicotiana tabacum and poplar, which occurs in two to three major transcripts. Mapping of primary 5' ends, northern hybridizations and quantitative real-time reverse transcription polymerase chain reaction (qPCR) experiments demonstrated that these transcripts originate from a promoter that is typical for the plastid-encoded RNA polymerase and are over their full length in antisense orientation to the gene ndhB and therefore were designated asRNA_ndhB. The asRNA_ndhB transcripts predominantly accumulate in young leaves and at physiological growth temperatures. Two nucleotide positions in the mRNA that are subject to C-to-U RNA editing and which were previously found to be sensitive to elevated temperatures are covered by asRNA_ndhB. Nevertheless, the correlation between the accumulation of asRNA_ndhB and RNA editing appeared weak in a temperature shift experiment. With asRNA_ndhB, we describe the first asRNA of plant chloroplasts that covers RNA editing sites, as well as a group II intron splice acceptor site, and that is under developmental control, raising the possibility that long asRNAs could be involved in RNA maturation or the control of RNA stability.

Ecological genomics of marine picocyanobacteria.

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production. Prochlorococcus was isolated around 20 years ago and is probably the most abundant photosynthetic organism on Earth. The genus comprises specific ecotypes which are phylogenetically distinct and differ markedly in their photophysiology, allowing growth over a broad range of light and nutrient conditions within the 45 degrees N to 40 degrees S latitudinal belt that they occupy. Synechococcus and Prochlorococcus are closely related, together forming a discrete picophytoplankton clade, but are distinguishable by their possession of dissimilar light-harvesting apparatuses and differences in cell size and elemental composition. Synechococcus strains have a ubiquitous oceanic distribution compared to that of Prochlorococcus strains and are characterized by phylogenetically discrete lineages with a wide range of pigmentation. In this review, we put our current knowledge of marine picocyanobacterial genomics into an environmental context and present previously unpublished genomic information arising from extensive genomic comparisons in order to provide insights into the adaptations of these marine microbes to their environment and how they are reflected at the genomic level.

Expression and phylogeny of the multiple antenna genes of the low-light-adapted strain Prochlorococcus marinus SS120 (Oxyphotobacteria).

In contrast to typical cyanobacteria, Prochlorococcus strains possess an intrinsic divinyl-chlorophyll (Chl) a/b-protein complex instead of phycobilisomes as the major light-harvesting system. These pigment-protein complexes are encoded by a variable number of pcb genes depending on the ecotype to which the Prochlorococcus strain belongs: low-light-adapted strains possess several pcb gene copies whereas only a single copy is present in high-light-adapted strains. In this study, the light-regulated expression of the seven pcb genes of Prochlorococcus marinus SS120 was examined. The pcbF gene was found to exhibit a high turnover and its mRNA could only be detected as a degraded product under all light conditions. Steady-state levels of transcripts originating from the six other pcb gene copies varied over several orders of magnitude but were not significantly differentially regulated by light intensity. Transcript levels of most pcb genes increased between 4.5 and 8.5 micromol quanta m(-2) s(-1), peaked at 45 micromol m(-2) s(-1) and decreased at the highest irradiance (72 micromol m(-2) s(-1)). A phylogenetic analysis of the Pcb proteins and other members of the six-helix Chl protein superfamily revealed that PcbC and PcbG make a separate cluster with regard to the other Pcbs from SS120. In contrast, Pcb sequences from four high-light-adapted Prochlorococcus sp. strains were found to cluster together and to be less variable than SS120 Pcbs. Thus, pcb genes likely evolved at a different rate in the two Prochlorococcus ecotypes. Their early multiplication and diversification is likely a key factor in the successful adaptation of some genotypes to very-low-light conditions.

Differential expression of antenna and core genes in Prochlorococcus PCC 9511 (Oxyphotobacteria) grown under a modulated light-dark cycle.

The continuous changes in incident solar light occurring during the day oblige oxyphototrophs, such as the marine prokaryote Prochlorococcus, to modulate the synthesis and degradation rates of their photosynthetic components finely. How this natural phenomenon influences the diel expression of photosynthetic genes has never been studied in this ecologically important oxyphotobacterium. Here, the high light-adapted strain Prochlorococcus sp. PCC 9511 was grown in large-volume continuous culture under a modulated 12 h-12 h light-dark cycle mimicking the conditions found in the upper layer of equatorial oceans. The pcbA gene encoding the major light-harvesting complex showed strong diel variations in transcript levels with two maxima, one before the onset of illumination and the other near the end of the photoperiod. In contrast, the mRNA level of psbA (encoding the reaction centre II subunit D1), the monocistronic transcript of psbD (encoding D2) and the dicistronic transcript of psbDC were all tightly correlated with light irradiance, with a minimum at night and a maximum at noon. The occurrence of a second peak during the dark period for the monocistronic transcript of psbC (encoding one of the PS II core Chl a antenna proteins) suggested the involvement of post-transcriptional regulation. Differential expression of the external antenna and core genes may constitute a mechanism of regulation of the antenna size to cope with the excess photon fluxes that Prochlorococcus cells experience in the upper layer of oceans around midday. The 5' ends of all transcripts were mapped, and a conserved motif, 5'-TTGATGA-3', was identified within the putative psbA and pcbA promoters.

Complete 5' and 3' end maturation of group II intron-containing tRNA precursors.

Higher plant chloroplasts provide the only experimentally validated example of functional tRNA genes that are disrupted by group II introns. Here, precursor transcripts for tRNA(Gly)(UCC), tRNA(Val)(UAC), and tRNA(Ala)(UGC) were investigated for processing of 5' leader and 3' trailer sequences in vivo. Use of intron-specific primer pairs and inclusion of a barley chloroplast splicing mutant specifically allowed us to evaluate the potential effect of intervening sequences that disrupt tRNA secondary and tertiary structures. The data suggest that (1) neither integrity of the dihydrouridine nor the anticodon domain is required for the nucleotidyltransferase-mediated addition of 3'-terminal CCA; (2) interruption of these two structural elements by group II introns does not interfere with nucleotide-specific 5' maturation by RNase P; (3) processing intermediates of chloroplast tRNAs can be 3' polyadenylated; and (4) plastid DNA-encoded proteins are not required for 3' and 5' maturation of plastid tRNAs.

Diel expression of cell cycle-related genes in synchronized cultures of Prochlorococcus sp. strain PCC 9511.

The cell cycle of the chlorophyll b-possessing marine cyanobacterium Prochlorococcus is highly synchronized under natural conditions. To understand the underlying molecular mechanisms we cloned and sequenced dnaA and ftsZ, two key cell cycle-associated genes, and studied their expression. An axenic culture of Prochlorococcus sp. strain PCC 9511 was grown in a turbidostat with a 12 h-12 h light-dark cycle for 2 weeks. During the light periods, a dynamic light regimen was used in order to simulate the natural conditions found in the upper layers of the world's oceans. This treatment resulted in strong cell cycle synchronization that was monitored by flow cytometry. The steady-state mRNA levels of dnaA and ftsZ were monitored at 4-h intervals during four consecutive division cycles. Both genes exhibited clear diel expression patterns with mRNA maxima during the replication (S) phase. Western blot experiments indicated that the peak of FtsZ concentration occurred at night, i.e., at the time of cell division. Thus, the transcript accumulation of genes involved in replication and division is coordinated in Prochlorococcus sp. strain PCC 9511 and might be crucial for determining the timing of DNA replication and cell division.

Nitrogen deprivation strongly affects photosystem II but not phycoerythrin level in the divinyl-chlorophyll b-containing cyanobacterium Prochlorococcus marinus.

Effects of nitrogen limitation on Photosystem II (PSII) activities and on phycoerythrin were studied in batch cultures of the marine oxyphotobacterium Prochlorococcus marinus. Dramatic decreases in photochemical quantum yields (F(V)/F(M)), the amplitude of thermoluminescence (TL) B-band, and the rate of Q(A) reoxidation were observed within 12 h of growth in nitrogen-limited conditions. The decline in F(V)/F(M) paralleled changes in the TL B-band amplitude, indicative of losses in PSII activities and formation of non-functional PSII centers. These changes were accompanied by a continuous reduction in D1 protein content. In contrast, nitrogen deprivation did not cause any significant reduction in phycoerythrin content. Our results refute phycoerythrin as a nitrogen storage complex in Prochlorococcus. Regulation of phycoerythrin gene expression in Prochlorococcus is different from that in typical phycobilisome-containing cyanobacteria and eukaryotic algae investigated so far.

The photosynthetic apparatus of Prochlorococcus: Insights through comparative genomics.

Within the vast oceanic gyres, a significant fraction of the total chlorophyll belongs to the light-harvesting antenna systems of a single genus, Prochlorococcus. This organism, discovered only about 10 years ago, is an extremely small, Chl b-containing cyanobacterium that sometimes constitutes up to 50% of the photosynthetic biomass in the oceans. Various Prochlorococcus strains are known to have significantly different conditions for optimal growth and survival. Strains which dominate the surface waters, for example, have an irradiance optimum for photosynthesis of 200 mumol photons m(-2) s(-1), whereas those that dominate the deeper waters photosynthesize optimally at 30-50 mumol photons m(-2) s(-1). These high and low light adapted 'ecotypes' are very closely related - less than 3% divergent in their 16S rRNA sequences - inviting speculation as to what features of their photosynthetic mechanisms might account for the differences in photosynthetic performance. Here, we compare information obtained from the complete genome sequences of two Prochlorococcus strains, with special emphasis on genes for the photosynthetic apparatus. These two strains, Prochlorococcus MED4 and MIT 9313, are representatives of high- and low-light adapted ecotypes, characterized by their low or high Chl b/a ratio, respectively. Both genomes appear to be significantly smaller (1700 and 2400 kbp) than those of other cyanobacteria, and the low-light-adapted strain has significantly more genes than its high light counterpart. In keeping with their comparative light-dependent physiologies, MED4 has many more genes encoding putative high-light-inducible proteins (HLIP) and photolyases to repair UV-induced DNA damage, whereas MIT 9313 possesses more genes associated with the photosynthetic apparatus. These include two pcb genes encoding Chl-binding proteins and a second copy of the gene psbA, encoding the Photosystem II reaction center protein D1. In addition, MIT 9313 contains a gene cluster to produce chromophorylated phycoerythrin. The latter represents an intermediate form between the phycobiliproteins of non-Chl b containing cyanobacteria and an extremely modified beta phycoerythrin as the sole derivative of phycobiliproteins still present in MED4. Intriguing features found in both Prochlorococcus strains include a gene cluster for Rubisco and carboxysomal proteins that is likely of non-cyanobacterial origin and two genes for a putative varepsilon and beta lycopene cyclase, respectively, explaining how Prochlorococcus may synthesize the alpha branch of carotenoids that are common in green organisms but not in other cyanobacteria.

Multiplication of antenna genes as a major adaptation to low light in a marine prokaryote.

Two ecotypes of the prokaryote Prochlorococcus adapted to distinct light niches in the ocean have been described recently. These ecotypes are characterized by their different (divinyl-) chlorophyll (Chl) a to Chl b ratios and 16S rRNA gene signatures, as well as by their significantly distinct irradiance optima for growth and photosynthesis [Moore, L. R., Rocap, G. & Chisholm, S. W. (1998) Nature (London) 393, 464-467]. However, the molecular basis of their physiological differences remained, so far, unexplained. In this paper, we show that the low-light-adapted Prochlorococcus strain SS120 possesses a gene family of seven transcribed genes encoding different Chl a/b-binding proteins (Pcbs). In contrast, Prochlorococcus sp. MED4, a high-light-adapted ecotype, possesses a single pcb gene. The presence of multiple antenna genes in another low-light ecotype (NATL2a), but not in another high-light ecotype (TAK9803-2), is demonstrated. Thus, the multiplication of pcb genes appears as a key factor in the capacity of deep Prochlorococcus populations to survive at extremely low photon fluxes.

A small and compact genome in the marine cyanobacterium Prochlorococcus marinus CCMP 1375: lack of an intron in the gene for tRNA(Leu)(UAA) and a single copy of the rRNA operon.

Data obtained by pulsed field gel electrophoresis revealed for Prochlorococcus marinus CCMP 1375 a genome size of 1.81+/-0.04 Mbp. This value is significantly smaller than for all other cyanobacteria investigated so far. The absence of an intron in the gene for tRNA(Leu)(UAA), which otherwise is widespread among cyanobacteria, and the additional finding that the ribosomal operon exists as a single copy suggest that the deletion of non-essential sequences played a major role in the evolution of P. marinus. A small genome may have been advantageous in the adaptation to very oligotrophic marine conditions.

Inter-organellar crosstalk in higher plants: impaired chloroplast development affects mitochondrial gene and transcript levels.

Co-ordination of gene expression between the three genomes present in plastids, mitochondria and nucleus is of crucial importance for plant cells. Previous studies revealed that in white leaves of the albostrians (Hordeum vulgare cv. Haisa) mutant, photosynthesis-related plastid and nuclear genes are expressed only at an extremely low level. The plastids of this mutant lack ribosomes, photosynthetic activity and have only rudimentary membrane systems. Here we report on the expression of mitochondrial genes in albostrians barley. Steady-state RNA levels of the mitochondrial genes encoding cytochrome oxidase or ATPase subunits, coxII, coxIII, atpA, atp6, atp9 and cob, were observed to be consistently elevated in the white leaves but not in roots. Investigation of mitochondrial DNA revealed an about three-fold enhanced mitochondrial gene copy number in white compared to green leaf cells, but no differential amplification of mitochondrial genes. Analysis of plants in which the white albostrians plastids were combined with a new nuclear background showed that the enhanced transcript levels were a consequence of the impaired plastids and not of the nuclear albostrians allele. Furthermore, plants bleached by the carotenoid biosynthesis inhibitor norflurazon also showed an enhanced mitochondrial transcript level. These findings allow the conclusion that lack of chloroplast activity in an otherwise fully differentiated leaf leads to an increase in mitochondrial gene copy number and an elevated level of mitochondrial transcripts. Our results indicate an influence of plastids on the genetic apparatus of mitochondria in leaves but not in roots.

Cloning and characterization of three cDNAs encoding chloroplast RNA-binding proteins from barley (Hordeum vulgare L.): differential regulation of expression by light and plastid development.

Three cDNAs encoding chloroplast RNA-binding proteins (RNBPs) were identified in a screen of barley albostrians mutant expression libraries, and their binding and expression characteristics were determined. Two of these proteins, designated cp31AHv and cp31BHv, are closely related to group II, whereas the third, cp33Hv, is more similar to group III of the nuclear-encoded chloroplast RNBPs of dicot plants. Analysis of RNA from sections of primary leaves by Northern hybridization showed that the expression of these genes correlates with the stage of leaf development. The steady state transcript levels of the two genes encoding cp31BHv and cp33Hv, but not of the gene for cp31AHv, were positively affected by light. Moreover, a plastid factor is required for activation of cp31AHv transcription as revealed by the low level of cp31AHv mRNA in white leaves of the albostrians mutant and of seedlings treated with Norflurazon. Therefore, we propose the existence of a light-independent plastid-derived signal chain that regulates the expression of cp31AHv.

Comparative analysis of splicing of the complete set of chloroplast group II introns in three higher plant mutants.

The barley mutant albostrians and the maize mutants crs1 and crs2 are defective in the splicing of various plastid group II introns. By analysing tRNA precursors and several mRNAs not previously examined, the investigation of in vivo splicing defects in these mutants has been completed. The albostrians mutation causes the loss of plastid ribosomes resulting secondarily in a disruption of splicing of all subgroup IIA introns in the chloroplast. Thus MatK, the only putative chloroplast intron-specific maturase of higher plants, might have evolved to function in splicing of multiple introns. We show that in the case of tRNA-Ala(UGC)the first step of splicing is affected, as suggested by the absence of lariat molecules. Thus the plastid-encoded splicing factor lacking in albostrians must participate in the formation of the catalytically active structure. In contrast, a mutation in the nuclear gene crs1 prevents splicing of only one intron but causes specific additional effects as precursor transcripts for tRNA-Ile(GAU), tRNA-Ala(UGC), tRNA-Lys(UUU)and tRNA-Val(UAC), but not tRNA-Gly(UCC), have significantly enhanced steady-state levels in this mutant. Our data provide evidence for a variety of splicing factors and pathways in the chloroplast, some encoded by nuclear and some by chloroplast genes, and possibly for a dual function of some of these factors.

Phycoerythrins of the oxyphotobacterium Prochlorococcus marinus are associated to the thylakoid membrane and are encoded by a single large gene cluster.

An intrinsic divinyl-chlorophyll a/b antenna and a particular form of phycobiliprotein, phycoerythrin (PE) III, coexist in the marine oxyphotobacterium Prochlorococcus marinus CCMP 1375. The genomic region including the cpeB/A operon of P. marinus was analysed. It encompasses 10,153 nucleotides that encode three structural phycobiliproteins and at least three (possibly five) different polypeptides analogous to cyanobacterial or red algal proteins involved either in the linkage of subunits or the synthesis and attachment of chromophoric groups. This gene cluster is part of the chromosome and is located within a distance of less than 110 kb from a previously characterized region containing the genes aspA-psbA-aroC. Whereas the Prochlorococcus phycobiliproteins are characterized by distinct deletions and amino acid replacements with regard to analogous proteins from other organisms, the gene arrangement resembles the organization of phycobiliprotein genes in some other cyanobacteria, in particular marine Synechococcus strains. The expression of two of the Prochlorococcus polypeptides as recombinant proteins in Escherichia coli allowed the production of individual homologous antisera to the Prochlorococcus alpha and beta PE subunits. Experiments using these sera show that the Prochlorococcus PEs are specifically associated to the thylakoid membrane and that the protein level does not significantly vary as a function of light irradiance or growth phase.

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.

Prochlorococcus, a marine photosynthetic prokaryote of global significance.

The minute photosynthetic prokaryote Prochlorococcus, which was discovered about 10 years ago, has proven exceptional from several standpoints. Its tiny size (0.5 to 0.7 microm in diameter) makes it the smallest known photosynthetic organism. Its ubiquity within the 40 degrees S to 40 degrees N latitudinal band of oceans and its occurrence at high density from the surface down to depths of 200 m make it presumably the most abundant photosynthetic organism on Earth. Prochlorococcus typically divides once a day in the subsurface layer of oligotrophic areas, where it dominates the photosynthetic biomass. It also possesses a remarkable pigment complement which includes divinyl derivatives of chlorophyll a (Chl a) and Chl b, the so-called Chl a2 and Chl b2, and, in some strains, small amounts of a new type of phycoerythrin. Phylogenetically, Prochlorococcus has also proven fascinating. Recent studies suggest that it evolved from an ancestral cyanobacterium by reducing its cell and genome sizes and by recruiting a protein originally synthesized under conditions of iron depletion to build a reduced antenna system as a replacement for large phycobilisomes. Environmental constraints clearly played a predominant role in Prochlorococcus evolution. Its tiny size is an advantage for its adaptation to nutrient-deprived environments. Furthermore, genetically distinct ecotypes, with different antenna systems and ecophysiological characteristics, are present at depth and in surface waters. This vertical species variation has allowed Prochlorococcus to adapt to the natural light gradient occurring in the upper layer of oceans. The present review critically assesses the basic knowledge acquired about Prochlorococcus both in the ocean and in the laboratory.

Expression of the psbA gene in the marine oxyphotobacteria Prochlorococcus spp.

The oxygenic photosynthetic prokaryotes Prochlorococcus marinus SS120 (CCMP1375) and Prochlorococcus sp. MED4 (CCMP 1378) were previously shown to exhibit different pigmentation and ecophysiological characteristics. The former strain has a much lower divinyl-Chl a to b ratio and is adapted to lower photon flux densities than the latter. In contrast to the cyanobacteria examined so far, both strains possess only one copy of the psbA gene, encoding the D1 protein of photosystem II core. In acclimated steady-state cultures, psbA transcript levels were always higher at high irradiances in both strains. Upon a shift from low to high light, the psbA transcript levels increased in both strains but more quickly in MED4 than in SS120. They decreased during the opposite shift. Iron-starved MED4 cells overexpressed psbA at all assayed irradiances, suggesting that this species, representative of populations from naturally iron-depleted oceanic areas, may have developed a particular compensation mechanism. The similar effects of DCMU and DBMIB on the expression of psbA suggest that light regulation of psbA in Prochlorococcus may be mediated by the electron transport chain. The energy state of cells could, however, also be involved in this regulation, since cultures of both strains subjected to darkness showed psbA levels significantly lower when glucose was added.

RNase P RNA from Prochlorococcus marinus: contribution of substrate domains to recognition by a cyanobacterial ribozyme.

The molecular organisation of the Prochlorococcus marinus rnpB gene and the catalytic activity of the encoded RNA were characterised. Kinetic parameters for several pre-tRNA substrates were comparable to those from other eubacterial RNase P RNAs, although unusually high cation concentrations were required. The CCA-end of pre-tRNAs is essential for efficient turnover despite the lack of the canonical binding motif in P. marinus RNase P RNA. A trnR gene is located only 38 nt upstream the rnpB 5' end on the complementary strand. This arrangement resembles those in the plastids of Cyanophora and Porphyra but not in any other bacterium.

Unique organization of the dnaA region from Prochlorococcus marinus CCMP1375, a marine cyanobacterium.

In order to study DNA replication control elements in cyanobacteria we cloned and sequenced the dnaA gene from the marine cyanobacterium Prochlorococcus marinus. The dnaA gene is ubiquitous among bacteria and encodes the DNA replication initiation factor DnaA. The deduced amino acid sequence of the P. marinus DnaA protein shows highest similarity to the DnaA protein from the freshwater cyanobacterium Synechocystis sp. PCC6803. Using a solid-phase DNA binding assay we demonstrated that both cyanobacterial DnaA proteins specifically recognize chromosomal origins, oriC, of Escherichia coli and Bacillus subtilis in vitro. The genetic environment of dnaA is not conserved between the two cyanobacteria. Upstream of the P. marinus dnaA gene we identified a gene encoding a putative ATP-binding cassette (ABC) transport protein. The gor gene encoding glutathione reductase lies downstream of dnaA. Comparison of the genetic structure of dnaA regions from 15 representative bacteria shows that the pattern of genes flanking dnaA is not universally conserved among them.

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.