Green life: Control of chloroplast gene transcription

A fully assembled plastid-encoded RNA polymerase complex detected in etioplasts and proplastids in Arabidopsis

The plastid-encoded genes of higher plants are transcribed by at least two types of RNA polymerases, the nuclear-encoded RNA polymerase (NEP) and the plastid-encoded RNA polymerase (PEP). In mature photosynthesizing leaves, the vast majority of the genes are transcribed by PEP. However, the regulatory mechanisms controlling plastid transcription during early light response is unclear. Chloroplast development is suggested to be associated with a shift in the usage of the primary RNA polymerase from NEP to PEP as the expression of the plastid-encoded photosynthesis genes is induced upon light exposure. Assembly of the PEP complex has been suggested as a rate-limiting step for full activation of plastid-encoded photosynthesis gene expression. However, two sigma factor mutants, sig2 and sig6, with reduced PEP activity, showed significantly lower expression of the plastid-encoded photosynthesis genes already in the dark and during the first hours of light exposure indicating that PEP activity is required for basal expression of plastid-encoded photosynthesis genes in the dark and during early light response. Furthermore, in etioplasts and proplastids a fully assembled PEP complex was revealed on Blue Native PAGE. Our results indicate that a full assembly of the PEP complex is possible in the dark and that PEP drives basal transcriptional activity of plastid-encoded photosynthesis genes in the dark. Assembly of the complex is most likely not a rate-limiting step for full activation of plastid-encoded photosynthesis gene expression which is rather achieved either by the abundance of the PEP complex or by some posttranslational regulation of the individual PEP components.

pTAC10, an S1-domain-containing component of the transcriptionally active chromosome complex, is essential for plastid gene expression in Arabidopsis thaliana and is phosphorylated by chloroplast-targeted casein kinase II

In higher plant chloroplasts, the plastid-encoded RNA polymerase (PEP) consists of four catalytic subunits and numerous nuclear-encoded accessory proteins, including pTAC10, an S1-domain-containing protein. In this study, pTAC10 knockout lines were characterized. Two ptac10 mutants had an albino phenotype and severely impaired chloroplast development. The pTAC10 genomic sequence fused to a four-tandem MYC tag driven by its own promoter functionally complemented the ptac10-1 mutant phenotype. pTAC10 was present in both the chloroplast stroma and thylakoids. Two-dimensional blue native polyacrylamide gel electrophoresis (BN-PAGE), and immunoblotting assays showed that pTAC10:MYC co-migrates with one of the PEP core subunits, RpoB. A comprehensive investigation of the plastid gene expression profiles by quantitative RT-PCR revealed that, compared with wild-type plants, the abundance of PEP-dependent plastid transcripts is severely decreased in the ptac10-1 mutant, while the amount of plastid transcripts exclusively transcribed by NEP either barely changes or even increases. RNA blot analysis confirmed that PEP-dependent chloroplast transcripts, including psaB, psbA and rbcL, substantially decrease in the ptac10-1 mutant. Immunoblotting showed reduced accumulation of most chloroplast proteins in the ptac10 mutants. These data indicate the essential role of pTAC10 in plastid gene expression and plastid development. pTAC10 interacts with chloroplast-targeted casein kinase 2 (cpCK2) in vitro and in vivo and can be phosphorylated by Arabidopsis cpCK2 in vitro at sites Ser95, Ser396 and Ser434. RNA-EMSA assays showed that pTAC10 is able to bind to the psbA, atpE and accD transcripts, suggesting a non-specific RNA-binding activity of pTAC10. The RNA affinity of pTAC10 was enhanced by phosphorylation and decreased by the amino acid substitution Ser434-Ala of pTAC10. These data show that pTAC10 is essential for plastid gene expression in Arabidopsis and that it can be phosphorylated by cpCK2.

Changes in the proteome of pad2-1, a glutathione depleted Arabidopsis mutant, during Pseudomonas syringae infection

The involvement of glutathione (GSH) in plant defense against pathogen invasion is an established fact. However, the molecular mechanism conferring this tolerance remains to be explored. Here, proteomic analysis of pad2-1, an Arabidopsis thaliana GSH-depleted mutant, in response to Pseudomonas syringae infection has been performed to explore the intricate position of GSH in defense against biotrophic pathogens. The pad2-1 mutant displayed severe susceptibility to P. syringae infection compared to the wild-type (Col-0) thus re-establishing a fundamental role of GSH in defense. Apart from general up-accumulation of energy metabolism-related protein-species in both infected Col-0 and pad2-1, several crucial defense-related protein-species were identified to be differentially accumulated. Leucine-rich repeat-receptor kinase (LRR-RK) and nucleotide-binding site-leucine-rich repeat resistance protein (NBS-LRR), known to play a pioneering role against pathogen attack, were only weakly up-accumulated in pad2-1 after infection. Transcriptional and post-transcriptional regulators like MYB-P1 and glycine-rich repeat RNA-binding protein (GRP) and several other stress-related protein-species like heat shock protein 17 (HSP17) and glutathione-S-transferase (GST) were also identified to be differentially regulated in pad2-1 and Col-0 in response to infection. Together, the present investigation reveals that the optimum GSH-level is essential for the efficient activation of plant defense signaling cascades thus conferring resistance to pathogen invasion.

Transcriptomic profiling of Arabidopsis thaliana mutant pad2.1 in response to combined cold and osmotic stress

The contribution of glutathione (GSH) in stress tolerance, defense response and antioxidant signaling is an established fact. In this study transcriptome analysis of pad2.1, an Arabidopsis thaliana mutant, after combined osmotic and cold stress treatment has been performed to explore the intricate position of GSH in the stress and defense signaling network in planta. Microarray data revealed the differential regulation of about 1674 genes in pad2.1 amongst which 973 and 701 were significantly up- and down-regulated respectively. Gene enrichment, functional pathway analysis by DAVID and MapMan analysis identified various stress and defense related genes viz. members of heat shock protein family, peptidyl prolyl isomerase (PPIase), thioredoxin peroxidase (TPX2), glutathione-S-transferase (GST), NBS-LRR type resistance protein etc. as down-regulated. The expression pattern of the above mentioned stress and defense related genes and APETALA were also validated by comparative proteomic analysis of combined stress treated Col-0 and pad2.1. Functional annotation noted down-regulation of UDP-glycosyl transferase, 4-coumarate CoA ligase 8, cinnamyl alcohol dehydrogenase 4 (CAD4), ACC synthase and ACC oxidase which are the important enzymes of phenylpropanoid, lignin and ethylene (ET) biosynthetic pathway respectively. Since the only difference between Col-0 (Wild type) and pad2.1 is the content of GSH, so, this study suggested that in addition to its association with specific stress responsive genes and proteins, GSH provides tolerance to plants by its involvement with phenylpropanoid, lignin and ET biosynthesis under stress conditions.

Redox activity of thioredoxin z and fructokinase-like protein 1 is dispensable for autotrophic growth of Arabidopsis thaliana

Redox modulation of protein activity by thioredoxins (TRXs) plays a key role in cellular regulation. Thioredoxin z (TRX z) and its interaction partner fructokinase-like protein 1 (FLN1) represent subunits of the plastid-encoded RNA polymerase (PEP), suggesting a role of both proteins in redox regulation of chloroplast gene expression. Loss of TRX z or FLN1 expression generates a PEP-deficient phenotype and renders the plants incapable to grow autotrophically. This study shows that PEP function in trx z and fln1 plants can be restored by complementation with redox-inactive TRX z C106S and FLN1 C105/106A protein variants, respectively. The complemented plants showed wild-type levels of chloroplast gene expression and were restored in photosynthetic capacity, indicating that redox regulation of PEP through TRX z/FLN1 per se is not essential for autotrophic growth. Promoter-reporter gene studies indicate that TRX z and FLN1 are expressed during early phases of leaf development while expression ceases at maturation. Taken together, our data support a model in which TRX z and FLN1 are essential structural components of the PEP complex and their redox activity might only play a role in the fine tuning of PEP function.

Toxicological Responses of Chlorella vulgaris to Dichloromethane and Dichloroethane

The aim of this study was to evaluate the acute toxicity effects of dichloromethane and dichloroethane on Chlorella vulgaris at the physiological and molecular level. Data showed that the cell number, chlorophyll a, and total protein content gradually decreased with increasing dichloromethane and dichloroethane concentrations over a 96-h exposure. Lower doses of two organic solvents had stimulatory effects on catalase and superoxide dismutase activity. Malondialdehyde showed a concentration-dependent increase in response to dichloromethane and dichloroethane exposure. Electron microscopy also showed that there were some chloroplast abnormalities in response to different concentrations of dichloromethane and dichloroethane exposure. Real-time polymerase chain reaction assay demonstrated that dichloromethane and dichloroethane reduced the transcript abundance of psaB, whereas that of psbC changed depending on the toxicant after 24 h of exposure. Dichloromethane and dichloroethane affected the activity of antioxidant enzymes, disrupted the chloroplast ultrastructure, and reduced transcription of photosynthesis-related genes in C. vulgaris, leading to metabolic disruption and cell death.

A purification strategy for analysis of the DNA/RNA-associated sub-proteome from chloroplasts of mustard cotyledons

Plant cotyledons are a tissue that is particularly active in plastid gene expression in order to develop functional chloroplasts from pro-plastids, the plastid precursor stage in plant embryos. Cotyledons, therefore, represent a material being ideal for the study of composition, function and regulation of protein complexes involved in plastid gene expression. Here, we present a pilot study that uses heparin-Sepharose and phospho-cellulose chromatography in combination with isoelectric focussing and denaturing SDS gel electrophoresis (two-dimensional gel electrophoresis) for investigating the nucleic acids binding sub-proteome of mustard chloroplasts purified from cotyledons. We describe the technical requirements for a highly resolved biochemical purification of several hundreds of protein spots obtained from such samples. Subsequent mass spectrometry of peptides isolated out of cut spots that had been treated with trypsin identified 58 different proteins within 180 distinct spots. Our analyses indicate a high enrichment of proteins involved in transcription and translation and, in addition, the presence of massive post-translational modification of this plastid protein sub-fraction. The study provides an extended catalog of plastid proteins from mustard being involved in gene expression and its regulation and describes a suitable purification strategy for further analysis of low abundant gene expression related proteins.

S1 domain-containing STF modulates plastid transcription and chloroplast biogenesis in Nicotiana benthamiana

• In this study, we examined the biochemical and physiological functions of Nicotiana benthamiana S1 domain-containing Transcription-Stimulating Factor (STF) using virus-induced gene silencing (VIGS), cosuppression, and overexpression strategies. • STF : green fluorescent protein (GFP) fusion protein colocalized with sulfite reductase (SiR), a chloroplast nucleoid-associated protein also present in the stroma. Full-length STF and its S1 domain preferentially bound to RNA, probably in a sequence-nonspecific manner. • STF silencing by VIGS or cosuppression resulted in severe leaf yellowing caused by disrupted chloroplast development. STF deficiency significantly perturbed plastid-encoded multimeric RNA polymerase (PEP)-dependent transcript accumulation. Chloroplast transcription run-on assays revealed that the transcription rate of PEP-dependent plastid genes was reduced in the STF-silenced leaves. Conversely, the exogenously added recombinant STF protein increased the transcription rate, suggesting a direct role of STF in plastid transcription. Etiolated seedlings of STF cosuppression lines showed defects in the light-triggered transition from etioplasts to chloroplasts, accompanied by reduced light-induced expression of plastid-encoded genes. • These results suggest that STF plays a critical role as an auxiliary factor of the PEP transcription complex in the regulation of plastid transcription and chloroplast biogenesis in higher plants.

Identification of essential subunits in the plastid-encoded RNA polymerase complex reveals building blocks for proper plastid development

The major RNA polymerase activity in mature chloroplasts is a multisubunit, Escherichia coli-like protein complex called PEP (for plastid-encoded RNA polymerase). Its subunit structure has been extensively investigated by biochemical means. Beside the "prokaryotic" subunits encoded by the plastome-located RNA polymerase genes, a number of additional nucleus-encoded subunits of eukaryotic origin have been identified in the PEP complex. These subunits appear to provide additional functions and regulation modes necessary to adapt transcription to the varying functional situations in chloroplasts. However, despite the enormous progress in genomic data and mass spectrometry techniques, it is still under debate which of these subunits belong to the core complex of PEP and which ones represent rather transient or peripheral components. Here, we present a catalog of true PEP subunits that is based on comparative analyses from biochemical purifications, protein mass spectrometry, and phenotypic analyses. We regard reproducibly identified protein subunits of the basic PEP complex as essential when the corresponding knockout mutants reveal an albino or pale-green phenotype. Our study provides a clearly defined subunit catalog of the basic PEP complex, generating the basis for a better understanding of chloroplast transcription regulation. In addition, the data support a model that links PEP complex assembly and chloroplast buildup during early seedling development in vascular plants.

The transcription machineries of plant mitochondria and chloroplasts: Composition, function, and regulation

Although genomes of mitochondria and plastids are very small compared to those of their bacterial ancestors, the transcription machineries of these organelles are of surprising complexity. With respect to the number of different RNA polymerases per organelle, the extremes are represented on one hand by chloroplasts of eudicots which use one bacterial-type RNA polymerase and two phage-type RNA polymerases to transcribe their genes, and on the other hand by Physcomitrella possessing three mitochondrial RNA polymerases of the phage type. Transcription of genes/operons is often driven by multiple promoters in both organelles. This review describes the principle components of the transcription machineries (RNA polymerases, transcription factors, promoters) and the division of labor between the different RNA polymerases. While regulation of transcription in mitochondria seems to be only of limited importance, the plastid genes of higher plants respond to exogenous and endogenous cues rather individually by altering their transcriptional activities.

Transcriptional control of photosynthesis genes: the evolutionarily conserved regulatory mechanism in plastid genome function

Chloroplast sensor kinase (CSK) is a bacterial-type sensor histidine kinase found in chloroplasts—photosynthetic plastids—in eukaryotic plants and algae. Using a yeast two-hybrid screen, we demonstrate recognition and interactions between: CSK, plastid transcription kinase (PTK), and a bacterial-type RNA polymerase sigma factor-1 (SIG-1). CSK interacts with itself, with SIG-1, and with PTK. PTK also interacts directly with SIG-1. PTK has previously been shown to catalyze phosphorylation of plastid-encoded RNA polymerase (PEP), suppressing plastid transcription nonspecifically. Phospho-PTK is inactive as a PEP kinase. Here, we propose that phospho-CSK acts as a PTK kinase, releasing PTK repression of chloroplast transcription, while CSK also acts as a SIG-1 kinase, blocking transcription specifically at the gene promoter of chloroplast photosystem I. Oxidation of the photosynthetic electron carrier plastoquinone triggers phosphorylation of CSK, inducing chloroplast photosystem II while suppressing photosystem I. CSK places photosystem gene transcription under the control of photosynthetic electron transport. This redox signaling pathway has its origin in cyanobacteria, photosynthetic prokaryotes from which chloroplasts evolved. The persistence of this mechanism in cytoplasmic organelles of photosynthetic eukaryotes is in precise agreement with the CoRR hypothesis for the function of organellar genomes: the plastid genome and its primary gene products are Co-located for Redox Regulation. Genes are retained in plastids primarily in order for their expression to be subject to this rapid and robust redox regulatory transcriptional control mechanism, whereas plastid genes also encode genetic system components, such as some ribosomal proteins and RNAs, that exist in order to support this primary, redox regulatory control of photosynthesis genes. Plastid genome function permits adaptation of the photosynthetic apparatus to changing environmental conditions of light quantity and quality.

The role of phosphorylation in redox regulation of photosynthesis genes psaA and psbA during photosynthetic acclimation of mustard

The long-term response (LTR) to light-quality gradients improves performance and survival of plants in dense stands. It involves redox-controlled transcriptional regulation of the plastome-encoded genes psaAB (encoding the P700 apoproteins of photosystem I) and psbA (encoding the D1 protein of photosystem II) and requires the action of plastid-localized kinases. To study the potential impact of phosphorylation events on plastid gene expression during the LTR, we analyzed mustard seedlings acclimated to light sources favoring either photosystem I or photosystem II. Primer extension analyses of psaA transcripts indicate that the redox regulation occurs at the principal bacterial promoters, suggesting that the plastid encoded RNA polymerase (PEP) is the target for redox signals. Chloroplast protein fractions containing PEP and other DNA-binding proteins were purified from mustard via heparin-Sepharose chromatography. The biochemical properties of these fractions were analyzed with special emphasis on promoter recognition and specificity, phosphorylation state, and kinase activity. The results demonstrate that the LTR involves the action of small DNA-binding proteins; three of them exhibit specific changes in the phosphorylation state. Auto-phosphorylation assays, in addition, exhibit large differences in the activity of endogenous kinase activities. Chloroplast run-on transcription experiments with the kinase inhibitor H7 and the reductant DTT indicate that phosphorylation events are essential for the mediation of redox signals toward psaA and psbA transcription initiation, but require the synergistic action of a thiol redox signal. The data support the idea that redox signals from the thylakoid membrane are linked to gene expression via phosphorylation events; however, this mediation appears to require a complex network of interacting proteins rather than a simple phosphorelay.

Potential regulation of gene expression in photosynthetic cells by redox and energy state: approaches towards better understanding

BACKGROUND

Photosynthetic electron transport is performed by a chain of redox components that are electrochemically connected in series. Its efficiency depends on the balanced action of the photosystems and on the interaction with the dark reaction. Plants are sessile and cannot escape from environmental conditions such as fluctuating illumination, limitation of CO(2) fixation by low temperatures, salinity, or low nutrient or water availability, which disturb the homeostasis of the photosynthetic process. Photosynthetic organisms, therefore, have developed various molecular acclimation mechanisms that maintain or restore photosynthetic efficiency under adverse conditions and counteract abiotic stresses. Recent studies indicate that redox signals from photosynthetic electron transport and reactive oxygen species (ROS) or ROS-scavenging molecules play a central role in the regulation of acclimation and stress responses.

SCOPE

The underlying signalling network of photosynthetic redox control is largely unknown, but it is already apparent that gene regulation by redox signals is of major importance for plants. Signalling cascades controlling the expression of chloroplast and nuclear genes have been identified and dissection of the different pathways is advancing. Because of the direction of information flow, photosynthetic redox signals can be defined as a distinct class of retrograde signals in addition to signals from organellar gene expression or pigment biosynthesis. They represent a vital signal of mature chloroplasts that report their present functional state to the nucleus. Here we describe possible problems in the elucidation of redox signalling networks and discuss some aspects of plant cell biology that are important for developing suitable experimental approaches.

CONCLUSIONS

The photosynthetic function of chloroplasts represents an important sensor that integrates various abiotic changes in the environment into corresponding molecular signals, which, in turn, regulate cellular activities to counterbalance the environmental changes or stresses.

Effects of glufosinate on antioxidant enzymes, subcellular structure, and gene expression in the unicellular green alga Chlorella vulgaris

Greater exposure to herbicide increases the likelihood of harmful effects in humans and the environment. Glufosinate, a non-selective herbicide, inhibits glutamine synthetase (GS) and thus blocks ammonium assimilation in plants. In the present study, the aquatic unicellular alga Chlorella vulgaris was chosen to assess the effects of acute glufosinate toxicity. We observed physiological changes during 12-96 h of exposure, and gene transcription during 6-48 h of exposure. Exposure to glufosinate increased malondialdehyde content by up to 2.73 times compared with the control, suggesting that there was some oxidative damage. Electron microscopy also showed that there were some chloroplast abnormalities in response to glufosinate. The activities of the antioxidant enzymes superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) also increased markedly in the presence of glufosinate. Maximum activities of SOD, POD, and CAT were 2.90, 2.91, and 2.48 times that of the control, respectively. These elevated activities may help alleviate oxidative damage. A real-time polymerase chain reaction (PCR) assay showed changes in transcript abundances of three photosynthetic genes, psaB, psbC, and rbcL. The results showed that glufosinate reduced the transcript abundances of the three genes after 12h exposure. The lowest abundances of psaB, psbC and rbcL transcripts in response to glufosinate exposure were 38%, 16% and 43% of those of the control, respectively. Our results demonstrate that glufosinate affects the activities of antioxidant enzymes, disrupts chloroplast ultrastructure, and reduces transcription of photosynthesis-related genes in C. vulgaris.

Chloroplast His-to-Asp signal transduction: a potential mechanism for plastid gene regulation in Heterosigma akashiwo (Raphidophyceae)

Background

Maintenance of homeostasis requires that an organism perceive selected physical and chemical signals within an informationally dense environment. Functionally, an organism uses a variety of signal transduction arrays to amplify and convert these perceived signals into appropriate gene transcriptional responses. These changes in gene expression serve to modify selective metabolic processes and thus optimize reproductive success. Here we analyze a chloroplast-encoded His-to-Asp signal transduction circuit in the stramenopile Heterosigma akashiwo (Hada) Hada ex Y. Hara et Chihara [syn. H. carterae (Hulburt) F.J.R. Taylor]. The presence, structure and putative function of this protein pair are discussed in the context of their evolutionary homologues.

Results

Bioinformatic analysis of the Heterosigma akashiwo chloroplast genome sequence revealed the presence of a single two-component His-to-Asp (designated Tsg1/Trg1) pair in this stramenopile (golden-brown alga). These data represent the first documentation of a His-to-Asp array in stramenopiles and counter previous reports suggesting that such regulatory proteins are lacking in this taxonomic cluster. Comparison of the 43 kDa H. akashiwo Tsg1 with bacterial sensor kinases showed that the algal protein exhibits a moderately maintained PAS motif in the sensor kinase domain as well as highly conserved H, N, G₁ and F motifs within the histidine kinase ATP binding site. Molecular modelling of the 27 kDa H. akashiwo Trg1 regulator protein was consistent with a winged helix-turn-helix identity – a class of proteins that is known to impact gene expression at the level of transcription. The occurrence of Trg1 protein in actively growing H. akashiwo cells was verified by Western analysis. The presence of a PhoB-like RNA polymerase loop in Trg1 and its homologues in the red-algal lineage support the hypothesis that Trg1 and its homologues interact with a sigma 70 (σ⁷⁰) subunit (encoded by rpoD) of a eubacterial type polymerase. Sequence analysis of H. akashiwo rpoD showed this nuclear-encoded gene has a well-defined 4.2 domain, a region that augments RNA polymerase interaction with transcriptional regulatory proteins and also serves in -35 promoter recognition. The presence/loss of the His-to-Asp pairs in primary and secondary chloroplast lineages is assessed.

Conclusion

His-to-Asp signal transduction components are found in most rhodophytic chloroplasts, as well as in their putative cyanobacterial progenitors. The evolutionary conservation of these proteins argues that they are important for the maintenance of chloroplast homeostasis. Our data suggest that chloroplast gene transcription may be impacted by the interaction of the His-to-Asp regulator protein (which is less frequently lost than the sensor protein) with the RNA polymerase σ⁷⁰ subunit.

Eukaryotic transcription factors in plastids--Bioinformatic assessment and implications for the evolution of gene expression machineries in plants

The expression of genes in higher plant chloroplasts includes a complex transcriptional regulation which can be explained only in part with the action of the actually known components of the transcriptional machinery. This suggests the existence of still unknown important regulatory factors which influence chloroplast transcription. In order to test if such factors could exist we performed in silico analyses of Arabidopsis genes encoding putative transcription factors looking for putative N-terminal chloroplast transit peptides in the amino acid sequences. Our results suggest that 48 (and maybe up to 100) transcription factors of eukaryotic origin are likely to be imported into plastids. None of them has been described yet. This set of transcription factors highly expands the actually known regulation capacity of the chloroplast transcription machinery and provides a possible explanation for the complex initiation patterns of chloroplast transcripts. As consequence of a massive import of eukaryotic transcription factors a comprehensive reconstruction of the ancient prokaryotic gene expression machinery must be assumed resulting in a novel compatible combination of eukaryotic and prokaryotic protein components. In turn, the opposite process has been induced in the nucleus by the integration of prokaryotic components of the plastid ancestor via its loss of genes during endosymbiosis. Thus, a mutual exchange of regulatory factors, i.e. transcription factors occurred which resulted in the unique signalling network of today's plants. An evolutionary model of how this could have emerged during endosymbiosis in a timely coordinated manner is proposed.

LexA regulates the bidirectional hydrogenase in the cyanobacterium Synechocystis sp. PCC 6803 as a transcription activator

The bidirectional NiFe-hydrogenase of Synechocystis sp. PCC 6803 is encoded by five genes (hoxEFUYH) which are transcribed as one unit. The transcription of the hox-operon is regulated by a promoter situated upstream of hoxE. The transcription start point was located at -168 by 5'Race. Several promoter probe vectors carrying different promoter fragments revealed two regions to be essential for the promoter activity. One is situated in the untranslated 5'leader region and the other is found -569 to -690 nucleotides upstream of the ATG. The region further upstream was shown to bind a protein. Even though an imperfect NtcA binding site was identified, NtcA did not bind to this region. The protein binding to the DNA was purified and found to be LexA by MALDI-TOF. The complete LexA and its DNA binding domain were overexpressed in Escherichia coli. Both were able to bind to two sites in the examined region in band-shift-assays. Accordingly, the hydrogenase activity of a LexA-depleted mutant was reduced. This is the first report on LexA acting not as a repressor but as a transcriptional activator. Furthermore, LexA is the first transcription factor identified so far for the expression of bidirectional hydrogenases in cyanobacteria.

Photosynthetic redox control of nuclear gene expression

Chloroplasts contain 3000-4000 different proteins but only a small subset of them is encoded in the plastid genome while the majority is encoded in the nucleus. Expression of these genes therefore requires a high degree of co-ordination between nucleus and chloroplast. This is achieved by a bilateral information exchange between both compartments including nucleus-to-plastid (anterograde) and plastid-to-nucleus (retrograde) signals. The latter represent a functional feedback control which couples the expression of nuclear encoded plastid proteins to the actual functional state of the organelle. The efficiency of photosynthesis is a very important parameter in this context since it is influenced by many environmental conditions and therefore represents a sensor for the residing environment. Components of the photosynthetic electron transport chain exhibit significant changes in their reduction/oxidation (redox) state depending on the photosynthetic electron flow and therefore serve as signalling parameters which report environmental influences on photosynthesis. Such redox signals control chloroplast and nuclear gene expression events and play an important role in the co-ordination of both genetic compartments. It is discussed here which photosynthetic parameters are known to control nuclear gene expression, how these signals are transduced toward the nucleus, and how they interact with other plastid retrograde signals and cytosolic light perception systems.

Redox regulation and modification of proteins controlling chloroplast gene expression

Chloroplasts are typical organelles of plant cells and represent the site of photosynthesis. As one very remarkable feature, they possess their own genome and a complete machinery to express the genetic information in it. The plastid gene expression machinery is a unique assembly of prokaryotic-, eukaryotic-, and phage-like components because chloroplasts acquired a great number of regulatory proteins during evolution. Such proteins can be found at all levels of gene expression. They significantly expand the functional and especially the regulatory properties of the "old" gene expression system that chloroplasts inherited from their prokaryotic ancestors. Recent results show that photosynthesis has a strong regulatory effect on plastid gene expression. The redox states of electron transport components, redox-active molecules coupled to photosynthesis, and pools of reactive oxygen species act as redox signals. They provide a functional feedback control, which couples the expression of chloroplast genes to the actual function of photosynthesis and, by this means, helps to acclimate the photosynthetic process to environmental cues. The redox signals are mediated by various specific signaling pathways that involve many of the "new" regulatory proteins. Chloroplasts therefore are an ideal model to study redox-regulated mechanisms in gene expression control. Because of the multiple origins of the expression machinery, these observations are of great relevance for many other biological systems.

A nuclear-encoded sigma factor, Arabidopsis SIG6, recognizes sigma-70 type chloroplast promoters and regulates early chloroplast development in cotyledons

Eubacterial-type multi-subunit plastid RNA polymerase (PEP) is responsible for the principal transcription activity in chloroplasts. PEP is composed of plastid-encoded core subunits and one of multiple nuclear-encoded sigma factors that confer promoter specificity on PEP. Thus, the replacement of sigma factors associated with PEP has been assumed to be a major mechanism for the switching of transcription patterns during chloroplast development. The null mutant (sig6-1) of plastid sigma factor gene AtSIG6 exhibited a cotyledon-specific pale green phenotype. Light-dependent chloroplast development was significantly delayed in the sig6-1 mutant. Genetic complementation of the mutant phenotype by the AtSIG6 cDNA demonstrated that AtSIG6 plays a key role in light-dependent chloroplast development. Northern and array-based global analyses for plastid transcripts revealed that the transcript levels of most PEP-dependent genes were greatly reduced in the sig6-1 mutant, but that the accumulation of nuclear-encoded RNA polymerase (NEP)-dependent transcripts generally increased. As the PEP alpha subunit and PEP-dependent trnV accumulated at normal levels in the sig6-1 mutant, the AtSIG6 knockout mutant probably retained functional PEP, and the transcriptional defects are likely to have been directly caused by AtSIG6 deficiency. Most of the AtSIG6-dependent genes are preceded by sigma70-type promoters comprised of conserved -35/-10 elements. Thus, AtSIG6 may act as a major general sigma factor in chloroplasts during early plant development. On the other hand, the mutant phenotype was restored in older seedlings. Arabidopsis probably contains another late general sigma factor, the promoter specificity of which widely overlaps with that of AtSIG6.

Plastid RNA polymerases, promoters, and transcription regulators in higher plants

Plastids are semiautonomous plant organelles exhibiting their own transcription-translation systems that originated from a cyanobacteria-related endosymbiotic prokaryote. As a consequence of massive gene transfer to nuclei and gene disappearance during evolution, the extant plastid genome is a small circular DNA encoding only ca. 120 genes (less than 5% of cyanobacterial genes). Therefore, it was assumed that plastids have a simple transcription-regulatory system. Later, however, it was revealed that plastid transcription is a multistep gene regulation system and plays a crucial role in developmental and environmental regulation of plastid gene expression. Recent molecular and genetic approaches have identified several new players involved in transcriptional regulation in plastids, such as multiple RNA polymerases, plastid sigma factors, transcription regulators, nucleoid proteins, and various signaling factors. They have provided novel insights into the molecular basis of plastid transcription in higher plants. This review summarizes state-of-the-art knowledge of molecular mechanisms that regulate plastid transcription in higher plants.

Function and regulation of the cyanobacterial genes lexA, recA and ruvB: LexA is critical to the survival of cells facing inorganic carbon starvation

The cyanobacterial genes lexA, recA and ruvB were analysed in Synechocystis PCC6803, which is shown here to be more radiation resistant than the other unicellular model strain Synechococcus PCC7942. We found that cyanobacteria do not have an Escherichia coli-type SOS regulon. The Synechocystis lexA and recA promoters were found to be strong and UV insensitive, unlike the ruvB promoter, which is weak and UV-C inducible. Yet, lexA and recA are regulated by UV-C, but the control is negative and occurs at the post-transcriptional level. Two novel conserved elements were characterized in the lexA promoter: (i) an unusually long crucial box 5'-TAAAATTTTGTATCTTTT-3' (-64, -47); and (ii) a negatively acting motif 5'-TAT GAT-3' (-42, -37). These elements were not found in the recA promoter, which appeared to be unusually simple in harbouring only a single crucial element (i.e. the canonical -10 box). RuvB, operating in recombination-dependent cellular processes, was found to be dispensable to cell growth, whereas LexA and RecA appeared to be critical to cell viability. Using DNA microarrays, we have identified 57 genes with expression that is altered, at least twofold, in response to LexA depletion. None of these genes is predicted to operate in DNA metabolism, arguing against the involvement of LexA in the regulation of DNA repair. Instead, most of the LexA-responsive genes were known to be involved in carbon assimilation or controlled by carbon availability. Consistently, the growth of the LexA-depleted strain was found to be strongly dependent on the availability of inorganic carbon.

Comparative Analysis of the Complete Plastid Genome Sequence of the Red Alga Gracilaria tenuistipitata var. liui Provides Insights into the Evolution of Rhodoplasts and Their Relationship to Other Plastids

We sequenced to completion the circular plastid genome of the red alga Gracilaria tenuistipitata var. liui. This is the first plastid genome sequence from the subclass Florideophycidae (Rhodophyta). The genome is composed of 183,883 bp and contains 238 predicted genes, including a single copy of the ribosomal RNA operon. Comparisons with the plastid genome of Porphyra pupurea reveal strong conservation of gene content and order, but we found major genomic rearrangements and the presence of coding regions that are specific to Gracilaria. Phylogenetic analysis of a data set of 41 concatenated proteins from 23 plastid and two cyanobacterial genomes support red algal plastid monophyly and a specific evolutionary relationship between the Florideophycidae and the Bangiales. Gracilaria maintains a surprisingly ancient gene content in its plastid genome and, together with other Rhodophyta, contains the most complete repertoire of plastid genes known in photosynthetic eukaryotes.

Blue light-induced transcription of plastid-encoded psbD gene is mediated by a nuclear-encoded transcription initiation factor, AtSig5

Light is one of the most important environmental factors regulating expression of photosynthesis genes. The plastid psbD gene encoding the photosystem II reaction center protein D2 is under the control of a unique blue light responsive promoter (BLRP) that is transcribed by a bacterial-type plastid RNA polymerase (PEP). Promoter recognition of PEP is mediated by one of the six nuclear-encoded sigma factors in Arabidopsis. The replacement of the plastid sigma factor associated with PEP may be the major mechanism for switching of plastid transcription pattern in response to environmental and developmental signals. This study demonstrates that AtSig5 is a unique sigma factor that is essential for psbD BLRP activity. A T-DNA insertional mutant with reduced AtSIG5 expression resulted in loss of primary transcripts from the psbD BLRP. Furthermore, transient overexpression of AtSig5 in dark-adapted protoplasts specifically elevated psbD and psbA transcription activities. On the other hand, overproduction of AtSig2 enhanced the transcription of psbA gene and trnE operon, but not psbD transcription. The AtSIG5 gene is phylogenetically distinct from other plastid sigma factors, and its expression is induced exclusively by blue light. We propose that AtSig5 acts as a mediator of blue light signaling that specifically activates the psbD BLRP in response to blue light in Arabidopsis.

Expression and regulation of the crucial plant-like ferredoxin of cyanobacteria

The Synechocystis fedI gene (petF, ssl0020) was found to be strongly expressed under the negative control of H2O2 or heavy metals, and the positive control of light fluence (regulation dependent on active photosynthesis) or carbon availability [under the control of NdhR, the regulator of the ndh3 operon encoding NAD(P)H dehydrogenase subunits]. The basic and constitutive promoter (BP) of fedI extending from -62 to +25 (relative to the transcription start point) is weakly active, presumably because it harbours a long (30 bp) spacer between the two crucial motifs: the -10 box (5'-TAgtAT-3', -13 to -8) and the '-35' box (5'-TTGctA-3', -49 to -44). BP strength is strongly enhanced by the two upstream regions, -113 to -82 and -151 to -114, mediating the 30-fold constitutive stimulation and the fourfold light activation respectively. Three well-conserved transcriptional elements were characterized for the first time, namely the -19 box (5'-TTTT-3') that is essential to transcription, and the two twice repeated elements that are both critical to light induction: the TTGyCA-3' box (-35 to -30, and -125 to -120) and the 5'-ATTTyA-3' box (-55 to -50, and -134 to -129). That two of these light induction motifs (5'-TTGtCA-3', -35 to -30; 5'-ATTTcA-3', -55 to -50) occur in the constitutive BP promoter indicate that in the fedI gene light activation and transcription per se are closely interacting. Interestingly, the fedI gene from marine strains was found to lack the three transcriptional elements presently described, as well as the 5'-AGGA-3' Shine-Dalgarno sequence, which are all conserved among the fedI from non-marine strains.

Redox regulation of chloroplast transcription

Chloroplasts are the important plant cell organelles where photosynthesis takes place. Throughout this process, reaction center proteins are degraded and subsequently replenished by redox-responsive gene expression. In addition to well defined posttranscriptional mechanisms at the RNA and protein level, the transcription of chloroplast DNA into RNA precursors has been a focal point of studies in this area. Evidence has become available for a central role of a redox-responsive protein kinase named plastid transcription kinase (PTK) because of its association with the chloroplast transcription complex. The recent cloning of the PTK gene has resulted in a full-length cDNA for a protein related to the catalytic alpha subunit of nucleocytoplasmic casein kinase (CK2), yet with an additional chloroplast transit peptide. The corresponding protein, termed cpCK2alpha, was shown to be associated with the major organellar RNA polymerase, PEP-A. Both authentic PTK and recombinant cpCK2alpha have comparable general properties in vitro, and both are subject to regulation by the redox-reactive reagent glutathione. Based on the physical and functional equivalence, it is anticipated that the cloned protein can help clarify the functional role of the transcription kinase in vivo, including the identification of interaction partners at the interface between photosynthetic redox signaling and gene expression.

Chloroplast redox signals: how photosynthesis controls its own genes

The photosynthetic apparatus of higher plants and algae is composed of plastid- and nuclear-encoded components, therefore the expression of photosynthesis genes needs to be highly coordinated. Expression is regulated by various factors, one of the most important of which is light. Photosynthesis functions as a sensor for such light signals, and the redox state of photosynthetic electron transport components and redox-active soluble molecules act as regulating parameters. This provides a feedback response loop in which the expression of photosynthesis genes is coupled to the function of the photosynthetic process, and highlights the dual role of photosynthesis in energy fixation and the reception of environmental information.

Redox control, redox signaling, and redox homeostasis in plant cells

Redox chemistry is a key feature of life. Oxidized substrates are reduced to synthesize functional molecules; reduced substrates are oxidized for energy supply. In addition, cells must fight against uncontrolled oxidation of essential constituents, a process that continuously occurs in an atmosphere of 21% O2. The redox situation is further complicated in plants with their highly reactive photosynthetic metabolism. To this end it is now well established that redox regulation is a central element in adjusting plant metabolism and development to the prevailing environmental conditions. This review introduces general redox chemistry and the main components of the cellular redox network, namely pyridine nucleotides, ascorbate, glutathione, lipoic acid, tocopherol, thioredoxins, glutaredoxins, peroxiredoxins, and other thiol proteins. Examples for redox sensing, transduction, redox-regulated enzymes and transcription, and the function of regulatory circuits are presented. Emphasis is placed on redox regulation of photosynthesis, which is the best understood metabolism governed by redox control on essentially all levels, ranging from gene transcription to translation, assembly and turnover, as well as short-term adaptation by state transition and enzyme activity. Increasing evidence shows the importance of redox regulation in the context of transport, plant development, and programmed cell death.

Salt- and glyphosate-induced increase in glyoxalase I activity in cell lines of groundnut (Arachis hypogaea)

Glyoxalase I (EC 4.4.1.5) activity has long been associated with rapid cell proliferation, but experimental evidence is forthcoming, linking its role to stress tolerance as well. Proliferative callus cultures of groundnut (Arachis hypogaea L. cv. JL24) showed a 3.3-fold increase in glyoxalase I activity during the logarithmic growth phase, correlating well with the data on FW gain and mitotic index. Inhibition of cell division decreased glyoxalase I activity and vice versa, thus further corroborating its role as a cell division marker enzyme. Cell lines of A. hypogaea selected in the presence of high salt (NaCl) and herbicide (glyphosate) concentrations, yielded 4.2- to 4.5-fold and 3.9- to 4.6-fold elevated glyoxalase I activity, respectively, in a dose dependent manner reflective of the level of stress tolerance. The stress-induced increase in enzyme activity was also accompanied by an increase in the glutathione content. Exogenous supplementation of glutathione could partially alleviate the growth inhibition of callus cultures induced by methylglyoxal and d-isoascorbic acid, but failed to recover the loss in glyoxalase I activity due to d-isoascorbic acid. The adaptive significance of elevated glyoxalase I activity in maintaining glutathione homeostasis has been discussed in view of our understanding on the role of glutathione in the integration of cellular processes with plant growth and development under stress conditions.

Novel nuclear-encoded proteins interacting with a plastid sigma factor, Sig1, in Arabidopsis thaliana

Sigma factor binding proteins are involved in modifying the promoter preferences of the RNA polymerase in bacteria. We found the nuclear encoded protein (SibI) that is transported into chloroplasts and interacts specifically with the region 4 of Sig1 in Arabidopsis. SibI and its homologue, T3K9.5 are novel proteins, which are not homologous to any protein of known function. The expression of sibI was tissue specific, light dependent, and developmentally timed. We suggest the transcriptional regulation by sigma factor binding proteins to function in the plastids of higher plant.

Plastid redox state and sugars: Interactive regulators of nuclear-encoded photosynthetic gene expression

Feedback regulation of photosynthesis by carbon metabolites has long been recognized, but the underlying cellular mechanisms that control this process remain unclear. By using an Arabidopsis cell culture, we show that a block in photosynthetic electron flux prevents the increase in transcript levels of chlorophyll a/b-binding protein and the small subunit of Rubisco that typically occurs when intracellular sugar levels are depleted. In contrast, the expression of the nitrate reductase gene, which is induced by sugars, is not affected. These findings were confirmed in planta by using Arabidopsis carrying the firefly luciferase reporter gene fused to the plastocyanin and chlorophyll a/b-binding protein 2 gene promoters. Transcription from both promoters increases on carbohydrate depletion. Blocking photosynthetic electron transport with 3-(3', 4'-dichlorophenyl)-1,1'-dimethylurea prevents this increase in transcription. We conclude that plastid-derived redox signaling can override the sugar-regulated expression of nuclear-encoded photosynthetic genes. In the sugar-response mutant, sucrose uncoupled 6 (sun6), plastocyanin-firefly luciferase transcription actually increases in response to exogenous sucrose rather than decreasing as in the wild type. Interestingly, plastid-derived redox signals do not influence this defective pattern of sugar-regulated gene expression in the sun6 mutant. A model, which invokes a positive inducer originating from the photosynthetic electron transport chain, is proposed to explain the nature of the plastid-derived signal.

Involvement of a nuclear-encoded basic helix-loop-helix protein in transcription of the light-responsive promoter of psbD

In the chloroplast psbD light-responsive promoter (LRP), a highly conserved sequence exists upstream from the bacterial -10/-35 elements. Multiple sequence-specific DNA binding proteins are predicted to bind to the conserved sequence as transcription factors. Using yeast one-hybrid screening of an Arabidopsis cDNA library, a possible DNA binding protein of the psbD LRP upstream sequence was identified. The protein, designated PTF1, is a novel protein of 355 amino acids (estimated molecular weight of 39.6) that contains a basic helix-loop-helix DNA binding motif in the predicted N-terminal region of the mature protein. Transient expression assay of PTF1-GFP fusion protein showed that PTF1 was localized in chloroplasts. Using the modified DNA sequence in the one-hybrid system, the ACC repeat was shown to be essential for PTF1 binding. The rate of psbD LRP mRNA accumulation was reduced in a T-DNA-inserted Arabidopsis ptf1 mutant. Compared with wild-type plants, the mutant had pale green cotyledons and its growth was inhibited under short-day conditions. These results suggest that PTF1 is a trans-acting factor of the psbD LRP.

Photosynthetic electron flow regulates transcription of the psaB gene in pea (Pisum sativum L.) chloroplasts through the redox state of the plastoquinone pool

Plants respond to changing light conditions by altering the stoichiometry between components of the photosynthetic electron transport chain of chloroplast thylakoids. We measured specific run-on transcription of the chloroplast genes psaB, psbA and rbcL in pea (Pisum sativum L.) seedlings grown under three different conditions of illumination: light selective for photosystem I (PSI-light); light selective for photosystem II (PSII-light); and a combination of PSI- and PSII-light (mixed light, ML). The transcriptional rate of the psaB gene increased under PSII-light and decreased under PSI-light, while the transcriptional rates of the psbA and rbcL genes were affected only in a non-specific way. Similar effects also occurred in plants grown under ML and switched to either PSI- or PSII-light for 4 h. Addition of the inhibitors of photosynthetic electron transport 3-(3,4 dichlorophenyl)-1,1-dimethylurea (DCMU) and 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB) influenced psaB transcription in isolated, illuminated chloroplasts: DCMU addition resulted in oxidation of the plastoquinone pool and decreased transcription of psaB; DBMIB addition resulted in reduction of the plastoquinone pool and increased transcription of psaB. The experimental results obtained in vivo and in vitro provide evidence for coupling between the redox state of plastoquinone and the rate of transcription of the psaB gene in pea.

The role of sigma factors in plastid transcription

Expression of plastid genes is controlled at both transcriptional and post-transcriptional levels in response to developmental and environmental signals. In many cases this regulation is mediated by nuclear-encoded proteins acting in concert with the endogenous plastid gene expression machinery. Transcription in plastids is accomplished by two distinct RNA polymerase enzymes, one of which resembles eubacterial RNA polymerases in both subunit structure and promoter recognition properties. The holoenzyme contains a catalytic core composed of plastid-encoded subunits, assembled with a nuclear-encoded promoter-specificity factor, sigma. Based on examples of transcriptional regulation in bacteria, it is proposed that differential activation of sigma factors may provide the nucleus with a mechanism to control expression of groups of plastid genes. Hence, much effort has focused on identifying and characterizing sigma-like factors in plants. While fractionation studies had identified several candidate sigma factors in purified RNA polymerase preparations, it was only 4 years ago that the first sigma factor genes were cloned from two photosynthetic eukaryotes, both of which were red algae. More recently this achievement has extended to the identification of families of sigma-like factor genes from several species of vascular plants. Now, efforts in the field are directed at understanding the roles in plastid transcription of each member of the rapidly expanding plant sigma factor gene family. Recent results suggest that accumulation of individual sigma-like factors is controlled by light, by plastid type and/or by a particular stage of chloroplast development. These data mesh nicely with accumulating evidence that the core sigma-binding regions of plastid promoters mediate regulated transcription in response to light-regime and plastid type or developmental state. In this review I will outline progress made to date in identifying and characterizing the sigma-like factors of plants, and in dissecting their potential roles in chloroplast gene expression.

The carbon metabolism-controlled Synechocystis gap2 gene harbours a conserved enhancer element and a Gram-positive-like -16 promoter box retained in some chloroplast genes

The two glyceraldehyde-3-phosphate dehydrogenase-encoding genes (gap) of Synechocystis were shown to be expressed as monocistronic transcripts. Whereas gap1 expression is slow and weak, gap2 gene induction is rapid and strong. Transcription of the gap2 gene was shown to depend on functional photosynthetic electron transport and on active carbon metabolism. The basal promoter of gap2 (P, -45 to +34, relative to the transcription start site) is controlled by three cis-acting elements designated A (-443 to -45), B (+34 to +50, in the untranslated leader region) and C (+50 to +167, in the coding region) that, together, promote a 100-fold stimulation of P activity. Element B was found to behave as a transcriptional enhancer, in that it was active regardless of its position, orientation and distance relative to P. All three cis-acting stimulatory elements exhibit a common 5'-agaTYAACg-3' nucleotide motif that appears to be conserved in cyanobacteria and may be the target for a transcriptional enhancer. We also report that gap2 transcription depends on a Gram-positive-like -16 promoter box (5'-TRTG-3') that was obviously conserved throughout the evolution of chloroplasts. This is the first report on the occurrence of a -16 promoter element in photoautotrophic organisms.

The multisubunit chloroplast RNA polymerase A from mustard (Sinapis alba L.). Integration of a prokaryotic core into a larger complex with organelle-specific functions

We previously identified two multisubunit plastid RNA polymerases termed A and B. The B enzyme has a bacterial-type polypeptide composition and is sensitive to the prokaryotic transcription inhibitor rifampicin (Rif); the A enzyme has a more complex subunit structure and is Rif-resistant. Here we report results of N-terminal sequencing and MS carried out with the A enzyme, which establish that the latter contains rpo gene products and is structurally related to the B enzyme. Furthermore, evidence is provided that the A enzyme can be converted into a Rif-sensitive enzyme form in a phosphorylation-dependent manner in vitro by a treatment that results in depletion of a beta-like subunit. Database searches using sequence information derived from additional polypeptides that are present in purified A preparations revealed sequence similarity with chloroplast proteins involved in RNA processing and redox control. This proteomics approach thus points to the complexity of the chloroplast transcription apparatus and its interconnections with post-transcriptional and signalling mechanisms.

Subcellular localization and rolling circle replication of peach latent mosaic viroid: hallmarks of group A viroids

We characterized the peach latent mosaic viroid (PLMVd) replication intermediates that accumulate in infected peach leaves and determined the tissue and subcellular localization of the RNA species. Using in situ hybridization, we showed that PLMVd strands of both plus and minus polarities concentrate in the cells forming the palisade parenchyma. At the cellular level, PLMVd was found to accumulate predominantly in chloroplasts. Northern blot analyses demonstrated that PLMVd replicates via a symmetric mode involving the accumulation of both circular and linear monomeric strands of both polarities. No multimeric conformer was detected, indicating that both strands self-cleave efficiently via their hammerhead sequences. Dot blot hybridizations revealed that PLMVd strands of both polarities accumulate equally but that the relative concentrations vary by more than 50-fold between peach cultivars. Taken together these results establish two hallmarks for the classification of viroids. Group A viroids (e.g., PLMVd), which possess hammerhead structures, replicate in the chloroplasts via the symmetric mode. By contrast, group B viroids, which share a conserved central region, replicate in the nucleus via an asymmetric mechanism. This is an important difference between self-cleaving and non-self-cleaving viroids, and the implications for the evolutionary origin and replication are discussed.

Targeted disruption of the plastid RNA polymerase genes rpoA, B and C1: molecular biology, biochemistry and ultrastructure

The plastid encoded RNA polymerase subunit genes rpoA, B and C1 of tobacco were disrupted individually by PEG-mediated plastid transformation. The resulting off-white mutant phenotype is identical for inactivation of the different genes. The mutants pass through a normal ontogenetic cycle including flower formation and production of fertile seeds. Their plastids reveal a poorly developed internal membrane system consisting of large vesicles and, occasionally, flattened membranes, reminiscent of stacked thylakoids. The rpo- material is capable of synthesising pigments and lipids, similar in composition but at lower amounts than the wild-type. Western analysis demonstrates that plastids contain nuclear-coded stroma and thylakoid polypeptides including terminally processed lumenal components of the Sec but not of the DeltapH thylakoid translocation machineries. Components using the latter route accumulate as intermediates. In striking contrast, polypeptides involved in photosynthesis encoded by plastid genes could not be detected by Western analysis, although transcription of plastid genes, including the rrn operon, by the plastid RNA polymerase of nuclear origin is found as expected. Remarkably, ultrastructural, sedimentation and Northern analyses as well as pulse experiments suggest that rpo- plastids contain functional ribosomes. The detection of the plastid-encoded ribosomal protein Rpl2 is consistent with these results. The findings demonstrate that the consequences of rpo gene disruption, and implicitly the integration of the two plastid polymerase types into the entire cellular context, are considerably more complex than presently assumed.

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.

Developmental stage-specific multi-subunit plastid RNA polymerases (PEP) in wheat

Most photosystem I and II plastid genes are transcribed by a plastid encoded Escherichia coli-like RNA polymerase (PEP). In this study, we show that both promoter selectivity and light-dependency of PEP change dramatically during development in wheat leaves. In the leaf tip, psbA and psbD promoter activities are light induced, whilst psbC, psbE and 16S rRNA promoters do not function efficiently irrespective of light conditions. In contrast to the leaf tip, in the basal portion all PEP promoters studied function in the dark as well as the light, except for psbD. Using in vitro transcription, we found that PEP in the illuminated leaf tip can initiate transcription from the -35 destructed psbA promoter, but the -35 element is essential for transcription in the basal portion. There is an extended -10 element in the psbA promoter, recognized by the PEP in the illuminated leaf tip or purified sigma 70-type Escherichia coli RNA polymerase but not by the PEP in the leaf base. These results suggest that during wheat leaf development, PEP in the leaf base that is functional for most PEP promoters even in the dark is replaced by the light-dependent PEP selectively transcribing the psbA and psbD promoters.

Characterization of two chloroplast RNA polymerase sigma factors from Zea mays: photoregulation and differential expression

Two distinct cDNAs encoding putative sigma factors of plastid RNA polymerase were isolated from Zea mays, a C4 plant. The deduced amino acid sequences of both cDNAs possess all four highly conserved domains proposed for recognition of -10 and -35 promoter elements, core complex binding, DNA binding, and melting. These two cDNAs are designated sig1 and sig2. Phylogenetic analysis of available plastid sigma factors indicated that they were probably the descendants of cyanobacterial principal sigma factors. Southern blots probed with sig1 and sig2 revealed that both genes exist in the maize nuclear genome as single-copy genes, but low-stringency hybridization suggested the presence of a multigene family of maize plastid sigma factors. Transcription of sig1 and sig2 is light inducible and tissue specific. Transcripts of sig1 and sig2 were abundant in greening leaf tissues; sig2 (but not sig1) was barely detectable in etiolated leaves and neither was detectable in roots. Immunological studies using a peptide antibody against an epitope in subdomain 2.4 of Sig1 revealed 50-kDa and 60-kDa immunoreactive proteins in maize chloroplasts. Reduced levels of the 60-kDa immunoreactive protein were detected in etioplasts, and no immunoreactive proteins were observed in roots. Collectively, the data suggest that the nuclear genes, sig1 and sig2, may play a role in differential expression of plastid genes during chloroplast biogenesis.

RNA polymerase subunits encoded by the plastid rpo genes are not shared with the nucleus-encoded plastid enzyme

Plastid genes in photosynthetic higher plants are transcribed by at least two RNA polymerases. The plastid rpoA, rpoB, rpoC1, and rpoC2 genes encode subunits of the plastid-encoded plastid RNA polymerase (PEP), an Escherichia coli-like core enzyme. The second enzyme is referred to as the nucleus-encoded plastid RNA polymerase (NEP), since its subunits are assumed to be encoded in the nucleus. Promoters for NEP have been previously characterized in tobacco plants lacking PEP due to targeted deletion of rpoB (encoding the beta-subunit) from the plastid genome. To determine if NEP and PEP share any essential subunits, the rpoA, rpoC1, and rpoC2 genes encoding the PEP alpha-, beta'-, and beta"-subunits were removed by targeted gene deletion from the plastid genome. We report here that deletion of each of these genes yielded photosynthetically defective plants that lack PEP activity while maintaining transcription specificity from NEP promoters. Therefore, rpoA, rpoB, rpoC1, and rpoC2 encode PEP subunits that are not essential components of the NEP transcription machinery. Furthermore, our data indicate that no functional copy of rpoA, rpoB, rpoC1, or rpoC2 that could complement the deleted plastid rpo genes exists outside the plastids.

NUCLEAR CONTROL OF PLASTID AND MITOCHONDRIAL DEVELOPMENT IN HIGHER PLANTS

The nucleus must coordinate organelle biogenesis and function on a cell and tissue-specific basis throughout plant development. The vast majority of plastid and mitochondrial proteins and components involved in organelle biogenesis are encoded by nuclear genes. Molecular characterization of nuclear mutants has illuminated chloroplast development and function. Fewer mutants exist that affect mitochondria, but molecular and biochemical approaches have contributed to a greater understanding of this organelle. Similarities between organelles and prokaryotic regulatory molecules have been found, supporting the prokaryotic origin of chloroplasts and mitochondria. A striking characteristic for both mitochondria and chloroplast is that most regulation is posttranscriptional.

The recombinant product of the Chryptomonas phi plastid gene hlpA is an architectural HU-like protein that promotes the assembly of complex nucleoprotein structures

The HlpA protein which is encoded by the hlpA gene in the plastid genome of the cryptomonad alga Chryptomonas phi is structurally related to the non-sequence-specific DNA-binding and DNA-bending HU family of chromatin-associated proteins. The expression of the HlpA protein complements the mutant phenotype of Bacillus subtilis cells impaired in the Hbsu protein (B. subtilis HU), as measured by the resistance of the cells to methylmethane sulphonate. To analyse the interactions of HlpA with DNA, we expressed the protein in Escherichia coli and purified it to homogeneity. HlpA interacts preferentially with four-way junction DNA or DNA minicircles, when compared with linear DNA, recognising DNA structure. HlpA and E. coli HU display comparable affinities for all types of DNA tested; however, HlpA exhibits a stronger tendency to self-associate in the presence of DNA. Accordingly, HlpA oligomerises more readily than HU in protein crosslinking experiments. In the presence of topoisomerase I, HlpA constrains negative superhelical turns in closed circular plasmid DNA. The HlpA protein mediates the joining of distant recombination sites into a complex nucleoprotein structure, as judged by beta-mediated site-specific recombination. The results presented provide evidence that HlpA is a functional plastid equivalent of nuclear and mitochondrial HMG1-like proteins and bacterial HU proteins.

Chloroplast endoribonuclease p54 involved in RNA 3'-end processing is regulated by phosphorylation and redox state

Chloroplast RNA-binding protein p54 is an endoribonuclease required for 3'end-processing of plastid precursor transcripts. We find that purified p54 can serve as a phosphate acceptor for protein kinases in vitro. Both the processing and RNA-binding activities of p54 are enhanced by phosphorylation and decreased by dephosphorylation. In addition, the enzyme is activated by the oxidized form of glutathione and inhibited by the reduced form, whereas other redox reagents that were tested showed no effect. Kinase treatment of p54 prior to oxidation by glutathione resulted in highest levels of activation, suggesting that phosphorylation and redox state act together to control p54 activity in vitro and possibly also in vivo.