Embracing polygenicity: a review of methods and tools for psychiatric genetics research

The availability of genome-wide genetic data on hundreds of thousands of people has led to an equally rapid growth in methodologies available to analyse these data. While the motivation for undertaking genome-wide association studies (GWAS) is identification of genetic markers associated with complex traits, once generated these data can be used for many other analyses. GWAS have demonstrated that complex traits exhibit a highly polygenic genetic architecture, often with shared genetic risk factors across traits. New methods to analyse data from GWAS are increasingly being used to address a diverse set of questions about the aetiology of complex traits and diseases, including psychiatric disorders. Here, we give an overview of some of these methods and present examples of how they have contributed to our understanding of psychiatric disorders. We consider: (i) estimation of the extent of genetic influence on traits, (ii) uncovering of shared genetic control between traits, (iii) predictions of genetic risk for individuals, (iv) uncovering of causal relationships between traits, (v) identifying causal single-nucleotide polymorphisms and genes or (vi) the detection of genetic heterogeneity. This classification helps organise the large number of recently developed methods, although some could be placed in more than one category. While some methods require GWAS data on individual people, others simply use GWAS summary statistics data, allowing novel well-powered analyses to be conducted at a low computational burden.

Influence of a nonaqueous phase liquid (NAPL) on biodegradation of phenanthrene

A series of batch reactor experiments was carried out to examine the effect of a nonaqueous phase liquid (NAPL) on the biodegradation of a hydrophobic solute. A mathematical program model that describes physical processes of solute solubilization and partitioning between the NAPL and aqueous phases as well as microbial degradation and oxygen utilization was used to analyze the test data. The model calculates the cumulative changes in concentration of substrate, cell mass, carbon dioxide, and dissolved oxygen as a function of time. The equations incorporate the effects of solute solubilization, partitioning, biodegradation, as well as oxygen availability. Hexadecane was used as the model NAPL and was not biodegraded in the timeframe of the experiments performed. The model solute was the polyaromatic hydrocarbon, phenanthrene. In agreement with several previous studies, experimental measurements showed that hexadecane increased rates of mineralization of 15 mg phenanthrene when present at low mass but decreased rates at high mass. Model results suggest that partitioning of the phenanthrene into the hexadecane phase limits bioavailability at high NAPL mass. Further the model suggests that mineralization rates were higher with the low NAPL mass because aqueous phenanthrene concentrations were higher in those treatments from ca. 20 to 40 h than in other treatments. Finally, experiments showed that the presence of hexadecane, at all masses tested, resulted in a lower cell yield, effectively increasing the amount of CO(2) produced during the experiment. Model results suggest that this is due to changes in phenanthrene metabolism that are induced by the presence of the hexadecane phase. Model studies aimed at increasing rates of biodegradation by modifying operating conditions are described along with practical approaches to implementing these modifications.

C-to-U conversion in the intercistronic ndhI/ ndhG RNA of plastids from monocot plants: conventional editing in an unconventional small reading frame?

Editing of plastid RNAs proceeds by C-to-U, in hornwort species also by extensive U-to-C, transitions, which predominantly lead to the restoration of codons for structurally and/or functionally important, conserved amino acid residues. So far, only one instance of editing outside coding regions has been reported - in the psbL/ psbF intergenic region of Ginkgo biloba. This site was proposed to have no functional importance. Here we present an evaluation of an editing site in the ndhI/ ndhG intergenic region in a related group of monocot plants. Efficient editing of this site, as well as the phylogenetic conservation of the resulting uridine residue, point at an important role for the sequence restored by editing. Two potential functions can be envisaged. (1) RNA secondary structure predictions suggest that the C-to-U conversion at this site can lead to a modified stem/loop structure of the ndhG 5' UTR, which could influence ndhG expression. (2) Alternatively, editing of the ndhI/ ndhG intergenic region may tag a so far unidentified small (12-codon) ORF, and lead to the restoration of a conserved phenylalanine codon. A screen with specific antibodies elicited against the putative peptide failed to detect such a peptide in chloroplast fractions. However, this failure may be attributable to its low and/or development-specific expression.

Remediation of metal-contaminated soil and sludge using biosurfactant technology

Development of environmentally benign approaches to remediation of metal-contaminated soils and sewage sludges are needed to replace currently used techniques of either landfilling or metal extraction using caustic or toxic agents. We report results from four application technologies that use a metal-chelating biosurfactant, rhamnolipid, for removal of metals or metal-associated toxicity from metal-contaminated waste. The four applications include: 1) removal of metals from sewage sludge; 2) removal of metals from historically contaminated soils; 3) combined biosurfactant/phytoremediation of metal-contaminated soil; and 4) use of biosurfactant to facilitate biodegradation of the organic component of a metal-organic co-contaminated soil (in this case the biosurfactant reduces metal toxicity). These four technologies are nondestructive options for situations where the final goal is the removal of bioavailable and leachable metal contamination while maintaining a healthy ecosystem. Some of the approaches outlined may require multiple treatments or long treatment times which must be acceptable to site land-use plans and to the stakeholders involved. However, the end-product is a soil, sediment, or sludge available for a broad range of land use applications.

Biodegradation during contaminant transport in porous media: 4. Impact of microbial lag and bacterial cell growth

Miscible-displacement experiments were conducted to examine the impact of microbial lag and bacterial cell growth on the transport of salicylate, a model hydrocarbon compound. The impacts of these processes were examined separately, as well as jointly, to determine their relative effects on biodegradation dynamics. For each experiment, a column was packed with porous medium that was first inoculated with bacteria that contained the NAH plasmid encoding genes for the degradation of naphthalene and salicylate, and then subjected to a step input of salicylate solution. The transport behavior of salicylate was non-steady for all cases examined, and was clearly influenced by a delay (lag) in the onset of biodegradation. This microbial lag, which was consistent with the results of batch experiments, is attributed to the induction and synthesis of the enzymes required for biodegradation of salicylate. The effect of microbial lag on salicylate transport was eliminated by exposing the column to two successive pulses of salicylate, thereby allowing the cells to acclimate to the carbon source during the first pulse. Elimination of microbial lag effects allowed the impact of bacterial growth on salicylate transport to be quantified, which was accomplished by determining a cell mass balance. Conversely, the impact of microbial lag was further investigated by performing a similar double-pulse experiment under no-growth conditions. Significant cell elution was observed and quantified for all conditions/systems. The results of these experiments allowed us to differentiate the effects associated with microbial lag and growth, two coupled processes whose impacts on the biodegradation and transport of contaminants can be difficult to distinguish.

RNA editing in higher plant plastids: oligoribonucleotide SSCP analysis allows the proof of base conversion directly at the RNA level

Plastid RNA editing of a number of transcripts at specific sites changes genomically encoded cytidines to nucleosides, which act like uridines in RT-PCR analyses. To study plastid-editing directly at the RNA level, we established a single-strand conformational polymorphism assay for the discrimination of small RNA molecules. The electrophoretic mobility of a oligoribonucleotide resulting from a RNase T1-digested and edited plastid mRNA was shown to be identical with a control RNA molecule containing a uridine at the editing site, whereas the unedited RNA behaved like a RNA molecule containing a cytidine at the respective position.

Stability constants for the complexation of various metals with a rhamnolipid biosurfactant

The presence of toxic metals in natural environments presents a potential health hazard for humans. Metal contaminants in these environments are usually tightly bound to colloidal particles and organic matter. This represents a major constraint to their removal using currently available in situ remediation technologies. One technique that has shown potential for facilitated metal removal from soil is treatment with an anionic microbial surfactant, rhamnolipid. Successful application of rhamnolipid in metal removal requires knowledge of the rhamnolipid-metal complexation reaction. Therefore, our objective was to evaluate the biosurfactant complexation affinity for the most common natural soil and water cations and for various metal contaminants. The conditional stability constant (log K) for each of these metals was determined using an ion-exchange resin technique. Results show the measured stability constants follow the order (from strongest to weakest): Al3+ > Cu2+ > Pb2+ > Cd2+ > Zn2+ > Fe3+ > Hg2+ > Ca2+ > Co2+ > Ni2+ > Mn2+ > Mg2+ > K+. These data indicate that rhamnolipid will preferentially complex metal contaminants such as lead, cadmium, and mercury in the presence of common soil or water cations. The measured rhamnolipid-metal stability constants were found in most cases to be similar or higher than conditional stability constants reported in the literature for metal complexation with acetic acid, oxalic acid, citric acid, and fulvic acids. These results help delineate the conditions under which rhamnolipid may be successfully applied as a remediation agent in the removal of metal contaminants from soil, as well as surface waters, ground water, and wastestreams.

Biosurfactant-enhanced solubilization of NAPL mixtures

Remediation of nonaqueous phase liquids (NAPLs) by conventional pump-and-treat methods (i.e., water flushing) is generally considered to be ineffective due to low water solubilities of NAPLs and to mass-transfer constraints. Chemical flushing techniques, such as surfactant flushing, can greatly improve NAPL remediation primarily by increasing the apparent solubility of NAPL contaminants. NAPLs at hazardous waste sites are often complex mixtures. However, the equilibrium and nonequilibrium mass-transfer characteristics between NAPL mixtures and aqueous surfactant solutions are not well understood. This research investigates the equilibrium solubilization behavior of two- and three-component NAPL mixtures (containing akylbenzenes) in biosurfactant solutions. NAPL solubilization is found to be ideal in water (i.e., obeys Raoult's Law), while solubilization in biosurfactant solutions was observed to be nonideal. Specifically, the relatively hydrophobic compounds in the mixture experienced solubility enhancements that were greater than those predicted by ideal enhanced solubilization theory, while the solubility enhancements for the relatively hydrophilic compounds were less than predicted. The degree of nonideality is shown to be a nonlinear function of the NAPL-phase mole fraction. Empirical relationships based on the NAPL-phase mole fraction and/or micelle-aqueous partition coefficients measured in single-component NAPL systems are developed to estimate values for the multicomponent partition coefficients. Empirical relationships that incorporate both the NAPL-phase mole fraction and single-component partition coefficients yield much improved estimates for the multicomponent partition coefficient.

The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization

The chloroplast chromosome of spinach (Spinacia oleracea) is a double-stranded circular DNA molecule of 150,725 nucleotide pairs. A comparison of this chromosome with those of the three other autotrophic dicotyledons for which complete DNA sequences of plastid chromosomes are available confirms a conserved overall structure. Three classes of open reading frames were distinguished: (1) genes of known function which include 108 unique loci, (2) three hypothetical chloroplast reading frames (ycfs) that are highly conserved interspecifically, and (3) species-specific or rapidly diverging 'open reading frames'. A detailed transcript study of one of the latter (ycf15) shows that these loci may be transcribed, but do not constitute protein-coding genes.

Pseudomonas aeruginosa rhamnolipids: biosynthesis and potential applications

Pseudomonas aeruginosa produces and secretes rhamnose-containing glycolipid biosurfactants called rhamnolipids. This review describes rhamnolipid biosynthesis and potential industrial and environmental applications of rhamnolipids. Rhamnolipid production is dependent on central metabolic pathways, such as fatty acid synthesis and dTDP-activated sugars, as well as on enzymes participating in the production of the exopolysaccharide alginate. Synthesis of these surfactants is regulated by a very complex genetic regulatory system that also controls different P. aeruginosa virulence-associated traits. Rhamnolipids have several potential industrial and environmental applications including the production of fine chemicals, the characterization of surfaces and surface coatings, as additives for environmental remediation, and as a biological control agent. Realization of this wide variety of applications requires economical commercial-scale production of rhamnolipids.

A rhamnolipid biosurfactant reduces cadmium toxicity during naphthalene biodegradation

A model cocontaminated system was developed to determine whether a metal-complexing biosurfactant, rhamnolipid, could reduce metal toxicity to allow enhanced organic biodegradation by a Burkholderia sp. isolated from soil. Rhamnolipid eliminated cadmium toxicity when added at a 10-fold greater concentration than cadmium (890 microM), reduced toxicity when added at an equimolar concentration (89 microM), and had no effect at a 10-fold smaller concentration (8.9 microM). The mechanism by which rhamnolipid reduces metal toxicity may involve a combination of rhamnolipid complexation of cadmium and rhamnolipid interaction with the cell surface to alter cadmium uptake.

Rhamnolipid-induced removal of lipopolysaccharide from Pseudomonas aeruginosa: effect on cell surface properties and interaction with hydrophobic substrates

Little is known about the interaction of biosurfactants with bacterial cells. Recent work in the area of biodegradation suggests that there are two mechanisms by which biosurfactants enhance the biodegradation of slightly soluble organic compounds. First, biosurfactants can solubilize hydrophobic compounds within micelle structures, effectively increasing the apparent aqueous solubility of the organic compound and its availability for uptake by a cell. Second, biosurfactants can cause the cell surface to become more hydrophobic, thereby increasing the association of the cell with the slightly soluble substrate. Since the second mechanism requires very low levels of added biosurfactant, it is the more intriguing of the two mechanisms from the perspective of enhancing the biodegradation process. This is because, in practical terms, addition of low levels of biosurfactants will be more cost-effective for bioremediation. To successfully optimize the use of biosurfactants in the bioremediation process, their effect on cell surfaces must be understood. We report here that rhamnolipid biosurfactant causes the cell surface of Pseudomonas spp. to become hydrophobic through release of lipopolysaccharide (LPS). In this study, two Pseudomonas aeruginosa strains were grown on glucose and hexadecane to investigate the chemical and structural changes that occur in the presence of a rhamnolipid biosurfactant. Results showed that rhamnolipids caused an overall loss in cellular fatty acid content. Loss of fatty acids was due to release of LPS from the outer membrane, as demonstrated by 2-keto-3-deoxyoctonic acid and sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis and further confirmed by scanning electron microscopy. The amount of LPS loss was found to be dependent on rhamnolipid concentration, but significant loss occurred even at concentrations less than the critical micelle concentration. We conclude that rhamnolipid-induced LPS release is the probable mechanism of enhanced cell surface hydrophobicity.

Disruption of plastid-encoded RNA polymerase genes in tobacco: expression of only a distinct set of genes is not based on selective transcription of the plastid chromosome

Plastids of higher plants operate with at least two distinct DNA-dependent RNA polymerases, which are encoded in the organelle (PEP) and in the nucleus (NEP), respectively. Plastid run-on assays and Northern analyses were employed to analyse gene expression in tobacco mutant plastids lacking the PEP genes rpoA, rpoB or rpoC1. Hybridisation of run-on transcripts to restriction fragments representing the entire tobacco plastid chromosome, as well as to selected plastid gene-specific probes, shows that all parts of the plastid DNA are transcribed in rpo-deficient plastids. In comparison to wild-type chloroplasts, which are characterized by preferential transcription of photosynthesis-related genes in the light, mutant plastids exhibit a different transcription pattern with less pronounced differences in the hybridisation intensities between the individual genes. The analysis of steady-state transcript patterns and transcription rates of selected genes in both types of plastids demonstrates that differences in transcription rates are not necessarily paralleled by corresponding changes in transcript levels. The accumulation of large transcripts in the mutant plastids indicates that processing of primary transcripts may be impaired in the absence of PEP. These data suggest that, contrary to the prevailing view, much of the regulation of NEP-driven plastid gene expression in the rpo-deficient mutants is not based on differential promoter usage but is exerted at post-transcriptional levels.

Complete nucleotide sequence of the Oenothera elata plastid chromosome, representing plastome I of the five distinguishable euoenothera plastomes

We describe the 159,443-bp [corrected] sequence of the plastid chromosome of Oenothera elata (evening primrose). The Oe. elata plastid chromosome represents type I of the five genetically distinguishable basic plastomes found in the subsection Euoenothera. The genus Oenothera provides an ideal system in which to address fundamental questions regarding the functional integration of the compartmentalised genetic system characteristic of the eukaryotic cell. Its highly developed taxonomy and genetics, together with a favourable combination of features in its genetic structure (interspecific fertility, stable heterozygous progeny, biparental transmission of organelles, and the phenomenon of complex heterozygosity), allow facile exchanges of nuclei, plastids and mitochondria, as well as individual chromosome pairs, between species. The resulting hybrids or cybrids are usually viable and fertile, but can display various forms of developmental disturbance.

Development of an agar lift-DNA/DNA hybridization technique for use in visualization of the spatial distribution of Eubacteria on soil surfaces

While microbial growth is well-understood in pure culture systems, less is known about growth in intact soil systems. The objective of this work was to develop a technique to allow visualization of the two-dimensional spatial distribution of bacterial growth on a homogenous soil surface. This technique is a two-step process wherein an agar lift is taken and analyzed using a universal gene probe. An agar lift is comprised of a thin layer of soil that is removed from a soil surface using an agar slab. The agar is incubated to allow for microbial growth, after which, colonies are transferred to a membrane for conventional bacterial colony DNA/DNA hybridization analysis. In this study, a eubacterial specific probe was used to demonstrate that growing bacterial populations on soil surfaces could be visualized. Results show that microbial growth and distribution was nonuniform across the soil surface. Spot supplementation of the soil with benzoate or glucose resulted in a localized microbial growth response. Since only growing colonies are detected, this technique should facilitate a greater understanding of the microbial distribution and its response to substrate addition in more heterogenous soil systems.

Factors influencing expression of luxCDABE and nah genes in Pseudomonas putida RB1353(NAH7, pUTK9) in dynamic systems

Bioluminescent reporter organisms have been successfully exploited as analytical tools for in situ determination of bioavailable levels of contaminants in static environmental samples. Continued characterization and development of such reporter systems is needed to extend the application of these bioreporters to in situ monitoring of degradation in dynamic environmental systems. In this study, the naphthalene-degrading, lux bioreporter bacterium Pseudomonas putida RB1353 was used to evaluate the relative influences of cell growth stage, cell density, substrate concentration, oxygen tension, and background carbon substrates on both the magnitude of the light response and the rate of salicylate disappearance. The effect of these variables on the lag time required to obtain maximum luminescence and degradation was also monitored. Strong correlations were observed between the first three factors and both the magnitude and induction time of luminescence and degradation rate. The maximum luminescence response to nonspecific background carbon substrates (soil extract broth or Luria broth) was 50% lower than that generated in response to 1 mg of sodium salicylate liter(-1). Oxygen tension was evaluated over the range of 0.5 to 40 mg liter(-1), with parallel inhibition to luminescence and degradation rate (20 mg of sodium salicylate liter(-1)) observed at 1.5 mg liter(-1) and below and no effect observed above 5 mg liter(-1). Oxygen tensions from 2 to 4 mg liter(-1) influenced the magnitude of luminescence but not the salicylate degradation rate. The results suggest that factors causing parallel shifts in the magnitude of both luminescence and degradation rate were influencing regulation of the nah operon promoters. For factors that cause nonparallel shifts, other regulatory mechanisms are explored. This study demonstrates that lux reporter bacteria can be used to monitor both substrate concentration and metabolic response in dynamic systems. However, each lux reporter system and application will require characterization and calibration.

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.

A promiscuous chloroplast DNA fragment is transcribed in plant mitochondria but the encoded RNA is not edited

The RNA editing processes in chloroplasts and mitochondira of higher plants show several similarities which are suggestive of common components and/or biochemical steps between the two plant organelles. The existence of various promiscuous DNA fragments of chloroplast origin in plant mitochondrial genomes allowed us to test the possibility that chloroplast sequences are also edited in mitochondria. An rpoB fragment transferred from chloroplasts to mitochondria in rice was chosen as it contains several editing sites, two of which match sequence motifs surrounding even non-homologous editing sites in both chloroplast and mitochondrial transcripts. Rice chloroplast and mitochondrial rpoB DNA and cDNA sequences were selectively amplified and the editing status of the cDNA sequences was determined. Three of the four potential rpoB editing sites previously detected in maize were found to be edited in the rice chloroplast rpoB transcript, whereas the fourth was found to remain unedited. In mitochondria, however, all four editing sites remain unmodified at the cDNA level. This indicates that the editing processes of higher plant mitochondria and chloroplasts are not identical and that organelle-specific factors are required for eliciting the respective editing events.

Editing of the chloroplast ndhB encoded transcript shows divergence between closely related members of the grass family (Poaceae)

The ndhB-encoded transcript from barley chloroplasts deviates from the genomic ndhB sequence by nine C-to-U transitions, which is the maximum number of editing events for a chloroplast mRNA reported so far. Comparison with ndhB transcripts from other chloroplast species shows that six of the nine editing sites observed in barley are structurally and functionally conserved in maize, rice and tobacco. The remaining three sites, however, show divergent patterns of conservation even within the three members of the grass family. The conservation of two of these sites in tobacco but not in the closely related graminean species suggests that divergence of the ndhB editing sites is caused by the loss of preexisting editing sites rather than by gain of new sites.

Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing

The nucleotide sequence of the chloroplast (cp) DNA from maize (Zea mays) has been completed. The circular double-stranded DNA, which consists of 140,387 base-pairs, contains a pair of inverted repeat regions (IRA and IRB) with 22,748 base-pairs each, which are separated by a small and a large single copy region (SSC and LSC) of 12,536 and 82,355 base-pairs, respectively. The gene content and the relative positions of a total of 104 genes (70 peptide-encoding genes, 30 tRNA genes and four rRNA genes) are identical with the chloroplast DNA of the closely related species rice (Oryza sativa). A detailed analysis of the two graminean plastomes allows the identification of hotspots of divergence which predominate in one region containing a cluster of tRNA genes and in two regions containing degenerated reading frames. One of these length differences is thought to reflect a gene transfer event from the plastome to the nucleus, which is followed by progressive degradation of the respective chloroplast gene resulting in gene fragments. The other divergent plastome region seems to be due to the complete loss of a plastid gene and its functional substitution by a nuclear encoded eukaryotic homologue. The rate of neutral nucleotide substitutions is significantly reduced for protein coding genes located in the inverted repeat regions. This indicates that the existence of inverted repeat regions confers increased genetic stability of the genes positioned in these regions as compared to genes located in the two single copy regions. Editing events cause the primary structures of several transcripts to deviate from the corresponding genomic sequences by C to U transitions. The unambiguous deduction of amino acid sequences from the nucleotide sequences of the corresponding genes is, therefore, not possible. A survey of the 25 editing positions identified in 13 different transcripts of the maize plastome shows that representatives of all protein coding gene classes are subject to editing. A strong bias exists for the second codon position and for certain codon transitions. Based on the number and the codon transition types, and taking into account the frequency of putative editing sites in all peptide encoding genes and unidentified reading frames, a total number of only few more than the experimentally verified 25 editing sites encoded in the maize plastome is estimated. This corresponds to 0.13% of amino acid positions which cannot be derived from the corresponding codons present in the corresponding genes.

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

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

The role of RNA editing in conservation of start codons in chloroplast genomes

Open reading frames (ORFs), encoded by the plastid genomes of tobacco, liverwort, rice and maize were aligned with a view to studying the conservation of translational start and stop codons created by RNA editing of homologous genes. It became evident that most of the homologous ORFs have conserved translation start and stop signals at the gene level. However, some of the ORFs show differences with respect to extensions of their 3' and 5' terminal regions. For example, the proposed N-termini of the ndhD-encoded peptides from different plant species are very variable in length and amino-acid composition. Sequence analysis of ndhD and the corresponding cDNA shows that editing of an ACG triplet in tobacco, spinach and snapdragon leads to the creation of an AUG codon, corresponding to the start codon in other species. Conservation of translational start codons of plastome-encoded genes can, therefore, be achieved by editing of transcripts, and the definition of plastome-encoded ORFs must take potential editing events into consideration.

RNA editing in maize chloroplasts is a processing step independent of splicing and cleavage to monocistronic mRNAs

The psbB operon contained in the plastomes of higher plants consists of the genes psbB, psbH, petB and petD. The primary transcript of this operon is subject to a series of processing steps which include cleavages resulting in four monocistronic mRNAs and splicing of the petB and petD transcripts. A search for editing sites within the two latter transcripts from maize led us to the detection of one editing site within the petB coding region which is conserved at the DNA level in other graminean species and in tobacco. This shows that editing must be considered as an additional processing step of the psbB operon encoded primary transcript. As is evident from cDNA sequences derived from the dicistronic and/or unspliced petB/D transcripts which are completely edited, editing is an early step of mRNA processing which precedes both splicing and cleavage to the monocistronic mRNAs and which must, therefore, be independent of the latter two steps. This conclusion is confirmed by a similar observation with the editing site of the rpl2 transcript which is contained in the polycistronic transcript of the rpoA operon, although here only partial editing is observed for the unspliced dicistronic rpl23/rpl2 transcript.

Identification of editing positions in the ndhB transcript from maize chloroplasts reveals sequence similarities between editing sites of chloroplasts and plant mitochondria

A comparison of the nucleotide sequences from genomic DNA and cDNA of the ndhB gene from maize chloroplasts shows that the ndhB transcript is edited by C-to-U transitions at six positions which appear to exist as editing sites also in the chloroplast ndhB genes from rice and tobacco but not from liverwort. In order to identify possible sequence determinants necessary for editing, the sequences surrounding the newly identified ndhB and previously identified ndhA editing sites were compared with each other and with editing sites observed in plant mitochondrial transcripts. Among the chloroplast editing sites two closely positioned ndhB sites show similarity by sharing a common octanucleotide. The existence of the identical octanucleotide in the ndhJ gene whose transcript is not edited at the respective position, shows, however, that this octanucleotide is not sufficient to elicit the editing process. On the other hand, several of the chloroplast editing sites show sequence similarities with certain sets of consensus sequences reported earlier for editing sites of plant mitochondria. This supports the view that the editing processes of both plant organelles share common components and/or mechanistic steps and that the consensus sequences are part of the determinants necessary for editing.

Internal editing of the maize chloroplast ndhA transcript restores codons for conserved amino acids

The NADH dehydrogenase subunit A (ndhA) gene from maize chloroplasts encodes a highly conserved peptide, which at several positions could be restored to consensus sequences by potential C-to-U editing of the codons involved. This gene was, therefore, chosen for analysis of its mRNA sequence in the form of amplified cDNA. A comparison of this cDNA sequence with the plastome-encoded ndhA sequence reveals four C-to-U editing sites, thereby demonstrating as a novel finding that chloroplast editing can also affect internal mRNA positions. All the edited codons restore amino acids that are conserved in the ndhA-encoded peptides of other chloroplast species. Alignment with homologous mitochondrial NADH-ubiquinone reductase subunit 1 (nad1) sequences of plant and even nonplant species shows that two of the editing positions restore universally conserved amino acids and that one editing site is even shared with nad1 mRNA of plant mitochondria. No editing sites could be detected in the cDNA derived from transcripts of the maize chloroplast RNA polymerase alpha-subunit (rpoA) gene.

Editing of a chloroplast mRNA by creation of an initiation codon

Primary mRNA transcripts in several systems are edited by single base substitutions, small deletions or insertions to yield functional messenger RNA species. Mitochondrial mRNAs in particular, including those from plants, seem to be the subject of extensive editing, unlike mRNAs encoded by chloroplast DNA, for which the prediction of amino-acid sequence from the corresponding gene sequence is generally unambiguous. Occasionally, however, an ACG codon appears at the 5' terminus of chloroplast genes, where the initiation codon ATG would be expected. Here we present evidence for a C----U editing that is responsible for the conversion of the ACG codon to an AUG initiation codon in the mRNA transcript from the rpl2 gene of the maize plastome, showing that mRNA editing can also occur in chloroplasts.

The ndhH genes of gramminean plastomes are linked with the junctions between small single copy and inverted repeat regions

The junctions JSA and JSB between the two inverted repeat regions IRA and IRB and the small single copy region of the maize chloroplast DNA have been identified by DNA sequencing. The JSA junction coincides with the initiation codon of the ndhH gene which is encoded by the adjacent region of the small single copy region. A comparison with the plastomes of rice, rye, tobacco and liverwort shows that linkage of this junction with the ndhH gene is specific for gramminean species. The amino acid sequences deduced from the ndhH genes show conserved histidine and cysteine residues which are likely to form a metal-binding domain.