Detection rates and false positive rates for Down's syndrome screening: how precisely can they be estimated and what factors influence their value?

Down's syndrome screening is currently carried out using a combination of biochemical markers measured in maternal serum samples; these include MSAFP, Total hCG, uE3 and Free beta-hCG. Recently a number of papers have compared the effectiveness of different combinations of these markers. Some recommend MSAFP, Total hCG and uE3 (triple test) while others advocate MSAFP and Free beta-hCG (double test). The cases put forward to support these tests rely on estimated detection and false positive rates for the proposed test. A recent paper by Wright used simulation techniques to estimate the effects of sampling error on such error rates. In prospective studies there are two methods commonly used for estimating these rates. We obtain formulae for the standard deviations of these estimates and show that one of them always gives a smaller standard error than the other. We also show that in such studies the accuracy of estimating detection rates and false positive rates depends not only upon the method of calculation but also on the age distribution of pregnant women and the parameters used to calculate patient specific risk. We show that these effects can result in estimation errors of such magnitude that many observed differences in detection rates could be of questionable significance, a conclusion also reached by Wright.

Chromosomal location and expression of the single-copy gene encoding high-mobility-group protein HMG-I/Y in Arabidopsis thaliana

A cDNA encoding the HMG-I/Y protein from Arabidopsis thaliana has been isolated and characterised by nucleotide sequencing. The 903 bp cDNA contains a 612 bp open reading frame encoding a protein of 204 amino acid residues showing homology to HMG-I/Y proteins from other plant species. The protein contains four copies of the 'AT-hook' motif which is involved in binding A/T-rich DNA. Southern blotting showed that the HMG-I/Y gene was present in a single copy in the Arabidopsis genome. The gene was localised to the top of chromosome 1 by RFLP analysis of F8 recombinant inbred lines. Northern blotting showed that the gene was expressed in all organs examined, with the highest expression in flowers and developing siliques.

Azide-sensitive thylakoid membrane insertion of chimeric cytochrome f polypeptides imported by isolated pea chloroplasts

Post-translational integration of cytochrome f into thylakoid membranes was observed after import by isolated pea chloroplasts of a chimeric protein consisting of the presequence of the small subunit of ribulose 1,5-bisphosphate carboxylase fused to the cytochrome f precursor. Import of a similar chimeric protein lacking the C-terminal 33 amino acid residues resulted in a soluble cytochrome f protein in the thylakoid lumen, indicating that the C-terminal region contains a stop-transfer sequence for membrane integration. Azide inhibited the insertion of cytochrome f into the thylakoid membrane, whereas the ionophores nigericin and valinomycin had little effect on membrane insertion. The precursor of the 33 kDa protein, but not the 23 kDa protein, of the photo-system II oxygen-evolving complex inhibited the thylakoid insertion of cytochrome f, suggesting competition for a component of the transport pathway. These experiments suggest that the post-translational insertion of cytochrome f into the thylakoid membrane uses a SecA-dependent pathway.

Chloroplast SRP54 interacts with a specific subset of thylakoid precursor proteins

Signal recognition particles (SRPs) have been identified in organisms as diverse as mycoplasma and mammals; in several cases these SRPs have been shown to play a key role in protein targeting. In each case the recognition of appropriate targeting signals is mediated by SRP subunits related to the 54-kDa protein of mammalian SRP (SRP54). In this study we have characterized the specificity of 54CP, a chloroplast homologue of SRP54 which is located in the chloroplast stroma. We have used a nascent chain cross-linking approach to detect the interactions of 54CP with heterologous endoplasmic reticulum-targeting signals. 54CP functions as a bona fide signal recognition factor which can discriminate between functional and non-functional targeting signals. Using a range of authentic thylakoid precursor proteins we found that 54CP discriminates between thylakoid-targeting signals, interacting with only a subset of protein precursors. Thus, the light-harvesting chlorophyll a/b-binding protein, cytochrome f, and the Rieske FeS protein all showed strong cross-linking products with 54CP. In contrast, no cross-linking to the 23- and 33-kDa proteins of the oxygen-evolving complex were detected. The selectivity of 54CP correlates with the hydrophobicity of the thylakoid-targeting signal and, in the case of light-harvesting chlorophyll a/b-binding protein, with previously determined transport/integration requirements. We propose that 54CP mediates the targeting of a specific subset of precursors to the thylakoid membrane, i.e. those with particularly hydrophobic signal sequences.

High mobility group proteins HMG-1 and HMG-I/Y bind to a positive regulatory region of the pea plastocyanin gene promoter

A 268 bp region (P268) of the pea plastocyanin gene promoter responsible for high-level expression has been shown to interact with the high mobility group proteins HMG-1 and HMG-I/Y isolated from pea shoot chromatin. cDNAs encoding an HMG-1 protein of 154 amino acid residues containing a single HMG-box and a C-terminal acidic tail and an HMG-I/Y-like protein of 197 amino acid residues containing four AT-hooks have been isolated and expressed in Escherichia coli to provide large amounts of full-length proteins. DNase I footprinting identified eight binding sites for HMG-I/Y and six binding sites for HMG-1 in P268. Inhibition of binding by the antibiotic distamycin, which binds in the minor groove of A/T-rich DNA, revealed that HMG-I/Y binding was 400-fold more sensitive than HMG-1 binding. Binding-site selection from a pool of random oligonucleotides indicated that HMG-I/Y binds to oligonucleotides containing stretches of five or more A/T bp and HMG-1 binds preferentially to oligonucleotides enriched in dinucleotides such as TpT and TpG.

Manipulating photosynthesis

The levels of individual photosynthetic proteins can be independently decreased by the Agrobacterium-mediated transformation of plants with antisense RNA constructs. Protocols for the introduction of such constructs into Agrobacterium, the Agrobacterium-mediated transformation of tobacco leaf disks, and the screening and analysis of the transgenic plants produced are described.

The regulation of component processes of photosynthesis in transgenic tobacco with decreased phosphoribulokinase activity

Tobacco plants (Nicotiana tabacum L.) transformed with an inverted cDNA encoding ribulose 5-phosphate kinase (phosphoribulokinase,PRK; EC 2.7.1.19) were employed to study the in vivo relationship between photosynthetic electron transport and the partitioning of electron transport products to major carbon metabolism sinks under conditions of elevated ATP concentrations and limited ribulose 1,5-bisphosphate (RuBP) regeneration. Simultaneous measurements of room temperature chlorophyll fluorescence and CO2 gas exchange were conducted on intact leaves. Under ambient CO2 concentrations and light intensities above those at which the plants were grown, transformants with only 5% of PRK activity showed 'down-regulation" of PS II activity and electron transport in response to a decrease in net carbon assimilation when compared to wild-type. This was manifested as a decline in the efficiency of PS II electron transport (ΦPS II), an increase in dissipation of excess absorbed light in the antennae of PS II and a decline in: total linear electron transport (J1), electron transport dedicated to carbon assimilation (JA) and electron transport allocated to photorespiration (JL). The transformants showed no alteration in the Rubisco specificity factor measured in vitro and calculated in vivo but had a relatively smaller ratio of RuBP oxygenation to carboxylation rates (vo/vc), due to a higher CO2 concentration at the carboxylation site (Cc). The relationship between ΦPS II and ΦCO 2was similar in transformants and wild-type under photorespiratory conditions demonstrating no change in the intrinsic relationship between PS II function and carbon assimilation, however, a novel result of this study is that this similar relationship occurred at different values of quantum flux, J1, JA, JL and vo/vc in the transformant. For both wild-type and transformants, an assessment was made of the possible presence of a third major sink for electron transport products, beside RuBP oxygenation and carboxylation, the data provided no evidence for such a sink.

The sequence surrounding the translation initiation codon of the pea plastocyanin gene increases translational efficiency of a reporter gene

The 5'-upstream region of the pea plastocyanin gene (petE) directed 5-10-fold higher levels of beta-glucuronidase (GUS) activity than the cauliflower mosaic virus 35S promoter in transgenic tobacco plants, although the levels of GUS mRNA were similar. The sequence (AAAAAUGG) around the translation initiation codon of petE enhanced translation of the GUS mRNA 10-fold compared to translation from the GUS translation initiation codon in transgenic tobacco plants and transfected protoplasts.

The N-terminal hydrophobic region of the mature phosphate translocator is sufficient for targeting to the chloroplast inner envelope membrane

To locate the sequence required for directing the phosphate translocator to the chloroplast inner envelope membrane, a series of chimeric proteins constituting parts of the phosphate translocator and the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, which is normally located in the stroma, has been produced. Reciprocal exchanges of the presequences and mature sequences of the phosphate translocator and the small subunit indicated that the phosphate translocator presequence contains stromal targeting information and that the mature protein is responsible for inner envelope membrane targeting. Chimeric proteins containing the N-terminal 46 amino acid residues of the phosphate translocator were directed to the inner envelope membrane. Subdivision of this region into its composite hydrophilic and hydrophobic regions showed that the hydrophobic region alone, which consists of amino acid residues 24 to 45, was able to direct the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase to the inner envelope membrane.

Protein translocation across chloroplast envelope membranes

Nuclear-encoded chloroplast proteins are imported from the cytosol into the chloroplast stroma by a common translocation machinery. Several components of the import apparatus, including GTP-binding proteins and Hsp70 proteins, have recently been identified and characterized. This review discusses the role of these proteins in chloroplast protein import.

Developmental, circadian and light regulation of wheat ferredoxin gene expression

A genomic clone encoding the precursor of wheat leaf ferredoxin has been isolated and characterised. The uninterrupted PetF gene encodes a polypeptide of 143 amino acid residues, consisting of an N-terminal presequence of 46 amino acid residues and a mature polypeptide of 97 amino acid residues. Southern blot analysis suggests that six copies of the PetF gene are present in the wheat haploid genome. Northern blot analysis has shown that the genes are both developmentally and light regulated in wheat seedlings and provides evidence that a circadian rhythm regulates the steady-state levels of ferredoxin transcripts. The intact wheat gene and several chimeric constructs, containing portions of the 5'-upstream region fused to the beta-glucuronidase reporter gene, have been introduced into tobacco plants, but levels of beta-glucuronidase activity above background were not detected, suggesting that the 5'-upstream region is unable to function as a promoter in tobacco plants.

HMG protein binding to an A/T-rich positive regulatory region of the pea plastocyanin gene promoter

Gel retardation assays using pea nuclear extracts have detected specific binding to regions of the promoter of the pea plastocyanin gene (petE). Several complexes which differ in sensitivity to competition with unlabelled promoter fragments and various DNA alternating copolymers, to heat treatment and to digestion with proteinase K have been detected. A protein factor, PCF1, forming one of these complexes was heat-stable and most sensitive to competition with poly(dAdT).poly(dAdT) compared to other alternating copolymers. DNase I footprinting assays showed that tracts of A/T-rich sequence within the -444 to -177 positive regulatory region of the petE promoter were protected in the presence of the pea nuclear extract. The factor PCF1 copurified with a high-mobility-group (HMG) protein preparation from pea chromatin. DNase I footprinting with the HMG protein preparation demonstrated that similar tracts of A/T-rich sequences within the promoter were protected. Southwestern-blot analysis of pea HMG proteins purified by gel filtration through Superose 12 detected a single DNA-binding species of 21 kDa. The properties of the factor PCF1 suggest that it is likely to be an HMG I protein.

Proteolytic removal of the C-terminal transmembrane region of cytochrome f during extraction from turnip and charlock leaves generates a water-soluble monomeric form of the protein

Water-soluble, monomeric cytochrome f purified from leaves of turnip (Brassica rapa) and charlock (Sinapis arvensis) is approximately 3 kDa smaller than the protein in chloroplast thylakoid membranes determined by SDS/PAGE. Sequencing the N-terminal and C-terminal regions of the monomeric protein, by automated Edman degradation and carboxypeptidase P digestion, suggested the loss of 33 amino acid residues at the C-terminus by comparison to sequences of cytochrome f from other higher plants. This was confirmed by the isolation and nucleotide sequencing of the turnip petA gene and by determination of the molecular mass of the monomeric turnip protein by electrospray mass spectrometry. The turnip petA gene encodes a protein of 320 amino acid residues consisting of a presequence of 35 amino acid residues and a mature protein of 285 amino acid residues. The molecular mass of the monomeric turnip protein was 28,160.2 +/- 5.4 Da, indicating cleavage after Gln252 of the mature protein. Electrospray mass spectrometry of the monomeric charlock protein indicated the presence of two main forms with molecular masses of 28,135.1 +/- 5.5 Da and 27,750.7 +/- 4.3 Da corresponding to cleavage after Gln252 and Leu249, respectively. Cleavage in this region of the cytochrome f polypeptide during extraction with butanone removes the single transmembrane span of the protein and liberates the water-soluble globular domain of cytochrome f.

The thylakoid-targeting domain of the chloroplast Rieske iron-sulfur protein is located in the N-terminal hydrophobic region of the mature protein

The thylakoid-targeting domain of the Rieske FeS protein has been located in the N-terminal 55 amino acids of the mature protein by importing chimeric and truncated precursor proteins into isolated pea chloroplasts. A chimeric protein consisting of the presequence of ribulose-bisphosphate carboxylase/oxygenase (Rubisco) small subunit fused to the mature Rieske protein sequence was imported by chloroplasts, processed in the stroma, and translocated into the thylakoids, indicating that the thylakoid-targeting information was located within the mature Rieske protein. A truncated Rieske protein precursor consisting of the presequence and the N-terminal 55 amino acids of the mature protein was imported by chloroplasts and routed to the thylakoids, indicating that the thylakoid-targeting domain of the Rieske protein is located within the predominantly hydrophobic N-terminal region of the mature protein. Chimeric proteins consisting of this truncated Rieske protein precursor fused to the mature Rubisco small subunit and to plastocyanin were efficiently imported by chloroplasts and translocated across the thylakoid membrane. A proton-motive force was necessary for thylakoid translocation of the mature Rieske protein, the truncated Rieske protein, and the fusion protein consisting of the truncated Rieske protein and the mature Rubisco small subunit. In contrast, plastocyanin and the fusion of the truncated Rieske protein with plastocyanin were translocated across the thylakoid membrane in the presence of nigericin and valinomycin, indicating that the energy requirement for thylakoid translocation was conferred by the passenger protein and not by the thylakoid-targeting sequence.

Expression of genes encoding the tobacco chloroplast phosphate translocator is not light-regulated and is repressed by sucrose

A cDNA encoding the complete precursor of the phosphate translocator of the chloroplast inner envelope membrane has been isolated from a tobacco leaf (Nicotiana tabacum cv. Samsun) lambda gt 11 library. The tobacco cDNA is 1546 bp in length and encodes a precursor protein of 401 amino acid residues with a deduced molecular weight of 43705. A putative processing site between Ala-73 and Ala-74 of the precursor protein is suggested by comparison with the N-terminal sequences of the pea and spinach proteins. Removal of the transit peptide produces the mature protein of 328 amino acid residues with a molecular weight of 36038. Southern blot analysis suggests there is probably one copy of the phosphate translocator gene in the pea haploid genome and two copies in the tobacco haploid genome, one derived from each ancestral parental genome. Messenger RNAs essentially equivalent in size to the cDNAs (approx. 1.6 kb) were detected in extracts of all organs examined from tobacco and pea, including leaves, stems, sepals, petals, seed-pods, tendrils and roots. An immunochemically related protein of a similar size to the phosphate translocator was detected in the equivalent pea organs. The levels of both mRNA and protein in non-photosynthetic organs were lower than those in photosynthetic organs. Tobacco phosphate translocator mRNA was present at high levels in etiolated tissue and did not increase significantly after 24 h illumination. Germination and growth of tobacco seedlings in the presence of sucrose caused a 3.3-fold decrease in the level of the phosphate translocator mRNA.

The pea plastocyanin promoter directs cell-specific but not full light-regulated expression in transgenic tobacco plants

A series of 5' deletions of the pea plastocyanin gene (petE) promoter fused to the beta-glucuronidase (GUS) reporter gene has been examined for expression in transgenic tobacco plants. Strong positive and negative cis-elements which modulate quantitative expression of the transgene in the light and the dark have been detected within the petE promoter. Disruption of a negative regulatory element at -784 bp produced the strongest photosynthesis-gene promoter so far described. Histochemical analysis demonstrated that all petE-GUS constructs directed expression in chloroplast-containing cells, and that a region from -176 bp to +4 bp from the translation start site was sufficient for such cell-specific expression. The petE-promoter fusions were expressed at high levels in etiolated transgenic tobacco seedlings but there was no marked induction of GUS activity in the light. The endogenous tobacco plastocyanin genes and the complete pea plastocyanin gene in transgenic tobacco plants were also expressed in the dark, but showed a three- to sevenfold increase in the light. This indicates a requirement for sequences 3' to the promoter for the full light response of the petE gene.

Cytochrome f: Structure, function and biosynthesis

Cytochrome f is an intrinsic membrane component of the cytochrome bf complex, transferring electrons from the Rieske FeS protein to plastocyanin in the thylakoid lumen. The protein is held in the thylakoid membrane by a single transmembrane span located near its C-terminus with a globular hydrophilic domain extending into the lumen. The globular domain of the turnip protein has recently been crystallised, offering the prospect of a detailed three-dimensional structure. Reaction with plastocyanin involves localised positive charges on cytochrome f interacting with the acidic patch on plastocyanin and electron transfer via the surface-exposed tyrosine residue (Tyr83) of plastocyanin. Apocytochrome f is encoded in the chloroplast genome and is synthesised with an N-terminal presequence which targets the protein to the thylakoid membrane. The synthesis of cytochrome f is coordinated with the synthesis of the other subunits of the cytochrome bf complex.

Import and processing of the precursor of the delta subunit of tobacco chloroplast ATP synthase

A cDNA clone encoding the complete precursor of the delta subunit of chloroplast ATP synthase has been isolated from a tobacco (Nicotiana tabacum) leaf cDNA library in lambda gt11. The 880 bp insert encodes a polypeptide of 248 amino acid residues, of which 61 residues constitute an N-terminal presequence and 187 residues make up the mature delta subunit. Transcription and translation of the cDNA in vitro produced a protein of 29 kDa which was imported by isolated pea chloroplasts and processed to the mature 20 kDa subunit. The delta subunit precursor was processed to the mature size by a processing peptidase present in pea stromal extracts. Hybridisation of the cDNA to Southern blots of tobacco genomic DNA suggests the presence of two genes in the haploid genome.

Import and processing of the precursor of the Rieske FeS protein of tobacco chloroplasts

cDNA clones encoding the precursor of the Rieske FeS protein of tobacco chloroplasts have been characterised and shown to derive from two different genes. The 5' ends of the corresponding transcripts have been cloned using primer extension and PCR. The nucleotide sequences of the cDNAs (and their 5' extensions) predict precursors for the tobacco proteins which differ in 4 amino acid residues out of a total of 228 residues and show high homology with the pea and spinach precursors. The tobacco precursor proteins contain N-terminal presequences of 49 amino acid residues which lack 17 amino acid residues present at the N-terminus of the spinach presequence. The 26 kDa precursor obtained by transcription and translation of one of these cDNAs in vitro was efficiently imported and correctly processed to the mature 20 kDa protein by isolated pea or tobacco chloroplasts. The precursor was also processed to its mature size by a peptidase present in the stroma of chloroplasts.

Import and processing of the precursor form of the gamma subunit of the chloroplast ATP synthase from tobacco

A cDNA clone encoding the complete precursor of the gamma subunit of chloroplast ATP synthase has been isolated from a tobacco (Nicotiana tabacum) leaf cDNA library in lambda gt11. The 1.4 kb insert encodes a polypeptide of 377 amino acid residues, of which 55 residues constitute an N-terminal presequence and 322 residues make up the mature gamma subunit. Hybridisation of the cDNA to Southern blots of tobacco genomic DNA indicates the presence of two genes in the haploid genome. Transcription and translation of the cDNA in vitro produced a protein of 41 kDa which was imported by isolated pea chloroplasts and processed to the mature 36 kDa subunit. The gamma subunit precursor was processed to the mature size by a processing peptidase of 180 kDa present in pea stromal extracts.

The surface-exposed tyrosine residue Tyr83 of pea plastocyanin is involved in both binding and electron transfer reactions with cytochrome f

Site-directed mutants of the pea plastocyanin gene in which the codon for the surface-exposed Tyr83 has been changed to codons for Phe83 and Leu83 have been expressed in transgenic tobacco plants. The mutant proteins have been purified to homogeneity and their conformations shown not to differ significantly from the wild-type plastocyanin by 1H-NMR and CD. Overall rate constants for electron transfer (k2) from cytochrome f to plastocyanin have been measured by stopped-flow spectrophotometry and rate constants for binding (ka) and association constants (KA) have been measured from the enhanced Soret absorption of cytochrome f on binding plastocyanin. These measurements allow the calculation of the intrinsic rate of electron transfer in the binary complex. An 8-fold decrease in the overall rate of electron transfer to the Phe83 mutant is due entirely to a decreased association constant for cytochrome f, whereas the 40-fold decrease in the overall rate of electron transfer to the Leu83 mutant is due to weaker binding and a lower intrinsic rate of electron transfer. This indicates that Tyr83 is involved in binding to cytochrome f and forms part of the main route of electron transfer.

A scaffold-associated DNA region is located downstream of the pea plastocyanin gene

Chromosomal scaffold-associated DNA has been isolated from pea leaf nuclei treated with lithium diiodosalicylate to remove histones and then digested with restriction enzymes to remove the DNA in chromosomal loops. A scaffold-associated region (SAR) of DNA has been identified 8 to 9 kb downstream of the single-copy pea plastocyanin gene in proximity to a repetitive sequence present in 300 copies in the pea haploid genome. Isolated restriction fragments from within the SAR can bind to scaffold preparations in a binding assay in vitro. The nucleotide sequence of the SAR indicates a 540-bp 77% A+T-rich region containing many sequence elements in common with SARs from other organisms. Sequences with homology to topoisomerase II binding sites, A-box and T-box sequences, and replication origins are present within this AT-rich region.