Cis-acting elements essential for light regulation of the nuclear gene encoding the A subunit of chloroplast glyceraldehyde 3-phosphate dehydrogenase in Arabidopsis thaliana

We report the characterization of cis-acting elements involved in light regulation of the nuclear gene (GapA) that encodes the A subunit of glyceraldehyde 3-phosphate dehydrogenase in Arabidopsis thaliana. Our previous deletion analyses indicate that the -277 to -195 upstream region of GapA is essential for light induction of the beta-glucuronidase reporter gene in transgenic tobacco (Nicotiana tabacum) plants. This region contains three direct repeats with the consensus sequence 5'-CAAATGAA(A/G)A-3' (Gap boxes). Our results show that 2-bp substitutions of the last four nucleotides (AA or GA) of the Gap boxes by CC abolish light induction of the beta-glucuronidase reporter gene in vivo and affect binding of the Gap box binding factor in vitro. We have also identified an additional cis-acting element, AE (Activation Element) box, that is involved in regulation of GapA. A combination of a Gap box trimer and an AE box dimer can confer light responsiveness of the cauliflower mosaic virus 35S promoter containing the -92 to +6 upstream sequence, whereas oligomers of Gap boxes or AE boxes alone cannot confer light responsiveness on the same promoter. These results suggest that Gap boxes and AE boxes function together as the light-responsive element of GapA.

Computed tomography in the diagnosis of organic bowel obstruction

BACKGROUND

This study examined the usefulness of computed tomography (CT) scan for cases of organic intestinal obstruction, with two simple criteria.

METHODS

One hundred and thirteen patients with clinical suspicion of bowel obstruction were referred for CT scans. A line was drawn between the dilated proximal, and the collapsed distal bowels. A careful search was conducted on this line for obstructive lesions. The results were reported to be organic obstruction if there was an abrupt change of caliber (Criterion I) or a soft tissue mass around the dilated bowel (Criterion II). The judgement based on the CT findings.

RESULTS

Eighty-eight cases proved to have bowel obstruction. With Criterion I, the sensitivity was 59.1%, and specificity, 88% with Criterion II, the sensitivity was 56.3% and specificity 100%. If either of them was considered to be a positive sign of organic obstruction, the sensitivity was 100%, the specificity 88% and the accuracy 97.3%. The nature of the obstructions were precisely predicted in 76 patients (86%).

CONCLUSIONS

With these two simple criteria, CT scan can achieve high accuracy and is a recommendation in virtually every instance when intestinal obstruction is suspected.

Effects of light and chloroplast functional state on expression of nuclear genes encoding chloroplast glyceraldehyde-3-phosphate dehydrogenase in long hypocotyl (hy) mutants and wild-type Arabidopsis thaliana

In a previous study of Arabidopsis thaliana (J. Dewdney, T.R. Conley, M.-C. Shih, H.M. Goodman [1993] Plant Physiol 103: 1115-1121), it was postulated that both blue light receptor- and phytochrome-mediated pathways contribute to regulation of the nuclear genes encoding A and B subunits of glyceraldehyde-3-phosphate dehydrogenase (GAPA and GAPB). Here were report on the involvement of a nuclear gene encoding a putative blue-light receptor (HY4) and of a nuclear gene encoding phytochrome A apoprotein (PHYA) in regulation of the GAPA and GAPB genes in response to blue and far-red light. Continuous light irradiation experiments with the hy4 mutant demonstrate that the HY4 gene product is required for full expression of GAPA, GAPB, and one or more of the nuclear genes encoding small subunits of of ribulose-1,5-bisphosphate carboxylase/oxygenase. Continuous light irradiation and fluence-response studies with the phyA-101 mutant show that phytochrome A functions in far-red light regulation of GAPA, GAPB, nuclear genes encoding small subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase, and CAB genes. Phytochromes A and B alone either do not participate in red light-mediated gene regulation or have redundant functions, as shown by analysis of phyA-101 and phyB-1 single mutants. In addition, the hypothesis that chloroplast-nucleus interactions affect GAPA and GAPB gene regulation was tested. Herbicide-mediated photooxidative damage to chloroplasts in A thaliana seedlings strongly decreased the maximum amount of GAPA and GAPB steady-state mRNA detected in continuous-light irradiation experiments. Full expression of the GAPB genes is dependent on the presence of functional chloroplasts.

A rapid method to study the relationship between IDDM and HLA-DQ beta 57 Asp

We have developed a rapid and simple method to detect the relation between HLA-DQ beta 57 Asp and Chinese IDDM patients. The method involved the selective amplification of a DNA fragment from the HLA-DQ B1 gene by using the mutagenic primers. After PCR, if the HLA-DQ beta 57 was Asp, then there was an artificially created restriction enzyme cutting site. We then can accurately obtain the results by enzyme digestion and electrophoresis. Sixty-nine IDDM patients and 30 nondiabetic control subjects were analyzed using this method. Twenty-two (42%) IDDM patients had non-Asp 57 homozygous, 31/45%) were Asp/non-Asp 57 heterozygous, and 9 (13%) had Asp-57 homozygous. Of the 30 control subjects, the number of cases for these three types were 6 (20%), 18 (60%), and 6 (20%), respectively. The relative risk of homozygous DQ beta 57 non-Asp in our group was 2.9 and the p value was greater than 0.05. Using this kind of approach, we were able to provide a simple, rapid, and non-radioactive method to detect whether the HLA DQ beta 57 was Asp or not.

Identification of a light-responsive region of the nuclear gene encoding the B subunit of chloroplast glyceraldehyde 3-phosphate dehydrogenase from Arabidopsis thaliana

We report here the identification of a cis-acting region involved in light regulation of the nuclear gene (GapB) encoding the B subunit of chloroplast glyceraldehyde 3-phosphate dehydrogenase from Arabidopsis thaliana. Our results show that a 664-bp GapB promoter fragment is sufficient to confer light induction and organ-specific expression of the Escherichia coli beta-glucuronidase reporter gene (Gus) in transgenic tobacco (Nicotiana tabacum) plants. Deletion analysis indicates that the -261 to -173 upstream region of the GapB gene is essential for light induction. This region contains four direct repeats with the consensus sequence 5'-ATGAA(A/G)A-3' (Gap boxes). Deletion of all four repeats abolishes light induction completely. In addition, we have linked a 109-bp (-263 to -152) GapB upstream fragment containing the four direct repeats in two orientations to the -92 to +6 upstream sequence of the cauliflower mosaic virus 35S basal promoter. The resulting chimeric promoters are able to confer light induction and to enhance leaf-specific expression of the Gus reporter gene in transgenic tobacco plants. Based on these results we conclude that Gap boxes are essential for light regulation and organ-specific expression of the GapB gene in A. thaliana. Using gel mobility shift assays we have also identified a nuclear factor from tobacco that interacts with GapA and GapB DNA fragments containing these Gap boxes. Competition assays indicate that Gap boxes are the binding sites for this factor. Although this binding activity is present in nuclear extracts from leaves and roots of light-grown or dark-treated tobacco plants, the activity is less abundant in nuclear extracts prepared from leaves of dark-treated plants or from roots of greenhouse-grown plants. In addition, our data show that this binding factor is distinct from the GT-1 factor, which binds to Box II and Box III within the light-responsive element of the RbcS-3A gene of pea.

Characterization of cis-acting elements in light regulation of the nuclear gene encoding the A subunit of chloroplast isozymes of glyceraldehyde-3-phosphate dehydrogenase from Arabidopsis thaliana

We have characterized cis-acting elements involved in light regulation of the nuclear gene (GapA) encoding the A subunit of chloroplast glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in Arabidopsis thaliana. Our results show that a 1.1-kb promoter fragment of the GapA gene is sufficient to confer light inducibility and organ specificity in transgenic Nicotiana tabacum (tobacco) plants, using the beta-glucuronidase gene of Escherichia coli as the reporter gene. Deletion analysis indicates that the -359 to -110 bp region of the GapA gene is necessary for light responsiveness. Within this region there are three copies of a decamer repeat (termed the Gap box) having the consensus sequence 5'-CAAATGAA(A/G)A-3', which has not been characterized in the promoter regions of other light-regulated genes. A deletion (to -247) producing loss of one copy of these elements from the GapA promoter reduces light induction by two- to threefold compared with a promoter deletion (to -359) with all three Gap boxes present, while deletion of all three Gap boxes (to -110) abolishes light induction completely. Gel mobility shift experiments using tobacco nuclei as the source of nuclear proteins show that GapA promoter fragments that contain these repeats bind strongly to a factor in the nuclear extract and that binding can be abolished by synthetic competitors consisting only of a monomer or dimer of the Gap box. Furthermore, a trimer, dimer, and monomer of the Gap box show binding activity and, like the authentic GapA promoter-derived probes, show binding activities that are correlated with Gap box copy number. These results strongly suggest that these repeats play important roles in light regulation of the GapA gene of A. thaliana.

Effects of blue and red light on expression of nuclear genes encoding chloroplast glyceraldehyde-3-phosphate dehydrogenase of Arabidopsis thaliana

We have characterized the effects of different light spectra on expression of the nuclear genes (GapA and GapB) encoding chloroplast glyceraldehyde-3-phosphate dehydrogenase in Arabidopsis thaliana. Steady-state mRNA levels for both genes in etiolated seedlings increased after a short exposure to red or blue light. However, these increases could not be reversed by immediate far-red light following the initial light treatment. In mature plants, a short light pulse, regardless of its spectrum, had no apparent effect on GapA or GapB mRNA levels in dark-adapted plants. In contrast, continuous exposure to red, blue, or white light resulted in increases of GapA and GapB mRNA levels, with blue and white light being far more efficient than red light. Similarly, continuous exposure of etiolated seedlings to red, blue, or white light also resulted in increased GapA and GapB mRNA levels. In addition, we show that illumination of red light-saturated Arabidopsis plants with continuous blue light results in further increases of GapA and GapB mRNA levels. Based on these results, we conclude that both blue light photoreceptor- and phytochrome-mediated pathways are involved in light regulation of GapA and GapB genes in Arabidopsis, with blue light acting as the dominant regulator.

Stress responses and metabolic regulation of glyceraldehyde-3-phosphate dehydrogenase genes in Arabidopsis

We report here effects of three environmental conditions, heat shock, anaerobic treatment, and carbon source supply, on expression of nuclear genes encoding chloroplast (GapA and GapB) and cytosolic (GapC) glyceraldehyde-3-phosphate dehydrogenase from Arabidopsis thaliana. The steady-state mRNA level of the GapC increased when Arabidopsis plants were transferred from normal growth condition to heat-shock, anaerobiosis, or increased sucrose supply conditions. In contrast, the steady-state mRNA levels for GapA and GapB genes were unaffected or decreased transiently under the same treatments. To identify the cis-acting regulatory elements, transgenic tobacco plants containing a 820-bp GapC 5'-flanking DNA fragment and beta-glucuronidase (Gus) fusion were constructed. Analyses of these transgenic plants indicate that this 820-bp DNA fragment is sufficient to confer both heat-shock and anaerobic responses. These results suggest that transcriptional level control is involved in regulation of GapC expression under these stress conditions. Histochemical analysis of Gus activity indicates that expression of the GapC is cell-type specific and is probably linked to the metabolic activity of the cells.

Cloning and chromosomal mapping of nuclear genes encoding chloroplast and cytosolic glyceraldehyde-3-phosphate-dehydrogenase from Arabidopsis thaliana

Both cDNA and genomic clones for the nuclear genes encoding chloroplast (cp) (gapA and gapB) and cytosolic (gapC) glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Arabidopsis thaliana have been isolated and characterized. Genomic Southern-blot analyses indicate that there is only one copy of each gapA, gapB and gapC gene in A. thaliana. Comparison of the deduced amino acid (aa) sequences shows that the A and B subunits are highly similar (80% positional aa identity), while there is less similarity between the cp and cytosolic subunits (45% aa identity). These relationships are consistent with the idea that the cp and cytosolic GAPDHs evolved from different lineages, as suggested in our previous study of tobacco GAPDHs [Shih et al., Cell 47 (1986) 73-80]. In addition, the chromosomal locations for the three gap genes were determined by restriction fragment length polymorphism mapping; the three gap genes are not closely linked, gapA (55.8 cM) and gapC (0.0 cM) are on chromosome 3, and gapB (51.3 cM) is on chromosome 1.

Quantitative analysis of low molecular weight polar compounds by continuous flow liquid secondary ion tandem mass spectrometry

Quantitative analyses of low molecular weight (100-200) polar compounds [1-methyl-4-phenylpyridine (MPP+), 2-amino-3-(methylamino)propanoic acid (synonyms, beta-(methyl-amino)-L-alanine or BMAA), and tryptophan] were conducted on a triple-stage quadrupole mass spectrometer configured for continuous flow liquid secondary ion mass spectrometry ionization (CF L-SIMS). It is shown that quantification by CF L-SIMS at subnanogram sensitivity can be precise (correlation coefficients greater than 0.99), accurate, specific, and routine for compounds not measurable by static L-SIMS. Successful analyses, however, are strongly dependent upon the stability of the film formed by the mobile phase on the probe tip. In our system, film stability is affected by mobile phase composition and flow rate, ion source and probe tip temperature, probe-tip and capillary alignment, film thickness, and sample composition.

Intron existence predated the divergence of eukaryotes and prokaryotes

Nucleotide sequences for the nuclear genes encoding chloroplast (GapA and GapB) and cytosolic (GapC) glyceraldehyde-3-phosphate dehydrogenases (GAPDHs) from Arabidopsis thaliana were determined. Comparison of nucleotide sequences indicates that the divergence of chloroplast and cytosolic GAPDH genes preceded the divergence of prokaryotes and eukaryotes. In addition, some intron-exon junctions are conserved among GapB, GapC, and chicken GAPDH genes. These results provide evidence at the molecular level to support the idea that introns existed before the divergence of prokaryotes and eukaryotes.

Differential light regulated expression of nuclear genes encoding chloroplast and cytosolic glyceraldehyde-3-phosphate dehydrogenase in Nicotiana tabacum

When tobacco (Nicotiana tabacum) plants were transferred from the dark to continuous white light, the steady-state mRNA levels transcribed from the nuclear genes encoding chloroplast (GapA and GapB) glyceraldehyde-3-phosphate dehydrogenase increased at least 30- to 50-fold, while the mRNA level for the cytosolic enzyme (GapC) increased only 10-fold. Kinetic analyses show that the rates of mRNA accumulation for GapA and GapB are identical reaching steady-state levels after 24-48 h in light. In contrast, mRNA accumulation for the GapC gene shows a completely different kinetic pattern, accumulating much faster than that of GapA and GapB. These results suggest that expression of GapC and GapA/B genes are controlled by different light regulated mechanisms and nuclear run-on analyses suggest that these effects are primarily due to increased transcription.

Melatonin secretion in humans assessed by measuring its metabolite, 6-sulfatoxymelatonin

Comparing a direct radioimmunoassay for 6-sulfatoxymelatonin (aMT6s) with an established gas chromatographic/mass spectrometric method for 6-hydroxymelatonin, we found a good correlation r = 0.94 (P less than 0.001, n = 100). aMT6s was stable, both in urine and plasma samples, without preservative, for at least two years at -20 degrees C and for five days at room temperature. Urinary excretion of aMT6s showed considerable inter-individual differences; however, the aMT6s excretion of any one individual was consistent over a four-day period, as assessed by continuous collection from 18 normal volunteers. Total 24-h urinary excretion of aMT6s was significantly correlated with the area under the curve of the respective profiles for plasma melatonin (r = 0.75, P = 0.0002) and plasma aMT6s (r = 0.70, P = 0.0005) for 22 healthy volunteers. At 24:00 h and 03:00 h, sampling plasma at 30-s intervals provided no evidence for episodic secretion (in short pulses) of either melatonin or aMT6s.

Evidence in favor of the symbiotic origin of chloroplasts: primary structure and evolution of tobacco glyceraldehyde-3-phosphate dehydrogenases

We report nucleotide sequences of cDNAs for the nuclear genes encoding chloroplast (GapA and GapB) and cytosolic (GapC) glyceraldehyde-3-phosphate dehydrogenases (GAPDH) from N. tabacum. Comparison of nucleotide sequences indicates that the GapA and GapB genes evolved following duplication of an ancestral gene about 450 million years ago. However, the divergence of GapA/B and GapC occurred much earlier in evolution than the divergence of GapC and GAPDH genes of animals and fungi, suggesting that chloroplast and cytosolic GAPDHs evolved from different lineages. Comparison of amino acid sequences shows that the chloroplast GAPDHs are related to GAPDHs found in thermophilic bacteria, while the cytosolic GAPDH is related to the GAPDH found in mesophilic prokaryotes. These results strongly support the symbiotic origin of chloroplasts.

Quantification of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine and 1-methyl-4-phenylpyridinium ion in brain tissue by gas chromatography/mass spectrometry

A sensitive gas chromatographic/mass spectrometric assay has been developed to quantify 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and 1-methyl-4-phenylpyridinium ion (MPP+) in brain tissue. MPTP was derivatized with isobutyl chloroformate and then analyzed using gas chromatography/mass spectrometry. MPP+, a known metabolite of MPTP, was reduced with NaB2H4 to 2H2-MPTP before derivatization. Deuterated isotopomers of MPTP and MPP+ were used as internal standards. The intra-assay coefficients of variation in the determination of 57.3 ng MPTP and 371.8 ng MPP+ in 100 mg of mouse brain tissue were 3.0% and 5.6% (n = 7), respectively. The detection limit corresponds to about 2 ng per sample of authentic MPTP.

Mutations that alter the DNA binding site for the bacteriophage lambda cII protein and affect the translation efficiency of the cII gene

The efficiency of translation of the cII gene of bacteriophage lambda is greatly reduced by the cII3059 mutation, a GUU----GAU (Val----Asp) change in the second cII codon. Mutations in the third and fourth codons of the cII gene, called ctr mutations, reverse this translation deficiency. Lambda cII3059 ctr-1, which has a GCA----ACA (Ala----Thr) change in the fourth cII codon, produces about half the normal level of cII activity in liquid cultures, and lambda cII3059 ctr-2 and lambda cII3059 ctr-3, which have identical CGT----CGC changes in the third codon, produce normal levels of cII activity in liquid culture. Since the cII protein of ctr-3 has the same primary sequence as that of lambda cII3059, the cII- phenotype of lambda cII3059 can be explained entirely by the deficiency of translating cII mRNA. We propose that ctr mutations increase translation efficiency by destabilizing a stable stem structure which can be formed by cII mRNA. The ctr mutations lie in an overlapping regulatory region which contains, in addition to sequence elements that influence the rate of cII translation, a region to which cII protein binds to activate transcription from the PRE promoter. The ctr-1 mutation alters the cII recognition sequence from 5'-T-T-G-C-N6T-T-G-C-3' to 5'-T-T-G-C-N6T-T-G-T-3', but has no effect on PRE activity. Since a C----T change in the first (5'-proximal) T-T-G-C sequence (to yield 5'-T-T-G-T-N6T-T-G-C) greatly lowers cII binding affinity, cII protein must not recognize the two T-T-G-C sequences in an identical manner.

Kinetic analysis of mutations affecting the cII activation site at the PRE promoter of bacteriophage lambda

Abortive initiation and run-off transcription assays were used to study the effects of cy mutations on activation of the phage lambda PRE promoter by cII gene product. Six point mutations in the repeated T-T-G-C sequences that flank the -35 consensus region of PRE decreased the apparent affinity of the promoter for cII protein by factors of 4-16 relative to the wild-type affinity. Kinetic analyses of transcription initiation in the presence and absence of cII protein demonstrated that five of the six mutations did not significantly affect the intrinsic interaction of RNA polymerase with PRE. Thus, these mutations differ from other cy mutations, including those in the -35 consensus region, which affect the formation of polymerase-PRE closed complexes or the isomerization of closed complexes to open complexes but do not affect the binding of cII protein. A sixth T-T-G-C mutation, cy3001, may affect intrinsic initiation by RNA polymerase as well as cII binding.

Role of cII protein in stimulating transcription initiation at the lambda PRE promoter. Enhanced formation and stabilization of open complexes

Abortive and productive initiation assays were used to study transcription initiation at the PRE promoter of phage lambda in vitro. Two parameters were measured: k2, the rate constant for the transition between closed and open complexes; and KB, the equilibrium constant for the initial binding of RNA polymerase to promoter DNA. In the absence of cII protein (which activates PRE) the PRE promoter was extremely weak as expected, with k2 = 4.0 X 10(-4) S-1 and KB = 1.0 X 10(7) M-1. The addition of cII protein resulted in about a 15-fold increase in KB and a 40-fold increase in k2. Thus, cII activation of PRE results both in enhanced binding of RNA polymerase to DNA to form closed complexes and in an enchanced rate of isomerization of closed to open complexes. In addition, we found that open complexes formed in the presence of cII protein were at least four times as stable as those formed in its absence. This suggests that RNA polymerase and cII protein may remain in close contact even after complexes are formed.