Multiple transcripts of a gene for a leucine-rich repeat receptor kinase from morning glory (Ipomoea nil) originate from different TATA boxes in a tissue-specific manner.

TATA boxes are the most common regulatory elements found in the promoters of eukaryotic genes because they are associated with basal transcription initiation by RNA polymerase II. Often only a single TATA element is found in a given promoter, and tissue-, stage- and/or stimulus-specific expression occurs because the TATA box is associated with other cis -acting elements that enhance or repress transcription. We used software tools for gene analysis to assist in locating potential TATA box(es) in an AT-rich region of the promoter of a gene, inrpk1, which codes for a leucine-rich receptor protein kinase in morning glory (Ipomoea nil). Through the use of RT-PCR and various combinations of forward primers bracketing most of the promoter region we were able to define the 5'-ends of transcripts in this region. The region was then targeted for analysis by RNA Ligase-Mediated-5' Rapid Amplification of cDNA Ends (RLM-5' RACE) to identify the transcript initiation site(s). Positioning of initiation sites with respect to TATA boxes identified by gene analysis tools allowed us to identify three operational TATA elements which regulate basal transcription from this gene. Two TATA boxes were responsible for all of the inrpk1 transcripts found in leaves and cotyledons, and about 25-30% of the transcripts in roots. A third TATA box was involved only in expression in roots and accounted for the remaining 50-70% of root transcripts. RNAs expressed from this element lack two potentially functional upstream AUG codons, and may be translated more efficiently than transcripts originating from the other TATA boxes.

Alternative transcript initiation and novel post-transcriptional processing of a leucine-rich repeat receptor-like protein kinase gene that responds to short-day photoperiodic floral induction in morning glory (Ipomoea nil).

A gene (inrpk1) encoding a putative receptor-like protein kinase was isolated from the Japanese morning glory, Ipo-moea (Pharbitis) nil Roth. cv. Violet. The receptor-like portion of the largest derived polypeptide contains 26 direct leucine-rich repeats (LRRs) in a single block, and the catalytic portion has all the conserved amino acid residues characteristic of Ser/Thr protein kinases. RNA blot analysis detected multiple transcripts in cotyledons. The largest (4.4 kb) transcript encodes the predicted full length polypeptide (INRPK1), whereas a 1.6 kb transcript apparently originates from a secondary transcription initiation site within the gene and potentially encodes a protein kinase identical to INRPK1 but lacking most of the LRRs. Two transcripts (ca. 2.7 and 2.6 kb) are created by alternative 3'-splicing of a large (ca. 1.4-1.5 kb) cryptic intron in the LRR region, creating one transcript (2.6 kb) potentially encoding a small, secretable polypeptide. The larger transcript encoding a polypeptide identical to INRPK1, but lacking 21 LRRs, predominates in vegetative roots. Competitive PCR indicates that inrpk1 mRNA increases 20-fold in cotyledons in response to a previously given single floral-inducing short-day (SD). No differences of this magnitude were detected in any other organs examined from plants similarly treated. This pattern of expression and differential processing suggests a role for inrpk1 in some aspect of SD photoperiodic-induced flowering in morning glory.

Seasonal expression of a dehydrin gene in sibling deciduous and evergreen genotypes of peach (Prunus persica [L.] Batsch).

A cDNA library was created from cold-acclimated bark tissue of peach and selectively probed using an antibody directed against the lysine-rich consensus region of dehydrin proteins. Several clones were thus obtained which had a high degree of sequence similarity to other dehydrin genes. Northern analysis, using clone 5a, indicated that a 1.8 kb transcript was seasonally expressed in sibling deciduous and evergreen genotypes of peach, and also inducible by water deficit in cv. Rio Oso Gem. The evergreen and deciduous genotypes differ significantly in both their ability to cold-acclimate and in the seasonal expression of the dehydrin transcript and protein. In both genotypes, the transcript was maximally expressed during winter and undetectable in May-July. The evergreen genotype (less cold-tolerant), however, displayed transcript accumulation which lagged behind and declined sooner than in the deciduous genotype. Protein expression was similar to transcript expression, however, protein expression in the evergreen genotype lagged considerably behind transcript accumulation in the fall. This indicates that several levels of regulation of dehydrin proteins may exist during cold acclimation. A genomic clone (G10a) was isolated which contained the full-length dehydrin gene, designated ppdhn1. The peach dehydrin gene encodes 472 amino acids with a predicted size of 50,020 Da. The encoded protein (PCA60) contains nine of the lysine-rich repeats characteristic of dehydrins and two DEYGNP motifs at the amino acid terminus. A genomic blot, probed with clone 5a under stringent conditions, indicated that one or two highly homologous genes are present in peach, whereas an additional member was detected under low-stringency conditions. It is suggested that several members of the dehydrin gene family may exist in peach that vary in their relation to ppdhn1.

Photosynthetic Characteristics of Segregates from Hybrids between Flaveria brownii (C4 Like) and Flaveria linearis (C3-C4).

Characteristics related to C4 photosynthesis were studied in reciprocal F1 hybrids and F2 plants from Flaveria brownii (C4 like) and Flaveria linearis (C3-C4). The reciprocal F1 plants differed in 13C/12C ratios of leaves and the percentage of 14C initially incorporated into C4 acids, being more like the pollen parents in these traits. They did not differ in apparent photosynthesis or in O2 inhibition of apparent photosynthesis and differed only slightly in CO2 compensation concentration at 175 [mu]mol quanta m-2 s-1 and 400 mL L-1 O2. The 13C/12C ratios of 78 F2 progeny from the two F1 plants exhibited a normal distribution centered between those of the parents, with a few values slightly higher and lower than the parents. Apparent photosynthesis at 130 [mu]L L-1 CO2 and inhibition of photosynthesis by O2 was nearly normally distributed in the F2 population, but no values for F2 plants approached those for F. brownii (15.4 [mu]mol m-2 s-1 and 7.8%, respectively). Distribution of the CO2 compensation concentration measured at 1000 [mu]mol quanta m-2 s-1 and 400 mL L-1 of O2 in the F2 population was skewed toward F. brownii with 72% of the progeny having values <9 [mu]L of CO2 L-1 compared to 1.5 and 27.2 [mu]L L-1 for F. brownii and F. linearis, respectively. Correlations among traits of F2 plants were low (coefficients of 0.30 to -0.49), indicating that the C4- related traits are not closely linked in segregating populations. Plants in the F2 population selected for high or low apparent photosynthesis at 130 [mu]L of CO2 L-1 (six each) did not rank consistently high or low for 13C/12C ratios, O2 inhibition of apparent photosynthesis, CO2 compensation concentration, or activities of phosphoenolpyruvate carboxylase or NADP-malic enzyme. This study confirms results of earlier work that indicates independent segregation of C4 traits and also shows that the C4-like parental type can be recovered, at least for some characteristics (13C/12C ratio), in segregating populations. Recovery of fully functional C4 plants awaits further experimentation with C4 x C3 or C4 x C3-C4 hybrid plants that produce fertile progeny.

Degree of C(4) Photosynthesis in C(4) and C(3)-C(4)Flaveria Species and Their Hybrids : I. CO(2) Assimilation and Metabolism and Activities of Phosphoenolpyruvate Carboxylase and NADP-Malic Enzyme.

The degree of C(4) photosynthesis was assessed in four hybrids among C(4), C(4)-like, and C(3)-C(4) species in the genus Flaveria using (14)C labeling, CO(2) exchange, (13)C discrimination, and C(4) enzyme activities. The hybrids incorporated from 57 to 88% of the (14)C assimilated in a 10-s exposure into C(4) acids compared with 26% for the C(3)-C(4) species Flaveria linearis, 91% for the C(4) species Flaveria trinervia, and 87% for the C(4)-like Flaveria brownii. Those plants with high percentages of (14)C initially fixed into C(4) acids also metabolized the C(4) acids quickly, and the percentage of (14)C in 3-phosphoglyceric acid plus sugar phosphates increased for at least a 30-s exposure to (12)CO(2). This indicated a high degree of coordination between the carbon accumulation and reduction phases of the C(4) and C(3) cycles. Synthesis and metabolism of C(4) acids by the species and their hybrids were highly and linearly correlated with discrimination against (13)C. The relationship of (13)C discrimination or (14)C metabolism to O(2) inhibition of photosynthesis was curvilinear, changing more rapidly at C(4)-like values of (14)C metabolism and (13)C discrimination. Incorporation of initial (14)C into C(4) acids showed a biphasic increase with increased activities of phosphoenolpyruvate carboxylase and NADP-malic enzyme (steep at low activities), but turnover of C(4) acids was linearly related to NADP-malic enzyme activity. Several other traits were closely related to the in vitro activity of NADP-malic enzyme but not phosphoenolpyruvate carboxylase. The data indicate that the hybrids have variable degrees of C(4) photosynthesis but that the carbon accumulation and reduction portions of the C(4) and C(3) cycles are well coordinated.

Isolation and characterization of cDNA clones for NADP-malic enzyme from leaves of Flaveria: transcript abundance distinguishes C3, C3-C4 and C4 photosynthetic types.

To study the control of enhanced synthesis of enzymes associated with C4 photosynthesis relative to non-C4 plants, we investigated the expression of NADP-malic enzyme (NADP-ME) in different photosynthetic types of Flaveria. Complementary DNA clones encoding NADP-ME were constructed using poly(A)+ RNA from leaves of Flaveria trinervia (C4) and F. linearis (C3-C4) and identified by homology to a cDNA clone (500 bp) encoding NADP-ME from maize (Zea mays L. [39]). The sequence of one clone from each species was determined. The Flaveria clones were 90% homologous over a 564 nucleotide region encoding the carboxy terminal end of the derived polypeptide; sequence similarity to the maize transcript in this region was 71%. Both Flaveria clones detected a 2/3 kb transcript by hybridization to poly(A)+ RNA from expanding leaves of F. trinervia, F. linearis and F. pringlei (C3). The level of transcripts paralleled previously observed NADP-ME activity and abundance differences determined in these species, suggesting that control of the expression of NADP-ME in different photosynthetic types is predominantly at the transcriptional/post-transcriptional level. Southern analysis of genomic DNAs from F. trinervia, F. linearis and F. pringlei indicated a low copy number for this gene in all three species.

Transfer of C(4) Photosynthetic Characters through Hybridization of Flaveria Species.

Transfer of C(4) photosynthetic traits was studied through hybridization of Flaveria trinervia (Spreng.) Mohr (C(4)) and Flaveria brownii A.M. Powell (C(4)-like) with Flaveria linearis Lag. (C(3)-C(4)) and the C(3) species Flaveria pringlei Gandoger (C(3)). Fertility was low, based on irregular chromosome pairing and low pollen stainability, except in F. brownii x F. linearis which had bivalent pairing and 76% stainable pollen. Hybrids had apparent photosynthesis values of 71 to 148% of the midparental means, while the CO(2) compensation concentration was similar to the C(4) or C(4)-like parent, except in hybrids having the C(3) species F. pringlei as a parent. Inhibition of apparent photosynthesis by O(2), and phosphoenolpyruvate carboxylase and NADP-malic enzyme activities and subunit levels in the hybrids were closer to the C(3) or C(3)-C(4) parent. The species F. brownii and F. trinervia were equal in their capacity to transfer reduced O(2) inhibition of AP and CO(2) compensation concentration values to hybrids with F. linearis (C(3)-C(4)), although hybrids with F. trinervia had higher PEPC activity. The O(2) inhibition of AP was correlated with the logarithm of activities of phosphoenolpyruvate carboxylase (r = -0.95) and NADP-malic enzyme (r = -0.87). These results confirm that C(4) traits can be transferred by hybridization of C(3)-C(4) and C(4) or C(4)-like species, with a higher degree of C(4) photosynthesis than exists in C(3)-C(4) species, and at least in F. brownii x F. linearis, fertile progeny are obtained.

Inheritance of c(4) enzymes associated with carbon fixation in flaveria species.

Activities and subunit levels of three C(4) enzymes were determined for F(1) hybrids between C(4) and C(3)-C(4)Flaveria species. For phosphoenolpyruvate carboxylase and pyruvate orthophosphate, dikinase, enzyme amounts in the hybrids were close to the mid-parent means. However, activity and subunit levels of NADP-malic enzyme were approximately one-half the mid-parent mean.

DNA and RNA Levels in Bundle Sheath and Mesophyll Cells of Pearl Millett (Pennisetum americanum).

The DNA content of bundle sheath cells and mesophyll protoplasts from the C(4) plant pearl millet (Pennisetum americanum, Tift 23DB) was determined by microspectrophotometry to be 1.8 to 2.3 and 3.2 to 4.0 picograms/nucleus, respectively. Measurement of RNA by ultraviolet spectroscopy indicated that bundle sheath cells contain twice as much RNA as mesophyll cells.

Floral-specific polypeptides of the Japanese morning glory.

Polypeptides from stems, leaves, sepals, corollas, stamens and pistils of the Japanese morning glory (Ipomoea nil Roth (Pharbitis nil Chois.)) were separated by one- and two-dimensional gel electrophoresis and visualized by silver staining. The majority of polypeptides were expressed in two or more organs, while those specific to only one organ were comparatively rate. Among the polypeptides of the former class were two which appeared to be floral-specific. A 46-kDa (kilodalton) polypeptide was expressed in corollas, stamens and pistils, whereas a 32-kDa polypeptide was observed only in extracts prepared from reproductive organs. Polypeptide spots from the various organs were compared with those from leaves, and it was found that sepals and stems shared 40-50% of their polypeptides with leaves, whereas corollas, stamens and pistils shared 20% or less. The latter organs shared 120 polypeptides or roughly 15% of those identified in the floral extracts. Floralorgan-specific polypeptides comprised nearly 10% of the total floral polypeptides identified.

Photosynthesis of F(1) Hybrids between C(4) and C(3)-C(4) Species of Flaveria.

Photosynthetic characteristics were studied in several F(1) hybrids between C(4) and C(3)-C(4) species of Flaveria. Stable carbon isotope ratios, O(2) inhibition of apparent photosynthesis, and phosphoenolpyruvate carboxylase activities in the hybrids were similar to the means for the parents. Values of CO(2) compensation concentrations were nearer to those of the C(4) parent and apparent photosynthesis was below that of both parents, being only 60 and 74% of that of the lowest (C(3)-C(4)) parent in two experiments. Reductions of CO(2) compensation concentration and O(2) inhibition of apparent photosynthesis as well as increases in carbon isotope ratios and phosphoenolpyruvate carboxylase activities compared to values in C(3)-C(4) species suggest transfer of a limited degree of C(4) photosynthesis to the F(1) hybrids. However, the lower apparent photosynthesis of the hybrids suggests that transfer of C(4) characteristics to non-C(4) species is detrimental unless characteristics associated with C(4) photosynthesis are fully developed. There was a highly significant negative correlation (r = -0.90) between CO(2) compensation concentration and the logarithm of phosphoenolpyruvate carboxylase activity in the parents and hybrids, suggesting involvement of this enzyme in controlling the CO(2) compensation concentration. Although bundle-sheath cells were more developed in leaves of hybrids than in C(3)-C(4) parents, they appeared to contain lower quantities of organelles than those of the C(4) parent. Reduced quantities of organelles in bundle-sheath cells could indicate incomplete compartmentation of partial pathways of the C(4) cycle in the hybrids. This may mean that the reduction of CO(2) compensation and O(2) inhibition of apparent photosynthesis relative to the C(3)-C(4) parents is less dependent on fully developed Kranz anatomy than is increased apparent photosynthesis.

Spontaneous induction of colicin E1 in Escherichia coli strains deficient in both exonucleases I and V.

Colicin E1 synthesis is spontaneously induced in pRSF2124-carrying strains of Escherichia coli deficient in exonucleases I (sbcB) and V (recB recC). In contrast, the specific activity of beta-lactamase, which is also encoded by pRSF2124, is not affected by the absence of these enzymes. These results suggest that colicin E1 induction is specific and does not result either from a significant change in overall plasmid transcription or copy number. Furthermore, the level of spontaneous induction was similar to that obtained with mitomycin C.

Immunological determination of phosphoenolpyruvate carboxylase and the large and small subunits of ribulose 1,5-bisphosphate carboxylase in leaves of the c(4) plant pearl millet.

The light-dependent development of the photosynthetic apparatus in the first leaf of the C(4) plant pearl millet (Pennisetum americanum) was monitored by immunologically determining the concentration of phospho-enolpyruvate carboxylase and ribulose 1,5-bisphosphate carboxylase. A competitive enzyme-linked immunosorbent assay procedure using antibodies to the monomeric subunit of phosphoenolpyruvate carboxylase and the large and small subunit of ribulose 1,5-bisphosphate carboxylase was used to quantitate the amounts of these polypeptides in the first leaf of etiolated seedlings and etiolated seedlings exposed to light for varying periods of time. Phosphoenolpyruvate carboxylase was present in etiolated tissue; however, light stimulated its synthesis nearly 23-fold. Maximum accumulation of phosphoenolpyruvate carboxylase occurred approximately 4 days after etiolated plants were placed in the light. Both the large subunit and the small subunit of ribulose 1,5-bisphosphate carboxylase were present in leaves of etiolated seedlings. Light also stimulated the synthesis of both of these polypeptides, but at different rates. In etiolated leaves there was approximately a 3-fold molar excess of the small subunit to large subunit. Exposure of the etiolated leaves to light resulted in the molar ratio of the large subunit to the small subunit increasing to approximately 0.72. These data indicate that the net synthesis of these two polypeptides is not coordinately regulated at all times.

Exonucleases I, III, and V are required for stability of ColE1-related plasmids in Escherichia coli.

The stability of two ColE1-related plasmids (pRSF2124 and pMB9) was examined in strains of Escherichia coli multiply deficient in exonucleases I (sbcB), III (xthA), or V (recB recC). Any combination of exonuclease I, III, and V deficiency resulted in dramatically decreased stability of both pRSF2124 and pMB9. Inactivation of the RecF pathway by introducing either recF or recJ mutations to the recB recC subcB background resulted in nearly wild-type levels of stability for both plasmids. In contrast, the introduction of uvrD3 uvr-257, uvrE100, or recL152 into the recB21 recC22 sbcB15 strain did not affect plasmid stability. Furthermore, the amount of plasmid DNA recovered from pRSF2124 or pMB9 transformants of a xthA1 sbcB15 strain was strikingly reduced relative to that of a wild-type control. Taken together, these results suggest that some aspect of DNA repair is required for stable maintenance of ColE1-related plasmids in E. coli.

A restriction endonuclease map of the chloroplast genome of pearl millet.

Chloroplast DNA from pearl millet (Pennisetum americanum) was used to construct recombinant plasmids. These plasmids contained 97 kilobase pairs of unique DNA sequences. The chloroplast DNA fragments in these plasmids were mapped with the restriction endonucleases SalI, SphI, XhoI, BglI and HpaI. The technique of overlapping hybridization or chromosome walking was used to orient these DNA fragments on a restriction endonuclease map of the chloroplast genome. The size of the chloroplast DNA from pearl millet was estimated in this fashion to be 127-138 kilobase pairs. Twenty one kilobase pairs of the cloned DNA fragments were represented twice on the genome as inverted repeats. Thus, the recombinant plasmids which were isolated contained approximately 86-93% of the nucleotide sequences in the chloroplast genome of pearl millet. Previously characterized cloned chloroplast DNA sequences from other plants were used as hybridization probes to locate the genes for the large subunit of ribulose 1,5-bisphosphate carboxylase, the ß-coupling factor of ATPase and the 32 kilodalton polypeptide of photo system 11 on the restriction endonuclease map of the pearl millet chloroplast genome.

In vitro coupled transcription-translation of linear DNA fragments in a lysate derived from a recB rna pnp strain of Escherichia coli.

A recB21 derivative (CLB7) of an Escherichia coli rna-19 pnp-7 strain (PR7) was constructed for use in examining the in vitro coupled transcription-translation of linear DNA. The expression of linearized DNAs in CLB7 (recB21 rna-19 pnp-7) lysates was enhanced significantly when compared with expression of the same DNAs in lysates prepared from the PR7 or the original recB21 (CF300) strains. In addition, the endogenous incorporation of [35S]methionine into protein was considerably reduced in CLB7 lysates relative to lysates derived from the original recB21 strain.

Increased expression of a eukaryotic gene in Escherichia coli through stabilization of its messenger RNA.

The expression of a cloned eukaryotic gene [catabolic dehydroquinase (3-dehydroquinate hydro-lyase, EC 4.2.1.10) (qa-2+) from Neurospora crassa] is dramatically increased (as much as 100-fold) in Escherichia coli strains deficient in polynucleotide phosphorylase (pnp) (polynucleotide: orthophosphate nucleotidyltransferase, EC 2.7.7.8) and RNase I (rna). The increased expression is controlled primarily by the absence of polynucleotide phosphorylase and appears to be specific for the eukaryotic gene. No increase in the specific activity of either chromosomal or plasmid-borne prokaryotic genes has been observed. In polynucleotide phosphorylase-deficient strains of E. coli the half-life of plasmid (pVK88, ampr qa-2+)-encoded mRNAs increases from 1.0 to 2.8 min. This increase must be due primarily to stabilization of the aq-2 mRNA because no increase in the half-lives of pBR322 vehicle mRNAs was observed in polynucleotide phosphorylase-deficient strains. These results suggest that there are inherent structural differences between prokaryotic and eukaryotic mRNAs.

Amplification in Escherichia coli of enzymes involved in genetic recombination: construction of hybrid ColE1 plasmids carrying the structural gene for exonuclease I.

Endo-R-HindIII restriction endonuclease fragments obtained from F30 and pMB9 plasmid DNAs were ligated in vitro and used to transform a recB21 recC22 sbcB15 strain of E. coli K-12. The inability of this strain to stably maintain pMB9 alone permitted the isolation of transformants that carried hybrid plasmids containing the sbcB+ allele. These transformants became sensitive to ultraviolet light and recombination defieient and showed a 25-fold increase in the level of exonuclease I activity. The stability of the sbcB hybrid plasmids and their effects on exonuclease I activity have also been determined in wild-type and recA1 genetic backgrounds. The presence of the plasmids results in a 7-fold increase in the level of exonuclease I in a wild-type strain and 15-fold increase in a recA1 strain. The increased activity in the recA1 mutant appears to be a result of increased plasmid stability in this genetic background.