Imprinted gene alterations in the kidneys of growth restricted offspring may be mediated by a long non-coding RNA

Altered epigenetic mechanisms have been previously reported in growth restricted offspring whose mothers experienced environmental insults during pregnancy in both human and rodent studies. We previously reported changes in the expression of the DNA methyltransferase Dnmt3a and the imprinted genes Cdkn1c (Cyclin-dependent kinase inhibitor 1C) and Kcnq1 (Potassium voltage-gated channel subfamily Q member 1) in the kidney tissue of growth restricted rats whose mothers had uteroplacental insufficiency induced on day 18 of gestation, at both embryonic day 20 (E20) and postnatal day 1 (PN1). To determine the mechanisms responsible for changes in the expression of these imprinted genes, we investigated DNA methylation of KvDMR1, an imprinting control region (ICR) that includes the promoter of the antisense long non-coding RNA Kcnq1ot1 (Kcnq1 opposite strand/antisense transcript 1). Kcnq1ot1 expression decreased by 51% in growth restricted offspring compared to sham at PN1. Interestingly, there was a negative correlation between Kcnq1ot1 and Kcnq1 in the E20 growth restricted group (Spearman's ρ = 0.014). No correlation was observed between Kcnq1ot1 and Cdkn1c expression in either group at any time point. Additionally, there was a 11.25% decrease in the methylation level at one CpG site within KvDMR1 ICR. This study, together with others in the literature, supports that long non-coding RNAs may mediate changes seen in tissues of growth restricted offspring.

CLAW: An automated Snakemake workflow for the assembly of chloroplast genomes from long-read data

Chloroplasts are photosynthetic organelles in algal and plant cells that contain their own genome. Chloroplast genomes are commonly used in evolutionary studies and taxonomic identification and are increasingly becoming a target for crop improvement studies. As DNA sequencing becomes more affordable, researchers are collecting vast swathes of high-quality whole-genome sequence data from laboratory and field settings alike. Whole tissue read libraries sequenced with the primary goal of understanding the nuclear genome will inadvertently contain many reads derived from the chloroplast genome. These whole-genome, whole-tissue read libraries can additionally be used to assemble chloroplast genomes with little to no extra cost. While several tools exist that make use of short-read second generation and third-generation long-read sequencing data for chloroplast genome assembly, these tools may have complex installation steps, inadequate error reporting, poor expandability, and/or lack scalability. Here, we present CLAW (Chloroplast Long-read Assembly Workflow), an easy to install, customise, and use Snakemake tool to assemble chloroplast genomes from chloroplast long-reads found in whole-genome read libraries (https://github.com/aaronphillips7493/CLAW). Using 19 publicly available reference chloroplast genome assemblies and long-read libraries from algal, monocot and eudicot species, we show that CLAW can rapidly produce chloroplast genome assemblies with high similarity to the reference assemblies. CLAW was designed such that users have complete control over parameterisation, allowing individuals to optimise CLAW to their specific use cases. We expect that CLAW will provide researchers (with varying levels of bioinformatics expertise) with an additional resource useful for contributing to the growing number of publicly available chloroplast genome assemblies.

Photosynthetic traits of Australian wild rice (Oryza australiensis) confer tolerance to extreme daytime temperatures

A wild relative of rice from the Australian savannah was compared with cultivated rice, revealing thermotolerance in growth and photosynthetic processes and a more robust carbon economy in extreme heat. Above ~ 32 °C, impaired photosynthesis compromises the productivity of rice. We compared leaf tissues from heat-tolerant wild rice (Oryza australiensis) with temperate-adapted O. sativa after sustained exposure to heat, as well as diurnal heat shock. Leaf elongation and shoot biomass in O. australiensis were unimpaired at 45 °C, and soluble sugar concentrations trebled during 10 h of a 45 °C shock treatment. By contrast, 45 °C slowed growth strongly in O. sativa. Chloroplastic CO₂ concentrations eliminated CO₂ supply to chloroplasts as the basis of differential heat tolerance. This directed our attention to carboxylation and the abundance of the heat-sensitive chaperone Rubisco activase (Rca) in each species. Surprisingly, O. australiensis leaves at 45 °C had 50% less Rca per unit Rubisco, even though CO₂ assimilation was faster than at 30 °C. By contrast, Rca per unit Rubisco doubled in O. sativa at 45 °C while CO₂ assimilation was slower, reflecting its inferior Rca thermostability. Plants grown at 45 °C were simultaneously exposed to 700 ppm CO₂ to enhance the CO₂ supply to Rubisco. Growth at 45 °C responded to CO₂ enrichment in O. australiensis but not O. sativa, reflecting more robust carboxylation capacity and thermal tolerance in the wild rice relative.

Slack as a virtual undergraduate dermatology community: a pilot study

Background

Dermatology is under‐represented in UK undergraduate curricula, and with a diagnostic and educational toolkit that is heavily centred on face‐to‐face (F2F) clinical examination, dermatology education has been disproportionately affected by the COVID‐19 pandemic. Online channel‐based messaging apps such as Slack offer an opportunity to engage students in remote, multimodal collaborative learning by reproducing a classroom environment in the virtual space.

Aim

To determine the feasibility, acceptability and proof of concept for an online Slack community in undergraduate dermatology education.

Methods

Undergraduate medical students participated in an online classroom for a 6‐week programme encompassing case‐based discussions, seminars and journal clubs. The platform was facilitated by junior doctors (n = 10) and patient educators (n = 6). Students and faculty completed a post‐course evaluation. Students additionally completed a pre‐ and post‐intervention dermatology quiz. Mixed methods analyses included quantitative analyses to explore data trends and qualitative phenomenographic analyses to assimilate key underlying themes.

Results

Students (n = 65) were enrolled to join the platform. The evaluation was completed by students (n = 52) from UK universities (n = 27). The majority of students (n = 27) interacted with the platform as passive observers (≤ 5 active interactions with the channel), with a small group (n = 4) of ‘super‐users’ (≥ 100 active interactions). The overall quality of the course was described as ‘excellent’ by 96% of participants and 100% of faculty.

Conclusion

A community‐based online classroom can act as an enjoyable, acceptable and collaborative means of delivering dermatology education to undergraduate medical students. Its ease of use and supportive nature may also facilitate patient involvement. Such advances may provide vital safeguards against the reduction in F2F learning that has accompanied the COVID‐19 pandemic.

Deep roots and soil structure

In this opinion article we examine the relationship between penetrometer resistance and soil depth in the field. Assuming that root growth is inhibited at penetrometer resistances > 2.5 MPa, we conclude that in most circumstances the increases in penetrometer resistance with depth are sufficiently great to confine most deep roots to elongating in existing structural pores. We suggest that deep rooting is more likely related to the interaction between root architecture and soil structure than it is to the ability of a root to deform strong soil. Although the ability of roots to deform strong soil is an important trait, we propose it is more closely related to root exploration of surface layers than deep rooting.

The effect of age and sex on cost of inpatient facility encounters among patients with multiple sclerosis

OBJECTIVE

To explore the effect of age and sex on cost of all-cause and multiple sclerosis (MS)-related inpatient facility encounters.

METHODS

Adult patients with an initial MS diagnosis were identified from a national managed-care database (IMS LifeLink Health Plans Database). The analysis included newly diagnosed MS patients with 12 months insurance eligibility before and after their first MS diagnosis. Inpatient facility encounters (stays) were analyzed for all-cause and MS-related events (ICD-9-CM = 340.XX), other demyelinating CNS disease (ICD-9-CM = 341.XX), rehabilitation (ICD-9-CM = V57.89), and a group of symptom-related diagnoses. Costs and length of stay were evaluated using a general linear model controlling for age and sex.

RESULTS

A total of 57,236 patients met study criteria; 74.3% were female. Mean age for females was 45.5 years and for males it was 47.5 years. In total, 17.0% had an all-cause inpatient stay in the 360-day post index, and 3.2% had an in patient stay with a MS relapse-related diagnosis as primary discharge diagnosis. Additional MS-related diagnoses that led to inpatient stays included other demyelinating CNS disease (0.3%), symptom-related diagnoses (1.0%), and rehabilitation (1.1%). All-cause inpatient cost was higher for males vs females across all age groups; however, cost for females increased at a greater rate as age increased (p = 0.0007). Symptom-related inpatient cost was flat for males, was lower for females than males at an average age of 30, and was greater for females than males at an average age of 60 (p = 0.0199). Cost for MS inpatient stays ($11,931), other demyelinating CNS-related stays ($14,931), and rehabilitation ($23,643) did not differ by age and sex. The average cost for any MS-related relapse inpatient stay was $13,761 and varied with increasing age (p < 0.0001).

CONCLUSION

Burden of illness for relapse among MS patients is substantial. Costs vary by age and sex depending on the discharge diagnosis. Inclusion of symptom-related and rehabilitation inpatient stays may account for an under-recognized proportion of total expenditures.

Porcine oxymyoglobin and lipid oxidation in vitro

The present study was carried out to investigate the effect of dietary α-tocopherol supplementation on porcine oxymyoglobin (OxyMb) and lipid oxidation (TBARS) in model lipid systems, and to determine the influence of 4-hydroxynonenal (4-HNE), a secondary product of lipid oxidation, on porcine OxyMb stability. Porcine metmyoglobin (MetMb) formation was greater in the presence of 4-HNE than the control (P<0.05). Western blot analyses confirmed the covalent modification of myoglobin (Mb) histidine residues by 4-HNE. When combined with microsomes, both equine and porcine OxyMb oxidation increased with time of incubation, and was greater at 37 than at 25 °C (P<0.05). Lower TBARS values were observed in microsomes prepared from vitamin E-supplemented than control pork livers (P<0.05). α-Tocopherol concentration did not affect OxyMb oxidation in microsomes at 25 or 37 °C (P>0.05). These results differ from those observed with beef muscle microsomes where both OxyMb and lipid oxidation were delayed with elevated α-tocopherol levels. These results suggest that the factors affecting Mb and lipid oxidation interactions may be species-dependent.

Engineering gibberellin metabolism in Solanum nigrum L. by ectopic expression of gibberellin oxidase genes

Gibberellins (GAs) control many aspects of plant development, including seed germination, shoot growth, flower induction and growth and fruit expansion. Leaf explants of Solanum nigrum (Black Nightshade; Solanaceae) were used for Agrobacterium-mediated delivery of GA-biosynthetic genes to determine the influence of their encoded enzymes on the production of bioactive GAs and plant stature in this species. Constructs were prepared containing the neomycin phosphotransferase (nptII) gene for kanamycin resistance as a selectable marker, and the GA-biosynthetic genes, their expression under the control of the CaMV 35S promoter. The GA-biosynthetic genes comprised AtGA20ox1, isolated from Arabidopsis thaliana, the product from which catalyses the formation of C(19)-GAs, and MmGA3ox1 and MmGA3ox2, isolated from Marah macrocarpus, which encode functionally different GA 3-oxidases that convert C(19)-GAs to biologically active forms. Increase in stature was observed in plants transformed with AtGA20ox1, MmGA3ox2 and MmGA3ox1 + MmGA3ox2, their presence and expression being confirmed by PCR and RT-PCR, respectively, accompanied by an increase in GA(1) content. Interestingly, MmGA3ox1 alone did not induce a sustained increase in plant height, probably because of only a marginal increase in bioactive GA(1) content in the transformed plants. The results are discussed in the context of regulating plant stature, since this strategy would decrease the use of chemicals to promote plant growth.

Impact of medication adherence to disease-modifying drugs on severe relapse, and direct and indirect costs among employees with multiple sclerosis in the US

OBJECTIVE

To compare rates of severe relapse and total direct and indirect costs over a 2-year period between US-based employees with multiple sclerosis (MS) who were adherent and non-adherent to disease-modifying drugs (DMDs).

METHODS

Employees with ≥1 MS diagnosis (ICD-9-CM: 340.x) and ≥1 DMD pharmacy claim between 1/1/2002-12/31/2007 were identified from a large US administrative claims database. Patients had continuous coverage ≥6 months before (baseline) and ≥24 months after (study period) their index date (first DMD claim). Adherence was measured using medication possession ratio (MPR) over the study period. Patients with MPR ≥80% were considered adherent (n = 448) and those with MPR <80% as non-adherent (n = 200). Multivariate analyses were used to compare rates of severe relapse (inpatient or Emergency Department visit with MS diagnosis) and costs in 2007 dollars between DMD adherent and non-adherent patients. Direct costs were calculated as reimbursements to providers for medical services and prescription drugs excluding DMDs. Indirect costs included disability and medically-related absenteeism costs.

RESULTS

DMD adherent patients were on average older (43.5 vs 41.8 years, p = 0.015) and more likely to be male (38.6% vs 26.0%, p = 0.002) compared with non-adherent patients. Adherent patients had lower rates of depression, higher rates of previous DMD use, and higher baseline MS-related costs. After adjusting for differences in baseline characteristics, DMD adherent patients had a lower rate of severe relapse (12.4% vs 19.9%, p = 0.013) and lower total (direct and indirect) costs ($14,095 vs $16,638, p = 0.048) over the 2-year study period.

CONCLUSIONS

In this study, DMD adherence was associated with a significantly lower rate of severe relapse and lower total costs over 2 years. Causality cannot be inferred because adherence and outcomes were measured over the same period. The study was subject to limitations associated with use of claims data and the absence of clinical measures.

Over-expression of a gibberellin 2-oxidase gene from Phaseolus coccineus L. enhances gibberellin inactivation and induces dwarfism in Solanum species

Gibberellins (GAs) are endogenous hormones that play a predominant role in regulating plant stature by increasing cell division and elongation in stem internodes. The product of the GA 2-oxidase gene from Phaseolus coccineus (PcGA2ox1) inactivates C(19)-GAs, including the bioactive GAs GA(1 )and GA(4), by 2beta-hydroxylation, reducing the availability of these GAs in plants. The PcGA2ox1 gene was introduced into Solanum melanocerasum and S. nigrum (Solanaceae) by Agrobacterium-mediated transformation with the aim of decreasing the amounts of bioactive GA in these plants and thereby reducing their stature. The transgenic plants exhibited a range of dwarf phenotypes associated with a severe reduction in the concentrations of the biologically active GA(1) and GA(4). Flowering and fruit development were unaffected. The transgenic plants contained greater concentrations of chlorophyll b (by 88%) and total chlorophyll (11%), although chlorophyll a and carotenoid contents were reduced by 8 and 50%, respectively. This approach may provide an alternative to the application of chemical growth retardants for reducing the stature of plants, particularly ornamentals, in view of concerns over the potential environmental and health hazards of such compounds.

Gibberellin metabolism: new insights revealed by the genes

The identification of most of the genes involved in the metabolic pathways for gibberellin hormones has helped us to understand these pathways and their regulation. Many of these enzymes are multifunctional and therefore fewer enzymes than might be expected are required to synthesize the various gibberellin structures. However, several of the enzymes are encoded by multiple genes that are regulated differently, adding unexpected genetic complexity. Several endogenous and environmental factors modify the expression of gibberellin biosynthesis genes, including developmental stage, hormonal status and light. A future challenge will be to dissect the complex, interacting pathways that mediate the regulation of gibberellin metabolism.

Induction of dwarfism in transgenic Solanum dulcamara by over-expression of a gibberellin 20-oxidase cDNA from pumpkin

The gibberellin (GA) 20-oxidase (CmGA20ox1) from immature pumpkin seed produces predominantly inactive tricarboxylic acid GAs. We expressed CmGA20ox1 under the control of the CaMV 35S promoter in Solanum dulcamara to assess the usefulness of this gene for reducing GA content in transgenic plants. All transgenic plants obtained were semi-dwarfs with smaller, deep-green leaves and highly pigmented stems compared to the wild-type. Such transformants flowered earlier than the wild-type plants and produced more fruit and more seeds per fruit. The transgene was efficiently expressed, producing high levels of CmGA20ox1 transcript and protein. Furthermore, the concentration of GA(1) was reduced in leaves of the transformants to approximately 20% or less of that in the wild-type and to about 40% or less in stems. The concentrations of other 13-hydroxylated GAs were also reduced, except for the tricarboxylic acid, GA(17), which accumulated in the transformants due to 13-hydroxylation of GA(25). By contrast, the concentrations of non-13-hydroxylated GAs, GA(4) and GA(34), were not consistently reduced, indicating that the effect of expressing the pumpkin gene may not be predictable. Transcript abundance for a native GA 20-oxidase gene was higher in the leaves and stems of S. dulcamara transformed with the pumpkin gene than in wild-type, reflecting the feedback control of 20-oxidase gene expression that serves as a homeostatic mechanism for GAs.

Bovine placental protease specificity toward muscle connective tissue proteins

Enzymes currently used to tenderize meat are not substrate-specific, resulting in extensive myofibrillar protein degradation that often produces an undesirable texture. Bovine placental metalloproteases, which selectively hydrolyze connective tissue proteins while leaving myofibrillar proteins intact, may tenderize meat without causing texture problems. Therefore, our objective was to extract and crudely purify bovine metalloproteases from bovine placenta for possible use as tenderizers in meat systems. Enzymes were extracted from homogenized tissue and purified by ammonium sulfate precipitation. Samples were collected before (crude enzyme) and after gel filtration on a Sephadex G-100 column. Spectrophotometric analysis identified one major peak (filtered enzyme). Gelatin, casein, and type I acid-soluble collagen zymography were used to determine substrate specificity. Beef myofibrillar proteins were incubated with crude and filtered enzyme fractions, enzymes quenched, and substrate degradation visualized using SDS-PAGE. Active gelatinases and collagenases exhibiting molecular weights of 57 to 65 kDa were detected on zymograms. Banding patterns from crude enzyme indicated two enzymes with both gelatinase and collagenase activity and a third enzyme with gelatinase activity only. Banding patterns from filtered enzyme indicated two enzymes with both gelatinase and collagenase activity. Proteolytic activity was not detected with casein, actin, or myosin heavy-chain substrates. Due to specificity for collagen and gelatin, these enzymes may be capable of improving the tenderness of certain cuts relatively high in connective tissue, while avoiding myofibrillar protein hydrolysis.

Manipulation of hormone biosynthetic genes in transgenic plants

Modification of plant hormone biosynthesis through the introduction of bacterial genes is a natural form of genetic engineering, which has been exploited in numerous studies on hormone function. Recently, biosynthetic pathways have been largely elucidated for most of the plant hormone classes, and genes encoding many of the enzymes have been cloned. These advances offer new opportunities to manipulate hormone content in order to study their mode of action and the regulation of their biosynthesis. Furthermore, this technology is providing the means to introduce agriculturally useful traits into crops.

Molecular cloning and functional expression of gibberellin 2- oxidases, multifunctional enzymes involved in gibberellin deactivation

A major catabolic pathway for the gibberellins (GAs) is initiated by 2beta-hydroxylation, a reaction catalyzed by 2-oxoglutarate-dependent dioxygenases. To isolate a GA 2beta-hydroxylase cDNA clone we used functional screening of a cDNA library from developing cotyledons of runner bean (Phaseolus coccineus L.) with a highly sensitive tritium-release assay for enzyme activity. The encoded protein, obtained by heterologous expression in Escherichia coli, converted GA9 to GA51 (2beta-hydroxyGA9) and GA51-catabolite, the latter produced from GA51 by further oxidation at C-2. The enzyme thus is multifunctional and is best described as a GA 2-oxidase. The recombinant enzyme also 2beta-hydroxylated other C19-GAs, although only GA9 and GA4 were converted to the corresponding catabolites. Three related cDNAs, corresponding to gene sequences present in Arabidopsis thaliana databases, also encoded functional GA 2-oxidases. Transcripts for two of the Arabidopsis genes were abundant in upper stems, flowers, and siliques, but the third transcript was not detected by Northern analysis. Transcript abundance for the two most highly expressed genes was lower in apices of the GA-deficient ga1-2 mutant of Arabidopsis than in wild-type plants and increased after treatment of the mutant with GA3. This up-regulation of GA 2-oxidase gene expression by GA contrasts GA-induced down-regulation of genes encoding the biosynthetic enzymes GA 20-oxidase and GA 3beta-hydroxylase. These mechanisms would serve to maintain the concentrations of biologically active GAs in plant tissues.

Modification of gibberellin production and plant development in Arabidopsis by sense and antisense expression of gibberellin 20-oxidase genes

Gibberellin (GA) 20-oxidase catalyses consecutive steps late in GA biosynthesis in plants. In Arabidopsis, the enzyme is encoded by a gene family of at least three members (AtGA20ox1, AtGA20ox2 and AtGA20ox3) with differential patterns of expression. The genes are regulated by feedback from bioactive GAs, suggesting that the enzymes may be involved in regulating GA biosynthesis. To investigate this, we produced transgenic Arabidopsis expressing sense or antisense copies of each of the GA 20-oxidase cDNAs. Over-expression of any of the cDNAs gave rise to seedlings with elongated hypocotyls; the plants flowered earlier than controls in both long and short days and were 25% taller at maturity. GA analysis of the vegetative rosettes showed a two- to threefold increase in the level of GA4, indicating that GA 20-oxidase normally limits bioactive GA levels. Plants expressing antisense copies of AtGA20ox1 had short hypocotyls and reduced rates of stem elongation. This was reflected in reduced levels of GA4 in both rosettes and shoot tips. In short days, flowering was delayed and the reduction in the rate of stem elongation was greater. Antisense expression of AtGA20ox2 had no apparent effects in long days, but stem growth in one transgenic line grown in short days was reduced by 20%. Expression of antisense copies of AtGA20ox3 had no visible effect, except for one transgenic line that had short hypocotyls. These results demonstrate that GA levels and, hence, plant growth and development can be modified by manipulation of GA 20-oxidase expression in transgenic plants.

Function and substrate specificity of the gibberellin 3beta-hydroxylase encoded by the Arabidopsis GA4 gene

cDNA corresponding to the GA4 gene of Arabidopsis thaliana L. (Heynh. ) was expressed in Escherichia coli, from which cell lysates converted [14C]gibberellin (GA)9 and [14C]GA20 to radiolabeled GA4 and GA1, respectively, thereby confirming that GA4 encodes a GA 3beta-hydroxylase. GA9 was the preferred substrate, with a Michaelis value of 1 microm compared with 15 microm for GA20. Hydroxylation of these GAs was regiospecific, with no indication of 2beta-hydroxylation or 2,3-desaturation. The capacity of the recombinant enzyme to hydroxylate a range of other GA substrates was investigated. In general, the preferred substrates contained a polar bridge between C-4 and C-10, and 13-deoxy GAs were preferred to their 13-hydroxylated analogs. Therefore, no activity was detected using GA12-aldehyde, GA12, GA19, GA25, GA53, or GA44 as the open lactone (20-hydroxy-GA53), whereas GA15, GA24, and GA44 were hydroxylated to GA37, GA36, and GA38, respectively. The open lactone of GA15 (20-hydroxy-GA12) was hydroxylated but less efficiently than GA15. In contrast to the free acid, GA25 19,20-anhydride was 3beta-hydroxylated to give GA13. 2,3-Didehydro-GA9 and GA5 were converted by recombinant GA4 to the corresponding epoxides 2, 3-oxido-GA9 and GA6.

Gibberellin biosynthesis from gibberellin A12-aldehyde in endosperm and embryos of Marah macrocarpus

Soluble enzyme preparations from embryos and endosperm of Marah macrocarpus (previously Echinocystis macrocarpa) were incubated with [14C4]gibberellin(GA)12-aldehyde, [14C4]GA12, [14C1] GA9, 2,3-didehydro[14C1]GA9, [14C1]GA20, and [17-13C, 3H]GA5. Embryo preparations converted GA12-aldehyde, GA12, and GA9 to GA4 and GA7; 2,3-didehydroGA9 to GA7; GA5 to GA3; and GA20 (incompletely) to GA1 and GA60, but not to GA3. Endosperm preparations converted GA12-aldehyde and GA12 to GA15, GA24, and GA9, but, unlike embryo preparations, not to GA4 or GA7. However, GA4 and GA7 were formed from GA9 and GA7 was formed from 2,3-didehydroGA9. Metabolism of GA5 to GA3 and GA20 to GA1 was low. 2,3-DidehydroGA9 accumulated when GA9 was incubated with a desalted endosperm preparation. A cDNA clone (M3-8), selected from an embryo-derived cDNA library using a DNA fragment generated by reverse transcriptase polymerase chain reaction, was expressed in Escherichia coli. The fusion protein converted GA12 to GA9 (major) and GA25 (minor); GA53 was metabolized less effectively and only to GA44. Thus, the M3-8 protein is functionally similar to GA 20-oxidases from Arabidopsis thaliana, Spinacia oleracea, and Pisum sativum, but different from that from Cucurbita maxima seeds, to which its amino acid sequence is most closely related. mRNA hybridizing to M3-8 accumulated in embryos and endosperm of M. macrocarpus, but was absent in vegetative tissues.

Isolation and transcript analysis of gibberellin 20-oxidase genes in pea and bean in relation to fruit development

PCR was used with degenerate primers based on conserved amino acid sequences in gibberellin (GA) 20-oxidases to isolate cDNA clones for these enzymes from young seeds of pea (Pisum sativum) and developing embryos of French bean (Phaseolus vulgaris). One GA 20-oxidase cDNA (Ps27-12) was obtained from pea and three (Pv 15-11, Pv73-1 and Pv85-26) from bean. Their identities were confirmed by demonstrating that fusion proteins expressed in Escherichia coli exhibited GA 20-oxidase activity, converting [14C]GA12 to [14C]GA9. The intermediates in this three-step reaction, GA15 and GA24, were also identified as products. The expression proteins from three of the clones (Ps27-12, Pv15-11 and Pv73-1) were also shown to convert GA53 to GA20, as effectively as they did GA12. On the basis of transcript levels measured by northern blot analysis, the pea GA 20-oxidase gene is most highly expressed in young leaves, fully expanded internodes, very young seeds (until 4 days after anthesis) and expanding pods (from 3 days after anthesis at least until day 6). Expression in pods from 3-day-old unpollinated ovaries is higher than in those from pollinated ovaries. Treatment of unpollinated ovaries with GA3 to induce parthenocarpic fruit-set severely reduced the amount of GA 20-oxidase mRNA, whereas treatment with 2,4-D, although inducing fruit-set, did not reduce the levels of these transcripts. Plant decapitation above an unpollinated ovary resulted in very high levels of GA 20-oxidase mRNA in the pod. The three GA 20-oxidase genes from French bean showed very different patterns of expression: Pv 15-1 was expressed in the roots, young leaves, and developing seeds, but most highly in immature cotyledons, while Pv73-1 has a similar expression pattern to Ps27-12, with transcripts found only in young seeds and young leaves, where it was particularly abundant. Transcripts corresponding to Pv85-26 were detected in developing seeds, and just traces in the young leaves. Southern blot analysis indicated that the bean GA 20-oxidases are each encoded by single-copy genes, whereas one more gene, homologous to Ps27-12, could also exist in pea.

Isolation and expression of three gibberellin 20-oxidase cDNA clones from Arabidopsis

Using degenerate oligonucleotide primers based on a pumpkin (Cucurbita maxima) gibberellin (GA) 20-oxidase sequence, six different fragments of dioxygenase genes were amplified by polymerase chain reaction from arabidopsis thaliana genomic DNA. One of these was used to isolate two different full-length cDNA clones, At2301 and At2353, from shoots of the GA-deficient Arabidopsis mutant ga1-2. A third, related clone, YAP169, was identified in the Database of Expressed Sequence Tags. The cDNA clones were expressed in Escherichia coli as fusion proteins, each of which oxidized GA12 at C-20 to GA15, GA24, and the C19 compound GA9, a precursor of bioactive GAs; the C20 tricarboxylic acid compound GA25 was formed as a minor product. The expression products also oxidized the 13-hydroxylated substrate GA53, but less effectively than GA12. The three cDNAs hybridized to mRNA species with tissue-specific patterns of accumulation, with At2301 being expressed in stems and inflorescences, At2353 in inflorescences and developing siliques, and YAP169 in siliques only. In the floral shoots of the ga1-2 mutant, transcript levels corresponding to each cDNA decreased dramatically after GA3 application, suggesting that GA biosynthesis may be controlled, at least in part, through down-regulation of the expression of the 20-oxidase genes.

Gibberellin-regulated expression in oat aleurone cells of two kinases that show homology to MAP kinase and a ribosomal protein kinase

cDNA fragments from ten different protein kinases expressed in Avena sativa aleurone cells were amplified from mRNA by RT-PCR with degenerate primers. These could be classified into five groups: Aspk1-3 showed homology to the Snf1-related protein kinases, Aspk4-5 to a wheat ABA up-regulated protein kinase, Aspk6-8 to the Ca-dependent, calmodulin-independent protein kinase family, Aspk9 encoded a MAP kinase and Aspk10 was closely related to a novel Arabidopsis ribosomal protein kinase. GA caused a rapid increase in transcripts hybridising to Aspk10, while inhibiting the dramatic accumulation of transcripts hybridising to Aspk9 that occurred in the absence of GA.

Cloning of two gibberellin-regulated cDNAs from Arabidopsis thaliana by subtractive hybridization: expression of the tonoplast water channel, gamma-TIP, is increased by GA3

The Arabidopsis ga1 mutant has very low levels of endogenous, active gibberellins and thus has an extreme dwarf phenotype; application of GA3 induces stem elongation and flower development. To test the hypothesis that GA action in this system involves changes in gene expression, we have cloned mRNAs whose abundance changes following GA application. A subtraction cloning scheme for the isolation of differentially regulated cDNAs was established, involving hybridization of single-stranded cDNA to biotinylated mRNA. cDNA populations enriched up to 150-fold in GA-regulated sequences were produced and cDNA libraries generated. Screening of these libraries has isolated two clones that identify mRNAs of ca. 1100 and 750 bases whose abundance is markedly increased 24 h after GA application. One of these clones encodes the vegetative form of the Arabidopsis tonoplast intrinsic protein (gamma-TIP), a water channel protein, the expression of which has recently been shown to be correlated with regions of cell expansion. The second clone is expressed only in the inflorescence and encodes a proline- and glycine-rich protein that may be a cell wall component.

A point mutation in the N-terminus of ribulose-1,5-bisphosphate carboxylase affects ribulose-1,5-bisphosphate binding

Mutagenesis in vitro of the gene encoding the large subunit of ribulose-1,5-bisphosphate carboxylase/ oxygenase (EC 4.1.1.39) from Anacystis nidulans was used to generate novel enzymes. Two conserved residues, threonine 4 and lysine 11 in the N-terminus were changed. The substitution of threonine 4 with serine or valine had little effect on the kinetic parameters. The substitution of lysine 11 with leucine, which is non-polar, increased the K m for ribulose-1,5-bisphosphate from 82 to 190 μM but its replacement with glutamine, which has polar properties, had no appreciable effect.

Nucleotide sequence and transcripts of the pea chloroplast gene encoding CFo subunit III of ATP synthase

The structure and expression of the pea chloroplast atpH gene, encoding ATP synthase CFo subunit III, have been investigated. The atpH gene is situated between the atpI and atpF genes for CFo subunits IV and I, and encodes a hydrophobic polypeptide of 81 amino acid residues which is very similar to subunit III from other species. Analysis of transcripts from the region of chloroplast DNA encoding ATP synthase subunits IV-III-I-alpha shows a complex pattern of transcription, with large transcripts potentially coding for several subunits and also smaller gene-specific transcripts. Two abundant transcripts of 660 nucleotides (nt) and 980 nt specific for atpH were identified. Primer extension and S1 nuclease protection mapping suggested that the 660-nt transcripts were produced by endonucleolytic processing at the sequence, 5'-UGGAAU.

The role of the N-terminus of the large subunit of ribulose-bisphosphate carboxylase investigated by construction and expression of chimaeric genes

The genes for the large and small subunits of ribulose bisphosphate carboxylase/oxygenase (Rubisco) from Anacystis nidulans have been expressed in Escherichia coli under the control of the lac promoter to produce active enzyme. The enzyme can be purified from the cells to yield up to 200 mg Rubisco/l cultured bacteria, and is indistinguishable from the enzyme extracted from A. nidulans. In order to investigate the role of the N-terminus of the large subunit in catalysis, chimaeric genes were constructed where the DNA coding for the 12 N-terminal amino acids in A. nidulans was replaced by DNA encoding the equivalent, but poorly conserved, region of either the wheat or maize large subunit. These genes, in constructs also containing the gene for the A. nidulans small subunit, were expressed in E. coli and produced enzymes with similar catalytic properties to the wild-type Rubisco of A. nidulans. In contrast, when the N-terminal region of the large subunit was replaced by unrelated amino acids encoded by the pUC8 polylinker, enzyme activity of the expressed protein was reduced by 90% under standard assay conditions, due to an approximately tenfold rise in the Km for ribulose 1,5-bisphosphate. This confirms that the N-terminus of the large subunit has a function in catalysis, either directly in substrate binding or in maintaining the integrity of the active site.

A sixth subunit of ATP synthase, an F0 component, is encoded in the pea chloroplast genome

DNA from pea and tobacco chloroplasts hybridizes specifically with probes derived from the gene for a membrane component, the a subunit of ATP synthase of the cyanobacterium, Synechococcus 6301. DNA sequence of the hybridizing region of the pea plastid DNA has revealed that it encodes a protein of 247 amino acids related in sequence to the a subunits of ATP synthase of Escherichia coli, Synechococcus and mitochondria. This is the sixth component of chloroplast ATP synthase that is plastid coded. The gene is located upstream from the genes for three other ATP synthase subunits and a transcript of 6 kb contains coding sequences from each of these genes. Thus the subunit a gene is part of a co-transcribed cluster of four ATP synthase genes arranged in the order a:c(or III):b(or I):alpha. Two other ATP synthase genes, those for beta and epsilon subunits, are known to form a separate cluster. These gene arrangements are most closely related to those found in the cyanobacterium, Synechococcus 6301. Hence, this finding provides strong evidence for a common origin for cyanobacteria and plant chloroplasts.

Synthesis of components of the cytochrome b-f complex by isolated pea chloroplasts

Three components of the cytochrome b-f complex, cytochrome f, cytochrome b-563 and a 15.2-kDa polypeptide, were labelled with radioactive amino acids in isolated pea chloroplasts incubated in the light with added Mg-ATP. The assembly of cytochrome b-563 (19.5 kDa) into the cytochrome complex required the presence of added Mg-ATP whereas cytochrome f (37.3 kDa) and the 15.2-kDa polypeptide were assembled in its absence. Incorporation of [35S]methionine into the polypeptide chain of cytochrome b-563 and the 15.2-kDa component was confirmed by peptide mapping of the products of partial digestion with papain.

Isolation and characterization of a cytochrome b-f complex from pea chloroplasts

A cytochrome b-f complex has been extracted from pea chloroplast membranes with octyl glucoside and cholate and has been purified by ammonium sulphate fractionation and polyacrylamide gel electrophoresis in the presence of Triton X-100 and sodium deoxycholate. The complex contains cytochromes f and b-563 in a ratio of 1:2, but shows very low levels of the Rieske iron sulphur centre and plastoquinol-plastocyanin oxidoreductase activity. The complex consists of four polypeptides of molecular weights 37300, 34000, 19500 and 15200. The complex is dissociated by electrophoresis in the presence of 2M urea to give pure preparations of cytochrome f and cytochrome b-563, which on sodium dodecylsulphate-polyacrylamide gel electrophoresis give single bands of apparent molecular weights 37300 and 19500 respectively.