June Simpson

Phosphate Availability Alters Architecture and Causes Changes in Hormone Sensitivity in the Arabidopsis Root System

The postembryonic developmental program of the plant root system is plastic and allows changes in root architecture to adapt to environmental conditions such as water and nutrient availability. Among essential nutrients, phosphorus (P) often limits plant productivity because of its low mobility in soil. Therefore, the architecture of the root system may determine the capacity of the plant to acquire this nutrient. We studied the effect of P availability on the development of the root system in Arabidopsis. We found that at P-limiting conditions (<50 μm), the Arabidopsis root system undergoes major architectural changes in terms of lateral root number, lateral root density, and primary root length. Treatment with auxins and auxin antagonists indicate that these changes are related to an increase in auxin sensitivity in the roots of P-deprived Arabidopsis seedlings. It was also found that the axr1-3, axr2-1, and axr4-1 Arabidopsis mutants have normal responses to low P availability conditions, whereas the iaa28-1mutant shows resistance to the stimulatory effects of low P on root hair and lateral root formation. Analysis of ethylene signaling mutants and treatments with 1-aminocyclopropane-1-carboxylic acid showed that ethylene does not promote lateral root formation under P deprivation. These results suggest that in Arabidopsis, auxin sensitivity may play a fundamental role in the modifications of root architecture by P availability.

Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms

Abstract A modification of the amplified fragment length polymorphism technique was developed for the determination of DNA methylation in dimorphic fungi representative of three of the major fungal taxa: Mucor rouxii, a zygomycete; Yarrowia lipolytica, an ascomycete; and Ustilago maydis, a basidiomycete. DNA obtained from the yeast or mycelial stages of the fungi was digested with a mixture of EcoRI, and one of the isoschizomers MspI and HpaII, whose ability to cleave at the sequence CpCpGpG is affected by the methylation state. The resulting fragments were ligated to primers and subjected to a double round of amplification by the polymerase chain reaction, radiolabeled in the second round, and separated by polyacrylamide gel electrophoresis. Comparison of patterns revealed differences indicative of fragments whose methylation state did or did not change during the dimorphic transition. These results indicate the usefulness of the method for the study of DNA methylation, demonstrate the universality of DNA methylation in fungi, and confirm that differential DNA methylation occurs during fungal morphogenesis.

Architecture and evolution of a minute plant genome

It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of whole-genome duplications (WGDs) and mobile element proliferation. However, extreme genome size reductions have been reported in the angiosperm family tree. Here we report the sequence of the 82-megabase genome of the carnivorous bladderwort plant Utricularia gibba. Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA. Unexpectedly, we identified at least three rounds of WGD in U. gibba since common ancestry with tomato (Solanum) and grape (Vitis). The compressed architecture of the U. gibba genome indicates that a small fraction of intergenic DNA, with few or no active retrotransposons, is sufficient to regulate and integrate all the processes required for the development and reproduction of a complex organism.

Analysis of Gene Expression and Physiological Responses in Three Mexican Maize Landraces under Drought Stress and Recovery Irrigation

Background Drought is one of the major constraints for plant productivity worldwide. Different mechanisms of drought-tolerance have been reported for several plant species including maize. However, the differences in global gene expression between drought-tolerant and susceptible genotypes and their relationship to physiological adaptations to drought are largely unknown. The study of the differences in global gene expression between tolerant and susceptible genotypes could provide important information to design more efficient breeding programs to produce maize varieties better adapted to water limiting conditions. Methodology/Principal Findings Changes in physiological responses and gene expression patterns were studied under drought stress and recovery in three Mexican maize landraces which included two drought tolerant (Cajete criollo and Michoacán 21) and one susceptible (85-2) genotypes. Photosynthesis, stomatal conductance, soil and leaf water potentials were monitored throughout the experiment and microarray analysis was carried out on transcripts obtained at 10 and 17 days following application of stress and after recovery irrigation. The two tolerant genotypes show more drastic changes in global gene expression which correlate with different physiological mechanisms of adaptation to drought. Differences in the kinetics and number of up- and down-regulated genes were observed between the tolerant and susceptible maize genotypes, as well as differences between the two tolerant genotypes. Interestingly, the most dramatic differences between the tolerant and susceptible genotypes were observed during recovery irrigation, suggesting that the tolerant genotypes activate mechanisms that allow more efficient recovery after a severe drought. Conclusions/Significance A correlation between levels of photosynthesis and transcription under stress was observed and differences in the number, type and expression levels of transcription factor families were also identified under drought and recovery between the three maize landraces. Gene expression analysis suggests that the drought tolerant landraces have a greater capacity to rapidly modulate more genes under drought and recovery in comparison to the susceptible landrace. Modulation of a greater number of differentially expressed genes of different TF gene families is an important characteristic of the tolerant genotypes. Finally, important differences were also noted between the tolerant landraces that underlie different mechanisms of achieving tolerance.

Light-inducible and tissue-specific expression of a chimaeric gene under control of the 5'-flanking sequence of a pea chlorophyll a/b-binding protein gene

We have investigated the regulatory functions of the 5′‐flanking sequences of a chlorophyll a/b‐binding protein gene from Pisum sativum, using the neomycin phosphotransferase (II) activity from Tn5 as an enzymatic reporter. We show that 0.4 kb of the upstream flanking sequences of this gene are sufficient for both organ‐specific and light‐regulated expression of our chimaeric constructs in transformed tobacco plants. In addition, we show that sequences farther upstream have a significant influence on the level of transcription of these constructions.

Photosynthesis-associated gene families: differences in response to tissue-specific and environmental factors

The endogenous small subunit of the ribulose-1,5-bisphosphate carboxylase gene rbcS and the light-harvesting chlorophyll a/b-binding protein gene (LHCP) of pea are expressed in a light-inducible manner and are active mainly in green chloroplast-containing tissue. Chimeric genes under control of the 5-flanking sequences of the rbcS ss3.6 or LHCP AB80 genes from pea were used to study the factors relating to the issue-specific and lightinducible expression of these nuclear-encoded genes in transgenic tobacco plants. The results show that plastid development plays a crucial role in the activation of expression of these chimeric genes. Particular members of each of the above gene families respond differently to tissue-specific and environmental factors. Furthermore, the light-inducible expression directed by the 5-flanking sequence of ss3.6 rbcSgene is not exclusively mediated by phytochrome, but probably is controlledin large part by another photoreceptor.

Characterization of Mexican Isolates of Colletotrichum lindemuthianum by Using Differential Cultivars and Molecular Markers

ABSTRACT Differential cultivars and molecular markers were used to analyze 59 isolates of the bean anthracnose pathogen, Colletotrichum lindemuthianum, from different regions of Mexico. Ten distinct races were determined, three of which had not been reported previously in Mexico. Isolates were found to infect only a narrow range of the differential cultivars used and were restricted to cultivars of Middle American origin. A comparison of random amplified polymorphic DNA and amplified fragment length polymorphism (AFLP) analyses was carried out on a subset of the fungal isolates. Determination of genetic distances based on AFLP data and production of a dendrogram demonstrated two levels of association: i) isolates classified into two major groups according to the type of cultivar or system of cultivation from which they originated, and ii) isolates could be classified into smaller subgroups generally associated with the geographic location from which they were obtained. Bootstrap analysis and determination of confidence intervals showed these geographic groupings to be extremely robust.

Light-inducible and tissue-specific pea lhcp gene expression involves an upstream element combining enhancer- and silencer-like properties

Studies in viral and mammalian cell systems have identified regulatory elements, collectively termed enhancers, which are cis-acting elements effective in either orientation and at both 5′ and 3′ ends of a gene, and which increase transcription when linked to either their own or a heterologous promoter gene system1–5. Certain upstream elements in yeast have also been shown to exert a negative effect on the rate of transcription of cell-cycle-specific genes and these have been called silencers6. Two of the best characterized plant gene families are those of the small subunit of the ribulose 1,5-bisphosphate carboxylase (rbcS) genes7 and the lightharvesting chlorophyll a/b-bind ing protein (lhcp) genes8. The first enhancer element in plants has recently been described showing that an upstream element of an rbcS gene could, in both orientations, confer light-inducible expression on a heterologous promoter/gene system9. We report here that a 247-base pair (bp) element from an lhcp gene acts not only as a light-inducible enhancer but also as a tissue-specific ‘silencer’.

Molecular characterization of two genes encoding betaine aldehyde dehydrogenase from amaranth. Expression in leaves under short-term exposure to osmotic stress or abscisic acid

A genomic clone (ahybadh4) and a cDNA (ahybadh17) both encoding betaine aldehyde dehydrogenase (BADH; EC 1.2.1.8) were isolated from the plant Amaranthus hypochondriacus L. The ahybadh4 gene extends 9 kilobases (kb) containing 15 exons with an open reading frame (ORF) of 501 amino acids (aa), a 1.3kb 5 untranslated region (UTR) and a 3 UTR of 0.3kb. The ahybadh17 cDNA encodes a BADH isoform of 500aa which contains 10aa substitutions with respect to AHYBADH4. Both encoded proteins share 98% identity at the amino acid level. Comparison of amaranth BADHs with other reported sequences showed high similarity. Analysis of ahybadh17 expression in amaranth leaves showed that mRNA and BADH protein are present in non-treated amaranth leaves and both transiently increased under short-term exposure to abscisic acid (ABA) and osmotic stress treatments.

Transgenic Plants: An Historical Perspective

The development of technologies that allow the introduction and functional expression of foreign genes in plant cells has extended in less than two decades to the production of transgenic plants with improved insect and disease resistance, seeds and fruits with enhanced nutritional qualities, and plants that are better adapted to adverse environmental conditions. Vaccines against serious human diseases and other important products have also been developed using transgenic plants. Many more agronomic and quality traits are currently being engineered in both academic and industrial laboratories, which are limited only by our poor knowledge of plant gene function. The emergence of new functional genomic strategies for the identification and characterization of genes promises to provide a wealth of information with an enormous potential to enhance traditional plant breeding and to genetically engineer plants for specific purposes. This chapter describes some of the highlights in the development of these technologies and some of the major achievements in production and commercialization of transgenic crops. We also discuss some of the biosafety issues related to release of this novel class of plants into the environment.