Andrea Hricová

The SCABRA3 Nuclear Gene Encodes the Plastid RpoTp RNA Polymerase, Which Is Required for Chloroplast Biogenesis and Mesophyll Cell Proliferation in Arabidopsis

In many plant species, a subset of the genes of the chloroplast genome is transcribed by RpoTp, a nuclear-encoded plastid-targeted RNA polymerase. Here, we describe the positional cloning of the SCABRA3 (SCA3) gene, which was found to encode RpoTp in Arabidopsis (Arabidopsis thaliana). We studied one weak (sca3-1) and two strong (sca3-2 and sca3-3) alleles of the SCA3 gene, the latter two showing severely impaired plant growth and reduced pigmentation of the cotyledons, leaves, stem, and sepals, all of which were pale green. The leaf surface was extremely crumpled in the sca3 mutants, although epidermal cell size and morphology were not perturbed, whereas the mesophyll cells were less densely packed and more irregular in shape than in the wild type. A significant reduction in the size, morphology, and number of chloroplasts was observed in homozygous sca3-2 individuals whose photoautotrophic growth was consequently perturbed. Microarray analysis showed that several hundred nuclear genes were differentially expressed in sca3-2 and the wild type, about one-fourth of which encoded chloroplast-targeted proteins. Quantitative reverse transcription-PCR analyses showed that the sca3-2 mutation alters the expression of the rpoB, rpoC1, clpP, and accD plastid genes and the SCA3 paralogs RpoTm and RpoTmp, which respectively encode nuclear-encoded mitochondrion or dually targeted RNA polymerases. Double-mutant analysis indicated that RpoTmp and SCA3 play redundant functions in plant development. Our findings support a role for plastids in leaf morphogenesis and indicate that RpoTp is required for mesophyll cell proliferation.

Arabidopsis RUGOSA2 encodes an mTERF family member required for mitochondrion, chloroplast and leaf development

Little is known about the mechanisms that control transcription of the mitochondrial and chloroplastic genomes, and their interplay within plant cells. Here, we describe the positional cloning of the Arabidopsis RUG2 gene, which encodes a protein that is dual-targeted to mitochondria and chloroplasts, and is homologous with the metazoan mitochondrial transcription termination factors (mTERFs). In the loss-of-function rug2 mutants, most organs were pale and showed reduced growth, and the leaves exhibited both green and pale sectors, with the latter containing sparsely packed mesophyll cells. Chloroplast and mitochondrion development were strongly perturbed in the rug2-1 mutant, particularly in pale leaf sectors, in which chloroplasts were abnormally shaped and reduced in number, thereby impairing photoautotrophic growth. As expected from the pleiotropic phenotypes caused by its loss-of-function alleles, the RUG2 gene was ubiquitously expressed. In a microarray analysis of the mitochondrial and chloroplastic genomes, 56 genes were differentially expressed between rug2-1 and the wild type: most mitochondrial genes were downregulated, whereas the majority of the chloroplastic genes were upregulated. Quantitative RT-PCR analyses showed that the rug2-1 mutation specifically increases expression of the RpoTp nuclear gene, which encodes chloroplastic RNA polymerase. Therefore, the RUG2 nuclear gene seems to be crucial for the maintenance of the correct levels of transcripts in the mitochondria and chloroplasts, which is essential for optimized functions of these organelles and proper plant development. Our results highlight the complexity of the functional interaction between these two organelles and the nucleus.

Flax anther culture: effect of genotype, cold treatment and media

We report on screening of wide range of flax cultivars for androgenic response and on testing of induction conditions for flax (Linum usitatissimum L.) anther culture and plant regeneration. Anthers were cultured on four different media: Mo, N6, MS and N&N supplemented with various combinations of growth regulators. The induction of callus formation from cultured anthers was the highest on N6 (with cultivar PR FGL 77 – 12 %) and N&N media (with cultivar Carolin – 2.8 %), preferentially after cold pretreatment (7days at 8 °C). Shoots were formed on calli derived from the microspores inside the cultured anthers on media N&N and N6 supplemented with 1 mg l−1 zeatin or 1 mg l−1BAP + 1 mg l−1NAA, respectively and elongated on MS medium supplemented with 2 mg l−1 zeatin. The highest number of shoots (120) was observed with cultivar Red Wing. Shoots were rooted on MS medium supplemented with 2 mg l−1IAA. Our experiments resulted in total in 62 % anther response and 155 plants regenerated and transferred into soil.

PORPHOBILINOGEN DEAMINASE deficiency alters vegetative and reproductive development and causes lesions in Arabidopsis.

The Arabidopsis rugosa1 (rug1) mutant has irregularly shaped leaves and reduced growth. In the absence of pathogens, leaves of rug1 plants have spontaneous lesions reminiscent of those seen in lesion-mimic mutants; rug1 plants also express cytological and molecular markers associated with defence against pathogens. These rug1 phenotypes are made stronger by dark/light transitions. The rug1 mutant also has delayed flowering time, upregulation of the floral repressor FLOWERING LOCUS C (FLC) and downregulation of the flowering promoters FT and SOC1/AGL20. Vernalization suppresses the late flowering phenotype of rug1 by repressing FLC. Microarray analysis revealed that 280 nuclear genes are differentially expressed between rug1 and wild type; almost a quarter of these genes are involved in plant defence. In rug1, the auxin response is also affected and several auxin-responsive genes are downregulated. We identified the RUG1 gene by map-based cloning and found that it encodes porphobilinogen deaminase (PBGD), also known as hydroxymethylbilane synthase, an enzyme of the tetrapyrrole biosynthesis pathway, which produces chlorophyll, heme, siroheme and phytochromobilin in plants. PBGD activity is reduced in rug1 plants, which accumulate porphobilinogen. Our results indicate that Arabidopsis PBGD deficiency impairs the porphyrin pathway and triggers constitutive activation of plant defence mechanisms leading to leaf lesions and affecting vegetative and reproductive development.

Agricultural recovery of a formerly radioactive area: II. Systematic proteomic characterization of flax seed development in the remediated Chernobyl area

Molecular characterization of crop plants grown in remediated, formerly radioactive, areas could establish a framework for future agricultural use of these areas. Recently, we have established a quantitative reference map for mature flax seed proteins (Linum usitatissimum L.) harvested from a remediated plot in Chernobyl town. Herein we describe results from our ongoing studies of this subject, and provide a proteomics-based characterization of developing flax seeds harvested from same field. A quantitative approach, based on 2-dimensional electrophoresis (2-DE) and tandem mass spectrometry, yielded expression profiles for 379 2-DE spots through seed development. Despite the paucity of genomic resources for flax, the identity for 102 proteins was reliably determined. These proteins were sorted into 11 metabolic functional classes. Proteins of unknown function comprise the largest group, and displayed a pattern of decreased abundance throughout seed development. Analysis of the composite expression profiles for metabolic protein classes revealed specific expression patterns during seed development. For example, there was an overall decrease in abundance of the glycolytic enzymes during seed development.

Plastid control of abaxial-adaxial patterning

Translational regulation, exerted by the cytosolic ribosome, has been shown to participate in the establishment of abaxial-adaxial polarity in Arabidopsis thaliana: many hypomorphic and null alleles of genes encoding proteins of the cytosolic ribosome enhance the leaf polarity defects of asymmetric leaves1 (as1) and as2 mutants. Here, we report the identification of the SCABRA1 (SCA1) nuclear gene, whose loss-of-function mutations also enhance the polarity defects of the as2 mutants. In striking contrast to other previously known enhancers of the phenotypes caused by the as1 and as2 mutations, we found that SCA1 encodes a plastid-type ribosomal protein that functions as a structural component of the 70S plastid ribosome and, therefore, its role in abaxial-adaxial patterning was not expected.

Methodological Approaches to Simple Enzyme Polymorphism Analyses of Amaranth Species (Amaranthus SP.)

Methodological Approaches to Simple Enzyme Polymorphism Analyses of Amaranth Species (Amaranthus SP.) Amaranths have drawn a great interest in last years as an agronomic crop, alternative energy source and ornamental plants around the world. Several of them are cultivated as the leaf vegetables, cereals, or as the colourful, quick growing garden plants. Increasing demand for the breeding and proteomic study in Amaranthus species led us to test some methodological approaches to enzyme polymorphism analysis. For these experiments genotypes of Amaranthus cruentus L. (genotype Ficha) and mutant line of hybrid K-433 were selected, characterized by a good seed quality and quantity, suitable for food production. The attention was devoted to test of published methodology, which were slightly modified for enzyme (ACP, ADH, CAT, DIA, GOT, IDH, MDH, PGD, PGI and PGM) multiplicity analysis for amaranths and testing of feasibility of chosen analysed organ weights, dimensions of Whatman No. 2 wicks and different volumes of extract buffer. Results from enzyme multiplicity analysis are presented by means of photographed fingerprints and phenotypes are expressed in diagrams where positions of zymograme bands are marked by using factors of relative mobility (Rm).

Revealing the seed proteome of the health benefitting grain amaranth (Amaranthus cruentus L.)

Amaranth, a staple food source in ancient Aztec, Maya and Inca cultures, has been recognised as a 21st century crop. This superfood, known as Inca wheat, attracts the worldwide attention of researchers and farmers for its superior agronomical and technological properties but especially because of its exceptional nutritive value. A combination of two-dimensional electrophoresis (2-DE) with MS facilitating the effective differentiation of 13 classes of Amaranthus cruentus L. “Ficha” mature seed proteins was used in the current study. The best resolution results in the 2-DE were obtained using immobilised pH gradients strips with a pH range of 5–8. Out of the 461 spots detected, 249 were successfully identified by LC-MS/MS analysis, making this the most inclusive protein profile of mature amaranth seed. Unknown proteins represented the most abundant class of proteins (59), the second most abundant category was related to energy (46) and then to seed storage proteins (43). These results expand the knowledge of the amaranth seed proteome and it is expected that the data presented here will contribute to further in-depth characterisation of Amaranthus seeds.

Unravelling Gene Function Through Mutagenesis

In recent years, plant research has received a significant boost, partly due to the huge amount of data derived from the sequencing projects of some genomes, especially those obtained in the model system Arabidopsis thaliana. The use of this crucifer in many plant biology laboratories all over the world, together with the development of new technologies, have considerably increased research resources for dissecting gene function. Forward and reverse genetic approaches are still fundamental for assessing gene function through the isolation and characterization of mutants. In this chapter, we first take an overview, using Arabidopsis as a reference, of the methodologies and procedures used to infer gene function in plants through mutagenesis screens and look at how high-throughput analysis of gene-indexed mutant collections is contributing to assessing plant gene function on a genomic scale. We then discuss the forward and reverse genetic approaches currently used in crops for understanding gene function, highlighting the importance of mutagenesis as a basis for generating useful genetic variants and its significance for crop improvement.

Visualization of gene expression by fluorescent multiplex reverse transcriptase-PCR amplification.

Many developmental and physiological analyses, population studies, and diagnostic tests can be performed by simply determining the presence or absence of a limited number of gene products. Here, we describe a rapid and sensitive procedure, based on the reverse transcription of total RNA samples followed by the co-amplification of specific complementary DNA molecules, for the simultaneous detection of different transcripts. Multiplex PCR amplification products are obtained in a single reaction mix containing several primer pairs, each of which includes a fluorescently labeled oligonucleotide; the amplification products are finally electrophoresed in an automated DNA sequencer controlled by fragment analysis software. The electropherograms obtained in this way allow a semiquantitative and efficient visualization of gene expression.