A fast, efficient and high-throughput procedure involving laser microdissection and RT droplet digital PCR for tissue-specific expression profiling of rice roots

Background

In rice, the cortex and outer tissues play a key role in submergence tolerance. The cortex differentiates into aerenchyma, which are air-containing cavities that allow the flow of oxygen from shoots to roots, whereas exodermis suberification and sclerenchyma lignification limit oxygen loss from the mature parts of roots by forming a barrier to root oxygen loss (ROL). The genes and their networks involved in the cellular identity and differentiation of these tissues remain poorly understood. Identification and characterization of key regulators of aerenchyma and ROL barrier formation require determination of the specific expression profiles of these tissues.

Results

We optimized an approach combining laser microdissection (LM) and droplet digital RT-PCR (ddRT-PCR) for high-throughput identification of tissue-specific expression profiles. The developed protocol enables rapid (within 3 days) extraction of high-quality RNA from root tissues with a low contamination rate. We also demonstrated the possibility of extracting RNAs from paraffin blocks stored at 4 °C without any loss of quality. We included a detailed troubleshooting guide that should allow future users to adapt the proposed protocol to other tissues and/or species. We demonstrated that our protocol, which combines LM with ddRT-PCR, can be used as a complementary tool to in situ hybridization for tissue-specific characterization of gene expression even with a low RNA concentration input. We illustrated the efficiency of the proposed approach by validating three of four potential tissue-specific candidate genes detailed in the RiceXpro database.

Conclusion

The detailed protocol and the critical steps required to optimize its use for other species will democratize tissue-specific transcriptome approaches combining LM with ddRT-PCR for analyses of plants.

Local signalling pathways regulate the Arabidopsis root developmental response to Mesorhizobium loti inoculation

Numerous reports have shown that various rhizobia can interact with non-host plant species, improving mineral nutrition and promoting plant growth. To further investigate the effects of such non-host interactions on root development and functions, we inoculated Arabidopsis thaliana with the model nitrogen fixing rhizobacterium Mesorhizobium loti (strain MAFF303099). In vitro, we show that root colonization by M. loti remains epiphytic and that M. loti cells preferentially grow at sites where primary and secondary roots intersect. Besides resulting in an increase in shoot biomass production, colonization leads to transient inhibition of primary root growth, strong promotion of root hair elongation and increased apoplasmic acidification in periphery cells of a sizeable part of the root system. Using auxin mutants, axr1-3 and aux1-100, we show that a plant auxin pathway plays a major role in inhibiting root growth but not in promoting root hair elongation, indicating that root developmental responses involve several distinct pathways. Finally, using a split root device, we demonstrate that root colonization by M. loti, as well as by the bona fide plant growth promoting rhizobacteria Azospirillum brasilense and Pseudomonas, affect root development via local transduction pathways restricted to the colonised regions of the root system.

Interact to survive: Phyllobacterium brassicacearum improves Arabidopsis tolerance to severe water deficit and growth recovery

Mutualistic bacteria can alter plant phenotypes and confer new abilities to plants. Some plant growth-promoting rhizobacteria (PGPR) are known to improve both plant growth and tolerance to multiple stresses, including drought, but reports on their effects on plant survival under severe water deficits are scarce. We investigated the effect of Phyllobacterium brassicacearum STM196 strain, a PGPR isolated from the rhizosphere of oilseed rape, on survival, growth and physiological responses of Arabidopsis thaliana to severe water deficits combining destructive and non-destructive high-throughput phenotyping. Soil inoculation with STM196 greatly increased the survival rate of A. thaliana under several scenarios of severe water deficit. Photosystem II efficiency, assessed at the whole-plant level by high-throughput fluorescence imaging (Fv/Fm), was related to the probability of survival and revealed that STM196 delayed plant mortality. Inoculated surviving plants tolerated more damages to the photosynthetic tissues through a delayed dehydration and a better tolerance to low water status. Importantly, STM196 allowed a better recovery of plant growth after rewatering and stressed plants reached a similar biomass at flowering than non-stressed plants. Our results highlight the importance of plant-bacteria interactions in plant responses to severe drought and provide a new avenue of investigations to improve drought tolerance in agriculture.

The PGPR strain Phyllobacterium brassicacearum STM196 induces a reproductive delay and physiological changes that result in improved drought tolerance in Arabidopsis

Understanding how biotic interactions can improve plant tolerance to drought is a challenging prospect for agronomy and ecology. Plant growth-promoting rhizobacteria (PGPR) are promising candidates but the phenotypic changes induced by PGPR under drought remain to be elucidated. We investigated the effects of Phyllobacterium brassicacearum STM196 strain, a PGPR isolated from the rhizosphere of oilseed rape, on two accessions of Arabidopsis thaliana with contrasting flowering time. We measured multiple morphophysiological traits related to plant growth and development in order to quantify the added value of the bacteria to drought-response strategies of Arabidopsis in soil conditions. A delay in reproductive development induced by the bacteria resulted in a gain of biomass that was independent of the accession and the watering regime. Coordinated changes in transpiration, ABA content, photosynthesis and development resulted in higher water-use efficiency and a better tolerance to drought of inoculated plants. Our findings give new insights into the ecophysiological bases by which PGPR can confer stress tolerance to plants. Rhizobacteria-induced delay in flowering time could represent a valuable strategy for increasing biomass yield, whereas rhizobacteria-induced improvement of water use is of particular interest in multiple scenarios of water availability.

The NRT2.5 and NRT2.6 genes are involved in growth promotion of Arabidopsis by the plant growth-promoting rhizobacterium (PGPR) strain Phyllobacterium brassicacearum STM196

The Phyllobacterium brassicacearum STM196 strain stimulates Arabidopsis thaliana growth and antagonizes high nitrate inhibition of lateral root development. A previous study identified two STM196-responsive genes, NRT2.5 and NRT2.6 (Mantelin et al., 2006, Planta 223: 591-603). We investigated the role of NRT2.5 and NRT2.6 in the plant response to STM196 using single and double Arabidopsis mutants. The single mutants were also crossed with an nrt2.1 mutant, lacking the major nitrate root transporter, to distinguish the effects of NRT2.5 and NRT2.6 from potential indirect effects of nitrate pools. The nrt2.5 and nrt2.6 mutations abolished the plant growth and root system architecture responses to STM196. The determination of nitrate content revealed that NRT2.5 and NRT2.6 do not play an important role in nitrate distribution between plant organs. Conversely, NRT2.5 and NRT2.6 appeared to play a role in the plant response independent of nitrate uptake. Using a nitrate reductase mutant, it was confirmed that the NRT2.5/NRT2.6-dependent plant signalling pathway is independent of nitrate-dependent regulation of root development. Our findings demonstrate that NRT2.5 and NRT2.6, which are preferentially expressed in leaves, play an essential role in plant growth promotion by the rhizospheric bacterium STM196.

The ethylene pathway contributes to root hair elongation induced by the beneficial bacteria Phyllobacterium brassicacearum STM196

In Arabidopsis roots, some epidermal cells differentiate into root hair cells. Auxin regulates root hair positioning, while ethylene controls cell elongation. Phyllobacterium brassicacearum STM196, a beneficial strain of plant growth promoting rhizobacteria (PGPR) isolated from the roots of field-grown oilseed rape, stimulates root hair elongation in Arabidopsis thaliana seedlings. We investigated the role of ethylene in the response of root hair cells to STM196 inoculation. While we could not detect a significant increase in ethylene biosynthesis, we could detect a slight activation of the ethylene signalling pathway. Consistent with this, an exhaustive survey of the root hair elongation response of mutants and transgenic lines affected in the ethylene pathway showed contrasting root hair sensitivities to STM196. We propose that local ethylene emission contributes to STM196-induceed root hair elongation.

The auxin-signaling pathway is required for the lateral root response of Arabidopsis to the rhizobacterium Phyllobacterium brassicacearum

Plant root development is highly responsive both to changes in nitrate availability and beneficial microorganisms in the rhizosphere. We previously showed that Phyllobacterium brassicacearum STM196, a plant growth-promoting rhizobacteria strain isolated from rapeseed roots, alleviates the inhibition exerted by high nitrate supply on lateral root growth. Since soil-borne bacteria can produce IAA and since this plant hormone may be implicated in the high nitrate-dependent control of lateral root development, we investigated its role in the root development response of Arabidopsis thaliana to STM196. Inoculation with STM196 resulted in a 50% increase of lateral root growth in Arabidopsis wild-type seedlings. This effect was completely abolished in aux1 and axr1 mutants, altered in IAA transport and signaling, respectively, indicating that these pathways are required. The STM196 strain, however, appeared to be a very low IAA producer when compared with the high-IAA-producing Azospirillum brasilense sp245 strain and its low-IAA-producing ipdc mutant. Consistent with the hypothesis that STM196 does not release significant amounts of IAA to the host roots, inoculation with this strain failed to increase root IAA content. Inoculation with STM196 led to increased expression levels of several IAA biosynthesis genes in shoots, increased Trp concentration in shoots, and increased auxin-dependent GUS staining in the root apices of DR5::GUS transgenic plants. All together, our results suggest that STM196 inoculation triggers changes in IAA distribution and homeostasis independently from IAA release by the bacteria.

PGPR-Arabidopsis interactions is a useful system to study signaling pathways involved in plant developmental control

Using their 1-amino cyclopropane-1-carboxylic acid (ACC) deaminase activity, many rhizobacteria can divert ACC from the ethylene biosynthesis pathway in plant roots. To investigate the role of this microbial activity in plant responses to plant growth-promoting rhizobacteria (PGPR), we analyzed the effects of acdS knock-out and wild-type PGPR strains on two phenotypic responses to inoculation—root hair elongation and root system architecture—in Arabidopsis thaliana . Our work shows that rhizobacterial AcdS activity has a negative effect on root hair elongation, as expected from the reduction of ethylene production rate in root cells, while it has no impact on root system architecture. This suggests that PGPR triggered root hair elongation is independent of ethylene biosynthesis or signaling pathway. In addition, it does indicate that AcdS activity alters local regulatory processes, but not systemic regulations such as those that control root architecture. Our work also indicates that root hair elongation induced by PGPR inoculation is probably an auxin-independent mechanism. These findings were unexpected since genetic screens for abnormal root hair development mutants led to the isolation of ethylene and auxin mutants. Our work hence shows that studying the interaction between a PGPR and the model plant Arabidopsis is a useful system to uncover new pathways involved in plant plasticity.

Expression and cellular localization of Atrab28 during arabidopsis embryogenesis

The maize abscisic acid (ABA)-responsive gene rab28 has been shown to be ABA-inducible in embryos and vegetative tissues, expression being mostly restricted to vascular elements during late embryogenesis. In the course of an expressed sequence tags (ESTs) programme, we have isolated an Arabidopsis thaliana gene, Atrab28, encoding the orthologue of maize rab28. The Atrab28 cDNA is 1090 bp long, including a poly(A)+ stretch, and encodes a polypeptide of 262 amino acids. Atrab28 antibody against the recombinant protein recognizes a polipeptide of about 30 kDa and pI 6, in close agreement with the predicted molecular mass and pI. As for maize rab28, expression studies with Atrab28 revealed high specificity for embryo tissues, transcription being stimulated by the transcriptional activator abi3. In contrast, Atrab28 was not induced in vegetative tissues by ABA, osmotic stress or dehydration. The expression of Atrab28 mRNA and the accumulation of Atrab28 protein was largely restricted to provascular tissues of mature embryos and in the seed coat outer tegument and embryo and silique epidermis, as revealed by in situ hybridization and immunocytochemistry with anti-Atrab28 antibodies.

A YAC contig map of Arabidopsis thaliana chromosome 3

We have constructed a YAC contig map of Arabidopsis thaliana chromosome 3. From an estimated total size of 25 Mb, about 21 Mb were covered by 148 clones arranged into nine YAC contigs, which represented most of the low-copy regions of the chromosome. YAC clones were anchored with 259 molecular markers, including 111 for which linkage information was previously available. Most of the genetic map was included in the YAC coverage, and more than 60% of the genetic markers from the reference recombinant inbred line map were anchored, giving a high level of integration between the genetic and physical maps. The submetacentric structure of the chromosome was confirmed by physical data; 3R (the top arm of the linkage map) was about 12 Mb, and 3L (the bottom arm of the linkage map) was about 9 Mb. This YAC physical map will aid in chromosome walking experiments and provide a framework for large-scale DNA sequencing of chromosome 3.

Sequencing and mapping the Arabidopsis genome: a weed model for real crops

Arabidopsis is a crucifer weed with a small genome of about 120 Mbp which has been chosen as a model species for plant molecular genetics. Four years ago, a consortium of nine French laboratories, including ours, initiated a project aimed at mapping the transcribed regions of the genome. The strategy employed was to systematically and randomly sequence cDNA clones isolated from libraries made from different tissues and organs of plants grown under various physiological conditions. The consortium released about 7,000 expressed sequenced tags (ESTs) in the dbEST database corresponding to approximately 3,500 unique genes. In the next phase of the programme, a YAC library with average inserts of 500 kbp has been prepared. We have now started to use the EST information to map the cDNA clones on these YACs. The most recent aspect of Arabidopsis sequencing is the ESSA (European Scientists Sequencing Arabidopsis) project, in which the aim is to describe 2.5 Mbp by the end of 1996. Genomic sequencing has revealed a very high gene density. Comparison of present genomic sequencing results with the EST data suggests that up to half of the genes might already be tagged with an EST. In collaboration with Carlos Quiros' group in Davis we have also analysed the conservation of a 30 kbp locus (Em 1, a late embryogenesis abundant protein gene) on chromosome 3 between Arabidopsis and several Brassica species. Progress on these various aspects will be reviewed. We shall also present some sequence comparisons between Arabidopsis and rice ESTs. These results suggest that it should be possible in the very near future to map a pool of common genes onto many different plant genomes. This should provide a common framework to integrate maps from different species and facilitate mapbased cloning of genes of agronomical importance.