Scaling nitrogen and carbon interactions: what are the consequences of biological buffering?

Arabidopsis Growth-Promotion and Root Architecture Responses to the Beneficial Rhizobacterium Phyllobacterium brassicacearum Strain STM196 Are Independent of the Nitrate Assimilatory Pathway

Phyllobacterium brassicacearum STM196, a plant growth-promoting rhizobacterium isolated from roots of oilseed rape, stimulates Arabidopsis growth. We have previously shown that the NRT2.5 and NRT2.6 genes are required for this growth promotion response. Since these genes are members of the NRT2 family of nitrate transporters, the nitrogen assimilatory pathway could be involved in growth promotion by STM196. We address this hypothesis using two nitrate reductase mutants, G5 deleted in the major nitrate reductase gene NIA2 and G′4-3 altered in both NIA1 and NIA2 genes. Both mutants had a reduced growth rate and STM196 failed to increase their biomass production on a medium containing NO3− as the sole nitrogen source. However, they both displayed similar growth promotion by STM196 when grown on an NH4+ medium. STM196 was able to stimulate lateral roots development of the mutants under both nutrition conditions. Altogether, our results indicate that the nitrate assimilatory metabolism is not a primary target of STM196 interaction and is not involved in the root developmental response. The NIA1 transcript level was reduced in the shoots of nrt2.5 and nrt2.6 mutants suggesting a role for this nitrate reductase isoform independently from its role in nitrate assimilation.

LeBoldus J, Keefover‐Ring K, Azeem M, Chen J, Macaya‐Sanz D, MacDonald WL, Muchero W, DiFazio SP. Host plant genetic control of associated fungal and insect species in a Populus hybrid cross

Plants employ a diverse set of defense mechanisms to mediate interactions with insects and fungi. These relationships can leave lasting impacts on host plant genome structure such as rapid expansion of gene families through tandem duplication. These genomic signatures provide important clues about the complexities of plant/biotic stress interactions and evolution. We used a pseudo-backcross hybrid family to identify quantitative trait loci (QTL) controlling associations between Populus trees and several common Populus diseases and insects. Using whole-genome sequences from each parent, we identified candidate genes that may mediate these interactions. Candidates were partially validated using mass spectrometry to identify corresponding QTL for defensive compounds. We detected significant QTL for two interacting fungal pathogens and three insects. The QTL intervals contained candidate genes potentially involved in physical and chemical mechanisms of host-plant resistance and susceptibility. In particular, we identified adjoining QTLs for a phenolic glycoside and Phyllocolpa sawfly abundance. There was also significant enrichment of recent tandem duplications in the genomic intervals of the native parent, but not the exotic parent. Tandem gene duplication may be an important mechanism for rapid response to biotic stressors, enabling trees with long juvenile periods to reach maturity despite many coevolving biotic stressors.

In Situ Study of Metabolic Response of Arabidopsis thaliana Leaves to Salt Stress by Neutral Desorption-Extractive Electrospray Ionization Mass Spectrometry

Salt stress is one of the most common factors limiting plant cultivation. In this study, metabolic responses to salt stress in Arabidopsis thaliana (A. thaliana) leaves were analyzed in situ by neutral desorption-extractive electrospray ionization mass spectrometry (ND-EESI-MS) without any sample pretreatment. Metabolic changes of A. thaliana leaves were observed in response to salt stress conditions, including the levels of serine, glutamic acid, arginine, cinnamic acid, ferulic acid, caffeic acid, protocatechuic acid, epicatechin, morin, myricetin, apigravin, and β-cotonefuran. The content of serine increased under 50, 100, and 200 mM NaCl salt stress, reaching the highest level at 200 mM NaCl, but decreased under the maximum concentration of 300 mM NaCl. A similar phenomenon was observed for arginine, glutamic acid, cinnamic acid, caffeic acid, ferulic acid, and epicatechin, respectively, involved in the metabolic pathway of shikimate-phenylpropanoid. Both principal component analysis (PCA) and partial least-squares discrimination analysis (PLS-DA) showed that the salt stress treatment groups of the higher concentrations (200 and 300 mM) could be well distinguished from those of the lower concentrations (50 and 100 mM) and the control. Marker metabolites, like m/z 261 (apigravin) and m/z 305 (β-cotonefuran), were assistantly selected from the fingerprints by variable importance for the projection (VIP). Our results indicated the potential of the ND-EESI-MS method for the rapid recognition of metabolic conditions in plant leaves under salt stress.

Advances and perspectives on the use of CRISPR/Cas9 systems in plant genomics research

Genome editing with site-specific nucleases has become a powerful tool for functional characterization of plant genes and genetic improvement of agricultural crops. Among the various site-specific nuclease-based technologies available for genome editing, the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems have shown the greatest potential for rapid and efficient editing of genomes in plant species. This article reviews the current status of application of CRISPR/Cas9 to plant genomics research, with a focus on loss-of-function and gain-of-function analysis of individual genes in the context of perennial plants and the potential application of CRISPR/Cas9 to perturbation of gene expression, and identification and analysis of gene modules as part of an accelerated domestication and synthetic biology effort.