Without roots there would be no rhizosphere and no rhizodeposition to fuel microbial activity. Although micro-organisms may view roots merely as a source of carbon supply this belies the fascinating complexity and diversity of root systems that occurs despite their common function. Here, we examine the physiological and genetic determinants of root growth and the complex, yet varied and flexible, root architecture that results. The main functions of root systems are also explored including how roots cope with nutrient acquisition from the heterogeneous soil environment and their ability to form mutualistic associations with key soil microorganisms (such as nitrogen fixing bacteria and mycorrhizal fungi) to aid them in their quest for nutrients. Finally, some key biotic and abiotic constraints on root development and function in the soil environment are examined and some of the adaptations roots have evolved to counter such stresses discussed.Keywords Root systems . Auxin . Root architecture . Soil heterogeneity . Abiotic and biotic stresses . Soil micro-organisms (including nitrogen-fixing bacteria and mycorrhizal fungi)Physiological and genetic determinants of root growth and achitecture A major difference between plant and animal development is that positional information rather than cell lineage determines cell fate in plants (Singh and Bhalla 2006). Post-embryonically, plant development is essentially driven by stem cells localized in apical regions of shoots and roots, and referred to as apical meristems. This particular characteristic allows plants, Plant Soil (

Long non-protein coding RNAs (npcRNA) represent an emerging class of riboregulators, which either act directly in this long form or are processed to shorter miRNA and siRNA. Genome-wide bioinformatic analysis of full-length cDNA databases identified 76 Arabidopsis npcRNAs. Fourteen npcRNAs were antisense to protein-coding mRNAs, suggesting cis-regulatory roles. Numerous 24-nt siRNA matched to five different npcRNAs, suggesting that these npcRNAs are precursors of this type of siRNA. Expression analyses of the 76 npcRNAs identified a novel npcRNA that accumulates in a dcl1 mutant but does not appear to produce trans-acting siRNA or miRNA. Additionally, another npcRNA was the precursor of miR869 and shown to be up-regulated in dcl4 but not in dcl1 mutants, indicative of a young miRNA gene. Abiotic stress altered the accumulation of 22 npcRNAs among the 76, a fraction significantly higher than that observed for the RNA binding protein-coding fraction of the transcriptome. Overexpression analyses in Arabidopsis identified two npcRNAs as regulators of root growth during salt stress and leaf morphology, respectively. Hence, together with small RNAs, long npcRNAs encompass a sensitive component of the transcriptome that have diverse roles during growth and differentiation.[Supplemental material is available online at www.genome.org.]Non-protein coding RNAs (npcRNAs) are a class of RNAs that do not encode proteins, but instead their function lies on the RNA molecule. They are a heterogeneous group and have been divided into different classes according to their length and function. With respect to length, npcRNAs can range from 20 to 27 nucleotides (nt) for the families of microRNAs (miRNAs) and small interfering RNAs (siRNAs), 20-300 nt for small RNAs commonly found as transcriptional and translational regulators, or up to and beyond 10,000 nt for medium and large RNAs involved in other processes, including splicing, gene inactivation, and translation (Costa 2007). We use the term non-protein-coding RNAs instead of noncoding RNAs as every sequence has the potential to be coding, and certain large npcRNAs might encode small oligopeptides, which could be translated under specific conditions as shown for a pentapeptide located inside rRNA, a canonical RNA in Escherichia coli (Tenson et al. 1996). In recent years, numerous novel npcRNA candidates have been identified in a variety of organisms from E. coli to Homo sapiens (Argaman et al. 2001;Storz et al. 2004;Washietl et al. 2005).Several strategies have been employed to detect and discover novel npcRNAs, including both experimental and computational screenings (Huttenhofer et al. 2002). Genomic approaches, such as tiling arrays and systematic sequencing of full-length cDNA libraries, in model organisms have recently revealed that much larger portions of eukaryote transcriptomes represent nonprotein-coding transcripts than previously believed (Okazaki et al. 2002;Numata et al. 2003;Rinn et al. 2003;Ota et al. 2004;Chekanova et al. 2007). Diverse npcRNAs, including a surpris...

A strict gluten-free diet (GFD) is the only currently available therapeutic treatment for patients with celiac disease (CD). Traditionally, treatment with a GFD has excluded wheat, barley and rye, while the presence of oats is a subject of debate. The most-recent research indicates that some cultivars of oats can be a safe part of a GFD. In order to elucidate the toxicity of the prolamins from oat varieties with low, medium, and high CD toxicity, the avenin genes of these varieties were cloned and sequenced, and their expression quantified throughout the grain development. At the protein level, we have accomplished an exhaustive characterization and quantification of avenins by RP-HPLC and an analysis of immunogenicity of peptides present in prolamins of different oat cultivars. Avenin sequences were classified into three different groups, which have homology with S-rich prolamins of Triticeae. Avenin proteins presented a lower proline content than that of wheat gliadin; this may contribute to the low toxicity shown by oat avenins. The expression of avenin genes throughout the development stages has shown a pattern similar to that of prolamins of wheat and barley. RP-HPLC chromatograms showed protein peaks in the alcohol-soluble and reduced-soluble fractions. Therefore, oat grains had both monomeric and polymeric avenins, termed in this paper gliadin- and glutenin-like avenins. We found a direct correlation between the immunogenicity of the different oat varieties and the presence of the specific peptides with a higher/lower potential immunotoxicity. The specific peptides from the oat variety with the highest toxicity have shown a higher potential immunotoxicity. These results suggest that there is wide range of variation of potential immunotoxicity of oat cultivars that could be due to differences in the degree of immunogenicity in their sequences.

In plants, a diverse group of cell surface receptor-like protein kinases (RLKs) plays a fundamental role in sensing external signals to regulate gene expression. Roots explore the soil environment to optimize their growth via complex signaling cascades, mainly analyzed in Arabidopsis thaliana. However, legume roots have significant physiological differences, notably their capacity to establish symbiotic interactions. These major agricultural crops are affected by environmental stresses such as salinity. Here, we report the identification of a leucine-rich repeat RLK gene, Srlk, from the legume Medicago truncatula. Srlk is rapidly induced by salt stress in roots, and RNA interference (RNAi) assays specifically targeting Srlk yielded transgenic roots whose growth was less inhibited by the presence of salt in the medium. Promoter-b-glucuronidase fusions indicate that this gene is expressed in epidermal root tissues in response to salt stress. Two Srlk-TILLING mutants also failed to limit root growth in response to salt stress and accumulated fewer sodium ions than controls. Furthermore, early salt-regulated genes are downregulated in Srlk-RNAi roots and in the TILLING mutant lines when submitted to salt stress. We propose a role for Srlk in the regulation of the adaptation of M. truncatula roots to salt stress.