Size does matter: piRNA and miRNA targeting.

Piwi-interacting RNAs (piRNAs) guide PIWI proteins to bind and cleave RNAs. Originally, piRNAs were described as a system for transposable element repression. Recently, Anzelon, Choudhury, Hughes et al. uncovered the structural basis for piRNA targeting, whereby they are recognized in a manner distinct from targeting by miRNAs.

Uncovering the Mechanical Code of DNA Using 'Loop-seq'.

DNA mechanical properties play a critical role in different biological processes. Basu and coworkers described a method that measures DNA mechanics on the genome scale. Access to a high-throughput tool for measuring DNA mechanics opens up new possibilities to investigate this phenomenon with respect to establishing the chromatin regulatory landscape.

Strigolactones and abscisic acid interactions affect plant development and response to abiotic stresses.

Strigolactones (SL) are the youngest group of plant hormones responsible for shaping plant architecture, especially the branching of shoots. However, recent studies provided new insights into the functioning of SL, confirming their participation in regulating the plant response to various types of abiotic stresses, including water deficit, soil salinity and osmotic stress. On the other hand, abscisic acid (ABA), commonly referred as a stress hormone, is the molecule that crucially controls the plant response to adverse environmental conditions. Since the SL and ABA share a common precursor in their biosynthetic pathways, the interaction between both phytohormones has been largely studied in the literature. Under optimal growth conditions, the balance between ABA and SL content is maintained to ensure proper plant development. At the same time, the water deficit tends to inhibit SL accumulation in the roots, which serves as a sensing mechanism for drought, and empowers the ABA production, which is necessary for plant defense responses. The SL-ABA cross-talk at the signaling level, especially regarding the closing of the stomata under drought conditions, still remains poorly understood. Enhanced SL content in shoots is likely to stimulate the plant sensitivity to ABA, thus reducing the stomatal conductance and improving the plant survival rate. Besides, it was proposed that SL might promote the closing of stomata in an ABA-independent way. Here, we summarize the current knowledge regarding the SL and ABA interactions by providing new insights into the function, perception and regulation of both phytohormones during abiotic stress response of plants, as well as revealing the gaps in the current knowledge of SL-ABA cross-talk.

Multi-omics insights into the positive role of strigolactone perception in barley drought response.

BACKGROUND: Drought is a major environmental stress that affects crop productivity worldwide. Although previous research demonstrated links between strigolactones (SLs) and drought, here we used barley (Hordeum vulgare) SL-insensitive mutant hvd14 (dwarf14) to scrutinize the SL-dependent mechanisms associated with water deficit response. RESULTS: We have employed a combination of transcriptomics, proteomics, phytohormonomics analyses, and physiological data to unravel differences between wild-type and hvd14 plants under drought. Our research revealed that drought sensitivity of hvd14 is related to weaker induction of abscisic acid-responsive genes/proteins, lower jasmonic acid content, higher reactive oxygen species content, and lower wax biosynthetic and deposition mechanisms than wild-type plants. In addition, we identified a set of transcription factors (TFs) that are exclusively drought-induced in the wild-type barley. CONCLUSIONS: Critically, we resolved a comprehensive series of interactions between the drought-induced barley transcriptome and proteome responses, allowing us to understand the profound effects of SLs in alleviating water-limiting conditions. Several new avenues have opened for developing barley more resilient to drought through the information provided. Moreover, our study contributes to a better understanding of the complex interplay between genes, proteins, and hormones in response to drought, and underscores the importance of a multidisciplinary approach to studying plant stress response mechanisms.

New insights into the function of mammalian Argonaute2.

Uncovering the mechanisms that recognise a microRNA (miRNA) target is 1 of the biggest challenges because the Ago-miRNA complex is able to overcome different derogations of complementarity when binding targets. However, the recently solved crystallographic structure of Argonaute2 (Ago2) and a high-throughput analysis that used repurposed sequencing techniques has brought us closer to achieving this goal.

Changes in plastid biogenesis leading to the formation of albino regenerants in barley microspore culture.

BACKGROUND: Microspore embryogenesis is potentially the most effective method of obtaining doubled haploids (DH) which are utilized in breeding programs to accelerate production of new cultivars. However, the regeneration of albino plants significantly limits the exploitation of androgenesis for DH production in cereals. Despite many efforts, the precise mechanisms leading to development of albino regenerants have not yet been elucidated. The objective of this study was to reveal the genotype-dependent molecular differences in chloroplast differentiation that lead to the formation of green and albino regenerants in microspore culture of barley. RESULTS: We performed a detailed analysis of plastid differentiation at successive stages of androgenesis in two barley cultivars, 'Jersey' and 'Mercada' that differed in their ability to produce green regenerants. We demonstrated the lack of transition from the NEP-dependent to PEP-dependent transcription in plastids of cv. 'Mercada' that produced mostly albino regenerants in microspore culture. The failed NEP-to-PEP transition was associated with the lack of activity of Sig2 gene encoding a sigma factor necessary for transcription of plastid rRNA genes. A very low level of 16S and 23S rRNA transcripts and impaired plastid translation machinery resulted in the inhibition of photomorphogenesis in regenerating embryos and albino regenerants. Furthermore, the plastids present in differentiating 'Mercada' embryos contained a low number of plastome copies whose replication was not always completed. Contrary to 'Mercada', cv. 'Jersey' that produced 90% green regenerants, showed the high activity of PEP polymerase, the highly increased expression of Sig2, plastid rRNAs and tRNAGlu, which indicated the NEP inhibition. The increased expression of GLKs genes encoding transcription factors required for induction of photomorphogenesis was also observed in 'Jersey' regenerants. CONCLUSIONS: Proplastids present in microspore-derived embryos of albino-producing genotypes did not pass the early checkpoints of their development that are required for induction of further light-dependent differentiation of chloroplasts. The failed activation of plastid-encoded RNA polymerase during differentiation of embryos was associated with the genotype-dependent inability to regenerate green plants in barley microspore culture. The better understanding of molecular mechanisms underlying formation of albino regenerants may be helpful in overcoming the problem of albinism in cereal androgenesis.

Whole Exome Sequencing-Based Identification of a Novel Gene Involved in Root Hair Development in Barley (Hordeum vulgare L.).

Root hairs play a crucial role in anchoring plants in soil, interaction with microorganisms and nutrient uptake from the rhizosphere. In contrast to Arabidopsis, there is a limited knowledge of root hair morphogenesis in monocots, including barley (Hordeum vulgare L.). We have isolated barley mutant rhp1.e with an abnormal root hair phenotype after chemical mutagenesis of spring cultivar 'Sebastian'. The development of root hairs was initiated in the mutant but inhibited at the very early stage of tip growth. The length of root hairs reached only 3% of the length of parent cultivar. Using a whole exome sequencing (WES) approach, we identified G1674A mutation in the HORVU1Hr1G077230 gene, located on chromosome 1HL and encoding a cellulose synthase-like C1 protein (HvCSLC1) that might be involved in the xyloglucan (XyG) synthesis in root hairs. The identified mutation led to the retention of the second intron and premature termination of the HvCSLC1 protein. The mutation co-segregated with the abnormal root hair phenotype in the F2 progeny of rhp1.e mutant and its wild-type parent. Additionally, different substitutions in HORVU1Hr1G077230 were found in four other allelic mutants with the same root hair phenotype. Here, we discuss the putative role of HvCSLC1 protein in root hair tube elongation in barley.

Barley strigolactone signalling mutant hvd14.d reveals the role of strigolactones in abscisic acid-dependent response to drought.

Strigolactones (SLs) are a group of plant hormones involved in many aspects of plant development and stress adaptation. Here, we investigated the drought response of a barley (Hordeum vulgare L.) mutant carrying a missense mutation in the gene encoding the SL-specific receptor HvD14. Our results clearly showed that hvd14.d mutant is hyper-sensitive to drought stress. This was illustrated by a lower leaf relative water content (RWC), impaired photosynthesis, disorganization of chloroplast structure, altered stomatal density and slower closure of stomata in response to drought in the mutant compared to the wild type parent cultivar Sebastian. Although the content of abscisic acid (ABA) and its derivatives remained unchanged in the mutant, significant differences in expression of genes related to ABA biosynthesis were observed. Moreover, hvd14.d was insensitive to ABA during seed germination. Analysis of Arabidopsis thaliana mutant atd14-1 also demonstrated that mutation in the SL receptor resulted in increased sensitivity to drought. Our results indicate that the drought-sensitive phenotype of barley SL mutant might be caused by a disturbed ABA metabolism and/or signalling pathways. These results together uncovered a link between SL signalling and ABA-dependent drought stress response in barley.

Key Hormonal Components Regulate Agronomically Important Traits in Barley.

The development and growth of plant organs is regulated by phytohormones, which constitute an important area of plant science. The last decade has seen a rapid increase in the unravelling of the pathways by which phytohormones exert their influence. Phytohormones function as signalling molecules that interact through a complex network to control development traits. They integrate metabolic and developmental events and regulate plant responses to biotic and abiotic stress factors. As such, they influence the yield and quality of crops. Recent studies on barley have emphasised the importance of phytohormones in promoting agronomically important traits such as tillering, plant height, leaf blade area and spike/spikelet development. Understanding the mechanisms of how phytohormones interact may help to modify barley architecture and thereby improve its adaptation and yield. To achieve this goal, extensive functional validation analyses are necessary to better understand the complex dynamics of phytohormone interactions and phytohormone networks that underlie the biological processes. The present review summarises the current knowledge on the crosstalk between phytohormones and their roles in barley development. Furthermore, an overview of how phytohormone modulation may help to improve barley plant architecture is also provided.

Regulation of Root Development and Architecture by Strigolactones under Optimal and Nutrient Deficiency Conditions.

Strigolactones (SLs) constitute a group of plant hormones which are involved in multiple aspects of plant growth and development. Beside their role in shoot and root development and plant architecture in general, SLs are also involved in plant responses to nutrient deficiency by promoting interactions with symbiotic organisms and via promotion of root elongation. Recent observations on the cross talk between SLs and other hormones demonstrate that the inhibition of adventitious root formation by ethylene is independent of SLs. Additionally, it was shown that root exposure to SLs leads to the accumulation of secondary metabolites, such as flavonols or antioxidants. These data suggest pleiotropic effects of SLs, that influence root development. The discovery that the commonly used synthetic SL analogue racGR24 might also mimic the function of other plant growth regulators, such as karrikins, has led us to consider the previously published publications under the new aspects. This review summarizes present knowledge about the function of SLs in shaping root systems under optimal and nutrient deficiency conditions. Results which appear inconsistent with the various aspects of root development are singled out.

Enhancement of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) accumulation in Arxula adeninivorans by stabilization of production.

BACKGROUND: In recent years the production of biobased biodegradable plastics has been of interest of researchers partly due to the accumulation of non-biodegradable plastics in the environment and to the opportunity for new applications. Commonly investigated are the polyhydroxyalkanoates (PHAs) poly(hydroxybutyrate) and poly(hydroxybutyrate-co-hydroxyvalerate) (PHB-V). The latter has the advantage of being tougher and less brittle. The production of these polymers in bacteria is well established but production in yeast may have some advantages, e.g. the ability to use a broad spectrum of industrial by-products as a carbon sources. RESULTS: In this study we increased the synthesis of PHB-V in the non-conventional yeast Arxula adeninivorans by stabilization of polymer accumulation via genetic modification and optimization of culture conditions. An A. adeninivorans strain with overexpressed PHA pathway genes for ß-ketothiolase, acetoacetyl-CoA reductase, PHAs synthase and the phasin gene was able to accumulate an unexpectedly high level of polymer. It was found that an optimized strain cultivated in a shaking incubator is able to produce up to 52.1% of the DCW of PHB-V (10.8 g L-1) with 12.3%mol of PHV fraction. Although further optimization of cultivation conditions in a fed-batch bioreactor led to lower polymer content (15.3% of the DCW of PHB-V), the PHV fraction and total polymer level increased to 23.1%mol and 11.6 g L-1 respectively. Additionally, analysis of the product revealed that the polymer has a very low average molecular mass and unexpected melting and glass transition temperatures. CONCLUSIONS: This study indicates a potential of use for the non-conventional yeast, A. adeninivorans, as an efficient producer of polyhydroxyalkanoates.

Root hair development in the grasses: what we already know and what we still need to know.

A priority in many crop improvement programs for a long time has been to enhance the tolerance level of plants to both abiotic and biotic stress. Recognition that the root system is the prime determinant of a plant's ability to extract both water and minerals from the soil implies that its architecture is an important variable underlying a cultivar's adaptation. The density and/or length of the root hairs (RHs) that are formed are thought to have a major bearing on the plant's performance under stressful conditions. Any attempt to improve a crop's root system will require a detailed understanding of the processes of RH differentiation. Recent progress in uncovering the molecular basis of root epidermis specialization has been recorded in the grasses. This review seeks to present the current view of RH differentiation in grass species. It combines what has been learned from molecular-based analyses, histological studies, and observation of the phenotypes of both laboratory- and field-grown plants.

Identification and functional analysis of the HvD14 gene involved in strigolactone signaling in Hordeum vulgare.

In this study, the barley HvD14 gene encoding α/ß hydrolase, which is involved in strigolactone (SL) signaling, was identified. Bioinformatics analysis revealed that the identified gene is an orthologue of the D14, AtD14 and PhDAD2 genes that have been described in rice, Arabidopsis thaliana and petunia, respectively. Using TILLING strategy, an hvd14.d mutant that carried the G725A transition, located in the second exon, was identified. This mutation led to the substitution of a highly conserved glycine-193 to glutamic acid in the conserved fragment of the α/ß hydrolase domain of the HvD14 protein. The plants that carry the hvd14.d allele were semi-dwarf and produced a higher number of tillers in comparison to the wild-type (WT) parent cultivar. Additionally, the root architecture of mutant plants was affected: the total length of the seminal roots was significantly reduced, and the density of the lateral roots was higher than in the WT. Plants with the hvd14.d allele were insensitive to treatment with GR24, which is the synthetic analogue of SL. Analysis of the indole-3-acetic acid (IAA) concentration in the lateral buds showed no differences between the WT and mutant plants. By contrast, the WT seedlings treated with GR24 developed a lower number of tillers, longer primary roots with a reduced number of lateral roots and had an increased concentration of IAA in lateral buds. This paper describes the first barley SL mutant and shows the potential functions of SLs in barley growth and development.

Induced variations in brassinosteroid genes define barley height and sturdiness, and expand the green revolution genetic toolkit.

Reduced plant height and culm robustness are quantitative characteristics important for assuring cereal crop yield and quality under adverse weather conditions. A very limited number of short-culm mutant alleles were introduced into commercial crop cultivars during the Green Revolution. We identified phenotypic traits, including sturdy culm, specific for deficiencies in brassinosteroid biosynthesis and signaling in semidwarf mutants of barley (Hordeum vulgare). This set of characteristic traits was explored to perform a phenotypic screen of near-isogenic short-culm mutant lines from the brachytic, breviaristatum, dense spike, erectoides, semibrachytic, semidwarf, and slender dwarf mutant groups. In silico mapping of brassinosteroid-related genes in the barley genome in combination with sequencing of barley mutant lines assigned more than 20 historic mutants to three brassinosteroid-biosynthesis genes (BRASSINOSTEROID-6-OXIDASE, CONSTITUTIVE PHOTOMORPHOGENIC DWARF, and DIMINUTO) and one brassinosteroid-signaling gene (BRASSINOSTEROID-INSENSITIVE1 [HvBRI1]). Analyses of F2 and M2 populations, allelic crosses, and modeling of nonsynonymous amino acid exchanges in protein crystal structures gave a further understanding of the control of barley plant architecture and sturdiness by brassinosteroid-related genes. Alternatives to the widely used but highly temperature-sensitive uzu1.a allele of HvBRI1 represent potential genetic building blocks for breeding strategies with sturdy and climate-tolerant barley cultivars.

Arabinogalactan proteins are involved in root hair development in barley.

The arabinogalactan proteins (AGPs) are involved in a range of plant processes, including cell differentiation and expansion. Here, barley root hair mutants and their wild-type parent cultivars were used, as a model system, to reveal the role of AGPs in root hair development. The treatment of roots with different concentrations of ßGlcY (a reagent which binds to all classes of AGPs) inhibited or totally suppressed the development of root hairs in all of the cultivars. Three groups of AGP (recognized by the monoclonal antibodies LM2, LM14, and MAC207) were diversely localized in trichoblasts and atrichoblasts of root hair-producing plants. The relevant epitopes were present in wild-type trichoblast cell walls and cytoplasm, whereas in wild-type atrichoblasts and in all epidermal cells of a root hairless mutant, they were only present in the cytoplasm. In all of cultivars the higher expression of LM2, LM14, and MAC207 was observed in trichoblasts at an early stage of development. Additionally, the LM2 epitope was detected on the surface of primordia and root hair tubes in plants able to generate root hairs. The major conclusion was that the AGPs recognized by LM2, LM14, and MAC207 are involved in the differentiation of barley root epidermal cells, thereby implying a requirement for these AGPs for root hair development in barley.

In silico analysis of the genes encoding proteins that are involved in the biosynthesis of the RMS/MAX/D pathway revealed new roles of Strigolactones in plants.

Strigolactones were described as a new group of phytohormones in 2008 and since then notable large number of their functions has been uncovered, including the regulation of plant growth and development, interactions with other organisms and a plant's response to different abiotic stresses. In the last year, investigations of the strigolactone biosynthesis pathway in two model species, Arabidopsis thaliana and Oryza sativa, resulted in great progress in understanding the functions of four enzymes that are involved in this process. We performed in silico analyses, including the identification of the cis-regulatory elements in the promoters of genes encoding proteins of the strigolactone biosynthesis pathway and the identification of the miRNAs that are able to regulate their posttranscriptional level. We also searched the databases that contain the microarray data for the genes that were analyzed from both species in order to check their expression level under different growth conditions. The results that were obtained indicate that there are universal regulations of expression of all of the genes that are involved in the strigolactone biosynthesis in Arabidopsis and rice, but on the other hand each stage of strigolactone production may be additionally regulated independently. This work indicates the presence of crosstalk between strigolactones and almost all of the other phytohormones and suggests the role of strigolactones in the response to abiotic stresses, such as wounding, cold or flooding, as well as in the response to biotic stresses.

Uncovering the mechanism of mitochondrial translation initiation in plants.

Mitochondrial translation differs significantly from that conducted in bacteria and plastids. Recent research conducted by Tran and colleagues has unveiled the plant-specific mechanisms of mitochondrial translation initiation. The authors identified two Arabidopsis thaliana (arabidopsis) mTRAN proteins that may bind to the 5' untranslated region (UTR) of mitochondrial mRNAs by recognising newly discovered A/U-rich motifs.

Proton-polarized states in DNA.

We observed signatures of a phase transition in the double-stranded DNA fragment of known length and sequences using a non-invasive semiconductor-electrolyte interface technique and statistical physics methods. Observations revealed a coherence peak in the electromotive force and a significant decline in calculated dynamic entropy at a critical temperature and pH. This behavior may arise from the dynamic interaction of proton (H+) pairs with opposite momentum and spin, carrying a charge q=2+ under critical conditions.

Strigolactone insensitivity affects differential shoot and root transcriptome in barley.

Strigolactones (SLs) are plant hormones that play a crucial role in regulating various aspects of plant architecture, such as shoot and root branching. However, the knowledge of SL-responsive genes and transcription factors (TFs) that control the shaping of plant architecture remains elusive. Here, transcriptomic analysis was conducted using the SL-insensitive barley mutant hvd14.d (carried mutation in SL receptor DWARF14, HvD14) and its wild-type (WT) to unravel the differences in gene expression separately in root and shoot tissues. This approach enabled us to select more than six thousand SL-dependent genes that were exclusive to each studied organ or not tissue-specific. The data obtained, along with in silico analyses, found several TFs that exhibited changed expression between the analyzed genotypes and that recognized binding sites in promoters of other identified differentially expressed genes (DEGs). In total, 28 TFs that recognize motifs over-represented in DEG promoters were identified. Moreover, nearly half of the identified TFs were connected in a single network of known and predicted interactions, highlighting the complexity and multidimensionality of SL-related signalling in barley. Finally, the SL control on the expression of one of the identified TFs in HvD14- and dose-dependent manners was proved. Obtained results bring us closer to understanding the signalling pathways regulating SL-dependent plant development.

Asymmetric growth of root epidermal cells is related to the differentiation of root hair cells in Hordeum vulgare (L.).

The root epidermis of most vascular plants harbours two cell types, namely trichoblasts (capable of producing a root hair) and atrichoblasts. Here, in vivo analysis, confocal laser-scanning microscopy, transmission electron microscopy, histological analysis, and three-dimensional reconstruction were used to characterize the cell types present in the barley root epidermis and their distribution in the tissue. Both trichoblasts and atrichoblasts were present in the wild-type cultivars and could be distinguished from one another at an early stage. Trichoblast/atrichoblast differentiation depended on asymmetric cell expansion after a period of symmetrical cell division. After asymmetric growth, only the shorter epidermal cells could produce root hairs, whereas the longer cells became atrichoblasts. Moreover, the root epidermis did not develop root hairs at all if the epidermal cells did not differentiate into two asymmetric cell types. The root hairless phenotype of bald root barley (brb) and root hairless 1.b (rhl1.b) mutants was caused by a mutation in a gene related to the asymmetric expansion of the root epidermal cells. Additionally, the results showed that the mechanism of trichoblast/atrichoblast differentiation is not evolutionally conserved across the subfamilies of the Poaceae; in the Pooideae subfamily, both asymmetric division and asymmetric cell expansion have been observed.