Plant Biol Research Articles

Virus-Induced Gene Silencing in Sweet Basil (Ocimum basilicum).

Virus-induced gene silencing (VIGS) is a powerful reverse genetic tool for rapid functional analysis of plant genes. Over the last decade, VIGS has been widely used for conducting rapid gene knockdown experiment in plants and played a crucial role in advancing applied and basic research in plant science. VIGS was studied extensively in model plants Arabidopsis and tobacco. Moreover, several non-model plants such as Papaver (Hileman et al., Plant J 44:334-341, 2005), Aquilegia (Gould and Kramer, Plant Methods 3:6, 2007), Catharanthus (Liscombe and O'Connor, Phytochemistry 72:1969-1977, 2011), Withania (Singh et al., Plant Biol J 13:1287-1299, 2015), and Ocimum (Misra et al., New Phytol 214:706-720, 2017) were also successfully explored. We have recently developed a robust protocol for VIGS in sweet basil (Ocimum basilicum). Sweet basil, a popular medicinal/aromatic herb, is being studied for the diversity of specialized metabolites produced in it.

A Transcriptional Network Makes Normal Tomato Fruit Not Purple

A Transcriptional Network Makes Normal Tomato Fruit Not Purple

Evolution, Initiation, and Diversity in Early Plant Embryogenesis.

During embryogenesis in plants, cell identities are specified de novo, starting from a single cell. By combining imaging, genomic profiling, and genetics, principles of early plant development have been unraveled in the dicotyledonous plant Arabidopsis. A central emerging question, however, is how well zygotic embryogenesis in Arabidopsis reflects homologous processes in other plant species, including early diverging, non-flowering, and non-seed plants. Here, we consider plant embryogenesis with an emphasis on its evolutionary history, the diverse modes of its initiation, and the concepts in pattern formation among morphologically distinct plant groups. Furthermore, we explore challenges and future directions in plant embryogenesis research.

Nucleo-cytoplasmic Partitioning of ARF Proteins Controls Auxin Responses in Arabidopsis thaliana.

The phytohormone auxin plays crucial roles in nearly every aspect of plant growth and development. The auxin response factor (ARF) transcription factor family regulates auxin-responsive gene expression and exhibits nuclear localization in regions of high auxin responsiveness. Here we show that the ARF7 and ARF19 proteins accumulate in micron-sized assemblies within the cytoplasm of tissues with attenuated auxin responsiveness. We found that the intrinsically disordered middle region and the folded PB1 interaction domain of ARFs drive protein assembly formation. Mutation of a single lysine within the PB1 domain abrogates cytoplasmic assemblies, promotes ARF nuclear localization, and results in an altered transcriptome and morphological defects. Our data suggest a model in which ARF nucleo-cytoplasmic partitioning regulates auxin responsiveness, providing a mechanism for cellular competence for auxin signaling.

Integrative Paleobotany: Affirming the Role of Fossils in Modern Plant Biology—Introduction and Dedication

Integrative Paleobotany: Affirming the Role of Fossils in Modern Plant Biology—Introduction and Dedication

Measuring Pectin Properties to Track Cell Wall Alterations During Plant-Pathogen Interactions.

Plant cell walls act both as a barrier to pathogen entry and as a source of signaling molecules that can modulate plant immunity. Cell walls consist mainly of three polymeric sugars: cellulose, pectin, and hemicellulose (Mohnen et al., Biomass Recalcitrance: deconstructing the plant cell wall for bioenergy, 2008). In Arabidopsis more than 50% of the primary cell wall is pectin (Zablackis et al., Plant Physiol 107:1129-1138, 1995). There are various types of pectin, but all pectins contain galacturonic acid subunits in their backbone (Harholt et al., Plant Physiol 153:384-395, 2010; Mohnen, Curr Opin Plant Biol 11:266-277, 2008). Many pathogens secrete pectin-degrading enzymes as part of their infection strategy (Espino et al., Proteomics 10:3020-3034, 2010; ten Have et al., Mol Plant-Microbe Interact 11:1009-1016, 1998). Pectin is synthesized in a highly esterified fashion and is de-esterified in the cell wall by pectin methylesterases (Harholt et al., Plant Physiol 153:384-395, 2010; Mohnen, Curr Opin Plant Biol 11:266-277, 2008). During plant-pathogen interactions, both the amount and the patterns of pectin methylesterification in the wall can be altered (Bethke et al., Plant Physiol 164:1093-1107, 2014; Lionetti et al., J Plant Physiol 169:1623-1630, 2012). Pectin methylesterifications influence mechanical properties of pectin, and pectins must be at least partially de-methylesterified to be substrates for pectin-degrading enzymes (Levesque-Tremblay et al., Planta 242:791-811, 2015). Additionally, alterations of pectin methylesterification or pectin content affect pathogen growth (Bethke et al., Plant Physiol 164:1093-1107, 2014; Lionetti et al., J Plant Physiol 169:1623-1630, 2012; Bethke et al., Plant Cell 28:537-556, 2016; Raiola et al., Mol Plant-Microbe Interact 24:432-440, 2011; Vogel et al., Plant Cell 14:2095-2106, 2002; Vogel et al., Plant J 40:968-978, 2004; Wietholter et al., Mol Plant-Microbe Interact 16:945-952, 2003). This chapter explains a simple protocol that can be used in any molecular biology laboratory to estimate total pectin content using a colorimetric assay and pectin composition using antibodies raised against specific pectin components.

Regulation of Seed Germination: The Involvement of Multiple Forces Exerted via Gibberellic Acid Signaling

Regulation of Seed Germination: The Involvement of Multiple Forces Exerted via Gibberellic Acid Signaling

Regulation of asymmetric polar auxin transport by PsPIN1 in endodermal tissues of etiolated Pisum sativum epicotyls: focus on immunohistochemical analyses.

This manuscript reportsthe production of specific polyclonal antibodies for PsPIN1, a putative auxin efflux carrier in Alaska pea (Pisum sativum L.) plants, and the cellular immunolocalization of PsPIN1. When pea seeds were set with the seed axis horizontal to the upper surface of a rockwool block, and allowed to germinate and grow for 3days in the dark, the epicotyl grew upward. On the other hand, the application of 2,3,5-triiodobenzoic acid (TIBA) inhibited graviresponse. In the subapical epicotyl regions, PsPIN1 has been found to localize in the basal side of the plasma membrane of cells in endodermal tissues. Asymmetric PsPIN1 localization between the proximal and distal sides of the epicotyl was observed, the total amounts of PsPIN1 being more abundant in the proximal side. The asymmetric PsPIN1 distribution between the proximal and distal sides of the epicotyl was well correlated with unequal polar auxin transport as well as asymmetric accumulation of mRNA of PsPIN1 (Ueda et al. in Biol Sci Space 26:32-41, 2012; Ueda et al. in Plant Biol 16(suppl 1):43-49, 2014). In the proximal side of an apical hook, PsPIN1 localized in the basal side of the plasma membrane of cells in endodermal tissues, whereas in the distal side, the abundant distribution of PsPIN1 localized in the basal-lower (endodermal) side of the basal plasma membrane, suggesting possible lateral auxin movement from the distal side to the proximal side in this region. The application of TIBA significantly reduced the amount of PsPIN1 in the proximal side of epicotyls, but little in the distal side. These results suggest that unequal auxin transport in epicotyls during the early growth stage of etiolated pea seedlings is derived from asymmetric PsPIN1 localization in the apical hook and subapical region of epicotyls, and that asymmetric transport between the proximal and distal sides of epicotyls is required for the graviresponse of epicotyls.

Retracted: Activities of carbohydrate-metabolism enzymes in pre-drought primed wheat plants under drought stress during grain filling.

Abid M, Tian Z, Hu J, Ullah A, Cui Y, Ali S, Jiang S, Zahoor R, Fan Y, Dong J and Dai T Activities of carbohydrate-metabolism enzymes in pre-drought primed wheat plants under drought stress during grain filling. J Integr Plant Biol Accepted Author Manuscript. doi:10.1111/jipb.12628.

The long and winding road: transport pathways for amino acids in Arabidopsis seeds.

Pathways for assimilates. During their life cycle, plants alternate between a haploid stage, the gametophyte, and a diploid stage, the sporophyte. In higher plants, meiosis generates the gametophyte deeply embedded in the maternal tissue of the flower. The megaspore mother cell undergoes meiosis, and then, the surviving megaspore of the four megaspores produced undergoes mitotic divisions and finally gives rise to the female gametophyte, consisting of the egg cell, two synergids, the central cell, which due to the fusion of two nuclei is diploid (double haploid) in Arabidopsis and most angiosperms and the antipods, whose number is not fixed and varies significantly between species (Yadegari and Drews in Plant Cell 16(Suppl):S133-S141, 2004). The maternal tissues that harbor the female gametophyte and the female gametophyte are referred to as the ovule (Fig.1). Double fertilization of the egg cell and the central cell by the two generative nuclei of the pollen leads to the diploid embryo and the endosperm, respectively (Hamamura et al. in Curr Opin Plant Biol 15:70-77, 2012). Upon fertilization, the ovule is referred to as the seed. Seeds combine two purposes: to harbor storage compounds for use by the embryo upon germination and to protect the embryo until the correct conditions for germination are encountered. As a consequence, seeds are the plant tissue that is of highest nutritional value and the human diet, by a considerable amount, consists of seeds or seed-derived products. Amino acids are of special interest, because plants serve as the main source for the so-called essential amino acids, that animals cannot synthesize de novo and are therefore often a limiting factor for human growth and development (WHO in Protein and amino acid requirements in human nutrition. WHO technical report series, WHO, Geneva, 2007). The plant embryo needs amino acids for general protein synthesis, and additionally they are used to synthesize storage proteins in the seeds of certain plants, e.g., legumes as a resource to support the growth of the seedling after germination. The support of the embryo depends on transport processes that occur between the mother plant and the seed tissues including the embryo. In this review, we will focus on the processes of unloading amino acids from the phloem and their post-phloem transport. We will further highlight similarities between amino acid transport and the transport of the main assimilate and osmolyte, sucrose. Finally, we will discuss similarities and differences between different plant species in terms of structural aspects but for the molecular aspects we are almost exclusively focusing on Arabidopsis. Fig.1 Vascularization of the Arabidopsis ovule and seed. Plants expressing ER-localized mCherry under control of the companion cell-specific SUC2 promoter and ER-localized GFP under control of the sieve element marker PD1 as described (Müller et al. 2015) are shown to visualize the phloem in the funiculus and the chalazal regions. a Overview over an ovule. FG: female gametophyte. b A magnification of the region marked by a square in panel a. c Overview over a seed. ES: endosperm; E: embryo. d A magnification of the region marked by a square in panel c. The arrows in b and d point to the terminal companion cell and arrowheads to terminal sieve elements.

Cellulose synthase complex organization and cellulose microfibril structure.

Cellulose consists of linear chains of β-1,4-linked glucose units, which are synthesized by the cellulose synthase complex (CSC). In plants, these chains associate in an ordered manner to form the cellulose microfibrils. Both the CSC and the local environment in which the individual chains coalesce to form the cellulose microfibril determine the structure and the unique physical properties of the microfibril. There are several recent reviews that cover many aspects of cellulose biosynthesis, which include trafficking of the complex to the plasma membrane and the relationship between the movement of the CSC and the underlying cortical microtubules (Bringmann et al. 2012 Trends Plant Sci.17, 666-674 (doi:10.1016/j.tplants.2012.06.003); Kumar & Turner 2015 Phytochemistry112, 91-99 (doi:10.1016/j.phytochem.2014.07.009); Schneider et al. 2016 Curr. Opin. Plant Biol.34, 9-16 (doi:10.1016/j.pbi.2016.07.007)). In this review, we will focus on recent advances in cellulose biosynthesis in plants, with an emphasis on our current understanding of the structure of individual catalytic subunits together with the local membrane environment where cellulose synthesis occurs. We will attempt to relate this information to our current knowledge of the structure of the cellulose microfibril and propose a model in which variations in the structure of the CSC have important implications for the structure of the cellulose microfibril produced.This article is part of a discussion meeting issue 'New horizons for cellulose nanotechnology'.

Genome-wide identification of leaf abscission associated microRNAs in sugarcane (Saccharum officinarum L.)

BackgroundSugarcane (Saccharum officinarum L.) is an economically important crop, mainly due to the production of sugar and biofuel (Azevedo RA, Carvalho RF, Cia MC, & Gratão PL, Trop Plant Biol 4:42-51, 2011). Grown mainly in tropical and subtropical countries, sugarcane is a highly polyploid plant with up to ten copies of each chromosome, which increases the difficulties of genome assembly and genetic, physiologic and biochemical analyses. The increasing demands of sugar and the increasing cost of sugarcane harvest require sugarcane varieties which can shed their leaves during the maturity time, so it is important to study the mechanism of leaf abscission in sugarcane.ResultsTo improve the understanding of miRNA roles in sugarcane leaf abscission, we reported the genome-wide characterization of miRNAs and their putative targets in sugarcane using deep sequencing for six small RNA libraries. In total, 93 conserved miRNAs and 454 novel miRNAs were identified in sugarcane using previously reported transcriptome as reference. Among them, 25 up-regulated and 13 down-regulated miRNAs were identified in leaf abscission sugarcane plants (LASP) compared to leaf packaging sugarcane plants (LPSP). Target prediction revealed several miRNA-mRNA modules including miR156-SPL, miR319-TPR2, miR396-GRF and miR408-LAC3 might be involved in the sugarcane leaf abscission. KEGG pathway enrichment analysis showed differentially expressed miRNAs may regulate pathways like “plant hormone signal transduction” and “plant-pathogen interaction”, which is consistent with previous transcriptome study. In addition, we identified 96 variant miRNAs with 135 single nucleotide polymorphisms (SNPs). The expression of sugarcane miRNAs and variant miRNAs were confirmed by qRT-PCR. We identified a possible poaceae specific miRNA called miR5384 for the first time in sugarcane.ConclusionsWe not only reported miR5384, a possible poaceae specific miRNA, for the first time in sugarcane but also presented some miRNA-mRNA modules including miR156-SPL, miR319-TPR2, miR396-GRF and miR408-LAC in sugarcane. These modules might be involved in the regulation of sugarcane leaf abscission during the maturity time. All of these findings may lay ground work for future application of sugarcane breeding program and benefit research studies of sugarcane miRNAs.

Salt-accumulating glands reveal metabolic complexity

Plant Science![Figure][1] Salt accumulating trichomes in ice plants are metabolically flexible. PHOTO: STEPHANIE STARR/ALAMY STOCK PHOTO The ice plant thrives in salty ocean-side mist. Barkla et al. used proteomics to identify proteins in these halophytes that are critical to the defense against too much salt. Specialized trichomes, known as epidermal bladder cells (EBCs), found on the surface of the ice plant can accumulate a concentration of over 1 M Na+. Several dozen proteins, including some involved in Crassulacean acid metabolism (CAM), as well as several transporters in the EBCs are responsive to salty conditions. Ionomics showed the accumulation of Mn, V, and Zn as well as NaCl. Thus, more than a storage tank for salty water, the EBC is metabolically nimble, shifting physiological and developmental systems in response to environmental conditions. BMC Plant Biol. 10.1186/s12870-016-0797-1 (2016). [1]: pending:yes

A Putative Chloroplast Thylakoid Metalloprotease VIRESCENT3 Regulates Chloroplast Development in Arabidopsis thaliana

The chloroplast is the site of photosynthesis and many other essential plant metabolic processes, and chloroplast development is an integral part of plant growth and development. Mutants defective in chloroplast development can display various color phenotypes including the intriguing virescence phenotype, which shows yellow/white coloration at the leaf base and greening toward the leaf tip. Through large scale genetic screens, we identified a series of new virescent mutants including virescent3-1 (vir3-1), vir4-1, and vir5-1 in Arabidopsis thaliana. We showed that VIR3 encodes a putative chloroplast metalloprotease by map-based cloning. Through site-directed mutagenesis, we showed that the conserved histidine 235 residue in the zinc binding motif HEAGH of VIR3 is indispensable for VIR3 accumulation in the chloroplast. The chloroplast localization of VIR3 was confirmed by the transient expression of VIR3-GFP in leaf protoplasts. Furthermore, taking advantage of transgenic lines expressing VIR3-FLAG, we demonstrated that VIR3 is an intrinsic thylakoid membrane protein that mainly resides in the stromal lamellae. Moreover, topology analysis using transgenic lines expressing a dual epitope-tagged VIR3 indicated that both the N and C termini of VIR3 are located in the stroma, and the catalytic domain of VIR3 is probably facing the stroma. Blue native gel analysis indicated that VIR3 is likely present as a monomer or part of a small complex in the thylakoid membrane. This work not only implicates VIR3 as a new factor involved in early chloroplast development but also provides more insight into the roles of chloroplast proteases in chloroplast biogenesis.

A Nucleolar PUF RNA-binding Protein with Specificity for a Unique RNA Sequence

PUF proteins are a conserved group of sequence specific RNA-binding proteins that bind to RNA in a modular fashion. The RNA-binding domain of PUF proteins typically consists of eight clustered Puf repeats. Plant genomes code for large families of PUF proteins that show significant variability in their predicted Puf repeat number, organization, and amino acid sequence. Here we sought to determine whether the observed variability in the RNA-binding domains of four plant PUFs results in a preference for nonclassical PUF RNA target sequences. We report the identification of a novel RNA binding sequence for a nucleolar Arabidopsis PUF protein that contains an atypical RNA-binding domain. The Arabidopsis PUM23 (APUM23) binding sequence was 10 nucleotides in length, contained a centrally located UUGA core element, and had a preferred cytosine at nucleotide position 8. These RNA sequence characteristics differ from those of other PUF proteins, because all natural PUFs studied to date bind to RNAs that contain a conserved UGU sequence at their 5' end and lack specificity for cytosine. Gel mobility shift assays validated the identity of the APUM23 binding sequence and supported the location of 3 of the 10 predicted Puf repeats in APUM23, including the cytosine-binding repeat. The preferred 10-nucleotide sequence bound by APUM23 is present within the 18S rRNA sequence, supporting the known role of APUM23 in 18S rRNA maturation. This work also reveals that APUM23, an ortholog of yeast Nop9, could provide an advanced structural backbone for Puf repeat engineering and target-specific regulation of cellular RNAs.

Optimizing Crops for Biocontrol of Pests and Disease.

Volatile compounds and extrafloral nectar are common defenses of wild plants; however, in crops they bear an as-yet underused potential for biological control of pests and diseases. Odor emission and nectar secretion are multigene traits in wild plants, and thus form difficult targets for breeding. Furthermore, domestication has changed the capacity of crops to express these traits. We propose that breeding crops for an enhanced capacity for tritrophic interactions and volatile-mediated direct resistance to herbivores and pathogens can contribute to environmentally-friendly and sustainable agriculture. Natural plant volatiles with antifungal or repellent properties can serve as direct resistance agents. In addition, volatiles mediating tritrophic interactions can be combined with nectar-based food rewards for carnivores to boost indirect plant defense.

Unlocking artemisinin's biosynthetic secrets

Plant Science![Figure][1] The malaria drug artemisinin is isolated from Artemisia annua plants PHOTO: © MANFRED RUCKSZIO/ALAMY The emergence of drug-resistant parasites presents a major barrier to controlling human malaria. Artemisinin is the recommended first-line treatment for uncomplicated mal aria, but demand outstrips drugmakers' ability to cultivate the source, the Chinese herb Artemisia annua . A better understanding of the biosynthetic pathway could enhance scientists' ability to produce artemisinin from yeast, increasing the drug's availability. Bryant et al. explored the proteome of artemisinin-producing hairs stripped off the plant, cross-matching with genomic information to identify proteins. Key to the final steps of artemisinin biosynthesis may be enzymes like cyclophilins and peroxidases, hinting that steps that can proceed nonenzymatically may nonetheless get an enzymatic turbo-boost. BMC Plant Biol. 15 , 175 (2015). [1]: pending:yes

Tobacco phytochelatin synthase (NtPCS1) plays important roles in cadmium and arsenic tolerance and in early plant development in tobacco

Phytochelatin synthase (PCS) catalyzes the synthesis of phytochelatins, which are involved in heavy metal detoxification in plants and other living organisms. Previously, we cloned a PCS1 gene from tobacco (Nicotiana tabacum) and showed that its expression in yeast (Saccharomyces cerevisiae) resulted in increased cadmium (Cd) tolerance and Cd accumulation (Kim et al., J Plant Biol 48:440–447, 2005). To examine the role of NtPCS1 in tobacco, we generated transgenic tobacco lines over-expressing NtPCS1 in the sense or antisense direction. Compared with other PCS1-expressing plants, NtPCS1-expressing tobacco exhibited a unique phenotype: increased tolerance to cadmium and arsenite, but no change in cadmium and arsenic accumulation. In addition, the antisense-NtPCS1 tobacco lines showed growth retardation in the early stage, suggesting that phytochelatin also plays a role in plant development. These results demonstrate that NtPCS1 plays important roles in metal(loid) tolerance as well as in growth and development in tobacco.

Spatiotemporal sequestration of miR165/166 by Arabidopsis Argonaute10 promotes shoot apical meristem maintenance.

Arabidopsis Argonaute10 (AGO10) specifically sequesters miR165 and miR166 and antagonizes their activity, thus regulating shoot apical meristem (SAM) development. However, where and when this sequestration acts is currently unclear. We show here that AGO10 represses miR165/166 activity in the embryo proper during early embryogenesis, through the apical and central regions of mature embryos, and eventually in the entire adaxial domain and vasculature of the cotyledons and leaf primordia. These locations are essentially identical to regions expressing PHABULOSA and REVOLUTA, mRNA targets of miR165/166. The Arabidopsis genome contains nine MIR165/166 genes. Sequestration of miR165/166 by the MIR165b, MIR166a, MIR166b, and MIR166g promoters efficiently rescues the SAM defect in ago10 mutants. Comparison of the expression patterns of AGO10 and the four MIR165/166 members suggests that AGO10 quenches the non-cell-autonomous activity of any miR165/166 that moves into AGO10-expressing niches. Thus, this study provides insight into how the spatiotemporal regulation of AGO10-miR165/166 activity affects SAM development.

Auxin Binding Protein 1 (ABP1): a matter of fact.

Science is a global community enterprise.Collectively,we contribute to building the knowledge tower by using bricks and mortar that should be strong,solid,and long lasting.A brick with defects may lead this tower,or a part there of,to collapse.When that happens,the community suffers,laying waste countless dedicated hours of work,especially by students and postdoctoral scholars.This is the reason ary