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bioRxiv2019

Transcriptome Dedifferentiation Observed in Animal Primary Cultures is Essential to Plant Reprogramming

Tissue culture environment liberate cells from ordinary laws of multi-cellular organisms. This liberation enables cells several behaviors, such as growth, dedifferentiation, acquisition of pluripotency, immortalization and reprogramming. Each phenomenon is relating to each other and hardly to determine. Recently, dedifferentiation of animal cell was determined and quantified in increasing information entropy of transcriptome. The increasing information entropy of transcriptome induced by tissue culture may reappear in plant cells too. Here we corroborated it. Measuring information entropies of transcriptomes during reprogramming of plant cells suggested that reprogramming is a combined phenomenon of dedifferentiation and re-differentiation.

plant biology↗

bioRxiv2019

Auxin export from proximal fruits drives arrest in competent inflorescence meristems

A well-defined set of regulatory pathways control entry into the reproductive phase in flowering plants [1]. Conversely, little is known about the mechanisms that control the end of the reproductive phase ( floral arrest), despite this being a critical process for optimising fruit and seed production. Complete fruit removal or lack of fertile fruit-set in male sterile mutants, for example male sterile1 (ms1), prevents timely floral arrest in the model plant Arabidopsis [2]. These observations formed the basis for Hensel and colleagues model in which end-of-flowering was proposed to result from a cumulative fruit/seed-derived signal that caused simultaneous global proliferative arrest (GPA) in all inflorescences [2]. Recent studies have suggested that end-of-flowering involves gene expression changes at the floral meristem which are at least in part controlled by the FRUITFULL-APETELA2 pathway [3,4], however there is limited understanding of how this process is controlled and the communication needed at the whole plant level. Here, we provide new information providing a framework for the fruit-to-meristem (F-M) communication implied by the GPA model [5]. We show that floral arrest in Arabidopsis is not global and does not occur synchronously between branches, but rather that the arrest of each inflorescence is a local process, driven by auxin export from fruit proximal to the inflorescence meristem (IM). Furthermore, we show that inflorescence meristems are only competent for floral arrest once they reach a certain developmental age. Understanding the regulation of floral arrest is of major importance for the future manipulation of flowering to extend and maximise crop yields.

plant biology↗

bioRxiv2019

Moisture-dependent morphing tunes the dispersal of dandelion diaspores

Animal migration is highly sensitised to environmental cues, but plant dispersal is considered largely passive. The common dandelion, Taraxacum officinale, bears an intricate haired pappus facilitating flight. The pappus enables the formation of a separated vortex ring during flight; however, the pappus structure is not static but reversibly changes shape by closing in response to moisture. We hypothesised that this leads to changed dispersal properties in response to environmental conditions. Using wind tunnel experiments for flow visualisation, particle image velocimetry, and flight tests we characterised the fluid mechanics effects of the pappus morphing. We also modelled dispersal to understand the impact of pappus morphing on diaspore distribution. Pappus morphing dramatically alters the fluid mechanics of diaspore flight. We found that when the pappus closes in moist conditions, the drag coefficient decreases and thus the falling velocity is greatly increased. Detachment of diaspores from the parent plant also substantially decreases. The change in detachment when the pappus closes increases dispersal distances by reducing diaspore release when wind speeds are low. We propose that moisture-dependent pappus-morphing is a form of informed dispersal allowing rapid responses to changing conditions.

plant biology↗

bioRxiv2019

HydroShoot: a functional-structural plant model for simulating hydraulic structure, gas and energy exchange dynamics of complex plant canopies under water deficit - application to grapevine (Vitis vinifera L.)

This paper aims at presenting HydroShoot, a functional-structural plant model (FSPM) that is developed to simulate gas-exchange rates of complex plant canopies under water deficit conditions, by scaling up gas-exchange rates from the leaf to the canopy levels. The main hypothesis is that simulating both the hydraulic structure of the shoot together with the energy budget of individual leaves is the asset for successfully achieving this up-scaling task. HydroShoot was hence built as the ensemble of three interacting modules: hydraulic which calculates the distribution of xylem water potential across shoot hydraulic segments, energy which calculates the complete energy budget of individual leaves, and exchange which calculates net assimilation and transpiration rates of individual leaves. HydroShoot was coupled with irradiance interception and soil water balance models, and was evaluated on virtual and real grapevines having strongly contrasted canopies, under well-watered and water-deficit conditions. HydroShoot captured accurately the impact of canopy architecture and the varying soil water deficit conditions on plant-scale gas-exchange rates and leaf-scale temperature and water potential distributions. Both shoot hydraulic structure and leaf energy budget simulations were, as postulated, required to adequately scaling-up leaf to canopy gas-exchange rates. Notwithstanding, simulating the hydraulic structure of the shoot was found far more necessary to adequately performing this scaling task than simulating leaf energy balance. That is, the intra-canopy variability of leaf water potential was a better predictor of the reduction of whole plant gas-exchange rates under water deficit than the intra-canopy variability of leaf temperature. We conclude therefore that simulating the shoot hydraulic structure is a prerequisite if FSPM's are to be used to assess gas-exchange rates of complex plant canopies as those of grapevines. Finally HydroShoot is available through the OpenAlea platform (https://github.com/openalea/hydroshoot) as a set of reusable modules.

plant biology↗

bioRxiv2019

Genome wide analysis of Ga1-s modifiers in maize

A one way reproductive barrier exists between most popcorn varieties and dent corn varieties grown in the United States. This barrier is predominantly controlled by the ga1 locus. Using data from a diverse population of popcorn accessions pollinated by a dent corn tester, we found that the non-reciprocal pollination barrier conferred by ga1 is more complex than previously described. Individual accessions ranged from 0% to 100% compatible with dent corn pollen. Using conventional genotyping-by-sequencing data from 371 popcorn accessions carrying Ga1-s, seven significant modifiers of dent pollen compatibility were identified on five chromosomes. One locus may either be a nonfunctional ga1 allele present within popcorn, or second necessary gene for the reproductive barrier in genetic linkage with ga1, while the other modifiers are clearly genetically unlinked. The existence of ga1 modifiers segregating in a popcorn genetic background may indicate selective pressure to allow gene flow between populations, which should be incorporated into future models of the impact of genetic incompatibility loci on gene flow in natural and agricultural plant populations.

plant biology↗

bioRxiv2019

Cell wall integrity signaling regulates cell wall regeneration via transcriptional activation in Chlamydomonas reinhardtii

An intact cell wall is critical for protecting the cell from osmotic challenges and harmful environments. Signaling mechanisms are necessary to monitor cell wall integrity and to regulate cell wall production and remodeling during growth and division cycles. The green alga, Chlamydomonas, has a proteinaceous cell wall of defined structure that is readily removed by gametolysin (g-lysin), a metalloprotease released during sexual mating. Naked cells treated with g-lysin induce the mRNA accumulation of > 100 cell wall-related genes within an hour, offering a system to study signaling and regulatory mechanisms for de novo cell wall assembly. Combining quantitative RT-PCR and luciferase reporter assays to probe transcript accumulation and promoter activity, we revealed that up to 500-fold upregulation of cell wall-related genes was driven at least partly by transcriptional activation upon g-lysin treatment. To investigate how naked cells trigger this rapid transcriptional activation, we tested whether osmotic stress and cell wall integrity are involved in this process. Under a constant hypotonic condition, comparable levels of cell wall-gene activation were observed by g-lysin treatment. In contrast, cells in an iso- or hypertonic condition showed up to 80% reduction in the g-lysin-induced gene activation, suggesting that hypotonic conditions are required for full-scale responses to g-lysin treatment. To test whether mechanical perturbation is involved, we isolated and examined a new set of cell wall mutants with defective or little cell walls. All cell wall mutants examined showed a constitutive upregulation of cell wall-related genes at the level, which would only be achieved by the g-lysin treatment in wild-type cells. Our study suggests a signaling that monitors mechanical defects of cell walls and regulates cell wall-gene expression in Chlamydomonas, which may relate to cell wall integrity signaling mechanisms in plants.

plant biology↗

bioRxiv2019

Prediction of prospective leaf morphology in lettuce based on intracellular chloroplast position

In the accumulation response, chloroplasts move toward weak blue light, staying at positions along the periclinal cell wall. By contrast, in the avoidance response, chloroplasts move away from strong blue light, escaping to positions along the anticlinal cell wall. The accumulation response maximizes light capture and the avoidance response reduces photodamage. The intracellular positioning of chloroplasts is important for optimizing photosynthesis and may have common signals with the regulators that determine leaf morphology, another factor that affects photosynthesis. Here, we propose that intracellular chloroplast position can be used to predict prospective leaf morphology in lettuce (Lactuca sativa). To test this, we induced the accumulation or avoidance response in lettuce cells through exposure to the appropriate strength of blue light and observed the growth of the plants. Our results indicated that leaf area increased in response to weak blue light inducing the accumulation response, and leaf thickness increased in response to strong blue light inducing the avoidance response.

plant biology↗

bioRxiv2019

Salicylic acid-driven association of LENRV and NIMIN1/NIMIN2 binding domain regions in the C-terminus of tobacco NPR1 transduces SAR signal

O_LINONEXPRESSOR OF PATHOGENESIS-RELATED (PR) GENES1 (NPR1) is the central regulator of salicylic acid (SA)-induced PR-1 gene expression and systemic acquired resistance (SAR). The mechanism how SA is transduced through NPR1 is discussed controversially. Previously, we showed that Arabidopsis and tobacco (Nt) NPR1 contain two domains in their C-terminal thirds with relevance to SA signaling. SA sensitivity of NPR1 relies on the arginine residue in the LENRV motif, and SA-induced NIM1-INTERACTING (NIMIN, N) proteins bind to a highly conserved sequence termed N1/N2 binding domain (BD). C_LIO_LIWe demonstrate that LENRV and N1/N2BD regions of tobacco NPR1, separated from each other, interact in yeast, in vitro, in plant and in animal cells. Physical association of LENRV and N1/N2BD parts is enhanced considerably by SA and functional analogs, but not by a non-functional analog. Furthermore, physical association requires R431 and is most effective with intact LENRV and N1/N2BD interfaces. C_LIO_LIAssociation of separated LENRV and N1/N2BD parts by SA reconstitutes a functional NtNPR1 C-terminus, displaying transcription activity and able to interact with TGA transcription factors at two distinct sites. C_LIO_LITobacco NIMIN proteins can assemble LENRV and N1/N2BD parts into ternary complexes suggesting that NIMINs shape the NPR1 C-terminus to modulate SA signaling. C_LI

plant biology↗

bioRxiv2019

The cloud forest in the Dominican Republic: diversity and conservation status

The study of the forest in rainy environments of the Dominican Republic reveals the presence of four types of vegetation formations, clearly differentiated from each other in terms of their floristic and biogeographical composition, and also significantly different from the rainforests of Cuba. This leads us to propose two new alliances and four plant associations located in northern mountain areas exposed to moisture-laden winds from the Atlantic: All. Rondeletio ochraceae-Clusion roseae (Ass. Cyatheo furfuracei-Prestoetum motanae; Ass. Ormosio krugii-Prestoetum montanae); and All. Rondeletio ochraceae-Didymopanion tremuli (Ass. Hyeronimo montanae-Magnolietum pallescentis; Hyeronimo dominguensis-Magnolietum hamorii). Due to human activity, some areas are very poorly conserved, as evidenced by the diversity index and the presence of endemic tree and plant elements. The worst conserved in terms of the relationship between characteristic plants vegetation (cloud forest) in areas with high rainfall in the Dominican Republic, along with its floristic diversity and state of conservation. Thanks to this study it has been possible to significantly increase the botanical knowledge of this important habitat.

plant biology↗

bioRxiv2019

Molecular Mechanisms Driving Bistable Switch Behavior in Xylem Cell Differentiation

Plant xylem cells conduct water and mineral nutrients. Although most plant cells are totipotent, xylem cells are unusual and undergo terminal differentiation. Many genes regulating this process are well characterized, including the VASCULAR-RELATED NAC DOMAIN7 (VND7), MYB46 and MYB83 transcription factors which are proposed to act in interconnected feed-forward loops. Much less is known regarding the dynamic behavior underlying the terminal transition to xylem cell differentiation. Here we utilize whole root and single cell data to mathematically model this relationship. These provide evidence for VND7 regulating bistable switching of cells in the root to a xylem cell identity, with additional features of hysteresis. We further determine that although MYB46 responds to VND7 induction, it is not inherently involved in executing the binary switch. A novel regulatory architecture is proposed that involves four downstream targets of VND7 that act in a cycle. These data provide an important model to study the emergent properties that may give rise to totipotency relative to terminal differentiation and reveal novel xylem cell subtypes.

plant biology↗

bioRxiv2019

Chloroplast cold-avoidance response in Marchantia polymorpha occurs independently of changes in endogenous phototropin expression

When exposed to fluctuating light intensity, chloroplasts move towards weak light (accumulation response), and away from strong light (avoidance response). In addition, cold treatment (5{degrees}C) induces the avoidance response even under weak light conditions (cold-avoidance response). These three responses are mediated by the phototropin (phot), which is a blue-light photoreceptor and has also been found to act as a thermosensory protein that perceives temperature variation. Our previous report indicated that cold-induced changes in phot biochemical activity initiate the cold-avoidance response. In this study, we further explored the induction mechanism of the cold-avoidance response in the liverwort Marchantia polymorpha and examined the relationship between changes in the amount of phot and the induction of the cold-avoidance response. The switch between the accumulation and avoidance responses occurs at a so-called transitional light intensity. Our physiological experiments revealed that a cold-mediated decrease in the transitional light intensity leads to the induction of the cold-avoidance response. While artificial overexpression of phot decreased the transitional light intensity as much as cold treatment did, the amount of endogenous phot remained unchanged by cold treatment in wild-type M. polymorpha. Taken together, these findings show that the cold-avoidance response is initiated by a cold-mediated reduction of the transitional light intensity, independent of the amount of endogenous phot. This study provides a clue to understand the mechanism underlying the switch in direction of chloroplast relocation in response to light and temperature.

plant biology↗

bioRxiv2019

Non-canonical Features of Pentatricopeptide Repeat Protein-Facilitated RNA Editing in Arabidopsis Chloroplasts

Cytosine (C) to uracil (U) RNA editing in plant mitochondria and chloroplasts is facilitated by site-specific pentatricopeptide repeat (PPR) editing factors. PPR editing factors contain multiple types of PPR motifs, and PPR motifs of the same type also show sequence variations. Therefore, no PPR motifs are invariant within a PPR protein or between different PPR proteins. This work evaluates the functional diversity of PPR motifs in CHLOROPLAST RNA EDITING FACTOR 3 (CREF3). The results indicate that previously overlooked features of PPR editing factors could also contribute to RNA editing activity. In particular, the N-terminal degenerated PPR motifs and the two L1-type PPR motifs in CREF3 are functionally indispensable. Furthermore, PPR motifs of the same type in CREF3 are not interchangeable. These non-canonical features of CREF3 have important implications on the understanding of PPR-facilitated RNA editing in plant organelles.

plant biology↗

bioRxiv2019

Glutathionylation primes soluble GAPDH for late collapse into insoluble aggregates

Protein aggregation is a complex physiological process, primarily determined by stress-related factors revealing the hidden aggregation propensity of proteins that otherwise are fully soluble. Here we report a mechanism by which glycolytic glyceraldehyde-3-phosphate dehydrogenase of Arabidopsis thaliana (AtGAPC1) is primed to form insoluble aggregates by the glutathionylation of its catalytic cysteine (Cys149). Following a lag phase, glutathionylated AtGAPC1 initiates a self-aggregation process resulting in the formation of branched chains of globular particles made of partially misfolded and totally inactive proteins. GSH molecules within AtGAPC1 active sites are suggested to provide the initial destabilizing signal. The following removal of glutathione by the formation of an alternative disulfide bond between Cys149 and Cys153 reinforces the aggregation process. Besides acting as a protective mechanism against overoxidation, S-glutathionylation of AtGAPC1 triggers an unexpected aggregation pathway with completely different and still unexplored physiological implications.

plant biology↗

bioRxiv2019

The Molecular Mass and Isoelectric Point of Plant Proteomes

A proteomic analysis of proteomes from 145 plant species revealed a pI range of 1.99 (epsin) to 13.96 (hypothetical protein). The molecular mass of the plant proteins ranged from 0.54 to 2236.8 kDa. A putative Type-I polyketide synthase (22244 amino acids) in Volvox carteri was found to be the largest protein in the plant kingdom and was not found in higher plant species. Titin (806.46 kDa) and misin/midasin (730.02 kDa) were the largest proteins identified in higher plant species. The pI and molecular weight of the plant proteome exhibited a trimodal distribution. An acidic pI (56.44% of proteins) was found to be predominant over a basic pI (43.34% of proteins) and the abundance of acidic pI proteins was higher in unicellular algae species relative to multicellular higher plants. In contrast, the seaweed, Porphyra umbilicalis, possesses a higher proportion of basic pI proteins (70.09%). Plant proteomes were also found to contain the amino acid, selenocysteine (Sec), which is the first report of the presence of this amino acid in plants. Additionally, plant proteomes also possess ambiguous amino acids Xaa (unknown), Asx (asparagine or aspartic acid), Glx (glutamine or glutamic acid), and Xle (leucine or isoleucine) as well.

plant biology↗

bioRxiv2019

Efficient callus induction and completion of regeneration in kenaf Hibiscus cannabinus

Kenaf, Hibiscus cannabinus, is a fiber-enriched plant belonging to Malvaceae and is an important fiber crop. The features of kenaf of being fast-growing and fiber-enriched suggest the potential for the use of kenaf in biomass and materials; however, the complete regeneration procedure, which is essential for genetic modification, is lacking. Here, we report the complete regeneration of kenaf from cotyledon explants achieved by callus induction on an improved callus-inducing medium and shoot induction on a shoot-inducing medium and by seed setting under a regulated growth condition in a chamber. Our complete regeneration method will enable the production of stably transformed kenaf that can improve the properties of kenaf as a material.

plant biology↗

bioRxiv2019

rhizoTrak: A flexible open source Fiji plugin for user-friendly manual annotation of time-series images from minirhizotrons

Background and aimsMinirhizotrons are commonly used to study root turnover which is essential for understanding ecosystem carbon and nutrient cycling. Yet, extracting data from minirhizotron images requires intensive annotation effort. Existing annotation tools often lack flexibility and provide only a subset of the required functionality. To facilitate efficient root annotation in minirhizotrons, we present the user-friendly open source tool rhizoTrak. Methods and resultsrhizoTrak builds on TrakEM2 and is publically available as Fiji plugin. It uses treelines to represent branching structures in roots and assigns customizable status labels per root segment. rhizoTrak offers configuration options for visualization and various functions for root annotation mostly accessible via keyboard shortcuts. rhizoTrak allows time-series data import and particularly supports easy handling and annotation of time series images. This is facilitated via explicit temporal links (connectors) between roots which are automatically generated when copying annotations from one image to the next. rhizoTrak includes automatic consistency checks and guided procedures for resolving conflicts. It facilitates easy data exchange with other software by supporting open data formats. ConclusionsrhizoTrak covers the full range of functions required for user-friendly and efficient annotation of time-series images. Its flexibility and open source nature will foster efficient data acquisition procedures in root studies using minirhizotrons.

plant biology↗

bioRxiv2019

Lotus japonicus symbiosis signaling genes and their role in the establishment of root-associated bacterial and fungal communities

The wild legume Lotus japonicus engages in mutualistic symbiotic relationships with arbuscular mycorrhiza (AM) fungi and nitrogen-fixing rhizobia. Using plants grown in natural soil and community profiling of bacterial 16S rRNA genes and fungal internal transcribed spacers (ITS), we examined here the role of the Lotus symbiosis genes RAM1, NFR5, SYMRK, and CCaMK in structuring bacterial and fungal root-associated communities. We found host genotype-dependent community shifts in the root and rhizosphere compartments that were mainly confined to bacteria in nfr5 or fungi in ram1 mutants, whilst symRK and ccamk plants displayed major changes across both microbial kingdoms. We observed in all AM mutant roots an almost complete depletion of a large number of Glomeromycota taxa that was accompanied by a concomitant enrichment of Helotiales and Nectriaceae fungi, suggesting compensatory niche replacement within the fungal community. A subset of Glomeromycota whose colonization is strictly dependent on the common symbiosis pathway was retained in ram1 mutants, indicating that RAM1 is dispensable for intraradical colonization by some Glomeromycoyta fungi. However, intraradical colonization by certain Burkholderiaceae taxa is dependent on AM root infection, thereby revealing a microbial interkingdom interaction. Our findings imply a broad role for Lotus symbiosis genes in structuring the root microbiota.

plant biology↗

bioRxiv2019

Comparative biomechanical characterization of maize brace roots within andbetween plants

Root lodging is responsible for significant crop losses world-wide. During root lodging, roots fail by breaking, buckling, or pulling out of the ground. In maize, above-ground roots, called brace roots, have been shown to reduce root lodging susceptibility. However, the underlying structural-functional properties of brace roots that prevent root lodging are poorly defined. In this study, we quantified structural mechanical properties, geometry, and bending moduli for brace roots from different whorls, genotypes, and reproductive stages. Using 3-point bend tests, we show that brace root mechanics are variable by whorl, genotype, and reproductive stage. Generally, we find that within each genotype and reproductive stage, the brace roots from the whorl closest to the ground had higher structural mechanical properties and a lower bending modulus than brace roots from the second whorl. There was additional variation between genotypes and reproductive stages. Specifically, genotypes with higher structural mechanical properties also had a higher bending modulus, and senesced brace roots had lower structural mechanical properties than hydrated brace roots. Collectively these results highlight the importance of considering whorl-of-origin, genotype, and reproductive stage for quantification of brace root mechanics, which is important for mitigating crop loss due to root mechanical failure.

plant biology↗