Molecular mechanisms of shade tolerance in plants Martinez‐Garcia, Jaime F.; Rodriguez‐Concepcion, Manuel
The New phytologist,
August 2023, 2023-08-00, 20230801, Letnik:
239, Številka:
4
Journal Article
Recenzirano
Odprti dostop
Summary
Shade tolerance is an ecological concept used in a wide range of disciplines, from plant physiology to landscaping or gardening. It refers to the strategy of some plants to persist and even ...thrive in environments with low light levels because of the shade produced by the vegetation proximity (e.g. in the understory). Shade tolerance influences the organization, structure, functioning, and dynamics of plant communities. However, little is known about its molecular and genetic basis. By contrast, there is a good understanding on how plants deal with the proximity of other plants, a divergent strategy used by most crops to respond to vegetation proximity. While generally shade‐avoiding species strongly elongate in response to the proximity of other plants, shade‐tolerant species do not. Here we review the molecular mechanisms that control the regulation of hypocotyl elongation in shade‐avoiding species as a reference framework to understand shade tolerance. Comparative studies indicate that shade tolerance is implemented by components also known to regulate hypocotyl elongation in shade‐avoiding species. These components, however, show differential molecular properties that explain how, in response to the same stimulus, shade‐avoiding species elongate while shade‐tolerant ones do not.
Basic helix-loop-helix proteins (bHLHs) are found throughout the three eukaryotic kingdoms and constitute one of the largest families of transcription factors. A growing number of bHLH proteins have ...been functionally characterized in plants. However, some of these have not been previously classified. We present here an updated and comprehensive classification of the bHLHs encoded by the whole sequenced genomes of Arabidopsis (Arabidopsis thaliana), Populus trichocarpa, Oryza sativa, Physcomitrella patens, and five algae species. We define a plant bHLH consensus motif, which allowed the identification of novel highly diverged atypical bHLHs. Using yeast two-hybrid assays, we confirm that (1) a highly diverged bHLH has retained protein interaction activity and (2) the two most conserved positions in the consensus play an essential role in dimerization. Phylogenetic analysis permitted classification of the 638 bHLH genes identified into 32 subfamilies. Evolutionary and functional relationships within subfamilies are supported by intron patterns, predicted DNA-binding motifs, and the architecture of conserved protein motifs. Our analyses reveal the origin and evolutionary diversification of plant bHLHs through differential expansions, domain shuffling, and extensive sequence divergence. At the functional level, this would translate into different subfamilies evolving specific DNA-binding and protein interaction activities as well as differential transcriptional regulatory roles. Our results suggest a role for bHLH proteins in generating plant phenotypic diversity and provide a solid framework for further investigations into the role carried out in the transcriptional regulation of key growth and developmental processes.
Summary
The bacterium Vibrio cholerae is a natural inhabitant of aquatic ecosystems across the planet. V. cholerae serogroups O1 and O139 are responsible for cholera outbreaks in developing countries ...accounting for 3–5 million infections worldwide and 28.800–130.000 deaths per year according to the World Health Organization. In contrast, V. cholerae serogroups other than O1 and O139, also designated as V. cholerae non‐O1/O139 (NOVC), are not associated with epidemic cholera but can cause other illnesses that may range in severity from mild (e.g. gastroenteritis, otitis, etc.) to life‐threatening (e.g. necrotizing fasciitis). Although generally neglected, NOVC‐related infections are on the rise and represent one of the most striking examples of emerging human diseases linked to climate change. NOVC strains are also believed to potentially contribute to the emergence of new pathogenic strains including strains with epidemic potential as a direct consequence of genetic exchange mechanisms such as horizontal gene transfer and genetic recombination. Besides general features concerning the biology and ecology of NOVC strains and their associated diseases, this review aims to highlight the most relevant aspects related to the emergence and potential threat posed by NOVC strains under a rapidly changing environmental and climatic scenario.
Light limitation caused by dense vegetation is one of the greatest threats to plant survival in natural environments. Plants detect such neighboring vegetation as a reduction in the red to far-red ...ratio (R:FR) of the incoming light. The low R:FR signal, perceived by phytochromes, initiates a set of responses collectively known as the shade avoidance syndrome, intended to reduce the degree of current or future shade from neighbors by overtopping such competitors or inducing flowering to ensure seed production. At the seedling stage these responses include increased hypocotyl elongation. We have systematically analyzed the Arabidopsis seedling response and the contribution of phyA and phyB to perception of decreased R:FR, at three different levels of photosynthetically active radiation. Our results show that the shade avoidance syndrome, induced by phyB deactivation, is gradually antagonized by phyA, operating through the so-called FR-High Irradiance Response, in response to high FR levels in a range that simulates plant canopy shade. The data indicate that the R:FR signal distinguishes between the presence of proximal, but non-shading, neighbors and direct foliar shade, via a intrafamily photosensory attenuation mechanism that acts to suppress excessive reversion toward skotomorphogenic development under prolonged direct vegetation shade.
Unlike the situation in animals, the final morphology of the plant body is highly modulated by the environment. During Arabidopsis development, intrinsic factors provide the framework for basic ...patterning processes. CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD‐ZIPIII) transcription factors are involved in embryo, shoot and root patterning. During vegetative growth HD‐ZIPIII proteins control several polarity set‐up processes such as in leaves and the vascular system. We have identified several direct target genes of the HD‐ZIPIII transcription factor REVOLUTA (REV) using a chromatin immunoprecipitation/DNA sequencing (ChIP‐Seq) approach. This analysis revealed that REV acts upstream of auxin biosynthesis and affects directly the expression of several class II HD‐ZIP transcription factors that have been shown to act in the shade‐avoidance response pathway. We show that, as well as involvement in basic patterning, HD‐ZIPIII transcription factors have a critical role in the control of the elongation growth that is induced when plants experience shade. Leaf polarity is established by the opposed actions of HD‐ZIPIII and KANADI transcription factors. Finally, our study reveals that the module that consists of HD‐ZIPIII/KANADI transcription factors controls shade growth antagonistically and that this antagonism is manifested in the opposed regulation of shared target genes.
In high density of vegetation, plants detect neighbors by perceiving changes in light quality through phytochrome photoreceptors. Close vegetation proximity might result in competition for resources, ...such as light. To face this challenge, plants have evolved two alternative strategies: to either tolerate or avoid shade. Shade-avoiding species generally adapt their development by inducing hypocotyl, stem, and petiole elongation, apical dominance and flowering, and decreasing leaf expansion and yield, a set of responses collectively known as the shade avoidance syndrome (SAS). The SAS responses have been mostly studied at the seedling stage, centered on the increase of hypocotyl elongation. After compiling the main findings about SAS responses in seedlings, this review is focused on the response to shade at adult stages of development, such as petioles of adult leaves, and the little information available on the SAS responses in reproductive tissues. We discuss these responses based on the knowledge about the molecular mechanisms and components with a role in regulating the SAS response of the hypocotyls of Arabidopsis thaliana. The transcriptional networks involved in this process, as well as the communication among the tissues that perceive the shade and the ones that respond to this stimulus will also be briefly commented.
The shade avoidance syndrome (SAS) refers to a set of plant responses initiated after perception by the phytochromes of light with a reduced red to far‐red ratio, indicative of vegetation proximity ...or shade. These responses, including elongation growth, anticipate eventual shading from potential competitor vegetation by overgrowing neighboring plants or flowering to ensure production of viable seeds for the next generation. In Arabidopsis thaliana seedlings, the SAS includes dramatic changes in gene expression, such as induction of PHYTOCHROME RAPIDLY REGULATED 1 (PAR1), encoding an atypical basic helix‐loop‐helix (bHLH) protein that acts as a transcriptional co‐factor to repress hypocotyl elongation. Indeed, PAR1 has been proposed to act fundamentally as a dominant negative antagonist of conventional bHLH transcription factors by forming heterodimers with them to prevent their binding to DNA or other transcription factors. Here we report the identification of PAR1‐interacting factors, including the brassinosteroid signaling components BR‐ENHANCED EXPRESSION (BEE) and BES1‐INTERACTING MYC‐LIKE (BIM), and characterize their role as networked positive regulators of SAS hypocotyl responses. We provide genetic evidence that these bHLH transcriptional regulators not only control plant growth and development under shade and non‐shade conditions, but are also redundant in the control of plant viability. Our results suggest that SAS responses are initiated as a consequence of a new balance of transcriptional regulators within the pre‐existing bHLH network triggered by plant proximity, eventually causing hypocotyls to elongate.
Organogelation is a promising alternative to provide structure and texture to vegetable oils and stability to solid-like water-in-oil emulsions. Within this framework, we investigate the effect of ...monoglycerides (MG; 0%–0.5%) in the microstructure, thermal and textural behavior of organogelled emulsions developed with candelilla wax (CW; 0.5%–4%), safflower oil, and water (20%). The emulsions were prepared by homogenization (200bars) at 65°C, cooling to 45°C or 47°C (Tout), and then storage at 5°C for 24h. To evaluate the effect of shearing and water addition we also developed CW–MG organogels (i.e., no water added) under similar conditions. Both systems were analyzed for solid phase content (SPC), texture, and microstructure. Independent of Tout, as CW and MG concentration increased in both systems the SPC increased also (P<0.05). In the organogelled emulsions with 3% CW, independent of MG and Tout, hardness (2245.7±270gf∗mm) was ≈80% of the organogels' hardness (2861.0±255.0gf∗mm). This behavior was associated with the lower SPC (≈20%) present in the emulsions. Additionally, the microphotographs of the emulsions showed that water droplet size decreases as MG concentration increased. This effect was partly associated with the interfacial effect of the MG, but mainly with the lower extent of coalescence resulting from the droplet immobilization by the crystal network developed by CW. The lower texture and the decrease in water droplet size as MG concentration increased were not observed in the 2% CW emulsions, particularly at MG concentrations higher than 0.25%. This in spite the 2% CW–MG organogels had higher SPC than the corresponding emulsions (P<0.05). These results suggested that MG affected the inter-crystal interactions in both the organogels and the emulsions. This phenomenon became more significant as the MG concentration increased with respect to the crystal mass.
•Candelilla wax (CW) and monoglycerides (MG) structured solid-like W/O emulsions.•The CW crystal network limited coalescence of water droplets.•The MG decreased the apparent droplet size of emulsions with 3% CW.•The organogelled emulsions with 3% CW had softer texture than the 3% CW organogels.•MG decreased the CW inter-crystal interactions in the organogels and the emulsions.
The new tools revolutionizing Vibrio science Baker‐Austin, Craig; Trinanes, Joaquin; Martinez‐Urtaza, Jaime
Environmental microbiology,
October 2020, 2020-10-00, 20201001, Letnik:
22, Številka:
10
Journal Article
Recenzirano
Summary
As microbiologists we live in exciting times. A variety of technical and conceptual developments, particularly in the last decade have revolutionized the field of microbiology, redrawing the ...landscape, and entirely redefining what is possible. Perhaps this paradigm shift is no more apparent than in the study of vibrios. The family Vibrionaceae are almost unique as a group of bacteria to study in microbiology: they are genomically, phylogenetically and functionally diverse yet a distinct group of environmental bacteria encompassing important human and animal pathogens as well as non‐pathogenic species such as ecologically critical symbionts. Sensitive to physiochemical stimuli, they are among the fasting replicating bacteria studied, capable of responding almost immediately to favourable environmental conditions such as those afforded by climate warming. Characterized by an unusual double chromosome and frequently carrying numerous cryptic plasmids – their genomes are often pockmarked with insertion elements, transposons, prophages and integrases – paying testament to past genomic promiscuity. With a strong affinity for environmental niches in freshwater and marine systems, they are among the most numerous bacteria present in our oceans, coasts and freshwater environments. As such they offer something for almost anyone interested in microbiology and represent an excellent example of field of microbiology that has benefitted hugely by advances across a gamut of disciplines – not just microbiological – but encompassing genomics, genetics, oceanography, ecological, earth observations sciences and data visualization, among others. We will briefly outline some of the most exciting, innovative and translational scientific advances that are currently being applied to these ecologically, environmentally and clinically important bacteria.
This research analyses how different cement mortars behave in terms of their physical and mechanical properties. Several components were necessary to make seven mixes of mortars, such as Portland ...cement, standard sand, and solid waste from a factory of sodium silicate, in addition to graphene oxide. Furthermore, graphene oxide (GO) was selected to reduce the micropores and increase the nanopores in the cement mortar. Hence, some tests were carried out to determine their density, humidity content, water absorption capacity, open void porosity, the alkali–silica reaction, as well as flexural and mechanical strength and acid resistance. Thus, standard-sand-manufactured mortars’ mechanical properties were proved to be slightly better than those manufactured with recycled waste; the mortars with this recycled aggregate presented problems of alkali–silica reaction. In addition, GO (in a ratio GO/cement = 0.0003) performed as a filler, improving the mechanical properties (30%), alkali–silica (80%), and acid resistance
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