Gravity sensing and responses in the coordination of the shoot gravitropic setpoint angle

Molecular mechanism of brassinosteroids involved in root gravity response based on transcriptome analysis

BACKGROUND

Brassinosteroids (BRs) are a class of phytohormones that regulate a wide range of developmental processes in plants. BR-associated mutants display impaired growth and response to developmental and environmental stimuli.

RESULTS

Here, we found that a BR-deficient mutant det2-1 displayed abnormal root gravitropic growth in Arabidopsis, which was not present in other BR mutants. To further elucidate the role of DET2 in gravity, we performed transcriptome sequencing and analysis of det2-1 and bri1-116, bri1 null mutant allele. Expression levels of auxin, gibberellin, cytokinin, and other related genes in the two mutants of det2-1 and bri1-116 were basically the same. However, we only found that a large number of JAZ (JASMONATE ZIM-domain) genes and jasmonate synthesis-related genes were upregulated in det2-1 mutant, suggesting increased levels of endogenous JA.

CONCLUSIONS

Our results also suggested that DET2 not only plays a role in BR synthesis but may also be involved in JA regulation. Our study provides a new insight into the molecular mechanism of BRs on the root gravitropism.

Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism

Root gravitropic bending represents a fundamental aspect of terrestrial plant physiology. Gravity is perceived by sedimentation of starch-rich plastids (statoliths) to the bottom of the central root cap cells. Following gravity perception, intercellular auxin transport is redirected downwards leading to an asymmetric auxin accumulation at the lower root side causing inhibition of cell expansion, ultimately resulting in downwards bending. How gravity-induced statoliths repositioning is translated into asymmetric auxin distribution remains unclear despite PIN auxin efflux carriers and the Negative Gravitropic Response of roots (NGR) proteins polarize along statolith sedimentation, thus providing a plausible mechanism for auxin flow redirection. In this study, using a functional NGR1-GFP construct, we visualized the NGR1 localization on the statolith surface and plasma membrane (PM) domains in close proximity to the statoliths, correlating with their movements. We determined that NGR1 binding to these PM domains is indispensable for NGR1 functionality and relies on cysteine acylation and adjacent polybasic regions as well as on lipid and sterol PM composition. Detailed timing of the early events following graviperception suggested that both NGR1 repolarization and initial auxin asymmetry precede the visible PIN3 polarization. This discrepancy motivated us to unveil a rapid, NGR-dependent translocation of PIN-activating AGCVIII kinase D6PK towards lower PMs of gravity-perceiving cells, thus providing an attractive model for rapid redirection of auxin fluxes following gravistimulation.

Identification of a major QTL and candidate genes analysis for branch angle in rapeseed (Brassica napus L.) using QTL-seq and RNA-seq

Introduction

Branching angle is an essential trait in determining the planting density of rapeseed (Brassica napus L.) and hence the yield per unit area. However, the mechanism of branching angle formation in rapeseed is not well understood.

Methods

In this study, two rapeseed germplasm with extreme branching angles were used to construct an F2 segregating population; then bulked segregant analysis sequencing (BSA-seq) and quantitative trait loci (QTL) mapping were utilized to localize branching anglerelated loci and combined with transcriptome sequencing (RNA-seq) and quantitative real-time PCR (qPCR) for candidate gene mining.

Results and discussion

A branching angle-associated quantitative trait loci (QTL) was mapped on chromosome C3 (C3: 1.54-2.65 Mb) by combining BSA-seq as well as traditional QTL mapping. A total of 54 genes had SNP/Indel variants within the QTL interval were identified. Further, RNA-seq of the two parents revealed that 12 of the 54 genes were differentially expressed between the two parents. Finally, we further validated the differentially expressed genes using qPCR and found that six of them presented consistent differential expression in all small branching angle samples and large branching angles, and thus were considered as candidate genes related to branching angles in rapeseed. Our results introduce new candidate genes for the regulation of branching angle formation in rapeseed, and provide an important reference for the subsequent exploration of its formation mechanism.

Cellular and physiological functions of SGR family in gravitropic response in higher plants

BACKGROUND

In plants, gravity directs bidirectional growth; it specifies upward growth of shoots and downward growth of roots. Due to gravity, roots establish robust anchorage and shoot, which enables to photosynthesize. It sets optimum posture and develops plant architecture to efficiently use resources like water, nutrients, CO2, and gaseous exchange. Hence, gravitropism is crucial for crop productivity as well as for the growth of plants in challenging climate. Some SGR members are known to affect tiller and shoot angle, organ size, and inflorescence stem in plants.

AIM OF REVIEW

Although the SHOOT GRAVITROPISM (SGR) family plays a key role in regulating the fate of shoot gravitropism, little is known about its function compared to other proteins involved in gravity response in plant cells and tissues. Moreover, less information on the SGR family's physiological activities and biochemical responses in shoot gravitropism is available. This review scrutinizes and highlights the recent developments in shoot gravitropism and provides an outlook for future crop development, multi-application scenarios, and translational research to improve agricultural productivity.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Plants have evolved multiple gene families specialized in gravitropic responses, of which the SGR family is highly significant. The SGR family regulates the plant's gravity response by regulating specific physiological and biochemical processes such as transcription, cell division, amyloplast sedimentation, endodermis development, and vacuole formation. Here, we analyze the latest discoveries in shoot gravitropism with particular attention to SGR proteins in plant cell biology, cellular physiology, and homeostasis. Plant cells detect gravity signals by sedimentation of amyloplast (starch granules) in the direction of gravity, and the signaling cascade begins. Gravity sensing, signaling, and auxin redistribution (organ curvature) are the three components of plant gravitropism. Eventually, we focus on the role of multiple SGR genes in shoot and present a complete update on the participation of SGR family members in gravity.

IGT/LAZY genes are differentially influenced by light and required for light-induced change to organ angle

BACKGROUND

Plants adjust their growth orientations primarily in response to light and gravity signals. Considering that the gravity vector is fixed and the angle of light incidence is constantly changing, plants must somehow integrate these signals to establish organ orientation, commonly referred to as gravitropic set-point angle (GSA). The IGT gene family contains known regulators of GSA, including the gene clades LAZY, DEEPER ROOTING (DRO), and TILLER ANGLE CONTROL (TAC).

RESULTS

Here, we investigated the influence of light on different aspects of GSA phenotypes in LAZY and DRO mutants, as well as the influence of known light signaling pathways on IGT gene expression. Phenotypic analysis revealed that LAZY and DRO genes are collectively required for changes in the angle of shoot branch tip and root growth in response to light. Single lazy1 mutant branch tips turn upward in the absence of light and in low light, similar to wild-type, and mimic triple and quadruple IGT mutants in constant light and high-light conditions, while triple and quadruple IGT/LAZY mutants show little to no response to changing light regimes. Further, the expression of IGT/LAZY genes is differentially influenced by daylength, circadian clock, and light signaling.

CONCLUSIONS

Collectively, the data show that differential expression of LAZY and DRO genes are required to enable plants to alter organ angles in response to light-mediated signals.

Peach LAZY1 and DRO1 protein-protein interactions and co-expression with PRAF/RLD family support conserved gravity-related protein interactions across plants

IGT/LAZY proteins play a central role in determining gravitropic set point angle and orientation of lateral organs across plant species. Recent work in model systems has demonstrated that interactions between IGT/LAZY proteins and BREVIS RADIX (BRX)-domain containing proteins, such as PH, RCC1, AND FYVE/RCC1-LIKE DOMAIN (PRAF/RLD), and BREVIS RADIX LIKE (BRXL) family members, are mechanistically important for setting gravitropic set point angle. Here, we identified peach PRAF/RLD proteins as interactors of the peach IGT/LAZY proteins PpeLAZY1 and DEEPER ROOTING 1 (PpeDRO1) from a yeast-two-hybrid screen. We also show that the BRX domains of these interacting proteins have high sequence similarity with PRAF/RLD and BRX family proteins from rice and Arabidopsis. Further, PpeLAZY1 and the peach PRAF/RLD interactors are all expressed at relatively high levels in leaf, meristem, and shoot tip tissues. Together, this evidence supports the importance and conservation of IGT/LAZY-BRX-domain interactions, which underlie setting gravitropic set point angle across angiosperms.

Aluminium stress-induced modulation of root gravitropism in pea (Pisum sativum) via auxin signalling

Aluminium (Al) toxicity stands out as a primary cause of crop failure in acidic soils. The root gravity setpoint angle (GSA), one of the important traits of the root system architecture (RSA), plays a pivotal role in enabling plants to adapt to abiotic stress. This study explored the correlation between GSA and Al stress using hydroponic culture with pea (Pisum sativum) plants. The findings revealed that under Al stress, GSA increased in newly developed lateral roots. Notably, this response remained consistent regardless of the treatment duration, extending for at least 3 days during the experiment. Furthermore, exposure to Al led to a reduction in both the size and quantity of starch granules, pivotal components linked to gravity perception. The accumulation of auxin in root transition zone increased. This variation was mirrored in the expression of genes linked to granule formation and auxin efflux, particularly those in the PIN-formed family. This developmental framework suggested a unique role for the root gravitropic response that hinges on starch granules and auxin transport, acting as mediators in the modulation of GSA under Al stress. Exogenous application of indole-3-acetic acid (IAA) and the auxin efflux inhibitor N-1-naphthylphthalamic acid (NPA) had an impact on the root gravitropic response to Al stress. The outcomes indicate that Al stress inhibited polar auxin transport and starch granule formation, the two processes crucial for gravitropism. This impairment led to an elevation in GSA and a reconfiguration of RSA. This study introduces a novel perspective on how plant roots react to Al toxicity, culminating in RSA modification in the context of acidic soil with elevated Al concentrations.

The Main Functions of Plastids

Plastids are semi-autonomous organelles like mitochondria and derive from a cyanobacterial ancestor that was engulfed by a host cell. During evolution, they have recruited proteins originating from the nuclear genome, and only parts of their ancestral metabolic properties were conserved and optimized to limit functional redundancy with other cell compartments. Furthermore, large disparities in metabolic functions exist among various types of plastids, and the characterization of their various metabolic properties is far from being accomplished. In this review, we provide an overview of the main functions, known to be achieved by plastids or shared by plastids and other compartments of the cell. In short, plastids appear at the heart of all main plant functions.

Synergism of vesicle trafficking and cytoskeleton during regulation of plant growth and development: A mechanistic outlook

The cytoskeleton is a fundamental component found in all eukaryotic organisms, serving as a critical factor in various essential cyto-biological mechanisms, particularly in the locomotion and morphological transformations of plant cells. The cytoskeleton is comprised of three main components: microtubules (MT), microfilaments (MF), and intermediate filaments (IF). The cytoskeleton plays a crucial role in the process of cell wall formation and remodeling throughout the growth and development of cells. It is a highly organized and regulated network composed of filamentous components. In the basic processes of intracellular transport, such as mitosis, cytokinesis, and cell polarity, the plant cytoskeleton plays a crucial role according to recent studies. The major flaws in the organization of the cytoskeletal framework are at the root of the aberrant organogenesis currently observed in plant mutants. The regulation of protein compartmentalization and abundance within cells is predominantly governed by the process of vesicle/membrane transport, which plays a crucial role in several signaling cascades.The regulation of membrane transport in eukaryotic cells is governed by a diverse array of proteins. Recent developments in genomics have provided new tools to study the evolutionary relationships between membrane proteins in different plant species. It is known that members of the GTPases, COP, SNAREs, Rabs, tethering factors, and PIN families play essential roles in vesicle transport between plant, animal, and microbial species. This Review presents the latest research on the plant cytoskeleton, focusing on recent developments related to the cytoskeleton and summarizing the role of various proteins in vesicle transport. In addition, the report predicts future research direction of plant cytoskeleton and vesicle trafficking, potential research priorities, and provides researchers with specific pointers to further investigate the significant link between cytoskeleton and vesicle trafficking.

Cell polarity linked to gravity sensing is generated by LZY translocation from statoliths to the plasma membrane

Organisms have evolved under gravitational force, and many sense the direction of gravity by means of statoliths in specialized cells. In flowering plants, starch-accumulating plastids, known as amyloplasts, act as statoliths to facilitate downstream gravitropism. The gravity-sensing mechanism has long been considered a mechanosensing process by which amyloplasts transmit forces to intracellular structures, but the molecular mechanism underlying this has not been elucidated. We show here that LAZY1-LIKE (LZY) family proteins involved in statocyte gravity signaling associate with amyloplasts and the proximal plasma membrane. This results in polar localization according to the direction of gravity. We propose a gravity-sensing mechanism by which LZY translocation to the plasma membrane signals the direction of gravity by transmitting information on the position of amyloplasts.

Design and synthesis of strong root gravitropism inhibitors with no concomitant growth inhibition

Herein, we describe a highly potent gravitropic bending inhibitor with no concomitant growth inhibition. Previously, we reported that (2Z,4E)-5-phenylpenta-2,4-dienoic acid (ku-76) selectively inhibits root gravitropic bending of lettuce radicles at 5 μM. Based on the structure-activity relationship study of ku-76 as a lead compound, we designed and synthesized various C4-substituted analogs of ku-76. Among the analogs, 4-phenylethynyl analog exhibited the highest potency for gravitropic bending inhibition, which was effective at only 0.01 μM. Remarkably, 4-phenylethynyl analog is much more potent than the known inhibitor, NPA. Substitution in the para position on the aromatic ring of 4-phenylethynyl group was tolerated without diminished activity. In addition, evaluation using Arabidopsis indicated that 4-phenylethynyl analog inhibits gravitropism by affecting auxin distribution in the root tips. Based on the effects on Arabidopsis phenotypes, 4-phenylethynyl analog may be a novel inhibitor that differs in action from the previously reported auxin transport inhibitors.

Current Knowledge about the Impact of Microgravity on Gene Regulation

Microgravity (µg) has a massive impact on the health of space explorers. Microgravity changes the proliferation, differentiation, and growth of cells. As crewed spaceflights into deep space are being planned along with the commercialization of space travelling, researchers have focused on gene regulation in cells and organisms exposed to real (r-) and simulated (s-) µg. In particular, cancer and metastasis research benefits from the findings obtained under µg conditions. Gene regulation is a key factor in a cell or an organism’s ability to sustain life and respond to environmental changes. It is a universal process to control the amount, location, and timing in which genes are expressed. In this review, we provide an overview of µg-induced changes in the numerous mechanisms involved in gene regulation, including regulatory proteins, microRNAs, and the chemical modification of DNA. In particular, we discuss the current knowledge about the impact of microgravity on gene regulation in different types of bacteria, protists, fungi, animals, humans, and cells with a focus on the brain, eye, endothelium, immune system, cartilage, muscle, bone, and various cancers as well as recent findings in plants. Importantly, the obtained data clearly imply that µg experiments can support translational medicine on Earth.

The Course of Mechanical Stress: Types, Perception, and Plant Response

Mechanical stimuli, together with the corresponding plant perception mechanisms and the finely tuned thigmomorphogenetic response, has been of scientific and practical interest since the mid-17th century. As an emerging field, there are many challenges in the research of mechanical stress. Indeed, studies on different plant species (annual/perennial) and plant organs (stem/root) using different approaches (field, wet lab, and in silico/computational) have delivered insufficient findings that frequently impede the practical application of the acquired knowledge. Accordingly, the current work distils existing mechanical stress knowledge by bringing in side-by-side the research conducted on both stem and roots. First, the various types of mechanical stress encountered by plants are defined. Second, plant perception mechanisms are outlined. Finally, the different strategies employed by the plant stem and roots to counteract the perceived mechanical stresses are summarized, depicting the corresponding morphological, phytohormonal, and molecular characteristics. The comprehensive literature on both perennial (woody) and annual plants was reviewed, considering the potential benefits and drawbacks of the two plant types, which allowed us to highlight current gaps in knowledge as areas of interest for future research.

Mechanosensing, from forces to structures

Sessile plants evolve diverse structures in response to complex environmental cues. These factors, in essence, involve mechanical stimuli, which must be sensed and coordinated properly by the plants to ensure effective growth and development. While we have accumulated substantial knowledge on plant mechanobiology, how plants translate mechanical information into three-dimensional structures is still an open question. In this review, we summarize our current understanding of plant mechanosensing at different levels, particularly using Arabidopsis as a model plant system. We also attempt to abstract the mechanosensing process and link the gaps from mechanical cues to the generation of complex plant structures. Here we review the recent advancements on mechanical response and transduction in plant morphogenesis, and we also raise several questions that interest us in different sections.