Changes in gravitational forces induce the modification of Arabidopsis thaliana silique pedicel positioning

A protocol for measuring the response of Arabidopsis roots to gravity and treatment for simulated microgravity

We present a protocol to quantify the response of both normal and mutant Arabidopsis seedlings to gravity and simulated microgravity under earth-normal gravity conditions. We describe the steps to simulate microgravity using a three-dimensional (3D) clinostat, which changes the rate and direction at random and consistently rotates the axis horizontally and vertically to counteract the standard gravity at the Earth's surface. We then detail the gravity stimulation experiment, followed by the assessment of root responses using ImageJ-based analysis. For complete details on the use and execution of this protocol, please refer to Xu et al. (2022).1.

BREVIPEDICELLUS and ERECTA control the expression of AtPRX17 to prevent Arabidopsis callus browning

Efficient in vitro callus generation is required for tissue culture propagation, a process that allows for plant regeneration and transgenic breeding for desired phenotypes. Identifying genes and regulatory elements that prevent impaired callus growth and callus browning is essential for the development of in vitro callus systems. Here, we show that the BREVIPEDICELLUS and ERECTA pathways in Arabidopsis calli converge to prevent callus browning, and positively regulate the expression of the isoperoxidase gene AtPRX17 in rapidly growing calli. Loss-of-function mutations in both BREVIPEDICELLUS and ERECTA resulted in markedly increased callus browning. Transgenic lines expressing 35S pro::AtPRX17 in the bp-5 er105 double mutant background fully rescued this phenotypic abnormality. Using in vivo (chromatin immunoprecipitation-PCR and transient expression) and in vitro (electrophoretic mobility shift assays) assays, we observed that the BREVIPEDICELLUS protein binds directly to the upstream sequence of AtPRX17 to promote its transcription during callus growth. ERECTA is a ubiquitous factor required for cell proliferation and growth. We show that ERECTA positively regulates the expression of the transcription factor WRKY6, which directly binds to a separate site on the AtPRX17 promoter, further increasing its expression. Our data reveal an important molecular mechanism involved in the regulation of peroxidase isozyme expression to reduce Arabidopsis callus browning.

Switching the Direction of Stem Gravitropism by Altering Two Amino Acids in AtLAZY1

From germination to flowering, gravity influences plant growth and development. A rice (Oryza sativa) mutant with a distinctly prostrate growth habit led to the discovery of a gene category that participates in the shaping of plant form by gravity. Each so-called LAZY gene includes five short regions of conserved sequence. The importance of each of these regions in the LAZY1 gene of Arabidopsis (Arabidopsis thaliana; AtLAZY1) was tested by mutating each region and measuring how well transgenic expression of the resulting protein variant rescued the large inflorescence branch angle of an atlazy1 mutant. The effect of each alteration on subcellular localization was also determined. Region I was required for AtLAZY1 to reside at the plasma membrane, which is necessary for its function. Mutating region V severely disrupted function without affecting subcellular localization. Regions III and IV could be mutated without large impact on function or localization. Altering region II with two conservative amino acid substitutions (L92A/I94A) had the profound effect of switching shoot gravity responses from negative (upward bending) to positive (downward bending), resulting in a "weeping" inflorescence phenotype. Mechanical weakness of the stem was ruled out as an explanation for the downward bending. Instead, experiments demonstrated that the L92A/I94A change to AtLAZY1 reversed the auxin gradient normally established across stems by the gravity-sensing mechanism. This discovery opens up new avenues for studying how auxin gradients form across organs and new approaches for engineering plant architecture for agronomic and other practical purposes.

The effect of simulated microgravity on the Brassica napus seedling proteome

The magnitude and the direction of the gravitational field represent an important environmental factor affecting plant development. In this context, the absence or frequent alterations of the gravity field (i.e. microgravity conditions) might compromise extraterrestrial agriculture and hence space inhabitation by humans. To overcome the deleterious effects of microgravity, a complete understanding of the underlying changes on the macromolecular level is necessary. However, although microgravity-related changes in gene expression are well characterised on the transcriptome level, proteomic data are limited. Moreover, information about the microgravity-induced changes in the seedling proteome during seed germination and the first steps of seedling development is completely missing. One of the valuable tools to assess gravity-related issues is 3D clinorotation (i.e. rotation in two axes). Therefore, here we address the effects of microgravity, simulated by a two-axial clinostat, on the proteome of 24- and 48-h-old seedlings of oilseed rape (Brassica napus L.). The liquid chromatography-MS-based proteomic analysis and database search revealed 95 up- and 38 downregulated proteins in the tryptic digests obtained from the seedlings subjected to simulated microgravity, with 42 and 52 annotations detected as being unique for 24- and 48-h treatment times, respectively. The polypeptides involved in protein metabolism, transport and signalling were annotated as the functional groups most strongly affected by 3-D clinorotation.

OsbZIP48, a HY5 Transcription Factor Ortholog, Exerts Pleiotropic Effects in Light-Regulated Development

Plants have evolved an intricate network of sensory photoreceptors and signaling components to regulate their development. Among the light signaling components identified to date, HY5, a basic leucine zipper (bZIP) transcription factor, has been investigated extensively. However, most of the work on HY5 has been carried out in Arabidopsis (Arabidopsis thaliana), a dicot. In this study, based on homology search and phylogenetic analysis, we identified three homologs of AtHY5 in monocots; however, AtHYH (HY5 homolog) homologs are absent in the monocots analyzed. Out of the three homologs identified in rice (Oryza sativa), we have functionally characterized OsbZIP48OsbZIP48 was able to complement the Athy5 mutant. OsbZIP48 protein levels are developmentally regulated in rice. Moreover, the OsbZIP48 protein does not degrade in dark-grown rice and Athy5 seedlings complemented with OsbZIP48, which is in striking contrast to AtHY5. In comparison with AtHY5, which does not cause any change in hypocotyl length when overexpressed in Arabidopsis, the overexpression of full-length OsbZIP48 in rice transgenics reduced the plant height considerably. Microarray analysis revealed that OsKO2, which encodes ent-kaurene oxidase 2 of the gibberellin biosynthesis pathway, is down-regulated in OsbZIP48^OE and up-regulated in OsbZIP48^KD transgenics as compared with the wild type. Electrophoretic mobility shift assay showed that OsbZIP48 binds directly to the OsKO2 promoter. The RNA interference lines and the T-DNA insertional mutant of OsbZIP48 showed seedling-lethal phenotypes despite the fact that roots were more proliferative during early stages of development in the T-DNA insertional mutant. These data provide credible evidence that OsbZIP48 performs more diverse functions in a monocot system like rice in comparison with its Arabidopsis ortholog, HY5.

Effects of hypergravity stimulus on global gene expression during reproductive growth in Arabidopsis

The life cycle of higher plants consists of successive vegetative and reproductive growth phases. Understanding effects of altered gravity conditions on the reproductive growth is essential, not only to elucidate how higher plants evolved under gravitational condition on Earth but also to approach toward realization of agriculture in space. In the present study, a comprehensive analysis of global gene expression of floral buds under hypergravity was carried out to understand effects of altered gravity on reproductive growth at molecular level. Arabidopsis plants grown for 20-26 days were exposed to hypergravity of 300 g for 24 h. Total RNA was extracted from flower buds and microarray (44 K) analysis performed. As a result, hypergravity up-regulated expression of a gene related to β-1,3-glucanase involved in pectin modification, and down-regulated β-galactosidase and amino acid transport, which supports a previous study reporting inhibition of pollen development and germination under hypergravity. With regard to genes related to seed storage accumulation, hypergravity up-regulated expression of genes of aspartate aminotransferase, and down-regulated those related to cell wall invertase and sugar transporter, supporting a previous study reporting promotion of protein body development and inhibition of starch accumulation under hypergravity, respectively. In addition, hypergravity up-regulated expression of G6PDH and GPGDH, which supports a previous study reporting promotion of lipid deposition under hypergravity. In addition, analysis of the metabolic pathway revealed that hypergravity substantially changed expression of genes involved in the biosynthesis of phytohormones such as abscisic acid and auxin.

Modulation of root-skewing responses by KNAT1 in Arabidopsis thaliana

The KNOTTED1 homeobox (KNOX) family transcription factors are essential for stem cell establishment and maintenance and regulate various aspects of development in all green plants. Expression patterns of the KNOX genes in the roots of plants have been reported, but their role in development remains unclear. Here we show how the KNAT1 gene is specifically involved in root skewing in Arabidopsis. The roots of two mutant alleles of KNAT1 (bp-1 and bp-5) exhibited exaggerated skewing to the right of gravity when grown on both vertical and tilted agar medium surfaces. This skewing phenotype was enhanced by treatments with low concentrations of propyzamide, and required auxin transport. The KNAT1 mutation substantially decreased basipetal auxin transport and increased auxin accumulation in the roots. Using a PIN2-GFP reporter and western blot analysis, we found that this alteration in auxin transport was accompanied by a decrease in PIN2 levels in the root tip. Decreased PIN2 expression in the mutant roots was not accompanied by reduced mRNA levels, suggesting that the KNAT1 mutations affected PIN2 expression at the posttranscriptional level. In vivo visualization of intracellular vacuolar targeting indicated that vacuolar degradation of PIN2-GFP was significantly promoted in the root tips of the bp allelic mutants. Together, these results demonstrate that KNAT1 negatively modulates root skewing, possibly by regulating auxin transport.

Characterization of photosystem I in rice (Oryza sativa L.) seedlings upon exposure to random positioning machine

To gain a better understanding of how photosynthesis is adapted under altered gravity forces, photosynthetic apparatus and its functioning were investigated in rice (Oryza sativa L.) seedlings grown in a random positioning machine (RPM). A decrease in fresh weight and dry weight was observed in rice seedlings grown under RPM condition. No significant changes were found in the chloroplast ultrastructure and total chlorophyll content between the RPM and control samples. Analyses of chlorophyll fluorescence and thermoluminescence demonstrate that PSII activity was unchanged under RPM condition. However, PSI activity decreased significantly under RPM condition. 77 K fluorescence emission spectra show a blue-shift and reduction of PSI fluorescence emission peak in the RPM seedlings. In addition, RPM caused a significant decrease in the amplitude of absorbance changes of P700 at 820 nm (A 820) induced by saturated far-red light. Moreover, the PSI efficiency (Φ I) decreased significantly under RPM condition. Immunoblot and blue native gel analyses further illustrate that accumulation of PSI proteins was greatly decreased in the RPM seedlings. Our results suggest that PSI, but not PSII, is down-regulated under RPM condition.

AtLAZY1 is a signaling component required for gravitropism of the Arabidopsis thaliana inflorescence

The present study identified a family of six A. thaliana genes that share five limited regions of sequence similarity with LAZY1, a gene in Oryza sativa (rice) shown to participate in the early gravity signaling for shoot gravitropism. A T-DNA insertion into the Arabidopsis gene (At5g14090) most similar to LAZY1 increased the inflorescence branch angle to 81° from the wild type value of 42°. RNA interference lines and molecular rescue experiments confirmed the linkage between the branch-angle phenotype and the gene consequently named AtLAZY1. Time-resolved gravitropism measurements of atlazy1 hypocotyls and primary inflorescence stems showed a significantly reduced bending rate during the first hour of response. The subcellular localization of AtLAZY1 protein was investigated to determine if the nuclear localization predicted from the gene sequence was observable and important to its function in shoot gravity responses. AtLAZY1 fused to green fluorescent protein largely rescued the branch-angle phenotype of atlazy1, and was observed by confocal microscopy at the cell periphery and within the nucleus. Mutation of the nuclear localization signal prevented detectable levels of AtLAZY1 in the nucleus without affecting the ability of the gene to rescue the atlazy1 branch-angle phenotype. These results indicate that AtLAZY1 functions in gravity signaling during shoot gravitropism, being a functional ortholog of rice LAZY1. The nuclear pool of the protein appears to be unnecessary for this function, which instead relies on a pool that appears to reside at the cell periphery.

A proteomic approach to analyzing responses of Arabidopsis thaliana root cells to different gravitational conditions using an agravitropic mutant, pin2 and its wild type

Background

Root gravitropsim has been proposed to require the coordinated, redistribution of the plant signaling molecule auxin within the root meristem, but the underlying molecular mechanisms are still unknown. PIN proteins are membrane transporters that mediate the efflux of auxin from cells. The PIN2 is important for the basipetal transport of auxin in roots and plays a critical role in the transmission of gravity signals perceived in the root cap to the root elongation zone. The loss of function pin2 mutant exhibits a gravity-insensitive root growth phenotype. By comparing the proteomes of wild type and the pin2 mutant root tips under different gravitational conditions, we hope to identify proteins involved in the gravity-related signal transduction.

Results

To identify novel proteins involved in the gravity signal transduction pathway we have carried out a comparative proteomic analysis of Arabidopsis pin2 mutant and wild type (WT) roots subjected to different gravitational conditions. These conditions included horizontal (H) and vertical (V) clinorotation, hypergravity (G) and the stationary control (S). Analysis of silver-stained two-dimensional SDS-PAGE gels revealed 28 protein spots that showed significant expression changes in altered gravity (H or G) compared to control roots (V and S). Whereas the majority of these proteins exhibited similar expression patterns in WT and pin2 roots, a significant number displayed different patterns of response between WT and pin2 roots. The latter group included 11 protein spots in the H samples and two protein spots in the G samples that exhibited an altered expression exclusively in WT but not in pin2 roots. One of these proteins was identified as annexin2, which was induced in the root cap columella cells under altered gravitational conditions.

Conclusions

The most interesting observation in this study is that distinctly different patterns of protein expression were found in WT and pin2 mutant roots subjected to altered gravity conditions. The data also demonstrate that PIN2 mutation not only affects the basipetal transport of auxin to the elongation zone, but also results in an altered expression of proteins in the root columella.