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Leucine-rich repeat (LRR)-containing proteins have been identified in diverse species, including plants. The diverse intracellular and extracellular LRR variants are responsible for numerous biological processes. We analyzed the expression patterns of Arabidopsis thaliana extracellular LRR (AtExLRR) genes, 10 receptor-like proteins, and 4 additional genes expressing the LRR-containing protein by a promoter: β -glucuronidase (GUS) study. According to in silico expression studies, several AtExLRR genes were expressed in a tissue- or stage-specific and abiotic/hormone stress-responsive manner, indicating their potential participation in specific biological processes. Based on the promoter: GUS assay, AtExLRRs were expressed in different cells and organs. A quantitative real-time PCR investigation revealed that the expressions of AtExLRR3 and AtExLRR9 were distinct under various abiotic stress conditions. This study investigated the potential roles of extracellular LRR proteins in plant growth, development, and response to various abiotic stresses. [ABSTRACT FROM AUTHOR]

Chloroplasts sense a variety of stimuli triggering several acclimation responses. One prominent response is the mechanism of state transitions, which enables rapid adaption to changes in illumination. Here, we investigated the link between divalent cations (calcium, magnesium, and manganese) and protein kinase activity in Arabidopsis chloroplasts. Our results show that manganese ions are the strongest activator of kinase activity in chloroplasts followed by magnesium ions, whereas calcium ions are not able to induce kinase activity. Additionally, the phosphorylation of specific protein bands is strongly reduced in chloroplasts of a cmt1 mutant, which is impaired in manganese import into chloroplasts, as compared to the wild‐type. These findings provide insights for the future characterization of chloroplast protein kinase activity and potential target proteins. [ABSTRACT FROM AUTHOR]

Background: Plant grows in nature facing various types of abiotic stresses for their normal growth and development. During abiotic stress, plants evolve different types of mechanisms to survive in a hostile environment. Phospholipase D (PLD) plays important role in the regulation of diverse cellular processes including stress responses in plants. Member of PLD genes are well studied in different model plants; however, their functions in the jute are not clear yet. Result: In the present study, a total of 12 and 11 PLD genes were identified in the genome of C. capsularis and C. olitorius, respectively. The presence of the two conserved HKD motifs in PLD genes except for CoPLDδ-2 in jute suggests their strong lipase activity. Twenty different motifs were found in the identified PLD genes, and PLD-β1, PLD-γ1, and all members of PLD-δ1 of both jute species contained the highest number of motifs. Phylogenetic analysis showed the close evolutionary relationship among the five groups of jute PLD proteins along with the PLD proteins from Arabidopsis. Tissue-specific expression pattern of PLDα1-2, PLD-α2, PLDβ1, PLDγ1, and PLDδ1 of two jute species suggested their involvement in plant growth and development. However, the expression pattern of PLDα1-2, PLDα1-3, PLD-α4, PLDδ1, and PLDδ3 indicated their association during waterlogging stress. In addition, PLD-α2, PLDβ1, and PLDδ2 seemed to be involved in drought stress as well as salinity stress. Conclusion: This genome-wide identification of jute PLD genes from C. capsularis and C. olitorius will help to further functional characterization of the PLD genes for developing stress-tolerant jute variety. [ABSTRACT FROM AUTHOR]

Malectin is a maltose-binding endoplasmic reticulum protein conserved in animals. In Arabidopsis thaliana, we identified four genes that encode malectin-like domain (MLD)- and leucine-rich repeat (LRR)-containing proteins (AtMLLRs): two were receptor-like proteins (AtMLLR1 and 2) and the other two were extracellular proteins (AtMLLR3 and 4). The promoter:G3GFP+promoter:GUS assay indicated the organ- and cell-specific expression of the AtMLLR2 and AtMLLR3 genes. Abbreviations: Cmr: chloramphenicol-resistance marker; G3GFP: G3 green fluorescent protein; GUS: β-glucuronidase; KD: kinase domain; LRR: leucine-rich repeat; MLD: malectin-like domain; RLK: receptor-like kinase; SP: signal peptide; TMD: transmembrane domain; Tnos: nopaline synthase terminator [ABSTRACT FROM AUTHOR]

Sumoylation regulates numerous cellular functions in plants as well as in other eukaryotic systems. However, the regulatory mechanisms controlling E3 small ubiquitin-related modifier ( SUMO) ligase are not well understood. Here, post-translational modification of the Arabidopsis E3 SUMO ligase At SIZ1 was shown to be specifically controlled by abiotic stresses. At SIZ1 ubiquitination was induced by exposure to heat stress in transgenic plants overexpressing the E3 ubiquitin ligase COP1. In addition, At SIZ1 ubiquitination was strongly enhanced in transgenic plants overexpressing SUMO isopeptidase ESD4 under heat stress. By contrast, drought stress induced sumoylation rather than ubiquitination of At SIZ1 and sumoylated forms of At SIZ1 accumulated in esd4 and cop1-4 mutants. Moreover, siz1 mutants were found to be tolerant to heat and drought stresses. Taken together, these results indicate that ubiquitination and sumoylation of At SIZ1 in response to abiotic stresses depend on the activities of COP1 and ESD4 and that the activity and stability of At SIZ1 can be specifically controlled by different abiotic stresses. [ABSTRACT FROM AUTHOR]

The classification methods of the electrical signal can be effectively applied for the identification of salt tolerance in plants. Biotechnology can help researchers discover genes and proteins related to plant electrical signals, thereby deciphering the biological mechanisms of electrical signal classification, but it is time-consuming and expensive only using biological technologies. Although protein interaction relationships can be predicted using deep learning, the relationships between plant electrical signals and proteins are unclear. This uncertainty can directly lead to protein information incompletion or lack of plant electrical signal data, which is not conducive to prediction performance. To this end, we propose a graph neural network model that integrates plant electrical signal features to discover electrical signal-related proteins (PMESP). In particular, the model constructs protein interaction relationships as a graph structure, where nodes represent proteins. To obtain sufficient feature information of these nodes, we develop an electrical signal feature extraction model based on a bidirectional long short-term memory and utilize a pre-trained neural network to extract the semantic information features of proteins. In the PMESP, the features of the electrical signals and proteins are fused as the input of graph convolutional neural network (GCN), the representations of pairs of nodes are calculated by multilayer GCNs, and then the new protein interaction relationships are predicted by the comparison of the scores between nodes connected by edges to the scores between any pair of nodes. We finally assemble a dataset containing the relationships between electrical signals and protein interactions, employ the method of light induced rhythmic bioelectrogenesis to collect data from Arabidopsis thaliana leaves under salt stress, and use weighted gene co-expression network analysis and crawler methods to obtain Arabidopsis thaliana protein interaction relationships. The results illustrate that the area under the receiver operating characteristic curve and area under precision-recall curve values of the model on the test set are 0.9624 and 0.9684 respectively, which are significantly higher than other link predicting models and previous existing methods. • Designing a graph neural network for protein–protein interaction prediction. • The network fuses plant electrical signal and protein features. • Deciphering the classification mechanisms of plant electrical signals. • Applications in the prediction of proteins that generate plant electrical signals. [ABSTRACT FROM AUTHOR]

Because environmental stress can reduce crop growth and yield, the identification of genes that enhance agronomic traits is increasingly important. Previous screening of full-length cDNA overexpressing (FOX) rice lines revealed that OsTIFY11b, one of 20 TIFY proteins in rice, affects plant size, grain weight, and grain size. Therefore, we analyzed the effect ofOsTIFY11band nine other TIFY genes on the growth and yield of corresponding TIFY-FOX lines. Regardless of temperature, grain weight and culm length were enhanced in lines overexpressing TIFY11 subfamily genes, exceptOsTIFY11e.The TIFY-FOX plants exhibited increased floret number and reduced days to flowering, as well as reduced spikelet fertility, andOsTIFY10b, in particular, enhanced grain yield by minimizing decreases in fertility. We suggest that the enhanced growth of TIFY-transgenic rice is related to regulation of the jasmonate signaling pathway, as inArabidopsis.Moreover, we discuss the potential application of TIFY overexpression for improving crop yield. [ABSTRACT FROM AUTHOR]

Plants and animals have many similarities in the recognition of pathogen-associated molecular patterns (PAMPs) through pattern recognition receptors (PRR). One such receptor, Toll-like receptor (TLR) 5in animals and FLS2 in plants are used for recognition of bacterial elicitor flagellin. Several reports have shown that animal pathogens can colonize plants and induce productive infections. Moreover, certain similarities have been found between transcriptomes of Arabidopsis thaliana plants infected by the plant pathogen Pseudomonas syringae pv. tomato and the human pathogen Escherichia coli O157:H7. Here we analyzed the transcriptomes of Arabidopsis thaliana wild type and fls2 mutant plants exposed to E. coli O157:H7. We found a substantial number of significantly up- and downregulated genes with only partial overlap between transcriptomes of wild type and mutant plants. We further compared our transcriptome data to that of the transcriptome of Arabidopsis plants exposed to Pseudomonas syringae , Pseudomonas fluorescens and E. coli O157:H7 using data from previously published experiments. We found very little overlap between our data and that from previously published work, with the largest overlap with the data from previous studies on plants exposed to E. coli O157:H7. Furthermore, our work shows that the FLS receptor likely plays an important role in the response to E. coli O157:H7 in Arabidopsis, however, there appear to be other means for recognition of infections with this pathogen. Our work also shows similarities in the transcriptome response of plants to plant and animal pathogens. [ABSTRACT FROM AUTHOR]

Tubby proteins are highly conserved in a wide range of multicellular organisms. The Tubby gene family was first verified in obese mice. In plants, 11 Tubby genes have been identified in Arabidopsis, 14 in rice, and 11 in poplar. However, there is very little information about Tubby-like proteins in wheat. In this study, we identified four Tubby-like protein genes (TaTULP1-TaTULP4) in wheat. A comparison of the gene structure showed a conserved exon number pattern in TaTULPs, although the length of the introns differed. With the exception of TaTULP2, TaTULPs had four exons. To identify the chromosome localization of TaTULPs, BLASTn analyses were performed using the URGI database to predict the chromosomal location of TaTULP genes. TaTULP1, 2, 3 and 4 genes were localized on chromosomes 4, 5, 7 and 2. All TaTULPs harbor a Tubby domain in their C-terminal region and an F-box domain in the N terminus. We investigated protein-protein interactions between the F-box domain of TaTULPs and various wheat SKP1-like proteins (TaSKPs) using the yeast two-hybrid system. TaTULP1, TaTULP3 and TaTULP4 were found to interact with TaSKP1, TaSKP3 and TaSKP6, whereas TaTULP2 showed no interaction with TaSKP proteins. TaTULP proteins tagged with green fluorescent protein were targeted to the Golgi apparatus in plant cells. Our analysis of TaTULPs will aid in understanding the functions of TaTULPs in plants. [ABSTRACT FROM AUTHOR]

A new highly sensitive whole-mount in situ hybridization method, based on tyramide signal amplification (TSA-MISH) was developed and a combined GFP detection and TSA-MISH procedure was applied for the first time in plants, to precisely define the spatial pattern of AtGUS1 and AtGUS2 expression in the root apex. β-glucuronidases (GUSs) belonging to the glycosyl hydrolases (GHs) 79 family, are widely distributed in plants, but their functional role has not yet been fully investigated. In the model system Arabidopsis Thaliana, three different AtGUS genes have been identified which encode proteins with putative different fates. Endogenous GUS expression has been detected in different organs and tissues, but the cyto-histological domains of gene expression remain unclear. The results here reported show co-expression of AtGUS1 and AtGUS2 in different functional zones of the root apex (the cap central zone, the root cap meristem, the staminal cell niche and the cortical cell layers of the proximal meristem), while AtGUS2 is exclusively expressed in the cap peripheral layer and in the epidermis in the elongation zone. Interestingly, both genes are not expressed in the stelar portion of the proximal meristem. A spatial (cortex vs. stele) and temporal (proximal meristem vs. transition zone) regulation of AtGUS1 and AtGUS2 expression is therefore active in the root apex. This expression pattern, although globally consistent with the involvement of GUS activity in both cell proliferation and elongation, clearly indicates that AtGUS1 and AtGUS2 could control distinct downstream process depending on the developmental context and the interaction with other players of root growth control. In the future, the newly developed approaches may well be very useful to dissect such interactions. [ABSTRACT FROM AUTHOR]

The article discusses research which examines repression of the flowering locus C (FLC) clade members by Vascular plant one-zinc fingeri 1 (VOZ1) and VOZ2 to control flowering in Arabidopsis thaliana. Topics discussed include identification of VOZ1 and VOZ 2 as phytochrome B-interacting factors, role of VOZ1 and VOZ2 in downregulation of FLC, repressor of flowering, and suppression of phenotypes of the voz1 voz2 mutant by vernalization in the Columbia and FRIGIDA (FRI)-containing accessions.

Arsenic (As) is a toxic pollutant that mainly enters the human body via plants. Therefore, understanding the strategy for reducing arsenic accumulation in plants is important to human health and the environment. Aquaporins are ubiquitous water channel proteins that bidirectionally transport water across cell membranes and play a role in the transportation of other molecules, such as glycerol, ammonia, boric acid, and arsenic acid. Previously, we observed that Arabidopsis PIP2;2, encoding a plasma membrane intrinsic protein, is highly expressed in NtCyc07 -expressing Arabidopsis, which shows a higher tolerance to arsenite (As(III)). In this study, we report that the overexpression of AtPIP2;2 enhanced As(III) tolerance and reduced As(III) levels in yeast. Likewise, AtPIP2;2 -overexpressing Arabidopsis exhibited improved As(III) tolerance and lower accumulation of As(III). In contrast, atpip2;2 knockout Arabidopsis showed reduced As(III) tolerance but no significant change in As(III) levels. Interestingly, the AtPIP2;2 transcript and protein levels were increased in roots and shoots of Arabidopsis in response to As(III). Furthermore, As(III) efflux was enhanced and As(III) influx/accumulation was reduced in AtPIP2;2 -expressing plants. The expression of AtPIP2;2 rescued the As(III)-sensitive phenotype of acr3 mutant yeast by reducing As levels and slightly reduced the As(III)-tolerant phenotype of fps1 mutant yeast by enhancing As content, suggesting that AtPIP2; 2 functions as a bidirectional channel of As(III), while the As(III) exporter activity is higher than the As(III) importer activity. All these results indicate that AtPIP2;2 expression promotes As(III) tolerance by decreasing As(III) accumulation through enhancing As(III) efflux in Arabidopsis. This finding can be applied to the generation of low arsenic crops for human health. Image 1 • Arsenic is a very toxic pollutant entering human bodies mainly via plants. • AtPIP2; 2 is a plasma membrane intrinsic protein in Arabidopsis. • AtPIP2; 2 enhances As(III) (arsenite) tolerance by reducing arsenite accumulation. • AtPIP2; 2 decreases arsenic accumulation by playing as an arsenite exporter. [ABSTRACT FROM AUTHOR]

Strontium (Sr) is an emerging environmental pollutant that has become a major global concern after the nuclear accident at the Fukushima Daiichi Nuclear Power Plant in 2011. Although many studies have demonstrated the harmful effects of Sr on plant growth and development at the physiological level, knowledge regarding how plants sense and respond to Sr stress at the molecular level is limited. Recent studies have suggested that microRNAs (miRNAs) function as key regulators of plant growth and development as well as in the responses of plants to environmental stresses, including salinity, drought, cold, nutrient starvation, and heavy metals. In this study, we examined the global expression profile of miRNAs under Sr stress using small RNA sequencing analysis in Arabidopsis to better understand the molecular basis of plant responses to Sr stress. To identify specific Sr-responsive miRNAs, we performed comparative miRNA expression profiling analysis using control, CaCl 2 -, and SrCl 2 -treated seedlings. Compared to the control treatment, the expressions of most miRNAs were considerably decreased in the Sr-treated seedlings. However, under Sr stress, the expressions of primary miRNAs (pri-miRNAs) and their target genes were significantly increased; the protein levels of HYPONASTIC LEAVES 1 (HYL1), one of the core components of the microprocessor complex, were strongly reduced despite the increased HYL1 mRNA expression. In addition, hyl1-2 mutant plants were shown to be more sensitive to Sr stress than wild-type plants. Collectively, our results strongly suggested that Sr stress may be associated with the disruption of miRNA biogenesis by reducing the protein level of HYL1, which is required to maintain proper growth and development for plants. Our findings further indicated that some miRNAs may play important roles in plant responses to Sr stress. • We determined the molecular basis for plant responses to Sr stress using miRNA. • Sr stress affected miRNA biogenesis and HYL1 protein accumulation in Arabidopsis. • The toxic effects of Sr on plant growth and development were concentration-dependent. • The hyl1-2 mutant, with reduced levels of miRNAs, was hypersensitive to Sr stress. • We demonstrated the importance of miRNA biogenesis in plant responses to Sr stress. [ABSTRACT FROM AUTHOR]