Genome-wide analysis and expression profiling of H-type Trx family in Phaseolus vulgaris revealed distinctive isoforms associated with symbiotic N2-fixing performance and abiotic stress response

Identification and expression analysis of phosphate transporter (PHT) genes in Brachypodium distachyon in response to phosphorus deficiency

Phosphorus (P) is a macronutrient that plays a crucial role in critical plant functions. Phosphate transporters (PHTs) ensure the acquisition and translocation of Pi in the plant, thereby playing a key role in maintaining normal plant growth under Pi deficiency conditions. In Brachypodium distachyon, the grass model system, the function of individual PHT genes, remains largely unknown. Here, we identified the complete PHT gene family in B. distachyon, for the first time, and analyzed their expression profiles under Pi deficiency. Overall, 25 PHT genes in B. distachyon (BdPHTs) were identified, which were divided into four clades (PHT1-4). BdPHT genes were found to be unevenly distributed across the five chromosomes. Both segmental and tandem duplication events contributed to PHT gene expansion in B. distachyon which underwent a strong purifying selection. Moreover, exon-intron organization and motif composition were conserved within each PHT group consolidating the classification of the phylogenetic tree. Motif composition differs among the four PHT groups, indicating their functional divergence. Gene expression analysis using real-time quantitative PCR revealed that two BdPHT1 genes (BdPHT1.9 and BdPHT1.10) were upregulated in leaves, and seven (BdPHT1.9, BdPHT1.8, BdPHT1.7, BdPHT1.11, BdPHT1.12, BdPHT1.5, and BdPHT1.13) in roots under P deficiency suggesting their involvement in P uptake and translocation. Therefore, these results lay the foundation for future functional analyses in B. distachyon to improve P deficiency tolerance in B. distachyon and other cereals.

Ubiquitin Ligase Gene OsPUB57 Negatively Regulates Rice Blast Resistance

The ubiquitination and degradation of proteins are widely involved in plant biotic and abiotic stress responses. E3 ubiquitin ligases play an important role in the ubiquitination of specific proteins. In this study, we identified the function of a U-box E3 ubiquitin ligase gene OsPUB57 in rice. Expression analyses revealed that OsPUB57 was mainly expressed in the aboveground part of rice. Drought, salt, cold, JA (jasmonic acid), PAMPs (pathogen-associated molecular patterns) or Magnaportheoryzae treatment could significantly suppress the expression of OsPUB57 in rice. Compared with wild-type plants, OsPUB57-overexpressing plants showed a decrease in resistance to M. oryzae, while the mutant plants exhibited an enhancement of M. oryzae resistance. The expression level detection indicated that OsPUB57 negatively regulates rice blast resistance, probably by down-regulating the expression of the defense-related genes OsPR1a and OsAOS2. This study provides a candidate gene for the genetic improvement of rice blast resistance.

Stilbene production as part of drought adaptation mechanisms in cultivated grapevine (Vitis vinifera L.) roots modulates antioxidant status

Stilbenes, naturally occurring polyphenolic secondary metabolites, play a pivotal role in adaptation of various plant species to biotic and abiotic factors. Recently, increased attention has been directed toward their potential to enhance plant stress tolerance. We evaluated drought tolerance of three grapevine varieties grown with different levels of water deficit. Throughout, we studied physiological mechanisms associated with drought stress tolerance, particularly stilbene accumulation in root tissues, using HPLC. Additionally, we explored the possible relationship between antioxidant potential and stilbene accumulation in response to water deficit. The results underscore the detrimental impact of water deficit on grapevine growth, water status, and membrane stability index, while revealing varying tolerance among the studied genotypes. Notably, Syrah variety had superior drought tolerance, compared to Razegui and Muscat d'Italie grapes. Under severe water deficit, Syrah exhibited a substantial increase in levels of stilbenic compounds, such as t-resveratrol, t-piceatannol, t-ɛ-viniferin, and t-piceid, in root tissues compared to other genotypes. This increase was positively correlated with total antioxidant activity (TAA), emphasizing the active role of resveratrol and its derivatives in total antioxidant potential. This demonstratres the potential involvement of resveratrol and its derivatives in enhancing antioxidant status of the drought-tolerant Syrah grape variety. Our findings suggest that these stilbenes may function as valuable markers in grapevine breeding programs, offering novel insights for the sustainable cultivation of grapevines in water-limited environments.

Unraveling the Role of the Liriodendron Thioredoxin (TRX) Gene Family in an Abiotic Stress Response

Thioredoxin (TRX) is a small protein with REDOX activity that plays a crucial role in a plant's growth, development, and stress resistance. The TRX family has been extensively studied in Arabidopsis, rice, and wheat, and so it is likely that its members have similar biological functions in Liriodendron that have not been reported in Liriodendron. In this study, we performed the genome-wide identification of the TRX gene family based on the Liriodendron chinense genome, leading to a total of 42 LcTRX gene members. A phylogenetic analysis categorized these 42 LcTRX proteins into 13 subfamilies. We further characterized their chromosome distributions, gene structures, conserved protein motifs, and cis-elements in the promoter regions. In addition, based on the publicly available transcriptome data for Liriodendron hybrid and following RT-qPCR experiments, we explored the expression patterns of LhTRXs to different abiotic stressors, i.e., drought, cold, and heat stress. Notably, we found that several LhTRXs, especially LhTRX-h3, were significantly upregulated in response to abiotic stress. In addition, the subcellular localization assay showed that LhTRX-h3 was mainly distributed in the cytoplasm. Subsequently, we obtained LhTRX-h3 overexpression (OE) and knockout (KO) callus lines in Liriodendron hybrid. Compared to the wild type (WT) and LhTRX-h3-KO callus proliferation of LhTRX-h3-OE lines was significantly enhanced with reduced reactive oxygen species (ROS) accumulation under drought stress. Our findings that LhTRX-h3 is sufficient to improve drought tolerance. and underscore the significance of the TRX gene family in environmental stress responses in Liriodendron.

Systematic analysis of Prx genes in the Brachypodium genus and their expression pattern under abiotic constraints

Peroxiredoxins (Prx) are ubiquitous peroxidases required for the removal of excess free radicals produced under stress conditions. Peroxiredoxin genes (Prx) in the Brachypodium genus were identified using bioinformatics tools and their expression profiles were determined under abiotic stress using RT-qPCR. The promoter regions of Prx genes contain several cis-acting elements related to stress response. In silico expression analysis showed that B. distachyon Prx genes (BdPrx) are tissue specific. RT-qPCR analysis revealed their differential expression when exposed to salt or PEG-induced dehydration stress. In addition, the upregulation of BdPrx genes was accompanied by accumulation of H2 O2 . Exogenous application of H2 O2 induced expression of almost all BdPrx genes. The identified molecular interaction network indicated that Prx proteins may contribute to abiotic stress tolerance by regulating key enzymes involved in lignin biosynthesis. Overall, our findings suggest the potential role of Prx genes in abiotic stress tolerance and lay the foundation for future functional analyses aiming to engineer genetically improved cereal lines.

Proteomic and Mutant Analysis of Hydrogenase Maturation Protein Gene hypE in Symbiotic Nitrogen Fixation of Mesorhizobium huakuii

Hydrogenases catalyze the simple yet important redox reaction between protons and electrons and H2, thus mediating symbiotic interactions. The contribution of hydrogenase to this symbiosis and anti-oxidative damage was investigated using the M. huakuii hypE (encoding hydrogenase maturation protein) mutant. The hypE mutant grew a little faster than its parental 7653R and displayed decreased antioxidative capacity under H2O2-induced oxidative damage. Real-time quantitative PCR showed that hypE gene expression is significantly up-regulated in all the detected stages of nodule development. Although the hypE mutant can form nodules, the symbiotic ability was severely impaired, which led to an abnormal nodulation phenotype coupled to a 47% reduction in nitrogen fixation capacity. This phenotype was linked to the formation of smaller abnormal nodules containing disintegrating and prematurely senescent bacteroids. Proteomics analysis allowed a total of ninety differentially expressed proteins (fold change > 1.5 or <0.67, p < 0.05) to be identified. Of these proteins, 21 are related to stress response and virulence, 21 are involved in transporter activity, and 18 are involved in energy and nitrogen metabolism. Overall, the HypE protein is essential for symbiotic nitrogen fixation, playing independent roles in supplying energy and electrons, in bacterial detoxification, and in the control of bacteroid differentiation and senescence.

Characterization of thioredoxin gene TaTrxh9 associated with heading-time regulation in wheat

Thioredoxins (Trxs) are thiol-disulfide oxidoreductase proteins that play important roles in a spectrum of processes linking redox regulation and signaling in plants. However, little is known about Trxs and their biological functions in wheat, one of the most important food crops worldwide. This study reports the identification and functional characterization of an h-type Trx gene, TaTrxh9, in wheat. Three homoeologs of TaTrxh9 were identified and the sequences in the coding region were highly consistent among the homoeologs. Protein characterization showed that a conserved Trx_family domain, as well as a typical active site with a dithiol signature (WCGPC), was included in TaTrxh9. Structural modeling demonstrated that TaTrxh9 could fold into a canonical thioredoxin structure consisting of five-stranded antiparallel beta sheets sandwiched between four alpha helices. The insulin disulfide reduction assay demonstrated that TaTrxh9 was catalytically active in vitro. TaTrxh9 overexpression in the Arabidopsis mutant trxh9 complemented the abnormal growth phenotypes of the mutant, suggesting is functionality in vivo. The transcription level of TaTrxh9 was higher in leaf tissues and it was differentially expressed during the development of wheat plants. Interestingly, barley stripe mosaic virus-mediated suppression of TaTrxh9 shortened the seedling-heading period of wheat. Furthermore, CRISPR-Cas9 mediated gene knockout confirmed that the TaTrxh9 mutation resulted in early heading of wheat. To our knowledge, this study is the first to report that Trxh is associated with heading-time regulation, which lays a foundation for further exploring the biological function of TaTrxh9 and provides new ideas for molecular breeding focusing on early heading in wheat.

Comprehensive identification, evolutionary patterns and the divergent response of PRX genes in Phaseolus vulgaris under biotic and abiotic interactions

Peroxiredoxins (Prxs) are novel cysteine-based peroxidases which are involved in protecting cells from oxidative damage by catalyzing the reduction of different peroxides. The present study addressed, for the first time, genome-wide identification, evolutionary patterns and expression dynamics of Phaseolus vulgaris Prx gene family (PvPrx). Nine Prx proteins were identified in P. vulgaris based on homology searches. The phylogeny analysis of Prxs from seven plant species revealed that Prx proteins can be clustered into four groups (1C-Prx, 2C-Prxs, PrxQ and type II Prxs). Both tandem and segmental duplication contributed to PvPrx gene family expansion. Intragenic reorganizations including gain/loss of exon/intron and insertions/deletions have also contributed to PvPrx gene diversification. The collinearity analysis revealed the presence of some orthologous Prx gene pairs between A. thaliana and P. vulgaris genomes. The Ka/Ks ratio indicated that two of the three PvPrx duplicated gene pairs have undergone a purifying selection. Redundant stress-related cis-acting elements were also found in the promoters of most PvPrx genes. RT q-PCR analysis revealed an upregulation of key PvPrx members in response to symbiosis and different abiotic factors. The upregulation of targeted PvPrx members, particularly in leaves exposed to salinity or drought, was accompanied by an accumulation of hydrogen peroxide (H₂O₂). When exogenously applied, H₂O₂ modulated almost all PvPrx genes, suggesting a potential H₂O₂-scavenging role for these proteins. Collectively, our analysis provided valuable information for further functional analysis of key PvPrx members to improve common bean stress tolerance and/or its symbiotic performance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03246-8.

Genome-wide identification, characterization and expression analysis of glutaredoxin gene family (Grxs) in Phaseolus vulgaris

Glutaredoxins (Grxs) are ubiquitous oxidoreductase proteins implicated in development and abiotic stress response mainly through maintaining redox homoeostasis. Here, we conducted the first systematic analysis of the Grx gene family (PvGrx) in the most popular legume Phaseolus vulgaris (common bean). A total of 50 PvGrx genes were identified, and divided into four classes (CC-type, CGFS-type, CPYC-type and Grl-type) based on the phylogenetic analysis. The different classes have different introns-exons structures and conserved motifs, indicating functional divergence in the PvGrx family. Both tandem and segmental duplications were found to be involved in the expansion of PvGrx family that underwent a purifying selection by excluding the deleterious loss-of-function mutations. Cis-acting regulatory elements and gene ontology analyses predicted their role of distinctive members in abiotic stress response and hormonal signalling. RNA-seq based expression analysis revealed their differential expression pattern during plant development. On the other hand, RT q-PCR analysis revealed that target PvGrx isoforms were associated with nodule organogenesis and symbiosis based on their expression profiles. In addition, a battery of PvGrx candidates were markedly upregulated by different abiotic stressors suggesting their broad spectrum of functions. These findings serve as a reference for functional analysis and genetic improvement in P. vulgaris and related legume species.

Delineation of mechanistic approaches of rhizosphere microorganisms facilitated plant health and resilience under challenging conditions

Sustainable agriculture demands the balanced use of inorganic, organic, and microbial biofertilizers for enhanced plant productivity and soil fertility. Plant growth-enhancing rhizospheric bacteria can be an excellent biotechnological tool to augment plant productivity in different agricultural setups. We present an overview of microbial mechanisms which directly or indirectly contribute to plant growth, health, and development under highly variable environmental conditions. The rhizosphere microbiomes promote plant growth, suppress pathogens and nematodes, prime plants immunity, and alleviate abiotic stress. The prospective of beneficial rhizobacteria to facilitate plant growth is of primary importance, particularly under abiotic and biotic stresses. Such microbe can promote plant health, tolerate stress, even remediate soil pollutants, and suppress phytopathogens. Providing extra facts and a superior understanding of microbial traits underlying plant growth promotion can stir the development of microbial-based innovative solutions for the betterment of agriculture. Furthermore, the application of novel scientific approaches for facilitating the design of crop-specific microbial biofertilizers is discussed. In this context, we have highlighted the exercise of "multi-omics" methods for assessing the microbiome's impact on plant growth, health, and overall fitness via analyzing biochemical, physiological, and molecular facets. Furthermore, the role of clustered regularly interspaced short palindromic repeats (CRISPR) based genome alteration and nanotechnology for improving the agronomic performance and rhizosphere microbiome is also briefed. In a nutshell, the paper summarizes the recent vital molecular processes that underlie the different beneficial plant-microbe interactions imperative for enhancing plant fitness and resilience under-challenged agriculture.