Overexpression of Genes to Enhance Abiotic Stress Tolerance in Arabidopsis.

Abiotic environmental stressors cause various types of damage to plants and cause significant loss in yield. Abiotic stress tolerance in plants refers to the ability to withstand environmental factors and maintain growth, development, and production. Since this tolerance is controlled by a gene or a set of genes, transgenic activating of these genes in plants often enhances tolerance under abiotic stress. Therefore, this methodology chapter describes a strategy and the corresponding protocols needed to induce a gene by an abiotic stressor, clone the corresponding cDNA into plasmids and Agrobacterium cells, and genetic transformation to the Arabidopsis plants using the floral dip method. The chapter also describes standard assays to evaluate the transgene's effect on the plant's tolerance. Finally, the techniques outlined in this chapter for cloning and generating transgenic plants tolerant to abiotic stress are a versatile approach that can be implemented across various plant species and genes.

Isolation and Identification of Growth-Promoting Bacteria from Plants Growing Under Abiotic Stresses.

Identification and isolation of plant growth-promoting bacteria (PGPB) are critical steps toward understanding the role of these bacteria in stress tolerance in plants. This procedure also provides essential knowledge about the microbes needed to formulate effective biofertilizers. This chapter describes culture-dependent and culture-independent strategies to identify and isolate PGPB. The culture-dependent strategy commonly involves growing PGPB on general and selective media. However, the culture-independent strategy involves next-generation sequencing technologies. A combination of both strategies would identify the structure of the bacterial communities and isolate bacteria from their environments. Therefore, this chapter describes a comprehensive strategy where the methods are sequentially applied to identify and isolate epiphytic and endophytic PGPB from a particular environmental sample. However, a single procedure can also be employed to identify and isolate a specific type of PGPB.

Functional Characterization and Localization of Plant-Growth Promoting Bacteria Grown Under Stressful Conditions.

Various bacterial species are associated with plant roots. However, symbiotic and free-living plant growth-promoting bacteria (PGPB) can only help plants to grow and develop under normal and stressful conditions. Several biochemical and in vitro assays were previously designed to differentiate between the PGPB and other plant-associated bacterial strains. This chapter describes and summarizes some of these assays and proposes a strategy to screen for PGPB. To determine the involvement of the PGPB in abiotic stress tolerance, assays for the ability to produce 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, ammonium, gibberellic acid (GA), indole acetic acid (IAA), and microbial volatile organic compounds (mVOCs) are described in this chapter. Additionally, assays to show the capacity to solubilize micronutrients such as potassium, phosphorus, and zinc by bacteria were also summarized in this chapter. To determine the contribution of the PGPB in biotic stress tolerance in plants, Fe-siderophore, hydrogen cyanide, and antibiotic and antifungal metabolites production assays were described. Moreover, assays to investigate the growth-promotion activities of a bacterium strain on plants, using the gnotobiotic root elongation, in vitro, and pots assays, were explained. Finally, an assay for the localization of endophytic bacterium in plant tissues was also presented in this chapter. Although the assays described in this chapter can give evidence of the nature of the mechanism behind the PGPB actions, other unknown growth-promoting means are yet to decipher, and until then, new methodologies will be developed.

The Effects of Salinity and Genotype on the Rhizospheric Mycobiomes in Date Palm Seedlings.

Salinity severely affects the health and productivity of plants, with root-associated microbes, including fungi, potentially playing a crucial role in mitigating this effect and promoting plant health. This study employed metagenomics to investigate differences in the structures of the epiphyte mycobiomes in the rhizospheres of seedlings of two distinct date palm cultivars with contrasting salinity tolerances, the susceptible cultivar, 'Zabad', and the tolerant cultivar, 'Umsila'. Next-generation sequencing (NGS) of the internal transcribed spacer (ITS) rRNA was utilized as a DNA barcoding tool. The sequencing of 12 mycobiome libraries yielded 905,198 raw sequences of 268,829 high-quality reads that coded for 135 unique and annotatable operational taxonomic units (OTUs). An OTU analysis revealed differences in the rhizofungal community structures between the treatments regardless of genotype, and non-metric dimensional scaling (N-MDS) analyses demonstrated distinct separations between the cultivars under saline stress. However, these differences were not detected under the control environmental conditions, i.e., no salinity. The rhizospheric fungal community included four phyla (Ascomycota, Basidiomycota, Chytridiomycota, and Mucoromycota), with differences in the abundances of Aspergillus, Clonostachys, and Fusarium genera in response to salinity, regardless of the genotype. Differential pairwise comparisons showed that Fusarium falciforme-solani and Aspergillus sydowii-versicolor increased in abundance under saline conditions, providing potential future in vitro isolation guidelines for plant growth-promoting fungi. This study highlights the intricate dynamics of the rhizosphere microbial communities in date palms and their responses to salt stress. Additionally, we found no support for the hypothesis that indigenous epiphytic fungal communities are significantly involved in salinity tolerance in date palms.

The Effect of Date Palm Genotypes on Rhizobacterial Community Structures under Saline Environments.

Some genotypes of date palms (Phoenix dactylifera L.) are salt-tolerant; however, salinity significantly affects others. This study aimed to determine the root epiphytic bacterial contributions to the salt tolerance mechanism in the date palm and to verify if the salt-tolerant "Umsila" and the salt-susceptible "Zabad" cultivars have different bacterial communities. Therefore, the epiphytic bacterial community structures were investigated in both cultivars when grown under control and salinity conditions. The proximal soils of the roots were collected, the DNA was extracted, and a culture-independent approach using Illumina® MiSeq™ sequence analysis was carried out to identify the changes in the bacterial community structures in the soil samples due to the changes in salinity and the genotypes of the plants based on 16S rRNA gene sequencing. While salt tolerance response differences were evident between the two cultivars, the 16S rRNA gene sequencing results revealed 771 operational taxonomic units (OTUs), including 62 that were differentially accumulated in response to salinity. The ordination analysis showed significant (p = 0.001) changes among the communities in response to salinity in both cultivars. However, the results showed that the two cultivars had distinct bacterial communities when grown under controlled conditions, whereas they had a more similar bacterial community structure when grown under salinity conditions. The plant genotype does not affect the epiphyte bacterial community structure under salinity, probably because salinity affects the plant-microbe interaction similarly in both cultivars. Also, the identified rhizospheric bacteria are not directly associated with the root's physiological processes in response to salinity.

Functional characterization and expression profiling of glyoxalase III genes in date palm grown under abiotic stresses.

Methylglyoxal (MG), a by-product of various metabolic processes, including glycolysis, is a highly reactive cytotoxic metabolite. The level of MG in the cell is maintained at a non-toxic level via MG detoxification pathways such as the universal glyoxalase system, including glyoxalase I/II/III enzymes. Glyoxalase III (DJ-1) can breakdown MG to d-lactate in a single step without reducing glutathione (GSH). Elucidating the function of the DJ-1 gene family may provide further knowledge about its role in plants under abiotic stresses. Here, we characterize four glyoxalase III genes (PdDJ-1B1, PdDJ-1B2, PdDJ-1C, and PdDJ-1D) encoding the conserved DJ-1 domain in the genome of the date palm, a crop with high drought and salinity tolerance. The expression level of the PdDJ-1 genes increased in date palm leaves upon salinity treatment. In addition, overexpression of PdDJ-1 genes in Escherichia coli and the complementation in yeast hsp31Δ knockout mutant cells enhanced their growth rate and reduced the accumulation of reactive oxygen species (ROS) under MG and oxidative stress conditions as shown by the flow cytometry assay. Subcellular localization using confocal microscopy revealed the accumulation of PdDJ-1B1, PdDJ-1C, and PdDJ-1D in the chloroplast, whereas PdDJ-1B2 was localized to the cytosol. Remarkably, constitutive expression of the PdDJ-1C gene in Arabidopsis thaliana Columbia (Col-0) resulted in the generation of non-viable albino plants implying that PdDJ-1C plays a critical function in chloroplast development. These findings suggest that PdDJ-1 protein has an important function in MG-detoxification and maintaining the redox balance in date palm plants under abiotic stress conditions.

Functional characterization of the Glyoxalase-I (PdGLX1) gene family in date palm under abiotic stresses.

Methylglyoxal (MG), a cytotoxic oxygenated short aldehyde, is a by-product of various metabolic reactions in plants, including glycolysis. The basal level of MG in plants is low, whereby it acts as an essential signaling molecule regulating multiple cellular processes. However, hyperaccumulation of MG under stress conditions is detrimental for plants as it inhibits multiple developmental processes, including seed germination, photosynthesis, and root growth. The evolutionarily conserved glyoxalase system is critical for MG detoxification, and it comprises of two-enzymes, the glyoxalase-I and glyoxalase-II. Here, we report the functional characterization of six putative glyoxalase-I genes from date palm (Phoenix dactylifera L.) (PdGLX1), by studying their gene expression under various environmental stress conditions and investigating their function in bacteria (Escherichia coli) and yeast (Saccharomyces cerevisiae) mutant cells. The putative PdGLX1 genes were initially identified using computational methods and cloned using molecular tools. The PdGLX1 gene expression analysis using quantitative PCR (qPCR) revealed differential expression under various stress conditions such as salinity, oxidative stress, and exogenous MG stress in a tissue-specific manner. Further, in vivo functional characterization indicated that overexpression of the putative PdGLX1 genes in E. coli enhanced their growth and MG detoxification ability. The putative PdGLX1 genes were also able to complement the loss-of-function MG hypersensitive GLO1 (YML004C) yeast mutants and promote growth by enhancing MG detoxification and reducing the accumulation of reactive oxygen species (ROS) under stress conditions as indicated by flow cytometry. These findings denote the potential importance of PdGLX1 genes in MG detoxification under stress conditions in the date palm.

A novel tonoplast Na+/H+ antiporter gene from date palm (PdNHX6) confers enhanced salt tolerance response in Arabidopsis.

KEY MESSAGE: A sodium hydrogen exchanger (NHX) gene from the date palm enhances tolerance to salinity in Arabidopsis plants. Plant sodium hydrogen exchangers/antiporters (NHXs) are pivotal regulators of intracellular Na+/K+ and pH homeostasis, which is essential for salt stress adaptation. In this study, a novel orthologue of Na+/H+ antiporter was isolated from date palm (PdNHX6) and functionally characterized in mutant yeast cells and Arabidopsis plants to assess the behavior of the transgenic organisms in response to salinity. Genetically transformed yeast cells with PdNHX6 were sensitive to salt stress when compared to the empty vector (EV) yeast cells. Besides, the acidity value of the vacuoles of the transformant yeast cells has significantly (p ≤ 0.05) increased, as indicated by the calibrated fluorescence intensity measurements and the fluorescence imagining analyses. This observation supports the notion that PdNHX6 might regulate proton pumping into the vacuole, a crucial salt tolerance mechanism in the plants. Consistently, the transient overexpression and subcellular localization revealed the accumulation of PdNHX6 in the tonoplast surrounding the central vacuole of Nicotiana benthamiana leaf epidermal cells. Stable overexpression of PdNHX6 in Arabidopsis plants enhanced tolerance to salt stress and retained significantly higher chlorophyll, water contents, and increased seed germination under salinity when compared to the wild-type plants. Despite the significant increase of Na+, transgenic Arabidopsis lines maintained a balanced Na+/K+ ratio under salt stress conditions. Together, the results obtained from this study imply that PdNHX6 is involved in the salt tolerance mechanism in plants by controlling K+ and pH homeostasis of the vacuoles.

Molecular Characterization of a Date Palm Vascular Highway 1-Interacting Kinase (PdVIK) Under Abiotic Stresses.

The date palm (Khalas) is an extremophile plant that can adapt to various abiotic stresses including drought and salinity. Salinity tolerance is a complex trait controlled by numerous genes. Identification and functional characterization of salt-responsive genes from the date palm is fundamental to understand salinity tolerance at the molecular level in this plant species. In this study, a salt-inducible vascular highway 1-interacting kinase (PdVIK) that is a MAP kinase kinase kinase (MAPKKK) gene from the date palm, was functionally characterized using in vitro and in vivo strategies. PdVIK, one of the 597 kinases encoded by the date palm genome possesses an ankyrin repeat domain and a kinase domain. The recombinant PdVIK protein exhibited phosphotyrosine activity against myelin basic protein (MBP) substrate. Overexpression of PdVIK in yeast significantly improved its tolerance to salinity, LiCl, and oxidative stresses. Transgenic Arabidopsis seedlings overexpressing PdVIK displayed improved tolerance to salinity, osmotic, and oxidative stresses as assessed by root growth assay. The transgenic lines grown in the soil also displayed modulated salt response, compared to wild-type controls as evaluated by the overall plant growth and proline levels. Likewise, the transgenic lines exhibited drought tolerance by maintaining better relative water content (RWC) compared to non-transgenic control plants. Collectively, these results implicate the involvement of PdVIK in modulating the abiotic stress response of the date palm.

Metabolomic analysis of date palm seedlings exposed to salinity and silicon treatments.

Silicon is known to promote plant growth as well as stress tolerance of plants. The current study was undertaken to assess the growth promoting effect of silicon on date palm seedling development as well as its ability to abate some of the negative effects of salinity. In this study, date palm seedlings were treated with silicon and sodium chloride salts, and the effect of these salts on some physiological parameters of the plants was determined. In addition, a global nontargeted metabolomics analysis was performed for the leaf and root tissues using liquid chromatography-mass spectrometry (LC-MS). The results showed that under non-stress conditions, silicon treatment enhanced the growth of the date palm seedlings, however, under salinity, silicon slightly mitigates the negative effects of salt stress on the date palm seedlings although it enhances the potassium accumulation under this condition. The global metabolomics analysis has identified a total of 1,101 significant differentially accumulated (p, q ≤ 0.05) metabolites in leaves and roots under silicon, salinity or their combination. A differential pairwise metabolic profile comparison revealed the accumulation of distinct metabolites in response to silicon and salinity treatments such as antioxidant compounds pyridoxine, cepharanthine, allithiamine, myristic acid and boldine; osmoregulators such as mucic acid; along with the accumulation of detoxification intermediates such as S-D-lactoylglutathione, beta-cyano-L-alanine and gamma-glutamyl-conjugates. In addition, histochemical analyses revealed that application of silicon significantly (p ≤ 0.05) enhanced the formation of the Casparian strip. Identification of the differentially accumulated metabolites could offer an insight into how silicon is able to promote growth and salinity tolerance in date palms.

Overexpression of a Metallothionein 2A Gene from Date Palm Confers Abiotic Stress Tolerance to Yeast and Arabidopsis thaliana.

Although the date palm tree is an extremophile with tolerance to drought and certain levels of salinity, the damage caused by extreme salt concentrations in the soil, has created a need to explore stress-responsive traits and decode their mechanisms. Metallothioneins (MTs) are low-molecular-weight cysteine-rich proteins that are known to play a role in decreasing oxidative damage during abiotic stress conditions. Our previous study identified date palm metallothionein 2A (PdMT2A) as a salt-responsive gene, which has been functionally characterized in yeast and Arabidopsis in this study. The recombinant PdMT2A protein produced in Escherichia coli showed high reactivity against the substrate 5'-dithiobis-2-nitrobenzoic acid (DTNB), implying that the protein has the property of scavenging reactive oxygen species (ROS). Heterologous overexpression of PdMT2A in yeast (Saccharomyces cerevisiae) conferred tolerance to drought, salinity and oxidative stresses. The PdMT2A gene was also overexpressed in Arabidopsis, to assess its stress protective function in planta. Compared to the wild-type control, the transgenic plants accumulated less Na+ and maintained a high K+/Na+ ratio, which could be attributed to the regulatory role of the transgene on transporters such as HKT, as demonstrated by qPCR assay. In addition, transgenic lines exhibited higher chlorophyll content, higher superoxide dismutase (SOD) activity and improved scavenging ability for reactive oxygen species (ROS), coupled with a better survival rate during salt stress conditions. Similarly, the transgenic plants also displayed better drought and oxidative stress tolerance. Collectively, both in vitro and in planta studies revealed a role for PdMT2A in salt, drought, and oxidative stress tolerance.

Functional Characterization of Date Palm Aquaporin Gene PdPIP1;2 Confers Drought and Salinity Tolerance to Yeast and Arabidopsis.

Recent studies on salinity tolerance in date palm revealed the discovery of salt-responsive genes including PdPIP1;2, a highly conserved aquaporin gene in plants, which was functionally characterized in this study to investigate its precise role in drought and salinity tolerance. Immunoblot assay showed a high level of PIP1 protein accumulation only in the leaves of date palm plants when grown under drought, an observation which may imply the involvement of PIP1;2 in CO2 uptake. Heterologous overexpression of PdPIP1;2 in yeast (Saccharomyces cerevisiae) improved tolerance to salinity and oxidative stress. While, heterologous overexpression of PdPIP1;2 in Arabidopsis had significantly (p < 0.05) increased biomass, chlorophyll content, and root length under drought and salinity. In addition, a significantly (p < 0.05) higher percentage of transgenic plants could be recovered by rewatering after drought stress, indicating the ability of the transgenic plants to maintain water and viability under drought. Transgenic plants under drought and salinity maintained significantly (p < 0.05) higher K+/Na+ ratios than wild type (WT) plants, an observation which may represent an efficient tolerance mechanism controlled by the transgene. Collectively, this study provided an insight on the mechanism by which PdPIP1;2 conferred tolerance to salt and drought stresses in date palm.

Neuropilin-1 promotes the oncogenic Tenascin-C/integrin ß3 pathway and modulates chemoresistance in breast cancer cells.

BACKGROUND: Neuropilin-1 (NRP-1), a non-tyrosine kinase glycoprotein receptor, is associated with poor prognosis breast cancer, however transcriptomic changes triggered by NRP-1 overexpression and its association with chemoresistance in breast cancer have not yet been explored. METHODS: BT-474 NRP-1 variant cells were generated by stable overexpression of NRP-1 in the BT-474 breast cancer cell line. RNA sequencing and qRT-PCR were conducted to identify differentially expressed genes. The role of an upregulated oncogene, Tenascin C (TNC) and its associated pathway was investigated by siRNA-mediated knockdown. Resistant variants of the control and BT-474 NRP-1 cells were generated by sequential treatment with four cycles of Adriamycin/Cyclophosphamide (4xAC) followed by four cycles of Paclitaxel (4xAC + 4xPAC). RESULTS: NRP-1 overexpression increased cellular tumorigenic behavior. RNA sequencing identified upregulation of an oncogene, Tenascin-C (TNC) and downregulation of several tumor suppressors in BT-474 NRP-1 cells. Additionally, protein analysis indicated activation of the TNC-associated integrin ß3 (ITGB3) pathway via focal adhesion kinase (FAK), Akt (Ser473) and nuclear factor kappa B (NF-kB) p65. siRNA-mediated TNC knockdown ablated the migratory capacity of BT-474 NRP-1 cells and inactivated FAK/Akt473 signaling. NRP-1 overexpressing cells downregulated breast cancer resistance protein (BCRP/ABCG2). Consequently, sequential treatment with Adriamycin/Cyclophosphamide (AC) cytotoxic drugs to generate resistant cells indicated that BT-474 NRP-1 cells increased sensitivity to treatment by inactivating NRP-1/ITGB3/FAK/Akt/NF-kB p65 signaling compared to wild-type BT-474 resistant cells. CONCLUSIONS: We thus report a novel mechanism correlating high baseline NRP-1 with upregulated TNC/ITGB3 signaling, but decreased ABCG2 expression, which sensitizes BT-474 NRP-1 cells to Adriamycin/Cyclophosphamide. The study emphasizes on the targetability of the NRP-1/ITGB3 axis and its potential as a predictive biomarker for chemotherapy response.

Identification of Candidate Genes Involved in the Salt Tolerance of Date Palm (Phoenix dactylifera L.) Based on a Yeast Functional Bioassay.

Although date palm is a relatively salt-tolerant plant, the molecular basis of this tolerance is complex and poorly understood. Therefore, this study aimed to identify the genes involved in salinity tolerance using a basic yeast functional bioassay. To achieve this, a date palm cDNA library was overexpressed in Saccharomyces cerevisiae cells. The expression levels of selected genes that make yeast cells tolerant to salt were subsequently validated in the leaf and root tissues of date palm seedlings using a quantitative PCR method. About 6000 yeast transformant cells were replica printed and screened on a synthetic minimal medium containing 1.0 M of NaCl. The screening results showed the presence of 62 salt-tolerant transformant colonies. Sequence analysis of the recombinant yeast plasmids revealed the presence of a group of genes with potential salt-tolerance functions, such as aquaporins (PIP), serine/threonine protein kinases (STKs), ethylene-responsive transcription factor 1 (ERF1), and peroxidases (PRX). The expression pattern of the selected genes endorsed the hypothesis that these genes may be involved in salinity tolerance, as they showed a significant (p < 0.05) overexpression trend in both the leaf and root tissues in response to salinity. The genes identified in this project are suitable candidates for the further functional characterization of date palms.

Differential DNA methylation and transcription profiles in date palm roots exposed to salinity.

As a salt-adaptive plant, the date palm (Phoenix dactylifera L.) requires a suitable mechanism to adapt to the stress of saline soils. There is growing evidence that DNA methylation plays an important role in regulating gene expression in response to abiotic stresses, including salinity. Thus, the present study sought to examine the differential methylation status that occurs in the date palm genome when plants are exposed to salinity, and to identify salinity responsive genes that are regulated by DNA methylation. To achieve these, whole-genome bisulfite sequencing (WGBS) was employed and mRNA was sequenced from salinity-treated and untreated roots. The WGBS analysis included 324,987,795 and 317,056,091 total reads of the control and the salinity-treated samples, respectively. The analysis covered about 81% of the total genomic DNA with about 40% of mapping efficiency of the sequenced reads and an average read depth of 17-fold coverage per DNA strand, and with a bisulfite conversion rate of around 99%. The level of methylation within the differentially methylated regions (DMRs) was significantly (p < 0.05, FDR ≤ 0.05) increased in response to salinity specifically at the mCHG and mCHH sequence contexts. Consistently, the mass spectrometry and the enzyme-linked immunosorbent assay (ELISA) showed that there was a significant (p < 0.05) increase in the global DNA methylation in response to salinity. mRNA sequencing revealed the presence of 6,405 differentially regulated genes with a significant value (p < 0.001, FDR ≤ 0.05) in response to salinity. Integration of high-resolution methylome and transcriptome analyses revealed a negative correlation between mCG methylation located within the promoters and the gene expression, while a positive correlation was noticed between mCHG/mCHH methylation rations and gene expression specifically when plants grew under control conditions. Therefore, the methylome and transcriptome relationships vary based on the methylated sequence context, the methylated region within the gene, the protein-coding ability of the gene, and the salinity treatment. These results provide insights into interplay among DNA methylation and gene expression, and highlight the effect of salinity on the nature of this relationship, which may involve other genetic and epigenetic players under salt stress conditions. The results obtained from this project provide the first draft map of the differential methylome and transcriptome of date palm when exposed to an abiotic stress.

Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula).

BACKGROUND: DNA methylation has a potential role in controlling gene expression and may, therefore, contribute to salinity adaptation in plants. Caliph medic (Medicago truncatula) is a model legume of moderate salinity tolerance capacity; however, a base-resolution DNA methylome map is not yet available for this plant. RESULTS: In this report, a differential whole-genome bisulfite sequencing (WGBS) was carried out using DNA samples extracted from root tissues exposed to either control or saline conditions. Around 50 million differentially methylated sites (DMSs) were recognized, 7% of which were significantly (p < 0.05, FDR < 0.05) altered in response to salinity. This analysis showed that 77.0% of the contexts of DMSs were mCHH, while only 9.1% and 13.9% were mCHG and mCG, respectively. The average change in methylation level was increased in all sequence contexts, ranging from 3.8 to 10.2% due to salinity stress. However, collectively, the level of the DNA methylation in the gene body slightly decreased in response to salinity treatment. The global increase in DNA methylation due to salinity was confirmed by mass spectrometry analysis. Gene expression analysis using qPCR did not reveal a constant relationship between the level of mCG methylation and the transcription abundance of some genes of potential importance in salinity tolerance, such as the potassium channel KAT3, the vacuolar H+-pyrophosphatase (V-PPase), and the AP2/ERF and bZIP transcription factors, implying the involvement of other epigenetic gene expression controllers. Computational functional prediction of the annotated genes that embrace DMSs revealed the presence of enzymes with potential cellular functions in biological processes associated with salinity tolerance mechanisms. CONCLUSIONS: The information obtained from this study illustrates the effect of salinity on DNA methylation and shows how plants can remodel the landscape of 5-methylcytosine nucleotide (5-mC) in the DNA across gene structures, in response to salinity. This remodeling varies between gene regions and between 5-mC sequence contexts. The mCG has a vague impact on the expression levels of a few selected potentially important genes in salt tolerant mechanisms.

Comparative transcriptome and translatome analysis in contrasting rice genotypes reveals differential mRNA translation in salt-tolerant Pokkali under salt stress.

BACKGROUND: Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is a highly salt-tolerant landrace, whereas IR29 is a salt-sensitive but widely cultivated genotype. Comparative analysis of these genotypes may offer a better understanding of the salinity tolerance mechanisms in rice. Although most stress-responsive genes are regulated at the transcriptional level, in many cases, changes at the transcriptional level are not always accompanied with the changes in protein abundance, which suggests that the transcriptome needs to be studied in conjunction with the proteome to link the phenotype of stress tolerance or sensitivity. Published reports have largely underscored the importance of transcriptional regulation during salt stress in these genotypes, but the regulation at the translational level has been rarely studied. Using RNA-Seq, we simultaneously analyzed the transcriptome and translatome from control and salt-exposed Pok and IR29 seedlings to unravel molecular insights into gene regulatory mechanisms that differ between these genotypes. RESULTS: Clear differences were evident at both transcriptional and translational levels between the two genotypes even under the control condition. In response to salt stress, 57 differentially expressed genes (DEGs) were commonly upregulated at both transcriptional and translational levels in both genotypes; the overall number of up/downregulated DEGs in IR29 was comparable at both transcriptional and translational levels, whereas in Pok, the number of upregulated DEGs was considerably higher at the translational level (544 DEGs) than at the transcriptional level (219 DEGs); in contrast, the number of downregulated DEGs (58) was significantly less at the translational level than at the transcriptional level (397 DEGs). These results imply that Pok stabilizes mRNAs and also efficiently loads mRNAs onto polysomes for translation during salt stress. CONCLUSION: Under salt stress, Pok is more efficient in maintaining cell wall integrity, detoxifying reactive oxygen species (ROS), translocating molecules and maintaining photosynthesis. The present study confirmed the known salt stress-associated genes and also identified a number of putative new salt-responsive genes. Most importantly, the study revealed that the translational regulation under salinity plays an important role in salt-tolerant Pok, but such regulation was less evident in the salt-sensitive IR29.

Genome Sequencing of Microbacterium sp. Yaish 1, a Bacterial Strain Isolated from the Rhizosphere of Date Palm Trees Affected by Salinity.

Microbacterium sp. strain Yaish 1 is a rhizospheric bacterium isolated from date palm orchards with high soil salinity. The genome was sequenced, and genes coding for growth-promoting 1-aminocyclopropane-1-carboxylate (ACC) deaminase, siderophore-producing proteins, and tryptophan biosynthesis proteins were identified. Here, we report the draft whole-genome sequencing of the strain.