Although the date palm tree is an extremophile with tolerance to drought and certain levels of sa... more 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.
Although date palm is a relatively salt-tolerant plant, the molecular basis of this tolerance is ... more 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.
Background: Neuropilin-1 (NRP-1), a non-tyrosine kinase glycoprotein receptor, is associated with... more 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.
The salinity tolerance mechanism in date palm through antioxidation has not been completely decip... more The salinity tolerance mechanism in date palm through antioxidation has not been completely deciphered to date. Therefore, this study aimed to investigate the role of various antioxidants in salinity tolerance. Two date palm cultivars, contrasting in salinity tolerance, were used as model plants in a comparative study designed to detect changes in growth, Na + and K + uptake, reactive oxygen species (ROS), and antioxidant accumulations, when plants were exposed to salt stress. The results showed that salinity treatment had a more substantial negative effect on the growth and photosynthetic pigmentation of the susceptible 'Zabad' cultivar than on the tolerant 'Umsila' cultivar, probably due to the ability of 'Umsila' to accumulate less Na + and more K + , to maintain a normal concentration of ROS and to produce more non-enzymatic antioxidants, including glutathione, phenolic compounds, flavonoids, and proline. Under salinity, 'Umsila' could also activate more superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX) than 'Zabad'. These results suggest that the tolerance of 'Umsila' is partially due to the balanced Na + and K + uptake and to the relatively high concentration of ROS-scavenging metabolites. Together, these results indicate that the antioxidant mechanism is crucial for salinity tolerance in date palms. However, other mechanisms may also be involved in this trait.
Background: Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is... more 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.
Background: Neuropilin-1 (NRP-1), a non-tyrosine kinase glycoprotein receptor, is associated with... more 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.
Background: DNA methylation has a potential role in controlling gene expression and may, therefor... more 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.
As a salt-adaptive plant, the date palm (Phoenix dactylifera L.) requires a suitable mechanism to... more 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.
Epigenetics in modern definition refers to the heritable alterations in gene expression which may... more Epigenetics in modern definition refers to the heritable alterations in gene expression which may lead to a variation in the phenotype without a change in the DNA sequence (Morris, 2001). Molecular events in epigenetics can take place naturally in cells but can also be modulated by environmental stressors. A combination of epigenetics and environmental stress dynamics lead scientists to investigate the impact of epigenetics on evolution in plants. The aim of the current research topic was to explore and update our understanding on epigenetic mechanism which may drive evolution in plants. The present edited volume includes original research and review articles describing epigenetic changes and their impact on the evolutionary adaptation mechanisms. The adjustment of gene expression is a key mechanism used by plants during growth and developmental processes. Because plants are immobile organisms, the control of gene expression becomes more essential when plants are subjected to inescapable environmental stressors (Yaish et al., 2017). The expression level of a particular gene is manipulated by a series of coordinated epigenetic events on the nucleosomes, which involve DNA methylation, histone post-transitional modifications and small RNA interference (Baulcombe and Dean, 2014). When exposed to stresses, plants tend to flower earlier than normal in order to skip the unfavorable conditions and produce seeds as soon as possible in order to conserve the species (Yaish et al., 2011). The resultant seeds may transfer the accumulated epigenetic information of the stressed plants to their progenies. Thus, this process may eventually lead to adaptive evolution. The transfer of epigenetic information over generations is called epigenetic transgenerational memory (Molinier et al., 2006). Such transgenerational epigenetic changes may be the result of heritable epialleles (Johannes et al., 2009), as well as through nucleosome recycling during cell division (Alabert et al., 2015). These findings are corroborated by the conclusions of the contribution by Iglesias and Cerdán that emphasized the essential role of nucleosome assembly on DNA replication processes and the stable epigenetic inheritance in plants. However, Iwasaki and Tricker, found in two other separate reviews published in this topic that the changes in chromatin can also be reverted to the default standard in order to reduce potentially negative impacts on the respective phenotype. On the other hand, Latzel et al. showed that epigenetic memory could be an essential motor which empowers environmental adaptation or intelligent behavior of clonal plants.
Microbacterium sp. strain Yaish 1 is a rhizospheric bacterium isolated from date palm orchards wi... more 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) deami-nase, siderophore-producing proteins, and tryptophan biosynthesis proteins were identified. Here, we report the draft whole-genome sequencing of the strain.
Bacillus aryabhattai strain SQU-R12 was isolated from date palm seedlings , where it showed a gro... more Bacillus aryabhattai strain SQU-R12 was isolated from date palm seedlings , where it showed a growth-promoting capacity by being able to synthesize indole-3-acetic acid phytohormone and reduce ethylene biosynthesis by producing 1-aminocyclopropane-1-carboxylic acid deaminase. The draft genome sequence of this strain is reported here.
DNA methylation is the most important epigenetic change affecting gene expression in plants grown... more DNA methylation is the most important epigenetic change affecting gene expression in plants grown under normal as well as under stress conditions. Therefore, researchers study differential DNA methyla-tion under distinct environmental conditions and their relationship with transcriptome abundance. Up to date, more than 25 methods and techniques are available to detect DNA methylation based on different principles. Bisulfite sequencing method is considered as a gold standard since it is able to distinguish 5-methylcytosine from cytosine using the bisulfite treatment. Therefore, it is useful for qualitative and semiquantitative measurement of DNA methylation. However, the reliability of data obtaining from this technique is mainly depending on the efficiency of bisulfite conversion and number of sequencing clones representing the target-converted sequence. Therefore, it is labor intensive and time-consuming. Revolution of next generation DNA sequencing (NGS) has allowed researches to combine conventional bisulfite sequencing methods with high-throughput Illumina sequencing in a technique called whole genome bisulfite sequencing (WGBS). This technique allows a single nucleotide resolution of 5-methylcytosine on a genome scale. WGBS technique workflow involves DNA fragmentation, processing through end blunting, terminal A(s) addition at 3′ end and adaptor ligation, bisulfite treatment, PCR amplification, sequencing libraries and assembling, and finally alignment with the reference genome and data analysis. Despite the fact that WGBS is more reliable than the conventional clone-based bisulfite sequencing, it is costly, requires large amount of DNA and its output data is not easily handled.
Ionic stress is one of the most important components of salinity and is brought about by excess N... more Ionic stress is one of the most important components of salinity and is brought about by excess Na + accumulation, especially in the aerial parts of plants. Since Na + interferes with K + homeostasis, and especially given its involvement in numerous metabolic processes, maintaining a balanced cytosolic Na + /K + ratio has become a key salinity tolerance mechanism. Achieving this homeostatic balance requires the activity of Na + and K + transporters and/or channels. The mechanism of Na + and K + uptake and translocation in glycophytes and halophytes is essentially the same, but glycophytes are more susceptible to ionic stress than halophytes. The transport mechanisms involve Na + and/or K + transporters and channels as well as non-selective cation channels. Thus, the question arises of whether the difference in salt tolerance between glycophytes and halophytes could be the result of differences in the proteins or in the expression of genes coding the transporters. The aim of this review is to seek answers to this question by examining the role of major Na + and K + transporters and channels in Na + and K + uptake, translocation and intracellular homeostasis in glycophytes. It turns out that these transporters and channels are equally important for the adaptation of glycophytes as they are for halophytes, but differential gene expression, structural differences in the proteins (single nucleotide substitutions, impacting affinity) and post-translational modifications (phosphorylation) account for the differences in their activity and hence the differences in tolerance between the two groups. Furthermore, lack of the ability to maintain stable plasma membrane (PM) potentials following Na +-induced depolarization is also crucial for salt stress tolerance. This stable membrane potential is sustained by the activity of Na + /H + antiporters such as SOS1 at the PM. Moreover, novel regulators of Na + and K + transport pathways including the Nax1 and Nax2 loci regulation of SOS1 expression and activity in the stele, and haem oxygenase involvement in stabilizing membrane potential by activating H +-ATPase activity, favorable for K + uptake through HAK/AKT1, have been shown and are discussed.
Date palms are able to grow under diverse abiotic stress conditions including in saline soils, wh... more Date palms are able to grow under diverse abiotic stress conditions including in saline soils, where microbial communities may be help in the plant’s salinity tolerance. These communities able to produce specific growth promoting substances can enhance date palm growth in a saline environment. However, these communities are poorly defined. In the work reported here, the date palm endophytic bacterial and fungal communities were identified using the pyrosequencing method, and the microbial differential abundance in the root upon exposure to salinity stress was estimated. Approximately 150,061 reads were produced from the analysis of six ribosomal DNA libraries, which were prepared from endophytic microorganisms colonizing date palm root tissues. DNA sequence analysis of these libraries predicted the presence of a variety of bacterial and fungal endophytic species, some known and others unknown. The microbial community compositions of 30% and 8% of the bacterial and fungal species, respectively, were significantly (p ≤ 0.05) altered in response to salinity stress. Differential enrichment analysis showed that microbe diversity indicated by the Chao, Shannon and Simpson indices were slightly reduced, however, the overall microbial community structures were not significantly affected as a consequence of salinity. This may reflect a buffering effect by the host plant on the internal environments that these communities are colonizing. Some of the endophytes identified in this study were strains that were previously isolated from saline and marine environments. This suggests possible interactions with the plant that are favorable to salinity tolerance in date palm.
Date palm (Phoenix dactylifera L.) is a major fruit tree in the Middle East and it is a plant con... more Date palm (Phoenix dactylifera L.) is a major fruit tree in the Middle East and it is a plant considered to be tolerant to a variety of abiotic stresses, including salinity. However, the physiological basis of its salinity tolerance is not fully known. The objective of this study was to screen Omani date palm cultivars for tolerance or susceptibility to salt stress. Seedlings from 10 commercially important date palm cultivars were subjected to 240 mM NaCl, and several physiological parameters related to salinity tolerance traits were evaluated upon treatment. The cultivars were divided into two groups based on the dry weight (DW) of their leaf and root tissues, a parameter which was used as an indication of healthy growth. The results revealed that photosynthesis, electrolyte leakage (EL), and the shoot K + /Na + ratio were all significantly reduced in the susceptible cultivars. In addition, the relative water content was higher in the tolerant cultivars in comparison with the susceptible ones. These results suggest that although date palm is tolerant to high salinity, there is variation in tolerance among different cultivars. Shoot Na + exclusion, photosynthesis, and membrane stability are apparently the main determinants of tolerance and can be used in salinity tolerance screening of date palm. The results have shown new very tolerant cultivars (Manoma and Umsila) that could serve as genetic resources for improved date palm tolerance to salinity.
Background: Date palm, as one of the most important fruit crops in North African and West Asian c... more Background: Date palm, as one of the most important fruit crops in North African and West Asian countries including Oman, is facing serious growth problems due to salinity, arising from persistent use of saline water for irrigation. Although date palm is a relatively salt-tolerant plant species, its adaptive mechanisms to salt stress are largely unknown.
Background: Date palm, as one of the most important fruit crops in North African and West Asian c... more Background: Date palm, as one of the most important fruit crops in North African and West Asian countries including Oman, is facing serious growth problems due to salinity, arising from persistent use of saline water for irrigation. Although date palm is a relatively salt-tolerant plant species, its adaptive mechanisms to salt stress are largely unknown.
Worldwide tetracycline resistance (Tc r) is increasing dramatically, causing serious environmenta... more Worldwide tetracycline resistance (Tc r) is increasing dramatically, causing serious environmental and health problems. A total of 201 samples were collected from chicken intestine, human feces and treated sewage effluent (TSE). One hundred and eighteen Escherichia coli strains were isolated and identified using MALDI-Biotyper. Single and multiplex PCR were used to screen isolates for 14 tet genes, among which only 7 tet genes (A, B, C, M, Q, W, 32) were found. Among the resistant isolates, tet A was the most frequent gene, followed by tet B and tet 32 while the rest of tet determinants occurred at a lower frequency. Many strains contained multiple Tc r determinants. Some strains contained 4 tet gene-combination, tet (A/B/C/32) and tet (A/B/M/32). The 4 tet gene combination is reported for the first time in this region. The Tc r isolates showed a high variation of tet gene combination. The increase in the resistance of tetracycline with high diversification is an indication of antibiotics overuse. Strict enforcement of regulation is urgently needed to control and prevent the spread of tetracycline resistant strains which are detrimental to the environment.
Date palm is an important crop plant in the arid and semi-arid regions supporting human populatio... more Date palm is an important crop plant in the arid and semi-arid regions supporting human population in the Middle East and North Africa. These areas have been largely affected by drought and salinity due to insufficient rainfall and improper irrigation practices. Date palm is a relatively salt-and drought-tolerant plant and more recently efforts have been directed to identifying genes and pathways that confer stress tolerance in this species. Quantitative real-time PCR (qPCR) is a promising technique for the analysis of stress-induced differential gene expression, which involves the use of stable reference genes for normalizing gene expression. In an attempt to find the best reference genes for date palm's drought and salinity research, we evaluated the stability of 12 most commonly used reference genes using the geNorm, NormFinder, BestKeeper statistical algorithms and the comparative ΔC T method. The comprehensive results revealed that HEAT SHOCK PROTEIN (HSP), UBIQUITIN (UBQ) and YTH domain-containing family protein (YT521) were stable in drought-stressed leaves whereas GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGE-NASE (GAPDH), ACTIN and TUBULIN were stable in drought-stressed roots. On the other hand, SMALL SUBUNIT RIBOSOMAL RNA (25S), YT521 and 18S ribosomal RNA (18S); and UBQ, ACTIN and ELONGATION FACTOR 1-ALPHA (eEF1a) were stable in leaves and roots, respectively, under salt stress. The stability of these reference genes was verified by using the abiotic stress-responsive CYTOSOLIC Cu/Zn SUPEROXIDE DISMUT-ASE (Cyt-Cu/Zn SOD), an ABA RECEPTOR, and a PROLINE TRANSPORTER 2 (PRO) genes. A combination of top 2 or 3 stable reference genes were found to be suitable for nor-malization of the target gene expression and will facilitate gene expression analysis studies aimed at identifying functional genes associated with drought and salinity tolerance in date palm.
In this report, a draft of the Enterobacter asburiae strain PDA134 genome was sequenced. This bac... more In this report, a draft of the Enterobacter asburiae strain PDA134 genome was sequenced. This bacterial strain was isolated from the root tissue of a date palm, where it has the ability to produce 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and indole-3-acetic acid (IAA) under salinity stress. Citation Yaish MW. 2016. Draft genome sequence of endophytic bacterium Enterobacter asburiae PDA134, isolated from date palm (Phoenix dactylifera L.) roots. Genome Announc 4(4):e00848-16.
Although the date palm tree is an extremophile with tolerance to drought and certain levels of sa... more 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.
Although date palm is a relatively salt-tolerant plant, the molecular basis of this tolerance is ... more 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.
Background: Neuropilin-1 (NRP-1), a non-tyrosine kinase glycoprotein receptor, is associated with... more 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.
The salinity tolerance mechanism in date palm through antioxidation has not been completely decip... more The salinity tolerance mechanism in date palm through antioxidation has not been completely deciphered to date. Therefore, this study aimed to investigate the role of various antioxidants in salinity tolerance. Two date palm cultivars, contrasting in salinity tolerance, were used as model plants in a comparative study designed to detect changes in growth, Na + and K + uptake, reactive oxygen species (ROS), and antioxidant accumulations, when plants were exposed to salt stress. The results showed that salinity treatment had a more substantial negative effect on the growth and photosynthetic pigmentation of the susceptible 'Zabad' cultivar than on the tolerant 'Umsila' cultivar, probably due to the ability of 'Umsila' to accumulate less Na + and more K + , to maintain a normal concentration of ROS and to produce more non-enzymatic antioxidants, including glutathione, phenolic compounds, flavonoids, and proline. Under salinity, 'Umsila' could also activate more superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX) than 'Zabad'. These results suggest that the tolerance of 'Umsila' is partially due to the balanced Na + and K + uptake and to the relatively high concentration of ROS-scavenging metabolites. Together, these results indicate that the antioxidant mechanism is crucial for salinity tolerance in date palms. However, other mechanisms may also be involved in this trait.
Background: Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is... more 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.
Background: Neuropilin-1 (NRP-1), a non-tyrosine kinase glycoprotein receptor, is associated with... more 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.
Background: DNA methylation has a potential role in controlling gene expression and may, therefor... more 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.
As a salt-adaptive plant, the date palm (Phoenix dactylifera L.) requires a suitable mechanism to... more 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.
Epigenetics in modern definition refers to the heritable alterations in gene expression which may... more Epigenetics in modern definition refers to the heritable alterations in gene expression which may lead to a variation in the phenotype without a change in the DNA sequence (Morris, 2001). Molecular events in epigenetics can take place naturally in cells but can also be modulated by environmental stressors. A combination of epigenetics and environmental stress dynamics lead scientists to investigate the impact of epigenetics on evolution in plants. The aim of the current research topic was to explore and update our understanding on epigenetic mechanism which may drive evolution in plants. The present edited volume includes original research and review articles describing epigenetic changes and their impact on the evolutionary adaptation mechanisms. The adjustment of gene expression is a key mechanism used by plants during growth and developmental processes. Because plants are immobile organisms, the control of gene expression becomes more essential when plants are subjected to inescapable environmental stressors (Yaish et al., 2017). The expression level of a particular gene is manipulated by a series of coordinated epigenetic events on the nucleosomes, which involve DNA methylation, histone post-transitional modifications and small RNA interference (Baulcombe and Dean, 2014). When exposed to stresses, plants tend to flower earlier than normal in order to skip the unfavorable conditions and produce seeds as soon as possible in order to conserve the species (Yaish et al., 2011). The resultant seeds may transfer the accumulated epigenetic information of the stressed plants to their progenies. Thus, this process may eventually lead to adaptive evolution. The transfer of epigenetic information over generations is called epigenetic transgenerational memory (Molinier et al., 2006). Such transgenerational epigenetic changes may be the result of heritable epialleles (Johannes et al., 2009), as well as through nucleosome recycling during cell division (Alabert et al., 2015). These findings are corroborated by the conclusions of the contribution by Iglesias and Cerdán that emphasized the essential role of nucleosome assembly on DNA replication processes and the stable epigenetic inheritance in plants. However, Iwasaki and Tricker, found in two other separate reviews published in this topic that the changes in chromatin can also be reverted to the default standard in order to reduce potentially negative impacts on the respective phenotype. On the other hand, Latzel et al. showed that epigenetic memory could be an essential motor which empowers environmental adaptation or intelligent behavior of clonal plants.
Microbacterium sp. strain Yaish 1 is a rhizospheric bacterium isolated from date palm orchards wi... more 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) deami-nase, siderophore-producing proteins, and tryptophan biosynthesis proteins were identified. Here, we report the draft whole-genome sequencing of the strain.
Bacillus aryabhattai strain SQU-R12 was isolated from date palm seedlings , where it showed a gro... more Bacillus aryabhattai strain SQU-R12 was isolated from date palm seedlings , where it showed a growth-promoting capacity by being able to synthesize indole-3-acetic acid phytohormone and reduce ethylene biosynthesis by producing 1-aminocyclopropane-1-carboxylic acid deaminase. The draft genome sequence of this strain is reported here.
DNA methylation is the most important epigenetic change affecting gene expression in plants grown... more DNA methylation is the most important epigenetic change affecting gene expression in plants grown under normal as well as under stress conditions. Therefore, researchers study differential DNA methyla-tion under distinct environmental conditions and their relationship with transcriptome abundance. Up to date, more than 25 methods and techniques are available to detect DNA methylation based on different principles. Bisulfite sequencing method is considered as a gold standard since it is able to distinguish 5-methylcytosine from cytosine using the bisulfite treatment. Therefore, it is useful for qualitative and semiquantitative measurement of DNA methylation. However, the reliability of data obtaining from this technique is mainly depending on the efficiency of bisulfite conversion and number of sequencing clones representing the target-converted sequence. Therefore, it is labor intensive and time-consuming. Revolution of next generation DNA sequencing (NGS) has allowed researches to combine conventional bisulfite sequencing methods with high-throughput Illumina sequencing in a technique called whole genome bisulfite sequencing (WGBS). This technique allows a single nucleotide resolution of 5-methylcytosine on a genome scale. WGBS technique workflow involves DNA fragmentation, processing through end blunting, terminal A(s) addition at 3′ end and adaptor ligation, bisulfite treatment, PCR amplification, sequencing libraries and assembling, and finally alignment with the reference genome and data analysis. Despite the fact that WGBS is more reliable than the conventional clone-based bisulfite sequencing, it is costly, requires large amount of DNA and its output data is not easily handled.
Ionic stress is one of the most important components of salinity and is brought about by excess N... more Ionic stress is one of the most important components of salinity and is brought about by excess Na + accumulation, especially in the aerial parts of plants. Since Na + interferes with K + homeostasis, and especially given its involvement in numerous metabolic processes, maintaining a balanced cytosolic Na + /K + ratio has become a key salinity tolerance mechanism. Achieving this homeostatic balance requires the activity of Na + and K + transporters and/or channels. The mechanism of Na + and K + uptake and translocation in glycophytes and halophytes is essentially the same, but glycophytes are more susceptible to ionic stress than halophytes. The transport mechanisms involve Na + and/or K + transporters and channels as well as non-selective cation channels. Thus, the question arises of whether the difference in salt tolerance between glycophytes and halophytes could be the result of differences in the proteins or in the expression of genes coding the transporters. The aim of this review is to seek answers to this question by examining the role of major Na + and K + transporters and channels in Na + and K + uptake, translocation and intracellular homeostasis in glycophytes. It turns out that these transporters and channels are equally important for the adaptation of glycophytes as they are for halophytes, but differential gene expression, structural differences in the proteins (single nucleotide substitutions, impacting affinity) and post-translational modifications (phosphorylation) account for the differences in their activity and hence the differences in tolerance between the two groups. Furthermore, lack of the ability to maintain stable plasma membrane (PM) potentials following Na +-induced depolarization is also crucial for salt stress tolerance. This stable membrane potential is sustained by the activity of Na + /H + antiporters such as SOS1 at the PM. Moreover, novel regulators of Na + and K + transport pathways including the Nax1 and Nax2 loci regulation of SOS1 expression and activity in the stele, and haem oxygenase involvement in stabilizing membrane potential by activating H +-ATPase activity, favorable for K + uptake through HAK/AKT1, have been shown and are discussed.
Date palms are able to grow under diverse abiotic stress conditions including in saline soils, wh... more Date palms are able to grow under diverse abiotic stress conditions including in saline soils, where microbial communities may be help in the plant’s salinity tolerance. These communities able to produce specific growth promoting substances can enhance date palm growth in a saline environment. However, these communities are poorly defined. In the work reported here, the date palm endophytic bacterial and fungal communities were identified using the pyrosequencing method, and the microbial differential abundance in the root upon exposure to salinity stress was estimated. Approximately 150,061 reads were produced from the analysis of six ribosomal DNA libraries, which were prepared from endophytic microorganisms colonizing date palm root tissues. DNA sequence analysis of these libraries predicted the presence of a variety of bacterial and fungal endophytic species, some known and others unknown. The microbial community compositions of 30% and 8% of the bacterial and fungal species, respectively, were significantly (p ≤ 0.05) altered in response to salinity stress. Differential enrichment analysis showed that microbe diversity indicated by the Chao, Shannon and Simpson indices were slightly reduced, however, the overall microbial community structures were not significantly affected as a consequence of salinity. This may reflect a buffering effect by the host plant on the internal environments that these communities are colonizing. Some of the endophytes identified in this study were strains that were previously isolated from saline and marine environments. This suggests possible interactions with the plant that are favorable to salinity tolerance in date palm.
Date palm (Phoenix dactylifera L.) is a major fruit tree in the Middle East and it is a plant con... more Date palm (Phoenix dactylifera L.) is a major fruit tree in the Middle East and it is a plant considered to be tolerant to a variety of abiotic stresses, including salinity. However, the physiological basis of its salinity tolerance is not fully known. The objective of this study was to screen Omani date palm cultivars for tolerance or susceptibility to salt stress. Seedlings from 10 commercially important date palm cultivars were subjected to 240 mM NaCl, and several physiological parameters related to salinity tolerance traits were evaluated upon treatment. The cultivars were divided into two groups based on the dry weight (DW) of their leaf and root tissues, a parameter which was used as an indication of healthy growth. The results revealed that photosynthesis, electrolyte leakage (EL), and the shoot K + /Na + ratio were all significantly reduced in the susceptible cultivars. In addition, the relative water content was higher in the tolerant cultivars in comparison with the susceptible ones. These results suggest that although date palm is tolerant to high salinity, there is variation in tolerance among different cultivars. Shoot Na + exclusion, photosynthesis, and membrane stability are apparently the main determinants of tolerance and can be used in salinity tolerance screening of date palm. The results have shown new very tolerant cultivars (Manoma and Umsila) that could serve as genetic resources for improved date palm tolerance to salinity.
Background: Date palm, as one of the most important fruit crops in North African and West Asian c... more Background: Date palm, as one of the most important fruit crops in North African and West Asian countries including Oman, is facing serious growth problems due to salinity, arising from persistent use of saline water for irrigation. Although date palm is a relatively salt-tolerant plant species, its adaptive mechanisms to salt stress are largely unknown.
Background: Date palm, as one of the most important fruit crops in North African and West Asian c... more Background: Date palm, as one of the most important fruit crops in North African and West Asian countries including Oman, is facing serious growth problems due to salinity, arising from persistent use of saline water for irrigation. Although date palm is a relatively salt-tolerant plant species, its adaptive mechanisms to salt stress are largely unknown.
Worldwide tetracycline resistance (Tc r) is increasing dramatically, causing serious environmenta... more Worldwide tetracycline resistance (Tc r) is increasing dramatically, causing serious environmental and health problems. A total of 201 samples were collected from chicken intestine, human feces and treated sewage effluent (TSE). One hundred and eighteen Escherichia coli strains were isolated and identified using MALDI-Biotyper. Single and multiplex PCR were used to screen isolates for 14 tet genes, among which only 7 tet genes (A, B, C, M, Q, W, 32) were found. Among the resistant isolates, tet A was the most frequent gene, followed by tet B and tet 32 while the rest of tet determinants occurred at a lower frequency. Many strains contained multiple Tc r determinants. Some strains contained 4 tet gene-combination, tet (A/B/C/32) and tet (A/B/M/32). The 4 tet gene combination is reported for the first time in this region. The Tc r isolates showed a high variation of tet gene combination. The increase in the resistance of tetracycline with high diversification is an indication of antibiotics overuse. Strict enforcement of regulation is urgently needed to control and prevent the spread of tetracycline resistant strains which are detrimental to the environment.
Date palm is an important crop plant in the arid and semi-arid regions supporting human populatio... more Date palm is an important crop plant in the arid and semi-arid regions supporting human population in the Middle East and North Africa. These areas have been largely affected by drought and salinity due to insufficient rainfall and improper irrigation practices. Date palm is a relatively salt-and drought-tolerant plant and more recently efforts have been directed to identifying genes and pathways that confer stress tolerance in this species. Quantitative real-time PCR (qPCR) is a promising technique for the analysis of stress-induced differential gene expression, which involves the use of stable reference genes for normalizing gene expression. In an attempt to find the best reference genes for date palm's drought and salinity research, we evaluated the stability of 12 most commonly used reference genes using the geNorm, NormFinder, BestKeeper statistical algorithms and the comparative ΔC T method. The comprehensive results revealed that HEAT SHOCK PROTEIN (HSP), UBIQUITIN (UBQ) and YTH domain-containing family protein (YT521) were stable in drought-stressed leaves whereas GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGE-NASE (GAPDH), ACTIN and TUBULIN were stable in drought-stressed roots. On the other hand, SMALL SUBUNIT RIBOSOMAL RNA (25S), YT521 and 18S ribosomal RNA (18S); and UBQ, ACTIN and ELONGATION FACTOR 1-ALPHA (eEF1a) were stable in leaves and roots, respectively, under salt stress. The stability of these reference genes was verified by using the abiotic stress-responsive CYTOSOLIC Cu/Zn SUPEROXIDE DISMUT-ASE (Cyt-Cu/Zn SOD), an ABA RECEPTOR, and a PROLINE TRANSPORTER 2 (PRO) genes. A combination of top 2 or 3 stable reference genes were found to be suitable for nor-malization of the target gene expression and will facilitate gene expression analysis studies aimed at identifying functional genes associated with drought and salinity tolerance in date palm.
In this report, a draft of the Enterobacter asburiae strain PDA134 genome was sequenced. This bac... more In this report, a draft of the Enterobacter asburiae strain PDA134 genome was sequenced. This bacterial strain was isolated from the root tissue of a date palm, where it has the ability to produce 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and indole-3-acetic acid (IAA) under salinity stress. Citation Yaish MW. 2016. Draft genome sequence of endophytic bacterium Enterobacter asburiae PDA134, isolated from date palm (Phoenix dactylifera L.) roots. Genome Announc 4(4):e00848-16.
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