Search

Plants have acquired sets of highly regulated and complex signaling pathways to respond to unfavorable environmental conditions during evolution. Calcium signaling, as a vital mechanism, enables plants to respond to external stimuli, including abiotic and biotic stresses, and coordinate the basic processes of the growth and development. In the present study, the calcium sensor families, including CBL and CIPK, were investigated in the halophyte plant, Aeluropus littoralis, with a comprehensive analysis. Here, six AlCBL genes, and twenty AlCIPK genes were presented. The analysis of the gene structure and conserved motifs, as well as physicochemical properties, showed that these genes are highly conserved during evolution. The expression levels of AlCBL genes and AlCIPK genes were evaluated under salt stress in leaf and root tissue. Based on the real-time RT-PCR results, AlCIPK gene family had a higher variation in mRNA abundance compared to the AlCBL gene family. The AlCIPKs were found to have a higher abundance in leaves than in roots. The results suggest that the interaction pattern of AlCBL genes with AlCIPK is tissue-specific, and different interactions can be expected in leaves and roots. Based on these patterns AlCIPK3.1 - AlCBL4.1 and AlCIPK1.2 - AlCBL4.4 can interact in root tissue, while the AlCBL10 has the potential to interact with the AlCIPK5, AlCIPK26 and AlCIPK12.3 in the leaf tissue. These findings provide valuable information on the structure and function of calcium sensor families in Aeluropus littoralis a halophyte plant, for future research on the biological function of CBLs and CIPKs on salt stress resistance.

Laccases are plant enzymes with essential functions during growth and development. These monophenoloxidases are involved in lignin polymerization, and their expression respond to environmental stress. However, studies of laccases in some plants and fungi have highlighted that many structural and functional aspects of these genes are still unknown. Here, the laccase gene family in Aeluropus littoralis (AlLAC) is described based on sequence structure and expression patterns under abiotic stresses and ABA treatment. Fifteen non-redundant AlLACs were identified from the A. littoralis genome, which showed differences in physicochemical characteristics and gene structure. Based on phylogenetic analysis, AlLACs and their orthologues were classified into five groups. A close evolutionary relationship was observed between LAC gene family members in rice and A. littoralis. According to the interaction network, AlLACs interact more with proteins involved in biological processes such as iron incorporation into the metallo-sulfur cluster, lignin catabolism, regulation of the symbiotic process and plant-type primary cell wall biogenesis. Gene expression analysis of selected AlLACs using real-time RT (reverse transcription)-PCR revealed that AlLACs are induced in response to abiotic stresses such as cold, salt, and osmotic stress, as well as ABA treatment. Moreover, AlLACs showed differential expression patterns in shoot and root tissues. Our findings indicate that AlLACs are preferentially involved in the late response of A. littoralis to abiotic stress.

During the response of plants to adverse stresses, aquaporin (AQP) plays a prominent role in membrane water transport based on received upstream signals. In addition, they have various physical parts for dealing with environmental stresses. Due to the importance of the AQP gene family, studies have been conducted investigating the function and regulatory system of these genes. However, many of their molecular aspects are still unknown. This study aims to carry out a genomic-wide investigation of the AQP gene family in durum wheat using bioinformatics tools and to investigate the expression patterns of some members in response to salt stress. Our results showed that there are 80 TtAQP genes in durum wheat, which are classified into four main groups based on phylogenetic analysis. Many duplications were observed between the members of the TtAQP gene family, and high diversity in response to post-translational modifications was observed between TtAQP family members. The expression pattern of TtAQP genes disclosed that these genes are primarily upregulated in response to salt stress. Besides, qPCR data revealed that TtAQPs are more induced in delayed responses to salinity stress. Overall, our findings illustrate that TtAQP members are diverse in terms of their structure, regulatory systems and expression levels.

Various kinds of primary metabolisms in plants are modulated through sulfate metabolism, and sulfotransferases (SOTs), which are engaged in sulfur metabolism, catalyze sulfonation reactions. In this study, a genome-wide approach was utilized for the recognition and characterization of SOT family genes in the significant nutritional crop potato (Solanum tuberosum L.). Twenty-nine putative StSOT genes were identified in the potato genome and were mapped onto the nine S. tuberosum chromosomes. The protein motifs structure revealed two highly conserved 5 '-phosphosulfate-binding (5 ' PSB) regions and a 3 '-phosphate-binding (3 ' PB) motif that are essential for sulfotransferase activities. The protein-protein interaction networks also revealed an interesting interaction between SOTs and other proteins, such as PRTase, APS-kinase, protein phosphatase, and APRs, involved in sulfur compound biosynthesis and the regulation of flavonoid and brassinosteroid metabolic processes. This suggests the importance of sulfotransferases for proper potato growth and development and stress responses. Notably, homology modeling of StSOT proteins and docking analysis of their ligand-binding sites revealed the presence of proline, glycine, serine, and lysine in their active sites. An expression essay of StSOT genes via potato RNA-Seq data suggested engagement of these gene family members in plants' growth and extension and responses to various hormones and biotic or abiotic stimuli. Our predictions may be informative for the functional characterization of the SOT genes in potato and other nutritional crops.

BAHD enzymes play a critical role in regulating plant metabolites and affecting cell stability. In the present study, BAHD gene family members were recognized in the genome of Theobroma cacao and characterized using available bioinformatics tools. We found 27 nonredundant putative tcBAHD genes in cacao for the first time. Our findings indicate that tcBAHD genes are diverse based on sequence structure, physiochemical properties, and function. In addition, tcBAHDs and their orthologous in G. raimnodii, and C. capsularis were clustered into five groups. According to phylogenetic analysis, BAHD family genes were probably evolve drastically after divergence. The divergence time of duplication events with purifying selection pressure was predicted to range from 1.82 MYA to 15.50 MYA. Pocket analysis revealed that SER amino acids play a key role in regulating the activity of tcBAHDs. Furthermore, cis-acting elements related to responsiveness of stress and hormone, especially ABA and MeJA, were observed in the promoter region of tcBAHD genes. RNA-seq analysis revealed that tcBAHD13 and tcBAHD26 are more involved in response to P. megakarya fungi. In conclusion, it seems that evolutionary processes, such as duplication events, caused a high diversity in the structure and function of tcBAHD genes.

Magnesium (Mg) is an element involved in various key cellular processes in plants. Mg transporter (MGT) genes play an important role in magnesium distribution and ionic balance maintenance. Here, MGT family members were identified and characterized in three species of the plant family Malvaceae, Theobroma cacao, Corchorus capsularis, and Gossypium hirsutum, to improve our understanding of their structure, regulatory systems, functions, and possible interactions. We identified 18, 41, and 16 putative non-redundant MGT genes from the genome of T. cacao, G. hirsutum, and C. capsularis, respectively, which clustered into three groups the maximum likelihood tree. Several segmental/tandem duplication events were determined between MGT genes. MGTs appear to have evolved slowly under a purifying selection. Analysis of gene promoter regions showed that MGTs have a high potential to respond to biotic/abiotic stresses and hormones. The expression patterns of MGT genes revealed a possible role in response to P. megakarya fungi in T. cacao, whereas MGT genes showed differential expression in various tissues and response to several abiotic stresses, including cold, salt, drought, and heat stress in G. hirsutum. The co-expression network of MGTs indicated that genes involved in auxin-responsive lipid metabolism, cell wall organization, and photoprotection can interact with MGTs.

The gibberellic acid-stimulated Arabidopsis (GASA/GAST) gene family is widely distributed in plants and involved in various physiological and biological processes. These genes also provide resistance to abiotic and biotic stresses, including antimicrobial, antiviral, and antifungal. We are interested in characterizing the GASA gene family and determining its role in various physiological and biological process in Theobroma cacao. Here, we report 17 tcGASA genes distributed on six chromosomes in T. cacao. The gene structure, promoter region, protein structure and biochemical properties, expression, and phylogenetics of all tcGASAs were analyzed. Phylogenetic analyses divided tcGASA proteins into five groups. Among 17 tcGASA genes, nine segmentally duplicating genes were identified which formed four pairs and cluster together in phylogenetic tree. Differential expression analyses revealed that most of the tcGASA genes showed elevated expression in the seeds (cacao food), implying their role in seed development. The differential expression of tcGASAs was recorded between the tolerant and susceptible cultivars of cacao, which indicating their possible role as fungal resistant. Our findings provide new insight into the function, evolution, and regulatory system of the GASA family genes in T.cacao and may suggest new target genes for development of fungi-resistant cacao varieties in breeding programs.