Genome-wide identification, phylogenetic classification of histone acetyltransferase genes, and their expression analysis in sugar beet (Beta vulgaris L.) under salt stress.

MAIN CONCLUSION: This study identified seven histone acetyltransferase-encoding genes (HATs) from Beta vulgaris L. (sugar beet) genome through bioinformatics tools and analyzed their expression profiles under salt stress. Sugar beet HATs are phylogenetically divided into four families: GNAT, MYST, CBP, and TAFII250. The BvHAT genes were differentially transcribed in leaves, stems, and roots of B. vulgaris salt-resistant (Casino) and -sensitive (Bravo) cultivars under salt stress. Histone acetylation is regulated by histone acetyltransferases (HATs), which catalyze ɛ-amino bond formation between lysine residues and acetyl groups with a cofactor, acetyl-CoA. Even though the HATs are known to participate in stress response and development in model plants, little is known about the functions of HATs in crops. In sugar beet (Beta vulgaris L.), they have not yet been identified and characterized. Here, an in silico analysis of the HAT gene family in sugar beet was performed, and their expression patterns in leaves, stems, and roots of B. vulgaris were analyzed under salt stress. Salt-resistant (Casino) and -sensitive (Bravo) beet cultivars were used for gene expression assays. Seven HATs were identified from sugar beet genome, and named BvHAG1, BvHAG2, BvHAG3, BvHAG4, BvHAC1, BvHAC2, and BvHAF1. The HAT proteins were divided into 4 groups including MYST, GNAT (GCN5, HAT1, ELP3), CBP and TAFII250. Analysis of cis-acting elements indicated that the BvHAT genes might be involved in hormonal regulation, light response, plant development, and abiotic stress response. The BvHAT genes were differentially expressed in leaves, stems, and roots under control and 300 mM NaCl. In roots of B. vulgaris cv. Bravo, the BvHAG1, BvHAG2, BvHAG4, BvHAF1, and BvHAC1 genes were dramatically expressed after 7 and 14 days of salt stress. Interestingly, the BvHAC2 gene was not expressed under both control and stress conditions. However, the expression of BvHAG2, BvHAG3, BvHAG4, BvHAC1, BvHAC2 genes showed a significant increase in response to salt stress in the roots of cv. Casino. This study provides new insights into the potential roles of histone acetyltransferases in sugar beet.

Heavy Metal Levels and Mineral Nutrient Status of Natural Walnut (Juglans regia L.) Populations in Kyrgyzstan: Nutritional Values of Kernels.

In this study, mineral nutrient and heavy metal (Al, Ca, Cd, Cu, Fe, K, Mg, Mn, Na, Ni, Pb, and Zn) contents of the walnut kernels and their co-located soil samples collected from the four different zones of natural walnut forests (Sary-Chelek, Arslanbap, and Kara-Alma in Jalal-Abad Region and Kara-Shoro in Osh Region) in Kyrgyzstan were investigated. The highest concentrations for all elements determined in the soil samples were observed in the Sary-Chelek zone whereas the Arslanbap zone was found to be having the lowest concentrations except Fe and Zn. The highest concentrations in the kernels of walnut samples were found to be in the Sary-Chelek zone for Ca, Fe, K, Mg, and Zn; in the Kara-Shoro zone for Cu; in the Arslanbap zone for Mn; and in the Kara-Alma zone for Na whereas the lowest concentrations were found to be in the Arslanbap zone for Ca, Fe, K, Mg, Na, and Zn and in the Sary-Chelek zone for Cu and Mn, respectively. Also, the levels of Al, Cd, Ni, and Pb in kernel samples could not be detected by ICP-OES because their levels were lower than the threshold detection point (10 µg.kg-1). Additionally, our data indicated that the walnut kernels from Kyrgyzstan have higher values for RDA (recommended daily allowances) in comparison with the walnut kernels from other countries.

Genome-wide identification and expression profiling of EIL gene family in woody plant representative poplar (Populus trichocarpa).

This study aimed to improve current understanding on ethylene-insensitive 3-like (EIL) members, least explored in woody plants such as poplar (Populus trichocarpa Torr. & Grey). Herein, seven putative EIL members were identified in P. trichocarpa genome and were roughly annotated either as EIN3-like sequence associated with ethylene pathway or EIL3-like sequences related with sulfur (S)-pathway. Motif-distribution pattern of proteins also corroborated this annotation. They were distributed on six chromosomes (chr1, 3, 4 and 8-10), and were revealed to encode a protein of 509-662 residues with nuclear localization. The presence of ethylene insensitive 3 (EIN3; PF04873) domain (covering first 80-280 residues from N-terminus) was confirmed by Hidden Markov Model-based search. The first half of EIL proteins (∼80-280 residues including EIN3 domain) was substantially conserved. The second half (∼300-600 residues) was considerably diverged. Additionally, first half of proteins harbored acidic, proline-rich and glutamine-rich sites, and supported the essentiality of these regions in the transcriptional-activation and protein-function. Moreover, identified six segmental and one-tandem duplications demonstrated the negative or purifying selective nature of mutations. Furthermore, expression profile analysis indicated the possibility of a crosstalk between EIN3- and EIL3-like genes, and co-expression networks implicated their interactions with very diverse panels of biological molecules.

Isolation of a transcription factor DREB1A gene from Phaseolus vulgaris and computational insights into its characterization: protein modeling, docking and mutagenesis.

A transcription factor DREB1A (dehydration-responsive element-binding 1A) gene was amplified and sequenced from the common bean (Phaseolus vulgaris). PvDREB1A had a 777 base pairs (bp) open reading frame encoding a protein of 225 residues. The protein sequence contained a conserved DNA-binding AP2 domain of about 60 residues and a nuclear localization signal (NLS) at N-terminus site. PvDREB1A demonstrated high homology with other DREB1 members only in AP2 domain and NLS site. The phylogenetic distribution of different DREB members showed three main groups as DREB1-3 and PvDREB1A was a member of DREB1 group. Homology modeling and secondary structure analyses revealed that PvDREB1A AP2 domain was packed into the three-stranded antiparallel beta sheets (ß1-3) and an alpha helix (α1) almost parallel to these beta sheets. Moreover, DNA-binding AP2 domain of PvDREB1A and GCC-box containing double helix DNA were docked. The docking analysis showed that PvDREB1A AP2 domain could bind to the major groove of the DNA by three-stranded antiparallel beta sheets, with residues Gly86 or Thr87 in ß1-sheet and Arg63 or Arg64 in ß3-sheet. The docked complex also indicated that AP2 domain has a preferential for the binding of GCC stretches in the double helix DNA. A total of 36 reliably estimated hot spots residues were identified with high mutability grade but none of these residues was essential for the protein function since they are located at outside the DNA-binding AP2 domain of PvDREB1A.

Genome-wide identification and expression analysis of sulfate transporter (SULTR) genes in potato (Solanum tuberosum L.).

MAIN CONCLUSION: Solanum tuberosum genome analysis revealed 12 StSULTR genes encoding 18 transcripts. Among genes annotated at group level ( StSULTR I-IV), group III members formed the largest SULTRs-cluster and were potentially involved in biotic/abiotic stress responses via various regulatory factors, and stress and signaling proteins. Employing bioinformatics tools, this study performed genome-wide identification and expression analysis of SULTR (StSULTR) genes in potato (Solanum tuberosum L.). Very strict homology search and subsequent domain verification with Hidden Markov Model revealed 12 StSULTR genes encoding 18 transcripts. StSULTR genes were mapped on seven S. tuberosum chromosomes. Annotation of StSULTR genes was also done as StSULTR I-IV at group level based mainly on the phylogenetic distribution with Arabidopsis SULTRs. Several tandem and segmental duplications were identified between StSULTR genes. Among these duplications, Ka/Ks ratios indicated neutral nature of mutations that might not be causing any selection. Two segmental and one-tandem duplications were calculated to occur around 147.69, 180.80 and 191.00 million years ago (MYA), approximately corresponding to the time of monocot/dicot divergence. Two other segmental duplications were found to occur around 61.23 and 67.83 MYA, which is very close to the origination of monocotyledons. Most cis-regulatory elements in StSULTRs were found associated with major hormones (such as abscisic acid and methyl jasmonate), and defense and stress responsiveness. The cis-element distribution in duplicated gene pairs indicated the contribution of duplication events in conferring the neofunctionalization/s in StSULTR genes. Notably, RNAseq data analyses unveiled expression profiles of StSULTR genes under different stress conditions. In particular, expression profiles of StSULTR III members suggested their involvement in plant stress responses. Additionally, gene co-expression networks of these group members included various regulatory factors, stress and signaling proteins, and housekeeping and some other proteins with unknown functions.