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Genome-wide exploration of silicon (Si) transporter genes, Lsi1 and Lsi2 in plants; insights into Si-accumulation status/capacity of plants
(Springer, 2017) Vatansever, Recep; Özyiğit, İbrahim İlker; Filiz, Ertuğrul; Gözükara, Nermin
Silicon (Si) is a nonessential, beneficial micronutrient for plants. It increases the plant stress tolerance in relation to its accumulation capacity. In this work, root Si transporter genes were characterized in 17 different plants and inferred for their Si-accumulation status. A total of 62 Si transporter genes (31 Lsi1 and 31 Lsi2) were identified in studied plants. Lsi1s were 261-324 residues protein with a MIP family domain whereas Lsi2s were 472-547 residues with a citrate transporter family domain. Lsi1s possessed characteristic sequence features that can be employed as benchmark in prediction of Si-accumulation status/capacity of the plants. Silicic acid selectivity in Lsi1s was associated with two highly conserved NPA (Asn-Pro-Ala) motifs and a Gly-Ser-Gly-Arg (GSGR) ar/R filter. Two NPA regions were present in all Lsi1 members but some Ala substituted with Ser or Val. GSGR filter was only available in the proposed high and moderate Si accumulators. In phylogeny, Lsi1s formed three clusters as low, moderate and high Si accumulators based on tree topology and availability of GSGR filter. Low-accumulators contained filters WIGR, AIGR, FAAR, WVAR and AVAR, high-accumulators only with GSGR filter, and moderate-accumulators mostly with GSGR but some with A/CSGR filters. A positive correlation was also available between sequence homology and Si-accumulation status of the tested plants. Thus, availability of GSGR selectivity filter and sequence homology degree could be used as signatures in prediction of Si-accumulation status in experimentally uncharacterized plants. Moreover, interaction partner and expression profile analyses implicated the involvement of Si transporters in plant stress tolerance.
Genome-wide exploration of metal tolerance protein (MTP) genes in common wheat (Triticum aestivum): insights into metal homeostasis and biofortification
(Springer, 2017) Vatansever, Recep; Filiz, Ertuğrul; Eroğlu, Seçkin
Metal transport process in plants is a determinant of quality and quantity of the harvest. Although it is among the most important of staple crops, knowledge about genes that encode for membrane-bound metal transporters is scarce in wheat. Metal tolerance proteins (MTPs) are involved in trace metal homeostasis at the sub-cellular level, usually by providing metal efflux out of the cytosol. Here, by using various bioinformatics approaches, genes that encode for MTPs in the hexaploid wheat genome (Triticum aestivum, abbreviated as Ta) were identified and characterized. Based on the comparison with known rice MTPs, the wheat genome contained 20 MTP sequences; named as TaMTP1-8A, B and D. All TaMTPs contained a cation diffusion facilitator (CDF) family domain and most members harbored a zinc transporter dimerization domain. Based on motif, phylogeny and alignment analysis, A, B and D genomes of TaMTP3-7 sequences demonstrated higher homology compared to TaMTP1, 2 and 8. With reference to their rice orthologs, TaMTP1s and TaMTP8s belonged to Zn-CDFs, TaMTP2s to Fe/Zn-CDFs and TaMTP3-7s to Mn-CDFs. Upstream regions of TaMTP genes included diverse cis-regulatory motifs, indicating regulation by developmental stage, tissue type and stresses. A scan of the coding sequences of 20 TaMTPs against published miRNAs predicted a total of 14 potential miRNAs, mainly targeting the members of most diverged groups. Expression analysis showed that several TaMTPs were temporally and spatially regulated during the developmental time-course. In grains, MTPs were preferentially expressed in the aleurone layer, which is known as a reservoir for high concentrations of iron and zinc. The work identified and characterized metal tolerance proteins in common wheat and revealed a potential involvement of MTPs in providing a sink for trace element storage in wheat grains.
Genome-wide identification of mildew resistance locus O (MLO) genes in tree model poplar (Populus trichocarpa): powdery mildew management in woody plants
(Springer, 2018) Filiz, Ertuğrul; Vatansever, Recep
Poplars are economically important fast growing trees. They are exposed to broad range of fungal diseases like powdery mildew (PM). MLOs (mildew resistance locus O), as plant susceptibility genes, act as negative regulators and whose loss-of-functions confer complete resistance to PM disease. Herein, work identified the MLO gene family members in poplar, a woody model species. A total of 26 identified MLOs (annotated as PtMLO1-26) were distributed on 14 poplar chromosomes either individually or in groups of two to four. PtMLO genes encoded a polypeptide of 341-593 residues with a characteristic MLO domain structure. One tandem and eight segmental duplications were revealed in PtMLO genes. PtMLO proteins anchored at plasma membrane and had putative 5-9 TMDs with extracellular/cytosolic N- and C-terminuses. They were rich in leucine (9.1-12.9%), which is reported to play roles in defense response signaling. The C-terminal calmodulin-binding domain (CaMBD), reported to modulate the signaling mechanism in the defense response, was completely preserved in all PtMLOs, except PtMLO6. This domain was partially absent in PtMLO6 which is inferred to be a different MLO type or a pseudogene with a lost/impaired function in PM response. Besides, second and third cytoplasmic loops that are critical for PM-susceptibility were identified in PtMLOs. Particularly, PtMLO17, 18, 19, and 24 genes, inferred from Arabidopsis-poplar comparative phylogeny, were identified as potential candidates that may be involved in poplar-PM resistance. Notably, inductions of 14 PtMLO genes were detected in probes of microarray data such as GSE56865, GSE16417, and GSE23726 under different fungal infections indicating their involvements in plant defense. Overall, this work provided a basis for woody plant genomics for the effective and better management of poplar-PM disease.
Genome-wide identification and expression profiling of EIL gene family in woody plant representative poplar (Populus trichocarpa)
(Elsevier Science Inc, 2017) Filiz, Ertuğrul; Vatansever, Recep; Özyiğit, İbrahim İlker; Uras, Mehmet Emin; Şen, Uğur; Anjum, Naser A.; Pereira, Eduarda
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 (chrl, 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 (similar to 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, praline-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. (C) 2017 Elsevier Inc. All rights reserved.
Genome-wide identification of galactinol synthase (GolS) genes in Solanum lycopersicum and Brachypodium distachyon
(Elsevier Sci Ltd, 2015) Filiz, Ertuğrul; Özyiğit, İbrahim İlker; Vatansever, Recep
GoIS genes stand as potential candidate genes for molecular breeding and/or engineering programs in order for improving abiotic stress tolerance in plant species. In this study, a total of six galactinol synthase (GolS)genes/proteins were retrieved for Solanum lycopersicum and Brachypodium distachyon. GolS protein sequences were identified to include glyco_transf_8 (PF01501) domain structure, and to have a close molecular weight (36.40-39.59 kDa) and amino acid length (318-347 aa) with a slightly acidic pI (5.35-6.40). The sub-cellular location was mainly predicted as cytoplasmic. S. lycopersicum genes located on chr 1 and 2, and included one segmental duplication while genes of B. distachyon were only on chr 1 with one tandem duplication. GoIS sequences were found to have well conserved motif structures. Cis-acting analysis was performed for three abiotic stress responsive elements, including ABA responsive element (ABRE), dehydration and cold responsive elements (DRE/CRT) and low-temperature responsive element (LTRE). ABRE elements were found in all GoIS genes, except for SIGoIS4; DRE/CRT was not detected in any GoIS genes and LTRE element found in SlGolS1 and BdGolS1 genes. AU analysis in UTR and ORF regions indicated that SlGolS and BdGoIS mRNAs may have a short half-life. SlGolS3 and SlG0lS4 genes may generate more stable transcripts since they included AATTAAA motif for polyadenylation signal POLASIG2. Seconder structures of SIGolS proteins were well conserved than that of BdGolS. Some structural divergences were detected in 3D structures and predicted binding sites exhibited various patterns in GoIS proteins. (C) 2015 Elsevier Ltd. All rights reserved.
Genome-wide identification and comparative analysis of EPSPS (aroA) genes in different plant species
(Springer India, 2016) Filiz, Ertuğrul; Koç, İbrahim
Shikimate pathway produces aromatic amino acids such as phenylalanine, tyrosine and tryptophan, which is essential for plant life. EPSPS (5-enolpyruvylshikimate-3-phosphate synthase, EC 2.5.1.1.9) (aroA) that observed in plants and bacteria plays an important role in shikimate pathway as being the sixth crucial enzyme. In this study, genome-wide comparative analyses of EPSPS genes were performed in different plant species, including Glycine max, Medicago truncatula, Brachypodium disctahyon, Zea mays, Chlamydomonas reinhardtii (green alga), and Physcomitrella patens (moss). One EPSPS gene was identified in M. truncatula, B. distachyon, Z. mays, and C. reinhardtii while two EPSPS genes identified in G. max and P. patens. Based on nucleotide diversity analyses of EPSPS genes, nucleotide diversity was found to be pi: 0.29 and theta: 0.34, respectively. Gene structure analysis revealed that 6 of 8 EPSPS genes (75 %) contained seven introns while the length of open reading frame (ORF) ranged from 1173 to 1611 bp. Two highly conserved motifs (LPGSKSLSNRILLLAAL and LFLGNAGTAMRPL) were detected in all plant species. All putative EPSPSs were predicted to be localized in chloroplast while 7 of 8 EPSPSs (87.5 %) contained N-glycosylation sites except for Chlamydomonas. Phylogenetic analyses showed that monocots, dicots, and moss were clustered in group A whereas green alga (C. reinhardtii) was located alone in group B. 3D structure analyses indicated that EPSP synthases contained N-terminal and C-terminal domains while electrostatic potential of EPSPSs were found to exhibit various patterns. In addition, ligand molecule glyphosate was docked with EPSPS of B. disctahyon and G. max. The result showed that there were strong favorable bonds between the proteins and the ligand with favorable conformation.
Genome-wide distribution of superoxide dismutase (SOD) gene families in Sorghum bicolor
(Tubitak Scientific & Technical Research Council Turkey, 2015) Filiz, Ertuğrul; Tombuloğlu, Hüseyin
Superoxide dismutases (SODs) are critical enzymes protecting cells against toxic superoxide radicals. To date, 3 types of SODs have been identified: Cu-ZnSODs, Fe-MnSODs, and NiSODs. In this study, a genome-wide analysis was performed in Sorghum bicolor to characterize SOD genes and proteins. Using several bioinformatics tools, we characterized a total of 8 SOD genes from the Sorghum genome. Gene structure, chromosomal distribution, tissue specific expression, conserved domain, and phylogenetic analyses of SOD genes were carried out. Additionally, 3-dimensional structures were determined and compared within each SbSOD protein. Chromosomal distributions revealed that the highest number of SOD genes was on chromosomes 1 and 10, with 2 members on each. Single segmental gene duplication was observed between the genes SbSOD2 and SbSOD5. Intron numbers of SbSOD genes ranged from 5 to 7. Motif analyses showed that SbSODs included 2 and 3 common motifs in Cu-ZnSOD and Fe-MnSODs, respectively. In addition, 3 functional domains were identified in SbSODs: 1) copper-zinc domain (Pfam: 00080) in Cu-ZnSOD; and 2) iron/manganese superoxide dismutases alpha-hairpin domain (Pfam: 00081) and 3) iron/manganese superoxide dismutases, C-terminal domain (Pfam: 02777) in Fe-MnSODs. Gene Ontology term enrichment analysis showed that 8 SOD genes have similar molecular functions and biological processes, and variable cellular components. Phylogenetic analysis revealed that Cu-ZnSODs (92%) and Fe-MnSODs (100%) were separated by high bootstrap values. Additionally, predicted motif structures and critical binding sites of SbSODs were found to be similar within each SOD group. The results of this study contribute to a better understanding of SOD genes and proteins in plants, especially in Sorghum taxa.
Genome-wide identification and analysis of growth regulating factor genes in Brachypodium distachyon: in silico approaches
(Tubitak Scientific & Technical Research Council Turkey, 2014) Filiz, Ertuğrul; Koç, İbrahim; Tombuloğlu, Hüseyin
Growth-regulating factor (GRF) genes may play important roles for regulating growth and development in different plant tissues and organs. Here we report the first genome-wide analysis of the GRF gene family in Brachypodium. We performed in silico comparative analysis of GRF genes, including their structure, duplication in the genome, conserved motifs, and phylogenetic relationship. At the end of the study, 10 BdGRF genes were identified. The highest number of GRF genes was identified on chromosome 1 with 5 members, whereas the least number of genes (only 1 member) was found on chromosomes 2, 4, and 5. Of those, a single segmental duplication was observed in the Brachypodium genome. Average exon and intron numbers were determined as 3 and 4, respectively. Motif analysis showed that WRC and QLQ residues were consistent in all GRF protein sequences. Gene Ontology terms showed that 10 BdGRF proteins grouped in the same biological function, biological process, and cellular component groups. In addition, we compared the new BdGRF proteins with the other monocot and dicot GRF proteins sequences. Phylogenetic analysis revealed that GRF proteins of monocot and dicot species were clustered together in a joined tree; in particular, the monocot species (Brachypodium, maize, and rice) were grouped into the same cluster with high bootstrap values. We assume that the results of this study will provide molecular insights about GRF proteins in grass species.
Genome-wide identification and expression analysis of sulfate transporter (SULTR) genes in potato (Solanum tuberosum L.)
(Springer, 2016) Vatansever, Recep; Koç, İbrahim; Özyiğit, İbrahim İlker; Şen, Uğur; Uras, Mehmet Emin; Anjum, Naser A.; Filiz, Ertuğrul
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.
Genome-Wide Identification and Comparative Analysis of Copper Transporter Genes in Plants
(Springer Heidelberg, 2017) Vatansever, Recep; Özyiğit, İbrahim İlker; Filiz, Ertuğrul
Copper (Cu) transporters have primary importance in maintenance of physiological limits of Cu home-ostasis in plants. However, structural characterization of Cu transporters in many plant species is still limited. In this study, a total of 78 potential Cu transporter genes were identified from 18 different plant species. Study revealed that Cu transporters could be characterized with a CTR protein family (PF04145) domain, three putative transmembrane domains (TMDs), a single exon number, and a basic character. Met-rich motifs at N-terminal region, MXXXM motif in TMD-2, and GXXXG motif in TMD-3 could be essential for Cu transport since they were highly conserved in all analyzed species. In phylogeny, a clear distinction was observed between Cu transporter sequences of lower and higher plants. General topological features of Cu transporters in higher plants-monocots and dicots-were highly conserved compared to lower plants. Identification of Cu transporter homologous in various plant species and their comparative analysis at gene and protein levels will become valuable theoretical basis for future studies aiming to further characterization and molecular manipulation of Cu transporters.
Genome-wide identification and expression analysis of sulphate transporter (SULTR) genes under sulfur deficiency in Brachypodium distachyon
(Springer India, 2017) Tombuloğlu, Hüseyin; Filiz, Ertuğrul; Aydın, Mehtap; Koç, İbrahim
Sulphur is an important mineral element for plant growth and development. It involves in a number of metabolic processes with crucial functions. This study has performed a genome-wide analysis of sulfate transporter (SULTR) genes in Brachypodium distachyon. Ten putative SULTR genes were identified in Brachypodium genome. BdSULTR genes included 6-17 exons encoding a protein of 647-693 residues with basic nature. BdSULTR proteins included both sulfate_transp (PF00916) and STAS (PF01740) domains. BdSULTRs were classified into 4 groups based on the phylogenetic distribution. Promoter regions of all BdSULTR genes, except for BdSULTR3;3 and 3;5 included the SURECOREATSULTR11 elements. A considerable structural overlap was identified between superimposed SULTR1;3 and 3;1 proteins, indicating that SULTR1 members may also involve in plant stress response/tolerance like SULTR3 members. Microarray and RNA-Seq analyses also revealed the differential expression of SULTR 1 and 3 genes under different biotic/abiotic stresses. Protein-protein interaction partners of BdSULTRs were mainly related with adenylyl-sulfate kinases, 5'-adenylylsulfate reductases, ATP sulfurylases, and acyl carrier proteins. Moreover, expression profiles of identified BdSULTR genes under S-deficiency were analyzed using RT-qPCR. It was revealed that BdSULTR1;1 and 3;1 are highly expressed in plant roots as similar to tenfold and similar to fivefold, respectively, while BdSULTR2 (similar to 15-fold) and 3;1 (similar to twofold) are abundantly expressed in leaf tissues.
Genome-wide identification and cadmium induced expression profiling of sulfate transporter (SULTR) genes in sorghum (Sorghum bicolor L.)
(Springer, 2018) Akbudak, M. Aydın; Filiz, Ertuğrul; Kontbay, Kübra
Sulfur is an essential element for all living organisms. Plants can convert inorganic sulfur into organic sulfur compounds by complex enzymatic steps. In this study, we conducted a genome-wide analysis of sulfate transporter genes (SULTRs) in the sorghum (Sorghum bicolor) genome and examined expression profiles of SbSULTR genes under 200 A mu M cadmium (Cd) exposure. As a result of sorghum genome analysis, 11 SULTR genes were identified, including SbSULTR1;1, SbSULTR1;2, SbSULTR1;3, SbSULTR2;1, SbSULTR2;2, SbSULTR3;1, SbSULTR3;2, SbSULTR3;3, SbSULTR3;4, SbSULTR3;5, and SbSULTR4. Given names are based on phylogeny and chromosomal locations. Except SbSULTR4, all SbSULTR proteins contained Sulfate_transp (PF00916), STAS (PF01740) domains and 12 trans-membrane domains. Phylogenetic analysis revealed that four major groups were identified such as SULTR1, 2, 3, and 4 groups and SULTR4 group was separated to other SULTR groups. In promotor sequences of SbSULTR genes, many diverse cis-acting elements were found mainly related with physiological processes such as light, stress and hormone responsiveness. The expression profiles of SbSULTR genes showed that SULTR1;2, 1;3, 3;3, and 3;5 genes up-regulated in root, while expression level of SULTR4 decreased under 200 A mu M Cd exposure. The predicted 3D structures of SULTR proteins showed some conformational changes, suggesting functional diversities of SbSULTRs. Finally, results of this study may contribute towards understanding SbSULTR genes and their regulations and roles in Cd stress in sorghum.
Genome-Wide Identification and Expression Profiling of Ascorbate Peroxidase (APX) and Glutathione Peroxidase (GPX) Genes Under Drought Stress in Sorghum (Sorghum bicolor L.)
(Springer, 2018) Akbudak, M. Aydın; Filiz, Ertuğrul; Vatansever, Recep; Kontbay, Kübra
APX and GPX are two crucial plant antioxidant enzymes. By protein homology search, nine APX and seven GPX members were identified in Sorghum bicolor genome. They were annotated based on chromosomal localizations as SbAPX1-9 and SbGPX1-7. APXs were distributed on six Sorghum chromosomes and encoded polypeptides of 250-474 residues with characteristic "peroxidase" domain, whereas GPXs were on five chromosomes and encoded proteins of 136-232 residues characterized by a "GSHPx" domain. The first about 1-90 amino acid residues in SbAPXs and about 60-70 amino acid residues in SbGPXs from N-terminus corresponded to transit peptides, and formed the main source of sequence variations. On the other hand, APXs/GPXs appeared to be significantly conserved at the amino acid sequence level. Residues in active and/or metal binding sites of these enzymes were also revealed with inference to their Arabidopsis counterparts. The combined Sorghum-Arabidopsis APX and GPX phylogenies allowed inferring functional roles to putative Sorghum sequences at cross-species level. In digital RNA-seq data from Sorghum, APXs within sensitive genotypes were relatively more responsive to drought compared to GPXs. Differentially upregulated APX4 and downregulated GPX2 suggested that their performance was synergistic. SbAPXs/GPXs expression in drought-exposed sorghum roots and leaves were quantified by Real-Time quantitative PCR (RT-qPCR). Drought-exposed plants morphologically demonstrated reductions in stem/root elongation and size, retardation in plant growth, and erected leaves. Expressions of APXs/GPXs were mostly upregulated in aboveground parts of drought-exposed plants, e.g., leaves while they were downregulated in roots. Furthermore, APX1 and APX5 in leaves, and APX8, APX9, GPX5, and GPX6 in roots showed significant changes in expression levels; therefore, their synergetic regulation during drought should be considered.
Genome-wide analysis of iron-regulated transporter 1 (IRT1) genes in plants
(Korean Soc Horticultural Science, 2015) Vatansever, Recep; Filiz, Ertuğrul; Özyiğit, İbrahim İlker
Iron (Fe) is an essential micronutrient required in a number of biological processes in plant species. Fe transporters are a type of broad-range metal transporter and have different families functioning in different compartments. This study focused on iron-regulated transporter 1 (IRT1), which are mainly responsible for Fe uptake from root, in 17 selected plant species with an emphasis on Brachypodium distachyon, Chlamydomonas reinhardtii, Solanum lycopersicum and Populus trichocarpa species. All IRT1 proteins were observed to belong to the ZIP (PF02535) protein family with eight transmembrane (TM) domains, and have a similar molecular weight (33.86-42.72 kDa, except for C. reinhardtii with 65.83 kDa) and amino acid length (324-408 aa, except for C. reinhardtii with 639 aa), with pI values of 5.31-7.16. The sub-cellular localization of these proteins was predicted to be the plasma membrane. Similar exon numbers were also detected with most genes having 2-3, except for C. reinhardtii (5), Physcomitrella patens (5) and Vitis vinifera (4). In a phylogenetic tree, monocot-dicot separation was not observed in main groups but some subgroups included only monocot or dicot proteins. Predicted interaction partner analysis of AtIRT1 (AT2G30080.1) pointed to main interaction partners either directly related with iron transport or that of other metal ion. The results of this study provide a theoretical reference for elucidating the structural and biological role of IRT1 genes/proteins in plant species.
Genome-wide and comparative analysis of bHLH38, bHLH39, bHLH100 and bHLH101 genes in Arabidopsis, tomato, rice, soybean and maize: insights into iron (Fe) homeostasis
(Springer, 2018) Kurt, Fırat; Filiz, Ertuğrul
Iron (Fe) is an essential element for plant life. Its deficiency impedes growth and development and excessive iron can cause the toxic effect via the Fenton reaction. Thus, plants have developed various mechanisms to acquire, distribute and utilize Fe for the maintenance of their iron homeostasis at cellular and systemic levels. A basic helix-loop-helix (bHLH) transcription factor family plays essential roles in many regulatory and development processes in plants. In this study, we aimed to understand the roles of bHLH38, bHLH39, bHLH100 and bHLH101 genes for Fe homeostasis in Arabidopsis, tomato, rice, soybean and maize species by using bioinformatics approaches. The gene/protein sequence analyses of these genes demonstrated that all bHLH proteins comprised helix-loop-helix DNA binding domain (PF00010) with varied exon numbers between 2 and 13. The phylogenetic analysis did not reveal a clear distinction between monocot and dicot plants. A total of 61 cis-elements were found in promotor sequences, including biotic and abiotic stress responsiveness, hormone responsiveness, and tissue specific expressions. The some structural divergences were identified in predicted 3D structures of bHLH proteins with different channels numbers. The co-expression network analysis demonstrated that bHLH39 and bHLH101 played more important roles in Fe regulation in Arabidopsis. The digital expression analysis showed various expression profiles of bHLH genes which were identified in developmental stages, anatomical parts, and perturbations. Particularly, bHLH39 and bHLH101 genes were found to be more active genes in Fe homeostasis. As a result, our findings can contribute to understanding of bHLH38, bHLH39, bHLH100 and bHLH101 genes in Fe homeostasis in plants.
Genome-wide analysis of response to low sulfur (LSU) genes in grass species and expression profiling of model grass species Brachypodium distachyon under S deficiency
(Tubitak Scientific & Technical Research Council Turkey, 2016) Tombuloğlu, Hüseyin; Ablazov, Abdugaffar; Filiz, Ertuğrul
Sulfur (S) affects the plant life cycle and crop yield and has nutritional importance for human and animal diet. Its deficiency is one of the major problems in agriculture. However, the plant-specific LSU (response to Low SUlfur) gene family has not been extensively analyzed in major plant species such as grasses. In this study, we have performed in silico genome-wide analysis of LSU genes in 6 grass species, including Brachypodium distachyon, Sorghum bicolor, Oryza sativa, Zea mays, Triticum aestivum, and Panicum virgatum. All identified LSU genes contained one exon encoding proteins of acidic character with cytoplasmic localization. In silico analysis of cis-elements revealed that sulfur-responsive elements (SURE boxes, SUlfur Response Element, GAGAC motif) were present in all LSU genes. In phylogenetic analysis, dicot and monocot LSU genes were separated. Expression profiles of B. distachyon BdLSU1 and BdLSU2 genes were analyzed by qRT-PCR method. Two Brachypodium LSU genes demonstrated different expression patterns when subjected to 48 h of S-depletion treatment. In roots, the BdLSU2 gene was upregulated, while BdLSU1 was downregulated. In leaves, expression levels were decreased for both genes. Analysis of the BdLSU expression under drought, cold, salt, and heat stresses was carried out based on the Brachypodium stress atlas. Results showed that BdLSU genes are not specific to S limitation; indeed, they may be involved in different stress conditions by cooperating with their interacting partner proteins. The results of this study could significantly contribute to the understanding of LSU genes in plants, particularly in grass species. These results may also support plant molecular studies by aiding the understanding of the sulfur assimilation pathway.
Genome-wide analysis of IQ67 domain (IQD) gene families in Brachypodium distachyon
(Southern Cross Publ, 2013) Filiz, Ertuğrul; Tombuloğlu, Hüseyin; Özyiğit, İbrahim İlker
In plants, Ca2+ concentration is important for the regulation of developmental processes and responses against biotic and abiotic stress factors. The eukaryotic Ca2+ binding protein calmodulin (CaM: CALcium MODULating protelN) was found in Arabidopsis which contains a characteristic plant-specific IQ67 (Ile, Glu) domain (IQD). In this study, a genome wide analysis was performed in Bracyhpodium distachyon to identify IQD genes. Using several bioinformatics tools, we determined 23 BdIQD genes which were distributed on all chromosomes and the highest gene number was detected on chromosome 2 including 12 IQD genes. 22 of the predicted proteins were considered to be basic proteins. Gene duplication analysis revealed that 8 of 23 BdIQD genes were involved in duplication event, either segmental or tandem. Phylogenetic analysis showed that two main groups were observed in joined tree with rice and Arabidopsis. Especially, monocot species (Brachypodium and rice) were grouped together with the highest bootstrap value (100%), whereas monocot and dicot species (Arabidopsis) were clustered with lower bootstrap values. Digital expression profile analysis indicated that the most of the BdIQD genes were expressed in leaves (8 genes) and flowers (6 genes), respectively. In conclusion, this comparative genomics analysis contributes to understanding IQD genes in grass species.
Genome-wide analyses of ATP sulfurylase (ATPS) genes in higher plants and expression profiles in sorghum (Sorghum bicolor) under cadmium and salinity stresses
(Academic Press Inc Elsevier Science, 2019) Akbudak, M. Aydın; Filiz, Ertuğrul
ATP sulfurylase (ATPS, EC: 2.7.7.4) is a crucial enzyme for sulfate assimilation pathway in both plastids and cytosol in plants. In this study, genome-wide and comparative analyses of ATPSs in 11 higher plant species, including sequence and structural analyses have been performed. Expression of ATPS genes in sorghum under cadmium (Cd) and salinity (NaCl) stresses were also investigated to provide a model experimental data for the regulation of ATPS genes under stress conditions. Thirty-one ATPS genes from 11 plant species were found. It showed that ATPSs from different species have high sequence divergences, which cause structural differences among them. Phylogenetic analysis has shown that there are two major types of ATPSs evolved in dicots while monocots were evolved to have one type of ATPs. Finally, expression analysis of ATPS genes revealed tissue and stress dependent expression pattern, which indicates expressions of ATPS genes are tightly regulated.
GENETIC DIVERSITY AND PHYLOGENETIC ANALYSES OF TURKISH RICE VARIETIES REVEALED BY ISSR MARKERS AND CHLOROPLAST trnL-F REGION
(Parlar Scientific Publications (P S P), 2018) Filiz, Ertuğrul; Uras, Mehmet Emin; Özyiğit, İbrahim İlker; Şen, Uğur; Güngör, Hüseyin
A set of 17 Turkish rice (Oryza sativa L.) varieties (TRVs) were characterized using inter simple sequence repeat (ISSR) markers to study genetic diversity. Also, the sequences of trnL((UAA))-F-(GAA) intergenic spacer (IGS) regions were used to evaluate the phylogenetic relationships of TRVs. According to ISSR data, the observed number of alleles (Na), effective number of alleles (Ne), Nei's gene diversity (h), Shannon's information index (I), and overall polymorphism were found as 1.62, 1.38, 0.22, 0.32, and 61.7%, respectively. The genetic distance values were identified between 1.732and 4.583, and replicon size varied from 200 bp to 1600 bp. The ISSR-UPGMA (unweighted pair group method with arithmetic mean) similarity tree and PCA (principal component analysis) exhibited different cluster topologies based on pedigree. All trnL-F regions were found as 306 bp in length, and GC content was found between 34.31% and 34.97%. The nucleotide diversities were found as pi: 0.00954 and theta: 0.03595, while Tajima's D was found as -0.382. The phylogenetic analyses revealed that trnL-F sequences are effective molecular tools in resolving phylogenetic relationships. Consequently, our findings could be useful in planning future Turkish rice breeding strategies for general rice germplasm improvement.
FIT (Fer-like iron deficiency-induced transcription factor) in plant iron homeostasis: genome-wide identification and bioinformatics analyses
(Springer India, 2019) Filiz, Ertuğrul; Kurt, Fırat
FIT (Fer-like iron deficiency-induced transcription factor) is one of the key regulators in uptake of iron (Fe) for plants. In this study, FIT genes from 10 plant species were identified at genome-wide scale and analyzed by computational tools. Our analyses showed that subcellular localizations of all FITs were in nucleus and FITs were generally acidic proteins. While a clear monocot-dicot divergence was observed, exon numbers were found as three and four for monocots and dicots, respectively. Arg and Leu were established as most repetitive amino acid residues in conserved regions of all FITs. All FITs had different shape and pocket numbers along with different secondary and tertiary structures despite they contained same domain structure as PF00010 (helix-loop-helix DNA-binding domain). We observed that FIT is an important target of several biological processes and a component of various metabolic pathways regulating root development and stress responses on exposure to various environmental stressors. Moreover, FITs seem to be located in heterochromatic area of chromosome and its transcription may also be upregulated on the exposure of stressors. The FITs were established to interact with Pi and Cu uptake machinery, other than iron acquisition, under Pi and Cu deficiency. Consequently, FITs can be proposed to take part in different and specific metabolic pathways together with Fe acquisition. The miRNA analyses showed that miRNAs targeting FITs take part in abiotic and biotic stress metabolism together with Pi uptake mechanism. Lastly, involvement of FIT in abiotic stress response was stimulated by phytohormones such as ABA and ethylene.