Fen Edebiyat Fakültesi / Faculty of Letters and Science
Permanent URI for this collectionhttps://hdl.handle.net/11727/1396
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Item Role Of Sulfur Metabolism In Acquiring Of Boron Tolerance In Arabidopsis Thaliana(TURKISH JOURNAL OF BOTANY, 2024) Yirmibes, Seda; Kayihan, Ceyhun; Cicek, Nuran; Ekmekci, YaseminThe purpose of this study was to assess whether sulfate treatment (pre- and combined) caused changes in the tolerance against boron (B) toxicity in Arabidopsis thaliana at the physiological, biochemical, and molecular levels. Germinated plants were grown in a controlled climate chamber (22 +/- 1 degrees C temperature, 16/8 s photoperiod, 200 mu mol m -2 s -1 light intensity and 50%-60% humidity) for 12 days. The sulfate pretreatment groups (PS-3B and PS-5B) were then transferred to nutrient medium containing Mg2SO4- type sulfate for 3 days. Afterward, they were transferred to petri dishes containing different boron concentrations (3 and 5 mM H3BO3), along with the nonpretreatment and combined (S+3B and S+5B) treatment groups, and exposed to boron toxicity for 10 days. The leaf area, plant biomass, and total chlorophyll content decreased significantly depending on the accumulation of B. Toxic levels of B adversely affected the structure and functionality of the photosynthetic apparatus. Changes were seen in the specific and phenomenological energy fluxes, quantum yields, and efficiency of the photosystem II (PSII) donor and acceptor sides. These changes led to decreases in the photosynthetic performance of the plants. Although B toxicity adversely affected the integrity of the membrane and the amount of photosynthetic pigment in the antenna and reaction centers (RCs), this effect was not at a level that completely blocked the functionality of the photosystems, and this negative effect was alleviated with the sulfate treatment. The increases in the antioxidant enzyme activities (especially peroxidase) and phenolic compounds with the sulfate treatment may have provided tolerance against toxicity and oxidative damage by regulating the defense systems. Moreover, B toxicity affected the relative expression of genes related to sulfate uptake, transport, and sulfur metabolism. In fact, the genes of sulfate transporters ( SULTR ); SULTR3;1, SULTR3;3, and SULTR3;5 were more expressed in PS-B group. The glutamate cysteine ligase (GSH1) and glutathione synthetase 1 (GSH2) relative gene expressions were increased in the treatment groups, indicating induced glutathione metabolism. In conclusion, plants may have acquired tolerance against B toxicity by assimilating sulfate, especially that provided by sulfate pretreatment.Item Advancements in QTL Mapping and GWAS Application in Plant Improvement(TURKISH JOURNAL OF BOTANY, 2024) Altaf, Muhammad Tanveer; Tatar, Muhammed; Ali, Amjad; Liaqat, Waqas; Mortazvi, Parnaz; Kayihan, Ceyhun; Olmez, Fatih; Nadeem, Muhammad Azhar; Javed, Jazib; Gou, Jin-Ying; Wang, Meng-Lu; Umar, Ummad Ud Din; Dasgan, Hayriye Yildiz; Kurt, Cemal; Yildiz, Mehtap; Mansoor, Sheikh; Dababat, Abdelfattah A.; Celiktas, Nafiz; Baloch, Faheem ShehzadIn modern plant breeding, molecular markers have become indispensable tools, allowing the precise identification of genetic loci linked to key agronomic traits. These markers provide critical insight into the genetic architecture of crops, accelerating the selection of desirable traits for sustainable agriculture. This review focuses on the advancements in quantitative trait locus (QTL) mapping and genome-wide association studies (GWASs), highlighting their effective roles in identifying complex traits such as stress tolerance, yield, disease resistance, and nutrient efficiency. QTL mapping identifies the significant genetic regions linked to desired traits, while GWASs enhance precision using larger populations. The integration of high-throughput phenotyping has further improved the efficiency and accuracyof QTL research and GWASs, enabling precise trait analysis across diverse conditions. Additionally, next-generation sequencing, clustered regularly interspaced short palindromic repeats (CRISPR) technology, and transcriptomics have transformed these methods, offering profound insights into gene function and regulation. Single-cell RNA sequencing further enhances our understanding of plant responses at the cellular level, especially under environmental stress. Despite this progress, however, challenges persist in optimizing methods, refining training populations, and integrating these tools into breeding programs. Future studies must aim to enhance genetic prediction models, incorporate advanced molecular technologies, and refine functional markers to tackle the challenges of sustainable agriculture.Item General guidelines for CRISPR/Cas-based genome editing in plants(2022) Aksoy, Emre; Yildirim, Kubilay; Kavas, Musa; Kayihan, Ceyhun; Yerlikaya, Bayram Ali; Calik, Irmak; Sevgen, Ilkay; Demirel, Ufuk; 36107373CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) technology is a versatile genome editing tool that has been used to improve agriculturally important plant traits. Due to its precision, CRISPR/Cas9 is more effective than either conventional plant breeding methods or standard genetic engineering approaches for the rapid development of new varieties resilient to climate change. In addition to knowledge in tissue culture-based plant transformation, effective gene-specific single guide RNA (sgRNA) design, prediction of its off-target effect and utilization of vectors, promoters, Cas proteins and terminators is required for CRISPR/Cas9. Various bioinformatics tools are available for the best sgRNA design and screening of the off-targets. Various tools are used in the delivery of CRISPR/Cas components into cells and the genome. Moreover, some recent studies proved the simultaneous silencing of different paralogs in the same family or several genes working in the same pathway by using multiple-target sgRNA designs. This review summarizes the type of promoters, Cas proteins, recognition sequences, and terminators available for the development of knock-out and overexpression plant lines. It also provides a general guideline for the development of genome-edited plants from the design of sgRNAs to the selection of non-transgenic genome-edited T-2 generation.Item The involvement of the induction of anthocyanin biosynthesis and transport in toxic boron responsive regulation in Arabidopsis thaliana(2021) Kayihan, Ceyhun; 0000-0003-1684-4147; AAW-8352-2021Recently, boron (B) has been found to form a complex with anthocyanin, which could be evidence for the B tolerance mechanisms that reduce free B in the leaf tissues of plants. However, the molecular mechanism of anthocyanin biosynthesis and transport has not been satisfactorily elucidated in plants exposed to toxic B. Therefore, the changes in expression levels of some of the phenylpropanoid pathway genes, early and late flavonoid biosynthetic genes, and transcription factors related to anthocyanin biosynthesis and transport were determined in Arabidopsis thaliana under B toxicity. Accordingly, 1 mM boric acid treatment did not cause any significant change in the expression levels of anthocyanin biosynthesis genes such as PAL1, PAL2, C4H, 4CL3, CHS, ANS and transcription factors such as MYBD and TT8 in Arabidopsis thaliana. However, 3 mM boric acid treatment induced the expression levels of anthocyanin biosynthesis genes such as C4H, 4CL3 and transcription factors including MYB75, MYB114 and anthocyanin transporter genes such as TT13 and TT19. In addition to B-anthocyanin, B-anthocyanins conjugated with glutathione (GSH) complexes can also participate in the internal B tolerance mechanism in plants. Therefore, the direct role of the B-anthocyanin complex without GSH conjugation needs to be determined. For this purpose, anthocyanin accumulation was determined in slim1 mutant Arabidopsis thaliana exposed to excess B because SLIM1 transcription factor activates sulfate acquisition for S assimilation, which generates cysteine, the substrate for GSH. Accordingly, it was gradually increased through increasing toxic B levels in both wild type (WT) and slim1 mutant plants. slim1 mutant had more anthocyanin accumulation than WT under control and all toxic B conditions. In conclusion, increases in expression levels of MYB75, MYB114, TT13, TT19 and in anthocyanin level in slim1 mutant in response to increased toxic B levels showed that anthocyanins may play a primary role in B tolerance in plants.Item Identification and expression profiling of toxic boron-responsive microRNAs and their targets in sensitive and tolerant wheat cultivars(2021) Kayihan, Doga Selin; Aksoy, Emre; Kayihan, Ceyhun; 0000-0003-1684-4147; AAW-8352-2021Post transcriptional gene regulation in wheat cultivars caused by boron (B) toxicity has not been reported to date. In this study, two wheat cultivars Bolal-2973 (B-tolerant) and Atay-85 (B-sensitive) were compared with regard to the transcriptional regulation of miR319, miR172 and miR398 and their plausible target genes in order to address differences in their performances under high B levels. The expression levels of Cu/ZnSOD gene were found to be greater in Atay exposed to toxic B compared to Bolal, as verified by stable expression level of miR398. In wheat cultivars, both toxic B concentrations might cause an induction of leaf senescence mechanism due to stable level of JA and ethylene-related miRNAs, miR172 and miR319. miR172 targeting transcription factor TOE1 was only induced under B toxicity in sensitive cultivar Atay. However, MY133 as target of miR319 was significantly upregulated under toxic B in both cultivars. Also, computational prediction of these miRNA targets in wheat was performed and their orthologs in Arabidopsis thaliana were determined. Functional protein association networks of proteins encoded by miRNA targets and gene ontology enrichment analyses of these genes were identified. We identified new sets of genes that are targets of miR172, miR319 and miR398 in T. aestivum. In addition, miR172, miR319 and miR398 are responsive to different nutrient deficiencies or toxicities such as Fe, P, B, S and Cu, suggesting crosstalk between the post-transcriptional regulatory mechanisms involving miRNAs in plants.Item Higher nisin yield is reached with glutathione and pyruvate compared with heme in Lactococcus lactis N8(2020) Ersoy, Zeynep Girgin; Kayihan, Ceyhun; Tunca, Sedef; 0000-0003-1684-4147; 31898248; Q-4515-2016There are different studies that aim to enhance the production of nisin by Lactococcus lactis since its chemical synthesis is not possible. In this study, glutathione (GSH) and pyruvate, which are known to reduce the oxidative stress of cells, have been shown to trigger the production of nisin at both transcriptional and translational levels in L. lactis cells grown under aerobic condition. Presence of GSH and pyruvate caused more nisin yield than the heme-supplemented medium. Moreover, the expression of genes that encode stress-related enzymes were apparently upregulated in the presence of GSH and pyruvate. It can be concluded that GSH and pyruvate contribute to the defense system of L. lactis cells and so that higher biomass was obtained which in turn enhance nisin production. Antioxidant effect of GSH and pyruvate was known; however, their stimulating effect on nisin production was shown for the first time in this study.Item The role of microRNAs in recovery rates of Arabidopsis thaliana after short term cryo-storage(2020) Ekinci, Muhammad Hamit; Kayihan, Doga Selin; Kayihan, Ceyhun; Ciftci, Yelda Ozden; 0000-0003-1684-4147; Q-4515-2016Key message The alteration of expression levels of cold- and oxidative stress-induced genes related-miRNAs play a crucial role in development of successful cryopreservation protocols. Cryopreservation is a safe and cost-effective long-term storage technique which helps to conserve plant germplasm in liquid nitrogen (LN). However, up to now, the molecular regulatory mechanisms that effect survival after cryopreservation have not been satisfactorily elucidated in plants. Thus, the aim of the study concerned to reveal out microRNA (miRNA)-based post-transcriptional regulations during different stages of cryopreservation in 48-h and 72-h in vitro germinated Arabidopsis thaliana since miRNAs not only regulate gene expression in developmental process of plants, but also control transcription in stress conditions by post-transcriptional degradation. Among the screened 10 miRNAs and their selected target genes, differential expression levels were detected in two tested germination time according to exposure of cryopreservation stages, as 6 miRNAs (miR393, miR397, miR398, miR159, miR169 and miR172) showed a mixed pattern in 48-h germinated seedlings while 6 miRNAs (miR397, miR398, miR159, miR169, miR172 and miR408) were significantly down-regulated in OD (Osmoprotection-Dehydration) and LD (Liquid nitrogen-Dilution) samples in comparison to control in 72-h germinated ones. The most striking expression change was obtained in miR393 as it was up-regulated 15-fold in LN treated 48-h seedlings while relatively lower amount induction (twofold) was recorded in cryopreserved 72-h seedlings. The concominant down-regulation of its target TIR1 and HOS1 expression and up-regulation of CBF1 and CBF3 and their downstream genes (COR15 and COR47) were also observed in cryopreserved 48-h germinated seedlings. Thus, the alteration of expression levels of cold-induced genes related-miRNAs plays a crucial role for successful cryopreservation.Item Transgenic tobacco plants overexpressing a cold-adaptive nitroreductase gene exhibited enhanced 2,4-dinitrotoluene detoxification rate at low temperature(2020) Kayihan, Doga Selin; Kayihan, Ceyhun; Ciftci, Yelda Ozden; 0000-0003-1684-4147; 32643388; Q-4515-2016Plants encounter many environmental factors such as low and high temperatures during phytoremediation processes. In this study, our aim was to produce the transgenic tobacco plants by using a newly characterized bacterial nitroreductase,Ntr, which was active at a broad range temperature in order to detoxify 2,4-dinitrotoluene (2,4-DNT) at lower temperature. The presence ofNtrand its heterologous expression was verified in T1 transgenic plants and their growing ability were determined under toxic amount of 2,4-DNT (35 mu M). Fresh weight and dry weight of transgenic plants were significantly higher than wild type (WT) under toxic 2,4-DNT at 22 degrees C, indicating higher growth capacity of the transgenics. Transgenic plants also showed a higher tolerance than WT when exposed to 2,4-DNT at 15 degrees C. Moreover, transformation rate of 2,4-DNT was gradually decreased through decreasing temperatures in WT media, however, it was increased through decreasing temperatures in transgenic plant TR3-25 media and it had the highest transformation rate (54%) of 2,4-DNT at 4 degrees C. Correlatively, 2,4-DNT treatment at 4 degrees C led to a significant decrease in H(2)O(2)level in transgenic plants. Thus, transgenic plants overexpressing nitroreductase might have an important advantage for phytoremediation of toxic nitroaromatic compounds in field applications at low temperatures.Item Moderate level of toxic boron causes differential regulation of microRNAs related to jasmonate and ethylene metabolisms in Arabidopsis thaliana(2019) Kayihan, Doga Selin; Kayihan, Ceyhun; Ciftci, Yelda Ozden; 0000-0003-1684-4147; Q-4515-2016Earlier our colleagues detected that the genes related to jasmonate (JA), ethylene, and cell wall modification were significantly regulated under boron (B) toxicity in wheat. Determination of regulation mechanisms of these novel genes under B toxicity is very important in Arabidopsis thaliana as a model plant. As key regulators, the microRNAs (miRNAs) regulate gene expression at the posttranscriptional level and respond to numerous abiotic stresses in plants. In this study, expression levels of miRNAs such as miR159, miR172, miR319, and miR394 targeting JA and ethylene-related transcription factors and also miR397 targeting laccase were determined in Arabidopsis thaliana under toxic B conditions. Stem-loop quantitative reverse transcription polymerase chain reaction was used to amplify mature miRNAs for expression analyses. Expression levels of miRNAs targeting transcription factors related to JA and ethylene metabolisms were induced remarkably in moderate B toxicity (condition 1B) but not in severe B toxicity (condition 3B). Most remarkable regulations were obtained in miR172 and miR319 in Arabidopsis thaliana. Expression level of miR397 did not remarkably change under B toxicity, indicating a lack of posttranscriptional regulation of laccase related to cell wall modification. Moreover, miRNAs targeting transcription factors related to JA and ethylene metabolisms might be oxidative stress-adaptive responses of Arabidopsis to B toxicity.Item Biotization of In Vitro Plants with Endophytic Beneficial Bacterium (PGP_invit) to Understand Plant-bacteria Interaction(2019) Turkolmez, Nil; Albayrak, Merve; Batool, Maria; Kayihan, Doga Selin; Ekinci, Hamit; Akkaya, Ozlem; Seker, Mine Gul; Kayihan, Ceyhun; Aydinoglu, Fatma; Ciftci, Yelda Ozden