Browsing by Author "Ciftci, Yelda Ozden"

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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
Determination of Physiological, Biochemical and Molecular Interactions Between Fraser's Photinia (Photinia x fraseri Dress.) and Its Endophytic Bacterium PGB_invit
(2022) Turkolmez, Nil; Karakaya, Merve; Ekinci, Muhammed Hamit; Lucas, Stuart James; Akkaya, Ozlem; Seker, Mine Gul; Kayihan, Ceyhun; Ciftci, Yelda Ozden
An endophytic beneficial bacterium was isolated and characterized from in vitro grown microshoots of Fraser's Photinia (Photinia x fraseri Dress.) in our previous studies. This bacterium, which is nominated as PGB_invit and determined as a member of Pseudorhodoplanes sp., has ability to fix nitrogen and produce plant growth promoting regulators such as indole acetic acid and gibberellic acid. Due to its beneficial traits, this specific bacterium promotes in vitro proliferation of Fraser's Photinia microshoots and enables microshoots to be conserved at 25 +/- 2oC for up to 16 months without requiring periodic subculture. Thus, the aim of the study is to identify physiological, biochemical and molecular influences of this bacterium together with determination of its localization in plant tissues. Our results showed that the optimum inoculum concentration of PGB_invit is 10(6) cfu ml(- 1) and the optimum incubation period is 60 days. Also, this study provides clear microscopic evidence of the endopyhtic bacterial colonization of GFP-labeled bacteria detected by confocal microscopy in Fraser's Photinia. Proline content was significantly enhanced in response to bacterial treatment whereas cellular H2O2 content was decreased. An increase in catalase activity was also detected, indicating that the results were consistent with the decrease in H2O2 content. Moreover, RNA sequencing (RNA-Seq) was also used to assess gene expression patterns and differential expression of five genes (predicted "MID1-Complementing Activity 1", Ubiquitin-conjugating enzyme E2, predicted "E3 ubiquitin-protein ligase RHA1B-like", 4-coumarate-CoA ligase-like 9, and methionine aminopeptidase 2B-like) between active and inactive form of the bacterium was confirmed by qRT-PCR. Among them, ubiquitin-conjugating enzyme E2 and predicted "E3 ubiquitin-protein ligase RHA1B-like genes which play important roles in plant immunity and stress were down-regulated in plant samples inoculated with bacteria which may demostrate that PGB_invit does not evoke plant immune system and has a positive effect on reducing stress on Fraser's Photinia. Key message PGB_invit (Pseudorhodoplanes sp.) has a positive impact on plants growth and development with several mechanisms. Besides its shown that PGB_invit is not act as a stress factor, as it does not cause a severe oxidative stress and thus can be used as a biofertilizer.
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-4515-2016
Earlier 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.
Regulation of boron toxicity responses via glutathione-dependent detoxification pathways at biochemical and molecular levels in Arabidopsis thaliana
(2019) Kayihan, Doga Selin; Kayihan, Ceyhun; Ciftci, Yelda Ozden; 0000-0002-9799-3648; Y-6244-2018
The fine-tuned regulation of the Halliwell-Asada cycle (ascorbate-glutathione pathway) in Arabidopsis thaliana under boron (B) toxicity was shown in our previous report. In this study, we investigated the expression levels of some members of the glutathione S-transferase (GST) superfamily, such as phi (GSTF2, GSTF6, GSTF7, and GSTF8), tau (GSTU19), and zeta (GSTZ1) classes in Arabidopsis thaliana that were exposed to 1 mM boric acid (1B) and 3 mM boric acid (3B). Additionally, the expression levels of genes for glutathione (GSH) and phytochelatin biosynthesis as well as miR169 and miR156 were evaluated in Arabidopsis thaliana exposed to 1B and 3B. Moreover, changes in the levels of total GST activity; GSH; and total, protein-bound, and nonprotein thiols were spectrophotometrically determined. GSH levels and nonprotein thiol content did not change significantly following both B-toxicity conditions. Expression levels of GSH1 and GSH2 stayed stable under 1B toxicity; however, GSH1 expression increased significantly under 3B conditions in Arabidopsis thaliana. The expression levels of four genes from phi class members of GST were not dramatically changed under B-toxicity conditions. However, the transcript levels of miR169, ATGSTU19, and ATGSTZ1 were significantly increased after 1B and 3B exposure. These GST genes may have a role in the dramatic increase of total GST activity under toxic B. To the best of our knowledge, this is the first report displaying an integrative view of high-B-induced regulation of GSH-dependent enzymatic machinery at different biological organization levels in Arabidopsis thaliana.
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-4515-2016
Key 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.
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-4515-2016
Plants 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.