Prediction of protein targets of kinetin using in silico and in vitro methods: a case study on spinach seed germination mechanism

Kinetin, a cytokinin which promotes seed germination by inhibiting the action of abscisic acid, is an important molecule known to trigger various molecular mechanisms by interacting with an array of proteins shown from experimental observations in various model organisms. We report here the prediction of most probable protein targets of kinetin from spinach proteome using in silico approaches. Inverse docking and ligand-based similarity search was performed using kinetin as molecule. The former method prioritized six spinach proteins, whereas the latter method provided a list of protein targets retrieved from several model organisms. The most probable protein targets were selected by comparing the rank list of docking and ligand similarity methods. Both of these methods prioritized chitinase as the most probable protein target (ΔG_pred = 5.064 kcal/mol) supported by the experimental structure of yeast chitinase 1 complex with kinetin (PDB: 2UY5) and Gliocladium roseum chitinase complex with 3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione (caffeine; 3G6M) which bears a 3D similarity of 0.43 with kinetin. An in vitro study to evaluate the effect of kinetin on spinach seed germination indicated that a very low concentration of kinetin (0.5 mg/l) did not show a significant effect compared to control in inducing seed germination process. Further, higher levels of kinetin (>0.5 mg/l) constituted an antagonist effect on spinach seed germination. It is anticipated that kinetin may have a molecular interaction with prioritized protein targets synthesized during the seed germination process and reduces growth. Thus, it appears that kinetin may not be a suitable hormone for enhancing spinach seed germination in vitro.

Electronic supplementary material

The online version of this article (doi:10.1007/s12154-015-0135-3) contains supplementary material, which is available to authorized users.     

Anthocyanin production in a callus line of <Emphasis Type="Italic">Panax sikkimensis</Emphasis> Ban

A root-derived callus line of Panax sikkimensis that stably accumulates anthocyanins was established by small cell aggregate selection method. The selected line showed a growth index of 221.36 and an anthocyanin content of 2.76 mg/g fw (7.076% dw) in 50–60 d of growth on a modified MS medium containing 4.5 μM 2,4-dichlorophenoxy acetic acid and 1.2 μM kinetin under 16-h light and 8-h dark photoperiodic conditions. Incubation under continuous light increased the growth index to 435.57 but led to a marginal dilution of anthocyanin content to 2.192 mg/g fw (6.928% dw). The purple-red pigment had absorption maximum at 528 nm. The selected callus line has shown sustained growth and productivity for more than 6 yr now. Interestingly, pigment accumulation in the selected line did not hinder the ginsenoside production in the callus tissue (0.9–1.2% fw).     

New Insights into the Chemical Composition,Pro-Inflammatory Cytokine Inhibition Profile of Davana (Artemisia pallens Wall. ex DC.) Essential Oil and cis-Davanone in Primary Macrophage Cells

Artemisia pallens Wall. ex DC., popularly known as davana, has gained considerable attention because of its unique fragrance, high economic value, and pharmacological properties. The compositional complexity of davana essential oil (DO) has been a challenge for quality control. In this study, the chemical profile of DO was developed using polarity-based fractionation and a combination of gas chromatographic (GC-FID), hyphenated chromatographic (GC/MS), and spectroscopic (Fourier-Transform Infra-Red, 1D, 2D-Nuclear Magnetic Resonance) techniques. The analysis led to the identification of ninety-nine compounds. Major components of the DO were cis-davanone (D3, 53.0 %), bicyclogermacrene (6.9 %), trans-ethyl cinnamate (4.9 %), davana ether isomer (3.4 %), spathulenol (2.8 %), cis-hydroxy davanone (2.4 %), and trans-davanone (2.1 %). The study led to identifying several co-eluting novel minor components, which could help determine the authenticity of DO. The rigorous column-chromatography led to the isolation of five compounds. Among these, bicyclogermacrene, trans-ethyl cinnamate, and spathulenol were isolated and characterized by spectroscopic methods for the first time from DO. Pharmacological profile revealed that the treatment of DO and D3 inhibited the production of pro-inflammatory cytokines (TNF-α, IL-6) induced by lipopolysaccharide (LPS) in primary macrophages without any cytotoxic effect after administration of their effective concentrations. The result of this study indicates the suitability of DO and D3 for further investigation for the treatment of chronic skin inflammatory conditions.     

Calcium mediated nitric oxide responses: Acquisition of nickel stress tolerance in cyanobacterium Nostoc muscorum ATCC 27893

Calcium (Ca²⁺) and nitric oxide (NO) are potentially active and multitasking signaling molecules which are known to regulate abiotic stresses in plants, but their interactive role in the acquisition of metal stress tolerance in cyanobacteria remains elusive. In current study the signaling role of Ca²⁺ (800 μM) and NO (10 μM SNP) on key physiological and biochemical attributes of the agriculturally and economically important cyanobacterium Nostoc muscorum ATCC 27893 subjected to Ni stress (2 μM) was examined. Results revealed that Ni at elevated level caused severe damages to the test organism but exogenous supplementation of Ca²⁺ and NO efficiently mitigated its toxic effects and up-regulated the growth, pigment contents, rate of photosynthesis (whole cell oxygen evolution and Chl a fluorescence indices: Kinetic traits: ΦP_0, Ψ₀, ΦE₀ and PI_ABS, along with Fv/F₀), nitrogen metabolism (NO₃￣ and NO₂￣ uptake, nitrate:NR and NiR; and ammonia:GS and GOGAT; assimilating enzymes), and boosted the enzymatic (SOD, POD, CAT and GST) along with non-enzymatic (proline, cysteine and NP-SH) antioxidants. Whereas the increased values of energy flux traits: (ABS/RC, TR₀/RC, DI₀/RC and ET₀/RC) along with F₀/Fv, rate of respiration, oxidative stress biomarkers (SOR, H₂O₂ and MDA), and activity of GDH enzyme exhibited lowering trends with application of Ca²⁺ and NO. Further, addition of EGTA (Ca²⁺ scavenger) and PTIO (NO scavenger) reversed the positive impacts of Ca²⁺ and NO and worsened the toxicity of Ni on test cyanobacterium, but the damages were more pronounced under PTIO application that demonstrated Ca²⁺ mediated signaling role of NO in Ni toxicity alleviation.