Exploring the specialized metabolome of the plant pathogen Streptomyces sp. 11-1-2.

Streptomyces bacteria are notable for producing chemically diverse specialized metabolites that exhibit various bioactivities and mediate interactions with different organisms. Streptomyces sp. 11-1-2 is a plant pathogen that produces nigericin and geldanamycin, both of which display toxic effects against various plants. Here, the 'One Strain Many Compounds' approach was used to characterize the metabolic potential of Streptomyces sp. 11-1-2. Organic extracts were prepared from 11-1-2 cultures grown on six different agar media, and the extracts were tested in antimicrobial and plant bioassays and were subjected to untargeted metabolomics and molecular networking. Most extracts displayed strong bioactivity against Gram-positive bacteria and yeast, and they exhibited phytotoxic activity against potato tuber tissue and radish seedlings. Several known specialized metabolites, including musacin D, galbonolide B, guanidylfungin A, meridamycins and elaiophylin, were predicted to be present in the extracts along with closely related compounds with unknown structure and bioactivity. Targeted detection confirmed the presence of elaiophylin in the extracts, and bioassays using pure elaiophylin revealed that it enhances the phytotoxic effects of geldanamycin and nigericin on potato tuber tissue. Overall, this study reveals novel insights into the specialized metabolites that may mediate interactions between Streptomyces sp. 11-1-2 and other bacteria and eukaryotic organisms.

Risk assessment of trace elements in vegetables grown in river Yamuna floodplain in Delhi.

Urban agriculture is common in fertile river floodplains of many developing countries. However, there is a risk of contamination in highly polluted regions. This study quantifies health risks associated with the consumption of vegetables grown in the floodplain of the urban river 'Yamuna' in the highly polluted yet data-scarce megacity Delhi, India. Six trace elements are analyzed in five kinds of vegetable samples. Soil samples from the cultivation area are also analyzed for elemental contamination. Ni, Mn, and Co are observed to be higher in leafy vegetables than others. Fruit and inflorescence vegetables are found to have higher concentrations of Cr, Pb, and Zn as compared to root vegetables. Transfer Factor indicates that Cr and Co have the highest and least mobility, respectively. Vegetable Pollution Index indicates that contamination levels follow as Cr > Ni > Pb > Zn. Higher Metal Pollution Index of leafy and inflorescence vegetables than root and fruit vegetables indicate that atmospheric deposition is the predominant source. Principal Component Analysis indicates that Pb and Cr have similar sources and patterns in accumulation. Among the analyzed vegetables, radish may pose a non-carcinogenic risk to the age group of 1-5 year. Carcinogenic risk is found to be potentially high due to Ni and Cr accumulation. Consumption of leafy vegetables was found to have relatively less risk than other vegetables due to lower Cr accumulation. Remediation of Cr and Ni in floodplain soil and regular monitoring of elemental contamination is a priority.

Comparative analysis of isothiocyanates in eight cruciferous vegetables and evaluation of the hepatoprotective effects of 4-(methylsulfinyl)-3-butenyl isothiocyanate (sulforaphene) from daikon radish (Raphanus sativus L.) sprouts.

The contributions of cruciferous vegetables to human health are widely recognised, particularly at the molecular level, where their isothiocyanates play a significant role. However, compared to the well-studied isothiocyanate 4-(methylsulfinyl)butyl isothiocyanate (sulforaphane) produced from broccoli sprouts, less is known about the pharmacological effects of other isothiocyanates and the stage of vegetables preferable to obtain their benefits. We analysed the quantity and quality of isothiocyanates produced in both the sprouts and mature stages of eight cruciferous vegetables using gas chromatography-mass spectrometry (GC-MS). Additionally, we investigated the hepatoprotective effects of isothiocyanates in a mouse model of acute hepatitis induced by carbon tetrachloride (CCl4). Furthermore, we explored the detoxification enzyme-inducing activities of crude sprout extracts in normal rats. Among the eight cruciferous vegetables, daikon radish (Raphanus sativus L.) sprouts produced the highest amount of isothiocyanates, with 4-(methylsulfinyl)-3-butenyl isothiocyanate (sulforaphene) being the dominant compound. The amount of sulforaphene in daikon radish sprouts was approximately 30 times that of sulforaphane in broccoli sprouts. Sulforaphene demonstrated hepatoprotective effects similar to sulforaphane in ameliorating CCl4-induced hepatic injury in mice. A crude extract of 3-day-old daikon radish sprouts upregulated the detoxifying enzyme glutathione S-transferase (GST) in the liver, whereas the crude extract of broccoli sprouts showed limited upregulation. This study highlights that daikon radish sprouts and sulforaphene have the potential to serve as functional food materials with hepatoprotective effects. Furthermore, daikon radish sprouts may exhibit more potent hepatoprotective effects compared to broccoli sprouts.

Biological and chemical characterization in relation to the yield of radish (Raphanus sativus L.) nourished with humus from plant residues.

The increase in prices of fertilizers, energy and other materials necessary for the industry triggered a global economic crisis. Reason that was investigated on the biological and chemical characteristics in relation to the yield of radish nourished with humus from plant residue. The objective was to determine the appropriate dose of humus to obtain greater yield and its relationship with the chemical and biological characteristics of the radish. It is based on applied methodology with an experimental approach; Therefore, the Completely Random Block Design model was used, which consisted of 3 blocks and 5 treatments that were T1 with 0, T2 with 4, T3 with 6, T4 with 8 and T5 with 10 t/ha of humus and They applied 15 days after sowing. The physical characteristics of the radish were evaluated and processed using analysis of variance and Duncan. Concentration of elements in leaves and stomatal density were also analyzed. It was determined that T5 stood out in total plant length with 28.95 cm, plant weight with 76.87 g, equatorial diameter with 4,404 cm and commercial yield with 20,296 t/ha. Nitrogen consumption in relation to yield with 247.44 kg/ha. Stomatal density 459 stomata/mm2 and profitability with 150% and nutrient concentration in leaves highlighted T4 with N, K, Ca, Mg, Mo and Zn. It concludes that T5 stood out with 20,296 t/ha, which differed by 26.04% in relation to the control (T1) with 15,011 t/ha. Therefore, this dose added nutrients to the soil that improved the availability for plant absorption and this influenced the concentration of nutrients in leaves such as N, P and Fe and stomatal density with 459 stomata/mm2, which had a response in good development, strengthening against environmental stress and therefore greater performance.

Impact of cobalt and proline foliar application for alleviation of salinity stress in radish.

Salinity stress ranks among the most prevalent stress globally, contributing to soil deterioration. Its negative impacts on crop productivity stem from mechanisms such as osmotic stress, ion toxicity, and oxidative stress, all of which impede plant growth and yield. The effect of cobalt with proline on mitigating salinity impact in radish plants is still unclear. That's why the current study was conducted with aim to explore the impact of different levels of Co and proline on radish cultivated in salt affected soils. There were four levels of cobalt, i.e., (0, 10, 15 and 20 mg/L) applied as CoSO4 and two levels of proline (0 and 0.25 mM), which were applied as foliar. The treatments were applied in a complete randomized design (CRD) with three replications. Results showed that 20 CoSO4 with proline showed improvement in shoot length (∼ 20%), root length (∼ 23%), plant dry weight (∼ 19%), and plant fresh weight (∼ 41%) compared to control. The significant increase in chlorophyll, physiological and biochemical attributes of radish plants compared to the control confirms the efficacy of 20 CoSO4 in conjunction with 10 mg/L proline for mitigating salinity stress. In conclusion, application of cobalt with proline can help to alleviate salinity stress in radish plants. However, multiple location experiments with various levels of cobalt and proline still needs in-depth investigations to validate the current findings.

Impact of changes in root biomass on the occurrence of internal browning in radish root.

The purpose of this study was to investigate the effects of root biomass during the later stage of growth on fatty acid composition and lipid peroxidation, and to clarify the physiological mechanisms by which these differences affect internal browning (IB) development in radish roots. Therefore, we controlled the enlargement of roots by changing the thinning period and generated plots composed of roots with different biomass in the latter half of growth. The earlier the radish seedlings were thinned, the more vigorous the root growth from an earlier stage was achieved. Earlier thinning caused IB from the early stage of root maturation, and IB severity progressed with subsequent age progression; however, IB damage did not occur when root size during the later growth stage was kept small by later thinning. Higher levels of hydrogen peroxide, peroxidase activity, NADPH-dependent reactive oxygen species (ROS) burst-related genes, and carbonyl compounds were detected in earlier-thinned large-sized roots compared to later-thinned small-sized ones. Compared with the latter small-sized roots, the former large-sized roots had a lower ratio of linoleic acid (18:2) and a higher ratio of α-linolenic acid (α-18:3). Furthermore, in earlier-thinned large-sized roots, higher levels of phospholipase- and/or lipoxygenase-related genes were detected compared to later-thinned small-sized ones. These facts suggest the possibility that root biomass in the later stage of growth affects the desaturation of membrane fatty acids, ROS concentration, and activity of fatty acid degrading enzymes, and controls the occurrence of IB injury through membrane oxidative degradation.

Oxytetracycline Increases the Residual Risk of Imidacloprid in Radish (Raphanus sativus) and Disturbs the Plant-Rhizosphere Microbiome Holobiont Homeostasis.

Antibiotics can be accidentally introduced into farmland by wastewater irrigation, and the environmental effects are still unclear. In this study, the effects of oxytetracycline on the residue of imidacloprid in soil and radishes were investigated. Besides, the rhizosphere microbiome and radish metabolome were analyzed. It showed that the persistence of imidacloprid in soil was unchanged, but the content of olefin-imidacloprid was increased by oxytetracycline. The residue of imidacloprid in radishes was increased by nearly 1.5 times, and the hazard index of imidacloprid was significantly raised by 1.5-4 times. Oxytetracycline remodeled the rhizosphere microbiome, including Actinobe, Elusimic, and Firmicutes, and influenced the metabolome of radishes. Especially, some amino acid metabolic pathways in radish were downregulated, which might be involved in imidacloprid degradation. It can be assumed that oxytetracycline increased the imidacloprid residue in radish through disturbing the plant-rhizosphere microbiome holobiont and, thus, increased the pesticide dietary risk.

Antinociceptive effects of Raphanus sativus sprouts involve the opioid and 5-HT1A serotonin receptors, cAMP/cGMP pathways, and the central activity of sulforaphane.

Raphanus sativus L. cv. Sango, commonly known as red radish, is widely consumed around the world as a vegetable, but its benefit in pain relief is not sufficiently investigated. This study aimed to evaluate the antinociceptive effects of R. sativus and a possible mechanism of action. An aqueous extract of R. sativus sprouts (AERSS) was investigated by parenteral (10, 30, and 100 mg kg-1, i.p.) and enteral (500 mg kg-1, p.o.) administration in the neurogenic and inflammatory phases of the formalin test, where gastric damage was also evaluated as a possible adverse effect. Ketorolac (5 mg kg-1, i.p.) was used as the reference drug. Endogenous opioid and 5-HT1A serotonin receptors, as well as the cAMP/NO-cGMP pathways, were explored in the study of a possible mechanism of action by using their corresponding antagonists: naloxone, 1 mg kg-1, i.p., WAY100635, 1 mg kg-1, i.p., and enzymatic activators or inhibitors, respectively. Sulforaphane (SFN), a known bioactive metabolite, was analyzed using electroencephalography (EEG) to evidence its central involvement. A significant and dose-dependent antinociceptive activity was observed with the AERSS resembling the antinociceptive effect of the reference drug, with an equivalent significant response with a dose of 500 mg kg-1, p.o. without causing gastric damage. The participation of the endogenous opioid and 5-HT1A serotonin receptors at central and peripheral levels was also observed, with a differential participation of cAMP/NO-cGMP. SFN as one metabolite produced significant changes in the EEG analysis, reinforcing its effects on the CNS. Our preclinical evidence supports the benefits of consuming Raphanus sativus cv. Sango sprouts for pain relief.

Investigation of CaMV-host co-evolution through synonymous codon pattern.

Cauliflower mosaic virus (CaMV) has a double-stranded DNA genome and is globally distributed. The phylogeny tree of 121 CaMV isolates was categorized into two primary groups, with Iranian isolates showing the greatest genetic variations. Nucleotide A demonstrated the highest percentage (36.95%) in the CaMV genome and the dinucleotide odds ratio analysis revealed that TC dinucleotide (1.34 ≥ 1.23) and CG dinucleotide (0.63 ≤ 0.78) are overrepresented and underrepresented, respectively. Relative synonymous codon usage (RSCU) analysis confirmed codon usage bias in CaMV and its hosts. Brassica oleracea and Brassica rapa, among the susceptible hosts of CaMV, showed a codon adaptation index (CAI) value above 0.8. Additionally, relative codon deoptimization index (RCDI) results exhibited the highest degree of deoptimization in Raphanus sativus. These findings suggest that the genes of CaMV underwent codon adaptation with its hosts. Among the CaMV open reading frames (ORFs), genes that produce reverse transcriptase and virus coat proteins showed the highest CAI value of 0.83. These genes are crucial for the creation of new virion particles. The results confirm that CaMV co-evolved with its host to ensure the optimal expression of its genes in the hosts, allowing for easy infection and effective spread. To detect the force behind codon usage bias, an effective number of codons (ENC)-plot and neutrality plot were conducted. The results indicated that natural selection is the primary factor influencing CaMV codon usage bias.

Insights into the effect of manganese-based nanomaterials on the distribution trait and nutrition of radish (Raphanus sativus L.).

Manganese (Mn) is one of the essential elements for plant growth and is involved in the process of photosynthesis and seed germination. Herein, we applied two Mn-based nanoparticles, MnO2 and Mn3O4, to the soil to investigate their effects on radish growth, antioxidant system, and nutrients. The radish plant height after treatment with 10 mg/kg of MnO2 and Mn3O4 NPs were increased, compare to the control. In radish's shoot, MnO2 NPs at high concentrations (100 mg/kg) increased MDA activity by 58 % compared to the control group, while exposure to Mn3O4 NPs at the same concentration decreased MDA activity by 14 %. The nutrient content of radishes, such as soluble sugar and vitamin C, was improved. Moreover, single particle inductively coupled plasma mass spectrometry (SP ICP-MS) was used to understand the patterns of migration of Mn-based NPs in radish and subsequent impact on nutrients. We found that Mn-based NPs accumulated mainly in the roots of radish. Interestingly, the accumulation characteristics of MnO2 NPs and Mn3O4 NPs were different. MnO2 NPs accumulated more in radish leaves than in fruits, while the accumulation of Mn3O4 NPs gradually decreased from roots to leaves. Finally, we determined the mineral element content of the leaves, fruits, and roots of radish, and found that the uptake of main metallic mineral elements (e.g. Cu, Fe, Mg, Zn, Na, K) was inhibited by the application of Mn-based NPs. These findings underscore the importance of considering species and multifaceted impacts of Mn-based NPs as nanofertilizers for their wide application in agriculture.

Uptake, accumulation and metabolism of UV-320 in vegetables and its impact on growth and quality.

UV-320 is classified as a Substance of Very High Concern (SVHC) by the European Chemicals Agency and has attracted significant attention due to its presence in the environment. Understanding the uptake, translocation and metabolic patterns of UV-320 in vegetables is essential for assessing their ability to bioaccumulate and potential risks to human health. In this study, we investigated the uptake and translocation of UV-320 in lettuce and radish by hydroponic experiments. The results showed that the root concentration factors (Croot/Csolution, RCF) of lettuce and radish were in the range of 47.9 to 464 mL/g and 194 to 787 mL/g, respectively. The transfer factors (Cshoot/Croot, TF) were observed to be 0.001-0.012 for lettuce and 0.02-0.05 for radish. Additionally, non-targeted screening identified twelve phase I and one phase II metabolites of UV-320 in vegetables, which were confirmed based on their molecular formulas and structures. The metabolic pathways involving oxidation, ketonylation and deamination were proposed in vegetables. Also, we have observed that UV-320 inhibits the growth of vegetables. Meanwhile, we evaluated the health risk of UV-320 in lettuce and radish and found that the consumption of lettuce is relatively safe, while the consumption of radish has a risk of HQ >1 for both adults and children, which should be seriously considered. This study provides valuable insights into the behavior and ecological risks of UV-320 in the environment.

Enzymatic properties of UDP-glycosyltransferase 89B1 from radish and modulation of enzyme catalytic activity via loop region mutation.

Glycosyltransferases (GTs), crucial enzymes in plants, alter natural substances through glycosylation, a process with extensive applications in pharmaceuticals, food, and cosmetics. This study narrows its focus to GT family 1, specifically UDP-glycosyltransferases (UGTs), which are known for glycosylating small phenolic compounds, especially hydroxybenzoates. We delve into the workings of Raphanus sativus glucosyltransferase (Rs89B1), a homolog of Arabidopsis thaliana UGT89B1, and its mutant to explore their glycosyltransferase activities toward hydroxybenzoates. Our findings reveal that Rs89B1 glycosylates primarily the para-position of mono-, di-, trihydroxy benzoic acids, and its substrate affinity is swayed by the presence and position of the hydroxyl group on the benzene ring of hydroxybenzoate. Moreover, mutations in the loop region of Rs89B1 impact both substrate affinity and catalytic activity. The study demonstrates that insertional/deletional mutations in non-conserved regions, which are distant from the UGT's recognition site, can have an effect on the UGT's substrate recognition site, which in turn affects acceptor substrate selectivity and glycosyltransferase activity. This research uncovers new insights suggesting that mutations in the loop region could potentially fine-tune enzyme properties and enhance its catalytic activity. These findings not only have significant implications for enzyme engineering in biotechnological applications but also contribute to a more profound understanding of this field.

Novel insights into the anti-asthmatic effect of Raphanus sativus L. (Raphani Semen): Targeting immune cells, inflammatory pathways and oxidative stress markers.

ETHNOPHARMACOLOGICAL RELEVANCE: Raphanus sativus L. is a well-known medicinal plant with traditional therapeutic applications in various common ailments including inflammation and asthma. AIMS OF THE STUDY: This study aimed to evaluate the chemical composition and anti-asthmatic potential of the hydro-methanolic extract of the leaves of R. sativus L. (Rs.Cr) using various in vitro and in vivo investigations. MATERIALS AND METHODS: The Rs.Cr was subjected to preliminary phytochemical analysis and HPLC profiling. The safety was assessed through oral acute toxicity tests in mice. The antiasthmatic effect of the extract was studied using milk-induced leukocytosis and ovalbumin (OVA)-induced allergic asthma models established in mice. While mast cell degranulation and passive paw anaphylaxis models were established in rats. Moreover, effect of the extract was studied on various oxidative and inflammatory makers. The antioxidant effect of the extract was also studied by in vitro DPPH method. RESULTS: The HPLC profiling of Rs.Cr showed the presence of important polyphenols in a considerable quantity. In toxicity evaluation, Rs.Cr showed no sign of morbidity or mortality with LD50 < 2000 mg/kg. The extract revealed significant mast cell disruption in a dose-dependent manner compared to the intoxicated group. Similarly, treatment with Rs.Cr and dexamethasone significantly (p < 0.001) reduced paw edema volume. Subcutaneous injection of milk at a dose of 4 mL/kg, after 24 h of its administration, showed an increase in the leukocyte count in the intoxicated group. Similarly, mice treated with dexamethasone and Rs.Cr respectively showed a significant decrease in leukocytes and eosinophils count in the ovalbumin-induced allergic asthma model. The extract presented a significant (p˂0.001) alleviative effect on the levels of SOD and GSH, MDA, IL-4, IL-5, and IL-13 in a dose-dependent manner as compared to the intoxicated group. Furthermore, the histological evaluation also revealed a notable decrease in inflammatory and goblet cell count with reduced mucus production. CONCLUSION: The current study highlights mechanism-based novel insights into the anti-asthmatic potential of R. sativus that also strongly supports its traditional use in asthma.

Combinatorial preparation and structural characterization of anthocyanins and aglycones from Purple-heart Radish for evaluation of physicochemical stability and pancreatic lipase inhibitory activity.

In this study, an efficient approach to preparation of different anthocyanins from Purple-heart Radish was developed by combining microwave-assisted extraction (MAE), macroporous resin purification (MRP) and ultrasound-assisted acid hydrolysis (UAAH) for evaluation of physicochemical stability and pancreatic lipase (PL) inhibitory activity. By optimization of MAE, MRP and UAAH processes, the anthocyanins reached the yield of 6.081 ± 0.106 mg/g, the purity of 78.54 ± 0.62 % (w/w) and the content of 76.29 ± 1.31 % (w/w), respectively. With high-resolution UHPLC-Q-Orbitrap/MS, 15 anthocyanins were identified as pelargonins with diverse glucosides and confirmed by pelargonidin standard. By glycosylation, pelargonins exhibited higher stability in different pH, temperature, light, metal ions environments than that of pelargonidin. However, PL inhibitory assay, kinetic analysis and molecular docking demonstrated that pelargonidin had higher PL inhibitory activity than pelargonins even though with similar binding sites and a dose-effect relationship. The above results revealed that the effect of glycosylation and deglycosylation on PL inhibitory activity and physicochemical stability.

A cooperative combination of non-targeted metabolomics and electronic tongue evaluation reveals the dynamic changes in metabolites and sensory quality of radish during pickling.

Pickled radish is a traditional fermented food with a unique flavor after long-term preservation. This study analyzed the organoleptic and chemical characteristics of pickled radish from different years to investigate quality changes during pickling. The results showed that the sourness, saltiness, and aftertaste-bitterness increased after pickling, and bitterness and astringency decreased. The levels of free amino acids, soluble sugars, total phenols, and total flavonoids initially decreased during pickling but increased with prolonged pickling. The diversity of organic acids also increased over time. Through non-targeted metabolomics analysis, 349 differential metabolites causing metabolic changes were identified to affect the quality formation of pickled radish mainly through amino acid metabolism, phenylpropane biosynthesis and lipid metabolism. Correlation analysis showed that L*, soluble sugars, lactic acid, and acetic acid were strongly associated with taste quality. These findings provide a theoretical basis for standardizing and scaling up traditional pickled radish production.

Phytochemical Profile, Bioactive Properties, and Se Speciation of Se-Biofortified Red Radish (Raphanus sativus), Green Pea (Pisum sativum), and Alfalfa (Medicago sativa) Microgreens.

The impact of selenium (Se) enrichment on bioactive compounds and sugars and Se speciation was assessed on different microgreens (green pea, red radish, and alfalfa). Sodium selenite and sodium selenate at a total concentration of 20 µM (1:1) lead to a noticeable Se biofortification (40-90 mg Se kg-1 DW). In green pea and alfalfa, Se did not negatively impact phenolics and antioxidant capacity, while in red radish, a significant decrease was found. Regarding photosynthetic parameters, Se notably increased the level of chlorophylls and carotenoids in green pea, decreased chlorophyll levels in alfalfa, and had no effect on red radish. Se treatment significantly increased sugar levels in green pea and alfalfa but not in red radish. Red radish had the highest Se amino acid content (59%), followed by alfalfa (34%) and green pea (28%). These findings suggest that Se-biofortified microgreens have the potential as functional foods to improve Se intake in humans.

Sustainable remediation of chromium-contaminated soils: boosting radish growth with deashed biochar and strigolactone.

Chromium (Cr) stress significantly hinders crop production by disrupting nutrient uptake, impairing plant growth, and contaminating soil, posing a substantial threat to agricultural sustainability. The use of deashed biochar (DAB) and strigolactone can be an effective solution to mitigate this issue. Deashed biochar enhances crop production by improving soil structure, water retention, and nutrient availability while mitigating the bioavailability of toxic substances. Strigolactone boosts plant growth by stimulating root growth, branching, shoot formation, and overall plant physiology. Nevertheless, the scientific rationale behind their collective use as an amendment to counter Cr stress remains to be substantiated. Therefore, in this study, a blend of DAB and strigolactone was employed as additives in radish cultivation, both in the absence of Cr stress and under the influence of 200Cr stress. Four treatments, i.e., 0, 20µM Strigolactone, DAB, and 20µM Strigolactone + DAB, were applied in four replications following a completely randomized design. Results demonstrate that 20µM Strigolactone + DAB produced significant improvement in radish shoot length (27.29%), root length (45.60%), plant fresh weight (33.25%), and plant dry weight (78.91%), compared to the control under Cr stress. Significant enrichment in radish chlorophyll a (20.41%), chlorophyll b (58.53%), and total chlorophyll (31.54%) over the control under Cr stress, prove the efficacy of 20µM Strigolactone + DAB treatment. In conclusion, 20µM Strigolactone + DAB is the recommended amendment for mitigating Cr stress in radish. Farmers should consider using Strigolactone + DAB amendments to combat Cr stress and enhance radish growth, contributing to a more resilient agricultural ecosystem.

The type VI secretion system of Stenotrophomonas rhizophila CFBP13503 limits the transmission of Xanthomonas campestris pv. campestris 8004 from radish seeds to seedlings.

Stenotrophomonas rhizophila CFBP13503 is a seedborne commensal bacterial strain, which is efficiently transmitted to seedlings and can outcompete the phytopathogenic bacterium Xanthomonas campestris pv. campestris (Xcc8004). The type VI secretion system (T6SS), an interference contact-dependent mechanism, is a critical component of interbacterial competition. The involvement of the T6SS of S. rhizophila CFBP13503 in the inhibition of Xcc8004 growth and seed-to-seedling transmission was assessed. The T6SS cluster of S. rhizophila CFBP13503 and nine putative effectors were identified. Deletion of two T6SS structural genes, hcp and tssB, abolished the competitive advantage of S. rhizophila against Xcc8004 in vitro. The population sizes of these two bacterial species were monitored in seedlings after inoculation of radish seeds with mixtures of Xcc8004 and either S. rhizophila wild-type (wt) strain or isogenic hcp mutant. A significant decrease in the population size of Xcc8004 was observed during confrontation with the S. rhizophila wt in comparison with T6SS-deletion mutants in germinated seeds and seedlings. We found that the T6SS distribution among 835 genomes of the Stenotrophomonas genus is scarce. In contrast, in all available S. rhizophila genomes, T6SS clusters are widespread and mainly belong to the T6SS group i4. In conclusion, the T6SS of S. rhizophila CFBP13503 is involved in the antibiosis against Xcc8004 and reduces seedling transmission of Xcc8004 in radish. The distribution of this T6SS cluster in the S. rhizophila complex could make it possible to exploit these strains as biocontrol agents against X. campestris pv. campestris.

Systematic analysis of Heat Shock Protein 70 (HSP70) gene family in radish and potential roles in stress tolerance.

The 70 kD heat shock proteins (HSP70s) represent a class of molecular chaperones that are widely distributed in all kingdoms of life, which play important biological roles in plant growth, development, and stress resistance. However, this family has not been systematically characterized in radish (Raphanus sativus L.). In this study, we identified 34 RsHSP70 genes unevenly distributed within nine chromosomes of R. sativus. Phylogenetic and multiple sequence alignment analyses classified the RsHSP70 proteins into six distinct groups (Group A-F). The characteristics of gene structures, motif distributions, and corresponding cellular compartments were more similar in closely linked groups. Duplication analysis revealed that segmental duplication was the major driving force for the expansion of RsHSP70s in radish, particularly in Group C. Synteny analysis identified eight paralogs (Rs-Rs) in the radish genome and 19 orthologs (Rs-At) between radish and Arabidopsis, and 23 orthologs (Rs-Br) between radish and Chinese cabbage. RNA-seq analysis showed that the expression change of some RsHSP70s were related to responses to heat, drought, cadmium, chilling, and salt stresses and Plasmodiophora brassicae infection, and the expression patterns of these RsHSP70s were significantly different among 14 tissues. Furthermore, we targeted a candidate gene, RsHSP70-23, the product of which is localized in the cytoplasm and involved in the responses to certain abiotic stresses and P. brassicae infection. These findings provide a reference for further molecular studies to improve yield and stress tolerance of radish.

Identification of vernalization-related genes and cold memory element (CME) required for vernalization response in radish (Raphanus sativus L.).

Floral transition is accelerated by exposure to long-term cold like winter in plants, which is called as vernalization. Acceleration of floral transition by vernalization is observed in a diversity of biennial and perennial plants including Brassicaceae family plants. Scientific efforts to understand molecular mechanism underlying vernalization-mediated floral transition have been intensively focused in model plant Arabidopsis thaliana. To get a better understanding on floral transition by vernalization in radish (Raphanus sativus L.), we investigated transcriptomic changes taking place during vernalization in radish. Thousands of genes were differentially regulated along time course of vernalization compared to non-vernalization (NV) sample. Twelve major clusters of DEGs were identified based on distinctive expression profiles during vernalization. Radish FLC homologs were shown to exert an inhibition of floral transition when transformed into Arabidopsis plants. In addition, DNA region containing RY motifs located within a Raphanus sativus FLC homolog, RsFLC1 was found to be required for repression of RsFLC1 by vernalization. Transgenic plants harboring disrupted RY motifs were impaired in the enrichment of H3K27me3 on RsFLC1 chromatin, thus resulting in the delayed flowering in Arabidopsis. Taken together, we report transcriptomic profiles of radish during vernalization and demonstrate the requirement of RY motif for vernalization-mediated repression of RsFLC homologs in radish (Raphanus sativus L.).