Effects of Endogenous Salicylic Acid During Calcium Deficiency-Induced Tipburn in Chinese Cabbage (<Emphasis Type="Italic">Brassica rapa</Emphasis> L. ssp. <Emphasis Type="Italic">pekinensis</Emphasis>)

By cultivating tipburn-susceptible plants in modified Hoagland’s medium containing of gradient exogenous calcium (Ca²⁺), we have shown that Ca²⁺ deficiency is one of the main causes of tipburn in Chinese cabbage (Brassica rapa L. ssp. pekinensis). The effect of endogenous plant Ca²⁺ concentrations on tipburn was also studied in a doubled haploid (DH) population consisting of 100 individuals, but no correlation was found. We then examined the expression of 12 Ca²⁺ transporter genes that function in cytosolic Ca²⁺ homeostasis in both tipburn-susceptible and tipburn-resistant plants under normal and tipburn-inducing conditions. Expression patterns for most of these genes differed between the two types of plants. Salicylic acid (SA) accumulated in response to conditions of calcium deficiency in our study, and both total SA and SA β-glucoside (SAG) in tipburn-susceptible plants was ～3-fold higher than it was in resistant plants following Ca²⁺ deficiency treatment. Also, the changes observed in SA levels correlated well with cell death patterns revealed by trypan blue staining. Therefore, we speculate that the cytoplasmic Ca²⁺ fluctuation-induced downstream signaling events, as well as SA signaling or other biological events, are involved in the plant defense response to tipburn in Chinese cabbage.     

Effect of calcium ions on electron transfer between hemes <Emphasis Type="Italic">a</Emphasis> and <Emphasis Type="Italic">a</Emphasis><Subscript>3</Subscript> in cytochrome <Emphasis Type="Italic">c</Emphasis> oxidase

Kinetics of the reduction of the hemes in cytochrome c oxidase in the presence of high concentration of ruthenium(III)hexaammine chloride was examined using a stopped-flow spectrophotometer. Upon mixing of the oxidized enzyme with dithionite and Ru(NH₃) ₆ ³⁺ , three well-resolved phases were observed: heme a reduction reaching completion within a few milliseconds is followed by two slow phases of heme a ₃ reduction. The difference spectrum of heme a ₃ reduction in the visible region is characterized by a maximum at ～612 nm, rather than at 603 nm as was believed earlier. It is shown that in the case of bovine heart cytochrome c oxidase containing a special cation-binding site in which reversible binding of calcium ion occurs, heme a ₃ reduction is slowed down by low concentrations of Ca²⁺. The effect is absent in the case of the bacterial cytochrome oxidase in which the cation-binding site contains a tightly bound Ca²⁺ ion. The data corroborate the inhibition of the cytochrome oxidase enzymatic activity by Ca²⁺ ions discovered earlier and indicate that the cation affects intramolecular electron transfer.     

Xylem sap chemistry: seasonal changes in timberline conifers <Emphasis Type="Italic">Pinus cembra</Emphasis>, <Emphasis Type="Italic">Picea abies</Emphasis>, and <Emphasis Type="Italic">Larix decidua</Emphasis>

The seasonal course of xylem sap parameters (electrical conductivity EC, potassium concentration [K⁺], and pH) of three conifers (Pinus cembra, Picea abies, and Larix decidua) growing at the alpine timberline was monitored. We also looked into possible effects of [K⁺] and pH on the difference in hydraulic conductivity (Δk_s). In all studied species, EC, [K⁺], and pH varied considerably over the year, with pH ranging between 7.3 (February) and 5.8 (June) and [K⁺] changing between 0.4 (January) and 2.5 mM (June). The Δk_s was overall low with positive values during winter (up to +20 %) and negative values in summer (-15 % in August). Samples perfused with alkaline solutions showed higher Δk_s. Xylem sap parameters in all conifers under study were surprisingly variable over the year thus indicating either effects upon seasonal changes in environmental factors or active adjustments, or both. Although Δk_s values over the year were minor, observed induction of Δk_s by high pH might indicate a role for hydraulic adjustment in harsh winter periods.     

Increase in Salt Tolerance of <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis> by <Emphasis Type="Italic">TaDi19</Emphasis>

The gene expression profile chip of salt-resistant wheat mutant RH8706-49 under salt stress was investigated. The overall length of the cDNA sequence of the probe was obtained using electronic cloning and RT-PCR. An unknown gene induced by salt was obtained, cloned, and named TaDi19 (Triticum aestivum drought-induced protein). No related report or research on the protein is available. qPCR analysis showed that gene expression was induced by many stresses, such as salt. Arabidopsis thaliana was genetically transferred using the overexpressing gene, which increased its salt tolerance. After salt stress, the transgenic plant demonstrated better physiological indicators (higher Ca²⁺ and lower Na⁺) than those of the wild-type plant. Results of non-invasive micro-test technology indicate that TaDi19-overexpressing A. thaliana significantly effluxed Na⁺ after salt treatment, whereas the wild-type plant influxed Na⁺. Chelating extracellular Ca²⁺ resulted in insignificant differences in salt tolerance between overexpressing and wild-type A. thaliana. Subcellular localization showed that the gene encoding protein was mainly located in the cell membrane and nucleus. TaDi19 was overexpressed in wild-type A. thaliana, and the transgenic lines were more salt-tolerant than the control A. thaliana. Thus, the wheat gene TaDi19 could increase the salt tolerance of A. thaliana.     

Haloperidol modulates ion transport in <Emphasis Type="Italic">Chara corallina</Emphasis> cells

The effects of haloperidol, an antagonist of D2 dopamine receptors, on the functioning of Ca²⁺, K⁺, and Cl^? ion channels in the membrane of Chara corallina cells and on the functional properties of their cytoskeleton was studied. Haloperidol blocked Ca²⁺ channels of the plasmalemma. In addition to bringing about a decrease in the amplitude of the calcium current, exposure to haloperidol decelerated the activation and inactivation of calcium channels. The effect of haloperidol was reversible; after it was removed, the characteristics of calcium current were restored. Haloperidol did not affect Ca²⁺-activated chloride channels. Haloperidol also inhibited microfilament-dependent motion of the cytoplasm. Cytoplasmic streaming was restored after haloperidol was removed from the extracellular solution. These results suggest that the concentration of free Ca²⁺ ions in the cytoplasm increases in the presence of haloperidol, and that Ca²⁺ channels of C. corallina plasmalemma possess specific binding sites both for dopamine receptors and for their antagonists.     

<Emphasis Type="Italic">Zunongwangia flava</Emphasis> sp. nov., belonging to the family <Emphasis Type="Italic">Flavobacteriaceae</Emphasis>, isolated from <Emphasis Type="Italic">Salicornia europaea</Emphasis>

A yellow pigmented bacterium designated strain MBLN094^T within the family Flavobacteriaceae was isolated from a halophyte Salicornia europaea on the coast of the Yellow Sea. This strain was a Gram-stain negative, aerobic, non-spore forming, rod-shaped bacterium. Phylogenetic analysis of the 16S rRNA gene sequence of strain MBLN094^T was found to be related to the genus Zunongwangia, exhibiting 16S rRNA gene sequence similarity values of 97.0, 96.8, 96.4, and 96.3% to Zunongwangia mangrovi P2E16^T, Z. profunda SM-A87^T, Z. atlantica 22II14-10F7^T, and Z. endophytica CPA58^T, respectively. Strain MBLN094^T grew at 20?37°C (optimum, 25?30°C), at pH 6.0?10.0 (optimum, 7.0?8.0), and with 0.5?15.0% (w/v) NaCl (optimum, 2.0?5.0%). Menaquinone MK-6 was the sole respiratory quinone. The polar lipids were phosphatidylethanolamine, two unidentified aminolipids, and four unidentified lipids. Major fatty acids were iso-C_17:0 3-OH, summed feature 3 (C_16:1ω6c and/or C16:1 ω7c), and iso-C_15:0. The genomic DNA G + C content was 37.4 mol%. Based on these polyphasic taxonomic data, strain MBLN094^T is considered to represent a novel species of the genus Zunongwangia, for which the name Zunongwangia flava sp. nov. is proposed. The type strain is MBLN094^T (= KCTC 62279^T = JCM 32262^T).     

Molecular cloning and characterization of calmodulin-like protein CaLP from the Scleractinian coral <Emphasis Type="Italic">Galaxea astreata</Emphasis>

Optimal temperature and light are both necessary conditions for coral survival. Light enhances calcification, and thermal stress disrupts Ca²⁺ homeostasis. As calcium is involved in many important metabolic activities, in this study, we cloned the calmodulin-like protein (CaLP) gene of one of the scleractinian corals, Galaxea astreata. We also detected the relative mRNA expression levels of gaCaLP using the calcium channel blocker verapamil and CaCl₂ treatment under conditions of light and dark, and compared expression levels under controlled temperature conditions. Full-length gaCaLP cDNA comprised 1290 nucleotides and contained 498 bp open reading frame that encoded a protein with 165 amino acids. With CaCl₂, expression levels of gaCaLP only increased in the presence of light, suggesting that light may be a restrictive factor in CaLP expression when sufficient calcium is available in the environment. In addition, after verapami treatment, we noted that a down regulation of gaCaLP, suggesting that the expression of CaLP is closely related to extracellular Ca²⁺ influx. Under temperature stress at both high (30 °C) and low (20 °C) temperatures, expression levels of gaCaLP showed an initial increase, followed by a decreasing trend as treatment progressed. Expression levels reached their maximum value at 24 h. This result showed that CaLP participated in a temperature stress response, and Ca²⁺ homeostasis was disrupted during stress. The findings of the present study will help determine the function and regulatory mechanisms of gaCaLP.     

Characterization of a novel <Emphasis Type="Italic">Acinetobacter baumannii</Emphasis> xanthine dehydrogenase expressed in <Emphasis Type="Italic">Escherichia coli</Emphasis>

Objective

To characterize a novel xanthine dehydrogenase (XDH) from Acinetobacter baumannii by recombinant expression in Escherichia coli and to assess its potential for industrial applications.

Results

The XDH gene cluster was cloned from A. baumannii CICC 10254, expressed heterologously in E. coli and purified to homogeneity. The purified recombinant XDH consisted of two subunits with the respective molecular weights of 87 kDa and 56 kDa according to SDS-PAGE. XDH catalysis was optimum at pH 8.5 and 40–45 °C, was stable under alkaline conditions (pH 7–11) and the half-inactivation temperature was 60 °C. The K _m, turnover number and catalytic efficiency for xanthine were 25 μM, 69 s^?1 and 2.7 μM^?1 s^?1, respectively, which is an improvement over XDHs characterized previously. A. baumannii XDH is less than 50 % identical to previously identified XDH orthologs from other species, and is the first from the Acinetobacter genus to be characterized.

Conclusion

The novel A. baumannii enzyme was found to be among the most active, thermostable and alkaline-tolerant XDH enzymes reported to date and has potential for use in industrial applications.

     

Characterization of a novel thermo-stable lipase from endophyte <Emphasis Type="Italic">Pseudomonas putida</Emphasis> in <Emphasis Type="Italic">Pistacia chinensis</Emphasis> Bunge

A novel lipolytic enzyme-producing endophytic strain PC2 was successfully isolated from the seeds of an ideal bioenergy plant Pistacia chinensis Bunge. Based on the analysis of morphology and 16S rRNA sequence, bacterial strain PC2 was identified as a subspecies of Pseudomonas putida, therefore named as P. putida PC2. Whole-genome sequencing showed PC2 contained a 1224-nucleotide lipase gene (named lip-PC2) predicted to encode a 407-amino-acid protein. Purified lipases from both the original PC2 strain and heterologously expressed Escherichia coli were nearly 50 kD with specific activity of 9.48 U/mL. LIP-PC2 displayed the maximal activity at 50°C or pH 8.0, and maintained above 80% relative activity in the range of from 40 to 60°C or pH in the range of from 6.0 to 8.0, indicating thermostable and alkaline properties. Enzyme activity was enhanced by Mg²⁺, Na⁺ and Mn²⁺, but strongly inhibited by Cu²⁺, Zn²⁺ Co²⁺, EDTA as well as organic solvents and surfactants. Additionally, the analysis of amino acid sequence and structure indicated that LIP-PC2 was a novel member belonging to family I.3 of bacterial lipolytic enzymes and its catalytic triad was consisted of Ser-200, Asp-342 and His-374.     

Molecular Cloning,Expression and Characterization of Pectin Methylesterase (<Emphasis Type="Italic">Ct</Emphasis>PME) from <Emphasis Type="Italic">Clostridium thermocellum</Emphasis>

Many phytopathogenic micro-organisms such as bacteria and fungi produce pectin methylesterases (PME) during plant invasion. Plants and insects also produce PME to degrade plant cell wall. In the present study, a thermostable pectin methylesterase (CtPME) from Clostridium thermocellum belonging to family 8 carbohydrate esterase (CE8) was cloned, expressed and purified. The amino acid sequence of CtPME exhibited similarity with pectin methylesterase from Erwinia chrysanthemi with 38% identity. The gene encoding CtPME was cloned into pET28a(+) vector and expressed using Escherichia coli BL21(DE3) cells. The recombinant CtPME expressed as a soluble protein and exhibited a single band of molecular mass approximately 35.2 kDa on SDS-PAGE gels. The molecular mass, 35.5 kDa of the enzyme, was also confirmed by MALDI-TOF MS analysis. Notably, highest protein concentration (11.4 mg/mL) of CtPME was achieved in auto-induction medium, as compared with LB medium (1.5 mg/mL). CtPME showed maximum activity (18.1 U/mg) against citrus pectin with >85% methyl esterification. The optimum pH and temperature for activity of CtPME were 8.5 and 50 °C, respectively. The enzyme was stable in pH range 8.0–9.0 and thermostable between 45 and 70 °C. CtPME activity was increased by 40% by 5 mM Ca²⁺ or Mg²⁺ ions. Protein melting curve of CtPME gave a peak at 80 °C. The peak was shifted to 85 °C in the presence of 5 mM Ca²⁺ ions, and the addition of 5 mM EDTA shifted back the melting peak to 80 °C. CtPME can be potentially used in food and textile industry applications.     

<Emphasis Type="Italic">Sphingorhabdus buctiana</Emphasis> sp. nov., isolated from fresh water,and reclassification of <Emphasis Type="Italic">Sphingopyxis contaminans</Emphasis> as <Emphasis Type="Italic">Sphingorhabdus contaminans</Emphasis> comb. nov.

A Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterial strain, designated T5^T, was isolated from the Chishui River in Maotai town, Guizhou Province, Southwest of China. Strain T5^T was found to grow optimally at pH 9.0 and 25 °C. The 16S rRNA gene sequence analysis indicated that strain T5^T belongs to the family Sphingomonadaceae within the phylum Proteobacteria; the strain T5^T clustered with the type strains of Sphingopyxis contaminans, Sphingorhabdus wooponensis and Sphingorhabdus rigui, with which it exhibits 16S rRNA gene sequence similarity values of 96.2–96.9%. The DNA G+C content was 58.5 mol%. The major respiratory quinone was Q-10 and the major polar lipid was phosphatidylethanolamine. The major polyamine was homospermidine and the major fatty acids were C_18:1 ω7c (37.5%) and C_16:1 ω7c (30.1%). On the basis of phylogenetic, phenotypic and genetic data, strain T5^T represents a novel species of the genus Sphingorhabdus, for which the name Sphingorhabdus buctiana sp. nov. is proposed. The type strain is T5^T (= CGMCC 1.12929^T = JCM 30114^T). It is also proposed that Sphingopyxis contaminans should be reclassified as a member of the genus Sphingorhabdus.     

Purification and Biochemical Characterization of Phytase Enzyme from <Emphasis Type="Italic">Lactobacillus coryniformis</Emphasis> (<Emphasis Type="Italic">MH121153</Emphasis>)

Phytase (myo-inositol hexaphosphate phosphohydrolase) belongs to phosphatases. It catalyzes the hydrolysis of phytate to less-phosphorylated inorganic phosphates and phytate. Phytase is used primarily for the feeding of simple hermit animals in order to increase the usability of amino acids, minerals, phosphorus and energy. In the present study, phytase isolation from the Lactobacillus coryniformis strain, isolated from Lor cheese sources, phytase purification and characterization were studied. The phytase was purified in simple three steps. The enzyme was obtained with 2.60% recovery and a specific activity of 202.25 (EU/mg protein). The molecular mass of the enzyme was determined to be 43.25 kDa with the sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) method. The optimum temperature and pH for the enzyme were found as 60 °C and 5.0 and respectively. To defined the substrate specificity of the phytase, the hydrolysis of several phosphorylated compounds by the purified enzyme was studied and sodium phytate showed high specificity. Furthermore, the effects of Ca²⁺, Ag⁺, Mg²⁺, Cu²⁺, Co²⁺, Pb²⁺, Zn²⁺ and Ni²⁺ metal ions on the enzyme were studied.     

<Emphasis Type="Italic">Pedobacter panacis</Emphasis> sp. nov., isolated from <Emphasis Type="Italic">Panax ginseng</Emphasis> soil

A novel strain, DCY108^T was isolated from soil of a Panax ginseng field, Yeoncheon province (38°04′N 126°57′E), Republic of Korea. Strain DCY108^T is Gram-negative, non-motile, non-flagellate, rod-shaped, and aerobic. The bacterium grows optimally at 25–30 °C, pH 6.5–7.0 and 1 % NaCl. Phylogenetically, strain DCY108^T is closely related to Pedobacter jejuensis JCM 18824^T, Pedobacter aquatilis JCM 13454^T, Pedobacter kyungheensis LMG 26577^T and the type strain of the genus Pedobacter heparinus DSM 2366^T. The DNA–DNA relatedness values between strain DCY108^T and its close phylogenetic neighbors were below 30.0 %. The DNA G+C content of strain DCY108^T was determined to be 45.1 mol%. The predominant quinone was menaquinone 7 (MK-7). The major polar lipids were identified as phosphatidylethanolamine and three unidentified aminolipids AL1, AL13 and AL17. Iso-C_15:00, iso-C_17:03OH and summed feature 3 (C_16:1 ω7c/C_16:1 ω6c) were identified as the major fatty acids present in strain DCY108^T. The results of physiological and biochemical tests allowed strain DCY108^T to be differentiated phenotypically from other recognized species belonging to the genus Pedobacter. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Pedobacter panacis sp. nov is proposed with the type strain designated as DCY108^T (=CCTCCAB 2015196^T = KCTC 42748^T).     

Testing the cost of reproduction with the rotifer <Emphasis Type="Italic">Brachionus</Emphasis><Emphasis Type="Italic">patulus</Emphasis> at different pH levels

In the present work, we tested the hypothesis that the cost of reproduction was evident under stressful conditions with the rotifer Brachionus patulus at different pH levels (5–10 at 1 unit intervals). We used sublethal pH levels (pH 5, 9, and 10) to simulate stressful conditions. We analyzed the correlations between age-specific fecundity (m ₁, m ₂, m ₃, …) versus future survival (l _x + 1, l _x + 2, l _x + 3, … for the entire lifespan) (survival costs) and future expectation of reproduction (\( V_{ 1}^{*} , \, V_{ 2}^{*} , \, V_{ 3}^{*} , \ldots \) for the entire lifespan) (reproductive costs), using the data obtained from life table demographic studies of B. patulus under stressful and favorable (pH 6, 7, and 8) pH levels. The results showed that significant negative correlations were observed between age-specific fecundity and future survival and future expectation of reproduction at all tested pH levels, indicating that costs of reproduction exist in the rotifer B. patulus under stressful and favorable pH conditions. However, the percentage of statistically significant negative correlations from total correlations of survival and reproductive costs differed greatly, depending on the tested pH conditions. The percentage of significant negative correlation of reproductive costs is significantly higher under stressful pH conditions (pH 5, 9, and 10) than favorable pH conditions (pH 6, 7, and 8). For survival costs, the same trends are also observed, suggesting that the costs of reproduction were more obvious under stressful pH than favorable pH.     

<Emphasis Type="Italic">Larkinella roseus</Emphasis> sp. nov., a species of the family <Emphasis Type="Italic">Cytophagaceae</Emphasis> isolated from beach soil

The taxonomic position of bacterial strain, designated 15J16-1T3A^T, recovered from a soil sample was established using a polyphasic approach. Phylogenic analysis based on the 16S rRNA gene sequence showed that strain 15J16-1T3A^T belonged to the family Cytophagaceae, phylum Bacteroidetes, and was most closely related to ‘Larkinella harenae’ 15J9-9 (95.9% similarity), Larkinella ripae 15J11-11^T (95.6%), Larkinella bovis M2TB15^T (94.7%), Larkinella arboricola Z0532^T (93.9%), and Larkinella insperata LMG 22510^T (93.5%). Cells were rod-shaped, Gram-stain-negative, aerobic, and nonmotile. The isolate grew on NA, R2A, TSA, but not on LB agar. The strain was able to grow at temperature range from 10°C to 30°C with an optimum at 25°C and pH 6–8. Menaquinone MK-7 was the predominant respiratory quinone. The major cellular fatty acids comprised C_16:1ω5c (48.6%) and C_15:0 iso (24.1%). Phosphatidylethanolamine, phosphatidylserine, and an unidentified lipid were the major polar lipids. The G + C content of the genomic DNA was 49.5 mol%. Strain 15J16-1T3A^T could be distinguished from its closest phylogenetic neighbors based on its phenotypic, genotypic, and chemotaxonomic features. Therefore, the isolate is considered to represent a novel species in the genus Larkinella, for which the name Larkinella roseus sp. nov. is proposed. The type strain is 15J16-1T3A^T (= KCTC 52004^T = JCM 31991^T).     

<Emphasis Type="Italic">Nibribacter flagellatus</Emphasis> sp. nov., isolated from rhizosphere of <Emphasis Type="Italic">Hibiscus syriacus</Emphasis> and emended description of the genus <Emphasis Type="Italic">Nibribacter</Emphasis>

A Gram-stain negative, aerobic, motile by flagella, rod-shaped strain (THG-T16^T) was isolated from rhizosphere of Hibiscus syriacus. Growth occurred at 10–40 °C (optimum 28–30 °C), at pH 6.0–8.0 (optimum 7.0) and at 0–1.0% NaCl (optimum 0%). Based on 16S rRNA gene sequence analysis, the near phylogenetic neighbours of strain THG-T16^T were identified as Nibribacter koreensis KACC 16450^T (98.6%), Rufibacter roseus KCTC 42217^T (94.7%), Rufibacter immobilis CCTCC AB 2013351^T (94.5%) and Rufibacter tibetensis CCTCC AB 208084^T (94.4%). The DNA G+C content of strain THG-T16^T was determined to be 46.7 mol%. DNA–DNA hybridization values between strain THG-T16^T and N. koreensis KACC 16450^T, R. roseus KCTC 42217^T, R. immobilis CCTCC AB 2013351^T, R.tibetensis CCTCC AB 208084^T were 33.5?±?0.5% (31.7?±?0.7% reciprocal analysis), 28.1?±?0.2% (25.2?±?0.2%), 17.1?±?0.9% (10.2?±?0.6%) and 8.1?±?0.3% (5.2?±?0.1%). The polar lipids were identified as phosphatidylethanolamine, two unidentified aminophospholipids, an unidentified aminolipid and three unidentified lipids. The quinone was identified as MK-7 and the polyamine as sym-homospermidine. The major fatty acids were identified as C_16:1 ω5c, C_17:1 ω6c, iso-C_15:0, summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c) and summed feature 4 (iso-C_17:1 I and/or anteiso-C_17:1 B). On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics, and DNA–DNA hybridization data, strain THG-T16^T represents a novel species of the genus Nibribacter, for which the name Nibribacter flagellatus sp. nov. is proposed. The type strain is THG-T16^T(=?KACC 19188^T?=?CCTCC AB 2016246^T).     

<Emphasis Type="Italic">Achromobacter panacis</Emphasis> sp. nov., isolated from rhizosphere of <Emphasis Type="Italic">Panax ginseng</Emphasis>

A novel strain DCY105^T was isolated from soil collected from the rhizosphere of ginseng (Panax ginseng), in Gochang, Republic of Korea. Strain DCY105^T is Gram-reaction-negative, white, non-motile, non-flagellate, rod-shaped and aerobic. The bacteria grow optimally at 30°C, pH 6.5–7.0 and in the absence of NaCl. Phylogenetically, strain DCY105^T is most closely related to Achromobacter marplatensis LMG 26219^T (96.81%). The DNA G+C content of strain DCY105^T was 64.4 mol%. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were amongst the major polar lipids. C_16:00, C_8:03OH and iso-C_17:03OH were identified as the major fatty acids present in DCY105^T. The results of physiological and biochemical tests allowed strain DCY105^T to be differentiated phenotypically from other recognized species belonging to the genus Achromobacter. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Achromobacter panacis sp. nov. is proposed with the type strain designated as DCY105^T (=CCTCCAB 2015193^T =KCTC 42751^T).     

<Emphasis Type="Italic">In silico</Emphasis> characterization and Molecular modeling of double-strand break repair protein <Emphasis Type="Italic">MRE11</Emphasis> from <Emphasis Type="Italic">Phoenix dactylifera</Emphasis> v deglet nour

Background

DNA double-strand breaks (DSBs) are highly cytotoxic and mutagenic. MRE11 plays an essential role in repairing DNA by cleaving broken ends through its 3′ to 5′ exonuclease and single-stranded DNA endonuclease activities.

Methods

The present study aimed to in silico characterization and molecular modeling of MRE11 from Phoenix dactylifera L cv deglet nour (DnMRE11) by various bioinformatic approaches. To identify DnMRE11 cDNA, assembled contigs from our cDNA libraries were analysed using the Blast2GO2.8 program.

Results

The DnMRE11 protein length was 726 amino acids. The results of HUMMER show that DnMRE11 is formed by three domains: the N-terminal core domain containing the nuclease and capping domains, the C-terminal half containing the DNA binding and coiled coil region. The structure of DnMRE11 is predicted using the Swiss-Model server, which contains the nuclease and capping domains. The obtained model was verified with the structure validation programs such as ProSA and QMEAN servers for reliability. Ligand binding studies using COACH indicated the interaction of DnMRE11 protein with two Mn²⁺ ions and dAMP. The ConSurf server predicted that residues of the active site and Nbs binding site have high conservation scores between plant species.

Conclusions

A model structure of DnMRE11 was constructed and validated with various bioinformatics programs which suggested the predicted model to be satisfactory. Further validation studies were conducted by COACH analysis for active site ligand prediction, and revealed the presence of six ligands binding sites and two ligands (2 Mn²⁺ and dAMP).