Formation mechanism of the internal structure of type I protein bodies in rice endosperm: relationship between the localization of prolamin species and the expression of individual genes

Rice prolamins, a group of seed storage proteins, are synthesized on the rough endoplasmic reticulum (ER) and form type I protein bodies (PB-Is) in endosperm cells. Rice prolamins are encoded by a multigene family. In this study, the spatial accumulation patterns of various prolamin species in rice endosperm cells were investigated to determine the mechanism of formation of the internal structure of PB-Is. Immunofluorescence microscopic analysis of mature endosperm cells showed that the 10 kDa prolamin is mainly localized in the core of the PB-Is, the 13b prolamin is localized in the inner layer surrounding the core and the outermost layer, and the 13a and 16 kDa prolamins are localized in the middle layer. Real-time RT-PCR analysis showed that expression of the mRNA for 10 kDa prolamin precedes expression of 13a, 13b-1 and 16 kDa prolamin in the developing stages. mRNA expression for 13b-2 prolamin occurred after that of the other prolamin species. Immunoelectron microscopy of developing seeds showed that the 10 kDa prolamin polypeptide initially accumulates in the ER, and then 13b, 13a, 16 kDa and 13b prolamins are stacked in layers within the ER. Studies with transgenic rice seeds expressing prolamin-GFP fusion proteins under the control of native and constitutive promoters indicated that the temporal expression pattern of prolamin genes influenced the localization of prolamin proteins within the PB-Is. These findings indicate that the control of gene expression of prolamin species contributes to the internal structure of PB-Is.     

Polypeptide Compositions and NH2-terminal Amino Acid Sequences of Proteins in Foxtail and Proso Millets

Seed protein of foxtail and proso millets were fractionated into polypeptides that were analyzed for their major protein, prolamin, and the NH₂-terminal amino acid sequences of the proteins were determined. The proteins extracted from foxtail and proso millets were 64.1% and 80.0% prolamin, respectively. The polypeptides of the prolamins were classified into two groups. The major polypeptides of 27-19 kDa were rich in leucine and alanine, whereas the 17-14 kDa polypeptides were rich in methionine and cysteine. Glutelin-like proteins that were extracted with a reducing reagent were high in proline content, the major polypeptides being 17 and 20 kDa. The NH₂-terminal amino acid sequence showed that the major polypeptides of prolamin were homologous to α-zein and a glutelin-like protein containing the Pro-Pro-Pro sequence, like the repetitive sequence of γ-zein. Although the prolamin consisted of a similar subunit to that of zein, polypeptides with various pI values were found among them.     

Thermal and chemical denaturation of Colocasia esculenta tuber agglutinin from α2β2 to unfolded state

The major tuber storage protein of Colocasia esculenta, is a monocot mannose-binding, widely used dietary lectin, containing two polypeptides of 12.0 and 12.4 kDa. By both gel filtration and dynamic light scattering at pH 7.2, the lectin has a α₂β₂ form of apparent molecular mass of 48.2 kDa and a hydrodynamic radius of 6.1 ± .2 nm; however, at pH 3, it migrates as αβ and has a reduced hydrodynamic radius of 4.6 ± .3 nm. Our circular dichroism spectroscopy studies show that the lectin retains approximately 100% of its secondary structure between pH 2–8, going down to ~90% for extreme acidic/alkaline conditions. The fluorescence emission maxima of 346 to 350 nm for pH 4 to 10 show that the tryptophan residues are relatively exposed. The unfolding is a simple two-state process, N₄ ? 4U, as seen in our denaturation scan profiles. These denaturation profiles, monitored separately by fluorescence, far-UV CD, and near-UV CD, are completely super imposable. Analyses of these profiles provide an estimate of several thermodynamic parameters at each guanidinium chloride concentration, including the melting temperature T_g, which is 346.9 K in 0 M, but lowers to 321.8 K in 3.6 M. Dimeric and tetrameric interfaces observed in the crystal structure for the same protein are used to rationalize solution data in some detail.     

Constant surface tension molecular dynamics simulations of lipid bilayers with trehalose

Surface areas and fluctuations evaluated from 50 ns molecular dynamics simulations of fully hydrated dipalmitoylphosphatidylcholine (DPPC) bilayers in a 1:2 trehalose:lipid ratio carried out at surface tensions 10, 17 and 25 dyn/cm/leaflet are compared with those of pure bilayers under the same conditions. Trehalose increases the surface area, as consistent with the surface tension lowering observed in simulations at constant area. The system bulk elastic modulus K _b  = 1.5 ± 0.3 × 10¹⁰ dyn/cm². It is independent of bilayer surface area and trehalose content within statistical error. In contrast, the area elastic modulus K _a shows a strong area dependence. At 64 Å²/lipid (the experimental surface area), K _a  = 138 ± 26 dyn/cm for a pure DPPC bilayer and 82 ± 10 dyn/cm for one with trehalose; i.e. trehalose increases fluidity of the bilayer surface at this area per lipid.     

Effect of the structure of dietary epoxylignan on its cytotoxic activity: relationship between the structure and the activity of 7,7′-epoxylignan and the introduction of apoptosis by caspase 3/7

We compared the cytotoxic activities of dietary epoxylignans and their stereoisomers and found (?)-verrucosin, which is (7S,7′R,8R,8′R)-7,7′-epoxylignan, to be the most cytotoxic epoxylignan against HeLa cells (IC₅₀ = 6.6 μM). On the other hand, the activity was about a factor of 10 less against HL-60. In this research on the relationship between the structure and cytotoxic activity of (?)-verrucosin 13, the 7-(4-methoxyphenyl)-7′-(3,4-dimethoxyphenyl) derivative 60, for which the activity (IC₅₀ = 2.4 μM) is three times greater than (?)-verrucosin 13, was discovered. The induction of apoptosis by caspase 3/7 was observed upon treatment with the (?)-verrucosin derivative.     

Characterization of tetrathionate hydrolase from the marine acidophilic sulfur-oxidizing bacterium,Acidithiobacillus thiooxidans strain SH

Tetrathionate hydrolase (4THase), a key enzyme of the S₄-intermediate (S4I) pathway, was partially purified from marine acidophilic bacterium, Acidithiobacillus thiooxidans strain SH, and the gene encoding this enzyme (SH-tth) was identified. SH-Tth is a homodimer with a molecular mass of 97 ± 3 kDa, and contains a subunit 52 kDa in size. Enzyme activity was stimulated in the presence of 1 M NaCl, and showed the maximum at pH 3.0. Although 4THases from A. thiooxidans and the closely related Acidithiobacillus caldus strain have been reported to be periplasmic enzymes, SH-Tth seems to be localized on the outer membrane of the cell, and acts as a peripheral protein. Furthermore, both 4THase activity and SH-Tth proteins were detected in sulfur-grown cells of strain SH. These results suggested that SH-Tth is involved in elemental sulfur-oxidation, which is distinct from sulfur-oxidation in other sulfur-oxidizing strains such as A. thiooxidans and A. caldus.     

Purification and partial characterization of phytase from rice bean (<Emphasis Type="Italic">Vigna umbellata</Emphasis> Thunb.) germinated seeds

Rice bean (Vigna umbellata Thunb.) phytase activity increased during germination and reached maximum at 72 h. The phytate content in seeds decreased with increase in germination time. Phytase was purified 32 fold from 72-h germinated cotyledons with final specific activity 2.22 U/mg. Native PAGE revealed a single band. On SDS PAGE, it revealed two bands with molecular mass 66 and 44 kDa. The native molecular mass was 110 kDa on size exclusion chromatography. The A₂₈₀/₂₆₀ ratio was 1.88. When the enzyme was excited at 295 nm, the emission maximum was observed at 330 nm. The FTIR results suggest that Lys, Tyr, Phe, Trp, Ser, Gln and Asn residues on the enzyme’s surface. The enzyme was stored at 4 °C, showed 12 % residual activity on 35th day which was improved to 53.6 and 65.7 %, respectively in the presence of additives ascorbic acid and acetaminophen. The optimum pH and temperature of enzyme were 4.0 and 40 °C, respectively. The energy of activation was 32.2 kJ/mol. The values of K _m and V _max were 0.197 mM and 2.35 μmol/min/mg protein, respectively with sodium phytate as substrate. Phytase showed broad substrate specificity. The k _cat/K _m ratio was the highest for sodium phytate.     

Purification and characterization of 2S albumin from Nelumbo nucifera

The 2S albumins are a group of seed storage proteins that have recently attracted considerable attention in the field of allergen science due to their allergenic potential. A new 2S albumin from seeds of Nelumbo nucifera (Nn-2S alb) was purified to electrophoretic homogeneity by the combination of ammonium sulfate fractionation, gel filtration, and ion exchange chromatography. The protein has a molecular mass of about 12 kDa estimated by SDS–PAGE, in good agreement with 12.5 ± 0.01 kDa determined by ESI–MS. Circular dichroism data showed that protein contained about 66% α-helices as estimated by K2D3, indicating that the protein was predominantly helical. The sedimentation coefficient (s°_20,w) of the predicted model was 1.72 ± 0.21 S. The predicted 3-dimensional structure of the Nn-2S alb revealed that the protein has a region of 12 amino acids which largely corresponds to the conserved immuno-dominant epitope of 2S allergens.     

Excluded volume of hard cylinders of variable aspect ratio

In this article, we report expressions for the excluded volume, v _ex and second virial coefficient, B ₂, of hard cylinders as a function of their aspect ratio (𝒜 = L/D), where L and D are the length and diameter of the cylinder, respectively. These expressions are valid for aspect ratio values within the interval 0.001 < 𝒜 < 100, that covers from thin plates to long rods and reproduce Monte Carlo (MC) simulation values. We compare these results with Onsager's predictions and with reported values of hard bodies of similar geometry, as cut spheres (CS), hard spherocylinders (HSC) and linear tangent hard sphere chains (LTHSC). Simulation values for v _ex were obtained with an overlap algorithm that is also presented in detail. The obtained results can be applied in theoretical and computer simulation studies of discotic liquid crystals.     

Cloning and characterization of a cDNA encoding a rice 13 kDa prolamin

Summary A cDNA library constructed from mRNAs obtained from developing rice endosperm was screened with a cDNA clone (RM7) of highest frequency of occurrence (1.8%). The translati) product directed by the mRNA which was hybrid-released from RM7 cDNA in a wheat germ cell-free system showed a molecular size of 13 kDa when coexisting with the protein body fraction of developing maize endosperm. A polypeptide sequence composed of 156 amino acids was deduced from the nucleotide sequence. By comparison with the 19 N-terminal amino acids obtained from Edman degradation of the isolated rice 13 kDa prolamin fraction, the signal sequence was determined as consisting of 19 amino acids. The deduced polypeptide is rich in hydrophobic amino acids such as Leu and Val, and also in Gln, but lacks Lys. Hence, the amino acid composition is consistent with that of rice 13 kDa rolamin. By homology with previously reported cereal prolamins, only a single octapeptide sequence, Gln-Gln-Gln-CysCys-Gln-Gln-Leu, which was observed in 15 kDa and 27 kDa zein, B- and -hordein, /- and -gliadin, and -secalin was conserved in the rice 10 kDa and 13 kDa prolamin. No repetitive sequences and/or sequences homologous to other cereal prolamins, except the above octapeptide, were observed for the mature 13 kDa prolamin polypeptide. The signal sequence region of the 13 kDa prolamin, however, shows homology of more than 65% in both the nucleotide sequence and the amino acid sequence with rice 10 kDa prolamin and maize zein.     

Bacteria and diatom resistance of silicones modified with PEO-silane amphiphiles

Silicone coatings with enhanced antifouling behavior towards bacteria, diatoms, and a diatom dominated slime were prepared by incorporating PEO-silane amphiphiles with varied siloxane tether lengths (a–c): α-(EtO)₃Si(CH₂)₂-oligodimethylsiloxane_n-block-poly(ethylene oxide)₈-OCH₃ [n = 0 (a), 4 (b), and 13 (c)]. Three modified silicone coatings (A–C) were prepared by the acid-catalyzed sol–gel cross-linking of a–c, respectively, each with a stoichiometric 2:3 M ratio of α, ω-bis(Si–OH)polydimethylsiloxane (M_n = 3,000 g mol^?1). The coatings were exposed to the marine bacterium Bacillus sp.416 and the diatom (microalga) Cylindrotheca closterium, as well as a mixed community of Bacillus sp. and C. closterium. In addition, in situ microfouling was assessed by maintaining the coatings in the Atlantic Ocean. Under all test conditions, biofouling was reduced to the highest extent on coating C which was prepared with the PEO-silane amphiphile having the longest siloxane tether length (c).     

Inhibitory effects on microbial growth of Botrytis cinerea and Erwinia carotovora on potato using of a biopolymer chitosan at different molecular weights

The antimicrobial efficiency of chitosan at different molecular weights (5, 37, 57 and 290 kDa) against Botrytis cinerea and Erwinia carotovora on potato (Solanum tuberosum L.) was investigated. In vitro study showed that chitosan of 37 kDa was the most active against E. carotovora (minimum inhibitory concentration (MIC) = 950 mg/L), whereas 5 kDa chitosan was the most active against B.cinerea. Coating of potato tubers with 100, 250 and 500 mg/L significantly decreased the rate of weight loss and chitosan of 37 kDa showed the best effect. The in vivo antibacterial effect indicated that all treatments (500, 1000 and 2000 mg/L) significantly inhibited the growth of E. carotovora compared with the control. The lowest decay incidence was observed with 37 kDa chitosan. However, the antifungal activity against B. cinerea inoculated of leaves showed no decay incidence at 500 and 1000 mg/L with 57 kDa chitosan after 48 h.     

<Superscript>1</Superscript>H, <Superscript>13</Superscript>C and <Superscript>15</Superscript>N backbone NMR chemical shift assignments of the C-terminal P4 domain of Ahnak

Ahnak is a ~?700 kDa polypeptide that was originally identified as a tumour-related nuclear phosphoprotein, but later recognized to play a variety of diverse physiological roles related to cell architecture and migration. A critical function of Ahnak is modulation of Ca²⁺ signaling in cardiomyocytes by interacting with the β subunit of the L-type Ca²⁺ channel (Ca_V1.2). Previous studies have identified the C-terminal region of Ahnak, designated as P3 and P4 domains, as a key mediator of its functional activity. We report here the nearly complete ¹H, ¹³C and ¹⁵N backbone NMR chemical shift assignments of the 11 kDa C-terminal P4 domain of Ahnak. This study lays the foundations for future investigations of functional dynamics, structure determination and interaction site mapping of the Ca_V1.2-Ahnak complex.     

Purification and partial characterization of the extradiol dioxygenase, 2′-carboxy-2,3-dihydroxybiphenyl 1,2-dioxygenase,in the fluorene degradation pathway from Rhodococcus sp. strain DFA3

Type II extradiol dioxygenase, 2′-carboxy-2,3-dihydroxybiphenyl 1,2-dioxygenase (FlnD1D2) involved in the fluorene degradation pathway of Rhodococcus sp. DFA3 was purified to homogeneity from a heterologously expressing Escherichia coli. Gel filtration chromatography and SDS-PAGE suggested that FlnD1D2 is an α₄β₄ heterooctamer and that the molecular masses of these subunits are 30 and 9.9 kDa, respectively. The optimum pH and temperature for enzyme activity were 8.0 and 30 °C, respectively. Assessment of metal ion effects suggested that exogenously supplied Fe²⁺ increases enzyme activity 3.2-fold. FlnD1D2 catalyzed meta-cleavage of 2′-carboxy-2,3-dihydroxybiphenyl homologous compounds, but not single-ring catecholic compounds. The K_m and k_cat/K_m values of FlnD1D2 for 2,3-dihidroxybiphenyl were 97.2 μM and 1.5 × 10^?2 μM^?1sec^?1, and for 2,2′,3-trihydroxybiphenyl, they were 168.0 μM and 0.5 × 10^?2 μM^?1sec^?1, respectively. A phylogenetic tree of the large and small subunits of type II extradiol dioxygenases suggested that FlnD1D2 constitutes a novel subgroup among heterooligomeric type II extradiol dioxygenases.     

Nitrilase superfamily aryl acylamidase from the halotolerant mangrove Streptomyces sp. 211726

A novel nitrilase superfamily amidase gene, designated azl13, was cloned from Streptomyces sp. 211726. Bioinformatic and biochemical analysis indicated that Azl13 belongs to a new subfamily in branch 13 of the nitrilase superfamily. His₆-Azl13 was expressed in Escherichia coli BL21(DE3) and had the expected molecular mass of 31 kDa, and the enzymatic activity was best at 40 °C, pH 8.0. His₆-Azl13 had amidase, aryl acylamidase, and acyl transferase activities, and it displayed an unusually wide substrate spectrum. His₆-Azl13 was most active on 4-guanidinobutyramide, which is probably its natural substrate, moderately active on short-chain aliphatic amides and weakly active hydrolyzing aromatic and heterocyclic amides. His₆-Azl13 also catalyzed acyl transfer to hydroxylamine from acetamide or the herbicide propanil. The substrate spectrum differs from that of the Pseudomonas amidase RamA, probably reflecting high salinity adaptation. The broad substrate spectrum of Azl13 is potentially useful for chemical synthesis and biodegradation.     

Ring-cleaving cyanuric acid amidohydrolase activity in the atrazine-mineralizing Ralstonia basilensis M91-3

The purpose of this study was to characterize the cyanuric acid amidohydrolase reaction in Ralstonia basilensis M91-3, an atrazine-mineralizing soil bacterium. This ring fission reaction is the last aromatic step in the degradative pathway of atrazine and other s-triazines. The products and molar stoichiometry of the cyanuric acid amidohydrolase reaction were one mol biuret (H₂N·CO·NH·CO·NH₂) and one mol CO₂ per mol cyanuric acid hydrolyzed, as confirmed by ¹³C-NMR and gas chromatography. The optimum pH and temperature, substrate specificity, and kinetic parameters were also characterized for the purified enzyme. The native enzyme had two forms of different sizes, 204?kDa and 160?kDa. Each was a tetramer or pentamer of 44?kDa and 33?kDa, respectively.     

<Emphasis Type="Bold">Role of microRNAs and their target genes in salinity response in plant</Emphasis>s

We examined the effects of 2,4-epibrassinolide (EBR) application on photosynthesis, antioxidant enzyme activity, and Rubisco activase (RCA) gene expression in wheat (Triticum aestivum L.) seedlings under a combination of drought and heat stress. The net photosynthetic rates (P_n) of wheat seedlings decreased significantly, the photosynthetic capability was inhibited, and the activities of superoxide (SOD), peroxidase (POD), catalase (CAT), and RCA as well as the initial and total activity of Rubisco declined under the combined stress. These decreases and inhibitory effects were significantly ameliorated by exogenous EBR application. Three subunits (45–46, 41–42, and 38–39 kDa) of RCA were observed in wheat seedlings. The abundances of the 38–39 kDa and 41–42 kDa subunits were significantly lower in plants subjected to stressful conditions than in unstressed plants. Interestingly, a marked increase in 45–46 kDa RCA was observed under heat or heat combined with drought stress. The abundance of 38–39 kDa RCA in seedlings exposed to heat, drought, or their combination was significantly enhanced by EBR pretreatment, which paralleled the changes in initial Rubisco activity and P_n, but was not consistent with observed mRNA abundance. These results indicated that the larger subunit of RCA (45–46 kDa), which is more thermostable and increased in response to moderate heat stress, and the smaller isoform (38–39 kDa) of RCA may play important roles in maintaining the photosynthetic capability by EBR under stress conditions.     

Purification and Characterization of Wild-Type and Mutant Tk1 Type Kinases From Caenorhabditis Elegans

Caenorhabditis elegans has a single deoxynucleoside kinase-like gene. The sequence is similar to that of human TK1, but besides accepting thymidine as a substrate, the C. elegans TK1 (CeTK1) also phosphorylates deoxyguanosine. In contrast to human TK1, the CeTK1 exclusively exists as a dimer with a molecular mass of ～60 kDa, even if incubated with ATP. Incubation with ATP induces a transition into a more active enzyme with a higher k_cat but unchanged K_m. This activation only occurs at an enzyme concentration in the incubation buffer of 0.5 μg/ml (8.42 nM) or higher. C-terminal deletion of the enzyme results in lower catalytic efficiency and stability.