Stress-induced early flowering is mediated by miR169 in Arabidopsis thaliana.

Plants interact with their environment and they often flower earlier under stress conditions, but how such stress-induced flowering is regulated remains poorly understood. Here evidence is presented that the miR169 family plays a key role in stress-induced flowering in plants. The microRNA (miRNA) miR169 family members are up-regulated in Arabidopsis, maize, and soybean under abiotic stresses. Overexpression of miR169d in Arabidopsis results in early flowering, and overexpression of the miR169d target gene, AtNF-YA2, especially a miR169d-resistant version of AtNF-YA2, results in late flowering. The results suggest that the miR169 family regulates stress-induced flowering by repressing the AtNF-YA transcription factor, which in turn reduces the expression of FLOWERING LOCUS C (FLC), allowing for the expression of FLC target genes such as FLOWERING LOCUS T (FT) and LEAFY (LFY) to promote flowering. It was shown that the expression of genes or miRNAs involved in the other flowering pathways, namely the photoperiod (CO), ambient temperature (SVP), ageing (miR156), and gibberelin (SOC1) pathways, was not affected in miR169d-overexpressing plants, suggesting that stress-induced early flowering is a novel signalling pathway mediated by miR169.

Rolling circle amplification-mediated long hairpin RNA library construction in plants.

Gene silencing has been used widely in gene function studies and crop plant modification. Long hairpin RNA (lhRNA) results in high efficiency of gene silencing; however, constructing multiple lhRNA vectors using traditional approaches is both time consuming and costly. Also, most of the existing approaches are based on sequence-specific cloning of individual sequences and are therefore not suitable for preparing hpRNA libraries from a pool of mixed target sequences. The rolling circle amplification (RCA)-mediated hairpin RNA (RMHR) construction system is suitable for generating hairpin libraries from any gene of interest or pool of genes. Using the RMHR system, a long-hairpin RNA (lhRNA) library is generated from an Arabidopsis cDNA population containing known and unknown genes. Our results indicate that the RMHR technique permits the rapid, efficient, and low-cost preparation of genome-wide lhRNA expression libraries.

Functional analysis of BnMAR element in transgenic tobacco plants.

Scaffold/matrix attachment regions (S/MARs) are defined as genomic DNA sequences, located at the physical boundaries of chromatin loops. Previous reports suggest that S/MARs elements may increase and stabilize the expression of transgene. In this study, DNA sequence with MAR characteristics has been isolated from B. napus . The BnMARs sequence was used to flank the CaMV35S-GUS-NOS expression cassette within the T-DNA of the plant expression vector pPZP212. These constructs were introduced into tobacco plants, respectively and the GUS reporter gene expression was investigated in stably transformed plants. When the forward BnMARs sequence was inserted into the upstream of CaMV35S promoter, the average GUS activities were much higher than those without BnMARs in transgenic tobacco. The GUS expression of M(+)35S:GUS, M(+)35S:GUSM(+) and M(+)35S:GUSM(-) constructs increased average 1.0-fold, with or without BnMARs located downstream of NOS. The GUS expression would not be affected when reverse BnMARs sequence inserted whether upstream of CaMV35S promoter or downstream of NOS. The GUS expression was affected a little when reverse BnMARs sequence was inserted the downstream of NOS and BnMARs could not act by serving as of promoter. The results showed that the presence of forward BnMARs sequence does have an obvious impact on enhancing downstream gene expression and its effect is unidirectional.

An intramolecular disulfide bond is required for the thermostability of methyl parathion hydrolase, OPHC2.

OPHC2, a methyl parathion hydrolase (MPH) from Pseudomonas pseudoalcaligenes C2-1 (CGMCC 1150), can degrade a wide range of organophosphate pesticides. Compared with other MPHs, OPHC2 exhibits high thermostability. Its thermostability mechanism, however, remains unknown. In the present study, sequence analysis demonstrated that two cysteines (Cys110 and Cys146) exist in OPHC2, but not in other MPHs. The three-dimensional structural model of OPHC2 performed by computer-assisted homology modelling revealed a potential stacking network with residues Cys110 and Cys146, which probably formed an intramolecular disulfide bond. Furthermore, both sodium dodecyl sulphate-polyacrylamide gel electrophoresis and thiol-titration analyses indicated that OPHC2 contains a disulfide bond. Substitution of the disulfide bond-forming cysteines with alanine, leucine or methionine residues substantially decreased the thermostability of OPHC2, suggesting that disulfide bond formation affects conformational stability. These results, combined with three-dimensional structural modelling, demonstrated that the formation of a C110-C146 disulfide bond may stabilise the conformation of OPHC2, contributing to its thermostability.

A simple artificial microRNA vector based on ath-miR169d precursor from Arabidopsis.

Artificial microRNA (amiRNA) is becoming a powerful tool for silencing genes in plants, and several amiRNA vectors have recently been developed based on the natural precursor structures of ath-miR159a, ath-miR164b, ath-miR172a, ath-miR319a and osa-miR528. In this study we generated a simple amiRNA vector (pAmiR169d) based on the structure of Arabidopsis miR169d precursor (pre-miR169d). Two unique restriction sites were created inside the stem region of pre-miR169d, which allows for the artificial miRNA sequences to be cloned as either ~80 bp synthetic oligonucleotides or PCR products. A beta-glucuronidase:green florescent protein fusion gene (GUS-GFP) was efficiently silenced in transient assays using a pAmiR169d-derived construct targeting the GUS-GFP sequence. 5'-RACE showed that the target GUS-GFP transcript was cleaved precisely at the expected position across nucleotides 10 and 11 of the artificial miRNA. Thus, pAmiR169d allows for both easy construction of artificial miRNA constructs and efficient silencing of target genes in plants.

Nesterenkonia alba sp. nov., an alkaliphilic actinobacterium isolated from the black liquor treatment system of a cotton pulp mill.

An alkaliphilic actinobacterium, designated strain CAAS 252(T), was isolated from the black liquor treatment system of a cotton pulp mill in Wuhan, China. Cells of strain CAAS 252(T) were Gram-positive, non-motile, non-endospore-forming, short rod-shaped, and grew optimally at 42 degrees C and pH 9-10 in the presence of 3 % (w/v) NaCl. Strain CAAS 252(T) contained MK-7, MK-8 and MK-9 as the major menaquinones and anteiso-C(17 : 0), anteiso-C(15 : 0) and C(16 : 0) as the predominant cellular fatty acids and had a peptidoglycan type of A4alpha, Lys-Gly-d-Asp. The DNA G+C content was 60.2 mol%. Based on analysis of 16S rRNA gene sequences (94.7-96.8 % similarity), DNA-DNA hybridization (<70 % relatedness) and chemotaxonomic characteristics, strain CAAS 252(T) belonged to the genus Nesterenkonia, but differed from all recognized species. Therefore, it is proposed that strain CAAS 252(T) represents a novel species of the genus Nesterenkonia, for which the name Nesterenkonia alba sp. nov. is proposed. The type strain is CAAS 252(T) (=CCTCC AB 207011(T)=DSM 19423(T)).

Rolling circle amplification-mediated hairpin RNA (RMHR) library construction in plants.

Long hairpin RNA (lhRNA) construct-induced gene silencing facilitates the study of gene function in plants and animals, but constructing multiple lhRNA vectors using traditional approaches is both time-consuming and costly. Also, most of the existing approaches are based on sequence-specific cloning of individual sequences, and are therefore not suitable for preparing hpRNA libraries from a pool of mixed target sequences. Here we describe a rolling-circle amplification (RCA)-mediated hpRNA (RMHR) construction system suitable for generating libraries of lhRNA constructs from any gene of interest or pool of genes. Using RMHR we successfully generated a lhRNA library from a Arabidopsis cDNA population containing known and unknown genes, with an average size of 500-800 bp for the inverted-repeat inserts. To validate the RMHR system, lhRNA constructs targeting the beta-glucuronidase (GUS) gene were tested using Agrobacterium infiltration and shown to be effective at inducing GUS silencing in tobacco leaves. Our results indicate that the RMHR technique permits rapid, efficient and low-cost preparation of genome-wide lhRNA expression libraries.

Nesterenkonia flava sp. nov., isolated from paper-mill effluent.

A Gram-positive, non-motile, rod-shaped, non-spore-forming bacterium, designated CAAS 251T, was isolated from paper-mill effluent in Wuhan, China. The organism grew optimally at 40-42 degrees C and at pH 9.0-10.0. The major menaquinones were MK-7, MK-8 and MK-9. The predominant cellular fatty acids were anteiso-C15:0 (34.78 %), anteiso-C17:0 (25.24 %) and C16:0 (13.37 %). The G+C content of the genomic DNA was 65.5 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain CAAS 251T belongs to the genus Nesterenkonia, having sequence identities ranging from 96.0 to 97.0 % with respect to eight recognized species of the genus Nesterenkonia. Data from DNA-DNA hybridization and physiological and biochemical tests indicated that strain CAAS 251T represents a novel species of the genus Nesterenkonia, for which the name Nesterenkonia flava sp. nov. is proposed. The type strain is CAAS 251T (=CCTCC AB 207010T=JCM 14814T).

Eukaryotic expression and antimicrobial spectrum determination of the peptide tachyplesin II.

Ta0-a, the gene encoding the mature antimicrobial peptide tachyplesin II, was engineered to optimize the coding sequence according to codon usage bias in yeast. Ta0-a was efficiently expressed in the methylotrophic yeast Pichia pastoris strain SMD1168. The recombinant peptide Ta0 reached 150mg/L after methanol induction for 6 d. Ta0 was rapidly purified to homogeneity by a single step of size-exclusion chromatography. The minimal lethal concentrations of Ta0 to the Escherichia coli strain K12 was 30 microg/mL. Ta0 exhibited a wide range of antimicrobial activity: the growth of 26 bacterial and fungal strains, including some typical food/feed spoilage microorganisms, was all substantially inhibited. This result indicates the potential practical application of the recombinant peptide in various industrial products.

Cloning and characterization of microRNAs from Brassica napus.

A library containing approximately 40,000 small RNA sequences was constructed for Brassica napus. Analysis of 3025 sequences obtained from this library resulted in the identification of 11 conserved miRNA families, which were validated by secondary structure prediction using surrounding sequences in the Brassica genome. Two 21 nt small RNA sequences reside within the arm of a pre-miRNA like stem-loop structure, making them likely candidates for novel non-conserved miRNAs in B. napus. Most of the conserved miRNAs were expressed at similar levels in a F1 hybrid B. napus line and its four double haploid progeny that showed marked variations in phenotypes, but many were differentially expressed between B. napus and Arabidopsis. The miR169 family was expressed at high levels in young leaves and stems, but was undetectable in roots and mature leaves, suggesting that miR169 expression is developmentally regulated in B. napus.

[Use of rpoB and 16S rDNA genes to analyze rumen bacterial diversity of goat using PCR and DGGE].

DNA extraction from the rumen of three species of goat (boer goat, Nanjiang yellow goat, Inner Mongolia cashmere goat) was followed by Polymerase Chain Reaction (PCR) amplification of the beta subunit of the RNA polymerase (rpoB) and 16S rDNA genes. PCR products were compared by Denaturing Gradient Gel Electrophoresis (DGGE) to compare the predominant bacterial community structure. The results showed the rpoB DGGE profiles comprised fewer bands than those of 16S rDNA profiles and were easier to analyze. The gene for rpo B is a single copy gene unlike 16S rDNA. So using the rpoB gene offeres a better alternative to the commonly used 16S rRNA gene for microbial community analyses based on DGGE. The bacteria community structure of different goats were similar to each other. The similarities within species were noticeably higher than that between species. Goat species were found to influence the rumen microbe community. Phylogenetic and sequence similarity analyses of the resultant 14 clone sequences in16S rDNA DGGE libraries revealed that 4 clone show similarity over 97% with that of database sequences, while the rest present similarity in a range of 89%-96%, and 13 clone of all were similar to those unidentified rumen bacteria. These results suggest that DGGE followed by clone technique is a practicable protocol to research the complex community of rumen microbe.

Functional expression of the keratinolytic serine protease gene sfp2 from Streptomyces fradiae var. k11 in Pichia pastoris.

We report the initial characterization and expression of sfp2, a gene encoding a keratinolytic serine protease from Streptomyces fradiae var. k11. Recombinant SFP2 was expressed in and secreted from the yeast Pichia pastoris with a final yield of 78 mg/L (136.2 U/mL caseinolytic activity) after 25 h of induction. The recombinant enzyme was purified using by ammonium sulfate precipitation and gel filtration chromatography to electrophoretic homogeneity, which was appropriately glycosylated and had a molecular mass of 26.0 kDa. The purified recombinant SFP2 was characterized. The optimal pHs and temperatures of SFP2 for proteolysis of casein and keratin azure were pH 10.0, 60 degrees C, and pH 9.0, 55 degrees C, respectively. SFP2 activity was stable from pH 3.0 to pH 11.0. The enzyme activity was inhibited by Co(2+) and Cr(3+) and enhanced by Ni(2+) and Cu(2+). The K(m) of 0.45 mmol/L and V(max) of 19.84 mmol/min mg were calculated using N-succinyl-Ala-Ala-Pro-Phe-pNA as a substrate. We tested the activity of SFP2 with soluble and insoluble substrates; SFP2 was more specific for keratinous substrates compared with proteinase K and other commercial proteases.

[Mutation research on Q23L and Q23LG272E in phytase derivated from Aspergillus fumigatus].

Aspergillus fumigatus wild-type phytase has many favorable properties, such as a good thermorstability and a broad pH optimum. However, the specific activity of the enzyme is relative low. A. fumigatus Q23L phytase resulted in a remarkable increase in specific activity around pH4.5 - 7.0, but the pH stability of Q23L was lower than A. fumigatus wild-type phytase. To increase the pH stability of Q23L, the mutant Q23LG272E was constructed by site-directed mutagenesis with PCR. The gene of A. fumigatus wild-type phytase and the mutant genes encoding the Q23LG272E and the Q23L were correctly expressed in Pichia pastoris GS115. Enzymes were purified and their enzymatic properties were determined. The results revealed that the specific activity of the Q23L improved remarkably, which increased from 51 u/mg of the wild type to 109 u/mg at pH5.5. Meanwhile, the pH stability of Q23L, decreased evidently, especially from pH3.0 to pH4.0.The pH stability of Q23LG272E in pH3.0 - 4.5 and pH6.5 - 7.0 has been improved compared with Q23L. The specific activity of Q23LG272E basically maintained at the level of Q23L. Analysis of 3-D structure and sequence similarity were used to reveal the presumable factors influencing the enzymatic properties of Q23LG272E, and discussion for the relationship between structure and function of phytase was given.

[Isolation and characterization of gamma-TMT gene promoter from Arabidopsis thaliana].

Vitamin E (Tocopherols) is lipid-soluble antioxidants and essential for human health. Gamma-tocopherol methyltransferase (delta-TMT), one of the key enzymes in tocopherol biosynthetic pathway in plants, converts delta,sigma-tocopherols into alpha,beta-tocopherols. In this study, we isolated the 1552 bp promoter of Arabidopsis TMT gene. The promoter was fused with GUS reporter gene and this expression cassette was introduced into wild Arabidopsis thaliana by Agrobacterium-mediated transformation. GUS staining shows that GUS gene is expressed in leaves, stems and flowers, with the highest expression in young leaves, stamens and stem apices, while not observable in roots, seeds and siliques. The data indicate that gamma-TMT gene promoter is likely to be expressed preferentially in some of the tissues of Arabidopsis.

Expression of organophosphorus hydrolase OPHC2 in Pichia pastoris: purification and characterization.

Organophosphorus hydrolase is able to hydrolyze phosphoester bonds and reduce the toxicity of organophosphorus compounds. In this work, recombinant organophosphorus hydrolase OPHC2 was successfully produced by Pichia pastoris at a high expression level (approximately 5.5 g/L) using 3 L high-cell-density fermentation. The expression level is higher than those produced in other expression systems. The results of the SDS-PAGE and the Western blot analyses showed a major 36 kDa polypeptide band, which was the same size as that from the original bacteria, Pseudomonas pseudoalcaligenes C2-1. The expressed enzyme was recovered from the culture supernatant and purified by a single-step purification procedure with a recovery rate of 72.78%. The main physiochemical features of the recombinant OPHC2, including its optimum temperature and pH for the reaction, its temperature and pH stability, and its sensitivity to some metal ions and chemical reagents, were also characterized. With methyl parathion as a substrate, the optimum temperature and pH for enzyme activity are 65 degrees C and pH 9.0, respectively. It also shows good thermal and pH stability.

[Improvement of the thermostability of xylanase by N-terminus replacement].

The hybrid xylanase TB was constructed by the substitution of the N-terminus segment of the Streptomyces olivaceoviridis xylanase XYNB with corresponding region of Thermomonosporafusca xylanase TfxA. The hybrid gene tb, encoding the TB, was correctly expressed in Escherichia coli BL21 and Pichia pastoris GS115. TB was purified and its enzymatic properties were determined. The results revealed that the optimal temperature and optimal pH of TB were at 70 degrees C and 6.0, which have been obviously improved compared with those of XYNB. The thermostability of TB were all about six-fold of XYNB's after incubating the properly diluted enzyme solutions at 80 degrees C and 90 degrees C for 3min, respectively. The pH stability of TB was 5 to approximately 9, which was narrower than that of XYNB. Still, TB remains a high specific activity as XYNB does. Analysis of a homology modeling and sequence similarity were used to reveal the factors influencing the enzymatic properties of TB and the discussion for the relationship between structure and function of xylanase was given.

[Gene cloning and expression of serine protease SFP2 from Streptomyces fradiae var. k11].

Extracellular serine protease SFP2 from Streptomyces fradiae var. k11 with high feather-degrading activity was purified. The partial amino acid sequences of internal peptide of purified SFP2 were determined, and the partial gene encoding SFP2 was cloned by PCR using the degenerate primers designed according to the amino acid sequences. Complete sfp2 gene was cloned by screening the genomic DNA library of Streptomyces fradiae var. k11. The Open Reading Frame of sfp2 including pre- pro-enzyme is 924bp long (EMBL Accession number: AJ784940). The signal peptide sequence is as long as 114bp, the precursor sequence is 810bp and the mature enzyme is 576bp long, encoding 191 amino acid resides with the putative molecular weight of 19.112kD. In E. coli and Bacillus subtilis, the two sequences encoding SFP2 pro-enzyme and mature enzyme were both expressed successfully. The pro-enzyme expressed had normal biological function and its mature product had normal enzymatic activity.

[Hydrophobic interaction between beta-sheet B1 and B2 in xylanase XYNB influencing the enzyme thermostability].

A homology modeling of xylanase XYNB from Streptomyces olivaceoviridis A1 was made by Swiss-Model. The hydrophobic Interaction between beta-sheet B1 and B2 in the tertiary structure model of XYNB was compared with other thermophilic xylanase. A T11Y mutation was introduced in XYNB by site-dirrected mutagenesis to improve the thermostability of the enzyme. The XYNB and mutant xylanase (XYNB') expressed in Pichia pastoris were purified and their enzymatic properties were determined. The result revealed that the thermostability of XYNB' was obviously higher than that of XYNB. The optimal temperature of XYNB' for its activity was 60 degrees C, similar to XYNB. But, compare to XYNB, the optimal pH value, the Km value and the specific activity of XYNB' had also been changed. The research results suggested that the aromatic interaction between beta-sheet B1 and B2 in xylanase should increase enzyme thermostability. The mutant xylanase XYNB' is a good material for further research in the relationship between structure and function of xylanase.

[Overexpression of Aspergillus candidus lactase and analysis of enzymatic properties].

The lactase gene lacb' from Aspergillus candidus was fused behind alpha-factor signal sequence in the Pichia pastoris expression vector pPIC9, then integrated into the genome of P. pastoris by recombination events. The P. pastoris recombinants for lactase overexpression were screened by enzyme activity analysis and SDS-PAGE. The lactase expressed in P. pastoris was glycosylated protein with an apparent molecular weight of 130 kD, while the deglycosylated lactase treated with Endo H had an apparent molecular weight of about 110 kD. The expression level of secreted lactase protein in recombinant P. pastoris was 6 mg/mL with enzymatic activity of 3600 U/mL in the 5 L fermenter, which was the highest among that of all kinds of recombinant strains reported now. The optimal pH and optimal temperature of the lactase are 5.2 and 60 degrees C. The Vmax, Km, and specific activity of the lactase are 3.3 micromol/min, 1.7 mmol/L and 706.5 +/- 2.6 U/mg, respectively. Compare to the lactase from Aspergillus oryzae ATCC 20423, the expressed lactase from A. candidus have better enzymatic properties including the high thermostability, high specific activity and wide pH range for enzyme reaction.

[Recent advances in structures and relative enzyme properties of xylanase].

Xylanase can hydrolyze xylans into xylooligosaccharides and D-xylose, and has great prospect for applications in feed industry, paper and pulp industry, food industry and environment science. The study of xylanase had been started in 1960's. With the development and application of the new technologies, such as molecular biology, structural biology and protein engineering, many progresses have been made in the research of structures and functions of xylanase. This paper reviews the research progress and trend in the structure correlating with the important properties of xylanase. Analyses of three-dimensional structures and properties of mutants have revealed that glutamine and aspartic acid residues are involved in the catalytic mechanism. The thermostability of xylanase correlated with many factors, such as disulfide bridges, salt bridges, aromatic interactions, cotent of arginine and proline, and some multidomain xylanase have thermostability domains in N or C terminal. But no single mechanism is responsible for the remarkable stability of xylanase. The isoelectic points and reaction pH of xylanase are influenced by hydrophobicity and content of electric charges. Many researches had demonstrated that aromatic amino acid, histidine, and tryptophan play an important role in improving enzyme-substrate affinity. The researches of structures and functions of xylanase are of great significance in understanding the catalytic mechanism and directing the improvement of xylanase properties to meet the application requirement.