Isolation and functional characterization of MxCS1: a gene encoding a citrate synthase in Malus xiaojinensis

Iron is one of the essential micronutrients required by all living organisms. In this study, we isolated a gene encoding putative citrate synthase (CS) from Malus xiaojinensis, designated as MxCS1. The MxCS1 gene encodes a protein of 473 amino acid residues with a predicted molecular mass of 52.5 kDa and a theoretical isoelectric point of 8.67. The expression of MxCS1 was enriched in the leaf rather than in phloem and root, however, its expression was hardly detected in the xylem. The gene expression was strongly induced by Fe stress treatment in the M. xiaojinensis seedlings. Over-expression of MxCS1 improved Fe deficiency tolerance in transgenic Arabidopsis. We argued that MxCS1 is a new member of the CS genes, and it may function as a regulator in response to iron stress in plants.     

Heterologous gene expression in continuous cultures of budding yeast

Summary In a previous paper we have studied the expression of -galactosidase from Escherichia coli, driven from the inducible GAL1-10/CYC1 hybrid promoter, in batch cultures of budding Saccharomyces cerevisiae and have described operating conditions for maximal productivity. In this paper we show that the plasmid instability in continuous cultures can be overcome by utilizing appropriate selection markers and a high copy number vector. The maximal level of expression is influenced by the dilution rate. Moreover, enzyme accumulation appears to depend also upon the degree of oxygenation. A possible explanation of these modulations is discussed, taking into account the interactions of the UAS-GAL and TATA-CYC1 elements. Offprint requests to: D. Porro     

水稻突触融合相关蛋白基因(OsKNOLLE)在酵母中的异源表达及在非生物胁迫中的作用初探

突触融合相关蛋白属于多功能蛋白家族SNARE(SolubleN-ethylmaleimide-sensitive factor attachment pro-tein receptor)的亚家族蛋白,这类家族在植物的许多生理过程中都起着非常重要的作用。为探明水稻突触融合相关蛋白OsKNOLLE(Syntaxin-related protein KNOLLE)的功能,文章从"中花11"水稻根中克隆OsKNOLLE基因的CDS序列并构建到酵母表达载体pYX212上,同时转化酿酒酵母菌株BY4741。通过比较不同酵母转化子在多种非生物因子胁迫下的表型,显示转OsKNOLLE酵母菌比对照菌适应逆境能力更强,表明OsKNOLLE与盐、Cu2+、H2O2、Cd2+、Hg2+胁迫相关,推测OsKNOLLE在植物对逆境的耐性中发挥重要作用。本研究为OsKNOLLE基因的研究提供方法支持,同时明确了其与不同非生物因子的相关性。     

湖北海棠MhPR1a基因的克隆与表达特性分析

以水杨酸诱导的湖北海棠[ Malus hupehensis (Pamp.) Rehd.]全长cDNA文库和基因组DNA为模板,克隆其PR1a基因(MhPR1a)的全编码区序列,并对该序列进行生物信息学分析;在此基础上利用荧光定量RT-PCR技术对湖北海棠根、茎和叶中该基因的表达特性及经过10μmol·L-1ABA、4℃低温处理及苹果蚜虫(Aphis citricola van der Goot)侵染后叶中该基因的表达特性进行了测定.结果表明:克隆获得的MhPR1a基因全长518 bp,最大开放阅读框为492 bp,编码162个氨基酸残基;编码的蛋白质为酸性蛋白,其相对分子质量为16 960,等电点pI 5.46;其基因组DNA序列与cDNA序列完全一致,说明MhPR1a基因内部没有内含子.湖北海棠MhPR1a基因与苹果(M.domestic Borkh.)和沙梨[Pyrus pyrifolia( Burm.f.)Nakai] PR1基因的cDNA序列及其编码的氨基酸序列同源性均较高,其中cDNA序列的同源性均为97％,氨基酸序列的同源性分别为95％和97％;系统树也显示MhPR1a基因编码的氨基酸序列与苹果和沙梨的亲缘关系最近,聚为一类.MhPR1a基因编码的氨基酸序列具有SCP保守结构域,含有1个信号肽和6个保守的半胱氨酸残基.在湖北海棠的叶、茎和根中MhPR1a基因均能表达,在根中的表达量最高.10 μmol·L-1ABA和4℃低温处理48 h后均可诱导MhPR1a基因的表达,且相对表达量明显高于对照(处理0h);苹果蚜虫也可诱导MhPR1a基因的表达,说明MhPR1a基因在湖北海棠抵抗植食昆虫和低温胁迫的过程中可能发挥着重要作用.     

Iron deficiency stress can induce MxNAS1 protein expression to facilitate iron redistribution in Malus xiaojinensis

• Iron (Fe) is a vital trace element in plants, and deficiency of this element in apple trees can reduce fruit quality. Nicotianamine (NA) is known to play an important role in Fe transport and endogenous hormone balance. In the present study, we investigated the role of a nicotianamine synthase 1 gene (MxNas1) in an apple species, Malus xiaojinensis, that has a more Fe‐efficient genotype than other apple species and ecotypes.
• To characterise the response of M. xiaojinensis to Fe deficiency, we used quantitative Q‐PCR to determine the level of expression of MxNas1 and Western blot to measure protein levels. Immunohistochemical staining and GFP fluorescence localisation of the MxNAS1 protein were also carried out. HPLC and polarised absorption spectrophotometry were performed to investigate the effects of overexpression of MxNas1 in order to elucidate the role of MxNAS1 in the cellular uptake of active Fe in tobacco suspension cells.
• We found that MxNas1 expression and protein levels were higher under Fe deficiency stress than under Fe sufficiency. Immunohistochemical staining showed that MxNAS1 was localised mainly in the epidermal and vascular tissues of the roots, vascular tissues of the stem and palisade cells of mature leaves, and in parenchyma cells of young leaves. MxNAS1 was mainly localised in the plasma membranes and vesicles of protoplasts. In addition, overexpression of MxNas1 in stable transgenic tobacco cells increased NA and active Fe content under Fe sufficiency.
• The results suggest that MxNas1 expression in M. xiaojinensis is induced in response to Fe deficiency stress, resulting in higher levels of the protein. MxNAS1 may be involved in the redistribution of Fe in M. xiaojinensis under Fe deficiency.

     

苹果属小金海棠的遗传多样性初步研究

用RAPD技术建立了苹果属小金海棠（Malus xiaojinensis）2个自然分布区的3个群体内随机选取的30株树（10株／每群体）及其相应的子代实生苗共6个群体、60个样本植株的分子标记。通过对15个3承机引物产生的81条RAPD这的统计,计算了不同群体RAPD多态性带的数目。用TREECON软件分析了不同群体及所有个体间的遗传关系,并用AMOVA技术分析了物种的遗传变异。结果是15个引物在全部分析个体中产生了58条多态性带,平均每引物3.8条。现有分布3个群体及其相应的子代实生苗群体的平均多态性带的数目都为1.5条左右。其中平均多态性带的数目最低的群体仅有0.7条,最高的群体也只有2.5条。遗传关系分析表明,2个自然分布区的不同群体间存在遗传分化现象。AMOVA分析显示小金海棠的遗传变异有相当一部分来源于群体间。     

Identifying functional relationships within sets of co-expressed genes by combining upstream regulatory motif analysis and gene expression information

Background

Existing clustering approaches for microarray data do not adequately differentiate between subsets of co-expressed genes. We devised a novel approach that integrates expression and sequence data in order to generate functionally coherent and biologically meaningful subclusters of genes. Specifically, the approach clusters co-expressed genes on the basis of similar content and distributions of predicted statistically significant sequence motifs in their upstream regions.

Results

We applied our method to several sets of co-expressed genes and were able to define subsets with enrichment in particular biological processes and specific upstream regulatory motifs.

Conclusions

These results show the potential of our technique for functional prediction and regulatory motif identification from microarray data.

     

Isolation and preliminary functional characterization of MxWRKY64, a new WRKY transcription factor gene from Malus xiaojinensis Cheng et Jiang

In Vitro Cellular & Developmental Biology - Plant - Malus xiaojinensis Cheng et Jiang is a special and significant germplasm resource of semi-dwarf apple in China. Abiotic stresses, such as Fe...     

Characterization of the MLO gene family in Rosaceae and gene expression analysis in Malus domestica

Background

Powdery mildew (PM) is a major fungal disease of thousands of plant species, including many cultivated Rosaceae. PM pathogenesis is associated with up-regulation of MLO genes during early stages of infection, causing down-regulation of plant defense pathways. Specific members of the MLO gene family act as PM-susceptibility genes, as their loss-of-function mutations grant durable and broad-spectrum resistance.

Results

We carried out a genome-wide characterization of the MLO gene family in apple, peach and strawberry, and we isolated apricot MLO homologs through a PCR-approach. Evolutionary relationships between MLO homologs were studied and syntenic blocks constructed. Homologs that are candidates for being PM susceptibility genes were inferred by phylogenetic relationships with functionally characterized MLO genes and, in apple, by monitoring their expression following inoculation with the PM causal pathogen Podosphaera leucotricha.

Conclusions

Genomic tools available for Rosaceae were exploited in order to characterize the MLO gene family. Candidate MLO susceptibility genes were identified. In follow-up studies it can be investigated whether silencing or a loss-of-function mutations in one or more of these candidate genes leads to PM resistance.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-618) contains supplementary material, which is available to authorized users.     

Heterologous expression of bacteriocin E-760 in Chlamydomonas reinhardtii and functional analysis

The use of antimicrobial peptides (AMPs) synthesized by bacteria (bacteriocins) is an alternative for combating multidrug resistant bacterial strains and their production by recombinant route is a viable option for their mass production. The bacteriocin E-760 isolated from the genus Enterococcus sp. has been shown to possess inhibitory activity against Gram-negative and Gram-positive bacteria. In this study, the expression of a chimeric protein coding for E-760 in the nucleus of C. reinhardtii was evaluated, as well as, its antibacterial activity. The synthetic gene E-760S was inserted into the genome of C. reinhardtii using Agrobacterium tumefaciens. A transgenic line was identified in TAP medium with hygromycin and also by PCR. The increment in the culture medium temperature of the transgenic strain at 35 °C for 10 minutes, increased the production level of the recombinant protein from 0.14 (Noninduced culture, NIC) to 0.36% (Induced culture, IC) of total soluble proteins (TSP); this was quantified by an ELISA assay. Recombinant E-760 possesses activity against Staphylococcus aureus in 0.34 U log, Streptococcus agalactiae in 0.48 U log, Enterococcus faecium in 0.36 U log, Pseudomonas aeruginosa in 2 U log and for Klebsiella pneumoniae, the activity was 0.07 U log. These results demonstrate that the nucleus transformation of C. reinhardtii can function as a stable expression platform for the production of the synthetic gene E-760 and it can potentially be used as an antibacterial agent.     

Heterologous protein expression in the methylotrophic yeast Pichia pastoris

During the past 15 years, the methylotrophic yeast Pichia pastoris has developed into a highly successful system for the production of a variety of heterologous proteins. The increasing popularity of this particular expression system can be attributed to several factors, most importantly: (1) the simplicity of techniques needed for the molecular genetic manipulation of P. pastoris and their similarity to those of Saccharomyces cerevisiae, one of the most well-characterized experimental systems in modern biology; (2) the ability of P. pastoris to produce foreign proteins at high levels, either intracellularly or extracellularly; (3) the capability of performing many eukaryotic post-translational modifications, such as glycosylation, disulfide bond formation and proteolytic processing; and (4) the availability of the expression system as a commercially available kit. In this paper, we review the P. pastoris expression system: how it was developed, how it works, and what proteins have been produced. We also describe new promoters and auxotrophic marker/host strain combinations which extend the usefulness of the system.     

Heterologous expression of the Bacillus pumilus endo-beta-xylanase (xynA) gene in the yeast Saccharomyces cerevisiae

The endo-beta-xylanase-encoding gene (xynA) of Bacillus pumilus PLS was isolated from a genomic DNA library and the open reading frame (ORF) was inserted in expression vectors for the yeast Saccharomyces cerevisiae. Plasmid pFN3 harboured the xynA ORF fused to the yeast mating pheromone alpha-factor signal sequence (MFalpha1s) under the control of the alcohol dehydrogenase II gene promotor (ADH2P) and terminator (ADH2T) sequences. In plasmid pFN4, the MFalpha1S-xynA ORF was brought under the control of the phosphoglycerate kinase I gene promotor (PGK1p) and terminator (PGK1T) sequences. Autoselective, recombinant S. cerevisiae [fur1::LEU2] strains bearing pFN3 or pFN4 secreted functional endo-beta-xylanase when grown in complex medium. Enzymatic activities in the culture supernatants reached maximum levels of 8.5 nkat/ml and 4.5 nkat/ml, respectively. The temperature and pH optimum for both the bacterial and the recombinant xylanase were 58 degrees C and pH 6.2.     

Common gene expression strategies revealed by genome-wide analysis in yeast

Background  

Gene expression is a two-step synthesis process that ends with the necessary amount of each protein required to perform its function. Since the protein is the final product, the main focus of gene regulation should be centered on it. However, because mRNA is an intermediate step and the amounts of both mRNA and protein are controlled by their synthesis and degradation rates, the desired amount of protein can be achieved following different strategies.     

Heterologous expression,purification, and functional characterization of recombinant ovine angiotensinogen in the methylotrophic yeast Pichia pastoris

Angiotensinogen (AGT), a glycosylated plasma noninhibitory serpin, serves as a precursor for angiotensin peptides which regulate blood pressure and electrolyte balance. AGT is specifically cleaved by renin to produce angiotensin-I, the first product of the angiotensin-processing cascade. Ovine angiotensinogen (oAGT) is considered an effective substrate for human renin and consequently finds application in clinical renin assays. In this study, oAGT was cloned into the genome of Pichia pastoris and expressed under the control of alcohol oxidase (AOX1) promoter for high-level production. Compared to the shake flask study, the high cell density cultivation in bioreactor resulted in multifold increase in oAGT titer (420 ± 9.26 mg/L), which is its highest reported titer to date. We purified recombinant oAGT to homogeneity using two chromatography steps. The characterization studies revealed oAGT underwent a two-state transition during thermal denaturation process as assessed by differential scanning fluorimetry, and the melting temperature (T_m) of the purified oAGT from P. pastoris was 48.3°C. Renin reactivity with recombinant oAGT from P. pastoris (0.51 nM angiotensin-I/min) was slightly lower than the renin reactivity for recombinant oAGT from Escherichia coli (0.67 nM angiotensin-I/min), possibly because of its mannosylated N-glycan content. Enhanced production of functionally active recombinant oAGT using P. pastoris expression system reported in this study envisage the effective utilization of oAGT in clinical studies related to renin in near future.     

TMD1 domain and CRAC motif determine the association and disassociation of MxIRT1 with detergent‐resistant membranes

Iron is essential for most living organisms. The iron‐regulated transporter1 (IRT1) plays a major role in iron uptake in roots, and its trafficking from endoplasmic reticulum (ER) to plasma membrane (PM) is tightly coordinated with changes in iron environment. However, studies on the IRT1 response are limited. Here, we report that Malus xiaojinesis IRT1 (MxIRT1) associates with detergent‐resistant membranes (DRMs, a biochemical counterpart of PM microdomains), whereas the PM microdomains are known platforms for signal transduction in the PM. Depending on the shift of MxIRT1 from microdomains to homogeneous regions in PM, MxIRT1‐mediated iron absorption is activated by the cholesterol recognition/interaction amino acid consensus (CRAC) motif of MxIRT1. MxIRT1 initially associates with DRMs in ER via its transmembrane domain 1 (TMD1), and thus begins DRMs‐dependent intracellular trafficking. Subsequently, MxIRT1 is sequestered in COPII vesicles via the ER export signal sequence in MxIRT1. These studies suggest that iron homeostasis is influenced by the CRAC motif and TMD1 domain due to their determination of MxIRT1‐DRMs association.      

Paternity and ploidy segregation of progenies derived from tetraploid Malus xiaojinensis

Apomixis is usually subdivided into parthenogenesis, apogamy, and apospory on the basis of different mechanisms of development and cytogenetic effects. Although most plants and animals undergo sexual reproduction to multiply, it is important to understand the role of apomixis in plant reproduction because of its useful applications in the breeding and propagation of some crops. Tetraploid Malus xiaojinensis Cheng et Jiang is a typical facultative apomictic plant species. Paternity and ploidy analyses of M. xiaojinensis seedlings were performed with flow cytometry in conjunction with microsatellite and single nucleotide polymorphism markers. The proportion of apomictic derived progeny of M. xiaojinensis × Malus baccata was 54.05, 53.96, and 43.55 % from 2008 to 2010, respectively. The progeny of M. xiaojinensis × M. baccata comprised hybrids of 2x, 3x, 4x, or 5x ploidy, whereas apomictic offspring were 2x, 3x, or 4x. Among the apomictic derived progeny, the ploidy of restituted apomictic progeny was 2x, 3x, or 4x, whereas that of nonrestituted apomictic progeny was 4x only. The proportions of the different types of apomictic derived progeny differed among the years 2008 to 2010. The ploidy of progeny from emasculated flowers also segregated into 2x, 3x, and 4x individuals. These results indicate that both parthenogenesis and unreduced meiotic diplospory play important roles in apomictic reproduction in M. xiaojinensis.     

Revealing signaling pathway deregulation by using gene expression signatures and regulatory motif analysis

Gene expression signatures consisting of tens to hundreds of genes have been found to be informative for different biological states. Recently, many computational methods have been proposed for biological interpretation of such signatures. However, there is a lack of methods for identifying cell signaling pathways whose deregulation results in an observed expression signature. We present a strategy for identifying such signaling pathways and evaluate the strategy using six human and mouse gene expression signatures.