From Proteomics to Structural Studies of Cytosolic/MitochondriaI-Type Thioredoxin Systems in Barley Seeds

Thioredoxins （Trx） are ubiquitous proteins that participate in thiol disulfide reactions via two active site cysteine residues, allowing Trx to reduce disulfide bonds in target proteins. Recent progress in proteome analysis has resulted in identification of a wide range of potential target proteins for Trx, indicating that Trx plays a key role in several aspects of cell metabolism. In contrast to other organisms, plants contain multiple forms of Trx that are classified based on their primary structures and sub-cellular localization. The reduction of cytosolic and mitochondrial types of Trx is dependent on NADPH and catalyzed by NADPH-dependent thioredoxin reductase （NTR）. In barley, two isoforms each of Trx and NTR have been identified and investigated using proteomics, gene expression, and structural studies. This review outlines the diverse roles suggested for cytosolic/mitochondrial-type Trx systems in cereal seeds and summarizes the current knowledge of the barley system including recent data on function, regulation, interactions, and structure. Directions for future research are discussed.     

Computational identification of novel family members of microRNA genes in Arabidopsis thaliana and Oryza sativa

MicroRNAs (miRNAs) are a class of endogenous small RNAs that play important regulatory roles in both animals and plants, miRNA genes have been intensively studied in animals, but not in plants. In this study, we adopted a homology search approach to identify homologs of previously validated plant miRNAs in Arabidopsis thaliana and Oryza sativa. We identified 20 potential miRNA genes in Arabidopsis and 40 in O. sativa, providing a relatively complete enumeration of family members for these miRNAs in plants. In addition, a greater number of Arabidopsis miRNAs (MIR168, MIR159 and MIR172) were found to be conserved in rice. With the novel homologs, most of the miRNAs have closely related fellow miRNAs and the number of paralogs varies in the different miRNA families. Moreover, a probable functional segment highly conserved on the elongated stem of pre-miRNA fold-backs of MIR319 and MIR159 family was identified. These results support a model of variegated miRNA regulation in plants, in which miRNAs with different functional elements on their pre-miRNA fold-backs can differ in their function or regulation, and closely related miRNAs can be diverse in their specificity or competence to downregulate target genes. It appears that the sophisticated regulation of miRNAs can achieve complex biological effects through qualitative and quantitative modulation of gene expression profiles in plants.     

Plant Cell Wall Matrix Polysaccharide Biosynthesis

The wall of an expanding plant cell consists primarily of cellulose microfibrils embedded in a matrix of hemicellulosic and pectic polysaccharides along with small amounts of structural and enzymatic proteins. Matrix polysaccharides are synthesized in the Golgi and exported to the cell wall by exocytosis, where they intercalate among cellulose microfibrils, which are made at the plasma membrane and directly deposited into the cell wall. Involvement of Golgi glucan synthesis in auxin-induced cell expansion has long been recognized; however, only recently have the genes corresponding to glucan synthases been identified. Biochemical purification was unsuccessful because of the labile nature and very low abundance of these enzymes. Mutational genetics also proved fruitless. Expression of candidate genes identified through gene expression profiling or comparative genomics in heterologous systems followed by functional characterization has been relatively successful. Several genes from the cellulose synthase-like （Csl） family have been found to be involved in the synthesis of various hemicellulosic glycans. The usefulness of this approach, however, is limited to those enzymes that probably do not form complexes consisting of unrelated proteins. Nonconventional approaches will continue to incrementally unravel the mechanisms of Golgi polysaccharide biosynthesis.     

Small auxin upregulated RNA （SAUR） gene family in maize： Identification,evolution, and its phylogenetic comparison with Arabidopsis,rice, and sorghum

Small auxin-up RNAs （.SAURs） are the early auxin- responsive genes represented by a large multigene family in plants. Here, we identified 79 SAUR gene family members from maize （Zea mays subsp, mays） by a reiterative database search and manual annotation. Phylogenetic analysis indicated that the SAUR proteins from Arabidopsis, rice, sorghum, and maize had divided into 16 groups. These genes were non-randomly distributed across the maize chromosomes, and segmental duplication and tandem duplication contributed to the expansion of the maize .SAUR gene family. Synteny analysis established ortholos~J relationships and functional linkages between SAUR genes in maize and sorghum genomes. We also found that the auxin-responsive elements were conserved in the upstream sequences of maize SAUR members. Selection analyses identified some significant site-specific constraints acted on most SAUR paralogs. Expression profiles based on microarray data have provided insights into the possible functional divergence among members of the .SAUR gene family. Quantitative real-time PCR analysis indicated that some of the 10 randomly selected ZmSAUR genes could be induced at least in maize shoot or root tissue tested. The results reveal a comprehensive overview of the maize .SAUR gene family and may pave the way for deciphering their function during pJant development.     

Bioinformatic identification of genes encoding Clq-domaincontaining proteins in zebrafish

C1q is the first subcomponent of classical pathway in the complement system and a major link between innate and acquired immunities. The globular （gC1q） domain similar with C1q was also found in many non-complement C1q-domain-containing （C1qDC） proteins which have similar crystal structure to that of the multifunctional tumor necrosis factor （TNF） ligand family, and also have diverse functions. In this study, we identified a total of 52 independent gene sequences encoding C1q-domain-containing proteins through comprehensive searches of zebrafish genome, cDNA and EST databases. In comparison to 31 orthologous genes in human and different numbers in other species, a significant selective pressure was suggested during vertebrate evolution. Domain organization of C1q-domain-containing （C1qDC） proteins mainly includes a leading signal peptide, a collagen-like region of variable length, and a C-terminal C1q domain. There are 11 highly conserved residues within the C1q domain, among which 2 are invariant within the zebrafish gene set. A more extensive database searches also revealed homologous C1qDC proteins in other vertebrates, invertebrates and even bacterium, but no homologous sequences for encoding C1qDC proteins were found in many species that have a more recent evolutionary history with zebrafish. Therefore, further studies on C1q-domain-containing genes among different species will help us understand evolutionary mechanism of innate and acquired immunities.     

In silico Analysis of Sequential,Structural and Functional Diversity of Wheat Cystatins and Its Implication in Plant Defense

Phytocystatins constitute a multigene family that regulates the activity of endogenous and/or exogenous cysteine proteinases.Cereal crops like wheat are continuously threatened by a multitude of pathogens,therefore cystatins offer to play a pivotal role in deciding the plant response.In order to study the need of having diverse specificities and activities of various cystatins,we conducted comparative analysis of six wheat cystatins(WCs) with twelve rice,seven barley,one sorghum and ten corn cystatin sequences employing different bioinformatics tools.The obtained results identified highly conserved signature sequences in all the cystatins considered.Several other motifs were also identified,based on which the sequences could be categorized into groups in congruence with the phylogenetic clustering.Homology modeling of WCs revealed 3D structural topology so well shared by other cystatins.Protein-protein interaction of WCs with papain supported the notion that functional diversity is a consequence of existing differences in amino acid residues in highly conserved as well as relatively less conserved motifs.Thus there is a significant conservation at the sequential and structural levels;however,concomitant variations maintain the functional diversity in this protein family,which constantly modulates itself to reciprocate the diversity while counteracting the cysteine proteinases.     

The distinct properties of natural and GM cry insecticidal proteins

The Cry toxins are a family of crystal-forming proteins produced by the bacterium Bacillus thuringiensis. Their mode of action is thought to be to create pores that disrupt the gut epithelial membranes of juvenile insects. These pores allow pathogen entry into the hemocoel, thereby killing the insect. Genes encoding a spectrum of Cry toxins, including Cry mutants, Cry chimaeras and other Cry derivatives, are used commercially to enhance insect resistance in genetically modified (GM) crops. In most countries of the world, such GM crops are regulated and must be assessed for human and environmental safety. However, such risk assessments often do not test the GM crop or its tissues directly. Instead, assessments rely primarily on historical information from naturally occurring Cry proteins and on data collected on Cry proteins (called ‘surrogates’) purified from laboratory strains of bacteria engineered to express Cry protein. However, neither surrogates nor naturally occurring Cry proteins are identical to the proteins to which humans or other nontarget organisms are exposed by the production and consumption of GM plants. To-date there has been no systematic survey of these differences. This review fills this knowledge gap with respect to the most commonly grown GM Cry-containing crops approved for international use. Having described the specific differences between natural, surrogate and GM Cry proteins this review assesses these differences for their potential to undermine the reliability of risk assessments. Lastly, we make specific recommendations for improving risk assessments.     

昆虫类钙粘蛋白与Bt Cry1A蛋白之间的相互作用

类钙粘蛋白(cadherin-likeprotein)位于昆虫中肠刷状缘膜囊泡(brushbordermembranevesicles,BBMV)上,是苏云金芽孢杆菌(Bacillusthuringiensis,Bt)产生的杀虫晶体蛋白(BtCry蛋白)的主要受体之一。它能够与BtCry蛋白结合,引起细胞膜的渗透性发生改变,促进BtCry蛋白对敏感昆虫的毒杀作用。类钙粘蛋白基因的突变还能导致敏感昆虫对BtCry蛋白产生抗性。因此,研究昆虫类钙粘蛋白与BtCry蛋白之间的相互作用,将有助于揭示BtCry蛋白杀虫作用机理。文章对昆虫类钙粘蛋白种类、结构特征、在昆虫体内的分布、及其与BtCry蛋白之间的相互作用等方面的研究现状进行详细论述。     

Antimicrobial peptides are not involved in Plutella xylostella resistance to Cry1Ac

Previous studies on Bacillus thuringiensis (Bt) resistance in the diamondback moth (DBM) Plutella xylostella have often focused on receptor proteins in the gut. In recent years, many studies have indicated that insect resistance to Bt is related to the immune system. Moreover, our group demonstrated that the expression of peptidoglycan recognition protein (PGRP) genes, which are located upstream of the insect humoral immune system signalling pathway, is significantly different between Cry1Ac-resistant and Cry1Ac-susceptible strains of DBM. Thus, whether antimicrobial peptides (AMPs), which are the major downstream effectors of the insect humoral immune system signalling pathway, are also related to the resistance of DBMs to Bt is a question worthy of in-depth study. In the present study, we sought to (a) clone the CDS of AMP genes expressed in DBMs and (b) explore the effect of the cloned AMPs on the biological characteristics and Bt resistance of DBMs. Here, we revealed three kinds of AMPs (PxDef, PxMor and PxCec), and each of their full-length CDSs was cloned. The recombinant PxDef, PxMor or PxCec proteins, which were expressed in a prokaryotic expression system, have a significant protective effect on DBMs in response to the complex microbial environment of the outside world but have no significant effect on the resistance of DBMs to Cry1Ac toxin. We believe that AMPs are not suitable as the primary entry point for studying the relationship between the immune system of DBMs and their resistance to Bt. This result will enable investigation of breakthrough ideas for further elucidating the mechanism of Bt impact on the insect immune system.     

转基因抗虫作物中苏云金芽孢杆菌Cry蛋白的食品安全问题

苏云金芽孢杆菌(Bt)微生物制剂是农业、林业和饮用水等领域用来控制靶标害虫幼虫的有效工具,至今已经有50余年的使用历史。同时其在美国、欧洲和其他一些国家被广泛用于经过认证的有机农业生产之中。目前已获审批的转基因Bt作物中最常使用的是Cry蛋白。Cry蛋白的作用机制、食品安全性以及致敏性已经经过啮齿类动物、农场动物和人体内试验和生物信息学研究的严格检验。Cry蛋白的杀虫作用只在靶标害虫的碱性消化道内,与中肠上皮细胞的特异蛋白受体结合才能起到杀虫作用,而其他非靶标生物体内(人类、猕猴、小鼠、大鼠和牛等)都被证明没有这种特异蛋白质受体。美国、欧洲和其他国家的管理机构都已经证实了转基因Bt作物和Cry蛋白在农作物和饮用水中残留的安全性。食物加工过程能够最大化地减少转基因作物中功能性Cry蛋白的摄入。转基因抗虫作物有利于降低农药杀虫剂的使用的同时,也能够有效防止玉米中伏马菌毒素的污染。     

苏云金杆菌Vip蛋白经历正向达尔文选择的证据

营养期杀虫蛋白(Vip)是苏云金杆菌在营养期所产生的一类新型杀虫蛋白,代表了第二代转基因杀虫蛋白,它能在一定程度上克服许多害虫对δ-内毒素低敏感或者不敏感的缺陷。但是,目前和已经深入研究的δ-内毒素相比较,有关Vip蛋白结构和功能关系方面的报道还甚少。本文采用最大似然方法和基于最大简约的滑窗分析对Vip蛋白的分子进化机制进行了评价。结果发现Vip蛋白在进化过程当中经历了正选择,并采用贝叶斯方法确定了16个正选择氨基酸残基。有意思的是所有这些正选择残基都位于Vip蛋白C端从705到809的区域。当把这些正选择残基定位到二级结构和三级结构时,发现绝大部分正选择残基都暴露在Vip蛋白空间结构的表面并且聚集在环的区域。推测Vip蛋白分子进化的机制应该是受到了正选择压力而不是功能约束的松弛。导致Vip蛋白C端多样性的潜在正选择压力可能是Vip蛋白为了在和目标昆虫之间竞争取得优势,或者是为了扩大Vip蛋白的杀虫范围。文中确定的经历了正选择残基很有可能是和昆虫宿主范围有关,因此可以为今后研究Vip蛋白的结构和功能提供相应的靶点。     

Expression of Cry1Ac cadherin receptors in insect midgut and cell lines

Cadherin-like proteins have been identified as putative receptors for the Bacillus thuringiensis Cry1A proteins in Heliothis virescens and Manduca sexta. Immunohistochemistry showed the cadherin-like proteins are present in the insect midgut apical membrane, which is the target site of Cry toxins. This subcellular localization is distinct from that of classical cadherins, which are usually present in cell-cell junctions. Immunoreactivity of the cadherin-like protein in the insect midgut was enhanced by Cry1Ac ingestion. We also generated a stable cell line Flp-InT-REX-293/Full-CAD (CAD/293) that expressed the H. virescens cadherin. As expected, the cadherin-like protein was mainly localized in the cell membrane. Interestingly, toxin treatment of CAD/293 cells caused this protein to relocalize to cell membrane subdomains. In addition, expression of H. virescens cadherin-like protein affects cell-cell contact and cell membrane integrity when the cells are exposed to activated Cry1Ab/Cry1Ac.     

Rapid cloning, identification, and application of one novel crystal protein gene cry30Fa1 from Bacillus thuringiensis

In this study, a fast and efficient strategy has been developed for identifying and isolating novel cry genes from Bacillus thuringiensis by combining the PCR-restriction fragment length polymorphism and the single-oligonucleotide nested-PCR method. Using this method, one novel holotype cry gene, cry30Fa1 , encoding a polypeptide of 687 amino acid residues with a molecular mass of 77.1 kDa, 74% identical to Cry30Aa1, was cloned from the B. thuringiensis strain BtMC28. Furthermore, the cry30Fa1 gene was successfully expressed in Escherichia coli BL21 (DE3). The Cry30Fa1 proteins, isolated from the cultures of recombinant E. coli , had remarkable insecticidal effects against Plutella xylostella and Aedes aegypti with LC50 at 6.477 and 15.359 μg mL⁻¹, respectively. Our results strongly suggest that this strategy is highly efficient and advantageous in terms of rapid cloning of holotype cry genes that have minimal identity to known genes. The cloning of the cry30Fa1 gene would be useful in the resources of the insecticidal crystal genes and may serve as an alternative choice of an insecticide for potential problems associated with insect resistance.     

Purification of the Cry1Ac protein of Bacillus thuringiensis and assessment against the Plutella xylostella and soil microbial community

The insecticidal toxin gene of Bacillus thuringiensis (Bt) is the most commonly used to develop insect‐resistant living modified organisms (LMOs). Insecticidal proteins produced in transgenic plants are released into the soil from the roots. In this study, possible effects of crystal 1Ac (Cry1Ac) protein on the soil microbial community in Korea were studied. To purify the insoluble Cry1Ac protein expressing Escherichia coli cells, we performed repeated sonication and PBS washing of the insoluble part and Cry1Ac protein was isolated in soluble form from the insoluble form using 100 mM Na₂CO₃ buffer (pH 9.6) without affinity bead. Also, size‐exclusion chromatography (SEC) was performed to increase the purity of the isolated Cry1Ac protein. The final protein product was identified as Cry1Ac protein through MALDI‐TOF. Insecticidal activity of Cry1Ac protein was demonstrated through the death of Plutella xylostella treated with Cry1Ac protein. Purely isolated Cry1Ac protein showed the same insecticidal activity as Cry1Ac expressed in LM crops. To investigate the change of soil microbial distribution using maize field soils treated with Cry1Ac protein, we isolated high quality metagenomic DNAs from buffer‐ and Cry1Ac protein‐treated soil groups, and analyzed the distribution of soil microorganisms through next‐generation sequencing (NGS) analysis. NGS results showed a similar microbial distribution in both buffer‐ and Cry1Ac protein‐treated samples. These results suggest a useful risk assessment method for domestic targeted insect and soil microorganisms using the Cry1Ac protein.     

苏云金芽孢杆菌Cry1Aa和Cry1Ca结构域交换对晶体形态和杀虫活性影响

通过体外重组的方法,实现了苏云金芽孢杆菌杀虫晶体蛋白Cry1Aa和Cry1Ca的功能性结构域Ⅰ、Ⅱ和Ⅲ的互换,得到了6株苏云金杆菌重组菌株BT-ACC,BT-AAC,BT-ACA,BT-CAA,BT-CCA和BT-CAC。SDS-PAGE和Westernblot分析表明,重组菌株BT-CAA和BT-CCA能表达产生135kDa左右的杂交晶体蛋白Cry1CAA和Cry1CCA,但其蛋白表达量较野生型Cry1Aa和Cry1Ca低。用牛胰蛋白酶对杂交晶体蛋白Cry1CAA、Cry1CCA及野生型Cry1Aa和Cry1Ca进行消化,证明所有晶体蛋白都能产生65kDa的活性毒素。电镜观察发现,野生菌株BT-Cry1Aa和BT-Cry1Ca形成典型的菱形晶体,而重组菌株BT-CCA和BT-CAA则形成球形或颗粒状杂交晶体。纯化晶体的生物测定显示,杂交晶体蛋白Cry1CAA和Cry1CCA对甜菜夜蛾的毒力比野生型晶体蛋白降低3~5倍,对棉铃虫的毒力比野生型晶体蛋白降低了190~260倍。研究结果表明,苏云金杆菌晶体蛋白不同结构域的相互作用会影响杂交晶体蛋白的表达、晶体形态和杀虫活性。