Re-programming DNA-binding specificity in zinc finger proteins for targeting unique address in a genome

Recent studies provide a glimpse of future potential therapeutic applications of custom-designed zinc finger proteins in achieving highly specific genomic manipulation. Custom-design of zinc finger proteins with tailor-made specificity is currently limited by the availability of information on recognition helices for all possible DNA targets. However, recent advances suggest that a combination of design and selection method is best suited to identify custom zinc finger DNA-binding proteins for known genome target sites. Design of functionally self-contained zinc finger proteins can be achieved by (a) modular protein engineering and (b) computational prediction. Here, we explore the novel functionality obtained by engineered zinc finger proteins and the computational approaches for prediction of recognition helices of zinc finger proteins that can raise our ability to re-program zinc finger proteins with desired novel DNA-binding specificities.     

烟草C2H2锌指蛋白转录因子家族成员的鉴定与表达分析

C2H2锌指蛋白转录因子家族在真核生物中具有重要的生物学功能,广泛参与植物叶的发生、花器官的调控、侧枝的形成及逆境胁迫等生命过程。植物C2H2锌指蛋白不仅结合DNA和RNA,而且与蛋白质之间相互作用。本研究利用普通烟草(Nicotiana tabacum)基因组数据库,运用Blastp比对,结合Pfam和SMART分析,鉴定了118条普通烟草C2H2锌指蛋白家族成员;对烟草C2H2锌指蛋白家族进行了进化树分析、结构域分析、物理化学性质分析、染色体定位、基因结构分析、三维结构分析及组织表达分析等。结果表明：不同成员的氨基酸长度差异较大;系统进化及结构域分析显示,所有C2H2家族成员可以被分为5个亚家族,同一亚家族成员之间在结构域和理化性质上呈现较高一致性;每个成员都含有C2H2结构域,在数量上存在较大差异;将所有基因家族成员定位在22条染色体上;组织表达分析表明,每个C2H2亚家族都有成员在不同组织中表达,在叶及根中有些基因的表达量较高。     

Computational predictions of common transcription factor binding sites on the genes of proline metabolism in plants

Proline, an imino acid, has been well documented to be associated with the stress response induced by abiotic factors such asdrought, cold and salinity in plants and biotic factors such as bacterial and fungal attacks. However, the regulatory mechanismscontrolling proline metabolism, intercellular and intracellular transport and connections of proline to other metabolic pathways arepoorly understood. F-MATCH analysis combined with composite module analysis (CMA) revealed that the binding sites matchingmatrices for O2 and OCSBF-1 were overrepresented in the promoters of differentially expressed proline metabolism genes. Thepresence of MYBAS1 consensus binding sites occurring in combination with O2 and OCSBF1 in the promoters of genes of prolinebiosynthesis pathway and SBF1 and GT1 consensus binding sites occurring in combination with O2 and OCSBF1 in the promotersof proline catabolic pathway genes suggest their involvement in modulation of proline metabolism and its accumulation in plants.