Ye Wenwu, Wang Yang, Dong Suomeng, Tyler Brett M, Wang Yuanchao
Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China.
BMC Genomics. 2013 Nov 28;14(1):839. doi: 10.1186/1471-2164-14-839.
Basic leucine zipper (bZIP) transcription factors are present exclusively in eukaryotes and constitute one of the largest and most diverse transcription factor families. The proteins are responsible for central developmental and physiological processes in plants, animals, and fungi, including the pathogenicity of fungal plant pathogens. However, there is limited understanding of bZIPs in oomycetes, which are fungus-like organisms in the kingdom Stramenopila. Oomycetes include many destructive plant pathogens, including the well-studied species Phytophthora sojae, which causes soybean stem and root rot.
Candidate bZIPs encoded in the genomes of P. sojae and four other oomycetes, two diatoms, and two fungal species were predicted using bioinformatic methods. Comparative analysis revealed expanded numbers of bZIP candidates in oomycetes, especially the Phytophthora species, due to the expansion of several novel bZIP classes whose highly conserved asparagines in basic DNA-binding regions were substituted by other residues such as cysteine. The majority of these novel bZIP classes were mostly restricted to oomycetes. The large number of novel bZIPs appears to be the result of widespread gene duplications during oomycete evolution. The majority of P. sojae bZIP candidates, including both conventional and novel bZIP classes, were predicted to contain canonical protein secondary structures. Detection of gene transcripts using digital gene expression profiling and qRT-PCR suggested that most of the candidates were not pseudogenes. The major transcriptional shifts of bZIPs occurred during the zoosporangia/zoospore/cyst and host infection stages. Several infection-associated bZIP genes were identified that were positively regulated by H2O2 exposure.
The identification of large classes of bZIP proteins in oomycetes with novel bZIP motif variants, that are conserved and developmentally regulated and thus presumably functional, extends our knowledge of this important family of eukaryotic transcription factors. It also lays the foundation for detailed studies of the roles of these proteins in development and infection in P. sojae and other oomycetes.
碱性亮氨酸拉链（bZIP）转录因子仅存在于真核生物中，是最大且最多样化的转录因子家族之一。这些蛋白质负责植物、动物和真菌的核心发育和生理过程，包括真菌植物病原体的致病性。然而，对于卵菌纲（属于不等鞭毛生物界的类似真菌的生物体）中的bZIP转录因子，人们了解有限。卵菌纲包括许多具有破坏性的植物病原体，其中包括被广泛研究的大豆疫霉，它会导致大豆茎腐病和根腐病。
利用生物信息学方法预测了大豆疫霉以及其他四种卵菌、两种硅藻和两种真菌基因组中编码的候选bZIP转录因子。比较分析表明，由于几个新的bZIP类别发生扩增，卵菌纲，尤其是疫霉属物种中的bZIP候选转录因子数量有所增加，这些新类别中碱性DNA结合区域高度保守的天冬酰胺被其他残基（如半胱氨酸）取代。这些新的bZIP类别大多仅限于卵菌纲。大量新的bZIP转录因子似乎是卵菌纲进化过程中广泛基因复制的结果。大豆疫霉的大多数bZIP候选转录因子，包括传统和新的bZIP类别，预计都含有典型的蛋白质二级结构。使用数字基因表达谱和定量逆转录聚合酶链反应检测基因转录本表明，大多数候选转录因子不是假基因。bZIP转录因子的主要转录变化发生在游动孢子囊/游动孢子/孢囊和宿主感染阶段。鉴定出了几个与感染相关的bZIP基因，它们受到过氧化氢暴露的正向调控。
在卵菌纲中鉴定出大量具有新bZIP基序变体的bZIP蛋白，这些变体保守且受发育调控，因此可能具有功能，这扩展了我们对这个重要的真核转录因子家族的认识。这也为详细研究这些蛋白质在大豆疫霉和其他卵菌的发育和感染中的作用奠定了基础。
