The Athb-1 and -2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities.

The Arabidopsis Athb-1 and -2 proteins are characterized by the presence of a homeodomain (HD) with a closely linked leucine zipper motif (Zip). We have suggested that the HD-Zip motif could, via dimerization of the leucine zippers, recognize dyad-symmetric DNA sequences. Here we report an analysis of the DNA binding properties of the Athb-1 homeodomain-leucine zipper (HD-Zip-1) domain in vitro. DNA binding analysis performed using random-sequence DNA templates showed that the HD-Zip-1 domain, but not the Athb-1 HD alone, binds to DNA. The HD-Zip-1 domain recognizes a 9 bp dyad-symmetric sequence [CAAT(A/T)ATTG], as determined by selecting high-affinity binding sites from random-sequence DNA. Gel retardation assays demonstrated that the HD-Zip-1 domain binds to DNA as a dimer. Moreover, the analysis of the DNA binding activity of Athb-1 derivatives indicated that a correct spatial relationship between the HD and the Zip is essential for DNA binding. Finally, we determined that the Athb-2 HD-Zip domain recognizes a distinct 9 bp dyad-symmetric sequence [CAAT(G/C)ATTG]. A model of DNA binding by the HD-Zip proteins is proposed.     

小黑杨HD-Zip转录因子家族生物信息学及应答盐胁迫分析

HD-Zip转录因子基因是植物中特有的一类蛋白家族,在植物生长发育和逆境应答胁迫过程中发挥重要作用。HD-Zip转录因子基因是由高度保守的同源异型结构域（HD）和亮氨酸拉链域（LZ）结构域构成的特殊结构模型。杨树HD-Zip转录因子家族共有63个基因,可被分为HD-ZipⅠ、HD-ZipⅡ、HD-ZipⅢ和HD-ZipⅣ四个亚家族。本文利用RNA-Seq分析了盐胁迫条件下HD-Zip基因家族在小黑杨根、茎、叶等不同组织的基因表达差异,从转录组水平揭示其应答胁迫环境的分子机制,结果表明,盐胁迫下在叶中有25个HD-Zip基因下调表达,21个基因上调表达;茎中有42个基因下调表达,11个基因上调表达;根中有26个基因下调表达,24个基因上调表达。另外,本文根据拟南芥HD-Zip转录因子家族基因的已知功能,预测了杨树HD-Zip转录因子同源基因的功能,并利用生物信息学方法分析了杨树HD-Zip转录因子蛋白序列的保守结构域、氨基酸组成和理化性质等,为进一步研究杨树HD-Zip转录因子基因功能提供参考。     

Crystal Structure of the cGMP-dependent Protein Kinase II Leucine Zipper and Rab11b Protein Complex Reveals Molecular Details of G-kinase-specific Interactions

cGMP-dependent protein kinase (PKG)-interacting proteins (GKIPs) mediate cellular targeting of PKG isoforms by interacting with their leucine zipper (LZ) domains. These interactions prevent aberrant signaling cross-talk between different PKG isotypes. To gain detailed insight into isotype-specific GKIP recognition by PKG, we analyzed the type II PKG leucine zipper domain and found that residues 40–83 dimerized and specifically interacted with Rab11b. Next, we determined a crystal structure of the PKG II LZ-Rab11b complex. The PKG II LZ domain presents a mostly nonpolar surface onto which Rab11b docks, through van der Waals interactions. Contact surfaces in Rab11b are found in switch I and II, interswitch, and the β1/N-terminal regions. This binding surface dramatically differs from that seen in the Rab11 family of interacting protein complex structures. Structural comparison with PKG Iα and Iβ LZs combined with mutagenic analysis reveals that GKIP recognition is mediated through surface charge interactions.