Genome-Wide Identification and Analysis of the TIFY Gene Family in Grape

Background

The TIFY gene family constitutes a plant-specific group of genes with a broad range of functions. This family encodes four subfamilies of proteins, including ZML, TIFY, PPD and JASMONATE ZIM-Domain (JAZ) proteins. JAZ proteins are targets of the SCF^COI1 complex, and function as negative regulators in the JA signaling pathway. Recently, it has been reported in both Arabidopsis and rice that TIFY genes, and especially JAZ genes, may be involved in plant defense against insect feeding, wounding, pathogens and abiotic stresses. Nonetheless, knowledge concerning the specific expression patterns and evolutionary history of plant TIFY family members is limited, especially in a woody species such as grape.

Methodology/Principal Findings

A total of two TIFY, four ZML, two PPD and 11 JAZ genes were identified in the Vitis vinifera genome. Phylogenetic analysis of TIFY protein sequences from grape, Arabidopsis and rice indicated that the grape TIFY proteins are more closely related to those of Arabidopsis than those of rice. Both segmental and tandem duplication events have been major contributors to the expansion of the grape TIFY family. In addition, synteny analysis between grape and Arabidopsis demonstrated that homologues of several grape TIFY genes were found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the divergence of lineages that led to grape and Arabidopsis. Analyses of microarray and quantitative real-time RT-PCR expression data revealed that grape TIFY genes are not a major player in the defense against biotrophic pathogens or viruses. However, many of these genes were responsive to JA and ABA, but not SA or ET.

Conclusion

The genome-wide identification, evolutionary and expression analyses of grape TIFY genes should facilitate further research of this gene family and provide new insights regarding their evolutionary history and regulatory control.     

茉莉酸信号途径中转录抑制因子JAZ蛋白家族的分子进化分析

茉莉酸在植物的生长发育、应激反应和次生代谢过程中起着重要的调控作用。转录抑制因子JAZ（Jasmonate ZIM-domain）蛋白则是茉莉酸信号从SCF^coi1受体复合物向下游茉莉酸应答基因转导的纽带。采用比较基因组学的方法。从多谱系的角度对植物JAZ蛋白家族进行分子进化分析并取得以下研究结果。（1）在藻类植物、苔藓植物、蕨类植物、裸子植物及单、双子叶植物6个不同谱系的15种代表植物基因组中,鉴定了82个JAZ同源基因,其中在低等藻类植物基因组中没有鉴定到JAZ同源基因,提示JAZ家族基因可能起源于陆生植物。（2）系统发育分析表明,在植物基因组中JAZ蛋白家族可分为10个保守的亚家族,而谱系特异扩增尤其是串联重复和区段重复可能是陆生植物JAZ家族基因扩增与进化的主要机制,并导致多个谱系特异的JAZ亚家族产生。（3）基因结构分析表明,JAZ家族基因含有0一7个数目不等、62—4222bp长度不等的内含子,提示在植物基因组进化过程中,JAZ家族基因可能发生内含-丢失或内含子插入缺失,进而导致基因外显子．内含子结构的多样性。该研究结果将为植物JAZ蛋白家族的深入研究提供参考。     

A computational study of elongation factor G (EFG) duplicated genes: diverged nature underlying the innovation on the same structural template

Background

Elongation factor G (EFG) is a core translational protein that catalyzes the elongation and recycling phases of translation. A more complex picture of EFG''s evolution and function than previously accepted is emerging from analyzes of heterogeneous EFG family members. Whereas the gene duplication is postulated to be a prominent factor creating functional novelty, the striking divergence between EFG paralogs can be interpreted in terms of innovation in gene function.

Methodology/Principal Findings

We present a computational study of the EFG protein family to cover the role of gene duplication in the evolution of protein function. Using phylogenetic methods, genome context conservation and insertion/deletion (indel) analysis we demonstrate that the EFG gene copies form four subfamilies: EFG I, spdEFG1, spdEFG2, and EFG II. These ancient gene families differ by their indispensability, degree of divergence and number of indels. We show the distribution of EFG subfamilies and describe evidences for lateral gene transfer and recent duplications. Extended studies of the EFG II subfamily concern its diverged nature. Remarkably, EFG II appears to be a widely distributed and a much-diversified subfamily whose subdivisions correlate with phylum or class borders. The EFG II subfamily specific characteristics are low conservation of the GTPase domain, domains II and III; absence of the trGTPase specific G2 consensus motif “RGITI”; and twelve conserved positions common to the whole subfamily. The EFG II specific functional changes could be related to changes in the properties of nucleotide binding and hydrolysis and strengthened ionic interactions between EFG II and the ribosome, particularly between parts of the decoding site and loop I of domain IV.

Conclusions/Significance

Our work, for the first time, comprehensively identifies and describes EFG subfamilies and improves our understanding of the function and evolution of EFG duplicated genes.     

WASP Family Proteins: Their Evolution and Its Physiological Implications

WASP family proteins control actin polymerization by activating the Arp2/3 complex. Several subfamilies exist, but their regulation and physiological roles are not well understood, nor is it even known if all subfamilies have been identified. Our extensive search reveals few novel WASP family proteins. The WASP, WASH, and SCAR/WAVE subfamilies are evolutionarily ancient, with WASH the most universally present, whereas WHAMM/JMY first appears in invertebrates. An unusual Dictyostelium WASP homologue that has lost the WH1 domain has retained its function in clathrin-mediated endocytosis, demonstrating that WASPs can function with a remarkably diverse domain topology. The WASH and SCAR/WAVE regulatory complexes are much more rigidly maintained; their domain topology is highly conserved, and all subunits are present or lost together, showing that the complexes are ancient and functionally interdependent. Finally, each subfamily has a distinctive C motif, indicating that this motif plays a specific role in each subfamily''s function, unlike the generic V and A motifs. Our analysis identifies which features are universally conserved, and thus essential, and which are branch-specific modifications. It also shows the WASP family is more widespread and diverse than currently appreciated and unexpectedly biases the physiological role of the Arp2/3 complex toward vesicle traffic.     

Structural Basis for Dimerization and Catalysis of a Novel Esterase from the GTSAG Motif Subfamily of the Bacterial Hormone-sensitive Lipase Family

Hormone-sensitive lipases (HSLs) are widely distributed in microorganisms, plants, and animals. Microbial HSLs are classified into two subfamilies, an unnamed new subfamily and the GDSAG motif subfamily. Due to the lack of structural information, the detailed catalytic mechanism of the new subfamily is not yet clarified. Based on sequence analysis, we propose to name the new subfamily as the GTSAG motif subfamily. We identified a novel HSL esterase E25, a member of the GTSAG motif subfamily, by functional metagenomic screening, and resolved its structure at 2.05 Å. E25 is mesophilic (optimum temperature at 50 °C), salt-tolerant, slightly alkaline (optimum pH at 8.5) for its activity, and capable of hydrolyzing short chain monoesters (C2–C10). E25 tends to form dimers both in the crystal and in solution. An E25 monomer contains an N-terminal CAP domain, and a classical α/β hydrolase-fold domain. Residues Ser¹⁸⁶, Asp²⁸², and His³¹² comprise the catalytic triad. Structural and mutational analyses indicated that E25 adopts a dimerization pattern distinct from other HSLs. E25 dimer is mainly stabilized by an N-terminal loop intersection from the CAP domains and hydrogen bonds and salt bridges involving seven highly conserved hydrophilic residues from the catalytic domains. Further analysis indicated that E25 also has some catalytic profiles different from other HSLs. Dimerization is essential for E25 to exert its catalytic activity by keeping the accurate orientation of the catalytic Asp²⁸² within the catalytic triad. Our results reveal the structural basis for dimerization and catalysis of an esterase from the GTSAG motif subfamily of the HSL family.     

苹果DREB转录因子家族全基因组鉴定与分析

DREB转录因子属于AP2/ERF转录因子家族,能够与DRE/CRT顺式作用元件特异性结合,调控与逆境应答基因的表达,因而在植物应对低温、干旱、高盐等逆境胁迫中发挥重要作用。该研究利用苹果全基因组数据,通过生物信息学手段鉴定苹果DREB转录因子家族成员,并分析DREB转录因子家族保守域特点与功能及表达情况。结果表明:从苹果全基因组中共鉴定出60个DREB转录因子家族成员,与拟南芥和水稻相比基本一致,通过引入拟南芥DREB基因进行系统发生分析,进一步可以将其细分为6个亚组;结构域和保守元件分析表明,DREB基因家族含有一个AP2保守结构域;染色体定位表明,苹果DREB基因分布于11条染色体上,部分基因存在串联复制现象;基因结构分析显示,该亚家族基因不含内含子。利用同源拟南芥RNA-Seq数据分析结果表明,DREB转录因子家族对低温、ABA调节等非生物胁迫具有调控作用,同时在DREB亚家族中每个亚组响应不同的非生物胁迫;通过分析DREB基因在不同组织中的表达情况,结果显示DREB基因在植物根部中的表达量最强,其次是叶。