CCCH-type zinc finger family in maize: genome-wide identification, classification and expression profiling under abscisic acid and drought treatments

Background

CCCH-type zinc finger proteins comprise a large protein family. Increasing evidence suggests that members of this family are RNA-binding proteins with regulatory functions in mRNA processing. Compared with those in animals, functions of CCCH-type zinc finger proteins involved in plant growth and development are poorly understood.

Methodology/Principal Findings

Here, we performed a genome-wide survey of CCCH-type zinc finger genes in maize (Zea mays L.) by describing the gene structure, phylogenetic relationships and chromosomal location of each family member. Promoter sequences and expression profiles of putative stress-responsive members were also investigated. A total of 68 CCCH genes (ZmC3H1-68) were identified in maize and divided into seven groups by phylogenetic analysis. These 68 genes were found to be unevenly distributed on 10 chromosomes with 15 segmental duplication events, suggesting that segmental duplication played a major role in expansion of the maize CCCH family. The Ka/Ks ratios suggested that the duplicated genes of the CCCH family mainly experienced purifying selection with limited functional divergence after duplication events. Twelve maize CCCH genes grouped with other known stress-responsive genes from Arabidopsis were found to contain putative stress-responsive cis-elements in their promoter regions. Seven of these genes chosen for further quantitative real-time PCR analysis showed differential expression patterns among five representative maize tissues and over time in response to abscisic acid and drought treatments.

Conclusions

The results presented in this study provide basic information on maize CCCH proteins and form the foundation for future functional studies of these proteins, especially for those members of which may play important roles in response to abiotic stresses.     

Comprehensive analysis of CCCH-type zinc finger gene family in citrus (Clementine mandarin) by genome-wide characterization

The CCCH-type zinc finger proteins comprise a large gene family of regulatory proteins and are widely distributed in eukaryotic organisms. The CCCH proteins have been implicated in multiple biological processes and environmental responses in plants. Little information is available, however, about CCCH genes in plants, especially in woody plants such as citrus. The release of the whole-genome sequence of citrus allowed us to perform a genome-wide analysis of CCCH genes and to compare the identified proteins with their orthologs in model plants. In this study, 62 CCCH genes and a total of 132 CCCH motifs were identified, and a comprehensive analysis including the chromosomal locations, phylogenetic relationships, functional annotations, gene structures and conserved motifs was performed. Distribution mapping revealed that 54 of the 62 CCCH genes are unevenly dispersed on the nine citrus chromosomes. Based on phylogenetic analysis and gene structural features, we constructed 5 subfamilies of 62 CCCH members and integrative subfamilies from citrus, Arabidopsis, and rice, respectively. Importantly, large numbers of SNPs and InDels in 26 CCCH genes were identified from Poncirus trifoliata and Fortunella japonica using whole-genome deep re-sequencing. Furthermore, citrus CCCH genes showed distinct temporal and spatial expression patterns in different developmental processes and in response to various stress conditions. Our comprehensive analysis of CleC3Hs is a valuable resource that further elucidates the roles of CCCH family members in plant growth and development. In addition, variants and comparative genomics analyses deepen our understanding of the evolution of the CCCH gene family and will contribute to further genetics and genomics studies of citrus and other plant species.     

Genome-wide survey and expression profiling of CCCH-zinc finger family reveals a functional module in macrophage activation

Previously, we have identified a novel CCCH zinc finger protein family as negative regulators of macrophage activation. To gain an overall insight into the entire CCCH zinc finger gene family and to evaluate their potential role in macrophage activation, here we performed a genome-wide survey of CCCH zinc finger genes in mouse and human. Totally 58 CCCH zinc finger genes in mouse and 55 in human were identified and most of them have not been reported previously. Phylogenetic analysis revealed that the mouse CCCH family was divided into 6 groups. Meanwhile, we employed quantitative real-time PCR to profile their tissue expression patterns in adult mice. Clustering analysis showed that most of CCCH genes were broadly expressed in all of tissues examined with various levels. Interestingly, several CCCH genes Mbnl3, Zfp36l2, Zfp36, Zc3h12a, Zc3h12d, Zc3h7a and Leng9 were enriched in macrophage-related organs such as thymus, spleen, lung, intestine and adipose. Consistently, a comprehensive assessment of changes in expression of the 58 members of the mouse CCCH family during macrophage activation also revealed that these CCCH zinc finger genes were associated with the activation of bone marrow-derived macrophages by lipopolysaccharide. Taken together, this study not only identified a functional module of CCCH zinc finger genes in the regulation of macrophage activation but also provided the framework for future studies to dissect the function of this emerging gene family.     

Characterization and phylogenetic analysis of environmental stress-responsive <Emphasis Type="Italic">SAP</Emphasis> gene family encoding A20/AN1 zinc finger proteins in tomato

Characterization of genes responsive to stress is important for efforts on improving stress tolerance of plants. To address components involved in stress tolerance of tomato (Solanum lycopersicum), a stress-responsive gene family encoding A20/AN1 zinc finger proteins was characterized. In the present study, 13 members of this gene family were cloned from tomato cultivar Pusa Ruby and named as Stress Associated Protein (SAP) genes. Out of 13 genes, 12 have been mapped on their respective chromosomes. Expression of these genes in response to cold, heat, salt, desiccation, wounding, abscisic acid, oxidative and submergence stresses was analysed. All tomato SAP genes were found to be responsive to one or other type of environmental stress. The phylogenetic analysis of these genes, along with their orthologs from Solanaceae species suggests the presence of a common set of SAP genes in the studied Solanaceae species. The present study characterizes a SAP gene family, which encodes A20/AN1 zinc finger containing proteins from tomato for the first time. Genes showing high expression in response to a particular stress can be exploited for improving stress tolerance of tomato and other Solanaceae members. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genome Wide Identification of C2H2-Type Zinc Finger Proteins of Tomato and Expression Analysis Under Different Abiotic Stresses

In plants, C2H2-type zinc finger proteins play important roles in multiple processes, including plant growth and development, as well as biotic and abiotic responses. In the present study, based on the presence of the C2H2 domain (CX2~4CX3FX5LX2HX3~5H), 112 C2H2-type zinc finger proteins were predicted in tomato. Through gene and protein structures analyses and phylogenetic analysis, the 112 C2H2-type zinc finger proteins were divided into five subfamilies. Members of the same subfamily shared similarities in gene and protein structures, while members of different subfamilies contained different numbers of the C2H2 domain. The tissue expression pattern analysis showed that 24 C2H2-type zinc finger proteins are constitutively expressed in all tissues, indicating that they may play important roles in the growth and development of all tissues. In addition, under chilling (4 °C), heat (42 °C), high salinity (200 Mm NaCl), and osmotic (20% PEG) stresses, members of C2H2-type zinc finger family were induced to varying degrees, which suggested that these genes were involved in multiple abiotic stress responses. This study will provide theoretical basis for further research of C2H2-type zinc finger proteins in tomato.

     

水稻种子发育期间特异锌指蛋白基因的筛选与分析

.锌指蛋白基因是植物基因组中最大最复杂的基因家族之一.大部分的锌指模体存在于转录因子中,它们在转录水平上参与植物生长发育及植物对生物和非生物胁迫的反应.为了解锌指蛋白基因在水稻种子发育中的作用,本研究通过多种数据库搜索获得了878个水稻锌指蛋白基因.从中选取311个利用RT-PCR技术分析它们在水稻成熟期根、茎、叶、花及不同发育阶段种子中的表达特征.结果发现,共有196个基因能在至少1个水稻器官中表达,其中10个为种子特异性表达基因.进一步分析发现,10个特异表达基因在水稻种子不同发育阶段中的表达具有种子阶段表达特异性.同时分析它们的基因及蛋白结构特点,结果显示它们的结构较简单,其中3个蛋白含有线粒体靶肽,5个蛋白含有CCCH锌指结构域.另外,分析种子特异性表达基因上游调控区的顺式作用元件,结果表明它们都含有TATA-box、CAAT-box和种子特异调控元件,除此之外还发现了光、激素和胁迫反应相关调控元件.这些结果为进一步研究它们在种子发育过程中的生物学功能提供了有用的线索.     

番茄AT-hook基因家族的鉴定及胁迫条件下的表达分析

AT-hook蛋白家族在植物生长发育、器官构建及逆境胁迫和激素信号应答中发挥重要作用。本研究在番茄基因组范围内,利用生物信息学方法对番茄AT-hook基因家族的成员、分布、结构和功能进行分析。结果表明,番茄AT-hook家族包含32个成员,分为3种类型,其中类型Ⅰ含有13个成员;遗传进化分析表明番茄AT-hook基因成员与拟南芥家族基因具有相似分类。利用实时荧光定量PCR对番茄32个基因开展组织表达分析,结果表明AT-hook基因具有表达差异,主要在根和花中表达较高。氧化胁迫分析结果表明,32个基因受ABA、SA、盐、高温和低温诱导表达,其中部分基因显著上调或下调表达,很可能参与了番茄逆境胁迫条件下的防御应答反应。本研究结果将为番茄AT-hook家族基因的深入研究提供依据,为进一步解析番茄AT-hook基因的功能奠定基础。     

Genome-Wide Analysis of Two-Component Systems and Prediction of Stress-Responsive Two-Component System Members in Soybean

In plants, the two-component systems (TCSs) play important roles in regulating diverse biological processes, including responses to environmental stress stimuli. Within the soybean genome, the TCSs consist of at least 21 histidine kinases, 13 authentic and pseudo-phosphotransfers and 18 type-A, 15 type-B, 3 type-C and 11 pseudo-response regulator proteins. Structural and phylogenetic analyses of soybean TCS members with their Arabidopsis and rice counterparts revealed similar architecture of their TCSs. We identified a large number of closely homologous soybean TCS genes, which likely resulted from genome duplication. Additionally, we analysed tissue-specific expression profiles of those TCS genes, whose data are available from public resources. To predict the putative regulatory functions of soybean TCS members, with special emphasis on stress-responsive functions, we performed comparative analyses from all the TCS members of soybean, Arabidopsis and rice and coupled these data with annotations of known abiotic stress-responsive cis-elements in the promoter region of each soybean TCS gene. Our study provides insights into the architecture and a solid foundation for further functional characterization of soybean TCS elements. In addition, we provide a new resource for studying the conservation and divergence among the TCSs within plant species and/or between plants and other organisms.     

Superfamily of ankyrin repeat proteins in tomato

The ankyrin repeat (ANK) protein family plays a crucial role in plant growth and development and in response to biotic and abiotic stresses. However, no detailed information concerning this family is available for tomato (Solanum lycopersicum) due to the limited information on whole genome sequences. In this study, we identified a total of 130 ANK genes in tomato genome (SlANK), and these genes were distributed across all 12 chromosomes at various densities. And chromosomal localizations of SlANK genes indicated 25 SlANK genes were involved in tandem duplications. Based on their domain composition, all of the SlANK proteins were grouped into 13 subgroups. A combined phylogenetic tree was constructed with the aligned SlANK protein sequences. This tree revealed that the SlANK proteins comprise five major groups. An analysis of the expression profiles of SlANK genes in tomato in different tissues and in response to stresses showed that the SlANK proteins play roles in plant growth, development and stress responses. To our knowledge, this is the first report of a genome-wide analysis of the tomato ANK gene family. This study provides valuable information regarding the classification and putative functions of SlANK genes in tomato.     

Multiple genes encoding zinc finger domains are expressed in human T cells

Proteins containing zinc finger domains have been implicated in developmental control of gene expression in Drosophila, Xenopus, mouse, and humans. Multiple cDNAs encoding zinc (II) finger structures were isolated from human cell lines of T-cell origin to explore whether zinc finger genes participate in the differentiation of human hematopoietic cells. Initial restriction analysis, genomic Southern blotting, and partial sequence comparisons revealed at least 30 nonoverlapping cDNAs designated cKox(1-30) encoding zinc finger motifs. Analysis of cKox1 demonstrated that Kox1 is a single-copy gene that is expressed in a variety of hematopoietic and nonhaematopoietic cell lines. cKox1 encodes 11 zinc fingers that were shown to bind zinc when expressed as a beta-gal-Kox1 fusion protein. Further analysis of the predicted amino acid sequence revealed a heptad repeat of leucines NH2-terminal to the finger region, which suggests a potential domain for homo- or heterodimer protein formation. On the basis of screening results it was estimated that approximately 70 zinc finger genes are expressed in human T cells. Zinc finger motifs are probably present in a large family of proteins with quite diverse and distinct functions. However, comparisons of individual finger regions in cKox1 with finger regions of cKox2 to cKox30 showed that some zinc fingers are highly conserved in their putative alpha-helical DNA binding region, supporting the notion of a zinc finger-specific DNA recognition code.     

A CCCH-type zinc finger nucleic acid-binding protein quantitatively confers resistance against rice bacterial blight disease

Bacterial blight is a devastating disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv oryzae (Xoo). Zinc finger proteins harboring the motif with three conserved cysteine residues and one histidine residue (CCCH) belong to a large family. Although at least 67 CCCH-type zinc finger protein genes have been identified in the rice genome, their functions are poorly understood. Here, we report that one of the rice CCCH-type zinc finger proteins, C3H12, containing five typical CX(8)-CX(5)-CX(3)-H zinc finger motifs, is involved in the rice-Xoo interaction. Activation of C3H12 partially enhanced resistance to Xoo, accompanied by the accumulation of jasmonic acid (JA) and induced expression of JA signaling genes in rice. In contrast, knockout or suppression of C3H12 resulted in partially increased susceptibility to Xoo, accompanied by decreased levels of JA and expression of JA signaling genes in rice. C3H12 colocalized with a minor disease resistance quantitative trait locus to Xoo, and the enhanced resistance of randomly chosen plants in the quantitative trait locus mapping population correlated with an increased expression level of C3H12. The C3H12 protein localized in the nucleus and possessed nucleic acid-binding activity in vitro. These results suggest that C3H12, as a nucleic acid-binding protein, positively and quantitatively regulates rice resistance to Xoo and that its function is likely associated with the JA-dependent pathway.     

香樟全基因组WRKY基因家族的鉴定与分析

WRKY转录因子基因家族是植物特有的一类基因,在植物次生代谢、生物和非生物胁迫中起着重要的调节作用。本研究通过生物信息学方法,在香樟(Cinnamomum camphora (L.) Presl.)全基因组中鉴定了60个WRKY基因(CcWRKY),并将其分为Group Ⅰ~ Ⅲ,其中,Group Ⅰ和Ⅲ的成员发生了收缩现象;片段复制是CcWRKY基因扩张的主要驱动力;Group Ⅰ有完整的WRKY结构域和锌指基序,但Group Ⅱ、Ⅲ存在结构域和锌指基序的丢失和变异现象;CcWRKY基因的启动子区域具有激素类和胁迫类响应顺式作用元件;基因表达分析结果显示,在贫瘠环境(未施肥)中大多数CcWRKY基因在香樟各个组织中高表达,而环境适宜(施肥)条件下,基因表达量降低。