Xiaojian Peng

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.

Systematic Analysis of Sequences and Expression Patterns of Drought-Responsive Members of the HD-Zip Gene Family in Maize

Background Members of the homeodomain-leucine zipper (HD-Zip) gene family encode transcription factors that are unique to plants and have diverse functions in plant growth and development such as various stress responses, organ formation and vascular development. Although systematic characterization of this family has been carried out in Arabidopsis and rice, little is known about HD-Zip genes in maize (Zea mays L.). Methods and Findings In this study, we described the identification and structural characterization of HD-Zip genes in the maize genome. A complete set of 55 HD-Zip genes (Zmhdz1-55) were identified in the maize genome using Blast search tools and categorized into four classes (HD-Zip I-IV) based on phylogeny. Chromosomal location of these genes revealed that they are distributed unevenly across all 10 chromosomes. Segmental duplication contributed largely to the expansion of the maize HD-ZIP gene family, while tandem duplication was only responsible for the amplification of the HD-Zip II genes. Furthermore, most of the maize HD-Zip I genes were found to contain an overabundance of stress-related cis-elements in their promoter sequences. The expression levels of the 17 HD-Zip I genes under drought stress were also investigated by quantitative real-time PCR (qRT-PCR). All of the 17 maize HD-ZIP I genes were found to be regulated by drought stress, and the duplicated genes within a sister pair exhibited the similar expression patterns, suggesting their conserved functions during the process of evolution. Conclusions Our results reveal a comprehensive overview of the maize HD-Zip gene family and provide the first step towards the selection of Zmhdz genes for cloning and functional research to uncover their roles in maize growth and development.

A novel maize homeodomain-leucine zipper (HD-Zip) I gene, Zmhdz10, positively regulates drought and salt tolerance in both rice and Arabidopsis.

Increasing evidence suggests that homeodomain-leucine zipper I (HD-Zip) I transcription factors play important roles in abiotic stress responses, but no HD-Zip I proteins have been reported in maize. Here, a drought-induced HD-Zip I gene, Zmhdz10, was isolated from maize and characterized for its role in stress responses. Real-time quantitative PCR showed that expression of Zmhdz10 was also induced by salt stress and ABA. Transient expression of Zmhdz10-green fluorescent protein (GFP) fusion proteins in onion cells showed a nuclear localization of Zmhdz10. Yeast hybrid assays demonstrated that Zmhdz10 has transactivation and DNA-binding activity in yeast cells. Overexpression of Zmhdz10 in rice led to enhanced tolerance to drought and salt stresses and increased sensitivity to ABA. Moreover, Zmhdz10 transgenic plants had lower relative electrolyte leakage (REL), lower malondialdehyde (MDA) and increased proline content relative to wild-type plants under stress conditions, which may contribute to enhanced stress tolerance. Zmhdz10 transgenic Arabidopsis plants also exhibited enhanced tolerance to drought and salt stresses that was concomitant with altered expression of stress/ABA-responsive genes, including Δ1-Pyrroline-5-carboxylate synthetase 1 (P5CS1), Responsive to dehydration 22 (RD22), Responsive to dehydration 29B (RD29B) and ABA-insensitive 1 (ABI1). Taken together, these results suggest that Zmhdz10 functions as a transcriptional regulator that can positively regulate drought and salt tolerance in plants through an ABA-dependent signaling pathway.

Whole-genome survey and characterization of MADS-box gene family in maize and sorghum

MADS-box genes comprise a large gene family, which codes for transcription factors, and play important functions in various aspects of flowering plant growth and development. However, little is known about the MADS-box genes in maize (Zea mays) and sorghum (Sorghum bicolor). Here, we performed a comprehensive bioinformatics analysis of the MADS-box gene family in the maize and sorghum genomes and identified 75 maize and 65 sorghum MADS-box genes. We subsequently carried out a comparative analysis of these genes, including the gene structure, phylogenetic relationship, conserved protein motifs, gene duplications, chromosomal locations and expression pattern between the two plants. According to these analyses, the MADS-box genes in both maize and sorghum were categorized into five (MIKCC, MIKC*, Mα, Mβ and Mγ) groups, and the MIKCC groups were further divided into 11 subfamilies. In addition, gene duplications of MADS-box genes were also investigated in the maize, sorghum, rice and Arabidopsis genomes. We found a higher percentage of MADS-box gene duplications in the maize and sorghum genomes, which contributed to the expansion of the MADS-box gene family. Furthermore, both tandem and segmental duplications played a major role in the MADS-box gene expansion in maize and sorghum. A survey of maize and sorghum EST sequences indicated that MADS-box genes exhibit a various expression pattern, suggesting diverse and novel functions of MADS-box gene families in the two plants. These results provided a useful reference for selection of candidate MADS-box genes for cloning and further functional analysis in both maize and sorghum.

Overexpression of a maize WRKY58 gene enhances drought and salt tolerance in transgenic rice

WRKY transcription factors (TFs) are reported to play crucial roles in the processes of plant growth and development, defense regulation and stress responses. In this study, a WRKY group IId TF, designated ZmWRKY58, was isolated from maize (Zea mays L.). Expression pattern analysis revealed that ZmWRKY58 was induced by drought, salt and abscisic acid treatments. Subcellular localization experiments in onion epidermal cells showed the presence of ZmWRKY58 in the nucleus. Overexpression of ZmWRKY58 in rice resulted in delayed germination and inhibited post-germination development. Further investigation showed that ZmWRKY58 overexpressing transgenic plants had higher survival rates and relative water contents, but lower malonaldehyde contents and relative electrical leakage compared with wild-type plants, following drought and salt stress treatments, suggesting that overexpression of ZmWRKY58 leads to enhanced tolerance to drought and salt stresses in transgenic rice. Additionally, yeast two-hybrid assay showed that ZmWRKY58 could interact with ZmCaM2, suggesting that ZmWRKY58 may function as a calmodulin binding protein. Taken together, these results suggest that ZmWRKY58 may act as a positive regulator involved in the drought and salt stress responses.

Molecular evolution of the HD-ZIP I gene family in legume genomes

Homeodomain leucine zipper I (HD-ZIP I) genes were used to increase the plasticity of plants by mediating external signals and regulating growth in response to environmental conditions. The way genomic histories drove the evolution of the HD-ZIP I family in legume species was described; HD-ZIP I genes were searched in Lotus japonicus, Medicago truncatula, Cajanus cajan and Phaseolus vulgaris, and then divided into five clades through phylogenetic analysis. Microsynteny analysis was made based on genomic segments containing the HD-ZIP I genes. Some pairs turned out to conform with syntenic genome regions, while others corresponded to those that were inverted, expanded, or contracted after the divergence of legumes. Besides, we dated their duplications by Ks analysis and demonstrated that all the blocks were formed after the monocot-dicot split; we observed Ka/Ks ratios representing strong purifying selections in the four legume species which might have been followed by gene loss and rearrangement.

Genomewide identification, classification and analysis of NAC type gene family in maize

NAC transcription factors comprise a large plant-specific gene family. Increasing evidence suggests that members of this family have diverse functions in plant growth and development. In this study, we performed a genomewide survey of NAC type genes in maize (Zea mays L.). A complete set of 148 nonredundant NAC genes (ZmNAC1–ZmNAC148) were identified in the maize genome using Blast search tools, and divided into 12 groups (a–l) based on phylogeny. Chromosomal location of these genes revealed that they are distributed unevenly across all 10 chromosomes. Segmental and tandem duplication contributed largely to the expansion of the maize NAC gene family. The Ka/Ks ratio suggested that the duplicated genes of maize NAC family mainly experienced purifying selection, with limited functional divergence after duplication events. Microarray analysis indicated most of the maize NAC genes were expressed across different developmental stages. Moreover, 19 maize NAC genes grouped with published stress-responsive genes from other plants were found to contain putative stress-responsive cis-elements in their promoter regions. All these stress-responsive genes belonged to the group d (stress-related). Further, these genes showed differential expression patterns over time in response to drought treatments by quantitative real-time PCR analysis. Our results reveal a comprehensive overview of the maize NAC, and form the foundation for future functional research to uncover their roles in maize growth and development.

PIGD: a database for intronless genes in the Poaceae

BackgroundIntronless genes are a feature of prokaryotes; however, they are widespread and unequally distributed among eukaryotes and represent an important resource to study the evolution of gene architecture. Although many databases on exons and introns exist, there is currently no cohesive database that collects intronless genes in plants into a single database.DescriptionIn this study, we present the Poaceae Intronless Genes Database (PIGD), a user-friendly web interface to explore information on intronless genes from different plants. Five Poaceae species, Sorghum bicolor, Zea mays, Setaria italica, Panicum virgatum and Brachypodium distachyon, are included in the current release of PIGD. Gene annotations and sequence data were collected and integrated from different databases. The primary focus of this study was to provide gene descriptions and gene product records. In addition, functional annotations, subcellular localization prediction and taxonomic distribution are reported. PIGD allows users to readily browse, search and download data. BLAST and comparative analyses are also provided through this online database, which is available at http://pigd.ahau.edu.cn/.ConclusionPIGD provides a solid platform for the collection, integration and analysis of intronless genes in the Poaceae. As such, this database will be useful for subsequent bio-computational analysis in comparative genomics and evolutionary studies.

Identification and characterization of the RCI2 gene family in maize (Zea mays)

Rare-cold-inducible (RCI2) genes are structurally conserved members that encode small, highly hydrophobic proteins involved in response to various abiotic stresses. Phylogenetic and functional analyses of these genes have been conducted in Arabidopsis, but an extensive investigation of the RCI2 gene family has not yet been carried out in maize. In the present study, 10 RCI2 genes were identified in a fully sequenced maize genome. Structural characterization and expression pattern analysis of 10 ZmRCI2s (Zea mays RCI2 genes) were subsequently determined. Sequence and phylogenetic analyses indicated that ZmRCI2s are highly conserved, and most of them could be grouped with their orthologues from other organisms. Chromosomal location analysis indicated that ZmRCI2s were distributed unevenly on seven chromosomes with two segmental duplication events, suggesting that maize RCI2 gene family is an evolutionarily conserved family. Putative stress-responsive cis-elements were detected in the 2-kb promoter regions of the 10 ZmRCI2s. In addition, the 10 ZmRCI2s showed different expression patterns in maize development based on transcriptome analysis. Further, microarray and quantitative real-time PCR (qRT-PCR) analysis showed that each maize RCI2 genes were responsive to drought stress, suggesting their important roles in drought stress response. The results of this work provide a basis for future cloning and application studies of maize RCI2 genes.

Different evolutionary patterns among intronless genes in maize genome.

Intronless genes, as a characteristic feature of prokaryotes, are an important resource for the study of the evolution of gene architecture in eukaryotes. In the study, 14,623 (36.87%) intronless genes in maize were identified and the percentage is greater than that of other monocots and algae. The number of maize intronless genes on each chromosome has a significant linear correlation with the number of total genes on the chromosome and the length of the chromosomes. Intronless genes in maize play important roles in translation and energy metabolism. Evolutionary analysis revealed that 2601 intronless genes conserved among the three domains of life and 2323 intronless genes that had no homology with genes of other species. These two sets of intronless genes were distinct in genetic features, physical locations and function. These results provided a useful source to understand the evolutionary patterns of related genes and genomes and some intronless genes are good candidates for subsequent functional analyses specifically.