Genome-wide comparative analyses of GATA transcription factors among seven Populus genomes.

GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. We identified 262 GATA genes (389 GATA TFs) from seven Populus genomes using the pipeline of GATA-TFDB. Alternative splicing forms of Populus GATA genes exhibit dynamics of GATA gene structures including partial or full loss of GATA domain and additional domains. Subfamily III of Populus GATA genes display lack CCT and/or TIFY domains. 21 Populus GATA gene clusters (PCs) were defined in the phylogenetic tree of GATA domains, suggesting the possibility of subfunctionalization and neofunctionalization. Expression analysis of Populus GATA genes identified the five PCs displaying tissue-specific expression, providing the clues of their biological functions. Amino acid patterns of Populus GATA motifs display well conserved manner of Populus GATA genes. The five Populus GATA genes were predicted as membrane-bound GATA TFs. Biased chromosomal distributions of GATA genes of three Populus species. Our comparative analysis approaches of the Populus GATA genes will be a cornerstone to understand various plant TF characteristics including evolutionary insights.

Genome-wide identification and analysis of the GATA transcription factor gene family in Ustilaginoidea virens.

In filamentous fungi, the conserved transcription factors play important roles in multiple cellular and developmental processes. The GATA proteins, a family of GATA-binding zinc finger transcription factors, play diverse functions in fungi. Ustilaginoidea virens is an economically important pathogen-causing rice false smut worldwide. To gain additional insight into the cellular and molecular mechanisms of this pathogen, in this study, we identified and functionally characterized seven GATA proteins from the U. virens genome (UvGATA). Sequences analysis indicated that these GATA proteins are divided into seven clades. The proteins in each clade contained conserved clade-specific sequences and structures, thus leading to the same motif serving different purposes in various contexts. The expression profiles of UvGATA genes at different infection stages and under H2O2 stress were detected. Results showed that the majority of UvGATA genes performed functions at both processes, thereby confirming the roles of these genes in pathogenicity and reactive oxygen species stress tolerance. This study provided an important starting point to further explore the biological functions of UvGATA genes and increased our understanding of their potential transcriptional regulatory mechanisms in U. virens.

Investigation of endoderm marker-genes during gastrulation and gut-development in the velvet worm Euperipatoides kanangrensis.

The ancestral state of animal gastrulation and its bearing for our understanding of bilaterian evolution still is one of the most controversially discussed topics in the field of evolutionary and developmental biology. One hypothesis, the so-called amphistomy scenario, suggests the presence of a slit-like blastopore in the last common ancestor of Bilateria. Onychophoran ontogeny at least superficially appears to support this scenario since a ventral groove clearly forms during gastrulation. The origin and nature of this groove, however, is another matter of ongoing controversy; i.e. the question of whether this structure actually represents the blastopore, or at least part of it. Recent research using genetic markers argued against the furrow representing a blastoporal structure. Here we investigate the origin of endoderm, which usually originates from the blastopore. We find conserved expression patterns of the endoderm- and gut-marker genes GATA456, GATA123, Hnf4 and fkh during gut development, and discuss the formation of the onychophoran gut in comparison with that in a range of arthropods. Despite expression of endodermal markers in and around the furrow we do not find convincing evidence that the furrow may be part of the blastopore, and thus we suggest that onychophoran development does not yield support for the amphistomy scenario.

GATA transcription factors in vertebrates: evolutionary, structural and functional interplay.

GATA transcription factors perform conserved and essential roles during animal development, including germ-layer specification, hematopoiesis, and cardiogenesis. The evolutionary history and the changes in selection pressures following duplication of the six GATA family members in vertebrates have not been completely understood. Recently, we explored multiple databases to find GATAs in different vertebrate species. Using these sequences, we have performed molecular phylogenetic analyses using Maximum Likelihood and Bayesian methods, and statistical tests of tree topologies, to ascertain the phylogenetic relationship and selection pressures among GATA proteins. Seventy-one full-length cDNA sequences from 24 vertebrate species were extracted from multiple databases. By phylogenetic analyses, we investigated the origin, conservation, and evolution of the GATAs. Six GATA genes in vertebrates might be formed by gene duplication. The inferred evolutionary transitions that separate members which belong to different gene clusters correlated with changes in functional properties. Selection analysis and protein structure analysis were combined to explain Darwinian selection in GATA sequences and these changes brought putative biological significance. 26 positive selection sites were detected in this process. This study reveals the evolutionary history of vertebrate GATA paralogous and positively selected sites likely relevant for the distinct functional properties of the paralogs. It provides a new perspective for understanding the origin and evolution and biological functions of GATAs, which will help to uncover the GATAs' biological roles, evolution and their relationship with associated diseases; in addition, other complex multidomain families and also larger superfamilies can be investigated in a similar way.