Dataset Information

DOF gene family expansion and diversification.

ABSTRACT: DOF (DNA binding with one finger) proteins are part of a plant-specific transcription factor (TF) gene family widely involved in plant development and stress responses. Many studies have uncovered their structural and functional characteristics in recent years, leading to a rising number of genome-wide identification study approaches, unveiling the DOF family expansion in angiosperm species. Nonetheless, these studies primarily concentrate on particular taxonomic groups. Identifying DOF TFs within less-represented groups is equally crucial, as it enhances our comprehension of their evolutionary history, contributions to plant phenotypic diversity, and role in adaptation. This review summarizes the main findings and progress of genome-wide identification and characterization studies of DOF TFs in Viridiplantae, exposing their roles as players in plant adaptation and a glimpse of their evolutionary history. We also present updated data on the identification and number of DOF genes in native and wild species. Altogether, these data, comprising a phylogenetic analysis of 2124 DOF homologs spanning 83 different species, will contribute to identifying new functional DOF groups, adding to our understanding of the mechanisms driving plant evolution and offering valuable insights into their potential applications.

SUBMITTER: Waschburger EL

PROVIDER: S-EPMC10842470 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

DOF gene family expansion and diversification.

Waschburger Edgar Luis EL Filgueiras João Pedro Carmo JPC Turchetto-Zolet Andreia Carina AC

Genetics and molecular biology 20240205 3 Suppl 1

DOF (DNA binding with one finger) proteins are part of a plant-specific transcription factor (TF) gene family widely involved in plant development and stress responses. Many studies have uncovered their structural and functional characteristics in recent years, leading to a rising number of genome-wide identification study approaches, unveiling the DOF family expansion in angiosperm species. Nonetheless, these studies primarily concentrate on particular taxonomic groups. Identifying DOF TFs with ...[more]

PMID: 38315880

Similar Datasets

Project description:Gene duplication facilitates functional diversification and provides greater phenotypic flexibility to an organism. Expanded gene families arise through repeated gene duplication but the extent of functional divergence that accompanies each paralogous gene is generally unexplored because of the difficulty in isolating the effects of single family members. The telomere-associated (TLO) gene family is a remarkable example of gene family expansion, with 14 members in the more pathogenic Candida albicans relative to two TLO genes in the closely-related species C. dubliniensis. TLO genes encode interchangeable Med2 subunits of the major transcriptional regulatory complex Mediator. To identify biological functions associated with each C. albicans TLO, expression of individual family members was regulated using a Tet-ON system and the strains were assessed across a range of phenotypes involved in growth and virulence traits. All TLOs affected multiple phenotypes and a single phenotype was often affected by multiple TLOs, including simple phenotypes such as cell aggregation and complex phenotypes such as virulence in a Galleria mellonella model of infection. No phenotype was regulated by all TLOs, suggesting neofunctionalization or subfunctionalization of ancestral properties among different family members. Importantly, regulation of three phenotypes could be mapped to individual polymorphic sites among the TLO genes, including an indel correlated with two phenotypes, growth in sucrose and macrophage killing. Different selective pressures have operated on the TLO sequence, with the 5' conserved Med2 domain experiencing purifying selection and the gene/clade-specific 3' end undergoing extensive positive selection that may contribute to the impact of individual TLOs on phenotypic variability. Therefore, expansion of the TLO gene family has conferred unique regulatory properties to each paralog such that it influences a range of phenotypes. We posit that the genetic diversity associated with this expansion contributed to C. albicans success as a commensal and opportunistic pathogen.

Project description:BACKGROUND: The chemokine family plays important roles in cell migration and activation. In humans, at least 44 members are known. Based on the arrangement of the four conserved cysteine residues, chemokines are now classified into four subfamilies, CXC, CC, XC and CX3C. Given that zebrafish is an important experimental model and teleost fishes constitute an evolutionarily diverse group that forms half the vertebrate species, it would be useful to compare the zebrafish chemokine system with those of mammals. Prior to this study, however, only incomplete lists of the zebrafish chemokine genes were reported. RESULTS: We systematically searched chemokine genes in the zebrafish genome and EST databases, and identified more than 100 chemokine genes. These genes were CXC, CC and XC subfamily members, while no CX3C gene was identified. We also searched chemokine genes in pufferfish fugu and Tetraodon, and found only 18 chemokine genes in each species. The majority of the identified chemokine genes are unique to zebrafish or teleost fishes. However, several groups of chemokines are moderately similar to human chemokines, and some chemokines are orthologous to human homeostatic chemokines CXCL12 and CXCL14. Zebrafish also possesses a novel species-specific subfamily consisting of five members, which we term the CX subfamily. The CX chemokines lack one of the two N-terminus conserved cysteine residues but retain the third and the fourth ones. (Note that the XC subfamily only retains the second and fourth of the signature cysteines residues.) Phylogenetic analysis and genome organization of the chemokine genes showed that successive tandem duplication events generated the CX genes from the CC subfamily. Recombinant CXL-chr24a, one of the CX subfamily members on chromosome 24, showed marked chemotactic activity for carp leukocytes. The mRNA was expressed mainly during a certain period of the embryogenesis, suggesting its role in the zebrafish development. CONCLUSION: The phylogenic and genomic organization analyses suggest that a substantial number of chemokine genes in zebrafish were generated by zebrafish-specific tandem duplication events. During such duplications, a novel chemokine subfamily termed CX was generated in zebrafish. Only two human chemokines CXCL12 and CXCL14 have the orthologous chemokines in zebrafish. The diversification observed in the numbers and sequences of chemokines in the fish may reflect the adaptation of the individual species to their respective biological environment.

Dataset Information

DOF gene family expansion and diversification.

Publications

DOF gene family expansion and diversification.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets