Dataset Information

A Comprehensive Phylogenetic Analysis of the MAP4K Family in the Green Lineage.

ABSTRACT: The kinase-mediated phosphorylation impacts every basic cellular process. While mitogen-activated protein kinase technology kinase kinases (MAP4Ks) are evolutionarily conserved, there is no comprehensive overview of the MAP4K family in the green lineage (Viridiplantae). In this study, we identified putative MAP4K members from representative species of the two core groups in the green lineage: Chlorophyta, which is a diverse group of green algae, and Streptophyta, which is mostly freshwater green algae and land plants. From that, we inferred the evolutionary relationships of MAP4K proteins through a phylogenetic reconstruction. Furthermore, we provided a classification of the MAP4Ks in the green lineage into three distinct.

SUBMITTER: Pan L

PROVIDER: S-EPMC8415026 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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A Comprehensive Phylogenetic Analysis of the MAP4K Family in the Green Lineage.

Pan Lixia L Fonseca De Lima Cassio Flavio CF Vu Lam Dai LD De Smet Ive I

Frontiers in plant science 20210813

The kinase-mediated phosphorylation impacts every basic cellular process. While mitogen-activated protein kinase technology kinase kinases (MAP4Ks) are evolutionarily conserved, there is no comprehensive overview of the MAP4K family in the green lineage (Viridiplantae). In this study, we identified putative MAP4K members from representative species of the two core groups in the green lineage: Chlorophyta, which is a diverse group of green algae, and Streptophyta, which is mostly freshwater green ...[more]

PMID: 34484252

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Project description:BackgroundTenascins are a family of glycoproteins found primarily in the extracellular matrix of embryos where they help to regulate cell proliferation, adhesion and migration. In order to learn more about their origins and relationships to each other, as well as to clarify the nomenclature used to describe them, the tenascin genes of the urochordate Ciona intestinalis, the pufferfish Tetraodon nigroviridis and Takifugu rubripes and the frog Xenopus tropicalis were identified and their gene organization and predicted protein products compared with the previously characterized tenascins of amniotes.ResultsA single tenascin gene was identified in the genome of C. intestinalis that encodes a polypeptide with domain features common to all vertebrate tenascins. Both pufferfish genomes encode five tenascin genes: two tenascin-C paralogs, a tenascin-R with domain organization identical to mammalian and avian tenascin-R, a small tenascin-X with previously undescribed GK repeats, and a tenascin-W. Four tenascin genes corresponding to tenascin-C, tenascin-R, tenascin-X and tenascin-W were also identified in the X. tropicalis genome. Multiple sequence alignment reveals that differences in the size of tenascin-W from various vertebrate classes can be explained by duplications of specific fibronectin type III domains. The duplicated domains are encoded on single exons and contain putative integrin-binding motifs. A phylogenetic tree based on the predicted amino acid sequences of the fibrinogen-related domains demonstrates that tenascin-C and tenascin-R are the most closely related vertebrate tenascins, with the most conserved repeat and domain organization. Taking all lines of evidence together, the data show that the tenascins referred to as tenascin-Y and tenascin-N are actually members of the tenascin-X and tenascin-W gene families, respectively.ConclusionThe presence of a tenascin gene in urochordates but not other invertebrate phyla suggests that tenascins may be specific to chordates. Later genomic duplication events led to the appearance of four family members in vertebrates: tenascin-C, tenascin-R, tenascin-W and tenascin-X.

Project description:BackgroundTranslation initiation in eukaryotes involves the recruitment of mRNA to the ribosome which is controlled by the translation factor eIF4E. eIF4E binds to the 5'-m7Gppp cap-structure of mRNA. Three dimensional structures of eIF4Es bound to cap-analogues resemble 'cupped-hands' in which the cap-structure is sandwiched between two conserved Trp residues (Trp-56 and Trp-102 of H. sapiens eIF4E). A third conserved Trp residue (Trp-166 of H. sapiens eIF4E) recognizes the 7-methyl moiety of the cap-structure. Assessment of GenBank NR and dbEST databases reveals that many organisms encode a number of proteins with homology to eIF4E. Little is understood about the relationships of these structurally related proteins to each other.ResultsBy combining sequence data deposited in the Genbank databases, we have identified sequences encoding 411 eIF4E-family members from 230 species. These sequences have been deposited into an internet-accessible database designed for sequence comparisons of eIF4E-family members. Most members can be grouped into one of three classes. Class I members carry Trp residues equivalent to Trp-43 and Trp-56 of H. sapiens eIF4E and appear to be present in all eukaryotes. Class II members, possess Trp-->Tyr/Phe/Leu and Trp-->Tyr/Phe substitutions relative to Trp-43 and Trp-56 of H. sapiens eIF4E, and can be identified in Metazoa, Viridiplantae, and Fungi. Class III members possess a Trp residue equivalent to Trp-43 of H. sapiens eIF4E but carry a Trp-->Cys/Tyr substitution relative to Trp-56 of H. sapiens eIF4E, and can be identified in Coelomata and Cnidaria. Some eIF4E-family members from Protista show extension or compaction relative to prototypical eIF4E-family members.ConclusionThe expansion of sequenced cDNAs and genomic DNAs from all eukaryotic kingdoms has revealed a variety of proteins related in structure to eIF4E. Evolutionarily it seems that a single early eIF4E gene has undergone multiple gene duplications generating multiple structural classes, such that it is no longer possible to predict function from the primary amino acid sequence of an eIF4E-family member. The variety of eIF4E-family members provides a source of alternatives on the eIF4E structural theme that will benefit structure/function analyses and therapeutic drug design.

Dataset Information

A Comprehensive Phylogenetic Analysis of the MAP4K Family in the Green Lineage.

Publications

A Comprehensive Phylogenetic Analysis of the MAP4K Family in the Green Lineage.

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