Large-scale examination of functional and sequence diversity of 2-oxoglutarate/Fe(II)-dependent oxygenases in Metazoa

Jia, Baolei; Tang, Ke; Chun, Byung Hee; Jeon, Che Ok

doi:10.1016/j.bbagen.2017.08.019

Cited by 27 publications

(26 citation statements)

References 58 publications

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“…S3). If 2 residues share a high MI score, they will most likely have been coevolving; that is, a mutation of 1 residue is linked to a specific compensatory mutation of the other residue to maintain a given enzymatic function (23). The MI network for the GLUTs revealed that amino acids located in the transmembrane part had higher MI values (top 10% of MI values), whereas those in extracellular and intracellular regions had relatively low values (Fig.…”

Section: Conservation and Coevolution Of Amino Acid Residues In The Mmentioning

confidence: 99%

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New insight into the classification and evolution of glucose transporters in the Metazoa

et al. 2019

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Because glucose is an essential energy source for living organisms, glucose transporters (GLUTs) are present in all species worldwide. Encoded by the solute carrier family 2 gene family, the GLUT proteins generally have 12 transmembrane helices (TMHs). In total, 14 GLUT proteins have been identified in humans (hGLUTs), and they are divided into 3 classes on the basis of their transport characteristics and sequence similarities. Herein, we report the use of protein sequence similarity networks (SSNs) to visualize the sequence trends of 4101 GLUT proteins across the Metazoa. The SSNs separated the metazoan proteins into 3 new classes that were different from the traditional classification system. In the new system, 9 of the 14 hGLUTs (hGLUT1–5, 7, 9, 11, and 14) were grouped into class I, 3 (hGLUT10, 12, and 13) were grouped into class II, and 2 (hGLUT6 and 8) were grouped into class III, as also supported by the phylogenetic tree. Multiple sequence alignments further showed that the conserved residues in each class were different. Furthermore, the hGLUTs in each class showed unique evolutionary characteristics, with similar nonsynonymous‐to‐synonymous divergence ratios and similar regions under conservative selection pressure. Of note, GLUTs with 3, 6, 18, 24, and 36 TMHs were identified among the metazoan genomes, and 1 Chinese hamster protein with 6 TMHs showed GLUT activity. In summary, this large‐scale sequence analysis provided new insights into the classification and evolution of GLUTs and further showed that gene duplication and fusion could have been important drivers during the evolution of these transporter molecules.—Jia, B., Yuan, D. P., Lan, W. J., Xuan, Y. H., Jeon, C. O. New insight into the classification and evolution of glucose transporters in the Metazoa. FASEB J. 33, 7519–7528 (2019). http://www.fasebj.org

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Section: Conservation and Coevolution Of Amino Acid Residues In The Mmentioning

confidence: 99%

“…The input metazoan sequences were retrieved from the InterPro database. In an SSN, each node indicates a protein, whereas the edge indicates that the 2 nodes share significant similarity with an e-value less than the selected cutoff (23)(24)(25).…”

Section: Construction Of the Ssnsmentioning

confidence: 99%

New insight into the classification and evolution of glucose transporters in the Metazoa

et al. 2019

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“…The input sequences were obtained from the Interpro database. Each node in the network indicates a protein, and an edge indicates that the two nodes connected by that edge are significantly similar, having an e-value less than the selected cutoff ( Jia et al, 2017 ).…”

Section: Methodsmentioning

confidence: 99%

Network Analysis of RAD51 Proteins in Metazoa and the Evolutionary Relationships With Their Archaeal Homologs

et al. 2018

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The RAD51 (DNA repair protein RAD51) recombinases are essential for homologous recombination, DNA repair, and genome stability. Overexpression of RAD51 proteins has been observed in many cancer cells, such as thyroid carcinoma, breast cancer, pancreatic cancer, and others. In Metazoa, there are multiple members of RAD51 (RAD51, RAD51B, RAD51C, RAD51D, DMC1) (DNA meiotic recombinase 1), XRCC2 (X-ray repair cross-complementing 2), and XRCC3. In this study, we used a protein sequence similarity network (SSN) to analyze the evolutionary relationship within this protein family. The SSN based on the RAD51 proteins from Metazoa indicated that there are several proteins that have yet to be functionally defined. The SSN based on the distribution of the proteins supports the hypothesis that horizontal gene transfer plays an important role in the evolution of RAD51 proteins. Multiple sequence alignments with structural information revealed that the amino acid residues for ATP and Mg2+ are highly conserved. The seven RAD51 proteins in humans are under different selective pressure: RAD51 and DMC1 are under stringent negative selection, while other proteins are subject to relatively relaxed negative selection. Furthermore, the expression levels of the seven genes in different tissues showed that the genes in the same cluster in the phylogenetic tree showed similar expression profiles. Finally, the SSN based on the RAD51 proteins from both eukaryotes and prokaryotes suggested that the eukaryotic RAD51 recombinases share a common ancestor with the archaeal homologs, but XRCC2 may have a different origin. These findings expand the understanding of the evolution and diversity of RAD51 recombinases in Metazoa.

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“…There are currently over 30 proteins identified in humans to belong to the JmjC group and most (but not all) of these have been associated with histone demethylation (reviewed in [58]). They can be further classified into subfamilies, which typically may share substrate specificity, dependent upon the presence of other domains, including the TUDOR, CXXC, PHD, FBOX, ARID, LRR and JmjN domains (reviewed in [59]; Table 2). As is the case for the TET enzymes, specific physiological and pathophysiological roles are increasingly been identified for different JmjC demethylases, notably in development and certain cancers (reviewed in [60,61]; Table 2).…”

Section: Histone Demethylation By the Jumonji Family Of 2-ogdd Proteinsmentioning

confidence: 99%

Dynamic regulation of epigenetic demethylation by oxygen availability and cellular redox

Lamadema

Burr

Brewer

2019

Free Radical Biology and Medicine

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Large-scale examination of functional and sequence diversity of 2-oxoglutarate/Fe(II)-dependent oxygenases in Metazoa

Cited by 27 publications

References 58 publications

New insight into the classification and evolution of glucose transporters in the Metazoa

New insight into the classification and evolution of glucose transporters in the Metazoa

Network Analysis of RAD51 Proteins in Metazoa and the Evolutionary Relationships With Their Archaeal Homologs

Dynamic regulation of epigenetic demethylation by oxygen availability and cellular redox

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