scholarly journals Key Role of Amino Acid Repeat Expansions in the Functional Diversification of Duplicated Transcription Factors

2015 ◽  
Vol 32 (9) ◽  
pp. 2263-2272 ◽  
Author(s):  
Núria Radó-Trilla ◽  
Krisztina Arató ◽  
Cinta Pegueroles ◽  
Alicia Raya ◽  
Susana de la Luna ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Amino Acid ◽  
Functional Diversification ◽  
Amino Acid Repeat ◽  
Repeat Expansions

scholarly journals Research Resource: Whole Transcriptome RNA Sequencing Detects Multiple 1α,25-Dihydroxyvitamin D3-Sensitive Metabolic Pathways in Developing Zebrafish

2012 ◽  
Vol 26 (9) ◽  
pp. 1630-1642 ◽  
Author(s):  
Theodore A. Craig ◽  
Yuji Zhang ◽  
Melissa S. McNulty ◽  
Sumit Middha ◽  
Hemamalini Ketha ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Fatty Acid ◽  
Amino Acid ◽  
Xenobiotic Metabolism ◽  
Peptide Hormones ◽  
Differentially Expressed ◽  
Dihydroxyvitamin D3 ◽  
Vitamin D Receptors ◽  
Whole Transcriptome

Abstract The biological role of vitamin D receptors (VDR), which are abundantly expressed in developing zebrafish (Danio rerio) as early as 48 h after fertilization, and before the development of a mineralized skeleton and mature intestine and kidney, is unknown. We probed the role of VDR in developing zebrafish biology by examining changes in expression of RNA by whole transcriptome shotgun sequencing (RNA-seq) in fish treated with picomolar concentrations of the VDR ligand and hormonal form of vitamin D3, 1α,25-dihydroxyvitamin D3 [1α,25(OH)2D3)].We observed significant changes in RNAs of transcription factors, leptin, peptide hormones, and RNAs encoding proteins of fatty acid, amino acid, xenobiotic metabolism, receptor-activator of NFκB ligand (RANKL), and calcitonin-like ligand receptor pathways. Early highly restricted, and subsequent massive changes in more than 10% of expressed cellular RNA were observed. At days post fertilization (dpf) 2 [24 h 1α,25(OH)2D3-treatment], only four RNAs were differentially expressed (hormone vs. vehicle). On dpf 4 (72 h treatment), 77 RNAs; on dpf 6 (120 h treatment) 1039 RNAs; and on dpf 7 (144 h treatment), 2407 RNAs were differentially expressed in response to 1α,25(OH)2D3. Fewer RNAs (n = 481) were altered in dpf 7 larvae treated for 24 h with 1α,25(OH)2D3vs. those treated with hormone for 144 h. At dpf 7, in 1α,25(OH)2D3-treated larvae, pharyngeal cartilage was larger and mineralization was greater. Changes in expression of RNAs for transcription factors, peptide hormones, and RNAs encoding proteins integral to fatty acid, amino acid, leptin, calcitonin-like ligand receptor, RANKL, and xenobiotic metabolism pathways, demonstrate heretofore unrecognized mechanisms by which 1α,25(OH)2D3 functions in vivo in developing eukaryotes.

scholarly journals Key role of amino acid repeat expansions in the functional diversification of duplicated transcription factors

2015 ◽  
Author(s):  
Núria Radó-Trilla ◽  
Krisztina Arató ◽  
Cinta Pegueroles ◽  
Alicia Raya ◽  
Susana de la Luna ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Amino Acid ◽  
Driving Forces ◽  
Gene Families ◽  
Low Complexity ◽  
Individual Gene ◽  
Genome Duplications ◽  
The Individual ◽  
Tf Gene

The high regulatory complexity of vertebrates has been related to two closely spaced whole genome duplications (2R-WGD) that occurred before the divergence of the major vertebrate groups. Following these events, many developmental transcription factors (TFs) were retained in multiple copies and subsequently specialized in diverse functions, whereas others reverted to their singleton state. TFs are known to be generally rich in amino acid repeats or low-complexity regions (LCRs), such as polyalanine or polyglutamine runs, which can evolve rapidly and potentially influence the transcriptional activity of the protein. Here we test the hypothesis that LCRs have played a major role in the diversification of TF gene duplicates. We find that nearly half of the TF gene families (107 out of 237) originated during the 2R-WGD contain LCRs, compared to only a small percentage of the non-duplicated TF genes used as a control (15 out of 115). At the individual gene level, we observe that twice as many duplicated TFs have gained LCRs as non-duplicated TFs. In addition, duplicated TFs preferentially accumulate certain LCR types, the most prominent of which are alanine repeats. We experimentally test the role of alanine-rich LCRs in two different TF gene families, PHOX2A/PHOX2B and LHX2/LHX9. In both cases, the presence of the alanine-rich LCR in one of the copies (PHOX2B and LHX2) significantly increases the capacity of the TF to activate transcription. Taken together, the results provide strong evidence that LCRs are important driving forces of evolutionary change in duplicated genes.

scholarly journals Chlorine-binding structures: role and organization in different proteins

2021 ◽  
Vol 93 (4) ◽  
pp. 5-17
Author(s):  
R. Yu. Marunych Ye. M. Makogonenko ◽  
◽  
O. O. Hrabovskyi ◽  
G. K. Bereznytskyj ◽  
L. V. Pyrogova ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Binding Site ◽  
Acid Composition ◽  
Chloride Binding ◽  
Channel Proteins ◽  
Transport Receptor ◽  
Receptor Channel

The review focuses on chloride-binding structures in the proteins of bacteria, plants, viruses and animals. The structure and amino acid composition of the chloride-binding site and its role in the functioning of structural, regulatory, transport, receptor, channel proteins, transcription factors and enzymes are considered. Data on the important role of chloride-binding structures and chloride anions in the polymerization of fibrin are presented.

The role of Forkhead Box O 3a (FoxO3a) Transcription Factors in the Pathogenesis of Pulmonary Fibrosis

Pneumologie ◽  
2012 ◽  
Vol 66 (06) ◽  
Author(s):  
HM Al-Tamari ◽  
M Eschenhagen ◽  
A Schmall ◽  
R Savai ◽  
HA Ghofrani ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Pulmonary Fibrosis ◽  
Forkhead Box
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