scholarly journals Ancestral reconstruction reveals mechanisms of ERK regulatory evolution

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Dajun Sang ◽  
Sudarshan Pinglay ◽  
Rafal P Wiewiora ◽  
Myvizhi E Selvan ◽  
Hua Jane Lou ◽  
...  

Protein kinases are crucial to coordinate cellular decisions and therefore their activities are strictly regulated. Previously we used ancestral reconstruction to determine how CMGC group kinase specificity evolved (Howard et al., 2014). In the present study, we reconstructed ancestral kinases to study the evolution of regulation, from the inferred ancestor of CDKs and MAPKs, to modern ERKs. Kinases switched from high to low autophosphorylation activity at the transition to the inferred ancestor of ERKs 1 and 2. Two synergistic amino acid changes were sufficient to induce this change: shortening of the β3-αC loop and mutation of the gatekeeper residue. Restoring these two mutations to their inferred ancestral state led to a loss of dependence of modern ERKs 1 and 2 on the upstream activating kinase MEK in human cells. Our results shed light on the evolutionary mechanisms that led to the tight regulation of a kinase that is central in development and disease.

2018 ◽  
Author(s):  
Dajun Sang ◽  
Sudarshan Pinglay ◽  
Sezen Vatansever ◽  
Hua Jane Lou ◽  
Benjamin Turk ◽  
...  

AbstractProtein kinases are crucial to coordinate cellular decisions and therefore their activities are strictly regulated. We used ancestral resurrection to uncover a mechanism underlying the evolution of kinase control within the ERK family of Mitogen Activated Protein Kinases (MAPKs). Kinase activities switched from high to low intrinsic autophosphorylation at the transition from the ancestors of ERKs1-5 and ERKs1-2. A shortening of the loop between β3-αC and a mutation in the gatekeeper residue drove this transition. Molecular dynamics simulations suggested that the change in the β3-αC loop length affected kinase cis-autophosphorylation by altering the positioning of catalytic residues and by allowing greater flexibility in the L16 kinase loop. This latter effect likely synergizes with the known role of gatekeeper mutations in facilitating domain closure and thus kinase activation, providing a rationale for the synergy between the two evolutionary mutations. Our results shed light on the evolutionary mechanisms that led to tight regulation of a central kinase in development and disease.


eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Conor J Howard ◽  
Victor Hanson-Smith ◽  
Kristopher J Kennedy ◽  
Chad J Miller ◽  
Hua Jane Lou ◽  
...  

Protein kinases have evolved diverse specificities to enable cellular information processing. To gain insight into the mechanisms underlying kinase diversification, we studied the CMGC protein kinases using ancestral reconstruction. Within this group, the cyclin dependent kinases (CDKs) and mitogen activated protein kinases (MAPKs) require proline at the +1 position of their substrates, while Ime2 prefers arginine. The resurrected common ancestor of CDKs, MAPKs, and Ime2 could phosphorylate substrates with +1 proline or arginine, with preference for proline. This specificity changed to a strong preference for +1 arginine in the lineage leading to Ime2 via an intermediate with equal specificity for proline and arginine. Mutant analysis revealed that a variable residue within the kinase catalytic cleft, DFGx, modulates +1 specificity. Expansion of Ime2 kinase specificity by mutation of this residue did not cause dominant deleterious effects in vivo. Tolerance of cells to new specificities likely enabled the evolutionary divergence of kinases.


Biomolecules ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 421
Author(s):  
Areetha R. D’Souza ◽  
Matthew R. Necelis ◽  
Alona Kulesha ◽  
Gregory A. Caputo ◽  
Olga V. Makhlynets

Antimicrobial peptides (AMPs) present a promising scaffold for the development of potent antimicrobial agents. Substitution of tryptophan by non-natural amino acid Azulenyl-Alanine (AzAla) would allow studying the mechanism of action of AMPs by using unique properties of this amino acid, such as ability to be excited separately from tryptophan in a multi-Trp AMPs and environmental insensitivity. In this work, we investigate the effect of Trp→AzAla substitution in antimicrobial peptide buCATHL4B (contains three Trp side chains). We found that antimicrobial and bactericidal activity of the original peptide was preserved, while cytocompatibility with human cells and proteolytic stability was improved. We envision that AzAla will find applications as a tool for studies of the mechanism of action of AMPs. In addition, incorporation of this non-natural amino acid into AMP sequences could enhance their application properties.


ChemBioChem ◽  
2014 ◽  
Vol 15 (12) ◽  
pp. 1755-1760 ◽  
Author(s):  
Moritz J. Schmidt ◽  
Annemarie Weber ◽  
Moritz Pott ◽  
Wolfram Welte ◽  
Daniel Summerer

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 35-35
Author(s):  
Sara L. Seegers ◽  
Amanda Lance ◽  
Lawrence J Druhan ◽  
Belinda R Avalos

CSF3R, the receptors for granulocyte colony stimulating factor, is a critical regulator of neutrophil production. Multiple CSF3R mRNA transcripts have been identified and are annotated in Genbank. The expression and function of the different CSF3R proteins have not been fully elucidated. We generated antibodies specific for two of the identified and annotated isoforms, V3 and V4. CSF3R-V4 is a truncated variant of V1 with a unique C-terminal 34 amino acids and this variant confers enhanced growth signals. Changes in the ratio of V1:V4 isoforms have been implicated in chemotherapy resistance and relapse of AML. CSF3R-V3 is a variant of V1 with a 27 amino acid insertion between two conserved domains in the cytoplasmic portion of the receptor involved in JAK/STAT activation, termed the box 1 and box 2. CSF3R-V3 produces reduced proliferative signaling in response to G-CSF. When V3 is co-expressed with V1, proliferative signaling is reduced in a concentration dependent manner. In order to generate custom rabbit polyclonal antibodies specific for CSF3R-V3 and CSF3R-V4 we used either a peptide that corresponds to a unique amino acid sequence present only in CSF3R-V3 or a peptide specific for a portion of the C-terminal amino acid sequence unique to the CSF3R-V4 isoform conjugated to an immunogenic carrier protein. These immunogens both produced robust immune responses, and the polyclonal antibodies were subsequently purified from bulk sera. Immunoblot analysis of lysates from Ba/F3 cells expressing CSF3R-V1 (V1), CSF3R-V3 (V3), or CSF3R-V4 (V4) demonstrated that both the custom generated anti-CSF3R-V3 and anti-CSF3R-V4 antibodies were very specific, recognizing only the appropriate CSF3R receptor isoform. All three CSF3R splice variants are recognized by commercially available anti-CSF3R (clone LMM741 to CD114), while the anti-CSF3R-V4 custom antibody and the custom anti-CSF3R-V3 antibody recognizes only the CSF3R-V4 and CSF3R-V3 isoforms, respectively. We next sought to detect the CSF3R receptor isoforms in primary human cells. Using our custom antibodies, we detected for the first time, both the CSF3R-V3 and CSF3R-V4 receptor forms in primary neutrophils isolated from healthy donors. Each of the CSF3R isoforms produce unique signaling, and we hypothesized that the observed differences in G-CSF-dependent signaling is produced by the expression level of each receptor isoform via both homodimerization and by heterodimerization of the receptor splice variant proteins. To investigate the potential for heterodimerization of the CSF3R-V1 with the V3 and V4 isoforms, we generated a CSF3R-V1 with a c-terminal epitope tag and co-expressed this construct with both CSF3R-V3 or CSF3R-V4. Immunoprecipitation with an antibody to the epitope tag (recognizing the V1 variant) followed by immunoblotting with the custom anti-V3 or anti-V4 antibodies demonstrated that both CSF3R-V3 and CSF3R-V4 co-immunoprecipitated with CSF3R-V1, in agreement with our hypothesis that the splice variants form receptor heterodimers. Of note, the CSF3R receptor heterodimers are detected even in the absence of G-CSF, thus demonstrating that CSF3R exist as a preformed receptor dimer in an inactive state. In conclusion, we have generated antibodies that specifically detect the CSF3R-V3 and the CSF3R-V4 receptor proteins. These are the first studies to demonstrate the expression of the CSF3R splice variants at the protein level, in both cell lines and primary human cells. In addition, these are the first studies to demonstrate the formation of heterodimers of the CSF3R splice variants, providing a mechanism for the observed alteration in ligand-dependent signaling produced under conditions of altered splice variant expression. Disclosures Avalos: Juno: Membership on an entity's Board of Directors or advisory committees; Best Practice-Br Med J: Patents & Royalties: receives royalties from a coauthored article on evaluation of neutropenia.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11722
Author(s):  
Paola María Sánchez-Martínez ◽  
Juan D. Daza ◽  
Julio Mario Hoyos

The skeleton of the middle ear of lizards is composed of three anatomical elements: columella, extracolumella, and tympanic membrane, with some exceptions that show modifications of this anatomy. The main function of the middle ear is transforming sound waves into vibrations and transmitting these to the inner ear. Most middle ear studies mainly focus on its functional aspects, while few describe the anatomy in detail. In lizards, the morphology of the columella is highly conservative, while the extracolumella shows variation in its presence/absence, size, and the number of processes present on the structure. In this work, we used diaphanized and double-stained specimens of 38 species of lizards belonging to 24 genera to study the middle ear’s morphology in a comparative framework. Results presented here indicate more variation in the morphology of the extracolumella than previously known. This variation in the extracolumella is found mainly in the pars superior and anterior processes, while the pars inferior and the posterior process are more constant in morphology. We also provide new information about the shape of gekkotan extracolumella, including traits that are diagnostic for the iguanid and gekkonid middle ear types. The data collected in this study were combined with information from published descriptive works. The new data included here refers to the length of the columella relative to the extracolumella central axis length, the general structure of the extracolumella, and the presence of the internal process. These characters were included in ancestral reconstruction analysis using Bayesian and parsimony approaches. The results indicate high levels of homoplasy in the variation of the columella-extracolumella ratio, providing a better understanding of the ratio variation among lizards. Additionally, the presence of four processes in the extracolumella is the ancestral state for Gekkota, Pleurodonta, and Xantusiidae, and the absence of the internal processes is the ancestral state for Gekkota, Gymnophthalmidae, and Scincidae; despite the fact that these groups convergently develop these character states, they could be used in combination with other characters to diagnose these clades. The posterior extension in the pars superior and an anterior process with some small and sharp projections is also a diagnostic trait for Gekkota. A more accurate description of each process of the extracolumella and its variation needs to be evaluated in a comprehensive analysis, including a greater number of species. Although the number of taxa sampled in this study is small considering the vast diversity of lizards, the results provide an overall idea of the amount of variation of the middle ear while helping to infer the evolutionary history of the lizard middle ear.


2018 ◽  
Vol 52 (3) ◽  
pp. 478-487 ◽  
Author(s):  
D. A. Karasev ◽  
A. V. Veselovsky ◽  
A. A. Lagunin ◽  
D. A. Filimonov ◽  
B. N. Sobolev

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