Divergent evolution of a protein-protein interaction revealed through ancestral sequence reconstruction and resurrection

AbstractThe postsynaptic density extends across the postsynaptic dendritic spine with Discs large (DLG) as the most abundant scaffolding protein. DLG dynamically alters the structure of the postsynaptic density, thus controlling the function and distribution of specific receptors at the synapse. PDZ domains make up one of the most abundant protein interaction domain families in animals. One important interaction governing postsynaptic architecture is that between the PDZ3 domain from DLG and cysteine-rich interactor of PDZ3 (CRIPT). However, little is know regarding functional evolution of the PDZ3:CRIPT interaction. Here, we subjected PDZ3 and CRIPT to ancestral sequence reconstruction, resurrection and biophysical experiments. We show that the PDZ3:CRIPT interaction is an ancient interaction, which was present in the last common ancestor of Eukaryotes, and that high affinity is maintained in most extant animal phyla. However, affinity is low in nematodes and insects, raising questions about the physiological function of the interaction in species from these animal groups. Our findings demonstrate how an apparently established protein-protein interaction involved in cellular scaffolding in bilaterians can suddenly be subject to dynamic evolution including possible loss of function.

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Divergent Evolution of a Protein–Protein Interaction Revealed through Ancestral Sequence Reconstruction and Resurrection

Molecular Biology and Evolution ◽

10.1093/molbev/msaa198 ◽

2020 ◽

Vol 38 (1) ◽

pp. 152-167

Author(s):

Louise Laursen ◽

Jelena Čalyševa ◽

Toby J Gibson ◽

Per Jemth

Keyword(s):

Protein Interaction ◽

Postsynaptic Density ◽

Ancestral Sequence ◽

Scaffolding Protein ◽

Divergent Evolution ◽

Last Common Ancestor ◽

Loss Of Function ◽

Protein Protein Interaction ◽

Ancestral Sequence Reconstruction ◽

Sequence Reconstruction

Abstract The postsynaptic density extends across the postsynaptic dendritic spine with discs large (DLG) as the most abundant scaffolding protein. DLG dynamically alters the structure of the postsynaptic density, thus controlling the function and distribution of specific receptors at the synapse. DLG contains three PDZ domains and one important interaction governing postsynaptic architecture is that between the PDZ3 domain from DLG and a protein called cysteine-rich interactor of PDZ3 (CRIPT). However, little is known regarding functional evolution of the PDZ3:CRIPT interaction. Here, we subjected PDZ3 and CRIPT to ancestral sequence reconstruction, resurrection, and biophysical experiments. We show that the PDZ3:CRIPT interaction is an ancient interaction, which was likely present in the last common ancestor of Eukaryotes, and that high affinity is maintained in most extant animal phyla. However, affinity is low in nematodes and insects, raising questions about the physiological function of the interaction in species from these animal groups. Our findings demonstrate how an apparently established protein–protein interaction involved in cellular scaffolding in bilaterians can suddenly be subject to dynamic evolution including possible loss of function.

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The molecular signal for the adaptation to cold temperature during early life on Earth

Biology Letters ◽

10.1098/rsbl.2013.0608 ◽

2013 ◽

Vol 9 (5) ◽

pp. 20130608 ◽

Cited By ~ 12

Author(s):

Mathieu Groussin ◽

Bastien Boussau ◽

Sandrine Charles ◽

Samuel Blanquart ◽

Manolo Gouy

Keyword(s):

Phylogenetic Trees ◽

Large Scale ◽

Common Ancestor ◽

Phylogenetic Signal ◽

Optimal Growth ◽

Ancestral Sequence ◽

Rate Variation ◽

Last Common Ancestor ◽

Ancestral Sequence Reconstruction ◽

Sequence Reconstruction

Several lines of evidence such as the basal location of thermophilic lineages in large-scale phylogenetic trees and the ancestral sequence reconstruction of single enzymes or large protein concatenations support the conclusion that the ancestors of the bacterial and archaeal domains were thermophilic organisms which were adapted to hot environments during the early stages of the Earth. A parsimonious reasoning would therefore suggest that the last universal common ancestor (LUCA) was also thermophilic. Various authors have used branch-wise non-homogeneous evolutionary models that better capture the variation of molecular compositions among lineages to accurately reconstruct the ancestral G + C contents of ribosomal RNAs and the ancestral amino acid composition of highly conserved proteins. They confirmed the thermophilic nature of the ancestors of Bacteria and Archaea but concluded that LUCA, their last common ancestor, was a mesophilic organism having a moderate optimal growth temperature. In this letter, we investigate the unknown nature of the phylogenetic signal that informs ancestral sequence reconstruction to support this non-parsimonious scenario. We find that rate variation across sites of molecular sequences provides information at different time scales by recording the oldest adaptation to temperature in slow-evolving regions and subsequent adaptations in fast-evolving ones.

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Faculty Opinions recommendation of An experimental phylogeny to benchmark ancestral sequence reconstruction.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.726740118.793524093 ◽

2016 ◽

Author(s):

Reinhard Sterner ◽

Rainer Merkl

Keyword(s):

Ancestral Sequence ◽

Ancestral Sequence Reconstruction ◽

Sequence Reconstruction

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Ancestral sequence reconstruction for protein engineers

Current Opinion in Structural Biology ◽

10.1016/j.sbi.2021.04.001 ◽

2021 ◽

Vol 69 ◽

pp. 131-141

Author(s):

Matthew A. Spence ◽

Joe A. Kaczmarski ◽

Jake W. Saunders ◽

Colin J. Jackson

Keyword(s):

Ancestral Sequence ◽

Ancestral Sequence Reconstruction ◽

Sequence Reconstruction

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Regulation of clathrin coat assembly by Eps15 homology domain–mediated interactions during endocytosis

Molecular Biology of the Cell ◽

10.1091/mbc.e11-04-0380 ◽

2012 ◽

Vol 23 (4) ◽

pp. 687-700 ◽

Cited By ~ 7

Author(s):

Ryohei Suzuki ◽

Junko Y. Toshima ◽

Jiro Toshima

Keyword(s):

Functional Diversity ◽

Protein Interaction ◽

Interaction Domain ◽

Protein Protein Interaction ◽

Molecular Events ◽

Biological Studies ◽

Eh Domain ◽

Actin Patch ◽

Lines Of Evidence

Clathrin-mediated endocytosis involves a coordinated series of molecular events regulated by interactions among a variety of proteins and lipids through specific domains. One such domain is the Eps15 homology (EH) domain, a highly conserved protein–protein interaction domain present in a number of proteins distributed from yeast to mammals. Several lines of evidence suggest that the yeast EH domain–containing proteins Pan1p, End3p, and Ede1p play important roles during endocytosis. Although genetic and cell-biological studies of these proteins suggested a role for the EH domains in clathrin-mediated endocytosis, it was unclear how they regulate clathrin coat assembly. To explore the role of the EH domain in yeast endocytosis, we mutated those of Pan1p, End3p, or Ede1p, respectively, and examined the effects of single, double, or triple mutation on clathrin coat assembly. We found that mutations of the EH domain caused a defect of cargo internalization and a delay of clathrin coat assembly but had no effect on assembly of the actin patch. We also demonstrated functional redundancy among the EH domains of Pan1p, End3p, and Ede1p for endocytosis. Of interest, the dynamics of several endocytic proteins were differentially affected by various EH domain mutations, suggesting functional diversity of each EH domain.

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Arabidopsis RADICAL-INDUCED CELL DEATH1 Belongs to the WWE Protein–Protein Interaction Domain Protein Family and Modulates Abscisic Acid, Ethylene, and Methyl Jasmonate Responses

The Plant Cell ◽

10.1105/tpc.021832 ◽

2004 ◽

Vol 16 (7) ◽

pp. 1925-1937 ◽

Cited By ~ 144

Author(s):

Reetta Ahlfors ◽

Saara Lång ◽

Kirk Overmyer ◽

Pinja Jaspers ◽

Mikael Brosché ◽

...

Keyword(s):

Abscisic Acid ◽

Methyl Jasmonate ◽

Protein Interaction ◽

Protein Family ◽

Interaction Domain ◽

Protein Protein Interaction ◽

Domain Protein

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Ancestral sequence reconstruction produces thermally stable enzymes with mesophilic enzyme-like catalytic properties

Scientific Reports ◽

10.1038/s41598-020-72418-4 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 2

Author(s):

Ryutaro Furukawa ◽

Wakako Toma ◽

Koji Yamazaki ◽

Satoshi Akanuma

Keyword(s):

Low Temperature ◽

Catalytic Properties ◽

Amino Acid Sequences ◽

Ancestral Sequence ◽

Kinetic Properties ◽

Reconstruction Technique ◽

Thermally Stable ◽

Ancestral Sequence Reconstruction ◽

Ancestral Sequences ◽

Sequence Reconstruction

Abstract Enzymes have high catalytic efficiency and low environmental impact, and are therefore potentially useful tools for various industrial processes. Crucially, however, natural enzymes do not always have the properties required for specific processes. It may be necessary, therefore, to design, engineer, and evolve enzymes with properties that are not found in natural enzymes. In particular, the creation of enzymes that are thermally stable and catalytically active at low temperature is desirable for processes involving both high and low temperatures. In the current study, we designed two ancestral sequences of 3-isopropylmalate dehydrogenase by an ancestral sequence reconstruction technique based on a phylogenetic analysis of extant homologous amino acid sequences. Genes encoding the designed sequences were artificially synthesized and expressed in Escherichia coli. The reconstructed enzymes were found to be slightly more thermally stable than the extant thermophilic homologue from Thermus thermophilus. Moreover, they had considerably higher low-temperature catalytic activity as compared with the T. thermophilus enzyme. Detailed analyses of their temperature-dependent specific activities and kinetic properties showed that the reconstructed enzymes have catalytic properties similar to those of mesophilic homologues. Collectively, our study demonstrates that ancestral sequence reconstruction can produce a thermally stable enzyme with catalytic properties adapted to low-temperature reactions.

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Classification of Nonenzymatic Homologues of Protein Kinases

Comparative and Functional Genomics ◽

10.1155/2009/365637 ◽

2009 ◽

Vol 2009 ◽

pp. 1-17 ◽

Cited By ~ 5

Author(s):

K. Anamika ◽

K. R. Abhinandan ◽

K. Deshmukh ◽

N. Srinivasan

Keyword(s):

Protein Kinase ◽

Protein Kinases ◽

Protein Interaction ◽

Transmembrane Domain ◽

Homo Sapiens ◽

Interaction Domain ◽

Protein Protein Interaction ◽

Domain 3 ◽

Eukaryotic Organisms ◽

And Function

Protein Kinase-Like Non-kinases (PKLNKs), which are closely related to protein kinases, lack the crucial catalytic aspartate in the catalytic loop, and hence cannot function as protein kinase, have been analysed. Using various sensitive sequence analysis methods, we have recognized 82 PKLNKs from four higher eukaryotic organisms, namely,Homo sapiens,Mus musculus,Rattus norvegicus, andDrosophila melanogaster. On the basis of their domain combination and function, PKLNKs have been classified mainly into four categories: (1) Ligand binding PKLNKs, (2) PKLNKs with extracellular protein-protein interaction domain, (3) PKLNKs involved in dimerization, and (4) PKLNKs with cytoplasmic protein-protein interaction module. While members of the first two classes of PKLNKs have transmembrane domain tethered to the PKLNK domain, members of the other two classes of PKLNKs are cytoplasmic in nature. The current classification scheme hopes to provide a convenient framework to classify the PKLNKs from other eukaryotes which would be helpful in deciphering their roles in cellular processes.

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