1
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Gizzio J, Thakur A, Haldane A, Post CB, Levy RM. Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases. Nat Commun 2024; 15:6545. [PMID: 39095350 PMCID: PMC11297160 DOI: 10.1038/s41467-024-50812-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
Protein kinases are molecular machines with rich sequence variation that distinguishes the two main evolutionary branches - tyrosine kinases (TKs) from serine/threonine kinases (STKs). Using a sequence co-variation Potts statistical energy model we previously concluded that TK catalytic domains are more likely than STKs to adopt an inactive conformation with the activation loop in an autoinhibitory folded conformation, due to intrinsic sequence effects. Here we investigate the structural basis for this phenomenon by integrating the sequence-based model with structure-based molecular dynamics (MD) to determine the effects of mutations on the free energy difference between active and inactive conformations, using a thermodynamic cycle involving many (n = 108) protein-mutation free energy perturbation (FEP) simulations in the active and inactive conformations. The sequence and structure-based results are consistent and support the hypothesis that the inactive conformation DFG-out Activation Loop Folded, is a functional regulatory state that has been stabilized in TKs relative to STKs over the course of their evolution via the accumulation of residue substitutions in the activation loop and catalytic loop that facilitate distinct substrate binding modes in trans and additional modes of regulation in cis for TKs.
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Affiliation(s)
- Joan Gizzio
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, PA, USA
- Department of Chemistry, Temple University, Philadelphia, PA, USA
| | - Abhishek Thakur
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, PA, USA
- Department of Chemistry, Temple University, Philadelphia, PA, USA
| | - Allan Haldane
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, PA, USA
- Department of Physics, Temple University, Philadelphia, PA, USA
| | - Carol Beth Post
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Ronald M Levy
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, PA, USA.
- Department of Chemistry, Temple University, Philadelphia, PA, USA.
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2
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Gizzio J, Thakur A, Haldane A, Levy RM. Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases. RESEARCH SQUARE 2024:rs.3.rs-4048991. [PMID: 38746330 PMCID: PMC11092858 DOI: 10.21203/rs.3.rs-4048991/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Protein kinases are molecular machines with rich sequence variation that distinguishes the two main evolutionary branches - tyrosine kinases (TKs) from serine/threonine kinases (STKs). Using a sequence co-variation Potts statistical energy model we previously concluded that TK catalytic domains are more likely than STKs to adopt an inactive conformation with the activation loop in an autoinhibitory "folded" conformation, due to intrinsic sequence effects. Here we investigated the structural basis for this phenomenon by integrating the sequence-based model with structure-based molecular dynamics (MD) to determine the effects of mutations on the free energy difference between active and inactive conformations, using a novel thermodynamic cycle involving many (n=108) protein-mutation free energy perturbation (FEP) simulations in the active and inactive conformations. The sequence and structure-based results are consistent and support the hypothesis that the inactive conformation "DFG-out Activation Loop Folded", is a functional regulatory state that has been stabilized in TKs relative to STKs over the course of their evolution via the accumulation of residue substitutions in the activation loop and catalytic loop that facilitate distinct substrate binding modes in trans and additional modes of regulation in cis for TKs.
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Affiliation(s)
- Joan Gizzio
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Abhishek Thakur
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Allan Haldane
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122
| | - Ronald M. Levy
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
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3
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Gizzio J, Thakur A, Haldane A, Post CB, Levy RM. Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584161. [PMID: 38559238 PMCID: PMC10979876 DOI: 10.1101/2024.03.08.584161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Protein kinases are molecular machines with rich sequence variation that distinguishes the two main evolutionary branches - tyrosine kinases (TKs) from serine/threonine kinases (STKs). Using a sequence co-variation Potts statistical energy model we previously concluded that TK catalytic domains are more likely than STKs to adopt an inactive conformation with the activation loop in an autoinhibitory "folded" conformation, due to intrinsic sequence effects. Here we investigated the structural basis for this phenomenon by integrating the sequence-based model with structure-based molecular dynamics (MD) to determine the effects of mutations on the free energy difference between active and inactive conformations, using a novel thermodynamic cycle involving many (n=108) protein-mutation free energy perturbation (FEP) simulations in the active and inactive conformations. The sequence and structure-based results are consistent and support the hypothesis that the inactive conformation "DFG-out Activation Loop Folded", is a functional regulatory state that has been stabilized in TKs relative to STKs over the course of their evolution via the accumulation of residue substitutions in the activation loop and catalytic loop that facilitate distinct substrate binding modes in trans and additional modes of regulation in cis for TKs.
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Affiliation(s)
- Joan Gizzio
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Abhishek Thakur
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Allan Haldane
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122
| | - Carol Beth Post
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907
| | - Ronald M. Levy
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
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4
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Ros-Rocher N, Brunet T. What is it like to be a choanoflagellate? Sensation, processing and behavior in the closest unicellular relatives of animals. Anim Cogn 2023; 26:1767-1782. [PMID: 37067637 PMCID: PMC10770216 DOI: 10.1007/s10071-023-01776-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/18/2023]
Abstract
All animals evolved from a single lineage of unicellular precursors more than 600 million years ago. Thus, the biological and genetic foundations for animal sensation, cognition and behavior must necessarily have arisen by modifications of pre-existing features in their unicellular ancestors. Given that the single-celled ancestors of the animal kingdom are extinct, the only way to reconstruct how these features evolved is by comparing the biology and genomic content of extant animals to their closest living relatives. Here, we reconstruct the Umwelt (the subjective, perceptive world) inhabited by choanoflagellates, a group of unicellular (or facultatively multicellular) aquatic microeukaryotes that are the closest living relatives of animals. Although behavioral research on choanoflagellates remains patchy, existing evidence shows that they are capable of chemosensation, photosensation and mechanosensation. These processes often involve specialized sensorimotor cellular appendages (cilia, microvilli, and/or filopodia) that resemble those that underlie perception in most animal sensory cells. Furthermore, comparative genomics predicts an extensive "sensory molecular toolkit" in choanoflagellates, which both provides a potential basis for known behaviors and suggests the existence of a largely undescribed behavioral complexity that presents exciting avenues for future research. Finally, we discuss how facultative multicellularity in choanoflagellates might help us understand how evolution displaced the locus of decision-making from a single cell to a collective, and how a new space of behavioral complexity might have become accessible in the process.
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Affiliation(s)
- Núria Ros-Rocher
- Evolutionary Cell Biology and Evolution of Morphogenesis Unit, Institut Pasteur, Université Paris-Cité, CNRS UMR3691, 25-28 Rue du Docteur Roux, 75015, Paris, France
| | - Thibaut Brunet
- Evolutionary Cell Biology and Evolution of Morphogenesis Unit, Institut Pasteur, Université Paris-Cité, CNRS UMR3691, 25-28 Rue du Docteur Roux, 75015, Paris, France.
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5
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Majumdar S, Di Palma F, Spyrakis F, Decherchi S, Cavalli A. Molecular Dynamics and Machine Learning Give Insights on the Flexibility-Activity Relationships in Tyrosine Kinome. J Chem Inf Model 2023; 63:4814-4826. [PMID: 37462363 PMCID: PMC10428216 DOI: 10.1021/acs.jcim.3c00738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Indexed: 08/15/2023]
Abstract
Tyrosine kinases are a subfamily of kinases with critical roles in cellular machinery. Dysregulation of their active or inactive forms is associated with diseases like cancer. This study aimed to holistically understand their flexibility-activity relationships, focusing on pockets and fluctuations. We studied 43 different tyrosine kinases by collecting 120 μs of molecular dynamics simulations, pocket and residue fluctuation analysis, and a complementary machine learning approach. We found that the inactive forms often have increased flexibility, particularly at the DFG motif level. Noteworthy, thanks to these long simulations combined with a decision tree, we identified a semiquantitative fluctuation threshold of the DGF+3 residue over which the kinase has a higher probability to be in the inactive form.
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Affiliation(s)
- Sarmistha Majumdar
- Computational
& Chemical Biology, Fondazione Istituto
Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
| | - Francesco Di Palma
- Computational
& Chemical Biology, Fondazione Istituto
Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
| | - Francesca Spyrakis
- Department
of Drug Science and Technology, University
of Turin, via Giuria
9, I-10125 Turin, Italy
| | - Sergio Decherchi
- Data
Science and Computation, Fondazione Istituto
Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
| | - Andrea Cavalli
- Computational
& Chemical Biology, Fondazione Istituto
Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
- Department
of Pharmacy and Biotechnology, University
of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy
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6
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Sabbarini IM, Reif D, McQuown AJ, Nelliat AR, Prince J, Membreno BS, Wu CCC, Murray AW, Denic V. Zinc-finger protein Zpr1 is a bespoke chaperone essential for eEF1A biogenesis. Mol Cell 2023; 83:252-265.e13. [PMID: 36630955 PMCID: PMC10016025 DOI: 10.1016/j.molcel.2022.12.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/15/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023]
Abstract
The conserved regulon of heat shock factor 1 in budding yeast contains chaperones for general protein folding as well as zinc-finger protein Zpr1, whose essential role in archaea and eukaryotes remains unknown. Here, we show that Zpr1 depletion causes acute proteotoxicity driven by biosynthesis of misfolded eukaryotic translation elongation factor 1A (eEF1A). Prolonged Zpr1 depletion leads to eEF1A insufficiency, thereby inducing the integrated stress response and inhibiting protein synthesis. Strikingly, we show by using two distinct biochemical reconstitution approaches that Zpr1 enables eEF1A to achieve a conformational state resistant to protease digestion. Lastly, we use a ColabFold model of the Zpr1-eEF1A complex to reveal a folding mechanism mediated by the Zpr1's zinc-finger and alpha-helical hairpin structures. Our work uncovers the long-sought-after function of Zpr1 as a bespoke chaperone tailored to the biogenesis of one of the most abundant proteins in the cell.
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Affiliation(s)
- Ibrahim M Sabbarini
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Dvir Reif
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alexander J McQuown
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Anjali R Nelliat
- Graduate Program in Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jeffrey Prince
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Britnie Santiago Membreno
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Colin Chih-Chien Wu
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vladimir Denic
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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7
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Gizzio J, Thakur A, Haldane A, Levy RM. Evolutionary divergence in the conformational landscapes of tyrosine vs serine/threonine kinases. eLife 2022; 11:83368. [PMID: 36562610 PMCID: PMC9822262 DOI: 10.7554/elife.83368] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/22/2022] [Indexed: 12/24/2022] Open
Abstract
Inactive conformations of protein kinase catalytic domains where the DFG motif has a "DFG-out" orientation and the activation loop is folded present a druggable binding pocket that is targeted by FDA-approved 'type-II inhibitors' in the treatment of cancers. Tyrosine kinases (TKs) typically show strong binding affinity with a wide spectrum of type-II inhibitors while serine/threonine kinases (STKs) usually bind more weakly which we suggest here is due to differences in the folded to extended conformational equilibrium of the activation loop between TKs vs. STKs. To investigate this, we use sequence covariation analysis with a Potts Hamiltonian statistical energy model to guide absolute binding free-energy molecular dynamics simulations of 74 protein-ligand complexes. Using the calculated binding free energies together with experimental values, we estimated free-energy costs for the large-scale (~17-20 Å) conformational change of the activation loop by an indirect approach, circumventing the very challenging problem of simulating the conformational change directly. We also used the Potts statistical potential to thread large sequence ensembles over active and inactive kinase states. The structure-based and sequence-based analyses are consistent; together they suggest TKs evolved to have free-energy penalties for the classical 'folded activation loop' DFG-out conformation relative to the active conformation, that is, on average, 4-6 kcal/mol smaller than the corresponding values for STKs. Potts statistical energy analysis suggests a molecular basis for this observation, wherein the activation loops of TKs are more weakly 'anchored' against the catalytic loop motif in the active conformation and form more stable substrate-mimicking interactions in the inactive conformation. These results provide insights into the molecular basis for the divergent functional properties of TKs and STKs, and have pharmacological implications for the target selectivity of type-II inhibitors.
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Affiliation(s)
- Joan Gizzio
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, United States.,Department of Chemistry, Temple University, Philadelphia, United States
| | - Abhishek Thakur
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, United States.,Department of Chemistry, Temple University, Philadelphia, United States
| | - Allan Haldane
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, United States.,Department of Physics, Temple University, Philadelphia, United States
| | - Ronald M Levy
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, United States.,Department of Chemistry, Temple University, Philadelphia, United States
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8
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Fierro Morales JC, Xue Q, Roh-Johnson M. An evolutionary and physiological perspective on cell-substrate adhesion machinery for cell migration. Front Cell Dev Biol 2022; 10:943606. [PMID: 36092727 PMCID: PMC9453864 DOI: 10.3389/fcell.2022.943606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Cell-substrate adhesion is a critical aspect of many forms of cell migration. Cell adhesion to an extracellular matrix (ECM) generates traction forces necessary for efficient migration. One of the most well-studied structures cells use to adhere to the ECM is focal adhesions, which are composed of a multilayered protein complex physically linking the ECM to the intracellular actin cytoskeleton. Much of our understanding of focal adhesions, however, is primarily derived from in vitro studies in Metazoan systems. Though these studies provide a valuable foundation to the cell-substrate adhesion field, the evolution of cell-substrate adhesion machinery across evolutionary space and the role of focal adhesions in vivo are largely understudied within the field. Furthering investigation in these areas is necessary to bolster our understanding of the role cell-substrate adhesion machinery across Eukaryotes plays during cell migration in physiological contexts such as cancer and pathogenesis. In this review, we review studies of cell-substrate adhesion machinery in organisms evolutionary distant from Metazoa and cover the current understanding and ongoing work on how focal adhesions function in single and collective cell migration in an in vivo environment, with an emphasis on work that directly visualizes cell-substrate adhesions. Finally, we discuss nuances that ought to be considered moving forward and the importance of future investigation in these emerging fields for application in other fields pertinent to adhesion-based processes.
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Affiliation(s)
| | | | - Minna Roh-Johnson
- Department of Biochemistry, University of Utah, Salt Lake City, UT, United States
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9
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Kawakami J, Brooks D, Zalmai R, Hartson SD, Bouyain S, Geisbrecht ER. Complex protein interactions mediate Drosophila Lar function in muscle tissue. PLoS One 2022; 17:e0269037. [PMID: 35622884 PMCID: PMC9140312 DOI: 10.1371/journal.pone.0269037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 05/12/2022] [Indexed: 11/28/2022] Open
Abstract
The type IIa family of receptor protein tyrosine phosphatases (RPTPs), including Lar, RPTPσ and RPTPδ, are well-studied in coordinating actin cytoskeletal rearrangements during axon guidance and synaptogenesis. To determine whether this regulation is conserved in other tissues, interdisciplinary approaches were utilized to study Lar-RPTPs in the Drosophila musculature. Here we find that the single fly ortholog, Drosophila Lar (Dlar), is localized to the muscle costamere and that a decrease in Dlar causes aberrant sarcomeric patterning, deficits in larval locomotion, and integrin mislocalization. Sequence analysis uncovered an evolutionarily conserved Lys-Gly-Asp (KGD) signature in the extracellular region of Dlar. Since this tripeptide sequence is similar to the integrin-binding Arg-Gly-Asp (RGD) motif, we tested the hypothesis that Dlar directly interacts with integrin proteins. However, structural analyses of the fibronectin type III domains of Dlar and two vertebrate orthologs that include this conserved motif indicate that this KGD tripeptide is not accessible and thus unlikely to mediate physical interactions with integrins. These results, together with the proteomics identification of basement membrane (BM) proteins as potential ligands for type IIa RPTPs, suggest a complex network of protein interactions in the extracellular space that may mediate Lar function and/or signaling in muscle tissue.
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Affiliation(s)
- Jessica Kawakami
- Department of Cell and Molecular Biology and Biochemistry, University of Missouri-Kansas City, Kansas City, MO, United States of America
| | - David Brooks
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
| | - Rana Zalmai
- Department of Cell and Molecular Biology and Biochemistry, University of Missouri-Kansas City, Kansas City, MO, United States of America
| | - Steven D. Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States of America
| | - Samuel Bouyain
- Department of Cell and Molecular Biology and Biochemistry, University of Missouri-Kansas City, Kansas City, MO, United States of America
| | - Erika R. Geisbrecht
- Department of Cell and Molecular Biology and Biochemistry, University of Missouri-Kansas City, Kansas City, MO, United States of America
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
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10
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Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in Monosiga brevicollis PDZ Domains Using Human PDZ Data. Molecules 2021; 26:molecules26196034. [PMID: 34641578 PMCID: PMC8512817 DOI: 10.3390/molecules26196034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 11/17/2022] Open
Abstract
Choanoflagellates are single-celled eukaryotes with complex signaling pathways. They are considered the closest non-metazoan ancestors to mammals and other metazoans and form multicellular-like states called rosettes. The choanoflagellate Monosiga brevicollis contains over 150 PDZ domains, an important peptide-binding domain in all three domains of life (Archaea, Bacteria, and Eukarya). Therefore, an understanding of PDZ domain signaling pathways in choanoflagellates may provide insight into the origins of multicellularity. PDZ domains recognize the C-terminus of target proteins and regulate signaling and trafficking pathways, as well as cellular adhesion. Here, we developed a computational software suite, Domain Analysis and Motif Matcher (DAMM), that analyzes peptide-binding cleft sequence identity as compared with human PDZ domains and that can be used in combination with literature searches of known human PDZ-interacting sequences to predict target specificity in choanoflagellate PDZ domains. We used this program, protein biochemistry, fluorescence polarization, and structural analyses to characterize the specificity of A9UPE9_MONBE, a M. brevicollis PDZ domain-containing protein with no homology to any metazoan protein, finding that its PDZ domain is most similar to those of the DLG family. We then identified two endogenous sequences that bind A9UPE9 PDZ with <100 μM affinity, a value commonly considered the threshold for cellular PDZ-peptide interactions. Taken together, this approach can be used to predict cellular targets of previously uncharacterized PDZ domains in choanoflagellates and other organisms. Our data contribute to investigations into choanoflagellate signaling and how it informs metazoan evolution.
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11
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Yeung W, Kwon A, Taujale R, Bunn C, Venkat A, Kannan N. Evolution of functional diversity in the holozoan tyrosine kinome. Mol Biol Evol 2021; 38:5625-5639. [PMID: 34515793 PMCID: PMC8662651 DOI: 10.1093/molbev/msab272] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The emergence of multicellularity is strongly correlated with the expansion of tyrosine kinases, a conserved family of signaling enzymes that regulates pathways essential for cell-to-cell communication. Although tyrosine kinases have been classified from several model organisms, a molecular-level understanding of tyrosine kinase evolution across all holozoans is currently lacking. Using a hierarchical sequence constraint-based classification of diverse holozoan tyrosine kinases, we construct a new phylogenetic tree that identifies two ancient clades of cytoplasmic and receptor tyrosine kinases separated by the presence of an extended insert segment in the kinase domain connecting the D and E-helices. Present in nearly all receptor tyrosine kinases, this fast-evolving insertion imparts diverse functionalities, such as post-translational modification sites and regulatory interactions. Eph and EGFR receptor tyrosine kinases are two exceptions which lack this insert, each forming an independent lineage characterized by unique functional features. We also identify common constraints shared across multiple tyrosine kinase families which warrant the designation of three new subgroups: Src module (SrcM), insulin receptor kinase-like (IRKL), and fibroblast, platelet-derived, vascular, and growth factor receptors (FPVR). Subgroup-specific constraints reflect shared autoinhibitory interactions involved in kinase conformational regulation. Conservation analyses describe how diverse tyrosine kinase signaling functions arose through the addition of family-specific motifs upon subgroup-specific features and coevolving protein domains. We propose the oldest tyrosine kinases, IRKL, SrcM, and Csk, originated from unicellular premetazoans and were coopted for complex multicellular functions. The increased frequency of oncogenic variants in more recent tyrosine kinases suggests that lineage-specific functionalities are selectively altered in human cancers.
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Affiliation(s)
- Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Annie Kwon
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Rahil Taujale
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Claire Bunn
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Aarya Venkat
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
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12
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Qiao Y, Choi JE, Tien JC, Simko SA, Rajendiran T, Vo JN, Delekta AD, Wang L, Xiao L, Hodge NB, Desai P, Mendoza S, Juckette K, Xu A, Soni T, Su F, Wang R, Cao X, Yu J, Kryczek I, Wang XM, Wang X, Siddiqui J, Wang Z, Bernard A, Fernandez-Salas E, Navone NM, Ellison SJ, Ding K, Eskelinen EL, Heath EI, Klionsky DJ, Zou W, Chinnaiyan AM. Autophagy Inhibition by Targeting PIKfyve Potentiates Response to Immune Checkpoint Blockade in Prostate Cancer. NATURE CANCER 2021; 2:978-993. [PMID: 34738088 PMCID: PMC8562569 DOI: 10.1038/s43018-021-00237-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Multi-tyrosine kinase inhibitors (MTKIs) have thus far had limited success in the treatment of castration-resistant prostate cancer (CRPC). Here, we report a phase I-cleared orally bioavailable MTKI, ESK981, with a novel autophagy inhibitory property that decreased tumor growth in diverse preclinical models of CRPC. The anti-tumor activity of ESK981 was maximized in immunocompetent tumor environments where it upregulated CXCL10 expression through the interferon gamma pathway and promoted functional T cell infiltration, which resulted in enhanced therapeutic response to immune checkpoint blockade. Mechanistically, we identify the lipid kinase PIKfyve as the direct target of ESK981. PIKfyve-knockdown recapitulated ESK981's anti-tumor activity and enhanced the therapeutic benefit of immune checkpoint blockade. Our study reveals that targeting PIKfyve via ESK981 turns tumors from cold into hot through inhibition of autophagy, which may prime the tumor immune microenvironment in advanced prostate cancer patients and be an effective treatment strategy alone or in combination with immunotherapies.
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Affiliation(s)
- Yuanyuan Qiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jae Eun Choi
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,School of Medicine, University of California, San Diego, California 92093, USA
| | - Jean C. Tien
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Stephanie A. Simko
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Thekkelnaycke Rajendiran
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Michigan Regional Comprehensive Metabolomics Resource Core, Ann Arbor, Michigan 48109, USA
| | - Josh N. Vo
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Andrew D. Delekta
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Lisha Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Nathan B. Hodge
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Parth Desai
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Sergio Mendoza
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Kristin Juckette
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Alice Xu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Tanu Soni
- Michigan Regional Comprehensive Metabolomics Resource Core, Ann Arbor, Michigan 48109, USA
| | - Fengyun Su
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Rui Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jiali Yu
- Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Ilona Kryczek
- Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Xiao-Ming Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xiaoju Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Javed Siddiqui
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Zhen Wang
- School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Amélie Bernard
- CNRS, Laboratoire de Biogenèse Membranaire, UMR5200; Université de Bordeaux, Laboratoire de Biogenèse Membranaire, UMR5200, 33000 Bordeaux, France.,Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Ester Fernandez-Salas
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Nora M. Navone
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Stephanie J. Ellison
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Ke Ding
- School of Pharmacy, Jinan University, Guangzhou 510632, China
| | | | - Elisabeth I. Heath
- Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
| | - Daniel J. Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Weiping Zou
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Urology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Correspondence to: Arul M. Chinnaiyan, Michigan Center for Translational Pathology, Rogel Cancer Center, 1500 East Medical Center Drive, Ann Arbor, Michigan 48109, USA. Phone: 734-615-4062; Fax: 734-615-4498;
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13
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Nagy LG, Varga T, Csernetics Á, Virágh M. Fungi took a unique evolutionary route to multicellularity: Seven key challenges for fungal multicellular life. FUNGAL BIOL REV 2020. [DOI: 10.1016/j.fbr.2020.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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14
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Miller WT. Temperature sensitivities of metazoan and pre-metazoan Src kinases. Biochem Biophys Rep 2020; 23:100775. [PMID: 32566764 PMCID: PMC7298416 DOI: 10.1016/j.bbrep.2020.100775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 11/24/2022] Open
Abstract
Homologous enzymes from different species display functional characteristics that correlate with the physiological and environmental temperatures encountered by the organisms. In this study, we have investigated the temperature sensitivity of the nonreceptor tyrosine kinase Src. We compared the temperature dependencies of c-Src and two Src kinases from single-celled eukaryotes, the choanoflagellate Monosiga brevicollis and the filasterean Capsaspora owczarzaki. Metazoan c-Src exhibits temperature sensitivity, with high activity at 30 °C and 37 °C. This sensitivity is driven by changes in substrate binding as well as maximal velocity, and it is dependent on the amino acid sequence surrounding tyrosine in the substrate. When tested with a peptide that displays temperature-dependent phosphorylation by c-Src, the enzymatic rates for the unicellular Src kinases show much less variation over the temperatures tested. The data demonstrate that unicellular Src kinases are temperature compensated relative to metazoan c-Src, consistent with an evolutionary adaptation to their environments.
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Affiliation(s)
- W. Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, 11794, USA
- Department of Veterans Affairs Medical Center, Northport, NY, 11768, USA
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15
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Li L, Liu D, Liu A, Li J, Wang H, Zhou J. Genomic Survey of Tyrosine Kinases Repertoire in Electrophorus electricus With an Emphasis on Evolutionary Conservation and Diversification. Evol Bioinform Online 2020; 16:1176934320922519. [PMID: 32546936 PMCID: PMC7249569 DOI: 10.1177/1176934320922519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/07/2020] [Indexed: 12/05/2022] Open
Abstract
Tyrosine kinases (TKs) play key roles in the regulation of multicellularity in
organisms and involved primarily in cell growth, differentiation, and
cell-to-cell communication. Genome-wide characterization of TKs has been
conducted in many metazoans; however, systematic information regarding this
superfamily in Electrophorus electricus (electric eel) is still
lacking. In this study, we identified 114 TK genes in the E
electricus genome and investigated their evolution, molecular
features, and domain architecture using phylogenetic profiling to gain a better
understanding of their similarities and specificity. Our results suggested that
the electric eel TK (EeTK) repertoire was shaped by whole-genome duplications
(WGDs) and tandem duplication events. Compared with other vertebrate TKs, gene
members in Jak, Src, and EGFR subfamily duplicated specifically, but with
members lost in Eph, Axl, and Ack subfamily in electric eel. We also conducted
an exhaustive survey of TK genes in genomic databases, identifying 1674 TK
proteins in 31 representative species covering all the main metazoan lineages.
Extensive evolutionary analysis indicated that TK repertoire in vertebrates
tended to be remarkably conserved, but the gene members in each subfamily were
very variable. Comparative expression profile analysis showed that electric
organ tissues and muscle shared a similar pattern with specific highly expressed
TKs (ie, epha7, musk, jak1, and pdgfra), suggesting that regulation of TKs might
play an important role in specifying an electric organ identity from its muscle
precursor. We further identified TK genes exhibiting tissue-specific expression
patterns, indicating that members in TKs participated in subfunctionalization
representing an evolutionary divergence required for the performance of
different tissues. This work generates valuable information for further gene
function analysis and identifying candidate TK genes reflecting their unique
tissue-function specializations in electric eel.
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Affiliation(s)
- Ling Li
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Dangyun Liu
- Department of Central Laboratory, The Affiliated Huaian No.1 People's Hospital, Nanjing Medical University, Huai'an, P.R. China
| | - Ake Liu
- Faculty of Biological Science and Technology, Changzhi University, Changzhi, P.R. China
| | - Jingquan Li
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Hui Wang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Jingqi Zhou
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
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16
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Jamroskovic J, Doimo M, Chand K, Obi I, Kumar R, Brännström K, Hedenström M, Nath Das R, Akhunzianov A, Deiana M, Kasho K, Sulis Sato S, Pourbozorgi PL, Mason JE, Medini P, Öhlund D, Wanrooij S, Chorell E, Sabouri N. Quinazoline Ligands Induce Cancer Cell Death through Selective STAT3 Inhibition and G-Quadruplex Stabilization. J Am Chem Soc 2020; 142:2876-2888. [PMID: 31990532 PMCID: PMC7307907 DOI: 10.1021/jacs.9b11232] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
The signal transducer
and activator of transcription 3 (STAT3)
protein is a master regulator of most key hallmarks and enablers of
cancer, including cell proliferation and the response to DNA damage.
G-Quadruplex (G4) structures are four-stranded noncanonical DNA structures
enriched at telomeres and oncogenes’ promoters. In cancer cells,
stabilization of G4 DNAs leads to replication stress and DNA damage
accumulation and is therefore considered a promising target for oncotherapy.
Here, we designed and synthesized novel quinazoline-based compounds
that simultaneously and selectively affect these two well-recognized
cancer targets, G4 DNA structures and the STAT3 protein. Using a combination
of in vitro assays, NMR, and molecular dynamics simulations, we show
that these small, uncharged compounds not only bind to the STAT3 protein
but also stabilize G4 structures. In human cultured cells, the compounds
inhibit phosphorylation-dependent activation of STAT3 without affecting
the antiapoptotic factor STAT1 and cause increased formation of G4
structures, as revealed by the use of a G4 DNA-specific antibody.
As a result, treated cells show slower DNA replication, DNA damage
checkpoint activation, and an increased apoptotic rate. Importantly,
cancer cells are more sensitive to these molecules compared to noncancerous
cell lines. This is the first report of a promising class of compounds
that not only targets the DNA damage cancer response machinery but
also simultaneously inhibits the STAT3-induced cancer cell proliferation,
demonstrating a novel approach in cancer therapy.
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Affiliation(s)
- Jan Jamroskovic
- Department of Medical Biochemistry and Biophysics , Umeå University , Umeå 90736 , Sweden
| | - Mara Doimo
- Department of Medical Biochemistry and Biophysics , Umeå University , Umeå 90736 , Sweden
| | - Karam Chand
- Department of Chemistry , Umeå University , Umeå 90736 , Sweden
| | - Ikenna Obi
- Department of Medical Biochemistry and Biophysics , Umeå University , Umeå 90736 , Sweden
| | - Rajendra Kumar
- Department of Chemistry , Umeå University , Umeå 90736 , Sweden
| | - Kristoffer Brännström
- Department of Medical Biochemistry and Biophysics , Umeå University , Umeå 90736 , Sweden
| | | | | | - Almaz Akhunzianov
- Department of Medical Biochemistry and Biophysics , Umeå University , Umeå 90736 , Sweden.,Institute of Fundamental Medicine and Biology , Kazan Federal University , Kazan 420008 , Russia
| | - Marco Deiana
- Department of Medical Biochemistry and Biophysics , Umeå University , Umeå 90736 , Sweden
| | - Kazutoshi Kasho
- Department of Medical Biochemistry and Biophysics , Umeå University , Umeå 90736 , Sweden
| | - Sebastian Sulis Sato
- Department of Integrative Medical Biology , Umeå University , Umeå 90736 , Sweden
| | - Parham L Pourbozorgi
- Department of Medical Biochemistry and Biophysics , Umeå University , Umeå 90736 , Sweden
| | - James E Mason
- Department of Radiation Sciences , Umeå University , Umeå 90736 , Sweden
| | - Paolo Medini
- Department of Integrative Medical Biology , Umeå University , Umeå 90736 , Sweden
| | - Daniel Öhlund
- Department of Radiation Sciences , Umeå University , Umeå 90736 , Sweden
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics , Umeå University , Umeå 90736 , Sweden
| | - Erik Chorell
- Department of Chemistry , Umeå University , Umeå 90736 , Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics , Umeå University , Umeå 90736 , Sweden
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17
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Moeller FU, Webster NS, Herbold CW, Behnam F, Domman D, Albertsen M, Mooshammer M, Markert S, Turaev D, Becher D, Rattei T, Schweder T, Richter A, Watzka M, Nielsen PH, Wagner M. Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta. Environ Microbiol 2019; 21:3831-3854. [PMID: 31271506 PMCID: PMC6790972 DOI: 10.1111/1462-2920.14732] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/25/2022]
Abstract
Marine sponges represent one of the few eukaryotic groups that frequently harbour symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. However, in most studies, direct demonstration of ammonia-oxidation by these archaea within sponges is lacking, and little is known about sponge-specific adaptations of ammonia-oxidizing archaea (AOA). Here, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and isotope-based functional assays. 'Candidatus Nitrosospongia ianthellae' is only distantly related to cultured AOA. It is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbour nitrite-oxidizing microbes. Furthermore, this AOA is equipped with an expanded set of extracellular subtilisin-like proteases, a metalloprotease unique among archaea, as well as a putative branched-chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge-associated, but not in free-living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic-like proteins, and a DNA-phosporothioation system, represent important adaptations of AOA to life within these ancient filter-feeding animals.
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Affiliation(s)
- Florian U. Moeller
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Nicole S. Webster
- Australian Institute of Marine ScienceTownsvilleQueenslandAustralia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular BiosciencesUniversity of QueenslandSt LuciaQueenslandAustralia
| | - Craig W. Herbold
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Faris Behnam
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Daryl Domman
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg University9220AalborgDenmark
| | - Maria Mooshammer
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Stephanie Markert
- Institute of Marine Biotechnology e.VGreifswaldGermany
- Institute of Pharmacy, Pharmaceutical BiotechnologyUniversity of GreifswaldGreifswaldGermany
| | - Dmitrij Turaev
- Centre for Microbiology and Environmental Systems Science, Division of Computational Systems BiologyUniversity of ViennaAustria
| | - Dörte Becher
- Institute of Microbiology, Microbial ProteomicsUniversity of GreifswaldGreifswaldGermany
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, Division of Computational Systems BiologyUniversity of ViennaAustria
| | - Thomas Schweder
- Institute of Marine Biotechnology e.VGreifswaldGermany
- Institute of Pharmacy, Pharmaceutical BiotechnologyUniversity of GreifswaldGreifswaldGermany
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem ResearchUniversity of ViennaAustria
| | - Margarete Watzka
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem ResearchUniversity of ViennaAustria
| | - Per Halkjaer Nielsen
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg University9220AalborgDenmark
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg University9220AalborgDenmark
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18
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Comparative genomics reveals the origin of fungal hyphae and multicellularity. Nat Commun 2019; 10:4080. [PMID: 31501435 PMCID: PMC6733946 DOI: 10.1038/s41467-019-12085-w] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 08/20/2019] [Indexed: 02/01/2023] Open
Abstract
Hyphae represent a hallmark structure of multicellular fungi. The evolutionary origins of hyphae and of the underlying genes are, however, hardly known. By systematically analyzing 72 complete genomes, we here show that hyphae evolved early in fungal evolution probably via diverse genetic changes, including co-option and exaptation of ancient eukaryotic (e.g. phagocytosis-related) genes, the origin of new gene families, gene duplications and alterations of gene structure, among others. Contrary to most multicellular lineages, the origin of filamentous fungi did not correlate with expansions of kinases, receptors or adhesive proteins. Co-option was probably the dominant mechanism for recruiting genes for hypha morphogenesis, while gene duplication was apparently less prevalent, except in transcriptional regulators and cell wall - related genes. We identified 414 novel gene families that show correlated evolution with hyphae and that may have contributed to its evolution. Our results suggest that hyphae represent a unique multicellular organization that evolved by limited fungal-specific innovations and gene duplication but pervasive co-option and modification of ancient eukaryotic functions.
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19
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Krishnan A, Degnan BM, Degnan SM. The first identification of complete Eph-ephrin signalling in ctenophores and sponges reveals a role for neofunctionalization in the emergence of signalling domains. BMC Evol Biol 2019; 19:96. [PMID: 31023220 PMCID: PMC6485061 DOI: 10.1186/s12862-019-1418-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 03/31/2019] [Indexed: 11/25/2022] Open
Abstract
Background Animals have a greater diversity of signalling pathways than their unicellular relatives, consistent with the evolution and expansion of these pathways occurring in parallel with the origin of animal multicellularity. However, the genomes of sponges and ctenophores – non-bilaterian basal animals – typically encode no, or far fewer, recognisable signalling ligands compared to bilaterians and cnidarians. For instance, the largest subclass of receptor tyrosine kinases (RTKs) in bilaterians, the Eph receptors (Ephs), are present in sponges and ctenophores, but their cognate ligands, the ephrins, have not yet been detected. Results Here, we use an iterative HMM analysis to identify for the first time membrane-bound ephrins in sponges and ctenophores. We also expand the number of Eph-receptor subtypes identified in these animals and in cnidarians. Both sequence and structural analyses are consistent with the Eph ligand binding domain (LBD) and the ephrin receptor binding domain (RBD) having evolved via the co-option of ancient galactose-binding (discoidin-domain)-like and monodomain cupredoxin domains, respectively. Although we did not detect a complete Eph-ephrin signalling pathway in closely-related unicellular holozoans or in other non-metazoan eukaryotes, truncated proteins with Eph receptor LBDs and ephrin RBDs are present in some choanoflagellates. Together, these results indicate that Eph-ephrin signalling was present in the last common ancestor of extant metazoans, and perhaps even in the last common ancestor of animals and choanoflagellates. Either scenario pushes the origin of Eph-ephrin signalling back much earlier than previously reported. Conclusions We propose that the Eph-LBD and ephrin-RBD, which were ancestrally localised in the cytosol, became linked to the extracellular parts of two cell surface proteins before the divergence of sponges and ctenophores from the rest of the animal kingdom. The ephrin-RBD lost the ancestral capacity to bind copper, and the Eph-LBD became linked to an ancient RTK. The identification of divergent ephrin ligands in sponges and ctenophores suggests that these ligands evolve faster than their cognate receptors. As this may be a general phenomena, we propose that the sequence-structure approach used in this study may be usefully applied to other signalling systems where no, or a small number of, ligands have been identified. Electronic supplementary material The online version of this article (10.1186/s12862-019-1418-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Arunkumar Krishnan
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia.,Present Address: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Bernard M Degnan
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sandie M Degnan
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia.
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20
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Kwon A, Scott S, Taujale R, Yeung W, Kochut KJ, Eyers PA, Kannan N. Tracing the origin and evolution of pseudokinases across the tree of life. Sci Signal 2019; 12:12/578/eaav3810. [PMID: 31015289 DOI: 10.1126/scisignal.aav3810] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein phosphorylation by eukaryotic protein kinases (ePKs) is a fundamental mechanism of cell signaling in all organisms. In model vertebrates, ~10% of ePKs are classified as pseudokinases, which have amino acid changes within the catalytic machinery of the kinase domain that distinguish them from their canonical kinase counterparts. However, pseudokinases still regulate various signaling pathways, usually doing so in the absence of their own catalytic output. To investigate the prevalence, evolutionary relationships, and biological diversity of these pseudoenzymes, we performed a comprehensive analysis of putative pseudokinase sequences in available eukaryotic, bacterial, and archaeal proteomes. We found that pseudokinases are present across all domains of life, and we classified nearly 30,000 eukaryotic, 1500 bacterial, and 20 archaeal pseudokinase sequences into 86 pseudokinase families, including ~30 families that were previously unknown. We uncovered a rich variety of pseudokinases with notable expansions not only in animals but also in plants, fungi, and bacteria, where pseudokinases have previously received cursory attention. These expansions are accompanied by domain shuffling, which suggests roles for pseudokinases in plant innate immunity, plant-fungal interactions, and bacterial signaling. Mechanistically, the ancestral kinase fold has diverged in many distinct ways through the enrichment of unique sequence motifs to generate new families of pseudokinases in which the kinase domain is repurposed for noncanonical nucleotide binding or to stabilize unique, inactive kinase conformations. We further provide a collection of annotated pseudokinase sequences in the Protein Kinase Ontology (ProKinO) as a new mineable resource for the signaling community.
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Affiliation(s)
- Annie Kwon
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Steven Scott
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Rahil Taujale
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Krys J Kochut
- Department of Computer Science, University of Georgia, Athens, GA 30602, USA
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA. .,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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21
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Featherston J, Arakaki Y, Hanschen ER, Ferris PJ, Michod RE, Olson BJSC, Nozaki H, Durand PM. The 4-Celled Tetrabaena socialis Nuclear Genome Reveals the Essential Components for Genetic Control of Cell Number at the Origin of Multicellularity in the Volvocine Lineage. Mol Biol Evol 2019; 35:855-870. [PMID: 29294063 DOI: 10.1093/molbev/msx332] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Multicellularity is the premier example of a major evolutionary transition in individuality and was a foundational event in the evolution of macroscopic biodiversity. The volvocine chlorophyte lineage is well suited for studying this process. Extant members span unicellular, simple colonial, and obligate multicellular taxa with germ-soma differentiation. Here, we report the nuclear genome sequence of one of the most morphologically simple organisms in this lineage-the 4-celled colonial Tetrabaena socialis and compare this to the three other complete volvocine nuclear genomes. Using conservative estimates of gene family expansions a minimal set of expanded gene families was identified that associate with the origin of multicellularity. These families are rich in genes related to developmental processes. A subset of these families is lineage specific, which suggests that at a genomic level the evolution of multicellularity also includes lineage-specific molecular developments. Multiple points of evidence associate modifications to the ubiquitin proteasomal pathway (UPP) with the beginning of coloniality. Genes undergoing positive or accelerating selection in the multicellular volvocines were found to be enriched in components of the UPP and gene families gained at the origin of multicellularity include components of the UPP. A defining feature of colonial/multicellular life cycles is the genetic control of cell number. The genomic data presented here, which includes diversification of cell cycle genes and modifications to the UPP, align the genetic components with the evolution of this trait.
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Affiliation(s)
- Jonathan Featherston
- Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa.,Agricultural Research Council, Biotechnology Platform, Pretoria, South Africa
| | - Yoko Arakaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Hongo, Japan
| | - Erik R Hanschen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
| | - Patrick J Ferris
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
| | - Richard E Michod
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
| | | | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Hongo, Japan
| | - Pierre M Durand
- Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa
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22
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Parca L, Ariano B, Cabibbo A, Paoletti M, Tamburrini A, Palmeri A, Ausiello G, Helmer-Citterich M. Kinome-wide identification of phosphorylation networks in eukaryotic proteomes. Bioinformatics 2019; 35:372-379. [PMID: 30016513 PMCID: PMC6361239 DOI: 10.1093/bioinformatics/bty545] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/06/2018] [Accepted: 07/12/2018] [Indexed: 01/10/2023] Open
Abstract
Motivation Signaling and metabolic pathways are finely regulated by a network of protein phosphorylation events. Unraveling the nature of this intricate network, composed of kinases, target proteins and their interactions, is therefore of crucial importance. Although thousands of kinase-specific phosphorylations (KsP) have been annotated in model organisms their kinase-target network is far from being complete, with less studied organisms lagging behind. Results In this work, we achieved an automated and accurate identification of kinase domains, inferring the residues that most likely contribute to peptide specificity. We integrated this information with the target peptides of known human KsP to predict kinase-specific interactions in other eukaryotes through a deep neural network, outperforming similar methods. We analyzed the differential conservation of kinase specificity among eukaryotes revealing the high conservation of the specificity of tyrosine kinases. With this approach we discovered 1590 novel KsP of potential clinical relevance in the human proteome. Availability and implementation http://akid.bio.uniroma2.it. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Luca Parca
- Department of Biology, Centro di Bioinformatica Molecolare, University of Rome “Tor Vergata”, Rome, Italy
| | - Bruno Ariano
- Department of Biology, Centro di Bioinformatica Molecolare, University of Rome “Tor Vergata”, Rome, Italy
| | - Andrea Cabibbo
- Department of Biology, Centro di Bioinformatica Molecolare, University of Rome “Tor Vergata”, Rome, Italy
| | - Marco Paoletti
- Department of Biology, Centro di Bioinformatica Molecolare, University of Rome “Tor Vergata”, Rome, Italy
| | - Annalaura Tamburrini
- Department of Biology, Centro di Bioinformatica Molecolare, University of Rome “Tor Vergata”, Rome, Italy
| | - Antonio Palmeri
- Department of Biology, Centro di Bioinformatica Molecolare, University of Rome “Tor Vergata”, Rome, Italy
| | - Gabriele Ausiello
- Department of Biology, Centro di Bioinformatica Molecolare, University of Rome “Tor Vergata”, Rome, Italy
| | - Manuela Helmer-Citterich
- Department of Biology, Centro di Bioinformatica Molecolare, University of Rome “Tor Vergata”, Rome, Italy
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Amacher JF, Hobbs HT, Cantor AC, Shah L, Rivero M, Mulchand SA, Kuriyan J. Phosphorylation control of the ubiquitin ligase Cbl is conserved in choanoflagellates. Protein Sci 2018; 27:923-932. [PMID: 29498112 PMCID: PMC5916117 DOI: 10.1002/pro.3397] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/27/2018] [Accepted: 02/28/2018] [Indexed: 12/23/2022]
Abstract
Cbl proteins are E3 ubiquitin ligases specialized for the regulation of tyrosine kinases by ubiquitylation. Human Cbl proteins are activated by tyrosine phosphorylation, thus setting up a feedback loop whereby the activation of tyrosine kinases triggers their own degradation. Cbl proteins are targeted to their substrates by a phosphotyrosine-binding SH2 domain. Choanoflagellates, unicellular eukaryotes that are closely related to metazoans, also contain Cbl. The tyrosine kinase complement of choanoflagellates is distinct from that of metazoans, and it is unclear if choanoflagellate Cbl is regulated similarly to metazoan Cbl. Here, we performed structure-function studies on Cbl from the choanoflagellate species Salpingoeca rosetta and found that it undergoes phosphorylation-dependent activation. We show that S. rosetta Cbl can be phosphorylated by S. rosetta Src kinase, and that it can ubiquitylate S. rosetta Src. We also compared the substrate selectivity of human and S. rosetta Cbl by measuring ubiquitylation of Src constructs in which Cbl-recruitment sites are placed in different contexts with respect to the kinase domain. Our results indicate that for both human and S. rosetta Cbl, ubiquitylation depends on proximity and accessibility, rather than being targeted toward specific lysine residues. Our results point to an ancient interplay between phosphotyrosine and ubiquitin signaling in the metazoan lineage.
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Affiliation(s)
- Jeanine F. Amacher
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCalifornia
- California Institute for Quantitative Biosciences, University of CaliforniaBerkeleyCalifornia
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyCalifornia
- Present address:
Department of ChemistryWestern Washington UniversityBellinghamWashington.
| | - Helen T. Hobbs
- Department of ChemistryUniversity of CaliforniaBerkeleyCalifornia
| | - Aaron C. Cantor
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCalifornia
- California Institute for Quantitative Biosciences, University of CaliforniaBerkeleyCalifornia
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyCalifornia
| | - Lochan Shah
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCalifornia
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyCalifornia
| | - Marco‐Jose Rivero
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCalifornia
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyCalifornia
| | - Sarah A. Mulchand
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCalifornia
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyCalifornia
| | - John Kuriyan
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCalifornia
- California Institute for Quantitative Biosciences, University of CaliforniaBerkeleyCalifornia
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyCalifornia
- Department of ChemistryUniversity of CaliforniaBerkeleyCalifornia
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
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24
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Nagy LG, Kovács GM, Krizsán K. Complex multicellularity in fungi: evolutionary convergence, single origin, or both? Biol Rev Camb Philos Soc 2018; 93:1778-1794. [DOI: 10.1111/brv.12418] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/23/2018] [Accepted: 03/28/2018] [Indexed: 12/22/2022]
Affiliation(s)
- László G. Nagy
- Synthetic and Systems Biology Unit; Institute of Biochemistry, BRC-HAS, 62 Temesvári krt; 6726 Szeged Hungary
| | - Gábor M. Kovács
- Department of Plant Anatomy; Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C; H-1117 Budapest Hungary
- Plant Protection Institute, Centre for Agricultural Research; Hungarian Academy of Sciences (MTA-ATK); PO Box 102, H-1525 Budapest Hungary
| | - Krisztina Krizsán
- Synthetic and Systems Biology Unit; Institute of Biochemistry, BRC-HAS, 62 Temesvári krt; 6726 Szeged Hungary
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25
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Abstract
Creolimax fragrantissima is a member of the ichthyosporean clade, the earliest branching holozoan lineage. The kinome of Creolimax is markedly reduced as compared to those of metazoans. In particular, Creolimax possesses a single non-receptor tyrosine kinase: CfrSrc, the homolog of c-Src kinase. CfrSrc is an active tyrosine kinase, and it is expressed throughout the lifecycle of Creolimax. In animal cells, the regulatory mechanism for Src involves tyrosine phosphorylation at a C-terminal site by Csk kinase. The lack of Csk in Creolimax suggests that a different mode of negative regulation must exist for CfrSrc. We demonstrate that CfrPTP-3, one of the 7 tyrosine-specific phosphatases (PTPs) in Creolimax, suppresses CfrSrc activity in vitro and in vivo. Transcript levels of CfrPTP-3 and two other PTPs are significantly higher than that of CfrSrc in the motile amoeboid and sessile multinucleate stages of the Creolimax life cycle. Thus, in the context of a highly reduced kinome, a pre-existing PTP may have been co-opted for the role of Src regulation. Creolimax represents a unique model system to study the adaptation of tyrosine kinase signaling and regulatory mechanisms.
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26
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Tong K, Wang Y, Su Z. Phosphotyrosine signalling and the origin of animal multicellularity. Proc Biol Sci 2018; 284:rspb.2017.0681. [PMID: 28768887 DOI: 10.1098/rspb.2017.0681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/26/2017] [Indexed: 12/21/2022] Open
Abstract
The evolution of multicellular animals (i.e. metazoans) from a unicellular ancestor is one of the most important yet least understood evolutionary transitions. Historically, given its indispensable functions in intercellular communication and exclusive presence in metazoans, phosphotyrosine (pTyr) signalling was considered a metazoan-specific evolutionary innovation that might have contributed to the origin of metazoan multicellularity. However, recent studies have led to a new understanding of pTyr signalling evolution and its role in the metazoan origin. Sequence analyses have unravelled a much earlier emergence of pTyr signalling in eukaryotic evolution. Even so, several distinct properties of holozoan pTyr signalling may have paved the way for a hypothesized functional transition of pTyr signalling at the multicellular origin, from environmental sensing to intercellular communication, and for it to evolve as a powerful intercellular signalling system for multicellularity. Biochemical analyses of premetazoan pTyr signalling components have further revealed the premetazoan origin of many key features of metazoan pTyr signalling, and the metazoan establishment of others, including the Csk-mediated negative regulation of the activity of Src, a conserved tyrosine kinase in the Holozoa. Finally, potential future directions are discussed, with a stress on the biological functions of premetazoan pTyr signalling via newly developed gene manipulation tools in non-animal holozoans.
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Affiliation(s)
- Kai Tong
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, People's Republic of China
| | - Yuyu Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, People's Republic of China
| | - Zhixi Su
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, People's Republic of China
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27
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Evolution, dynamics and dysregulation of kinase signalling. Curr Opin Struct Biol 2018; 48:133-140. [DOI: 10.1016/j.sbi.2017.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 12/31/2022]
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28
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Plattner H. Evolutionary Cell Biology of Proteins from Protists to Humans and Plants. J Eukaryot Microbiol 2017; 65:255-289. [PMID: 28719054 DOI: 10.1111/jeu.12449] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/04/2017] [Accepted: 07/07/2017] [Indexed: 01/10/2023]
Abstract
During evolution, the cell as a fine-tuned machine had to undergo permanent adjustments to match changes in its environment, while "closed for repair work" was not possible. Evolution from protists (protozoa and unicellular algae) to multicellular organisms may have occurred in basically two lineages, Unikonta and Bikonta, culminating in mammals and angiosperms (flowering plants), respectively. Unicellular models for unikont evolution are myxamoebae (Dictyostelium) and increasingly also choanoflagellates, whereas for bikonts, ciliates are preferred models. Information accumulating from combined molecular database search and experimental verification allows new insights into evolutionary diversification and maintenance of genes/proteins from protozoa on, eventually with orthologs in bacteria. However, proteins have rarely been followed up systematically for maintenance or change of function or intracellular localization, acquirement of new domains, partial deletion (e.g. of subunits), and refunctionalization, etc. These aspects are discussed in this review, envisaging "evolutionary cell biology." Protozoan heritage is found for most important cellular structures and functions up to humans and flowering plants. Examples discussed include refunctionalization of voltage-dependent Ca2+ channels in cilia and replacement by other types during evolution. Altogether components serving Ca2+ signaling are very flexible throughout evolution, calmodulin being a most conservative example, in contrast to calcineurin whose catalytic subunit is lost in plants, whereas both subunits are maintained up to mammals for complex functions (immune defense and learning). Domain structure of R-type SNAREs differs in mono- and bikonta, as do Ca2+ -dependent protein kinases. Unprecedented selective expansion of the subunit a which connects multimeric base piece and head parts (V0, V1) of H+ -ATPase/pump may well reflect the intriguing vesicle trafficking system in ciliates, specifically in Paramecium. One of the most flexible proteins is centrin when its intracellular localization and function throughout evolution is traced. There are many more examples documenting evolutionary flexibility of translation products depending on requirements and potential for implantation within the actual cellular context at different levels of evolution. From estimates of gene and protein numbers per organism, it appears that much of the basic inventory of protozoan precursors could be transmitted to highest eukaryotic levels, with some losses and also with important additional "inventions."
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Affiliation(s)
- Helmut Plattner
- Department of Biology, University of Konstanz, P. O. Box M625, Konstanz, 78457, Germany
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29
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Rensing SA. (Why) Does Evolution Favour Embryogenesis? TRENDS IN PLANT SCIENCE 2016; 21:562-573. [PMID: 26987708 DOI: 10.1016/j.tplants.2016.02.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/14/2016] [Accepted: 02/19/2016] [Indexed: 05/05/2023]
Abstract
Complex multicellular organisms typically possess life cycles in which zygotes (formed by gamete fusion) and meiosis occur. Canonical animal embryogenesis describes development from zygote to birth. It involves polarisation of the egg/zygote, asymmetric cell divisions, establishment of axes, symmetry breaking, formation of organs, and parental nutrition (at least in early stages). Similar developmental patterns have independently evolved in other eukaryotic lineages, including land plants and brown algae. The question arises whether embryo-like structures and associated developmental processes recurrently emerge because they are local optima of the evolutionary landscape. To understand which evolutionary principles govern complex multicellularity, we need to analyse why and how similar processes evolve convergently - von Baer's and Haeckel's phylotypic stage revisited in other phyla.
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Affiliation(s)
- Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
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30
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Weir ME, Mann JE, Corwin T, Fulton ZW, Hao JM, Maniscalco JF, Kenney MC, Roman Roque KM, Chapdelaine EF, Stelzl U, Deming PB, Ballif BA, Hinkle KL. Novel autophosphorylation sites of Src family kinases regulate kinase activity and SH2 domain-binding capacity. FEBS Lett 2016; 590:1042-52. [PMID: 27001024 DOI: 10.1002/1873-3468.12144] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/18/2016] [Accepted: 03/17/2016] [Indexed: 01/10/2023]
Abstract
Src family tyrosine kinases (SFKs) are critical players in normal and aberrant biological processes. While phosphorylation importantly regulates SFKs at two known tyrosines, large-scale phosphoproteomics have revealed four additional tyrosines commonly phosphorylated in SFKs. We found these novel tyrosines to be autophosphorylation sites. Mimicking phosphorylation at the C-terminal site to the activation loop decreased Fyn activity. Phosphomimetics and direct phosphorylation at the three SH2 domain sites increased Fyn activity while reducing phosphotyrosine-dependent interactions. While 68% of human SH2 domains exhibit conservation of at least one of these tyrosines, few have been found phosphorylated except when found in cis to a kinase domain.
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Affiliation(s)
- Marion E Weir
- Department of Biology, University of Vermont, Burlington, VT, USA
| | - Jacqueline E Mann
- Department of Medical Laboratory and Radiation Sciences, University of Vermont, Burlington, VT, USA
| | - Thomas Corwin
- Otto-Warburg Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Zachary W Fulton
- Department of Biology, University of Vermont, Burlington, VT, USA.,Department of Biology and Physical Education, Norwich University, Northfield, VT, USA
| | - Jennifer M Hao
- Department of Biology, University of Vermont, Burlington, VT, USA
| | | | - Marie C Kenney
- Department of Biology, University of Vermont, Burlington, VT, USA
| | | | - Elizabeth F Chapdelaine
- Department of Biology, University of Vermont, Burlington, VT, USA.,Department of Biology and Physical Education, Norwich University, Northfield, VT, USA
| | - Ulrich Stelzl
- Otto-Warburg Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Paula B Deming
- Department of Medical Laboratory and Radiation Sciences, University of Vermont, Burlington, VT, USA
| | - Bryan A Ballif
- Department of Biology, University of Vermont, Burlington, VT, USA
| | - Karen L Hinkle
- Department of Biology, University of Vermont, Burlington, VT, USA.,Department of Biology and Physical Education, Norwich University, Northfield, VT, USA
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31
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Hydrophobic Core Variations Provide a Structural Framework for Tyrosine Kinase Evolution and Functional Specialization. PLoS Genet 2016; 12:e1005885. [PMID: 26925779 PMCID: PMC4771162 DOI: 10.1371/journal.pgen.1005885] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 01/30/2016] [Indexed: 02/07/2023] Open
Abstract
Protein tyrosine kinases (PTKs) are a group of closely related enzymes that have evolutionarily diverged from serine/threonine kinases (STKs) to regulate pathways associated with multi-cellularity. Evolutionary divergence of PTKs from STKs has occurred through accumulation of mutations in the active site as well as in the commonly conserved hydrophobic core. While the functional significance of active site variations is well understood, relatively little is known about how hydrophobic core variations contribute to PTK evolutionary divergence. Here, using a combination of statistical sequence comparisons, molecular dynamics simulations, mutational analysis and in vitro thermostability and kinase assays, we investigate the structural and functional significance of key PTK-specific variations in the kinase core. We find that the nature of residues and interactions in the hydrophobic core of PTKs is strikingly different from other protein kinases, and PTK-specific variations in the core contribute to functional divergence by altering the stability and dynamics of the kinase domain. In particular, a functionally critical STK-conserved histidine that stabilizes the regulatory spine in STKs is selectively mutated to an alanine, serine or glutamate in PTKs, and this loss-of-function mutation is accommodated, in part, through compensatory PTK-specific interactions in the core. In particular, a PTK-conserved phenylalanine in the I-helix appears to structurally and functionally compensate for the loss of STK-histidine by interacting with the regulatory spine, which has far-reaching effects on enzyme activity, inhibitor sensing, and stability. We propose that hydrophobic core variations provide a selective advantage during PTK evolution by increasing the conformational flexibility, and therefore the allosteric potential of the kinase domain. Our studies also suggest that Tyrosine Kinase Like kinases such as RAF are intermediates in PTK evolutionary divergence inasmuch as they share features of both PTKs and STKs in the core. Finally, our studies provide an evolutionary framework for identifying and characterizing disease and drug resistance mutations in the kinase core. Proteins evolve new functions through accumulation of mutations in the primary sequence. Understanding how naturally occurring mutations shape protein function can provide insights into how non-natural mutations contribute to disease. Here, we identify sequence variants associated with the functional specialization of tyrosine kinases, a large and medically important class of proteins associated with the evolution of complex multicellular functions and diseases such as cancer. We find that mutations distal from the active site contribute to functional specialization by altering the stability, activity and dynamics of the kinase core. Our findings have implications for understanding the evolution of allosteric regulation in tyrosine kinases, and in predicting the structural and functional impact of disease and drug resistance mutations in the kinase core.
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32
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Van Roey K, Davey NE. Motif co-regulation and co-operativity are common mechanisms in transcriptional, post-transcriptional and post-translational regulation. Cell Commun Signal 2015; 13:45. [PMID: 26626130 PMCID: PMC4666095 DOI: 10.1186/s12964-015-0123-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/24/2015] [Indexed: 01/01/2023] Open
Abstract
A substantial portion of the regulatory interactions in the higher eukaryotic cell are mediated by simple sequence motifs in the regulatory segments of genes and (pre-)mRNAs, and in the intrinsically disordered regions of proteins. Although these regulatory modules are physicochemically distinct, they share an evolutionary plasticity that has facilitated a rapid growth of their use and resulted in their ubiquity in complex organisms. The ease of motif acquisition simplifies access to basal housekeeping functions, facilitates the co-regulation of multiple biomolecules allowing them to respond in a coordinated manner to changes in the cell state, and supports the integration of multiple signals for combinatorial decision-making. Consequently, motifs are indispensable for temporal, spatial, conditional and basal regulation at the transcriptional, post-transcriptional and post-translational level. In this review, we highlight that many of the key regulatory pathways of the cell are recruited by motifs and that the ease of motif acquisition has resulted in large networks of co-regulated biomolecules. We discuss how co-operativity allows simple static motifs to perform the conditional regulation that underlies decision-making in higher eukaryotic biological systems. We observe that each gene and its products have a unique set of DNA, RNA or protein motifs that encode a regulatory program to define the logical circuitry that guides the life cycle of these biomolecules, from transcription to degradation. Finally, we contrast the regulatory properties of protein motifs and the regulatory elements of DNA and (pre-)mRNAs, advocating that co-regulation, co-operativity, and motif-driven regulatory programs are common mechanisms that emerge from the use of simple, evolutionarily plastic regulatory modules.
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Affiliation(s)
- Kim Van Roey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany.
- Health Services Research Unit, Operational Direction Public Health and Surveillance, Scientific Institute of Public Health (WIV-ISP), 1050, Brussels, Belgium.
| | - Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland.
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33
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Reinecke J, Caplan S. Endocytosis and the Src family of non-receptor tyrosine kinases. Biomol Concepts 2015; 5:143-55. [PMID: 25372749 DOI: 10.1515/bmc-2014-0003] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 02/12/2014] [Indexed: 11/15/2022] Open
Abstract
The regulated intracellular transport of nutrient, adhesion, and growth factor receptors is crucial for maintaining cell and tissue homeostasis. Endocytosis, or endocytic membrane trafficking, involves the steps of intracellular transport that include, but are not limited to, internalization from the plasma membrane, sorting in early endosomes, transport to late endosomes/lysosomes followed by degradation, and/or recycling back to the plasma membrane through tubular recycling endosomes. In addition to regulating the localization of transmembrane receptor proteins, the endocytic pathway also controls the localization of non-receptor molecules. The non-receptor tyrosine kinase c-Src (Src) and its closely related family members Yes and Fyn represent three proteins whose localization and signaling activities are tightly regulated by endocytic trafficking. Here, we provide a brief overview of endocytosis, Src function and its biochemical regulation. We will then concentrate on recent advances in understanding how Src intracellular localization is regulated and how its subcellular localization ultimately dictates downstream functioning. As Src kinases are hyperactive in many cancers, it is essential to decipher the spatiotemporal regulation of this important family of tyrosine kinases.
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34
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Constitutive Activity in an Ancestral Form of Abl Tyrosine Kinase. PLoS One 2015; 10:e0131062. [PMID: 26090675 PMCID: PMC4474922 DOI: 10.1371/journal.pone.0131062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 05/28/2015] [Indexed: 11/19/2022] Open
Abstract
The c-abl proto-oncogene encodes a nonreceptor tyrosine kinase that is found in all metazoans, and is ubiquitously expressed in mammalian tissues. The Abl tyrosine kinase plays important roles in the regulation of mammalian cell physiology. Abl-like kinases have been identified in the genomes of unicellular choanoflagellates, the closest relatives to the Metazoa, and in related unicellular organisms. Here, we have carried out the first characterization of a premetazoan Abl kinase, MbAbl2, from the choanoflagellate Monosiga brevicollis. The enzyme possesses SH3, SH2, and kinase domains in a similar arrangement to its mammalian counterparts, and is an active tyrosine kinase. MbAbl2 lacks the N-terminal myristoylation and cap sequences that are critical regulators of mammalian Abl kinase activity, and we show that MbAbl2 is constitutively active. When expressed in mammalian cells, MbAbl2 strongly phosphorylates cellular proteins on tyrosine, and transforms cells much more potently than mammalian Abl kinase. Thus, MbAbl2 appears to lack the autoinhibitory mechanism that tightly constrains the activity of mammalian Abl kinases, suggesting that this regulatory apparatus arose more recently in metazoan evolution.
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35
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Kipryushina YO, Yakovlev KV, Odintsova NA. Vascular endothelial growth factors: A comparison between invertebrates and vertebrates. Cytokine Growth Factor Rev 2015; 26:687-95. [PMID: 26066416 DOI: 10.1016/j.cytogfr.2015.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 04/21/2015] [Indexed: 01/08/2023]
Abstract
This review aims to summarize recent data concerning the structure and role of the members of the vascular endothelial growth factor (VEGF) and vascular endothelial growth factor receptor (VEGFR) families in the context of early development, organogenesis and regeneration, with a particular emphasis on the role of these factors in the development of invertebrates. Homologs of VEGF and/or VEGFR have been found in all Eumetazoa, in both Radiata and Bilateria, where they are expressed in the descendants of different germ layers and play a pivotal role in the development of animals with and without a vascular system. VEGF is a well-known angiogenesis regulator, but this factor also control cell migration during neurogenesis and the development of branching organs (the trachea) in invertebrate and vertebrate species. A possible explanation for the origin of Vegf/Vegfr in the animal kingdom and a pathway of Vegf/Vegfr evolution are discussed.
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Affiliation(s)
- Yulia O Kipryushina
- Laboratory of Cytotechnology, A.V. Zhirmunsky Institute of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Palchevsky Str. 17, 690041 Vladivostok, Russia; Far Eastern Federal University, Sukhanova Str. 8, 690950 Vladivostok, Russia.
| | - Konstantin V Yakovlev
- Laboratory of Cytotechnology, A.V. Zhirmunsky Institute of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Palchevsky Str. 17, 690041 Vladivostok, Russia
| | - Nelly A Odintsova
- Laboratory of Cytotechnology, A.V. Zhirmunsky Institute of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Palchevsky Str. 17, 690041 Vladivostok, Russia; Far Eastern Federal University, Sukhanova Str. 8, 690950 Vladivostok, Russia
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36
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Hatzihristidis T, Desai N, Hutchins AP, Meng TC, Tremblay ML, Miranda-Saavedra D. A Drosophila-centric view of protein tyrosine phosphatases. FEBS Lett 2015; 589:951-66. [PMID: 25771859 DOI: 10.1016/j.febslet.2015.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 03/02/2015] [Accepted: 03/02/2015] [Indexed: 12/30/2022]
Abstract
Most of our knowledge on protein tyrosine phosphatases (PTPs) is derived from human pathologies and mouse knockout models. These models largely correlate well with human disease phenotypes, but can be ambiguous due to compensatory mechanisms introduced by paralogous genes. Here we present the analysis of the PTP complement of the fruit fly and the complementary view that PTP studies in Drosophila will accelerate our understanding of PTPs in physiological and pathological conditions. With only 44 PTP genes, Drosophila represents a streamlined version of the human complement. Our integrated analysis places the Drosophila PTPs into evolutionary and functional contexts, thereby providing a platform for the exploitation of the fly for PTP research and the transfer of knowledge onto other model systems.
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Affiliation(s)
- Teri Hatzihristidis
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue, Montreal, Québec H3A 1A3, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Nikita Desai
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue, Montreal, Québec H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Andrew P Hutchins
- Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Tzu-Ching Meng
- Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan; Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Michel L Tremblay
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue, Montreal, Québec H3A 1A3, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada; Department of Biochemistry, McGill University, Montreal, Quebec, Canada.
| | - Diego Miranda-Saavedra
- World Premier International (WPI) Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita 565-0871, Osaka, Japan; Centro de Biología Molecular Severo Ochoa, CSIC/Universidad Autónoma de Madrid, 28049 Madrid, Spain; IE Business School, IE University, María de Molina 31 bis, 28006 Madrid, Spain.
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Cock JM, Collén J. Independent Emergence of Complex Multicellularity in the Brown and Red Algae. EVOLUTIONARY TRANSITIONS TO MULTICELLULAR LIFE 2015. [DOI: 10.1007/978-94-017-9642-2_16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Abstract
The first animals arose more than six hundred million years ago, yet they left little impression in the fossil record. Nonetheless, the cell biology and genome composition of the first animal, the Urmetazoan, can be reconstructed through the study of phylogenetically relevant living organisms. Comparisons among animals and their unicellular and colonial relatives reveal that the Urmetazoan likely possessed a layer of epithelium-like collar cells, preyed on bacteria, reproduced by sperm and egg, and developed through cell division, cell differentiation, and invagination. Although many genes involved in development, body patterning, immunity, and cell-type specification evolved in the animal stem lineage or after animal origins, several gene families critical for cell adhesion, signaling, and gene regulation predate the origin of animals. The ancestral functions of these and other genes may eventually be revealed through studies of gene and genome function in early-branching animals and their closest non-animal relatives.
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Affiliation(s)
- Daniel J Richter
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3200; ,
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Schultheiss KP, Craddock BP, Suga H, Miller WT. Regulation of Src and Csk nonreceptor tyrosine kinases in the filasterean Ministeria vibrans. Biochemistry 2014; 53:1320-9. [PMID: 24520931 PMCID: PMC4033911 DOI: 10.1021/bi4016499] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The development of the phosphotyrosine-based signaling system predated the evolution of multicellular animals. Single-celled choanoflagellates, the closest living relatives to metazoans, possess numerous tyrosine kinases, including Src family nonreceptor tyrosine kinases. Choanoflagellates also have Csk (C-terminal Src kinase), the enzyme that regulates Src in metazoans; however, choanoflagellate Csk kinases fail to repress the cognate Src. Here, we have cloned and characterized Src and Csk kinases from Ministeria vibrans, a filasterean (the sister group to metazoans and choanoflagellates). The two Src kinases (MvSrc1 and MvSrc2) are enzymatically active Src kinases, although they have low activity toward mammalian cellular proteins. Unexpectedly, MvSrc2 has significant Ser/Thr kinase activity. The Csk homologue (MvCsk) is enzymatically inactive and fails to repress MvSrc activity. We suggest that the low activity of MvCsk is due to sequences in the SH2-kinase interface, and we show that a point mutation in this region partially restores MvCsk activity. The inactivity of filasterean Csk kinases is consistent with a model in which the stringent regulation of Src family kinases arose more recently in evolution, after the split between choanoflagellates and multicellular animals.
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Affiliation(s)
- Kira P Schultheiss
- Department of Physiology and Biophysics, Stony Brook University , Stony Brook, New York 11794, United States
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40
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Simon M, Plattner H. Unicellular Eukaryotes as Models in Cell and Molecular Biology. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 309:141-98. [DOI: 10.1016/b978-0-12-800255-1.00003-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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41
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Kaneko T, Joshi R, Feller SM, Li SS. Phosphotyrosine recognition domains: the typical, the atypical and the versatile. Cell Commun Signal 2012; 10:32. [PMID: 23134684 PMCID: PMC3507883 DOI: 10.1186/1478-811x-10-32] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 10/09/2012] [Indexed: 12/21/2022] Open
Abstract
SH2 domains are long known prominent players in the field of phosphotyrosine recognition within signaling protein networks. However, over the years they have been joined by an increasing number of other protein domain families that can, at least with some of their members, also recognise pTyr residues in a sequence-specific context. This superfamily of pTyr recognition modules, which includes substantial fractions of the PTB domains, as well as much smaller, or even single member fractions like the HYB domain, the PKCδ and PKCθ C2 domains and RKIP, represents a fascinating, medically relevant and hence intensely studied part of the cellular signaling architecture of metazoans. Protein tyrosine phosphorylation clearly serves a plethora of functions and pTyr recognition domains are used in a similarly wide range of interaction modes, which encompass, for example, partner protein switching, tandem recognition functionalities and the interaction with catalytically active protein domains. If looked upon closely enough, virtually no pTyr recognition and regulation event is an exact mirror image of another one in the same cell. Thus, the more we learn about the biology and ultrastructural details of pTyr recognition domains, the more does it become apparent that nature cleverly combines and varies a few basic principles to generate a sheer endless number of sophisticated and highly effective recognition/regulation events that are, under normal conditions, elegantly orchestrated in time and space. This knowledge is also valuable when exploring pTyr reader domains as diagnostic tools, drug targets or therapeutic reagents to combat human diseases.
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Affiliation(s)
- Tomonori Kaneko
- Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada.
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Schultheiss KP, Suga H, Ruiz-Trillo I, Miller WT. Lack of Csk-mediated negative regulation in a unicellular SRC kinase. Biochemistry 2012; 51:8267-77. [PMID: 22998693 DOI: 10.1021/bi300965h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phosphotyrosine-based signaling plays a vital role in cellular communication in multicellular organisms. Unexpectedly, unicellular choanoflagellates (the closest phylogenetic group to metazoans) possess numbers of tyrosine kinases that are comparable to those in complex metazoans. Here, we have characterized tyrosine kinases from the filasterean Capsaspora owczarzaki, a unicellular protist representing the sister group to choanoflagellates and metazoans. Two Src-like tyrosine kinases have been identified in C. owczarzaki (CoSrc1 and CoSrc2), both of which have the arrangement of SH3, SH2, and catalytic domains seen in mammalian Src kinases. In Capsaspora cells, CoSrc1 and CoSrc2 localize to punctate structures in filopodia that may represent primordial focal adhesions. We have cloned, expressed, and purified both enzymes. CoSrc1 and CoSrc2 are active tyrosine kinases. Mammalian Src kinases are normally regulated in a reciprocal fashion by autophosphorylation in the activation loop (which increases activity) and by Csk-mediated phosphorylation of the C-terminal tail (which inhibits activity). Similar to mammalian Src kinases, the enzymatic activities of CoSrc1 and CoSrc2 are increased by autophosphorylation in the activation loop. We have identified a Csk-like kinase (CoCsk) in the genome of C. owczarzaki. We cloned, expressed, and purified CoCsk and found that it has no measurable tyrosine kinase activity. Furthermore, CoCsk does not phosphorylate or regulate CoSrc1 or CoSrc2 in cells or in vitro, and CoSrc1 and CoSrc2 are active in Capsaspora cell lysates. Thus, the function of Csk as a negative regulator of Src family kinases appears to have arisen with the emergence of metazoans.
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Affiliation(s)
- Kira P Schultheiss
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794, USA
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