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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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3
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Hehenberger E, Eitel M, Fortunato SAV, Miller DJ, Keeling PJ, Cahill MA. Early eukaryotic origins and metazoan elaboration of MAPR family proteins. Mol Phylogenet Evol 2020; 148:106814. [PMID: 32278076 DOI: 10.1016/j.ympev.2020.106814] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 03/24/2020] [Accepted: 04/01/2020] [Indexed: 01/01/2023]
Abstract
The membrane-associated progesterone receptor (MAPR) family consists of heme-binding proteins containing a cytochrome b5 (cytb5) domain characterized by the presence of a MAPR-specific interhelical insert region (MIHIR) between helices 3 and 4 of the canonical cytb5-domain fold. Animals possess three MAPR genes (PGRMC-like, Neuferricin and Neudesin). Here we show that all three animal MAPR genes were already present in the common ancestor of the opisthokonts (comprising animals and fungi as well as related single-celled taxa). All three MAPR genes acquired extensions C-terminal to the cytb5 domain, either before or with the evolution of animals. The archetypical MAPR protein, progesterone receptor membrane component 1 (PGRMC1), contains phosphorylated tyrosines Y139 and Y180. The combination of Y139/Y180 appeared in the common ancestor of cnidarians and bilaterians, along with an early embryological organizer and synapsed neurons, and is strongly conserved in all bilaterian animals. A predicted protein interaction motif in the PGRMC1 MIHIR is potentially regulated by Y139 phosphorylation. A multilayered model of animal MAPR function acquisition includes some pre-metazoan functions (e.g., heme binding and cytochrome P450 interactions) and some acquired animal-specific functions that involve regulation of strongly conserved protein interaction motifs acquired by animals (Metazoa). This study provides a conceptual framework for future studies, against which especially PGRMC1's multiple functions can perhaps be stratified and functionally dissected.
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Affiliation(s)
- Elisabeth Hehenberger
- Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Michael Eitel
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sofia A V Fortunato
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Michael A Cahill
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia; ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Canberra, ACT 2601, Australia.
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Erwin DH. The origin of animal body plans: a view from fossil evidence and the regulatory genome. Development 2020; 147:147/4/dev182899. [DOI: 10.1242/dev.182899] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
ABSTRACT
The origins and the early evolution of multicellular animals required the exploitation of holozoan genomic regulatory elements and the acquisition of new regulatory tools. Comparative studies of metazoans and their relatives now allow reconstruction of the evolution of the metazoan regulatory genome, but the deep conservation of many genes has led to varied hypotheses about the morphology of early animals and the extent of developmental co-option. In this Review, I assess the emerging view that the early diversification of animals involved small organisms with diverse cell types, but largely lacking complex developmental patterning, which evolved independently in different bilaterian clades during the Cambrian Explosion.
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Affiliation(s)
- Douglas H. Erwin
- Department of Paleobiology, MRC-121, National Museum of Natural History, PO Box 37012, Washington, DC 20013-7012, USA
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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5
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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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