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Rauniyar K, Bokharaie H, Jeltsch M. Expansion and collapse of VEGF diversity in major clades of the animal kingdom. Angiogenesis 2023; 26:437-461. [PMID: 37017884 PMCID: PMC10328876 DOI: 10.1007/s10456-023-09874-9] [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: 01/20/2023] [Accepted: 03/17/2023] [Indexed: 04/06/2023]
Abstract
Together with the platelet-derived growth factors (PDGFs), the vascular endothelial growth factors (VEGFs) form the PDGF/VEGF subgroup among cystine knot growth factors. The evolutionary relationships within this subgroup have not been examined thoroughly to date. Here, we comprehensively analyze the PDGF/VEGF growth factors throughout all animal phyla and propose a phylogenetic tree. Vertebrate whole-genome duplications play a role in expanding PDGF/VEGF diversity, but several limited duplications are necessary to account for the temporal pattern of emergence. The phylogenetically oldest PDGF/VEGF-like growth factor likely featured a C-terminus with a BR3P signature, a hallmark of the modern-day lymphangiogenic growth factors VEGF-C and VEGF-D. Some younger VEGF genes, such as VEGFB and PGF, appeared completely absent in important vertebrate clades such as birds and amphibia, respectively. In contrast, individual PDGF/VEGF gene duplications frequently occurred in fish on top of the known fish-specific whole-genome duplications. The lack of precise counterparts for human genes poses limitations but also offers opportunities for research using organisms that diverge considerably from humans. Sources for the graphical abstract: 326 MYA and older [1]; 72-240 MYA [2]; 235-65 MYA [3].
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Affiliation(s)
- Khushbu Rauniyar
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Biocenter 2, (Viikinkaari 5E), P.O. Box. 56, 00790, Helsinki, Finland
| | - Honey Bokharaie
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Biocenter 2, (Viikinkaari 5E), P.O. Box. 56, 00790, Helsinki, Finland
| | - Michael Jeltsch
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Biocenter 2, (Viikinkaari 5E), P.O. Box. 56, 00790, Helsinki, Finland.
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Wihuri Research Institute, Helsinki, Finland.
- Helsinki One Health, University of Helsinki, Helsinki, Finland.
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Wang X, Weber GF. Quantitative Analysis of Protein Evolution: The Phylogeny of Osteopontin. Front Genet 2021; 12:700789. [PMID: 34484297 PMCID: PMC8415472 DOI: 10.3389/fgene.2021.700789] [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: 04/26/2021] [Accepted: 07/19/2021] [Indexed: 11/13/2022] Open
Abstract
The phylogenetic analysis of proteins conventionally relies on the evaluation of amino acid sequences or coding sequences. Individual amino acids have measurable features that allow the translation from strings of letters (amino acids or bases) into strings of numbers (physico-chemical properties). When the letters are converted to measurable properties, such numerical strings can be evaluated quantitatively with various tools of complex systems research. We build on our prior phylogenetic analysis of the cytokine Osteopontin to validate the quantitative approach toward the study of protein evolution. Phylogenetic trees constructed from the number strings differentiate among all sequences. In pairwise comparisons, autocorrelation, average mutual information and box counting dimension yield one number each for the overall relatedness between sequences. We also find that bivariate wavelet analysis distinguishes hypermutable regions from conserved regions of the protein. The investigation of protein evolution via quantitative study of the physico-chemical characteristics pertaining to the amino acid building blocks broadens the spectrum of applicable research tools, accounts for mutation as well as selection, gives assess to multiple vistas depending on the property evaluated, discriminates more accurately among sequences, and renders the analysis more quantitative than utilizing strings of letters as starting points.
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Affiliation(s)
- Xia Wang
- Department of Mathematical Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Georg F Weber
- Academic Health Center, University of Cincinnati, Cincinnati, OH, United States
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Yang J, Ding H, Kan X. Codon usage patterns and evolution of HSP60 in birds. Int J Biol Macromol 2021; 183:1002-1012. [PMID: 33971236 DOI: 10.1016/j.ijbiomac.2021.05.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 11/27/2022]
Abstract
Heat shock protein 60 (HSP60) is highly conserved from prokaryotic to eukaryotic organisms, acting as molecular chaperone and other vital biological functions. In spite of increasing knowledge of HSP60, its evolutionary mechanism on functional adaption is still far from completely understood. Moreover, analysis of codon usage bias (CUB) is a powerful tool to understand evolutionary association studies. However, so far, as we know, no scientific work on CUB of HSP60 in birds has been reported. In this study, we provide a comprehensive analysis on the codon usage and molecular evolution of HSP60 across birds. The results indicated that HSP60 had a weak codon usage bias with high ENC values (range from 52.66 to 61), low RSCU, and A/T-ending codons were mostly preferred. Meanwhile, it was considered that mutation, natural selection, and genetic drift combined to shape codon usage patterns with different strength proportions among various birds for HSP60. Then, the LRT tests suggested that different lineages of birds might be under similar selective pressures. Besides, the two positive selection sites (151 and 131) were detected and might undergo radical changes. These findings would contribute to understand function diversity and molecular evolution of HSP60 in birds.
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Affiliation(s)
- Jianke Yang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China; School of Preclinical Medicine, Wannan Medical College, Wuhu, Anhui, China
| | - Hengwu Ding
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China; Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu, Anhui, China
| | - Xianzhao Kan
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China; Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu, Anhui, China.
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Menter DG, Kopetz S, Hawk E, Sood AK, Loree JM, Gresele P, Honn KV. Platelet "first responders" in wound response, cancer, and metastasis. Cancer Metastasis Rev 2017; 36:199-213. [PMID: 28730545 PMCID: PMC5709140 DOI: 10.1007/s10555-017-9682-0] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Platelets serve as "first responders" during normal wounding and homeostasis. Arising from bone marrow stem cell lineage megakaryocytes, anucleate platelets can influence inflammation and immune regulation. Biophysically, platelets are optimized due to size and discoid morphology to distribute near vessel walls, monitor vascular integrity, and initiate quick responses to vascular lesions. Adhesion receptors linked to a highly reactive filopodia-generating cytoskeleton maximizes their vascular surface contact allowing rapid response capabilities. Functionally, platelets normally initiate rapid clotting, vasoconstriction, inflammation, and wound biology that leads to sterilization, tissue repair, and resolution. Platelets also are among the first to sense, phagocytize, decorate, or react to pathogens in the circulation. These platelet first responder properties are commandeered during chronic inflammation, cancer progression, and metastasis. Leaky or inflammatory reaction blood vessel genesis during carcinogenesis provides opportunities for platelet invasion into tumors. Cancer is thought of as a non-healing or chronic wound that can be actively aided by platelet mitogenic properties to stimulate tumor growth. This growth ultimately outstrips circulatory support leads to angiogenesis and intravasation of tumor cells into the blood stream. Circulating tumor cells reengage additional platelets, which facilitates tumor cell adhesion, arrest and extravasation, and metastasis. This process, along with the hypercoagulable states associated with malignancy, is amplified by IL6 production in tumors that stimulate liver thrombopoietin production and elevates circulating platelet numbers by thrombopoiesis in the bone marrow. These complex interactions and the "first responder" role of platelets during diverse physiologic stresses provide a useful therapeutic target that deserves further exploration.
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Affiliation(s)
- David G Menter
- Department of Gastrointestinal Medical Oncology, M. D. Anderson Cancer Center, Room#: FC10.3004, 1515 Holcombe Boulevard--Unit 0426, Houston, TX, 77030, USA.
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, M. D. Anderson Cancer Center, Room#: FC10.3004, 1515 Holcombe Boulevard--Unit 0426, Houston, TX, 77030, USA
| | - Ernest Hawk
- Office of the Vice President Cancer Prevention & Population Science, M. D. Anderson Cancer Center, Unit 1370, 1515 Holcombe Boulevard, Houston, TX, 77054, USA
| | - Anil K Sood
- Gynocologic Oncology & Reproductive Medicine, M. D. Anderson Cancer Center, Unit 1362, 1515 Holcombe Boulevard, Houston, TX, 77054, USA
- Department of Cancer Biology, M. D. Anderson Cancer Center, Unit 1362, 1515 Holcombe Boulevard, Houston, TX, 77054, USA
- Center for RNA Interference and Non-Coding RNA The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Jonathan M Loree
- Department of Gastrointestinal Medical Oncology, M. D. Anderson Cancer Center, Room#: FC10.3004, 1515 Holcombe Boulevard--Unit 0426, Houston, TX, 77030, USA
| | - Paolo Gresele
- Department of Medicine, Section of Internal and Cardiovascular Medicine, University of Perugia, Via E. Dal Pozzo, 06126, Perugia, Italy
| | - Kenneth V Honn
- Bioactive Lipids Research Program, Department of Pathology, Wayne State University, 431 Chemistry Bldg, 5101 Cass Avenue, Detroit, MI, 48202, USA
- Department of Pathology, Wayne State University, 431 Chemistry Bldg, 5101 Cass Avenue, Detroit, MI, 48202, USA
- Cancer Biology Division, Wayne State University School of Medicine, 431 Chemistry Bldg, 5101 Cass Avenue, Detroit, MI, 48202, USA
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Brunet FG, Volff JN, Schartl M. Whole Genome Duplications Shaped the Receptor Tyrosine Kinase Repertoire of Jawed Vertebrates. Genome Biol Evol 2016; 8:1600-13. [PMID: 27260203 PMCID: PMC4898815 DOI: 10.1093/gbe/evw103] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The receptor tyrosine kinase (RTK) gene family, involved primarily in cell growth and differentiation, comprises proteins with a common enzymatic tyrosine kinase intracellular domain adjacent to a transmembrane region. The amino-terminal portion of RTKs is extracellular and made of different domains, the combination of which characterizes each of the 20 RTK subfamilies among mammals. We analyzed a total of 7,376 RTK sequences among 143 vertebrate species to provide here the first comprehensive census of the jawed vertebrate repertoire. We ascertained the 58 genes previously described in the human and mouse genomes and established their phylogenetic relationships. We also identified five additional RTKs amounting to a total of 63 genes in jawed vertebrates. We found that the vertebrate RTK gene family has been shaped by the two successive rounds of whole genome duplications (WGD) called 1R and 2R (1R/2R) that occurred at the base of the vertebrates. In addition, the Vegfr and Ephrin receptor subfamilies were expanded by single gene duplications. In teleost fish, 23 additional RTK genes have been retained after another expansion through the fish-specific third round (3R) of WGD. Several lineage-specific gene losses were observed. For instance, birds have lost three RTKs, and different genes are missing in several fish sublineages. The RTK gene family presents an unusual high gene retention rate from the vertebrate WGDs (58.75% after 1R/2R, 64.4% after 3R), resulting in an expansion that might be correlated with the evolution of complexity of vertebrate cellular communication and intracellular signaling.
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Affiliation(s)
- Frédéric G Brunet
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, UMR5242 CNRS, Université Claude Bernard Lyon I, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, UMR5242 CNRS, Université Claude Bernard Lyon I, Lyon, France
| | - Manfred Schartl
- Physiologische Chemie, Biozentrum, University of Würzburg, Am Hubland, and Comprehensive Cancer Center, University Clinic Würzburg, Würzburg, Germany Texas Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, USA
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