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Barrera-Redondo J, Lotharukpong JS, Drost HG, Coelho SM. Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra. Genome Biol 2023; 24:54. [PMID: 36964572 PMCID: PMC10037820 DOI: 10.1186/s13059-023-02895-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: 08/26/2022] [Accepted: 03/10/2023] [Indexed: 03/26/2023] Open
Abstract
We present GenEra ( https://github.com/josuebarrera/GenEra ), a DIAMOND-fueled gene-family founder inference framework that addresses previously raised limitations and biases in genomic phylostratigraphy, such as homology detection failure. GenEra also reduces computational time from several months to a few days for any genome of interest. We analyze the emergence of taxonomically restricted gene families during major evolutionary transitions in plants, animals, and fungi. Our results indicate that the impact of homology detection failure on inferred patterns of gene emergence is lineage-dependent, suggesting that plants are more prone to evolve novelty through the emergence of new genes compared to animals and fungi.
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Affiliation(s)
- Josué Barrera-Redondo
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
| | - Jaruwatana Sodai Lotharukpong
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Hajk-Georg Drost
- Computational Biology Group, Department of Molecular Biology, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
| | - Susana M Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
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Csaba G. Provocation of life functions at a unicellular eukaryote level by extremely low doses of mammalian hormones: Evidences of hormesis. Acta Microbiol Immunol Hung 2019; 67:1-5. [PMID: 31813260 DOI: 10.1556/030.66.2019.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/15/2019] [Indexed: 11/19/2022]
Abstract
Hormones, characteristic to higher ranked animals, are synthesized, stored, and secreted by unicellular eukaryote animals. The unicells also have receptors for recognizing these materials and transmit the message into the cells for provoking response. The hormones are effective in very low concentrations (down to 10-21 M) and opposite effects of lower and higher concentrations can be observed. However, sometimes linear concentration effects can be found, which means that hormesis exists, nevertheless uncertain, as it is in the phase of formation (evolutionary experimentation). Hormesis, by transformation (fixation) of cytoplasmic receptor-like membrane components to receptors in the presence of the given hormone, likely helps the development of unicellular endocrine character and by this the evolution of endocrine system. The effect by extremely low concentrations of hormones had been forced by the watery way of unicellular life, which could establish the physiological concentrations of hormones in the blood of higher ranked animals. This means that hormetic low doses are the normal, effective concentrations and the high concentrations are artificial, consequently could be dangerous.
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Affiliation(s)
- György Csaba
- 1 Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
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Csaba G. Insulin at a unicellular eukaryote level. Cell Biol Int 2013; 37:267-75. [DOI: 10.1002/cbin.10054] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 01/11/2013] [Indexed: 11/09/2022]
Affiliation(s)
- György Csaba
- Department of Genetics, Cell and Immunobiology; Semmelweis University; Budapest; Hungary
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Oertel BG, Vermehren J, Zimmermann M, Huynh TT, Doehring A, Ferreiros N, Senzel S, Schmitz-Rixen T, Erbe M, Geisslinger G, Harder S, Angst MS, Lötsch J. Necessity and Risks of Arterial Blood Sampling in Healthy Volunteer Studies. Clin Pharmacokinet 2012; 51:629-38. [DOI: 10.1007/s40262-012-0001-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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The Prokaryotic Origin and Evolution of Eukaryotic Chemosignaling Systems. ACTA ACUST UNITED AC 2009; 39:793-804. [DOI: 10.1007/s11055-009-9190-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Indexed: 10/20/2022]
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Shpakov AO, Pertseva MN. Chapter 4 Signaling Systems of Lower Eukaryotes and Their Evolution. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2008; 269:151-282. [DOI: 10.1016/s1937-6448(08)01004-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Martynova MG. Proliferation and Differentiation Processes in the Heart Muscle Elements in Different Phylogenetic Groups. ACTA ACUST UNITED AC 2004; 235:215-50. [PMID: 15219784 DOI: 10.1016/s0074-7696(04)35005-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
This article reviews, discusses, and summarizes data about the generative behavior of muscle tissue cells, the mechanisms of its regulation, and the organization of the endocrine function of the heart in the main phylogenetic groups. With respect to the ratio of processes of proliferation and differentiation, cell organization, and growth mechanism, muscle tissues of propulsive organs can be divided into three types, each revealed in one of three main groups of animals, lophotrochozoans, ecdysozoans, and chordates. Ecdysterone is likely to play the key role in the regulation of proliferation and differentiation processes in the heart muscle of crustaceans, and, most probably, also of molluscs. In each of the three main phylogenetic groups the endocrine function of the heart consisting of secretion of natriuretic peptides has a peculiar organization. Vertebrate cardiomyocytes are known to combine contractile and endocrine differentiation. Such functional dualism is absent in heart muscle elements of Lophotrochozoa and Ecdysozoa; in the heart of lopfotrochozoans, secretion of natriuretic peptides is performed by endothelial cells and their derivatives. Homology of the heart muscle in the animal kingdom as well as possible mechanisms of genomic and epigenomic regulation of different types of cardiomyogenesis are discussed.
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Affiliation(s)
- Marina G Martynova
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
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Plesneva SA, Shpakov AO, Kuznetsova LA, Pertseva MN. A dual role of protein kinase C in insulin signal transduction via adenylyl cyclase signaling system in muscle tissues of vertebrates and invertebrates. Biochem Pharmacol 2001; 61:1277-91. [PMID: 11322932 DOI: 10.1016/s0006-2952(01)00592-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Further decoding of a novel adenylyl cyclase signaling mechanism (ACSM) of the action of insulin and related peptides detected earlier (Pertseva et al. Comp Biochem Physiol B Biochem Mol Biol 1995;112:689-95 and Pertseva et al. Biochem Pharmacol 1996;52:1867-74) was carried out with special attention given to the role of protein kinase C (PKC) in the ACSM. It was shown for the first time that transduction of the insulin signal via the ACSM followed by adenylyl cyclase (AC, EC 4.6.1.1) activation was blocked in the muscle tissues of rat and mollusc Anodonta cygnea in the presence of pertussis toxin, inducing the impairment of G(i)-protein function, wortmannin, an inhibitor of phosphatidylinositol 3-kinase (PI3-K), and calphostin C, a blocker of PKC. The cholera toxin treatment of muscle membranes led to an increase in basal AC activity and a decrease in enzyme insulin reactivity. Phorbol ester and diacylglycerol activation of PKC (acute treatment) induced the inhibition of the insulin AC activating effect. This negative influence was also observed in the case of the AC system activated by biogenic amines. It was first concluded that the ACSM of insulin action involves the following signaling chain: receptor tyrosine kinase => G(i) (betagamma) => PI3-K => PKCzeta (?) => G(s) => AC => adenosine 3',5'-cyclic monophosphate. It was also concluded that the PKC system has a dual role in the ACSM: (1) a regulatory role (PKC sensitive to phorbol esters) that is manifested as a negative feedback modulation of insulin signal transduction via the ACSM; (2) a transductory role, which consists in direct participation of atypical PKC (PKCzeta) in the process of insulin signal transduction via the ACSM.
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Affiliation(s)
- S A Plesneva
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez au. 44, 194223, St. Petersburg, Russia
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Christensen ST, Leick V, Rasmussen L, Wheatley DN. Signaling in unicellular eukaryotes. INTERNATIONAL REVIEW OF CYTOLOGY 1997; 177:181-253. [PMID: 9378617 DOI: 10.1016/s0074-7696(08)62233-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Aspects of intercellular and intracellular signaling systems in cell survival, proliferation, differentiation, chemosensory behavior, and programmed cell death in free-living unicellular eukaryotes have been reviewed. Comparisons have been made with both bacteria and metazoa. The central organisms were flagellates (Trypanosoma, Leishmania, and Crithidia), slime molds (Dictyostelium), yeast cells (Saccharomyces cerevisiae), and ciliates (Paramecium, Euplotes, and Tetrahymena). There are two novel aspects in this review. First, cellular responses are viewed in an evolutionary perspective, rather than from the more prevailing one, in which the unicellular eukaryotes are seen by the mammalian organisms. Second, results obtained with cell cultures in minimal, chemically defined nutrient media at low cell densities where intercellular signaling is strongly reduced are discussed. These results shed light on control mechanisms and their cooperation inside the living cell. Intracellular systems have many common features in unicellular and multicellular organisms.
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Affiliation(s)
- S T Christensen
- Department of Medical Biochemistry and Genetics, Panum Institute, University of Copenhagen, Denmark
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Zakelj-Mavric M, Kastelic-Suhadolc T, Plemenitas A, Rizner TL, Belic I. Steroid hormone signalling system and fungi. Comp Biochem Physiol B Biochem Mol Biol 1995; 112:637-42. [PMID: 8590379 DOI: 10.1016/0305-0491(95)00113-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Three components of the steroid hormone signalling system, 17 beta-hydroxysteroid dehydrogenase, androgen binding proteins and steroid hormone signalling molecule testosterone were determined in the filamentous fungus Cochliobolus lunatus for the first time in a fungus. Their possible role in C. lunatus is discussed in comparison with their role in mammalian steroid hormone signalling system. The results are in accordance with the hypothesis, that the elements of primordial signal transduction system should exist in present day eukaryotic microorganisms.
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Affiliation(s)
- M Zakelj-Mavric
- Institute of Biochemistry, Medical Faculty, Ljubljana, Slovenia
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Pheromones, social behaviour and the functions of secondary metabolism in bacteria. Trends Ecol Evol 1995; 10:126-9. [DOI: 10.1016/s0169-5347(00)89013-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Phylogeny and Ontogeny of Chemical Signaling: Origin and Development of Hormone Receptors. INTERNATIONAL REVIEW OF CYTOLOGY 1994. [DOI: 10.1016/s0074-7696(08)62095-1] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Bolander FF. Molecular Evolution of the Endocrine System. Mol Endocrinol 1994. [DOI: 10.1016/b978-0-12-111231-8.50020-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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