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Moelling K. Epigenetics and transgenerational inheritance. J Physiol 2024; 602:2537-2545. [PMID: 37772441 DOI: 10.1113/jp284424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/15/2023] [Indexed: 09/30/2023] Open
Abstract
Epigenetic modifications can alter the function of genes. The epigenetics changes are caused by environmental effects, which lead to chemical modifications of the DNA or the chromatin. The mechanisms involve the influence of small interfering siRNAs on gene silencing. Epigenetic changes normally last only during the life-time of an individual and are erased in embryos and eggs for a naive progeny. The genomes are reprogrammed and the chemical modifications removed to restart the next generation. However, there are mechanisms that allow the genome to escape from such a clearing effect so that modifications can be transmitted to one or more subsequent generations. In the germline of animal cells small RNAs, including piRNAs, have evolved which guarantee a higher degree of fidelity for transmission of genetic information, guarding especially against the detrimental effect caused by transposon activity. piRNA is essential for transposon silencing for survival of a species and protection of subsequent generations. Inactivation of piRNA results in abundant transposon activity and sperm infertility. The effect in humans has been described but is less distinct. Some stress-induced epigenetic changes are transitory in mice and can be reversed by a change of environment or lifestyle.
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Affiliation(s)
- Karin Moelling
- Institute Medical Microbiology, University Zürich, Zurich, Switzerland
- Max Planck Institute of Molecular Genetics, Berlin, Germany
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W B Jr M, A S R, P M, F B. Cellular and Natural Viral Engineering in Cognition-Based Evolution. Commun Integr Biol 2023; 16:2196145. [PMID: 37153718 PMCID: PMC10155641 DOI: 10.1080/19420889.2023.2196145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Neo-Darwinism conceptualizes evolution as the continuous succession of predominately random genetic variations disciplined by natural selection. In that frame, the primary interaction between cells and the virome is relegated to host-parasite dynamics governed by selective influences. Cognition-Based Evolution regards biological and evolutionary development as a reciprocating cognition-based informational interactome for the protection of self-referential cells. To sustain cellular homeorhesis, cognitive cells collaborate to assess the validity of ambiguous biological information. That collective interaction involves coordinate measurement, communication, and active deployment of resources as Natural Cellular Engineering. These coordinated activities drive multicellularity, biological development, and evolutionary change. The virome participates as the vital intercessory among the cellular domains to ensure their shared permanent perpetuation. The interactions between the virome and the cellular domains represent active virocellular cross-communications for the continual exchange of resources. Modular genetic transfers between viruses and cells carry bioactive potentials. Those exchanges are deployed as nonrandom flexible tools among the domains in their continuous confrontation with environmental stresses. This alternative framework fundamentally shifts our perspective on viral-cellular interactions, strengthening established principles of viral symbiogenesis. Pathogenesis can now be properly appraised as one expression of a range of outcomes between cells and viruses within a larger conceptual framework of Natural Viral Engineering as a co-engineering participant with cells. It is proposed that Natural Viral Engineering should be viewed as a co-existent facet of Natural Cellular Engineering within Cognition-Based Evolution.
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Affiliation(s)
- Miller W B Jr
- Banner Health Systems - Medicine, Paradise Valley, Arizona, AZ, USA
- CONTACT Miller W B Jr Paradise Valley, Arizona, AZ85253, USA
| | - Reber A S
- Department of Psychology, University of British Columbia, Vancouver, BC, Canada
| | - Marshall P
- Department of Engineering, Evolution 2.0, Oak Park, IL, USA
| | - Baluška F
- Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
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Abstract
α-Amino acids are essential molecular constituents of life, twenty of which are privileged because they are encoded by the ribosomal machinery. The question remains open as to why this number and why this 20 in particular, an almost philosophical question that cannot be conclusively resolved. They are closely related to the evolution of the genetic code and whether nucleic acids, amino acids, and peptides appeared simultaneously and were available under prebiotic conditions when the first self-sufficient complex molecular system emerged on Earth. This report focuses on prebiotic and metabolic aspects of amino acids and proteins starting with meteorites, followed by their formation, including peptides, under plausible prebiotic conditions, and the major biosynthetic pathways in the various kingdoms of life. Coenzymes play a key role in the present analysis in that amino acid metabolism is linked to glycolysis and different variants of the tricarboxylic acid cycle (TCA, rTCA, and the incomplete horseshoe version) as well as the biosynthesis of the most important coenzymes. Thus, the report opens additional perspectives and facets on the molecular evolution of primary metabolism.
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Affiliation(s)
- Andreas Kirschning
- Institute of Organic ChemistryLeibniz University HannoverSchneiderberg 1B30167HannoverGermany
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Abstract
The effect of the on-going COVID-19 pandemic on global healthcare systems has underlined the importance of timely and cost-effective point-of-care diagnosis of viruses. The need for ultrasensitive easy-to-use platforms has culminated in an increased interest for rapid response equipment-free alternatives to conventional diagnostic methods such as polymerase chain reaction, western-blot assay, etc. Furthermore, the poor stability and the bleaching behavior of several contemporary fluorescent reporters is a major obstacle in understanding the mechanism of viral infection thus retarding drug screening and development. Owing to their extraordinary surface-to-volume ratio as well as their quantum confinement and charge transfer properties, nanomaterials are desirable additives to sensing and imaging systems to amplify their signal response as well as temporal resolution. Their large surface area promotes biomolecular integration as well as efficacious signal transduction. Due to their hole mobility, photostability, resistance to photobleaching, and intense brightness, nanomaterials have a considerable edge over organic dyes for single virus tracking. This paper reviews the state-of-the-art of combining carbon-allotrope, inorganic and organic-based nanomaterials with virus sensing and tracking methods, starting with the impact of human pathogenic viruses on the society. We address how different nanomaterials can be used in various virus sensing platforms (e.g. lab-on-a-chip, paper, and smartphone-based point-of-care systems) as well as in virus tracking applications. We discuss the enormous potential for the use of nanomaterials as simple, versatile, and affordable tools for detecting and tracing viruses infectious to humans, animals, plants as well as bacteria. We present latest examples in this direction by emphasizing major advantages and limitations.
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Affiliation(s)
- Muqsit Pirzada
- Technical University of Berlin, Faculty of Natural Sciences and Maths, Straße des 17. Juni 124, Berlin 10623, Germany. .,Institute of Materials Science, Faculty of Engineering, Kiel University, Kaiserstr 2, 24143 Kiel, Germany
| | - Zeynep Altintas
- Technical University of Berlin, Faculty of Natural Sciences and Maths, Straße des 17. Juni 124, Berlin 10623, Germany. .,Institute of Materials Science, Faculty of Engineering, Kiel University, Kaiserstr 2, 24143 Kiel, Germany
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bin Umair M, Akusa FN, Kashif H, Seerat-e-Fatima, Butt F, Azhar M, Munir I, Ahmed M, Khalil W, Sharyar H, Rafique S, Shahid M, Afzal S. Viruses as tools in gene therapy, vaccine development, and cancer treatment. Arch Virol 2022; 167:1387-1404. [PMID: 35462594 PMCID: PMC9035288 DOI: 10.1007/s00705-022-05432-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/28/2022] [Indexed: 12/11/2022]
Abstract
Using viruses to our advantage has been a huge leap for humanity. Their ability to mediate horizontal gene transfer has made them useful tools for gene therapy, vaccine development, and cancer treatment. Adenoviruses, adeno-associated viruses, retroviruses, lentiviruses, alphaviruses, and herpesviruses are a few of the most common candidates for use as therapeutic agents or efficient gene delivery systems. Efforts are being made to improve and perfect viral-vector-based therapies to overcome potential or reported drawbacks. Some preclinical trials of viral vector vaccines have yielded positive results, indicating their potential as prophylactic or therapeutic vaccine candidates. Utilization of the oncolytic activity of viruses is the future of cancer therapy, as patients will then be free from the harmful effects of chemo- or radiotherapy. This review discusses in vitro and in vivo studies showing the brilliant therapeutic potential of viruses.
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Affiliation(s)
- Musab bin Umair
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Fujimura Nao Akusa
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Hadia Kashif
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Seerat-e-Fatima
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Fatima Butt
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Marium Azhar
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Iqra Munir
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Muhammad Ahmed
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Wajeeha Khalil
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Hafiz Sharyar
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Shazia Rafique
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Muhammad Shahid
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Samia Afzal
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
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Chen Q, Zhang X, Shi J, Yan M, Zhou T. Origins and evolving functionalities of tRNA-derived small RNAs. Trends Biochem Sci 2021; 46:790-804. [PMID: 34053843 PMCID: PMC8448906 DOI: 10.1016/j.tibs.2021.05.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/22/2021] [Accepted: 05/03/2021] [Indexed: 12/14/2022]
Abstract
Transfer RNA (tRNA)-derived small RNAs (tsRNAs) are among the most ancient small RNAs in all domains of life and are generated by the cleavage of tRNAs. Emerging studies have begun to reveal the versatile roles of tsRNAs in fundamental biological processes, including gene silencing, ribosome biogenesis, retrotransposition, and epigenetic inheritance, which are rooted in tsRNA sequence conservation, RNA modifications, and protein-binding abilities. We summarize the mechanisms of tsRNA biogenesis and the impact of RNA modifications, and propose how thinking of tsRNA functionality from an evolutionary perspective urges the expansion of tsRNA research into a wider spectrum, including cross-tissue/cross-species regulation and harnessing of the 'tsRNA code' for precision medicine.
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Affiliation(s)
- Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA.
| | - Xudong Zhang
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Junchao Shi
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Menghong Yan
- Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China; Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA.
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Kirschning A. The coenzyme/protein pair and the molecular evolution of life. Nat Prod Rep 2020; 38:993-1010. [PMID: 33206101 DOI: 10.1039/d0np00037j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2020What was first? Coenzymes or proteins? These questions are archetypal examples of causal circularity in living systems. Classically, this "chicken-and-egg" problem was discussed for the macromolecules RNA, DNA and proteins. This report focuses on coenzymes and cofactors and discusses the coenzyme/protein pair as another example of causal circularity in life. Reflections on the origin of life and hypotheses on possible prebiotic worlds led to the current notion that RNA was the first macromolecule, long before functional proteins and hence DNA. So these causal circularities of living systems were solved by a time travel into the past. To tackle the "chicken-and-egg" problem of the protein-coenzyme pair, this report addresses this problem by looking for clues (a) in the first hypothetical biotic life forms such as protoviroids and the last unified common ancestor (LUCA) and (b) in considerations and evidence of the possible prebiotic production of amino acids and coenzymes before life arose. According to these considerations, coenzymes and cofactors can be regarded as very old molecular players in the origin and evolution of life, and at least some of them developed independently of α-amino acids, which here are evolutionarily synonymous with proteins. Discussions on "chicken-and-egg" problems open further doors to the understanding of evolution.
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Affiliation(s)
- Andreas Kirschning
- Institut für Organische Chemie und Zentrum für Biomolekulare Wirkstoffchemie (BMWZ), Leibniz Universität Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
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Affiliation(s)
- Karin Moelling
- Inst for Medical MicrobiologyUniversity Zürich Gloriastr 30 8006 Zürich Switzerland
- Max Planck Institute for Molecular Genetics Ihnestr 73 14195 Berlin Germany
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