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Protein-Based Infection, Inheritance, and Memory
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Protein-Based Infection, Inheritance, and Memory

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 16858

Special Issue Editors

Prof. Dr. Yury O. Chernoff

E-Mail Website
Guest Editor
1. School of Biological Sciences, Georgia Institute of Technology, Krone Engineered Biosystems Building, 950 Atlantic Drive, Atlanta, GA 30332-2000, USA
2. Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia
Interests: yeast genetics; protein biosynthesis, misfolding and aggregation; protein quality control; amyloids; prions; chaperones and stress response; protein-based inheritance
Dr. Anton Nizhnikov

E-Mail Website
Guest Editor
Institute of Agricultural Microbiology, Russian Academy of Sciences, and St. Petersburg State University, St. Petersburg, Russia
Interests: prion; amyloid; protein structure; proteomics; yeast; bacteria; protein aggregate; chaperone; protein fibril; amyloidogenic region

Special Issue Information

Dear Colleagues,

Overwhelming evidence, mostly accumulated relatively recently, has demonstrated that the templated proliferation of protein isoforms can result in the reproduction and amplification of information encoded in the protein structure. Therefore, self-perpetuating protein isoforms can become carriers of biological information that are not directly encoded in DNA sequences. Transmissible protein isoforms (prions) manifest themselves as infectious agents causing diseases, including some devastating diseases in humans and other mammals. In yeast and other fungi, prions manifest themselves as heritable elements, transmitted via cytoplasm. At the molecular level, many prions are based on fibrous cross-β aggregates (amyloids), although other molecular mechanisms for the transmission of protein-based information are also being uncovered. Self-perpetuating protein isoforms have also been implicated in cellular memory. Such non-heritable molecular memory devices found in yeast have been termed mnemons. The ability of proteins to serve as information templates challenges existing biological paradigms and opens additional pathways for information transfer in biological systems, potentially playing a role in adaptation and evolution. The current issue will cover molecular mechanisms controlling the ability of proteins to serve as information carriers in infection, inheritance, and memory.

Prof. Dr. Yury O. Chernoff
Dr. Anton Nizhnikov
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Aggregation
  • amyloid
  • epigenetics
  • mnemon
  • non-Mendelian inheritance
  • prion
  • protein conformation

Published Papers (6 papers)

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Editorial

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4 pages, 192 KiB  
Editorial
Overview of the Special Issue “Protein-Based Infection, Inheritance, and Memory”
by Yury O. Chernoff and Anton A. Nizhnikov
Int. J. Mol. Sci. 2023, 24(14), 11280; https://doi.org/10.3390/ijms241411280 - 10 Jul 2023
Viewed by 656
Abstract
The Special Issue “Protein-Based Infection, Inheritance, and Memory” includes a set of experimental and review papers covering different aspects of protein memory, infection, and inheritance [...] Full article
(This article belongs to the Special Issue Protein-Based Infection, Inheritance, and Memory)

Research

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11 pages, 2720 KiB  
Article
Septin Defects Favour Symmetric Inheritance of the Budding Yeast Deceptive Courtship Memory
by Fozia Akhtar, Bastien Brignola and Fabrice Caudron
Int. J. Mol. Sci. 2023, 24(3), 3003; https://doi.org/10.3390/ijms24033003 - 03 Feb 2023
Cited by 1 | Viewed by 1186
Abstract
Mnemons are prion-like elements that encode cellular memories of past cellular adaptations and do not spread to progenies during cell divisions. During the deceptive courtship in budding yeast, the Whi3 mnemon (Whi3mnem) condenses into a super-assembly to encode a mating pheromone [...] Read more.
Mnemons are prion-like elements that encode cellular memories of past cellular adaptations and do not spread to progenies during cell divisions. During the deceptive courtship in budding yeast, the Whi3 mnemon (Whi3mnem) condenses into a super-assembly to encode a mating pheromone refractory state established in the mother cell. Whi3mnem is confined to the mother cell such that their daughter cells have the ability to respond to the mating pheromone. Confinement of Whi3mnem involves its association with the endoplasmic reticulum membranes and the compartmentalization of these membranes by the lateral membrane diffusion barrier at the bud neck, the limit between the mother cell and the bud. However, during the first cell division after the establishment of the pheromone refractory state, this adaptation is more likely to be inherited by the daughter cell than in subsequent cell divisions. Here, we show that the first cell division is associated with larger daughter cells and cytokinesis defects, traits that are not observed in subsequent cell divisions. The cytoskeletal septin protein shows aberrant localisation in these divisions and the septin-dependent endoplasmic reticulum membrane diffusion barrier is weakened. Overall, these data suggest that cytokinesis defects associated with prolonged cell division can alter the confinement and inheritance pattern of a cellular memory. Full article
(This article belongs to the Special Issue Protein-Based Infection, Inheritance, and Memory)
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15 pages, 1444 KiB  
Article
Human RAD51 Protein Forms Amyloid-like Aggregates In Vitro
by Daniel V. Kachkin, Kirill V. Volkov, Julia V. Sopova, Alexander G. Bobylev, Sergei A. Fedotov, Sergei G. Inge-Vechtomov, Oxana V. Galzitskaya, Yury O. Chernoff, Aleksandr A. Rubel and Anna Y. Aksenova
Int. J. Mol. Sci. 2022, 23(19), 11657; https://doi.org/10.3390/ijms231911657 - 01 Oct 2022
Cited by 2 | Viewed by 2039
Abstract
RAD51 is a central protein of homologous recombination and DNA repair processes that maintains genome stability and ensures the accurate repair of double-stranded breaks (DSBs). In this work, we assessed amyloid properties of RAD51 in vitro and in the bacterial curli-dependent amyloid generator [...] Read more.
RAD51 is a central protein of homologous recombination and DNA repair processes that maintains genome stability and ensures the accurate repair of double-stranded breaks (DSBs). In this work, we assessed amyloid properties of RAD51 in vitro and in the bacterial curli-dependent amyloid generator (C-DAG) system. Resistance to ionic detergents, staining with amyloid-specific dyes, polarized microscopy, transmission electron microscopy (TEM), X-ray diffraction and other methods were used to evaluate the properties and structure of RAD51 aggregates. The purified human RAD51 protein formed detergent-resistant aggregates in vitro that had an unbranched cross-β fibrillar structure, which is typical for amyloids, and were stained with amyloid-specific dyes. Congo-red-stained RAD51 aggregates demonstrated birefringence under polarized light. RAD51 fibrils produced sharp circular X-ray reflections at 4.7 Å and 10 Å, demonstrating that they had a cross-β structure. Cytoplasmic aggregates of RAD51 were observed in cell cultures overexpressing RAD51. We demonstrated that a key protein that maintains genome stability, RAD51, has amyloid properties in vitro and in the C-DAG system and discussed the possible biological relevance of this observation. Full article
(This article belongs to the Special Issue Protein-Based Infection, Inheritance, and Memory)
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Review

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21 pages, 3034 KiB  
Review
Noninvasive Diagnostics of Renal Amyloidosis: Current State and Perspectives
by Sergei A. Fedotov, Maria S. Khrabrova, Anastasia O. Anpilova, Vladimir A. Dobronravov and Aleksandr A. Rubel
Int. J. Mol. Sci. 2022, 23(20), 12662; https://doi.org/10.3390/ijms232012662 - 21 Oct 2022
Cited by 4 | Viewed by 4452
Abstract
Amyloidoses is a group of diseases characterized by the accumulation of abnormal proteins (called amyloids) in different organs and tissues. For systemic amyloidoses, the disease is related to increased levels and/or abnormal synthesis of certain proteins in the organism due to pathological processes, [...] Read more.
Amyloidoses is a group of diseases characterized by the accumulation of abnormal proteins (called amyloids) in different organs and tissues. For systemic amyloidoses, the disease is related to increased levels and/or abnormal synthesis of certain proteins in the organism due to pathological processes, e.g., monoclonal gammopathy and chronic inflammation in rheumatic arthritis. Treatment of amyloidoses is focused on reducing amyloidogenic protein production and inhibition of its aggregation. Therapeutic approaches critically depend on the type of amyloidosis, which underlines the importance of early differential diagnostics. In fact, the most accurate diagnostics of amyloidosis and its type requires analysis of a biopsy specimen from the disease-affected organ. However, absence of specific symptoms of amyloidosis and the invasive nature of biomaterial sampling causes the late diagnostics of these diseases, which leads to a delayed treatment, and significantly reduces its efficacy and patient survival. The establishment of noninvasive diagnostic methods and discovery of specific amyloidosis markers are essential for disease detection and identification of its type at earlier stages, which enables timely and targeted treatment. This review focuses on current approaches to the diagnostics of amyloidoses, primarily with renal involvement, and research perspectives in order to design new specific tests for early diagnosis. Full article
(This article belongs to the Special Issue Protein-Based Infection, Inheritance, and Memory)
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16 pages, 3878 KiB  
Review
Propagation and Dissemination Strategies of Transmissible Spongiform Encephalopathy Agents in Mammalian Cells
by Stefanie-Elisabeth Heumüller, Annika C. Hornberger, Alina S. Hebestreit, André Hossinger and Ina M. Vorberg
Int. J. Mol. Sci. 2022, 23(6), 2909; https://doi.org/10.3390/ijms23062909 - 08 Mar 2022
Cited by 7 | Viewed by 2505
Abstract
Transmissible spongiform encephalopathies or prion disorders are fatal infectious diseases that cause characteristic spongiform degeneration in the central nervous system. The causative agent, the so-called prion, is an unconventional infectious agent that propagates by converting the host-encoded cellular prion protein PrP into ordered [...] Read more.
Transmissible spongiform encephalopathies or prion disorders are fatal infectious diseases that cause characteristic spongiform degeneration in the central nervous system. The causative agent, the so-called prion, is an unconventional infectious agent that propagates by converting the host-encoded cellular prion protein PrP into ordered protein aggregates with infectious properties. Prions are devoid of coding nucleic acid and thus rely on the host cell machinery for propagation. While it is now established that, in addition to PrP, other cellular factors or processes determine the susceptibility of cell lines to prion infection, exact factors and cellular processes remain broadly obscure. Still, cellular models have uncovered important aspects of prion propagation and revealed intercellular dissemination strategies shared with other intracellular pathogens. Here, we summarize what we learned about the processes of prion invasion, intracellular replication and subsequent dissemination from ex vivo cell models. Full article
(This article belongs to the Special Issue Protein-Based Infection, Inheritance, and Memory)
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27 pages, 1627 KiB  
Review
β-Barrels and Amyloids: Structural Transitions, Biological Functions, and Pathogenesis
by Anna I. Sulatskaya, Anastasiia O. Kosolapova, Alexander G. Bobylev, Mikhail V. Belousov, Kirill S. Antonets, Maksim I. Sulatsky, Irina M. Kuznetsova, Konstantin K. Turoverov, Olesya V. Stepanenko and Anton A. Nizhnikov
Int. J. Mol. Sci. 2021, 22(21), 11316; https://doi.org/10.3390/ijms222111316 - 20 Oct 2021
Cited by 12 | Viewed by 5060
Abstract
Insoluble protein aggregates with fibrillar morphology called amyloids and β-barrel proteins both share a β-sheet-rich structure. Correctly folded β-barrel proteins can not only function in monomeric (dimeric) form, but also tend to interact with one another—followed, in several cases, by formation of higher [...] Read more.
Insoluble protein aggregates with fibrillar morphology called amyloids and β-barrel proteins both share a β-sheet-rich structure. Correctly folded β-barrel proteins can not only function in monomeric (dimeric) form, but also tend to interact with one another—followed, in several cases, by formation of higher order oligomers or even aggregates. In recent years, findings proving that β-barrel proteins can adopt cross-β amyloid folds have emerged. Different β-barrel proteins were shown to form amyloid fibrils in vitro. The formation of functional amyloids in vivo by β-barrel proteins for which the amyloid state is native was also discovered. In particular, several prokaryotic and eukaryotic proteins with β-barrel domains were demonstrated to form amyloids in vivo, where they participate in interspecies interactions and nutrient storage, respectively. According to recent observations, despite the variety of primary structures of amyloid-forming proteins, most of them can adopt a conformational state with the β-barrel topology. This state can be intermediate on the pathway of fibrillogenesis (“on-pathway state”), or can be formed as a result of an alternative assembly of partially unfolded monomers (“off-pathway state”). The β-barrel oligomers formed by amyloid proteins possess toxicity, and are likely to be involved in the development of amyloidoses, thus representing promising targets for potential therapy of these incurable diseases. Considering rapidly growing discoveries of the amyloid-forming β-barrels, we may suggest that their real number and diversity of functions are significantly higher than identified to date, and represent only “the tip of the iceberg”. Here, we summarize the data on the amyloid-forming β-barrel proteins, their physicochemical properties, and their biological functions, and discuss probable means and consequences of the amyloidogenesis of these proteins, along with structural relationships between these two widespread types of β-folds. Full article
(This article belongs to the Special Issue Protein-Based Infection, Inheritance, and Memory)
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