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Prion Volume 10, 2016 - Issue 3
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Review

Prions, amyloids, and RNA: Pieces of a puzzle

Anton A. NizhnikovDept. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia;Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg Branch, St. Petersburg, Russia;All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, RussiaCorrespondence[email protected];
,
Kirill S. AntonetsDept. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia;Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg Branch, St. Petersburg, Russia
,
Stanislav A. BondarevDept. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
,
Sergey G. Inge-VechtomovDept. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia;Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg Branch, St. Petersburg, Russia
&
Irina L. DerkatchDepartment of Neuroscience, College of Physicians and Surgeons of Columbia University, Columbia University, New York, NY, USACorrespondence[email protected]
Pages 182-206 | Received 01 Feb 2016, Accepted 17 Apr 2016, Published online: 01 Jun 2016

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Polina B. Drozdova, Yury A. Barbitoff, Mikhail V. Belousov, Rostislav K. Skitchenko, Tatyana M. Rogoza, Jeremy Y. Leclercq, Andrey V. Kajava, Andrew G. Matveenko, Galina A. Zhouravleva & Stanislav A. Bondarev. (2020) Estimation of amyloid aggregate sizes with semi-denaturing detergent agarose gel electrophoresis and its limitations. Prion 14:1, pages 118-128.
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Jay Rasmussen, Mathias Jucker & Lary C. Walker. (2017) Aβ seeds and prions: How close the fit?. Prion 11:4, pages 215-225.
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Tomasz Zajkowski, Michael D. Lee, Siddhant Sharma, Alec Vallota‐Eastman, Mikołaj Kuska, Małgorzata Malczewska & Lynn J. Rothschild. (2023) Conserved functions of prion candidates suggest a primeval role of protein self‐templating. Proteins: Structure, Function, and Bioinformatics 91:9, pages 1298-1315.
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Elmira I. Yakupova, Liya G. Bobyleva, Sergey A. Shumeyko, Ivan M. Vikhlyantsev & Alexander G. Bobylev. (2021) Amyloids: The History of Toxicity and Functionality. Biology 10:5, pages 394.
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Sabine M. Ulamec, David J. Brockwell & Sheena E. Radford. (2020) Looking Beyond the Core: The Role of Flanking Regions in the Aggregation of Amyloidogenic Peptides and Proteins. Frontiers in Neuroscience 14.
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Yu. V. Andreychuk, S. P. Zadorsky, A. S. Zhuk, E. I. Stepchenkova & S. G. Inge-Vechtomov. (2020) Relationship between Type I and Type II Template Processes: Amyloids and Genome Stability. Molecular Biology 54:5, pages 661-683.
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Maria S. Rubel, Sergey A. Fedotov, Anastasia V. Grizel, Julia V. Sopova, Oksana A. Malikova, Yury O. Chernoff & Aleksandr A. Rubel. (2020) Functional Mammalian Amyloids and Amyloid-Like Proteins. Life 10:9, pages 156.
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Sergei Y. Grishin, Evgeniya I. Deryusheva, Andrey V. Machulin, Olga M. Selivanova, Anna V. Glyakina, Elena Y. Gorbunova, Leila G. Mustaeva, Vyacheslav N. Azev, Valentina V. Rekstina, Tatyana S. Kalebina, Alexey K. Surin & Oxana V. Galzitskaya. (2020) Amyloidogenic Propensities of Ribosomal S1 Proteins: Bioinformatics Screening and Experimental Checking. International Journal of Molecular Sciences 21:15, pages 5199.
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Julia V. Sopova, Elena I. Koshel, Tatiana A. Belashova, Sergey P. Zadorsky, Alexandra V. Sergeeva, Vera A. Siniukova, Alexandr A. Shenfeld, Maria E. Velizhanina, Kirill V. Volkov, Anton A. Nizhnikov, Daniel V. Kachkin, Elena R. Gaginskaya & Alexey P. Galkin. (2019) RNA-binding protein FXR1 is presented in rat brain in amyloid form. Scientific Reports 9:1.
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Yury V. Malovichko, Anton A. Nizhnikov & Kirill S. Antonets. (2019) Repertoire of the Bacillus thuringiensis Virulence Factors Unrelated to Major Classes of Protein Toxins and Its Role in Specificity of Host-Pathogen Interactions. Toxins 11:6, pages 347.
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K. S. Antonets, M. V. Belousov, M. E. Belousova & A. A. Nizhnikov. (2019) The Gln3 Transcriptional Regulator of Saccharomyces cerevisiae Manifests Prion-Like Properties upon Overproduction. Biochemistry (Moscow) 84:4, pages 441-451.
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Yury V. Malovichko, Kirill S. Antonets, Anna R. Maslova, Elena A. Andreeva, Sergey G. Inge-Vechtomov & Anton A. Nizhnikov. (2019) RNA Sequencing Reveals Specific Transcriptomic Signatures Distinguishing Effects of the [SWI+] Prion and SWI1 Deletion in Yeast Saccharomyces cerevisiae. Genes 10:3, pages 212.
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Corey J. Wilson, Andreas S. Bommarius, Julie A. Champion, Yury O. Chernoff, David G. Lynn, Anant K. Paravastu, Chen Liang, Ming-Chien Hsieh & Jennifer M. Heemstra. (2018) Biomolecular Assemblies: Moving from Observation to Predictive Design. Chemical Reviews 118:24, pages 11519-11574.
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Bandana Kumari, Ravindra Kumar, Vipin Chauhan & Manish Kumar. (2018) Comparative functional analysis of proteins containing low-complexity predicted amyloid regions. PeerJ 6, pages e5823.
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Carl Peter J. Maury. (2018) Amyloid and the origin of life: self-replicating catalytic amyloids as prebiotic informational and protometabolic entities. Cellular and Molecular Life Sciences 75:9, pages 1499-1507.
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Pavithra Chandramowlishwaran, Meng Sun, Kristin L. Casey, Andrey V. Romanyuk, Anastasiya V. Grizel, Julia V. Sopova, Aleksandr A. Rubel, Carmen Nussbaum-Krammer, Ina M. Vorberg & Yury O. Chernoff. (2018) Mammalian amyloidogenic proteins promote prion nucleation in yeast. Journal of Biological Chemistry 293:9, pages 3436-3450.
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Stanislav A Bondarev, Olga V Bondareva, Galina A Zhouravleva & Andrey V Kajava. (2018) BetaSerpentine: a bioinformatics tool for reconstruction of amyloid structures. Bioinformatics 34:4, pages 599-608.
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Mikhail V. Belousov, Stanislav A. Bondarev, Anastasiia O. Kosolapova, Kirill S. Antonets, Anna I. Sulatskaya, Maksim I. Sulatsky, Galina A. Zhouravleva, Irina M. Kuznetsova, Konstantin K. Turoverov & Anton A. Nizhnikov. (2018) M60-like metalloprotease domain of the Escherichia coli YghJ protein forms amyloid fibrils. PLOS ONE 13:1, pages e0191317.
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Kirill Antonets & Anton Nizhnikov. (2017) Predicting Amyloidogenic Proteins in the Proteomes of Plants. International Journal of Molecular Sciences 18:10, pages 2155.
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K. S. Antonets, S. F. Kliver, D. E. Polev, A. R. Shuvalova, E. A. Andreeva, S. G. Inge-Vechtomov & A. A. Nizhnikov. (2017) Distinct mechanisms of phenotypic effects of inactivation and prionization of Swi1 protein in Saccharomyces cerevisiae. Biochemistry (Moscow) 82:10, pages 1147-1157.
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Jeremy D. Baker, Lindsey B. Shelton, Dali Zheng, Filippo Favretto, Bryce A. Nordhues, April Darling, Leia E. Sullivan, Zheying Sun, Parth K. Solanki, Mackenzie D. Martin, Amirthaa Suntharalingam, Jonathan J. Sabbagh, Stefan Becker, Eckhard Mandelkow, Vladimir N. Uversky, Markus Zweckstetter, Chad A. Dickey, John Koren & Laura J. Blair. (2017) Human cyclophilin 40 unravels neurotoxic amyloids. PLOS Biology 15:6, pages e2001336.
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