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Article: Excessive G-U transversions in novel allele variants in SARS-CoV-2 genomes.

Panchin, Alexander Y / Panchin, Yuri V

2020 Volume 8, Page(s) e9648

Abstract: Background: SARS-CoV-2 is a novel coronavirus that causes COVID-19 infection, with a closest known relative found in bats. For this virus, hundreds of genomes have been sequenced. This data provides insights into SARS-CoV-2 adaptations, determinants of ... ...

Abstract	Background: SARS-CoV-2 is a novel coronavirus that causes COVID-19 infection, with a closest known relative found in bats. For this virus, hundreds of genomes have been sequenced. This data provides insights into SARS-CoV-2 adaptations, determinants of pathogenicity and mutation patterns. A comparison between patterns of mutations that occurred before and after SARS-CoV-2 jumped to human hosts may reveal important evolutionary consequences of zoonotic transmission. Methods: We used publically available complete genomes of SARS-CoV-2 to calculate relative frequencies of single nucleotide variations. These frequencies were compared with relative substitutions frequencies between SARS-CoV-2 and related animal coronaviruses. A similar analysis was performed for human coronaviruses SARS-CoV and HKU1. Results: We found a 9-fold excess of G-U transversions among SARS-CoV-2 mutations over relative substitution frequencies between SARS-CoV-2 and a close relative coronavirus from bats (RaTG13). This suggests that mutation patterns of SARS-CoV-2 have changed after transmission to humans. The excess of G-U transversions was much smaller in a similar analysis for SARS-CoV and non-existent for HKU1. Remarkably, we did not find a similar excess of complementary C-A mutations in SARS-CoV-2. We discuss possible explanations for these observations.
Keywords	covid19
Language	English
Publishing date	2020-07-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.9648
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Article ; Online: Apoptotic gene loss in Cnidaria is associated with transition to parasitism.

Neverov, Alexander M / Panchin, Alexander Y / Mikhailov, Kirill V / Batueva, Marina D / Aleoshin, Vladimir V / Panchin, Yuri V

Scientific reports

2023 Volume 13, Issue 1, Page(s) 8015

Abstract: The phylum Cnidaria consists of several morphologically diverse classes including Anthozoa, Cubozoa, Hydrozoa, Polypodiozoa, Scyphozoa, Staurozoa, and Myxozoa. Myxozoa comprises two subclasses of obligate parasites-Myxosporea and Malacosporea, which ... ...

Abstract	The phylum Cnidaria consists of several morphologically diverse classes including Anthozoa, Cubozoa, Hydrozoa, Polypodiozoa, Scyphozoa, Staurozoa, and Myxozoa. Myxozoa comprises two subclasses of obligate parasites-Myxosporea and Malacosporea, which demonstrate various degrees of simplification. Myxosporea were previously reported to lack the majority of core protein domains of apoptotic proteins including caspases, Bcl-2, and APAF-1 homologs. Other sequenced Cnidaria, including the parasite Polypodium hydriforme from Polypodiozoa do not share this genetic feature. Whether this loss of core apoptotic proteins is unique to Myxosporea or also present in its sister subclass Malacosporea was not previously investigated. We show that the presence of core apoptotic proteins gradually diminishes from free-living Cnidaria to Polypodium to Malacosporea to Myxosporea. This observation does not favor the hypothesis of catastrophic simplification of Myxosporea at the genetic level, but rather supports a stepwise adaptation to parasitism that likely started from early parasitic ancestors that gave rise to Myxozoa.
MeSH term(s)	Animals ; Cnidaria/genetics ; Phylogeny ; Hydrozoa/genetics ; Myxozoa ; Anthozoa ; Cubozoa
Language	English
Publishing date	2023-05-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-34248-y
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Article ; Online: Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes

Panchin, Alexander Y. / Panchin, Yuri V.

PeerJ

2020 Volume 8, Page(s) e9648

Abstract: Background SARS-CoV-2 is a novel coronavirus that causes COVID-19 infection, with a closest known relative found in bats. For this virus, hundreds of genomes have been sequenced. This data provides insights into SARS-CoV-2 adaptations, determinants of ... ...

Abstract	Background SARS-CoV-2 is a novel coronavirus that causes COVID-19 infection, with a closest known relative found in bats. For this virus, hundreds of genomes have been sequenced. This data provides insights into SARS-CoV-2 adaptations, determinants of pathogenicity and mutation patterns. A comparison between patterns of mutations that occurred before and after SARS-CoV-2 jumped to human hosts may reveal important evolutionary consequences of zoonotic transmission. Methods We used publically available complete genomes of SARS-CoV-2 to calculate relative frequencies of single nucleotide variations. These frequencies were compared with relative substitutions frequencies between SARS-CoV-2 and related animal coronaviruses. A similar analysis was performed for human coronaviruses SARS-CoV and HKU1. Results We found a 9-fold excess of G–U transversions among SARS-CoV-2 mutations over relative substitution frequencies between SARS-CoV-2 and a close relative coronavirus from bats (RaTG13). This suggests that mutation patterns of SARS-CoV-2 have changed after transmission to humans. The excess of G–U transversions was much smaller in a similar analysis for SARS-CoV and non-existent for HKU1. Remarkably, we did not find a similar excess of complementary C–A mutations in SARS-CoV-2. We discuss possible explanations for these observations.
Keywords	General Biochemistry, Genetics and Molecular Biology ; General Neuroscience ; General Agricultural and Biological Sciences ; General Medicine ; covid19
Language	English
Publisher	PeerJ
Publishing country	us
Document type	Article ; Online
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.9648
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Article ; Online: Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes

Alexander Y. Panchin / Yuri V. Panchin

PeerJ, Vol 8, p e

2020 Volume 9648

Abstract	Background SARS-CoV-2 is a novel coronavirus that causes COVID-19 infection, with a closest known relative found in bats. For this virus, hundreds of genomes have been sequenced. This data provides insights into SARS-CoV-2 adaptations, determinants of pathogenicity and mutation patterns. A comparison between patterns of mutations that occurred before and after SARS-CoV-2 jumped to human hosts may reveal important evolutionary consequences of zoonotic transmission. Methods We used publically available complete genomes of SARS-CoV-2 to calculate relative frequencies of single nucleotide variations. These frequencies were compared with relative substitutions frequencies between SARS-CoV-2 and related animal coronaviruses. A similar analysis was performed for human coronaviruses SARS-CoV and HKU1. Results We found a 9-fold excess of G–U transversions among SARS-CoV-2 mutations over relative substitution frequencies between SARS-CoV-2 and a close relative coronavirus from bats (RaTG13). This suggests that mutation patterns of SARS-CoV-2 have changed after transmission to humans. The excess of G–U transversions was much smaller in a similar analysis for SARS-CoV and non-existent for HKU1. Remarkably, we did not find a similar excess of complementary C–A mutations in SARS-CoV-2. We discuss possible explanations for these observations.
Keywords	SARS-CoV-2 ; COVID-19 ; Mutations ; Transversions ; Evolution ; Mutagenesis ; Medicine ; R ; Biology (General) ; QH301-705.5 ; covid19
Subject code	572
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Corrigendum to "Comparative Analysis of Context-Dependent Mutagenesis Using Human and Mouse Models".

Medvedeva, Sofya A / Panchin, Alexander Y / Alexeevski, Andrei V / Spirin, Sergey A / Panchin, Yuri V

BioMed research international

2020 Volume 2020, Page(s) 4657615

Abstract: This corrects the article DOI: 10.1155/2013/989410.]. ...

Abstract	[This corrects the article DOI: 10.1155/2013/989410.].
Language	English
Publishing date	2020-07-20
Publishing country	United States
Document type	Journal Article ; Published Erratum
ZDB-ID	2698540-8
ISSN	2314-6141 ; 2314-6133
ISSN (online)	2314-6141
ISSN	2314-6133
DOI	10.1155/2020/4657615
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Article ; Online: Corrigendum to “Comparative Analysis of Context-Dependent Mutagenesis Using Human and Mouse Models”

Sofya A. Medvedeva / Alexander Y. Panchin / Andrei V. Alexeevski / Sergey A. Spirin / Yuri V. Panchin

BioMed Research International, Vol

2020 Volume 2020

Keywords	Medicine ; R
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Are there gap junctions without connexins or pannexins?

Slivko-Koltchik, Georgy A / Kuznetsov, Victor P / Panchin, Yuri V

BMC evolutionary biology

2019 Volume 19, Issue Suppl 1, Page(s) 46

Abstract: Background: Gap junctions (GJ) are one of the most common forms of intercellular communication. GJs are assembled from proteins that form channels connecting the cytoplasm of adjacent cells. They are considered to be the main or the only type of ... ...

Abstract	Background: Gap junctions (GJ) are one of the most common forms of intercellular communication. GJs are assembled from proteins that form channels connecting the cytoplasm of adjacent cells. They are considered to be the main or the only type of intercellular channels and the universal feature of all multicellular animals. Two unrelated protein families are currently considered to be involved in this function, namely, connexins and pannexins (pannexins/innexins). Pannexins were hypothesized to be the universal GJ proteins of multicellular animals, distinct from connexins that are characteristic of chordates only. Here we have revised this supposition by applying growing high throughput sequencing data from diverse metazoan species. Results: Pannexins were found in Chordates, Ctenophores, Cnidarians, and in the most major groups of bilateral protostomes. Yet some metazoans appear to have neither connexins nor pannexins in their genomes. We detected no connexins or pannexins/innexins homologues in representatives of all five classes of echinoderms and their closest relatives hemichordates with available genomic sequences. Despite this, our intracellular recordings demonstrate direct electrical coupling between blastomeres at the 2-cell embryo of the echinoderm (starfish Asterias rubens). In these experiments, carboxyfluorescein fluorescent dye did not diffuse between electrically coupled cells. This excludes the possibility that the observed electrical coupling is mediated by incomplete cytoplasm separation during cleavage. Conclusion: Functional GJs are present in representatives of the clade that lack currently recognized GJ protein families. New undiscovered protein families utilized for intercellular channels are predicted. It is possible that the new type(s) of intercellular channels are present in parallel to pannexin and connexin gap junctions in animal groups, other than Echinodermata.
MeSH term(s)	Animals ; Cell Communication ; Connexins/metabolism ; Echinodermata/cytology ; Echinodermata/genetics ; Echinodermata/metabolism ; Gap Junctions/metabolism ; Genome
Chemical Substances	Connexins
Language	English
Publishing date	2019-02-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2041493-6
ISSN	1471-2148 ; 1471-2148
ISSN (online)	1471-2148
ISSN	1471-2148
DOI	10.1186/s12862-019-1369-4
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Article ; Online: Midichlorians--the biomeme hypothesis: is there a microbial component to religious rituals?

Panchin, Alexander Y / Tuzhikov, Alexander I / Panchin, Yuri V

Biology direct

2014 Volume 9, Page(s) 14

Abstract: Background: Cutting edge research of human microbiome diversity has led to the development of the microbiome-gut-brain axis concept, based on the idea that gut microbes may have an impact on the behavior of their human hosts. Many examples of behavior- ... ...

Abstract	Background: Cutting edge research of human microbiome diversity has led to the development of the microbiome-gut-brain axis concept, based on the idea that gut microbes may have an impact on the behavior of their human hosts. Many examples of behavior-altering parasites are known to affect members of the animal kingdom. Some prominent examples include Ophiocordyceps unilateralis (fungi), Toxoplasma gondii (protista), Wolbachia (bacteria), Glyptapanteles sp. (arthropoda), Spinochordodes tellinii (nematomorpha) and Dicrocoelium dendriticum (flat worm). These organisms belong to a very diverse set of taxonomic groups suggesting that the phenomena of parasitic host control might be more common in nature than currently established and possibly overlooked in humans. Presentation of the hypothesis: Some microorganisms would gain an evolutionary advantage by encouraging human hosts to perform certain rituals that favor microbial transmission. We hypothesize that certain aspects of religious behavior observed in the human society could be influenced by microbial host control and that the transmission of some religious rituals could be regarded as the simultaneous transmission of both ideas (memes) and parasitic organisms. Testing the hypothesis: We predict that next-generation microbiome sequencing of samples obtained from gut or brain tissues of control subjects and subjects with a history of voluntary active participation in certain religious rituals that promote microbial transmission will lead to the discovery of microbes, whose presence has a consistent and positive association with religious behavior. Our hypothesis also predicts a decline of participation in religious rituals in societies with improved sanitation. Implications of the hypothesis: If proven true, our hypothesis may provide insights on the origin and pervasiveness of certain religious practices and provide an alternative explanation for recently published positive associations between parasite-stress and religiosity. The discovery of novel microorganisms that affect host behavior may improve our understanding of neurobiology and neurochemistry, while the diversity of such organisms may be of interest to evolutionary biologists and religious scholars. Reviewers: This article was reviewed by Prof. Dan Graur, Dr. Rob Knight and Dr. Eugene Koonin.
MeSH term(s)	Animals ; Bacteria/metabolism ; Ceremonial Behavior ; Humans ; Models, Biological ; Religion
Language	English
Publishing date	2014-07-02
Publishing country	England
Document type	Journal Article
ISSN	1745-6150
ISSN (online)	1745-6150
DOI	10.1186/1745-6150-9-14
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Article ; Online: Genomic analysis reveals cryptic diversity in aphelids and sheds light on the emergence of Fungi.

Mikhailov, Kirill V / Karpov, Sergey A / Letcher, Peter M / Lee, Philip A / Logacheva, Maria D / Penin, Aleksey A / Nesterenko, Maksim A / Pozdnyakov, Igor R / Potapenko, Evgenii V / Sherbakov, Dmitry Y / Panchin, Yuri V / Aleoshin, Vladimir V

Current biology : CB

2022 Volume 32, Issue 21, Page(s) 4607–4619.e7

Abstract: Over the past decade, molecular phylogenetics has reshaped our understanding of the fungal tree of life by unraveling a hitherto elusive diversity of the protistan relatives of Fungi. Aphelida constitutes one of these novel deep branches that precede the ...

Abstract	Over the past decade, molecular phylogenetics has reshaped our understanding of the fungal tree of life by unraveling a hitherto elusive diversity of the protistan relatives of Fungi. Aphelida constitutes one of these novel deep branches that precede the emergence of osmotrophic fungal lifestyle and hold particular significance as the pathogens of algae. Here, we obtain and analyze the genomes of aphelid species Amoeboaphelidium protococcarum and Amoeboaphelidium occidentale. Genomic data unmask the vast divergence between these species, hidden behind their morphological similarity, and reveal hybrid genomes with a complex evolutionary history in two strains of A. protococcarum. We confirm the proposed sister relationship between Aphelida and Fungi using phylogenomic analysis and chart the reduction of characteristic proteins involved in phagocytic activity in the evolution of Holomycota. Annotation of aphelid genomes demonstrates the retention of actin nucleation-promoting complexes associated with phagocytosis and amoeboid motility and also reveals a conspicuous expansion of receptor-like protein kinases, uncharacteristic of fungal lineages. We find that aphelids possess multiple carbohydrate-processing enzymes that are involved in fungal cell wall synthesis but do not display rich complements of algal cell-wall-processing enzymes, suggesting an independent origin of fungal plant-degrading capabilities. Aphelid genomes show that the emergence of Fungi from phagotrophic ancestors relied on a common cell wall synthetic machinery but required a different set of proteins for digestion and interaction with the environment.
MeSH term(s)	Eukaryota/physiology ; Phylogeny ; Genomics ; Plants/genetics ; Fungi/genetics ; Fungi/metabolism ; Genome, Fungal ; Evolution, Molecular
Language	English
Publishing date	2022-09-19
Publishing country	England
Document type	Journal Article
ZDB-ID	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2022.08.071
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Article: Evolution of gap junction proteins--the pannexin alternative.

Panchin, Yuri V

The Journal of experimental biology

2005 Volume 208, Issue Pt 8, Page(s) 1415–1419

Abstract: Gap junctions provide one of the most common forms of intercellular communication. They are composed of membrane proteins that form a channel that is permeable to ions and small molecules, connecting the cytoplasm of adjacent cells. Gap junctions serve ... ...

Abstract	Gap junctions provide one of the most common forms of intercellular communication. They are composed of membrane proteins that form a channel that is permeable to ions and small molecules, connecting the cytoplasm of adjacent cells. Gap junctions serve similar functions in all multicellular animals (Metazoa). Two unrelated protein families are involved in this function; connexins, which are found only in chordates, and pannexins, which are ubiquitous and present in both chordate and invertebrate genomes. The involvement of mammalian pannexins to gap junction formation was recently confirmed. Now it is necessary to consider the role of pannexins as an alternative to connexins in vertebrate intercellular communication.
MeSH term(s)	Amino Acid Sequence ; Animals ; Brain/physiology ; Cell Communication/genetics ; Cell Communication/physiology ; Connexins/genetics ; Connexins/physiology ; Evolution, Molecular ; Molecular Sequence Data ; Multigene Family/genetics ; Multigene Family/physiology ; Nerve Tissue Proteins ; Phylogeny ; Protein Conformation ; Sequence Alignment ; Vertebrates/genetics ; Vertebrates/physiology
Chemical Substances	Connexins ; Nerve Tissue Proteins ; PANX1 protein, human
Language	English
Publishing date	2005-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	218085-6
ISSN	1477-9145 ; 0022-0949
ISSN (online)	1477-9145
ISSN	0022-0949
DOI	10.1242/jeb.01547
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