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Approaches for the Reconstruction of Protein Families’ and Superfamilies’ Evolution...
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Approaches for the Reconstruction of Protein Families’ and Superfamilies’ Evolution with Consequences for De Novo Protein Design

A special issue of Biology (ISSN 2079-7737).

Deadline for manuscript submissions: closed (28 February 2022) | Viewed by 16694

Special Issue Editor

Dr. Marcel Zamocky

E-Mail Website
Guest Editor
Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
Interests: molecular phylogeny analysis; heterologous protein expression; peroxidases; catalase; phylogenetic analysis; reactive oxygen species; oxidative stress
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

I invite you to submit your original work and reviews for the new issue of Biology (MDPI) with the title “Approaches for the Reconstruction of Protein Families’ and Superfamilies’ Evolution with Consequences for de Novo Protein Design.” The focus of this broadly formulated issue topic is to get an up-to-date overview of various important achievements in the analysis of molecular evolution and structure–function relationships in diverse protein families and superfamilies originating from various organisms (both prokaryotic and/or eukaryotic). It will surely be interesting to compare convergent and divergent pathways of molecular evolution for distinct proteins based on experimental data and resolved structures and to find out possible unifying rules. Additionally, the search for archetypal subfamilies and the sequences and structures of reconstructed ancestors is of essential importance. This topic has already frequently been present in the literature of the last two decades, but the purpose of this Special Issue is to bring together current research outcomes from various experts and teams in one place to get a rather comprehensive overview of the capacity and possibilities of convergent and divergent modes of evolution within protein folds for future perspectives of specific approach for de novo protein design.

Dr. Marcel Zamocky
Guest Editor

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. Biology is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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

  • protein family evolution 
  • protein superfamily 
  • convergent evolution 
  • divergent evolution 
  • molecular phylogeny 
  • horizontal gene transfer 
  • structure–function relationship 
  • de novo protein design

Related Special Issue

Published Papers (3 papers)

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Research

Jump to: Review

18 pages, 3442 KiB  
Article
Deep Insights into the Specific Evolution of Fungal Hybrid B Heme Peroxidases
by Marcel Zámocký, Miloš Musil, Maksym Danchenko, Peter Ferianc, Katarína Chovanová, Peter Baráth, Andrej Poljovka and David Bednář
Biology 2022, 11(3), 459; https://0-doi-org.brum.beds.ac.uk/10.3390/biology11030459 - 17 Mar 2022
Cited by 4 | Viewed by 5089
Abstract
In this study, we focus on a detailed bioinformatics analysis of hyBpox genes, mainly within the genomes of Sclerotiniaceae (Ascomycota, Leotiomycetes), which is a specifically evolved fungal family of necrotrophic host generalists and saprophytic or biotrophic host specialists. Members of the genus Sclerotium [...] Read more.
In this study, we focus on a detailed bioinformatics analysis of hyBpox genes, mainly within the genomes of Sclerotiniaceae (Ascomycota, Leotiomycetes), which is a specifically evolved fungal family of necrotrophic host generalists and saprophytic or biotrophic host specialists. Members of the genus Sclerotium produce only sclerotia and no fruiting bodies or spores. Thus, their physiological role for peroxidases remains open. A representative species, S. cepivorum, is a dangerous plant pathogen causing white rot in Allium species, particularly in onions, leeks, and garlic. On a worldwide basis, the white rot caused by this soil-borne fungus is apparently the most serious threat to Allium-crop production. We have also found very similar peroxidase sequences in the related fungus S. sclerotiorum, although with minor yet important modifications in the architecture of its active centre. The presence of ScephyBpox1-specific mRNA was confirmed by transcriptomic analysis. The presence of Hybrid B peroxidase at the protein level as the sole extracellular peroxidase of this fungus was confirmed in the secretome of S. cepivorum through detailed proteomic analyses. This prompted us to systematically search for all available genes coding for Hybrid B heme peroxidases in the whole fungal family of Sclerotiniaceae. We present here a reconstruction of their molecular phylogeny and analyse the unique aspects of their conserved-sequence features and structural folds in corresponding ancestral sequences. Full article
(This article belongs to the Special Issue Approaches for the Reconstruction of Protein Families’ and Superfamilies’ Evolution with Consequences for De Novo Protein Design)
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12 pages, 2670 KiB  
Article
Going Forward and Back: The Complex Evolutionary History of the GPx
by Thomaz Stumpf Trenz, Camila Luiza Delaix, Andreia Carina Turchetto-Zolet, Marcel Zamocky, Fernanda Lazzarotto and Márcia Margis-Pinheiro
Biology 2021, 10(11), 1165; https://0-doi-org.brum.beds.ac.uk/10.3390/biology10111165 - 12 Nov 2021
Cited by 14 | Viewed by 3789
Abstract
There is large diversity among glutathione peroxidase (GPx) enzymes regarding their function, structure, presence of the highly reactive selenocysteine (SeCys) residue, substrate usage, and reducing agent preference. Moreover, most vertebrate GPxs are very distinct from non-animal GPxs, and it is still unclear if [...] Read more.
There is large diversity among glutathione peroxidase (GPx) enzymes regarding their function, structure, presence of the highly reactive selenocysteine (SeCys) residue, substrate usage, and reducing agent preference. Moreover, most vertebrate GPxs are very distinct from non-animal GPxs, and it is still unclear if they came from a common GPx ancestor. In this study, we aimed to unveil how GPx evolved throughout different phyla. Based on our phylogenetic trees and sequence analyses, we propose that all GPx encoding genes share a monomeric common ancestor and that the SeCys amino acid was incorporated early in the evolution of the metazoan kingdom. In addition, classical GPx and the cysteine-exclusive GPx07 have been present since non-bilaterian animals, but they seem to have been lost throughout evolution in different phyla. Therefore, the birth-and-death of GPx family members (like in other oxidoreductase families) seems to be an ongoing process, occurring independently across different kingdoms and phyla. Full article
(This article belongs to the Special Issue Approaches for the Reconstruction of Protein Families’ and Superfamilies’ Evolution with Consequences for De Novo Protein Design)
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Review

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28 pages, 26629 KiB  
Review
Siglecs as Therapeutic Targets in Cancer
by Jackwee Lim, Duygu Sari-Ak and Tanaya Bagga
Biology 2021, 10(11), 1178; https://0-doi-org.brum.beds.ac.uk/10.3390/biology10111178 - 13 Nov 2021
Cited by 27 | Viewed by 6548
Abstract
Hypersialylation is a common post-translational modification of protein and lipids found on cancer cell surfaces, which participate in cell-cell interactions and in the regulation of immune responses. Sialic acids are a family of nine-carbon α-keto acids found at the outermost ends of glycans [...] Read more.
Hypersialylation is a common post-translational modification of protein and lipids found on cancer cell surfaces, which participate in cell-cell interactions and in the regulation of immune responses. Sialic acids are a family of nine-carbon α-keto acids found at the outermost ends of glycans attached to cell surfaces. Given their locations on cell surfaces, tumor cells aberrantly overexpress sialic acids, which are recognized by Siglec receptors found on immune cells to mediate broad immunomodulatory signaling. Enhanced sialylation exposed on cancer cell surfaces is exemplified as “self-associated molecular pattern” (SAMP), which tricks Siglec receptors found on leukocytes to greatly down-regulate immune responsiveness, leading to tumor growth. In this review, we focused on all 15 human Siglecs (including Siglec XII), many of which still remain understudied. We also highlighted strategies that disrupt the course of Siglec-sialic acid interactions, such as antibody-based therapies and sialic acid mimetics leading to tumor cell depletion. Herein, we introduced the central roles of Siglecs in mediating pro-tumor immunity and discussed strategies that target these receptors, which could benefit improved cancer immunotherapy. Full article
(This article belongs to the Special Issue Approaches for the Reconstruction of Protein Families’ and Superfamilies’ Evolution with Consequences for De Novo Protein Design)
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