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Protein Biosynthesis: From Mechanism to Structure

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: closed (31 January 2022) | Viewed by 2757

Special Issue Editors


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Guest Editor
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
Interests: protein biosynthesis; gene expression regulation; ribosome profiling; antibiotics targeting ribosomes; antibiotic resistance mechanisms

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Guest Editor
Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA
Interests: protein biosynthesis; gene expression regulation; chromatin; chromatin remodeling; transcription; structural biology; cryo-EM; algorithms

Special Issue Information

Dear Colleagues,

Protein biosynthesis is a fundamental process in every living cell, during which the ribosome and associated factors translate the information encoded in mRNA into polypeptides. The precise control of this process lies at the heart of cellular response to stress and adaptation to the surrounding environment. Although the field of protein biosynthesis is over eighty years old, the regulation of gene expression at the translational level remains an underexplored area. The role of ribosomes in gene expression regulation was neglected for decades. However, the more recent experimental evidence suggests that ribosomes may take the role of regulatory elements in response to changing environmental conditions. Further, in addition to a set of elongation and recycling factors which are conserved and necessary for the functioning of translation initiation, evolution has selected a number of proteins that can help to maintain and preserve translation under stress conditions. Such specialized translation factors help protein biosynthesis machinery to respond rapidly and specifically to, e.g., nutrient deficiency or antibiotic stress. Indeed, translational machinery is one of the major targets for the action of a plethora of antibiotics. However, in many cases, the exact modes of action, physiological responses, and related resistance mechanisms remain vague.

Recent technological advances in next-generation sequencing, single-particle cryo-EM, and cryotomography Cryo-ET methods and many others have opened new avenues and approaches to translation research. In this Special Issue, we would like to welcome discoveries related to this wonderfully broad topic and encompassing all aspects of protein biosynthesis.

Dr. Agata L. Starosta
Dr. Jean-Paul Armache
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. Molecules is an international peer-reviewed open access semimonthly 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 biosynthesis
  • Translation
  • Ribosome
  • Gene expression regulation ribosome profiling
  • Antibiotics targeting ribosomes
  • Ribosome-related antibiotic resistance mechanisms

Published Papers (1 paper)

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Research

16 pages, 3950 KiB  
Article
A Uniform Benchmark for Testing SsrA-Derived Degrons in the Escherichia coli ClpXP Degradation Pathway
by Maria Magdalena Klimecka, Anna Antosiewicz, Matylda Anna Izert, Patrycja Emanuela Szybowska, Piotr Krzysztof Twardowski, Clara Delaunay and Maria Wiktoria Górna
Molecules 2021, 26(19), 5936; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26195936 - 30 Sep 2021
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Abstract
The ssrA degron is commonly used in fusion proteins to control protein stability in bacteria or as an interaction module. These applications often rely on the modular activities of the ssrA tag in binding to the SspB adaptor and in engaging the ClpXP [...] Read more.
The ssrA degron is commonly used in fusion proteins to control protein stability in bacteria or as an interaction module. These applications often rely on the modular activities of the ssrA tag in binding to the SspB adaptor and in engaging the ClpXP protease. However, a comparison of these activities for a substantial standard set of degron variants has not been conducted previously, which may hinder the development of new variants optimized exclusively for one application. Here, we strive to establish a benchmark that will facilitate the comparison of ssrA variants under uniform conditions. In our workflow, we included methods for expression and purification of ClpX, ClpP, SspB and eGFP-degrons, assays of ClpX ATPase activity, of eGFP-degron binding to SspB and for measuring eGFP-degron degradation in vitro and in vivo. Using uniform, precise and sensitive methods under the same conditions on a range of eGFP-degrons allowed us to determine subtle differences in their properties that can affect their potential applications. Our findings can serve as a reference and a resource for developing targeted protein degradation approaches. Full article
(This article belongs to the Special Issue Protein Biosynthesis: From Mechanism to Structure)
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