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In Silico Analysis of Bacterial Translation Factors Reveal Distinct Translation Event Specific Pi Values Soma Jana and Partha P

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In Silico Analysis of Bacterial Translation Factors Reveal Distinct Translation Event Specific Pi Values Soma Jana and Partha P Jana and Datta BMC Genomics (2021) 22:220 https://doi.org/10.1186/s12864-021-07472-x RESEARCH ARTICLE Open Access In silico analysis of bacterial translation factors reveal distinct translation event specific pI values Soma Jana and Partha P. Datta* Abstract Background: Protein synthesis is a cellular process that takes place through the successive translation events within the ribosome by the event-specific protein factors, namely, initiation, elongation, release, and recycling factors. In this regard, we asked the question about how similar are those translation factors to each other from a wide variety of bacteria? Hence, we did a thorough in silico study of the translation factors from 495 bacterial sp., and 4262 amino acid sequences by theoretically measuring their pI and MW values that are two determining factors for distinguishing individual proteins in 2D gel electrophoresis in experimental procedures. Then we analyzed the output from various angles. Results: Our study revealed the fact that it’s not all same, or all random, but there are distinct orders and the pI values of translation factors are translation event specific. We found that the translation initiation factors are mainly basic, whereas, elongation and release factors that interact with the inter-subunit space of the intact 70S ribosome during translation are strictly acidic across bacterial sp. These acidic elongation factors and release factors contain higher frequencies of glutamic acids. However, among all the translation factors, the translation initiation factor 2 (IF2) and ribosome recycling factor (RRF) showed variable pI values that are linked to the order of phylogeny. Conclusions: From the results of our study, we conclude that among all the bacterial translation factors, elongation and release factors are more conserved in terms of their pI values in comparison to initiation and recycling factors. Acidic properties of these factors are independent of habitat, nature, and phylogeny of the bacterial species. Furthermore, irrespective of the different shapes, sizes, and functions of the elongation and release factors, possession of the strictly acidic pI values of these translation factors all over the domain Bacteria indicates that the acidic nature of these factors is a necessary criterion, perhaps to interact into the partially enclosed rRNA rich inter- subunit space of the translating 70S ribosome. Keywords: Ribosome, Translation, Translation factors, Isoelectric point, Molecular weight, Phylogeny * Correspondence: [email protected] Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, WB PIN 741246, India © The Author(s). 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Jana and Datta BMC Genomics (2021) 22:220 Page 2 of 11 Background that the bacterial translational elongation and release The translation is a complex universal biological process factors have similar pI value distribution, and that was that takes place in a large macromolecular machine strictly acidic throughout the domain Bacteria. Irrespect- called ribosome in all living organisms. It is an energy- ive of the habitat, nature, or the phylogeny of the bacter- exhaustive cellular process. In Escherichia coli, 40% of ial species as well as irrespective of the different shapes, the total cellular energy is utilized by the translation sys- sizes, and functions of the elongation and release factors, tem [1]. With the help of specific protein factors and these factors had strictly acidic pI values. We believe, aminoacyl tRNAs, ribosomes carry out protein synthesis our study indicates that the charge distribution of these following the decoding of the genetic information from factors might play important roles in the fidelity of the mRNA in successive events, namely, initiation, elong- process of translation. ation, and termination (release and recycling). The pro- tein factors that are involved in the successive events are Results initiation factors (IF), elongation factors (EF), release fac- We studied 495 bacterial species throughout the domain tors (RF), and ribosome recycling factors (RRF). Here, of Bacteria. The habitats of these bacteria are very differ- the accurate coordination of every participant protein ent from each other. The nature of these bacteria in factor is necessary to perform the process successfully. terms of cell shape (coccus or bacillus), intracellular Based on several years of biochemical and structural bio- metabolic reactions (aerobic or anaerobic), and even the logical studies worldwide, fairly detailed knowledge of way they respond to the external environments (meso- the mechanisms of cellular protein synthesis is now philic or thermophilic or psychrophilic) are distinct [9]. known [2–4]. However, in the broad aspect, which char- Here, we studied the following bacterial phyla, such as acteristics of the translation factors i.e., IF, EF and RF Deinococcus-Thermus, Chlorobi, Actinobacteria, Firmi- are necessary to be conserved for the accuracy of the cutes, Chlamydiae, Fusobacteria, Spirochaetes, Chloro- universal process of protein synthesis among the differ- flexi, Tenericutes, Cyanobacteria, Bacteroidetes, ent kinds of organisms need to be investigated. Thermotogae, Acidobacteria, Aquificae, Caldiserica, In this study, we focused on the charge distribution (in Chrysiogenetes, Deferribacteres, Elusimicrobia, Fibrobac- terms of acidic and basic properties) of the translation teres, Gemmatimonadetes, Lentisphaerae, Nitrospirae, factors throughout the domain Bacteria to comprehend Planctomycetes, Thermodesulfobacteria, Verrucomicro- the importance of the influence of the charge distribu- bia, and Proteobacteria [10]. tion of these factors on their accommodation on the ribosome and thus in their functions during this process of translation. For this, we made use of the principle of pI and molecular weight value distribution of translation the 2D gel electrophoresis [5], whereby, we computed protein factors the pI values using the “Compute pI/Mw tool – In the process of translation, we found a unique pattern ExPASy” (https://web.expasy.org/compute_pi/) online of pI value distribution as depicted in Fig. 1a, (see Add- webserver. This web server calculates the pI values of itional file 1; Table S1). The initiation factors, IF1, and proteins using pK values of amino acids as defined in IF3 were strictly basic except IF2. Conversely, the elong- [6–8], which were determined by examining polypeptide ation and release factors were strictly acidic. On the migration in an immobilized pH gradient (between pH other hand, like IF2, RRF also showed a broad range of 4.5 to 7.3) gel environment with 9.2 M and 9.8 M urea at pI value distribution ranging from acidic to basic. All the 15 °C or 25 °C. In that study, the authors determined the four quartiles of initiation factor 1 (IF1) and initiation focusing positions of 29 polypeptides of known amino factor 3 (IF3) were above pI 7. The elongation factor Tu acid sequence within a narrow range of immobilized pH (EF-Tu), elongation factor G (EF-G), elongation factor 4 gradients i.e., between pH 4.5 to 7.3 under denaturing (EF-4), & elongation factor P (EF-P) and the release fac- conditions with 9.2 M and 9.8 M urea at 15 °C or 25 °C, tor 1 (RF1), release factor 2 (RF2), & release factor 3 respectively. They separately calculated the pI values of (RF3) had all the four quartiles in the acidic range. For those proteins from their amino acid sequences. The the comprehensive in silico study, along with the pI comparison of isoelectric points of the proteins calcu- values, we also studied the molecular weight (MW) lated from their amino acid sequences showed reliably value distribution of these translation protein factors good accuracy with the experimentally determined pl (Fig. 1b), (see Additional file 1; Table S1). Like pI values. The reliability of the tool is broad, except for the value distribution, the protein IF2 showed a wide range study of highly basic proteins and small proteins. As the of variations in MW value distribution as well (Fig. 1b). translational factors are not highly basic and also not too All the other proteins showed precise MW value distri- small, we believed our study was within the scope of the bution. A surprising observation is to be noted here that above mentioned web-based method. Our study revealed although RRF proteins showed a highly variable pI value Jana and Datta BMC Genomics (2021) 22:220 Page 3 of 11 Fig. 1 Box plot diagram
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