In silico analysis of bacterial translation factors reveal distinct translation event specific pI values

Initiation Factor ◽

Acidic Property ◽

Release Factors ◽

Translation Factors ◽

70S Ribosome ◽

Abstract Background Protein synthesis is a cellular process that takes place through the successive translation events within the ribosome with the help of the event-specific protein factors, namely, initiation, elongation, release, and recycling factors. The translation process is fundamental to all organisms living in the wide variety of environments. In this regard, we asked the questions 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, wherein we theoretically measured their pI and MW values that are the two determining factors for distinguishing individual proteins in 2D gel electrophoresis. Then we analyzed the output from various angles. Results Our study revealed that, not all the pI values are same or random, but there is a distinct order, such that 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. Further analysis revealed that the acidic property of those factors is due to the higher frequencies of glutamic acids. However, two translation factors, the translation initiation factor 2 (IF2) and the ribosome recycling factor (RRF) showed variable pI values. Remarkably, the variability of the pI values of these two factors showed distinct lineage with the order of phylogeny. Conclusion From our results 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, or the phylogeny of the bacterial species. Furthermore; irrespective of the different shapes, sizes, and functions of the elongation and release factors, possession of their strictly acidic pI values indicate 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.

In silico analysis of bacterial translation factors reveal distinct translation event specific pI values

BMC Genomics ◽

10.1186/s12864-021-07472-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Soma Jana ◽

Partha P. Datta

Keyword(s):

Translation Initiation ◽

In Silico ◽

Bacterial Species ◽

Amino Acid Sequences ◽

Initiation Factor ◽

Release Factors ◽

Translation Factors ◽

70S Ribosome ◽

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.

Cloning and characterization of hIF2, a human homologue of bacterial translation initiation factor 2, and its interaction with HIV-1 matrix

Biochemical Journal ◽

10.1042/0264-6021:3420097 ◽

1999 ◽

Vol 342 (1) ◽

pp. 97 ◽

Cited By ~ 7

Author(s):

Stuart A. WILSON ◽

Carmen SIEIRO-VAZQUEZ ◽

Nicholas J. EDWARDS ◽

Oleg IOURIN ◽

Elaine D. BYLES ◽

...

Keyword(s):

Translation Initiation ◽

Initiation Factor ◽

Human Homologue ◽

Initiation Factor 2 ◽

Bacterial Translation Initiation ◽

Translation Initiation Factor 2 ◽

Hiv 1 ◽

A Conserved Structural Motif at the N Terminus of Bacterial Translation Initiation Factor IF2

Journal of Biological Chemistry ◽

10.1074/jbc.m212960200 ◽

2003 ◽

Vol 278 (18) ◽

pp. 16320-16328 ◽

Cited By ~ 19

Author(s):

Brian Søgaard Laursen ◽

Kim Kusk Mortensen ◽

Hans Uffe Sperling-Petersen ◽

David W. Hoffman

Keyword(s):

Translation Initiation ◽

Structural Motif ◽

Initiation Factor ◽

N Terminus ◽

Bacterial Translation Initiation ◽

Molecular Structure and Functional Elucidation of IF-3 Protein of Chloroflexus Aurantiacus Involved in Protein Biosynthesis: An In-Silico Approach

10.26434/chemrxiv.14342372.v1 ◽

2021 ◽

Author(s):

Abu Saim Mohammad Saikat

Keyword(s):

Translation Initiation ◽

Protein Interactions ◽

In Silico ◽

Tertiary Structure ◽

Protein Biosynthesis ◽

Initiation Factor ◽

Chloroflexus Aurantiacus ◽

Protein Protein Interactions ◽

Functional Interpretation

Chloroflexus aurantiacus is a thermophilic bacterium that produces a multitude of proteins within its genome. Bioinformatics strategies can facilitate comprehending this organism through functional and structural interpretation assessments. This study aimed to allocate the structure and function through an in-silico approach required for bacterial protein biosynthesis. This in-silico viewpoint provides copious properties, including the physicochemical properties, subcellular location, three-dimensional structure, protein-protein interactions, and functional elucidation of the protein (WP_012256288.1). The STRING program is utilized for the explication of protein-protein interactions. The in-silico investigation documented the protein's hydrophilic nature with predominantly alpha (α) helices in its secondary structure. The tertiary-structure model of the protein has been shown to exhibit reasonably high consistency based on various quality assessment methods. The functional interpretation suggested that the protein can act as a translation initiation factor, a protein required for translation and protein biosynthesis. Protein-protein interactions also demonstrated high credence that the protein interconnected with 30S ribosomal subunit involved in protein synthesis. This study is bioinformatically examined that the protein (WP_012256288.1) is affiliated in protein biosynthesis as a translation initiation factor IF-3 of C. aurantiacus.

Structural and Functional Elucidation of IF-3 Protein of Chloroflexus aurantiacus Involved in Protein Biosynthesis: An In-Silico Approach

10.26434/chemrxiv.14342372.v2 ◽

2021 ◽

Author(s):

Abu Saim Mohammad Saikat ◽

Md. Ekhlas Uddin ◽

Tasnim Ahmad ◽

Shahriar Mahmud ◽

Md. Abu Sayeed Imran ◽

...

Keyword(s):

Translation Initiation ◽

Protein Interactions ◽

In Silico ◽

Tertiary Structure ◽

Protein Biosynthesis ◽

Initiation Factor ◽

Chloroflexus Aurantiacus ◽

Protein Protein Interactions ◽

Functional Interpretation

Chloroflexus aurantiacus is a thermophilic bacterium that produces a multitude of proteins within its genome. Bioinformatics strategies can facilitate comprehending this organism through functional and structural interpretation assessments.This study aimed to allocate the structure and function through an in-silico approach required for bacterial protein biosynthesis. This in-silico viewpoint provides copious properties, including the physicochemical properties, subcellular location, three-dimensional structure, protein-protein interactions, and functional elucidation of the protein (WP_012256288.1). The STRING program is utilized for the explication of protein-protein interactions. The in-silico investigation documented the protein's hydrophilic nature with predominantly alpha (α) helices in its secondary structure.The tertiary-structure model of the protein has been shown to exhibit reasonably high consistency based on various quality assessment methods.The functional interpretation suggested that the protein can act as a translation initiation factor, a protein required for translation and protein biosynthesis. Protein-protein interactions also demonstrated high credence that the protein interconnected with 30S ribosomal subunit involved in protein synthesis. This study is bioinformatically examined that the protein (WP_012256288.1) is affiliated in protein biosynthesis as a translation initiation factor IF-3 of C. aurantiacus.