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

Initiation Factor ◽

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.

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 ◽

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 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

BioMed Research International ◽

10.1155/2021/9050026 ◽

2021 ◽

Vol 2021 ◽

pp. 1-10

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 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 is aimed at allocating 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 bioinformatically examined that the protein (WP_012256288.1) is affiliated in protein biosynthesis as a translation initiation factor IF-3 of C. aurantiacus.

OseIF3h Regulates Plant Growth and Pollen Development at Translational Level Presumably through Interaction with OsMTA2

Plants ◽

10.3390/plants10061101 ◽

2021 ◽

Vol 10 (6) ◽

pp. 1101

Author(s):

Yuqing Huang ◽

Peng Zheng ◽

Xuejiao Liu ◽

Hao Chen ◽

Jumin Tu

Keyword(s):

Plant Growth ◽

Translation Initiation ◽

Pollen Development ◽

Messenger Rna ◽

Protein Biosynthesis ◽

Initiation Factor ◽

Sequencing Data ◽

Knock Out ◽

Translational Level

The initiation stage of protein biosynthesis is a sophisticated process tightly regulated by numerous initiation factors and their associated components. However, the mechanism underlying translation initiation has not been completely understood in rice. Here, we showed knock-out mutation of the rice eukaryotic translation initiation factor 3 subunit h (OseIF3h) resulted in plant growth retardation and seed-setting rate reduction as compared to the wild type. Further investigation demonstrated an interaction between OseIF3h and OsMTA2 (mRNA adenosine methylase 2), a rice homolog of METTL3 (methyltransferase-like 3) in mammals, which provided new insight into how N6-methyladenosine (m6A) modification of messenger RNA (mRNA) is engaged in the translation initiation process in monocot species. Moreover, the RIP-seq (RNA immunoprecipitation sequencing) data suggested that OseIF3h was involved in multiple biological processes, including photosynthesis, cellular metabolic process, precursor metabolites, and energy generation. Therefore, we infer that OseIF3h interacts with OsMTA2 to target a particular subset of genes at translational level, regulating plant growth and pollen development.

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 ◽

Bacterial Translation

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.

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

10.21203/rs.3.rs-75549/v1 ◽

2020 ◽

Author(s):

SOMA JANA ◽

Partha Pratim Datta

Keyword(s):

Translation Initiation ◽

In Silico ◽

Bacterial Species ◽

Initiation Factor ◽

Acidic Property ◽

Release Factors ◽

Translation Factors ◽

70S Ribosome ◽

Bacterial Translation

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.

CELL SYSTEMS BIOLOGY OF TRANSLATION FACTORS AND PROTEASOME-TARGETED PROTEIN COMPLEXES ASSOCIATED WITH AGC KINASE SCH9

10.31219/osf.io/zsby9 ◽

2020 ◽

Author(s):

Alex Sobko

Keyword(s):

Protein Synthesis ◽

Protein Kinase ◽

Protein Interactions ◽

Cell Cycle Progression ◽

Protein Complexes ◽

Initiation Factor ◽

Functional Connections ◽

Translation Factors

Sch9 appears to be the Saccharomyces cerevisiae homolog of protein kinase B and S6 kinase and is involved in the control of numerous nutrient-sensitive processes, including regulation of cell size, cell cycle progression, and stress resistance. Sch9 has also been implicated in the regulation of replicative and chronological life span. The availability of data from global studies of protein-protein interactions now makes it possible to predict and validate functional connections between Sch9, its putative substrates, and other proteins. Sch9 appears to be involved in control of biosynthetic and catabolic pathways. Thus, the analysis of Sch9-associated proteins indicates that this kinase may be involved in regulation of protein synthesis. Sch9 forms a complex with, and, presumably, phosphorylates starvation- and stress-induced protein kinase GCN2, which, in turn, phosphorylates translation initiation factor eIF2alpha. Sch9 also interacts with translation factors Arc1, Pab1 and prion-like protein Sup35. Thus, Sch9 may be part of the mechanism that relays availability of nutrients to utilization of glucose and to the rates of protein synthesis. One of the interesting outcomes of the proteome-wide analysis of protein-protein interactions in yeast is the finding that Sch9 associates with Shp1, Cdc48, and Ufd1, which form a complex responsible for the recognition and targeting of ubiquitinated proteins to the proteasome for degradation. It is unknown and remains to be elucidated, whether mammalian homologues of Sch9 are also associated with the proteins involved in translation/protein synthesis and proteasomal degradation.

A specific eIF4A paralog facilitates LARP1-mediated translation repression during mTORC1 inhibition

10.1101/2021.09.18.460932 ◽

2021 ◽

Author(s):

Yuichi Shichino ◽

Mari Mito ◽

Kazuhiro Kashiwagi ◽

Mari Takahashi ◽

Takuhiro Ito ◽

...

Keyword(s):

Translation Initiation ◽

Protein Interactions ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Ribosome Profiling ◽

Initiation Factor ◽

Mtor Inhibition ◽

Translation Repression

AbstractEukaryotic translation initiation factor (eIF) 4A — a DEAD-box RNA-binding protein — plays an essential role in translation initiation. Two mammalian eIF4A paralogs, eIF4A1 and eIF4A2, have been assumed to be redundant because of their high homology, and the difference in their functions has been poorly understood. Here, we show that eIF4A1, but not eIF4A2, enhances translational repression during the inhibition of mechanistic target of rapamycin complex 1 (mTORC1), an essential kinase complex controlling cell proliferation. RNA-immunoprecipitation sequencing (RIP-Seq) of the two eIF4A paralogs revealed that eIF4A1 preferentially binds to mRNAs containing terminal oligopyrimidine (TOP) motifs, whose translation is rapidly repressed upon mTOR inhibition. This biased interaction depends on a La-related RNA-binding protein, LARP1. Ribosome profiling revealed that the deletion of EIF4A1, but not EIF4A2, rendered the translation of TOP mRNAs resistant to mTOR inactivation. Moreover, eIF4A1 enhances the affinity between TOP mRNAs and LARP1 and thus ensures stronger translation repression upon mTORC1 inhibition. Our data show that the distinct protein interactions of these highly homologous translation factor paralogs shape protein synthesis during mTORC1 inhibition and provide a unique example of the repressive role of a universal translation activator.

In silico analysis reveals p53 responsive ribosomal protein and eukaryotic translation initiation factor genes: a route for p53 to influence ribosome assembly and translation

Matters ◽

10.19185/matters.201603000013 ◽

2016 ◽

Author(s):

Gnaneshwar Yadav

Keyword(s):

Ribosomal Protein ◽

Translation Initiation ◽

In Silico ◽

Initiation Factor ◽

Ribosome Assembly ◽

Eukaryotic Translation Initiation Factor ◽

Eukaryotic Translation ◽

Eukaryotic Translation Initiation

Conformational ordering of intrinsically disordered peptides for targeting translation initiation

10.1101/2020.08.20.230268 ◽

2020 ◽

Author(s):

Christopher J Brown ◽

Chandra S Verma ◽

David P Lane ◽

Dilraj Lama

Keyword(s):

Translation Initiation ◽

Protein Interactions ◽

Bound State ◽

Initiation Factor ◽

Structural Reorganization ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Conformational Ordering ◽

Natural Amino Acids

AbstractIntrinsically disordered regions (IDRs) in proteins can regulate their activity by facilitating protein-protein interactions (PPIs) as exemplified in the recruitment of the eukaryotic translation initiation factor 4E (eIF4E) protein by the protein eIF4G. Deregulation of this PPI module is central to a broad spectrum of cancer related malignancies and its targeted inhibition through bioactive peptides is a promising strategy for therapeutic intervention. We have employed a structure-guided approach to rationally develop peptide derivatives from the intrinsically disordered eIF4G scaffold by incorporating non-natural amino acids that facilitates disorder-to-order transition. The conformational heterogeneity of these peptides and the degree of structural reorganization required to adopt the optimum mode of interaction with eIF4E underscores their differential binding affinities. The presence of a pre-structured local helical element in the ensemble of structures was instrumental in the efficient docking of the peptides on to the protein surface. These insights were exploited to further design features into the peptide to propagate bound-state conformations in solution which resulted in the generation of a potent eIF4E binder. The study illustrates the molecular basis of eIF4E recognition by a disordered epitope from eIF4G and its modulation to generate peptides that can potentially attenuate translation initiation in oncology.