In silico functional prediction of hypothetical proteins from the core genome of <i>Corynebacterium pseudotuberculosis</i> biovar <i>ovis</i>

Araújo, Carlos; Blanco, Iago; Souza, Luciana; Tiwari, Sandeep; Pereira, Lino César; Ghosh, Preetam; Azevedo, Vasco; Silva, Artur da Costa da Luiz; Folador, Adriana Ribeiro Carneiro

doi:10.7717/peerj.9643

Cited by 12 publications

(10 citation statements)

References 83 publications

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“…glutamicum strains, which is somewhat higher than C . pseudotuberculosis core genes (26.1%) at sub-species level [ 70 ]. The number of cloud genes (strain-specific genes) was considerably large and covered 47.78% of the pan-genome, similar to C .…”

Section: Discussionmentioning

confidence: 99%

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Comprehensive analysis of genomic variation, pan-genome and biosynthetic potential of Corynebacterium glutamicum strains

Rahman,

Shimul,

Parvez

2024

PLoS ONE

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Corynebacterium glutamicum is a non-pathogenic species of the Corynebacteriaceae family. It has been broadly used in industrial biotechnology for the production of valuable products. Though it is widely accepted at the industrial level, knowledge about the genomic diversity of the strains is limited. Here, we investigated the comparative genomic features of the strains and pan-genomic characteristics. We also observed phylogenetic relationships among the strains based on average nucleotide identity (ANI). We found diversity between strains at the genomic and pan-genomic levels. Less than one-third of the C. glutamicum pan-genome consists of core genes and soft-core genes. Whereas, a large number of strain-specific genes covered about half of the total pan-genome. Besides, C. glutamicum pan-genome is open and expanding, which indicates the possible addition of new gene families to the pan-genome. We also investigated the distribution of biosynthetic gene clusters (BGCs) among the strains. We discovered slight variations of BGCs at the strain level. Several BGCs with the potential to express novel bioactive secondary metabolites have been identified. Therefore, by utilizing the characteristic advantages of C. glutamicum, different strains can be potential applicants for natural drug discovery.

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Section: Discussionmentioning

confidence: 99%

“…The number of cloud genes (strain-specific genes) was considerably large and covered 47.78% of the pan-genome, similar to C . pseudotuberculosis cloud genes (42.34%) [ 70 ]. The low percentage of core genes in C .…”

Section: Discussionmentioning

confidence: 99%

Comprehensive analysis of genomic variation, pan-genome and biosynthetic potential of Corynebacterium glutamicum strains

Rahman,

Shimul,

Parvez

2024

PLoS ONE

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“…These hypothetical proteins were found to constitute a major portion of microbial genomes. From recent studies, it was evident that functional characterization of hypothetical proteins (HPs) could provide additional understanding of the physiological architecture of the cell ( Rabbi et al, 2021 ; Araújo et al, 2020 ; Pranavathiyani et al, 2020 ; Sen and Verma, 2020 ; da Costa et al, 2018 ; Naqvi et al, 2015 ; Shahbaaz et al, 2013 ). Genomic analysis of Pseudomonas sp.…”

Section: Introductionmentioning

confidence: 99%

Investigating the Functional Role of Hypothetical Proteins From an Antarctic Bacterium Pseudomonas sp. Lz4W: Emphasis on Identifying Proteins Involved in Cold Adaptation

et al. 2022

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Exploring the molecular mechanisms behind bacterial adaptation to extreme temperatures has potential biotechnological applications. In the present study, Pseudomonas sp. Lz4W, a Gram-negative psychrophilic bacterium adapted to survive in Antarctica, was selected to decipher the molecular mechanism underlying the cold adaptation. Proteome analysis of the isolates grown at 4°C was performed to identify the proteins and pathways that are responsible for the adaptation. However, many proteins from the expressed proteome were found to be hypothetical proteins (HPs), whose function is unknown. Investigating the functional roles of these proteins may provide additional information in the biological understanding of the bacterial cold adaptation. Thus, our study aimed to assign functions to these HPs and understand their role at the molecular level. We used a structured insilico workflow combining different bioinformatics tools and databases for functional annotation. Pseudomonas sp. Lz4W genome (CP017432, version 1) contains 4493 genes and 4412 coding sequences (CDS), of which 743 CDS were annotated as HPs. Of these, from the proteome analysis, 61 HPs were found to be expressed consistently at the protein level. The amino acid sequences of these 61 HPs were submitted to our workflow and we could successfully assign a function to 18 HPs. Most of these proteins were predicted to be involved in biological mechanisms of cold adaptations such as peptidoglycan metabolism, cell wall organization, ATP hydrolysis, outer membrane fluidity, catalysis, and others. This study provided a better understanding of the functional significance of HPs in cold adaptation of Pseudomonas sp. Lz4W. Our approach emphasizes the importance of addressing the “hypothetical protein problem” for a thorough understanding of mechanisms at the cellular level, as well as, provided the assessment of integrating proteomics methods with various annotation and curation approaches to characterize hypothetical or uncharacterized protein data. The MS proteomics data generated from this study has been deposited to the ProteomeXchange through PRIDE with the dataset identifier–PXD029741.

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“…Due to the obvious similarity with known proteins, homology-based functional annotation may be used to assign functions to HPs. 21 , 24 - 26 Bioinformatics approaches, particularly protein-protein interactions, can aid in the proper characterization of the biological processes in which HPs are involved. 27 The objective of this study was to assign functions to the hypothetical proteins encoded within the genomes of the V. parahaemolyticus isolates to identify novel proteins that might aid to better understand the pathogenesis and virulence mechanism of the bacteria as well as identify new therapeutic targets employing computational approaches.…”

Section: Introductionmentioning

confidence: 99%

Functional Analysis of Hypothetical Proteins of Vibrio parahaemolyticus Reveals the Presence of Virulence Factors and Growth-Related Enzymes With Therapeutic Potential

Shahrear

Zinnia

Sany

et al. 2022

Bioinform Biol Insights

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Vibrio parahaemolyticus, an aquatic pathogen, is a major concern in the shrimp aquaculture industry. Several strains of this pathogen are responsible for causing acute hepatopancreatic necrosis disease as well as other serious illness, both of which result in severe economic losses. The genome sequence of two pathogenic strains of V. parahaemolyticus, MSR16 and MSR17, isolated from Bangladesh, have been reported to gain a better understanding of their diversity and virulence. However, the prevalence of hypothetical proteins (HPs) makes it challenging to obtain a comprehensive understanding of the pathogenesis of V. parahaemolyticus. The aim of the present study is to provide a functional annotation of the HPs to elucidate their role in pathogenesis employing several in silico tools. The exploration of protein domains and families, similarity searches against proteins with known function, gene ontology enrichment, along with protein-protein interaction analysis of the HPs led to the functional assignment with a high level of confidence for 656 proteins out of a pool of 2631 proteins. The in silico approach used in this study was important for accurately assigning function to HPs and inferring interactions with proteins with previously described functions. The HPs with function predicted were categorized into various groups such as enzymes involved in small-compound biosynthesis pathway, iron binding proteins, antibiotics resistance proteins, and other proteins. Several proteins with potential druggability were identified among them. In addition, the HPs were investigated in search of virulent factors, which led to the identification of proteins that have the potential to be exploited as vaccine candidate. The findings of the study will be effective in gaining a better understanding of the molecular mechanisms of bacterial pathogenesis. They may also provide an insight into the process of evaluating promising targets for the development of drugs and vaccines against V. parahaemolyticus.

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In silico functional prediction of hypothetical proteins from the core genome of Corynebacterium pseudotuberculosis biovar ovis

Cited by 12 publications

References 83 publications

Comprehensive analysis of genomic variation, pan-genome and biosynthetic potential of Corynebacterium glutamicum strains

Comprehensive analysis of genomic variation, pan-genome and biosynthetic potential of Corynebacterium glutamicum strains

Investigating the Functional Role of Hypothetical Proteins From an Antarctic Bacterium Pseudomonas sp. Lz4W: Emphasis on Identifying Proteins Involved in Cold Adaptation

Functional Analysis of Hypothetical Proteins of Vibrio parahaemolyticus Reveals the Presence of Virulence Factors and Growth-Related Enzymes With Therapeutic Potential

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