NetGenes: A Database of Essential Genes Predicted Using Features From Interaction Networks

Prediction of Essential Proteins of Klebsiella pneumoniae using Integrative Bioinformatics and Systems Biology Approach: Unveiling New Avenues for Drug Discovery

Klebsiella pneumoniae is an opportunistic multidrug-resistant bacterial pathogen responsible for various health care-associated infections. The prediction of proteins that are essential for the survival of bacterial pathogens can greatly facilitate the drug development and discovery pipeline toward target identification. To this end, the present study reports a comprehensive computational approach integrating bioinformatics and systems biology-based methods to identify essential proteins of K. pneumoniae involved in vital processes. From the proteome of this pathogen, we predicted a total of 854 essential proteins based on sequence, protein-protein interaction (PPI) and genome-scale metabolic model methods. These predicted essential proteins are involved in vital processes for cellular regulation such as translation, metabolism, and biosynthesis of essential factors, among others. Cluster analysis of the PPI network revealed the highly connected modules involved in the basic functionality of the organism. Further, the predicted consensus set of essential proteins of K. pneumoniae was evaluated by comparing them with existing resources (NetGenes and PATHOgenex) and literature. The findings of this study offer guidance toward understanding cell functionality, thereby facilitating the understanding of pathogen systems and providing a way forward to shortlist potential therapeutic candidates for developing novel antimicrobial agents against K. pneumoniae. In addition, the research strategy presented herein is a fusion of sequence and systems biology-based approaches that offers prospects as a model to predict essential proteins for other pathogens.

Recent advances in the characterization of essential genes and development of a database of essential genes

Over the past few decades, there has been a significant interest in the study of essential genes, which are crucial for the survival of an organism under specific environmental conditions and thus have practical applications in the fields of synthetic biology and medicine. An increasing amount of experimental data on essential genes has been obtained with the continuous development of technological methods. Meanwhile, various computational prediction methods, related databases and web servers have emerged accordingly. To facilitate the study of essential genes, we have established a database of essential genes (DEG), which has become popular with continuous updates to facilitate essential gene feature analysis and prediction, drug and vaccine development, as well as artificial genome design and construction. In this article, we summarized the studies of essential genes, overviewed the relevant databases, and discussed their practical applications. Furthermore, we provided an overview of the main applications of DEG and conducted comprehensive analyses based on its latest version. However, it should be noted that the essential gene is a dynamic concept instead of a binary one, which presents both opportunities and challenges for their future development.

Identification of discriminant features from stationary pattern of nucleotide bases and their application to essential gene classification

Introduction: Essential genes are essential for the survival of various species. These genes are a family linked to critical cellular activities for species survival. These genes are coded for proteins that regulate central metabolism, gene translation, deoxyribonucleic acid replication, and fundamental cellular structure and facilitate intracellular and extracellular transport. Essential genes preserve crucial genomics information that may hold the key to a detailed knowledge of life and evolution. Essential gene studies have long been regarded as a vital topic in computational biology due to their relevance. An essential gene is composed of adenine, guanine, cytosine, and thymine and its various combinations. Methods: This paper presents a novel method of extracting information on the stationary patterns of nucleotides such as adenine, guanine, cytosine, and thymine in each gene. For this purpose, some co-occurrence matrices are derived that provide the statistical distribution of stationary patterns of nucleotides in the genes, which is helpful in establishing the relationship between the nucleotides. For extracting discriminant features from each co-occurrence matrix, energy, entropy, homogeneity, contrast, and dissimilarity features are computed, which are extracted from all co-occurrence matrices and then concatenated to form a feature vector representing each essential gene. Finally, supervised machine learning algorithms are applied for essential gene classification based on the extracted fixed-dimensional feature vectors. Results: For comparison, some existing state-of-the-art feature representation techniques such as Shannon entropy (SE), Hurst exponent (HE), fractal dimension (FD), and their combinations have been utilized. Discussion: An extensive experiment has been performed for classifying the essential genes of five species that show the robustness and effectiveness of the proposed methodology.

Bacterial genome reductions: Tools, applications, and challenges

Bacterial cells are widely used to produce value-added products due to their versatility, ease of manipulation, and the abundance of genome engineering tools. However, the efficiency of producing these desired biomolecules is often hindered by the cells’ own metabolism, genetic instability, and the toxicity of the product. To overcome these challenges, genome reductions have been performed, making strains with the potential of serving as chassis for downstream applications. Here we review the current technologies that enable the design and construction of such reduced-genome bacteria as well as the challenges that limit their assembly and applicability. While genomic reductions have shown improvement of many cellular characteristics, a major challenge still exists in constructing these cells efficiently and rapidly. Computational tools have been created in attempts at minimizing the time needed to design these organisms, but gaps still exist in modelling these reductions in silico. Genomic reductions are a promising avenue for improving the production of value-added products, constructing chassis cells, and for uncovering cellular function but are currently limited by their time-consuming construction methods. With improvements to and the creation of novel genome editing tools and in silico models, these approaches could be combined to expedite this process and create more streamlined and efficient cell factories.