https://dr.ntu.edu.sg/bitstream/10356/148810/2/Solubilization%20and%20characterization%20of%20extracellular%20proteins%20from%20anammox%20granular%20sludge.pdf

Solubilization and characterization of extracellular proteins from anammox granular sludge

Although gene-finding in bacterial genomes is relatively straightforward, the automated assignment of gene function is still challenging, resulting in a vast quantity of hypothetical sequences of unknown function. But how prevalent are hypothetical sequences across bacteria, what proportion of genes in different bacterial genomes remain unannotated, and what factors affect annotation completeness? To address these questions, we surveyed over 27 000 bacterial genomes from the Genome Taxonomy Database, and measured genome annotation completeness as a function of annotation method, taxonomy, genome size, 'research bias' and publication date. Our analysis revealed that 52 and 79 % of the average bacterial proteome could be functionally annotated based on protein and domain-based homology searches, respectively. Annotation coverage using protein homology search varied significantly from as low as 14 % in some species to as high as 98 % in others. We found that taxonomy is a major factor influencing annotation completeness, with distinct trends observed across the microbial tree (e.g. the lowest level of completeness was found in the Patescibacteria lineage). Most lineages showed a significant association between genome size and annotation incompleteness, likely reflecting a greater degree of uncharacterized sequences in 'accessory' proteomes than in 'core' proteomes. Finally, research bias, as measured by publication volume, was also an important factor influencing genome annotation completeness, with early model organisms showing high completeness levels relative to other genomes in their own taxonomic lineages. Our work highlights the disparity in annotation coverage across the bacterial tree of life and emphasizes a need for more experimental characterization of accessory proteomes as well as understudied lineages.

An assessment of genome annotation coverage across the bacterial tree of life

Prioritization of potential drug targets against P. aeruginosa by core proteomic analysis using computational subtractive genomics and Protein-Protein interaction network.

Microorganisms represent the most abundant biomass on the planet; however, because of several cultivation technique limitations, most of this genetic patrimony has been inaccessible. Due to the advent of metagenomic methodologies, such limitations have been overcome. Prevailing over these limitations enabled the genetic pool of non-cultivable microorganisms to be exploited for improvements in the development of biotechnological products. By utilising a metagenomic approach, we identified a new gene related to biosurfactant production and hydrocarbon degradation. Environmental DNA was extracted from soil samples collected on the banks of the Jundiai River (Natal, Brazil), and a metagenomic library was constructed. Functional screening identified the clone 3C6, which was positive for the biosurfactant protein and revealed an open reading frame (ORF) with high similarity to sequences encoding a hypothetical protein from species of the family Halobacteriaceae. This protein was purified and exhibited biosurfactant activity. Due to these properties, this protein was named metagenomic biosurfactant protein 1 (MBSP1). In addition, E. coli RosettaTM (DE3) strain cells transformed with the MBSP1 clone showed an increase in aliphatic hydrocarbon degradation. In this study, we described a single gene encoding a protein with marked tensoactive properties that can be produced in a host cell, such as Escherichia coli, without substrate dependence. Furthermore, MBSP1 has been demonstrated as the first protein with these characteristics described in the Archaea or Bacteria domains.

/pdf/mbsp1-a-biosurfactant-protein-derived-from-a-metagenomic-1qkr9zk0zs.pdf

MBSP1: a biosurfactant protein derived from a metagenomic library with activity in oil degradation.

PIEZO channels are stretch-activated channels involved in wound sealing and cell proliferation in many cell types. A recent study focussing on lung cancer (LC), using next-generation sequencing analysis, has indicated that PIEZO functions were implicated in LC development. However, the expression and role of PIEZO channels in non-small cell LC (NSCLC) progression require elucidation. In the current study, we investigated the gene expression and alteration frequency in human NSCLC tissue, accessed the prognostic roles of PIEZO channels in NSCLC patients, and further studied the effect of PIEZOs in NSCLC cell proliferation and tumor growth in vivo. The mRNA expression of PIEZO1 and 2 was clearly decreased in NSCLC tumor tissue compared with that in matched adjacent non-tumor tissue. In human NSCLC tissues, PIEZO1 gene expression exhibits a highly deep deletion rate, and PIEZO2 mainly exhibits mutation in gene expression. High mRNA expression of PIEZO channels was found to correlate with better overall survival (OS) for NSCLC patients, especially for patients with lung adenocarcinoma (LUAD), but not for patients with lung squamous cell carcinoma (LUSC). The prognostic role of PIEZO channels was more sensitive in female patients than male patients, and more sensitive in patients at earlier stages than patients at latter stages. Knockdown of PIEZO1 or PIEZO2 in NSCLC cells significantly promoted cell migration in vitro and tumor growth in vivo. These results indicate the critical prognostic values of the PIEZO channels in NSCLC. This information will be beneficial to understand the pathological mechanism of NSCLC and to generate effective therapeutic approaches for NSCLC patients.

/pdf/loss-of-stretch-activated-channels-piezos-accelerates-non-eop5z7f5kj.pdf

Loss of stretch-activated channels, PIEZOs, accelerates non-small cell lung cancer progression and cell migration

Hypothetical Proteins are the proteins that are predicted to be expressed from an open reading frame (ORF), constituting a substantial fraction of proteomes in both prokaryotes and eukaryotes. Genome projects have led to the identification of many therapeutic targets, the putative function of the protein and their interactions. In this review we have enlisted various methods. Annotation linked to structural and functional prediction of hypothetical proteins assist in the discovery of new structures and functions serving as markers and pharmacological targets for drug designing, discovery and screening. Mass spectrometry is an analytical technique for validating protein characterisation. Matrix-assisted laser desorption ionization–mass spectrometry (MALDI-MS) is an efficient analytical method. Microarrays and Protein expression profiles help understanding the biological systems through a systems-wide study of proteins and their interactions with other proteins and non-proteinaceous molecules to control complex processes in cells and tissues and even whole organism. Next generation sequencing technology accelerates multiple areas of genomics research.

Annotation and curation of uncharacterized proteins- challenges

Cigarette smoking leads to serious epidemics in humans, creating torsion of infection in epithelial cells lining the respiratory tracts. Several researchers in the recent past have theorized that the next generation sequencing (NGS), especially transcriptome sequencing has enhanced understanding lung cancers and other epithelial epidemics. Conversely, pathogenesis specific to lung cancer with respect to molecular fraction of genomic ribonucleic acid has some mutant effect in various populations like smokers with lung cancer, healthy never smokers and vice versa. We review the impending impact of NGS data while providing insights into the biology of lung cancer affecting various populations, which we believe would be an add-on service for predictive biology approaches. Furthermore, we conclude what would be the outcome of such analysis for Indian population. Bioinformatics analysis was performed using various tools. We identified five genes namely epidermal growth factor receptor, Kirsten rat sarcoma, adenomatosis polyposis down regulated-1, N-ethylmaleimide-sensitive factor attachment protein, gamma and Piezo type mechanosensitive ion channel component 2 whose role was implicated in lung cancer and further analysis has to be performed to check whether or not the genes are indeed completely involved in causing lung cancer.

Next generation sequencing analysis of lung cancer datasets: A functional genomics perspective

Tumour suppressor protein 53 (TP53 or simply p53) is a well known protein linked to apoptosis, cell signalling, cascading and several myriad functions in cells. Many diseases are linked to p53 though analysis show only 216 interaction partners. Whether p53 plays an important role in cardiovascular diseases (CVD) remains uncertain. Through this bioinformatical analysis, we propose that p53 might play a major role in CVD whilst being linked to Hypoxia and Lupus. There could be evidence by pull down assay studies. Whether its interactants play a role in CVD remains to be studied using experiments, though the interaction maps show possible affect on other diseases.

/pdf/toward-understanding-the-role-of-p53-in-cardiovascular-w3j7ka9lu3.pdf

Mohanalatha Chandrasekharan

Papers

Annotation and curation of uncharacterized proteins- challenges

Next generation sequencing analysis of lung cancer datasets: A functional genomics perspective

Toward understanding the role of p53 in cardiovascular diseases