Commentary - Journal of Systems Biology & Proteome Research (2021) Volume 2, Issue 1
Microbial proteomics related to microbial activity.
Department of Biochemistry, University of St. Petersburg, 199178 St. Petersburg, Russia
- Corresponding Author:
- Ekaterina Romanovskaya
Department of Biochemistry,
University of St. Petersburg
Accepted date:September 6, 2021
Citation:Romanovskaya E . Microbial proteomics related to microbial activity. J Syst Biol Proteome Res 2021 ;2(1):3
Microbial proteomics helps to spot the proteins related to microbial activity, antimicrobial resistant mechanism and microbial host-pathogens interactions. Microbial activity of pathogens is often confirmed by using the 2-D gel-based and gel-free method. The dried cells of microorganisms like algae, bacteria, actinomycetes and fungi used as food and feed are collectively referred to as 'microbial protein'. The utilization of microbial protein as food has several advantages over conventional proteins. Microbial proteins are healthy source of vitamins, carotenes and carbohydrates. Bacteria use proteins for several purposes like structure, as enzymes, or for transport. Protein synthesis takes several steps working together. Antibiotics that prevent protein synthesis won’t cure bacterial infections. The yeast used for several strains are tested for single cell protein production from whey, notably yeasts. The most k.lactis had been used. But other yeasts, like Candida pseudotropicalis, Torulopsis cremoris and Candida kefir have also been studied.
As a cornerstone of proteomic studies, protein identification lays a firm foundation for further proteomic exploration, like cellular localization, protein quantitation, and protein–protein interactions. MS is that the most comprehensive and universal tool in large-scale proteomics, especially within the application of protein identification before MS analyses, separation technologies are required to isolate incredibly complex protein samples whose performance are extremely related to the identification results. Major separation technologies are often divided into two categories: gel-based and gel-free methods. Among gel-free methods, LC plays a dominant role in separation before MS analyses. The sufficient resolution and high detection capacity of the classic coupled approach MS immensely contribute to the identification of proteins. Multidimensional protein information technology is another popular method that addresses the separation problem by integrating several LC technologies. Multidimensional protein information technology is employed for high-complexity proteomic samples containing proteins with large dynamic range. However, the identification status relies ultimately on the performance of the next spectrometer. Linear trap quadrupole was smoothly utilized during a large-scale proteomic analysis of tubercle bacillus , during which the protein identification results were wont to improve gene annotations in Sanger and therefore the Institute for Genomic Research databases.Shotgun approaches, which are incorporated methods of Multidimensional protein information technology and MS analyses, were employed to examine the proteomes of Scheffersomyces stipites during xylose fermentation under oxygen restriction. Huang et al. Identified 958 non-redundant proteins, from which unique expression patterns were found in biological processes and metabolic pathways, including alternative respiration salicylhydroxamic acid pathway, activation of glyoxylate cycle, and expression of galactose enzymes. Both gel-based and gel-free methods have their own advantages and limitations when including MS to spot proteins. 2-DE-MS has a clear difficulty in detecting membrane and hydrophobic proteins; hence, its detection range must be improved. On the opposite hand, the utilization of high-throughput LC/MS strategy is usually limited by its high cost. Some studies used a mixture of gel-based and gel-free strategies to spot more proteins. Furthermore, subcellular fractionation followed by protein enrichment technique can provide a better resolution in proteomic identification, but can also introduce some bias. Recently, many studies have resorted to label-free methods to quantification. Instead of labelling targets with stable isotopes, label-free techniques directly compare the height information from the MS dataset to estimate protein abundances. Spectral counts, which are now increasingly used, are proportional to the relative abundance of the protein within the sample.
Conclusively, metabolic labelling is usually restricted to microbes and cell culture, whereas chemical labelling is specially limited to a couple of amino acids which will be tagged. Although label-free methods also suffer from run-torun variations in separate experiments they will determine absolutely the level of proteins during a complete sample. Advancement of proteomics in cellular physiology of microorganisms. The abilities of microorganisms to endure severe environmental stresses, like heat, extreme pH, hyper osmosis, radio action, dry, and toxic compounds or pollutants, and to infect their hosts, are of great value in both basic and applied research. To date, microbial proteomics has been successfully applied to certain hotspot problems with interest, like stress responses, extreme environment adaptation, and microbial pathogenicity.