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BMC Bioinformatics Mar 2017Protein-protein interactions (PPIs) can offer compelling evidence for protein function, especially when viewed in the context of proteome-wide interactomes. Bacteria...
BACKGROUND
Protein-protein interactions (PPIs) can offer compelling evidence for protein function, especially when viewed in the context of proteome-wide interactomes. Bacteria have been popular subjects of interactome studies: more than six different bacterial species have been the subjects of comprehensive interactome studies while several more have had substantial segments of their proteomes screened for interactions. The protein interactomes of several bacterial species have been completed, including several from prominent human pathogens. The availability of interactome data has brought challenges, as these large data sets are difficult to compare across species, limiting their usefulness for broad studies of microbial genetics and evolution.
RESULTS
In this study, we use more than 52,000 unique protein-protein interactions (PPIs) across 349 different bacterial species and strains to determine their conservation across data sets and taxonomic groups. When proteins are collapsed into orthologous groups (OGs) the resulting meta-interactome still includes more than 43,000 interactions, about 14,000 of which involve proteins of unknown function. While conserved interactions provide support for protein function in their respective species data, we found only 429 PPIs (~1% of the available data) conserved in two or more species, rendering any cross-species interactome comparison immediately useful. The meta-interactome serves as a model for predicting interactions, protein functions, and even full interactome sizes for species with limited to no experimentally observed PPI, including Bacillus subtilis and Salmonella enterica which are predicted to have up to 18,000 and 31,000 PPIs, respectively.
CONCLUSIONS
In the course of this work, we have assembled cross-species interactome comparisons that will allow interactomics researchers to anticipate the structures of yet-unexplored microbial interactomes and to focus on well-conserved yet uncharacterized interactors for further study. Such conserved interactions should provide evidence for important but yet-uncharacterized aspects of bacterial physiology and may provide targets for anti-microbial therapies.
Topics: Bacillus subtilis; Bacteria; Bacterial Proteins; Evolution, Molecular; Humans; Protein Interaction Mapping; Proteome; Salmonella enterica
PubMed: 28298180
DOI: 10.1186/s12859-017-1585-0 -
Cold Spring Harbor Perspectives in... Sep 2016Protein synthesis occurs on macromolecular machines, called ribosomes. Bacterial ribosomes and the translational machinery represent one of the major targets for... (Review)
Review
Protein synthesis occurs on macromolecular machines, called ribosomes. Bacterial ribosomes and the translational machinery represent one of the major targets for antibiotics in the cell. Therefore, structural and biochemical investigations into ribosome-targeting antibiotics provide not only insight into the mechanism of action and resistance of antibiotics, but also insight into the fundamental process of protein synthesis. This review summarizes the recent advances in our understanding of protein synthesis, particularly with respect to X-ray and cryoelectron microscopy (cryo-EM) structures of ribosome complexes, and highlights the different steps of translation that are targeted by the diverse array of known antibiotics. Such findings will be important for the ongoing development of novel and improved antimicrobial agents to combat the rapid emergence of multidrug resistant pathogenic bacteria.
Topics: Anti-Bacterial Agents; Bacterial Proteins; Cryoelectron Microscopy; Protein Biosynthesis; Ribosomes
PubMed: 27481773
DOI: 10.1101/cshperspect.a025361 -
Toxins Aug 2014To intoxicate cells, pore-forming bacterial toxins are evolved to allow for the transmembrane traffic of different substrates, ranging from small inorganic ions to... (Review)
Review
To intoxicate cells, pore-forming bacterial toxins are evolved to allow for the transmembrane traffic of different substrates, ranging from small inorganic ions to cell-specific polypeptides. Recent developments in single-channel electrical recordings, X-ray crystallography, protein engineering, and computational methods have generated a large body of knowledge about the basic principles of channel-mediated molecular transport. These discoveries provide a robust framework for expansion of the described principles and methods toward use of biological nanopores in the growing field of nanobiotechnology. This article, written for a special volume on "Intracellular Traffic and Transport of Bacterial Protein Toxins", reviews the current state of applications of pore-forming bacterial toxins in small- and macromolecule-sensing, targeted cancer therapy, and drug delivery. We discuss the electrophysiological studies that explore molecular details of channel-facilitated protein and polymer transport across cellular membranes using both natural and foreign substrates. The review focuses on the structurally and functionally different bacterial toxins: gramicidin A of Bacillus brevis, α-hemolysin of Staphylococcus aureus, and binary toxin of Bacillus anthracis, which have found their "second life" in a variety of developing medical and technological applications.
Topics: Animals; Bacterial Proteins; Bacterial Toxins; Biological Transport; Biosensing Techniques; Drug Delivery Systems; Humans; Neoplasms; Pore Forming Cytotoxic Proteins
PubMed: 25153255
DOI: 10.3390/toxins6082483 -
Current Genetics May 2016Nε-acetylation is emerging as an abundant post-translational modification of bacterial proteins. Two mechanisms have been identified: one is enzymatic, dependent on an... (Review)
Review
Nε-acetylation is emerging as an abundant post-translational modification of bacterial proteins. Two mechanisms have been identified: one is enzymatic, dependent on an acetyltransferase and acetyl-coenzyme A; the other is non-enzymatic and depends on the reactivity of acetyl phosphate. Some, but not most, of those acetylations are reversed by deacetylases. This review will briefly describe the current status of the field and raise questions that need answering.
Topics: Acetylation; Acetyltransferases; Bacterial Proteins; Humans; Organophosphates; Protein Processing, Post-Translational
PubMed: 26660885
DOI: 10.1007/s00294-015-0552-4 -
Microbiology (Reading, England) Sep 2013Misfolding and aggregation of proteins have a negative impact on all living organisms. In recent years, aggregation has been studied in detail due to its involvement in... (Review)
Review
Misfolding and aggregation of proteins have a negative impact on all living organisms. In recent years, aggregation has been studied in detail due to its involvement in neurodegenerative diseases, including Alzheimer's, Parkinson's and Huntington's diseases, and type II diabetes--all associated with accumulation of amyloid fibrils. This research highlighted the central importance of protein homeostasis, or proteostasis for short, defined as the cellular state in which the proteome is both stable and functional. It implicates an equilibrium between synthesis, folding, trafficking, aggregation, disaggregation and degradation. In accordance with the eukaryotic systems, it has been documented that protein aggregation also reduces fitness of bacterial cells, but although our understanding of the cellular protein quality control systems is perhaps most detailed in bacteria, the use of bacterial proteostasis as a drug target remains little explored. Here we describe protein aggregation as a normal physiological process and its role in bacterial virulence and we shed light on how bacteria defend themselves against the toxic threat of aggregates. We review the impact of aggregates on bacterial viability and look at the ways that bacteria use to maintain a balance between aggregation and functionality. The proteostasis in bacteria can be interrupted via overexpression of proteins, certain antibiotics such as aminoglycosides, as well as antimicrobial peptides--all leading to loss of cell viability. Therefore intracellular protein aggregation and disruption of proteostatic balance in bacteria open up another strategy that should be explored towards the discovery of new antimicrobials.
Topics: Animals; Bacteria; Bacterial Infections; Bacterial Proteins; Humans; Protein Folding; Virulence
PubMed: 23894132
DOI: 10.1099/mic.0.069575-0 -
Annual Review of Biophysics 2010Some bacteria contain organelles or microcompartments consisting of a large virion-like protein shell encapsulating sequentially acting enzymes. These organized... (Review)
Review
Some bacteria contain organelles or microcompartments consisting of a large virion-like protein shell encapsulating sequentially acting enzymes. These organized microcompartments serve to enhance or protect key metabolic pathways inside the cell. The variety of bacterial microcompartments provide diverse metabolic functions, ranging from CO(2) fixation to the degradation of small organic molecules. Yet they share an evolutionarily related shell, which is defined by a conserved protein domain that is widely distributed across the bacterial kingdom. Structural studies on a number of these bacterial microcompartment shell proteins are illuminating the architecture of the shell and highlighting its critical role in controlling molecular transport into and out of microcompartments. Current structural, evolutionary, and mechanistic ideas are discussed, along with genomic studies for exploring the function and diversity of this family of bacterial organelles.
Topics: Bacteria; Bacterial Proteins; Biological Evolution; Organelles
PubMed: 20192762
DOI: 10.1146/annurev.biophys.093008.131418 -
Microbiological Research Jan 2011Investigation of protein-protein interactions has arisen as a comprehensive approach for understanding bacterial physiology as well as pathogenesis. From this point of... (Review)
Review
Investigation of protein-protein interactions has arisen as a comprehensive approach for understanding bacterial physiology as well as pathogenesis. From this point of view, bacterial membrane as a place of contact with outer milieu seems to be crucial compartment and therefore, investigation of lipophilic proteins and their interactions is inevitable. Unfortunately, several methods developed for the analysis of protein interaction suffer from their labour intensiveness and underrepresent integral membrane proteins. Therefore, blue native polyacrylamide gel electrophoresis (BN-PAGE) with its simplicity and suitability for lipophilic entities has been widely employed in microbiological research. For investigation of membrane proteins interactions BN-PAGE became a method of choice. The efficacy in this area was proven by the elucidation not only of the stoichiometry, but also dynamic changes of several complexes involved in energetic metabolism, secretion and transport systems, localized both in inner as well as in outer membrane. Moreover, BN-PAGE was also successfully applied on peripheral membrane and cytoplasmic proteins and enabled complex analysis of interactomes of several microorganisms. This review shows BN-PAGE as a potent tool in microbiological fundamental research ranging from Archaea, through Gram-positive and Gram-negative bacteria to Chlamydia.
Topics: Archaea; Archaeal Proteins; Bacteria; Bacterial Proteins; Electrophoresis, Polyacrylamide Gel; Membrane Proteins; Protein Interaction Mapping
PubMed: 20171065
DOI: 10.1016/j.micres.2010.01.005 -
Molecular Microbiology Sep 2021Bacterial Type IV secretion systems (T4SSs) are a functionally heterogeneous group of nanomachines that can deliver substrates into a wide range of target cells. The...
Bacterial Type IV secretion systems (T4SSs) are a functionally heterogeneous group of nanomachines that can deliver substrates into a wide range of target cells. The Helicobacter pylori Cag T4SS has an important role in the pathogenesis of gastric cancer. CagA, the only effector protein known to be secreted by the H. pylori Cag T4SS, enters human gastric cells and causes alterations in intracellular signaling that are linked to cancer pathogenesis. Understanding the molecular mechanisms by which CagA is delivered into gastric cells has been hindered by the lack of robust methods for monitoring this process. A publication in this issue of Molecular Microbiology describes a split luciferase assay for monitoring T4SS-mediated translocation of CagA into host cells. The use of this translocation reporter allowed the quantification of CagA translocation in real-time assays, thereby facilitating the analysis of the kinetics of CagA delivery. This system also allowed the tracking of several types of CagA fusion proteins and confirmed that protein unfolding is important for secretion by the Cag T4SS. This commentary discusses T4SS-dependent delivery of H. pylori CagA into host cells and the use of the split luciferase system for monitoring bacterial protein secretion and delivery into target cells.
Topics: Antigens, Bacterial; Bacterial Proteins; Biological Transport; Helicobacter Infections; Helicobacter pylori; Humans; Signal Transduction; Stomach; Type IV Secretion Systems
PubMed: 34250669
DOI: 10.1111/mmi.14784 -
Molecules (Basel, Switzerland) Oct 2021Analytical ultracentrifugation is a versatile approach for analysing the molecular mass, molecular integrity (degradation/aggregation), oligomeric state and... (Comparative Study)
Comparative Study Review
Analytical ultracentrifugation is a versatile approach for analysing the molecular mass, molecular integrity (degradation/aggregation), oligomeric state and association/dissociation constants for self-association, and assay of ligand binding of kinase related membrane proteins and glycans. It has the great property of being matrix free-providing separation and analysis of macromolecular species without the need of a separation matrix or membrane or immobilisation onto a surface. This short review-designed for the non-hydrodynamic expert-examines the potential of modern sedimentation velocity and sedimentation equilibrium and the challenges posed for these molecules particularly those which have significant cytoplasmic or extracellular domains in addition to the transmembrane region. These different regions can generate different optimal requirements in terms of choice of the appropriate solvent (aqueous/detergent). We compare how analytical ultracentrifugation has contributed to our understanding of two kinase related cellular or bacterial protein/glycan systems (i) the membrane erythrocyte band 3 protein system-studied in aqueous and detergent based solvent systems-and (ii) what it has contributed so far to our understanding of the enterococcal VanS, the glycan ligand vancomycin and interactions of vancomycin with mucins from the gastrointestinal tract.
Topics: Bacteria; Bacterial Proteins; Ligands; Membrane Proteins; Molecular Weight; Polysaccharides; Protein Kinases; Ultracentrifugation
PubMed: 34641622
DOI: 10.3390/molecules26196080 -
Toxins Aug 2015Mass spectrometry has recently become a powerful technique for bacterial identification. Mass spectrometry approaches generally rely upon introduction of the bacteria... (Review)
Review
Mass spectrometry has recently become a powerful technique for bacterial identification. Mass spectrometry approaches generally rely upon introduction of the bacteria into a matrix-assisted laser-desorption time-of-flight (MALDI-TOF) mass spectrometer with mass spectrometric recognition of proteins specific to that organism that form a reliable fingerprint. With some bacteria, such as Bacillus anthracis and Clostridium botulinum, the health threat posed by these organisms is not the organism itself, but rather the protein toxins produced by the organisms. One such example is botulinum neurotoxin (BoNT), a potent neurotoxin produced by C. botulinum. There are seven known serotypes of BoNT, A-G, and many of the serotypes can be further differentiated into toxin variants, which are up to 99.9% identical in some cases. Mass spectrometric proteomic techniques have been established to differentiate the serotype or toxin variant of BoNT produced by varied strains of C. botulinum. Detection of potent biological toxins requires high analytical sensitivity and mass spectrometry based methods have been developed to determine the enzymatic activity of BoNT and the anthrax lethal toxins produced by B. anthracis. This enzymatic activity, unique for each toxin, is assessed with detection of the toxin-induced cleavage of strategically designed peptide substrates by MALDI-TOF mass spectrometry offering unparalleled specificity. Furthermore, activity assays allow for the assessment of the biological activity of a toxin and its potential health risk. Such methods have become important diagnostics for botulism and anthrax. Here, we review mass spectrometry based methods for the enzymatic activity of BoNT and the anthrax lethal factor toxin.
Topics: Antigens, Bacterial; Bacillus anthracis; Bacterial Proteins; Bacterial Toxins; Botulinum Toxins, Type A; Clostridium botulinum; Neurotoxins; Proteomics; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 26404376
DOI: 10.3390/toxins7093497