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Methods in Molecular Biology (Clifton,... 2017Proteins often do not function as single substances but rather as team players in a dynamic network. Growing evidence shows that protein-protein interactions are crucial...
Proteins often do not function as single substances but rather as team players in a dynamic network. Growing evidence shows that protein-protein interactions are crucial in many biological processes in living cells. Genetic (such as yeast two-hybrid, Y2H) and biochemical (such as co-immunoprecipitation, co-IP) methods are the methods commonly used at the beginning of a study to identify the interacting proteins. Immunoprecipitation (IP), a method using a target protein-specific antibody in conjunction with Protein A/G affinity beads, is a powerful tool to identify molecules that interact with specific proteins. Therefore, co-IP is considered to be one of the standard methods of identifying or confirming the occurrence of protein-protein interaction events in vivo. Co-IP experiments can identify proteins via direct or indirect interactions or in a protein complex. Here, we use Agrobacterium type VI secretion system (T6SS) sheath components TssB-TssC interaction as an example to describe the principle, procedure, and experimental problems of co-IP.
Topics: Agrobacterium; Bacterial Proteins; Immunoprecipitation; Multiprotein Complexes; Protein Binding; Protein Interaction Mapping; Proteins; Staphylococcal Protein A
PubMed: 28667615
DOI: 10.1007/978-1-4939-7033-9_17 -
Trends in Microbiology Aug 2020Colonization of the human stomach with Helicobacter pylori strains containing the cag pathogenicity island is a risk factor for development of gastric cancer. The cag... (Review)
Review
Colonization of the human stomach with Helicobacter pylori strains containing the cag pathogenicity island is a risk factor for development of gastric cancer. The cag pathogenicity island contains genes encoding a secreted effector protein (CagA) and components of a type IV secretion system (Cag T4SS). The molecular architecture of the H. pylori Cag T4SS is substantially more complex than that of prototype T4SSs in other bacterial species. In this review, we discuss recent discoveries pertaining to the structure and function of the Cag T4SS and its role in gastric cancer pathogenesis.
Topics: Animals; Antigens, Bacterial; Bacterial Proteins; Genomic Islands; Helicobacter Infections; Helicobacter pylori; Humans; Mice; Protein Conformation; Stomach; Stomach Neoplasms; Type IV Secretion Systems
PubMed: 32451226
DOI: 10.1016/j.tim.2020.02.004 -
Microbiology (Reading, England) May 2019The Type VI secretion system (T6SS) is a protein nanomachine that is widespread in Gram-negative bacteria and is used to translocate effector proteins directly into... (Review)
Review
The Type VI secretion system (T6SS) is a protein nanomachine that is widespread in Gram-negative bacteria and is used to translocate effector proteins directly into neighbouring cells. It represents a versatile bacterial weapon that can deliver effectors into distinct classes of target cells, playing key roles in inter-bacterial competition and bacterial interactions with eukaryotic cells. This versatility is underpinned by the ability of the T6SS to deliver a vast array of effector proteins, with many distinct activities and modes of interaction with the secretion machinery. Recent work has highlighted the importance and diversity of interactions mediated by T6SSs within polymicrobial communities, and offers new molecular insights into effector delivery and action in target cells.
Topics: Animals; Bacterial Proteins; Gram-Negative Bacteria; Gram-Negative Bacterial Infections; Humans; Type VI Secretion Systems
PubMed: 30893029
DOI: 10.1099/mic.0.000789 -
Vitamins and Hormones 2022Photoreceptor proteins enable living organisms to sense light and transduce this signal into biochemical outputs to elicit appropriate cellular responses. Their light... (Review)
Review
Photoreceptor proteins enable living organisms to sense light and transduce this signal into biochemical outputs to elicit appropriate cellular responses. Their light sensing is typically mediated by covalently or noncovalently bound molecules called chromophores, which absorb light of specific wavelengths and modulate protein structure and biological activity. Known photoreceptors have been classified into about ten families based on the chromophore and its associated photosensory domain in the protein. One widespread photoreceptor family uses coenzyme B or 5'-deoxyadenosylcobalamin, a biological form of vitamin B, to sense ultraviolet, blue, or green light, and its discovery revealed both a new type of photoreceptor and a novel functional facet of this vitamin, best known as an enzyme cofactor. Large strides have been made in our understanding of how these B-based photoreceptors function, high-resolution structural descriptions of their functional states are available, as are details of their unusual photochemistry. Additionally, they have inspired notable applications in optogenetics/optobiochemistry and synthetic biology. Here, we provide an overview of what is currently known about these B-based photoreceptors, their discovery, distribution, molecular mechanism of action, and the structural and photochemical basis of how they orchestrate signal transduction and gene regulation, and how they have been used to engineer optogenetic control of protein activities in living cells.
Topics: Bacterial Proteins; Humans; Vitamin B 12; Vitamins
PubMed: 35337618
DOI: 10.1016/bs.vh.2022.01.007 -
FEMS Microbiology Reviews Jan 2020Protein aggregation occurs as a consequence of perturbations in protein homeostasis that can be triggered by environmental and cellular stresses. The accumulation of... (Review)
Review
Protein aggregation occurs as a consequence of perturbations in protein homeostasis that can be triggered by environmental and cellular stresses. The accumulation of protein aggregates has been associated with aging and other pathologies in eukaryotes, and in bacteria with changes in growth rate, stress resistance and virulence. Numerous past studies, mostly performed in Escherichia coli, have led to a detailed understanding of the functions of the bacterial protein quality control machinery in preventing and reversing protein aggregation. However, more recent research points toward unexpected diversity in how phylogenetically different bacteria utilize components of this machinery to cope with protein aggregation. Furthermore, how persistent protein aggregates localize and are passed on to progeny during cell division and how their presence impacts reproduction and the fitness of bacterial populations remains a controversial field of research. Finally, although protein aggregation is generally seen as a symptom of stress, recent work suggests that aggregation of specific proteins under certain conditions can regulate gene expression and cellular resource allocation. This review discusses recent advances in understanding the consequences of protein aggregation and how this process is dealt with in bacteria, with focus on highlighting the differences and similarities observed between phylogenetically different groups of bacteria.
Topics: Bacteria; Bacterial Proteins; Gene Expression Regulation, Bacterial; Phylogeny; Protein Aggregates; Protein Folding; Species Specificity
PubMed: 31633151
DOI: 10.1093/femsre/fuz026 -
Advances in Experimental Medicine and... 2021Bacteria are able to inhabit and survive vastly diverse environments. This enormous adaptive capacity depend on their ability to perceive cues from the micro-environment...
Bacteria are able to inhabit and survive vastly diverse environments. This enormous adaptive capacity depend on their ability to perceive cues from the micro-environment and process this information accordingly to mount appropriate metabolic responses and ultimately sustain homeostasis. From systems perspective, microbial cells conceal significant degree of organismal complexity, which may only be managed by continuous bulk cellular information flow and processing, inside the cell, between other cells and the environment. In this respect, reversible covalent modification of proteins is one of the universal mode of information flow mechanism used to regulate metabolism in all organisms. More than 30 types of post translational modifications have been identified, where phosphorylation constitutes nearly half of them. Bacterial cells possess several modes of phosphoprotein mediated information flow mechanisms. Histidine kinases and two component systems, bacterial tyrosine kinases, Hanks type serine/threonine kinases, atypical serine kinases and arginine kinases have been identified in many species.
Topics: Bacteria; Bacterial Proteins; Phosphorylation; Protein Kinases; Protein Processing, Post-Translational; Protein Serine-Threonine Kinases
PubMed: 33539021
DOI: 10.1007/978-3-030-49844-3_12 -
Methods in Molecular Biology (Clifton,... 2017Protein function is generally dependent on its subcellular localisation. In Gram-negative bacteria such as Escherichia coli, a protein can be targeted to five different...
Protein function is generally dependent on its subcellular localisation. In Gram-negative bacteria such as Escherichia coli, a protein can be targeted to five different compartments: the cytoplasm, the inner membrane, the periplasm, the outer membrane and the extracellular medium. Different approaches can be used to determine the protein localisation within a cell such as in silico identification of protein signal sequences and motifs, electron microscopy and immunogold labelling, optical fluorescence microscopy, and biochemical technics. In this chapter, we describe a simple and efficient method to isolate the different compartments of Escherichia coli by a fractionation method and to determine the presence of the protein of interest. For inner membrane proteins we propose a method to discriminate between integral and peripheral membrane proteins.
Topics: Bacterial Proteins; Cell Fractionation; Escherichia coli; Gram-Negative Bacteria; Solubility
PubMed: 28667601
DOI: 10.1007/978-1-4939-7033-9_3 -
Biotechnology Advances Dec 2021Protein acetylation is an evolutionarily conserved posttranslational modification. It affects enzyme activity, metabolic flux distribution, and other critical... (Review)
Review
Protein acetylation is an evolutionarily conserved posttranslational modification. It affects enzyme activity, metabolic flux distribution, and other critical physiological and biochemical processes by altering protein size and charge. Protein acetylation may thus be a promising tool for metabolic regulation to improve target production and conversion efficiency in fermentation. Here we review the role of protein acetylation in bacterial physiology and metabolism and describe applications of protein acetylation in fermentation engineering and strategies for regulating acetylation status. Although protein acetylation has become a hot topic, the regulatory mechanisms have not been fully characterized. We propose future research directions in protein acetylation.
Topics: Acetylation; Bacteria; Bacterial Proteins; Lysine; Protein Processing, Post-Translational
PubMed: 34624455
DOI: 10.1016/j.biotechadv.2021.107842 -
Nature Reviews. Microbiology Sep 2015Distinct cellular functions are executed by separate groups of proteins, organized into complexes or functional modules, which are ultimately interconnected in cell-wide... (Review)
Review
Distinct cellular functions are executed by separate groups of proteins, organized into complexes or functional modules, which are ultimately interconnected in cell-wide protein networks. Understanding the structures and operational modes of these networks is one of the next great challenges in biology, and microorganisms are at the forefront of research in this field. In this Review, we present our current understanding of bacterial protein networks, their general properties and the tools that are used for systematically mapping and characterizing them. We then discuss two well-studied examples, the chemotaxis network and the cell cycle network in Escherichia coli, to illustrate how network architecture promotes function.
Topics: Bacterial Proteins; Gene Expression Regulation, Bacterial; Protein Interaction Maps
PubMed: 26256789
DOI: 10.1038/nrmicro3508 -
Trends in Microbiology Sep 2017Protein acetylation is a universal post-translational modification which is found in both eukaryotes and prokaryotes. This process is achieved enzymatically by the... (Review)
Review
Protein acetylation is a universal post-translational modification which is found in both eukaryotes and prokaryotes. This process is achieved enzymatically by the protein acetyltransferase Pat, and nonenzymatically by metabolic intermediates (e.g., acetyl phosphate) in bacteria. Protein acetylation plays a role in bacterial chemotaxis, metabolism, DNA replication, and other cellular processes. Recently, accumulating evidence has suggested that protein acetylation might be involved in bacterial virulence because a number of bacterial virulence factors are acetylated. In this review, we summarize the progress in understanding bacterial protein acetylation and discuss how it mediates bacterial virulence.
Topics: Acetylation; Acetyltransferases; Bacteria; Bacterial Proteins; Carbon; Nitrogen; Protein Processing, Post-Translational; Proteins; Proteomics; Virulence
PubMed: 28462789
DOI: 10.1016/j.tim.2017.04.001