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Biomolecules Dec 2023Phytochromes are photoreceptors of plants, fungi, slime molds bacteria and heterokonts. These biliproteins sense red and far-red light and undergo light-induced changes... (Review)
Review
Phytochromes are photoreceptors of plants, fungi, slime molds bacteria and heterokonts. These biliproteins sense red and far-red light and undergo light-induced changes between the two spectral forms, Pr and Pfr. Photoconversion triggered by light induces conformational changes in the bilin chromophore around the ring C-D-connecting methine bridge and is followed by conformational changes in the protein. For plant phytochromes, multiple phytochrome interacting proteins that mediate signal transduction, nuclear translocation or protein degradation have been identified. Few interacting proteins are known as bacterial or fungal phytochromes. Here, we describe how the interacting partners were identified, what is known about the different interactions and in which context of signal transduction these interactions are to be seen. The three-dimensional arrangement of these interacting partners is not known. Using an artificial intelligence system-based modeling software, a few predicted and modulated examples of interactions of bacterial phytochromes with their interaction partners are interpreted.
Topics: Phytochrome; Bacterial Proteins; Artificial Intelligence; Plants; Signal Transduction; Light
PubMed: 38275750
DOI: 10.3390/biom14010009 -
Nature Jan 2024AlphaFold2 (ref. ) has revolutionized structural biology by accurately predicting single structures of proteins. However, a protein's biological function often depends...
AlphaFold2 (ref. ) has revolutionized structural biology by accurately predicting single structures of proteins. However, a protein's biological function often depends on multiple conformational substates, and disease-causing point mutations often cause population changes within these substates. We demonstrate that clustering a multiple-sequence alignment by sequence similarity enables AlphaFold2 to sample alternative states of known metamorphic proteins with high confidence. Using this method, named AF-Cluster, we investigated the evolutionary distribution of predicted structures for the metamorphic protein KaiB and found that predictions of both conformations were distributed in clusters across the KaiB family. We used nuclear magnetic resonance spectroscopy to confirm an AF-Cluster prediction: a cyanobacteria KaiB variant is stabilized in the opposite state compared with the more widely studied variant. To test AF-Cluster's sensitivity to point mutations, we designed and experimentally verified a set of three mutations predicted to flip KaiB from Rhodobacter sphaeroides from the ground to the fold-switched state. Finally, screening for alternative states in protein families without known fold switching identified a putative alternative state for the oxidoreductase Mpt53 in Mycobacterium tuberculosis. Further development of such bioinformatic methods in tandem with experiments will probably have a considerable impact on predicting protein energy landscapes, essential for illuminating biological function.
Topics: Cluster Analysis; Mutation; Protein Conformation; Proteins; Sequence Alignment; Machine Learning; Rhodobacter sphaeroides; Bacterial Proteins; Protein Folding
PubMed: 37956700
DOI: 10.1038/s41586-023-06832-9 -
Nature Jan 2024Bacteria encode hundreds of diverse defence systems that protect them from viral infection and inhibit phage propagation. Gabija is one of the most prevalent anti-phage...
Bacteria encode hundreds of diverse defence systems that protect them from viral infection and inhibit phage propagation. Gabija is one of the most prevalent anti-phage defence systems, occurring in more than 15% of all sequenced bacterial and archaeal genomes, but the molecular basis of how Gabija defends cells from viral infection remains poorly understood. Here we use X-ray crystallography and cryo-electron microscopy (cryo-EM) to define how Gabija proteins assemble into a supramolecular complex of around 500 kDa that degrades phage DNA. Gabija protein A (GajA) is a DNA endonuclease that tetramerizes to form the core of the anti-phage defence complex. Two sets of Gabija protein B (GajB) dimers dock at opposite sides of the complex and create a 4:4 GajA-GajB assembly (hereafter, GajAB) that is essential for phage resistance in vivo. We show that a phage-encoded protein, Gabija anti-defence 1 (Gad1), directly binds to the Gabija GajAB complex and inactivates defence. A cryo-EM structure of the virally inhibited state shows that Gad1 forms an octameric web that encases the GajAB complex and inhibits DNA recognition and cleavage. Our results reveal the structural basis of assembly of the Gabija anti-phage defence complex and define a unique mechanism of viral immune evasion.
Topics: Bacteria; Bacterial Proteins; Bacteriophages; Cryoelectron Microscopy; Crystallography, X-Ray; Deoxyribonucleases; DNA, Viral; Immune Evasion; Protein Multimerization
PubMed: 37992757
DOI: 10.1038/s41586-023-06855-2 -
MBio Jan 2024Microbes use protein toxins as important tools to attack neighboring cells, microbial or eukaryotic, and for self-killing when attacked by viruses. These toxins work...
Microbes use protein toxins as important tools to attack neighboring cells, microbial or eukaryotic, and for self-killing when attacked by viruses. These toxins work through different mechanisms to inhibit cell growth or kill cells. Microbes also use antitoxin proteins to neutralize the toxin activities. Here, we developed a comprehensive database called Toxinome of nearly two million toxins and antitoxins that are encoded in 59,475 bacterial genomes. We described the distribution of bacterial toxins and identified that they are depleted by bacteria that live in hot and cold temperatures. We found 5,161 cases in which toxins and antitoxins are densely clustered in bacterial genomes and termed these areas "Toxin Islands." The Toxinome database is a useful resource for anyone interested in toxin biology and evolution, and it can guide the discovery of new toxins.
Topics: Bacterial Proteins; Bacterial Toxins; Bacteria; Antitoxins; Genome, Bacterial
PubMed: 38117054
DOI: 10.1128/mbio.01911-23 -
Nature Communications Oct 2023The spirochete bacterial pathogen Borrelia (Borreliella) burgdorferi (Bbu) affects more than 10% of the world population and causes Lyme disease in about half a million...
The spirochete bacterial pathogen Borrelia (Borreliella) burgdorferi (Bbu) affects more than 10% of the world population and causes Lyme disease in about half a million people in the US annually. Therapy for Lyme disease includes antibiotics that target the Bbu ribosome. Here we present the structure of the Bbu 70S ribosome obtained by single particle cryo-electron microscopy at 2.9 Å resolution, revealing a bound hibernation promotion factor protein and two genetically non-annotated ribosomal proteins bS22 and bL38. The ribosomal protein uL30 in Bbu has an N-terminal α-helical extension, partly resembling the mycobacterial bL37 protein, suggesting evolution of bL37 and a shorter uL30 from a longer uL30 protein. Its analogy to proteins uL30m and mL63 in mammalian mitochondrial ribosomes also suggests a plausible evolutionary pathway for expansion of protein content in mammalian mitochondrial ribosomes. Computational binding free energy predictions for antibiotics reflect subtle distinctions in antibiotic-binding sites in the Bbu ribosome. Discovery of these features in the Bbu ribosome may enable better ribosome-targeted antibiotic design for Lyme disease treatment.
Topics: Animals; Humans; Cryoelectron Microscopy; Bacterial Proteins; Ribosomes; Ribosomal Proteins; Lyme Disease; Anti-Bacterial Agents; Mammals
PubMed: 37907464
DOI: 10.1038/s41467-023-42266-7 -
ELife Dec 2023The conformational state of a structural protein in bacteria can vary, depending on the concentration level of potassium ions or the nucleotide bound to it.
The conformational state of a structural protein in bacteria can vary, depending on the concentration level of potassium ions or the nucleotide bound to it.
Topics: Actins; Bacterial Proteins; Nucleotides; Bacteria
PubMed: 38088194
DOI: 10.7554/eLife.93719 -
Nature Reviews. Microbiology Mar 2024Considerable progress has been made in recent years in the structural and molecular biology of type IV secretion systems in Gram-negative bacteria. The latest advances... (Review)
Review
Considerable progress has been made in recent years in the structural and molecular biology of type IV secretion systems in Gram-negative bacteria. The latest advances have substantially improved our understanding of the mechanisms underlying the recruitment and delivery of DNA and protein substrates to the extracellular environment or target cells. In this Review, we aim to summarize these exciting structural and molecular biology findings and to discuss their functional implications for substrate recognition, recruitment and translocation, as well as the biogenesis of extracellular pili. We also describe adaptations necessary for deploying a breadth of processes, such as bacterial survival, host-pathogen interactions and biotic and abiotic adhesion. We highlight the functional and structural diversity that allows this extremely versatile secretion superfamily to function under different environmental conditions and in different bacterial species. Additionally, we emphasize the importance of further understanding the mechanism of type IV secretion, which will support us in combating antimicrobial resistance and treating type IV secretion system-related infections.
Topics: Type IV Secretion Systems; Fimbriae, Bacterial; Bacteria; Gram-Negative Bacteria; DNA; Bacterial Proteins
PubMed: 37814112
DOI: 10.1038/s41579-023-00974-3 -
Nature Sep 2023Many animal- and plant-pathogenic bacteria use a type III secretion system to deliver effector proteins into host cells. Elucidation of how these effector proteins...
Many animal- and plant-pathogenic bacteria use a type III secretion system to deliver effector proteins into host cells. Elucidation of how these effector proteins function in host cells is critical for understanding infectious diseases in animals and plants. The widely conserved AvrE-family effectors, including DspE in Erwinia amylovora and AvrE in Pseudomonas syringae, have a central role in the pathogenesis of diverse phytopathogenic bacteria. These conserved effectors are involved in the induction of 'water soaking' and host cell death that are conducive to bacterial multiplication in infected tissues. However, the exact biochemical functions of AvrE-family effectors have been recalcitrant to mechanistic understanding for three decades. Here we show that AvrE-family effectors fold into a β-barrel structure that resembles bacterial porins. Expression of AvrE and DspE in Xenopus oocytes results in inward and outward currents, permeability to water and osmolarity-dependent oocyte swelling and bursting. Liposome reconstitution confirmed that the DspE channel alone is sufficient to allow the passage of small molecules such as fluorescein dye. Targeted screening of chemical blockers based on the predicted pore size (15-20 Å) of the DspE channel identified polyamidoamine dendrimers as inhibitors of the DspE/AvrE channels. Notably, polyamidoamines broadly inhibit AvrE and DspE virulence activities in Xenopus oocytes and during E. amylovora and P. syringae infections. Thus, we have unravelled the biochemical function of a centrally important family of bacterial effectors with broad conceptual and practical implications in the study of bacterial pathogenesis.
Topics: Animals; Bacterial Proteins; Cell Death; Fluorescein; Liposomes; Oocytes; Plant Cells; Plant Diseases; Porins; Protein Folding; Solutions; Water; Xenopus laevis; Osmolar Concentration
PubMed: 37704725
DOI: 10.1038/s41586-023-06531-5 -
MBio Oct 2023Secreted virulence factors play a critical role in bacterial pathogenesis. Virulence effectors not only help bacteria to overcome the host immune system but also aid in...
Secreted virulence factors play a critical role in bacterial pathogenesis. Virulence effectors not only help bacteria to overcome the host immune system but also aid in establishing infection. , which causes tuberculosis in humans, encodes various virulence effectors. Triggers that modulate the secretion of virulence effectors in are yet to be fully understood. To gain mechanistic insight into the secretion of virulence effectors, we performed high-throughput proteomic studies. With the help of system-level protein-protein interaction network analysis and empirical validations, we unravelled a link between phosphorylation and secretion. Taking the example of the well-known virulence factor of CFP10, we show that the dynamics of CFP10 phosphorylation strongly influenced bacterial virulence and survival and . This study presents the role of phosphorylation in modulating the secretion of virulence factors.
Topics: Humans; Mycobacterium tuberculosis; Bacterial Proteins; Antigens, Bacterial; Phosphorylation; Virulence; Proteomics; Virulence Factors
PubMed: 37791794
DOI: 10.1128/mbio.01232-23 -
Frontiers in Immunology 2023
Topics: Humans; Female; Immunity, Mucosal; Bacterial Proteins
PubMed: 37854596
DOI: 10.3389/fimmu.2023.1282709