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International Journal of Molecular... Jun 2023A commercial strain of () 4597 bacteria was shown to reduce food intake and promote weight loss, effects possibly induced by the bacterial protein ClpB, an...
A commercial strain of () 4597 bacteria was shown to reduce food intake and promote weight loss, effects possibly induced by the bacterial protein ClpB, an antigen-mimetic of the anorexigenic α-melanocyte-stimulating hormone. A decrease in the basal plasma glucose levels was also observed in overweight fasted humans and mice receiving . However, it is not known whether influences sweet taste preference and whether its protein extract or ClpB are sufficient to increase glucose tolerance; these are the objectives tested in the present study. C57BL/6J male mice were kept under standard diet and were gavaged daily for 17 days with a suspension of (4.5 × 10 CFU/animal) or with total protein extract (5 μg/animal) or saline as a control. Sweet taste preference was analyzed via a brief-access licking test with sucrose solution. Glucose tolerance tests (GTT) were performed after the intraperitoneal (IP) or intragastric (IG) glucose administration at the 9th and 15th days of gavage, respectively. The expression of regulatory peptides' mRNA levels was assayed in the hypothalamus. In another experiment performed in non-treated C57BL/6J male mice, effects of acute IP administration of recombinant ClpB protein on glucose tolerance were studied by both IP- and IG-GTT. Mice treated with the protein extract showed an improved glucose tolerance in IP-GTT but not in IG-GTT. Both groups treated with bacteria or protein extract showed a reduction of pancreatic tissue weight but without significant changes to basal plasma insulin. No significant effects of bacteria or its total protein extract administration were observed on the sweet taste preference, insulin tolerance and expression of regulatory peptides' mRNA in the hypothalamus. Acute administration of ClpB in non-treated mice increased glucose tolerance during the IP-GTT but not the IG-GTT, and reduced basal plasma glucose levels. We conclude that both the protein extract introduced orally and the ClpB protein administered via IP improve glucose tolerance probably by acting at the glucose postabsorptive level. Moreover, probiotic does not seem to influence the sweet taste preference. These results justify future testing of both the protein extract and ClpB protein in animal models of diabetes.
Topics: Humans; Mice; Male; Animals; Hafnia alvei; Blood Glucose; Bacterial Proteins; Mice, Inbred C57BL; Glucose; Insulins
PubMed: 37445766
DOI: 10.3390/ijms241310590 -
Biomaterials Science Nov 2023Fimbriae are long filamentous polymeric protein structures located upon the surface of bacteria. Often implicated in pathogenicity, the biosynthesis and function of... (Review)
Review
Fimbriae are long filamentous polymeric protein structures located upon the surface of bacteria. Often implicated in pathogenicity, the biosynthesis and function of fimbriae has been a productive topic of study for many decades. Evolutionary pressures have ensured that fimbriae possess unique structural and mechanical properties which are advantageous to bacteria. These properties are also difficult to engineer with well-known synthetic and natural fibres, and this has raised an intriguing question: can we exploit the unique properties of bacterial fimbriae in useful ways? Initial work has set out to explore this question by using Capsular antigen fragment 1 (Caf1), a fimbriae expressed naturally by . These fibres have evolved to 'shield' the bacterium from the immune system of an infected host, and thus are rather bioinert in nature. Caf1 is, however, very amenable to structural mutagenesis which allows the incorporation of useful bioactive functions and the modulation of the fibre's mechanical properties. Its high-yielding recombinant synthesis also ensures plentiful quantities of polymer are available to drive development. These advantageous features make Caf1 an archetype for the development of new polymers and materials based upon bacterial fimbriae. Here, we cover recent advances in this new field, and look to future possibilities of this promising biopolymer.
Topics: Antigens, Bacterial; Bacterial Proteins; Fimbriae, Bacterial; Polymers; Materials Science; Yersinia pestis
PubMed: 37791425
DOI: 10.1039/d3bm01075a -
Nature Feb 2024To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage. In...
To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage. In bacteria, two families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats and environmental stressors have confounded their discovery. Here, by combining cryogenic electron microscopy, genetics and biochemistry, we identify Balon, a new hibernation factor in the cold-adapted bacterium Psychrobacter urativorans. We show that Balon is a distant homologue of the archaeo-eukaryotic translation factor aeRF1 and is found in 20% of representative bacteria. During cold shock or stationary phase, Balon occupies the ribosomal A site in both vacant and actively translating ribosomes in complex with EF-Tu, highlighting an unexpected role for EF-Tu in the cellular stress response. Unlike typical A-site substrates, Balon binds to ribosomes in an mRNA-independent manner, initiating a new mode of ribosome hibernation that can commence while ribosomes are still engaged in protein synthesis. Our work suggests that Balon-EF-Tu-regulated ribosome hibernation is a ubiquitous bacterial stress-response mechanism, and we demonstrate that putative Balon homologues in Mycobacteria bind to ribosomes in a similar fashion. This finding calls for a revision of the current model of ribosome hibernation inferred from common model organisms and holds numerous implications for how we understand and study ribosome hibernation.
Topics: Bacterial Proteins; Peptide Elongation Factor Tu; Protein Biosynthesis; Ribosomal Proteins; Ribosomes; Psychrobacter; Cryoelectron Microscopy; Cold-Shock Response; Peptide Termination Factors
PubMed: 38355796
DOI: 10.1038/s41586-024-07041-8 -
Nucleic Acids Research Jul 2023Coordination of bacterial stress response mechanisms is critical for long-term survival in harsh environments for successful host infection. The general and specific...
Coordination of bacterial stress response mechanisms is critical for long-term survival in harsh environments for successful host infection. The general and specific stress responses of well-studied Gram-negative pathogens like Escherichia coli are controlled by alternative sigma factors, archetypically RpoS. The deadly hospital pathogen Acinetobacter baumannii is notoriously resistant to environmental stresses, yet it lacks RpoS, and the molecular mechanisms driving this incredible stress tolerance remain poorly defined. Here, using functional genomics, we identified the transcriptional regulator DksA as a master regulator for broad stress protection and virulence in A. baumannii. Transcriptomics, phenomics and in vivo animal studies revealed that DksA controls ribosomal protein expression, metabolism, mutation rates, desiccation, antibiotic resistance, and host colonization in a niche-specific manner. Phylogenetically, DksA was highly conserved and well-distributed across Gammaproteobacteria, with 96.6% containing DksA, spanning 88 families. This study lays the groundwork for understanding DksA as a major regulator of general stress response and virulence in this important pathogen.
Topics: Animals; Bacterial Proteins; Acinetobacter baumannii; Escherichia coli Proteins; Escherichia coli; Sigma Factor; Gene Expression Regulation, Bacterial
PubMed: 37158230
DOI: 10.1093/nar/gkad341 -
Journal of Bacteriology Oct 2023Membranes are a universal barrier to all cells. Phospholipids, essential bacterial membrane components, are composed of a polar head and apolar fatty acid (FA) chains....
Membranes are a universal barrier to all cells. Phospholipids, essential bacterial membrane components, are composed of a polar head and apolar fatty acid (FA) chains. Most bacterial FAs are synthesized by the Type II FA synthesis pathway (FASII). In Streptococcaceae, Enterococci, and , a unique feedback mechanism controls the FASII gene expression. FabT, encoded in the FASII main locus, is the repressor, and it is activated by long-chain acyl-acyl carrier protein (acyl-ACP). Many Streptococci, , but not , possess two ACPs. The AcpA-encoding gene is within the FASII locus and is coregulated with the FASII genes. Acyl-AcpA is the end product of FASII. The AcpB-encoding gene is in operon with encoding an acyl-ACP:phosphate acyltransferase. The role of acyl-AcpB as FabT corepressor is controversial. , which causes a wide variety of diseases ranging from mild non-invasive to severe invasive infections, possesses AcpB. In this study, by comparing the expression of FabT-controlled genes in an -deleted mutant with those in a wild-type and in a mutant strain, grown in the presence or absence of exogenous FAs, we show that AcpB is the FabT main corepressor. Its deletion impacts membrane FA composition and bacterial adhesion to eucaryotic cells, highlighting the importance of FASII control. Membrane composition is crucial for bacterial growth or interaction with the environment. Bacteria synthesize fatty acids (FAs), membrane major constituents, via the Type II FAS (FASII) pathway. Streptococci control the expression of the FASII genes via a transcriptional repressor, FabT, with acyl-acyl carrier proteins (ACPs) as corepressor. that causes a wide variety of diseases ranging from mild non-invasive to severe invasive infections possesses two ACPs. , but not , is a FASII gene. In this study, we show that acyl-AcpBs are FabT main corepressors. Also, AcpB deletion has consequences on the membrane FA composition and bacterial adhesion to host cells. In addition to highlighting the importance of FASII control in the presence of exogeneous FAs for the adaptation of bacteria to their environment, our data indicate that FASII gene repression is mediated by a corepressor whose gene expression is not repressed in the presence of exogenous FAs.
Topics: Streptococcus pyogenes; Co-Repressor Proteins; Fatty Acids; Operon; Bacterial Proteins
PubMed: 37811985
DOI: 10.1128/jb.00274-23 -
Microbiology Spectrum Aug 2023The use of antibiotics has led to the emergence of multidrug-resistant (MDR) bacteria, and there is an urgent need to find alternative treatments to alleviate this...
The use of antibiotics has led to the emergence of multidrug-resistant (MDR) bacteria, and there is an urgent need to find alternative treatments to alleviate this pressure. The type VI secretion system (T6SS) is a protein delivery system present in bacterial cells that secretes effectors that participate in bacterial virulence. Given the potential for the transformation of these effectors into antimicrobial peptides (AMPs), we designed T6SS effectors into AMPs that have a membrane-disrupting effect. These effectors kill bacteria by altering the membrane potential and increasing the intracellular reactive oxygen species (ROS) content. Moreover, AMPs also have a significant therapeutic effect both and . This finding suggests that it is possible to modify bacterial components of bacteria themselves to create compounds that fight bacteria. This study first identified and modified the T6SS effector into positively charged alpha-helical peptides. These peptides have good antibacterial and bactericidal effects on G+ bacteria and G- bacteria. This study broadens the source of AMPs and makes T6SS effectors more useful.
Topics: Type VI Secretion Systems; Bacterial Proteins; Antimicrobial Peptides; Bacteria; Anti-Bacterial Agents
PubMed: 37470717
DOI: 10.1128/spectrum.00308-23 -
MSystems Jun 2023Despite deep interest in how environments shape microbial communities, whether redox conditions influence the sequence composition of genomes is not well known. We...
Despite deep interest in how environments shape microbial communities, whether redox conditions influence the sequence composition of genomes is not well known. We predicted that the carbon oxidation state () of protein sequences would be positively correlated with redox potential (Eh). To test this prediction, we used taxonomic classifications for 68 publicly available 16S rRNA gene sequence data sets to estimate the abundances of archaeal and bacterial genomes in river & seawater, lake & pond, geothermal, hyperalkaline, groundwater, sediment, and soil environments. Locally, of community reference proteomes (i.e., all the protein sequences in each genome, weighted by taxonomic abundances but not by protein abundances) is positively correlated with Eh corrected to pH 7 (Eh7) for the majority of data sets for bacterial communities in each type of environment, and global-scale correlations are positive for bacterial communities in all environments. In contrast, archaeal communities show approximately equal frequencies of positive and negative correlations in individual data sets, and a positive pan-environmental correlation for archaea only emerges after limiting the analysis to samples with reported oxygen concentrations. These results provide empirical evidence that geochemistry modulates genome evolution and may have distinct effects on bacteria and archaea. IMPORTANCE The identification of environmental factors that influence the elemental composition of proteins has implications for understanding microbial evolution and biogeography. Millions of years of genome evolution may provide a route for protein sequences to attain incomplete equilibrium with their chemical environment. We developed new tests of this chemical adaptation hypothesis by analyzing trends of the carbon oxidation state of community reference proteomes for microbial communities in local- and global-scale redox gradients. The results provide evidence for widespread environmental shaping of the elemental composition of protein sequences at the community level and establish a rationale for using thermodynamic models as a window into geochemical effects on microbial community assembly and evolution.
Topics: Bacterial Proteins; RNA, Ribosomal, 16S; Proteome; Geologic Sediments; Phylogeny; Archaea; Bacteria; Carbon; Oxidation-Reduction
PubMed: 37289197
DOI: 10.1128/msystems.00014-23 -
Annual Review of Microbiology Sep 2023LysR-type transcriptional regulators (LTTRs) form one of the largest families of bacterial regulators. They are widely distributed and contribute to all aspects of... (Review)
Review
LysR-type transcriptional regulators (LTTRs) form one of the largest families of bacterial regulators. They are widely distributed and contribute to all aspects of metabolism and physiology. Most are homotetramers, with each subunit composed of an N-terminal DNA-binding domain followed by a long helix connecting to an effector-binding domain. LTTRs typically bind DNA in the presence or absence of a small-molecule ligand (effector). In response to cellular signals, conformational changes alter DNA interactions, contact with RNA polymerase, and sometimes contact with other proteins. Many are dual-function repressor-activators, although different modes of regulation may occur at multiple promoters. This review presents an update on the molecular basis of regulation, the complexity of regulatory schemes, and applications in biotechnology and medicine. The abundance of LTTRs reflects their versatility and importance. While a single regulatory model cannot describe all family members, a comparison of similarities and differences provides a framework for future study.
Topics: Transcription Factors; Bacterial Proteins; Bacteria; DNA; Protein Binding
PubMed: 37285554
DOI: 10.1146/annurev-micro-050323-040543 -
Microbial Physiology 2024The denitrifying betaproteobacterium Aromatoleum aromaticum EbN1T is a facultative anaerobic degradation specialist and belongs to the environmental bacteria studied... (Review)
Review
The denitrifying betaproteobacterium Aromatoleum aromaticum EbN1T is a facultative anaerobic degradation specialist and belongs to the environmental bacteria studied best on the proteogenomic level. This review summarizes the current state of knowledge about the anaerobic and aerobic degradation (to CO2) of 47 organic growth substrates (23 aromatic, 21 aliphatic, and 3 amino acids) as well as the modes of respiratory energy conservation (denitrification vs. O2-respiration). The constructed catabolic network is comprised of 256 genes, which occupy ∼7.5% of the coding regions of the genome. In total, 219 encoded proteins have been identified by differential proteomics, yielding a proteome coverage of ∼74% of the network. Its degradation section is composed of 31 peripheral and 4 central pathways, with several peripheral modules (e.g., for 4-ethylphenol, 2-phenylethylamine, indoleacetate, and phenylpropanoids) discovered only after the complete genome [Arch Microbiol. 2005 Jan;183(1):27-36] and a first proteomic survey [Proteomics. 2007 Jun;7(13):2222-39] of A. aromaticum EbN1T were reported. The activation of recalcitrant aromatic compounds involves a suite of biochemically intriguing reactions ranging from C-H-bond activation (e.g., ethylbenzene dehydrogenase) via carboxylation (e.g., acetophenone carboxylase) to oxidative deamination (e.g., benzylamine), reductive dearomatization (benzoyl-CoA), and epoxide-forming oxygenases (e.g., phenylacetyl-CoA). The peripheral reaction sequences are substrate-specifically induced, mediated by specific transcriptional regulators with in vivo response thresholds in the nanomolar range. While lipophilic substrates (e.g., phenolics) enter the cells via passive diffusion, polar ones require active uptake that is driven by specific transporters. Next to the protein repertoire for canonical complexes I-III, denitrification, and O2-respiration (low- and high-affinity oxidases), the genome encodes an Ndh-II, a tetrathionate reductase, two ETF:quinone oxidoreductases, and two Rnf-type complexes, broadening the electron transfer flexibility of the strain. Taken together, the detailed catabolic network presented here forms a solid basis for future systems biology-level studies with A. aromaticum EbN1T.
Topics: Bacterial Proteins; Anaerobiosis; Metabolic Networks and Pathways; Aerobiosis; Proteome; Proteomics; Denitrification; Rhodocyclaceae
PubMed: 37816339
DOI: 10.1159/000534425 -
Biochimica Et Biophysica Acta.... Jun 2024Iron‑sulfur (Fe-S) clusters are one of the most ancient and versatile inorganic cofactors present in the three domains of life. Fe-S clusters are essential cofactors... (Review)
Review
Iron‑sulfur (Fe-S) clusters are one of the most ancient and versatile inorganic cofactors present in the three domains of life. Fe-S clusters are essential cofactors for the activity of a large variety of metalloproteins that play crucial physiological roles. Fe-S protein biogenesis is a complex process that starts with the acquisition of the elements (iron and sulfur atoms) and their assembly into an Fe-S cluster that is subsequently inserted into the target proteins. The Fe-S protein biogenesis is ensured by multiproteic systems conserved across all domains of life. Here, we provide an overview on how bacterial genetics approaches have permitted to reveal and dissect the Fe-S protein biogenesis process in vivo.
Topics: Iron-Sulfur Proteins; Bacterial Proteins; Iron; Sulfur; Bacteria
PubMed: 38719030
DOI: 10.1016/j.bbamcr.2024.119746