Bacterial Microcompartment-Dependent 1,2-Propanediol Utilization of Propionibacterium freudenreichii

Bacterial microcompartments (BMCs) are proteinaceous prokaryotic organelles that enable the utilization of substrates such as 1,2-propanediol and ethanolamine. BMCs are mostly linked to the survival of particular pathogenic bacteria by providing a growth advantage through utilization of 1,2-propanediol and ethanolamine which are abundantly present in the human gut. Although a 1,2-propanediol utilization cluster was found in the probiotic bacterium Propionibacterium freudenreichii, BMC-mediated metabolism of 1,2-propanediol has not been demonstrated experimentally in P. freudenreichii. In this study we show that P. freudenreichii DSM 20271 metabolizes 1,2-propanediol in anaerobic conditions to propionate and 1-propanol. Furthermore, 1,2-propanediol induced the formation of BMCs, which were visualized by transmission electron microscopy and resembled BMCs found in other bacteria. Proteomic analysis of 1,2-propanediol grown cells compared to L-lactate grown cells showed significant upregulation of proteins involved in propanediol-utilization (pdu-cluster), DNA repair mechanisms and BMC shell proteins while proteins involved in oxidative phosphorylation were down-regulated. 1,2-Propanediol utilizing cells actively produced vitamin B12 (cobalamin) in similar amounts as cells growing on L-lactate. The ability to metabolize 1,2-propanediol may have implications for human gut colonization and modulation, and can potentially aid in delivering propionate and vitamin B12in situ.

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Anaerobic growth of Listeria monocytogenes on rhamnose is stimulated by Vitamin B12 and bacterial microcompartment dependent 1,2-propanediol utilization

10.1101/2021.04.20.440696 ◽

2021 ◽

Author(s):

Zhe Zeng ◽

Siming Li ◽

Sjef Boeren ◽

Eddy J. Smid ◽

Richard A. Notebaart ◽

...

Keyword(s):

Listeria Monocytogenes ◽

Vitamin B12 ◽

Anaerobic Growth ◽

Physiological Effects ◽

Human Intestine ◽

Human Pathogens ◽

Bacterial Microcompartment ◽

Food Borne ◽

Transmission Electron ◽

Shell Proteins

AbstractThe food-borne pathogen Listeria monocytogenes is able to form proteinaceous organelles called bacterial microcompartments (BMCs) that optimize the utilization of substrates, such as 1,2-propanediol, and confer an anaerobic growth advantage. Rhamnose is a deoxyhexose sugar abundant in a range of environments including the human intestine, and can be degraded in anaerobic conditions into 1,2-propanediol, next to acetate and lactate. Rhamnose-derived 1,2-propanediol has been found to link with BMCs in a limited number of commensal human colonic species and some human pathogens such as Salmonella enterica, but the involvement of BMCs in rhamnose metabolism and potential physiological effects on L. monocytogenes are still unknown. In this study, we firstly test the effect of rhamnose uptake and utilization on anaerobic growth of L. monocytogenes EGDe without and with added vitamin B12, followed by metabolic analysis. We unveil that the vitamin B12-dependent activation of pdu stimulates metabolism and anaerobic growth of L. monocytogenes EGDe on rhamnose via 1,2-propanediol degradation into 1-propanol and propionate. Transmission electron microscopy of pdu-induced cells shows that BMCs are formed and additional proteomics experiments confirm expression of pdu BMC shell proteins and enzymes. Finally, we discuss physiological effects and energy efficiency of L. monocytogenes pdu BMC-driven anaerobic rhamnose metabolism and impact on competitive fitness in environments such as the human intestine.

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Metabolic profiling analysis of the vitamin B 12 producer Propionibacterium freudenreichii

MicrobiologyOpen ◽

10.1002/mbo3.1199 ◽

2021 ◽

Vol 10 (3) ◽

Author(s):

Jiao Liu ◽

Yongfei Liu ◽

Jie Wu ◽

Huan Fang ◽

Zhaoxia Jin ◽

...

Keyword(s):

Metabolic Profiling ◽

Vitamin B ◽

Propionibacterium Freudenreichii ◽

Metabolic Profiling Analysis ◽

Vitamin B 12 ◽

Profiling Analysis

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Levofloxacin and Moxifloxacin Increase Human Gut Colonization by Candida Species

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.50.1.405.2006 ◽

2006 ◽

Vol 50 (1) ◽

pp. 405-405

Keyword(s):

Candida Species ◽

Human Gut ◽

Gut Colonization

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Engineering Bacterial Microcompartment Shells: Chimeric Shell Proteins and Chimeric Carboxysome Shells

ACS Synthetic Biology ◽

10.1021/sb500226j ◽

2014 ◽

Vol 4 (4) ◽

pp. 444-453 ◽

Cited By ~ 58

Author(s):

Fei Cai ◽

Markus Sutter ◽

Susan L. Bernstein ◽

James N. Kinney ◽

Cheryl A. Kerfeld

Keyword(s):

Bacterial Microcompartment ◽

Shell Proteins

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A Bacterial Microcompartment Is Used for Choline Fermentation byEscherichia coli536

Journal of Bacteriology ◽

10.1128/jb.00764-17 ◽

2018 ◽

Vol 200 (10) ◽

Cited By ~ 12

Author(s):

Taylor I. Herring ◽

Tiffany N. Harris ◽

Chiranjit Chowdhury ◽

Sujit Kumar Mohanty ◽

Thomas A. Bobik

Keyword(s):

Electron Microscopy ◽

Heart Disease ◽

Gene Cluster ◽

Transcriptional Regulator ◽

Human Gut ◽

Content Type ◽

E Coli ◽

Bacterial Microcompartment ◽

New Type ◽

Insight Into

ABSTRACTBacterial choline degradation in the human gut has been associated with cancer and heart disease. In addition, recent studies found that a bacterial microcompartment is involved in choline utilization byProteusandDesulfovibriospecies. However, many aspects of this process have not been fully defined. Here, we investigate choline degradation by the uropathogenEscherichia coli536. Growth studies indicatedE. coli536 degrades choline primarily by fermentation. Electron microscopy indicated that a bacterial microcompartment was used for this process. Bioinformatic analyses suggested that the choline utilization (cut) gene cluster ofE. coli536 includes two operons, one containing three genes and a main operon of 13 genes. Regulatory studies indicate that thecutXgene encodes a positive transcriptional regulator required for induction of the maincutoperon in response to choline supplementation. Each of the 16 genes in thecutcluster was individually deleted, and phenotypes were examined. ThecutX,cutY,cutF,cutO,cutC,cutD,cutU, andcutVgenes were required for choline degradation, but the remaining genes of thecutcluster were not essential under the conditions used. The reasons for these varied phenotypes are discussed.IMPORTANCEHere, we investigate choline degradation inE. coli536. These studies provide a basis for understanding a new type of bacterial microcompartment and may provide deeper insight into the link between choline degradation in the human gut and cancer and heart disease. These are also the first studies of choline degradation inE. coli536, an organism for which sophisticated genetic analysis methods are available. In addition, thecutgene cluster ofE. coli536 is located in pathogenicity island II (PAI-II536) and hence might contribute to pathogenesis.

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Potential Decontamination of Drinking Water Pathogens through k-Carrageenan Integrated Green Bottle Fly Bio-Synthesized Silver Nanoparticles

Molecules ◽

10.3390/molecules25081936 ◽

2020 ◽

Vol 25 (8) ◽

pp. 1936 ◽

Cited By ~ 1

Author(s):

M. A. Abu-Saied ◽

Mohamed Elnouby ◽

Tarek Taha ◽

Muhammad El-shafeey ◽

Ali G. Alshehri ◽

...

Keyword(s):

Electron Microscopy ◽

Antimicrobial Activity ◽

Silver Nanoparticles ◽

Drinking Water ◽

Pathogenic Bacteria ◽

Polymeric Nanoparticles ◽

Wide Distribution ◽

Spectrophotometric Analysis ◽

Transmission Electron ◽

Green Bottle

The wide distribution of infections-related pathogenic microbes is almost related to the contamination of food and/or drinking water. The current applied treatments face some limitations. In the current study, k-carrageenan polymer was used as supporting material for the proper/unreleased silver nanoparticles that showed strong antimicrobial activity against six pathogenic bacteria and yeast. The bio-extract of the pupa of green bottle fly was used as the main agent for the synthesis of silver nanoparticles. The qualitative investigation of biologically synthesized silver nanoparticles was determined using UV-Vis spectrophotometric analysis; however, the size of nanoparticles was in range of 30–100 nm, as confirmed by scanning electron microscopy (SEM), transmission electron microscopy (TEM), and particle size analyzer. The proper integration of silver nanoparticles into the polymeric substrate was also characterized through fourier transform infrared (FT-IR), thermogravimetric analysis (TGA), SEM, and tensile strength. The antimicrobial activity of k-carrageenan/silver nanoparticles against Gram positive, Gram negative, and yeast pathogens was highly effective. These results indicate the probable exploitation of the polymeric/nanoparticles composite as an extra stage in water purification systems in homes or even at water treatment plants.

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Potential of Inulin-Fructooligosaccharides Extract Produced from Red Onion (Allium cepa var. viviparum (Metz) Mansf.) as an Alternative Prebiotic Product

Plants ◽

10.3390/plants10112401 ◽

2021 ◽

Vol 10 (11) ◽

pp. 2401

Author(s):

Jakkrit Aisara ◽

Pairote Wongputtisin ◽

Somkid Deejing ◽

Chutamas Maneewong ◽

Kridsada Unban ◽

...

Keyword(s):

Pathogenic Bacteria ◽

Probiotic Bacterium ◽

Degree Of Polymerization ◽

Inhibitory Effects ◽

Commercial Cultivation ◽

Gastrointestinal Conditions ◽

Free Glucose ◽

Probiotic Lactobacilli ◽

Bifidogenic Effect

Red onion is a popular ingredient in many Thai dishes and has recently been promoted for commercial cultivation. In this study, inulin-fructooligosaccharides (inulin-FOSs) were extracted from red onions in a simplified extraction method. The extract contained 24.00 ± 0.38 g/L free glucose, fructose and sucrose, while the level of FOSs was recorded at 74.0 ± 2.80 g/L with a degree of polymerization of 4.1. The extract was resistant to simulated gastrointestinal conditions, while selectively promoting probiotic lactobacilli. These outcomes resulted in inhibitory effects against various pathogenic bacteria. The in vitro batch culture fermentation of the extract by natural mixed culture indicated that an unknown sugar identified as neokestose was more rapidly fermented than 1-kestose and other longer-chain inulin-FOSs. Notably, neokestose selectively encouraged a bifidogenic effect, specifically in terms of the growth of Bifidobacteirum breve, which is an infant-type probiotic bacterium. This is the first report to state that neokestose could selectively enhance the bifidogenic effect. In summary, inulin-FOSs extract should be recognized as a multifunctional ingredient that can offer benefits in food and pharmaceutical applications.

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Linking the Salmonella enterica 1,2-propanediol utilization bacterial microcompartment shell to the enzymatic core via the shell protein PduB

10.1101/2021.10.27.466122 ◽

2021 ◽

Author(s):

Nolan W Kennedy ◽

Carolyn E Mills ◽

Charlotte H Abrahamson ◽

Andre Archer ◽

Michael C Jewett ◽

...

Keyword(s):

Salmonella Enterica ◽

Carbon Sources ◽

Enzyme Concentration ◽

Fluorescent Reporters ◽

Shell Protein ◽

Bacterial Microcompartment ◽

Enzyme Encapsulation ◽

Transmission Electron ◽

Serovar Typhimurium ◽

Enzymatic Machinery

Bacterial microcompartments (MCPs) are protein-based organelles that house the enzymatic machinery for metabolism of niche carbon sources, allowing enteric pathogens to outcompete native microbiota during host colonization. While much progress has been made toward understanding MCP biogenesis, questions still remain regarding the mechanism by which core MCP enzymes are enveloped within the MCP protein shell. Here we explore the hypothesis that the shell protein PduB is responsible for linking the shell of the 1,2-propanediol utilization (Pdu) MCP from Salmonella enterica serovar Typhimurium LT2 to its enzymatic core. Using fluorescent reporters, we demonstrate that all members of the Pdu enzymatic core are encapsulated in Pdu MCPs. We also demonstrate that PduB is the sole protein responsible for linking the entire Pdu enzyme core to the MCP shell. Using MCP purifications, transmission electron microscopy, and fluorescence microscopy we find that shell assembly can be decoupled from the enzymatic core, as apparently empty MCPs are formed in Salmonella strains lacking PduB. Mutagenesis studies also reveal that PduB is incorporated into the Pdu MCP shell via a conserved, lysine-mediated hydrogen bonding mechanism. Finally, growth assays and systems-level pathway modeling reveal that unencapsulated pathway performance is strongly impacted by enzyme concentration, highlighting the importance of minimizing polar effects when conducting these functional assays. Together, these results provide insight into the mechanism of enzyme encapsulation within Pdu MCPs and demonstrate that the process of enzyme encapsulation and shell assembly are separate processes in this system, a finding that will aid future efforts to understand MCP biogenesis.

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Identification and Regulation of a Novel Citrobacter rodentium Gut Colonization Fimbria (Gcf)

Journal of Bacteriology ◽

10.1128/jb.02486-14 ◽

2015 ◽

Vol 197 (8) ◽

pp. 1478-1491 ◽

Cited By ~ 2

Author(s):

Gustavo G. Caballero-Flores ◽

Matthew A. Croxen ◽

Verónica I. Martínez-Santos ◽

B. Brett Finlay ◽

José L. Puente

Keyword(s):

Escherichia Coli ◽

Intestinal Epithelium ◽

Pathogenic Bacteria ◽

Critical Role ◽

Growth Conditions ◽

Citrobacter Rodentium ◽

Content Type ◽

Gut Colonization ◽

Successful Infection

ABSTRACTThe Gram-negative enteric bacteriumCitrobacter rodentiumis a natural mouse pathogen that has been extensively used as a surrogate model for studying the human pathogens enteropathogenic and enterohemorrhagicEscherichia coli. All three pathogens produce similar attaching and effacing (A/E) lesions in the intestinal epithelium. During infection, these bacteria employ surface structures called fimbriae to adhere and colonize the host intestinal epithelium. ForC. rodentium, the roles of only a small number of its genome-carried fimbrial operons have been evaluated. Here, we report the identification of a novelC. rodentiumcolonization factor, calledgutcolonizationfimbria (Gcf), which is encoded by a chaperone-usher fimbrial operon. AgcfAmutant shows a severe colonization defect within the first 10 days of infection. Thegcfpromoter is not active inC. rodentiumunder severalin vitrogrowth conditions; however, it is readily expressed in aC. rodentiumΔhns1mutant lacking the closest ortholog of theEscherichia colihistone-like nucleoid structuring protein (H-NS) but not in mutants with deletion of the other four genes encoding H-NS homologs. H-NS binds to the regulatory region ofgcf, further supporting its direct role as a repressor of thegcfpromoter that starts transcription 158 bp upstream of the start codon of its first open reading frame. Thegcfoperon possesses interesting novel traits that open future opportunities to expand our knowledge of the structure, regulation, and function during infection of these important bacterial structures.IMPORTANCEFimbriae are surface bacterial structures implicated in a variety of biological processes. Some have been shown to play a critical role during host colonization and thus in disease. Pathogenic bacteria possess the genetic information for an assortment of fimbriae, but their function and regulation and the interplay between them have not been studied in detail. This work provides new insights into the function and regulation of a novel fimbria called Gcf that is important for early establishment of a successful infection byC. rodentiumin mice, despite being poorly expressed underin vitrogrowth conditions. This discovery offers an opportunity to better understand the individual role and the regulatory mechanisms controlling the expression of specific fimbrial operons that are critical during infection.

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Bacteroidales Secreted Antimicrobial Proteins Target Surface Molecules Necessary for Gut Colonization and Mediate Competition In Vivo

mBio ◽

10.1128/mbio.01055-16 ◽

2016 ◽

Vol 7 (4) ◽

Cited By ~ 34

Author(s):

Kevin G. Roelofs ◽

Michael J. Coyne ◽

Rahul R. Gentyala ◽

Maria Chatzidaki-Livanis ◽

Laurie E. Comstock

Keyword(s):

Sequence Similarity ◽

Interference Competition ◽

Sensitive Strain ◽

Strain Level ◽

Surface Molecule ◽

Antimicrobial Proteins ◽

Human Gut ◽

Gut Colonization ◽

Target Molecules

ABSTRACT We recently showed that human gut Bacteroidales species secrete antimicrobial proteins (BSAPs), and we characterized in vitro the first such BSAP produced by Bacteroides fragilis . In this study, we identified a second potent BSAP produced by the ubiquitous and abundant human gut species Bacteroides uniformis . The two BSAPs contain a membrane attack complex/perforin (MACPF) domain but share very little sequence similarity. We identified the target molecules of BSAP-sensitive cells and showed that each BSAP targets a different class of surface molecule: BSAP-1 targets an outer membrane protein of sensitive B. fragilis strains, and BSAP-2 targets the O-antigen glycan of lipopolysaccharide (LPS) of sensitive B. uniformis strains. Species-wide genomic and phenotypic analyses of B. fragilis and B. uniformis showed that BSAP-producing strains circumvent killing by synthesizing an orthologous nontargeted surface molecule. The BSAP genes are adjacent to the gene(s) encoding their target replacements, suggesting coacquisition. Using a gnotobiotic mouse competitive-colonization model, we found that the BSAP surface targets are important for colonization of the mammalian gut, thereby explaining why they are maintained in sensitive strains and why they were replaced rather than deleted in BSAP-producing strains. Using isogenic BSAP-producing, -sensitive, and -resistant strains, we show that a BSAP-producing strain outcompetes a sensitive strain but not a resistant strain in the mammalian gut. Human gut metagenomic datasets reveal that BSAP-1-sensitive strains do not cooccur with BSAP-1-producing strains in human gut microbiotas, further supporting the idea that BSAPs are important competitive factors with relevance to the strain-level composition of the human gut microbiota. IMPORTANCE We know relatively little about the ecology of the human intestinal microbiota and the combination of factors that dictate which strains and species occupy an individual’s gut microbial community. Interference competition, mediated by bacterial factors that directly harm other members, is beginning to be appreciated as important in contributing to species- and strain-level dynamics of abundant gut bacteria. Here, we show that gut Bacteroidales secrete antimicrobial proteins (BSAPs) that antagonize strains of the same species. We show that BSAPs target molecules of sensitive cells that are important for gut colonization and therefore are maintained in sensitive cells. In an experimental animal model of gut colonization, a BSAP-1-producing strain antagonized and outcompeted an isogenic sensitive strain. Furthermore, metagenomic analyses showed that BSAP-1-producing and -sensitive strains are not found together in human gut microbiotas. These data suggest that BSAPs are strong ecological drivers shaping the strain-level composition of gut communities.

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