scholarly journals Elucidation of an anaerobic pathway for metabolism of l-carnitine–derived γ-butyrobetaine to trimethylamine in human gut bacteria

2021 ◽  
Vol 118 (32) ◽  
pp. e2101498118
Author(s):  
Lauren J. Rajakovich ◽  
Beverly Fu ◽  
Maud Bollenbach ◽  
Emily P. Balskus
Keyword(s):  
Gene Cluster ◽  
Human Disease ◽  
Genetic Basis ◽  
Human Gut ◽  
Metabolizing Enzymes ◽  
Associated Bacteria ◽  
Microbial Function ◽  
Dietary Nutrient ◽  
Anoxic Environment

Trimethylamine (TMA) is an important gut microbial metabolite strongly associated with human disease. There are prominent gaps in our understanding of how TMA is produced from the essential dietary nutrient l-carnitine, particularly in the anoxic environment of the human gut where oxygen-dependent l-carnitine–metabolizing enzymes are likely inactive. Here, we elucidate the chemical and genetic basis for anaerobic TMA generation from the l-carnitine–derived metabolite γ-butyrobetaine (γbb) by the human gut bacterium Emergencia timonensis. We identify a set of genes up-regulated by γbb and demonstrate that the enzymes encoded by the induced γbb utilization (bbu) gene cluster convert γbb to TMA. The key TMA-generating step is catalyzed by a previously unknown type of TMA-lyase enzyme that utilizes a putative flavin cofactor to catalyze a redox-neutral transformation. We identify additional cultured and uncultured host-associated bacteria that possess the bbu gene cluster, providing insights into the distribution of anaerobic γbb metabolism. Lastly, we present genetic, transcriptional, and metabolomic evidence that confirms the relevance of this metabolic pathway in the human gut microbiota. These analyses indicate that the anaerobic pathway is a more substantial contributor to TMA generation from l-carnitine in the human gut than the previously proposed aerobic pathway. The discovery and characterization of the bbu pathway provides the critical missing link in anaerobic metabolism of l-carnitine to TMA, enabling investigation into the connection between this microbial function and human disease.

scholarly journals Elucidation of an anaerobic pathway for metabolism of L-carnitine-derived γ-butyrobetaine to trimethylamine in human gut bacteria

2021 ◽  
Author(s):  
Lauren J. Rajakovich ◽  
Beverly Fu ◽  
Maud Bollenbach ◽  
Emily P. Balskus
Keyword(s):  
Gene Cluster ◽  
Human Disease ◽  
Gut Bacteria ◽  
Human Gut ◽  
Critical Gap ◽  
Genetic Components ◽  
Carnitine Metabolism ◽  
Dietary Nutrient ◽  
New Type ◽  
Anoxic Environment

ABSTRACTTrimethylamine (TMA) is an important gut microbial metabolite strongly associated with human disease. There are prominent gaps in our understanding of how TMA is produced from the essential dietary nutrient L-carnitine, particularly in the anoxic environment of the human gut where oxygen-dependent L-carnitine-metabolizing enzymes are likely inactive. Here, we elucidate the chemical and genetic basis for anaerobic TMA generation from the L-carnitine-derived metabolite γ-butyrobetaine (γbb) by the human gut bacterium Emergencia timonensis. We identify a set of genes upregulated by γbb and demonstrate that the enzymes encoded by the induced γbb utilization (bbu) gene cluster convert γbb to TMA. The key TMA-generating step is catalyzed by a previously unknown type of TMA-lyase enzyme that utilizes a flavin cofactor to catalyze a redox neutral transformation. We identify additional cultured and uncultured host-associated bacteria that possess the bbu gene cluster, providing insights into the distribution of anaerobic γbb metabolism. Lastly, we present genetic, transcriptional, and metabolomic evidence that confirms the relevance of this metabolic pathway in the human gut microbiota. These analyses indicate that the anaerobic pathway is a more substantial contributor to TMA generation from L-carnitine in the human gut than the previously proposed aerobic pathway. The discovery and characterization of the bbu pathway provides the critical missing link in anaerobic metabolism of L-carnitine to TMA, enabling investigation into the connection between this microbial function and human disease.SIGNIFICANCETrimethylamine (TMA) is a disease-associated metabolite produced in the human body exclusively by microbes. Gut microbes generate TMA from essential nutrients consumed in the human diet, including L-carnitine. However, our understanding of the biochemical mechanisms involved in these transformations is incomplete. In this work, we define the biochemical pathway and genetic components in gut bacteria required for anaerobic production of TMA from γ-butyrobetaine, a metabolite derived from L-carnitine. This discovery identifies a new type of TMA-producing enzyme and fills a critical gap in our knowledge of L-carnitine metabolism to TMA in the anaerobic environment of the human gut. This knowledge will enable evaluation of the link between L-carnitine metabolism and human disease, and the design of potential therapeutics.

scholarly journals Characterization and Detection of a Widely Distributed Gene Cluster That Predicts Anaerobic Choline Utilization by Human Gut Bacteria

mBio ◽  
2015 ◽  
Vol 6 (2) ◽  
Author(s):  
Ana Martínez-del Campo ◽  
Smaranda Bodea ◽  
Hilary A. Hamer ◽  
Jonathan A. Marks ◽  
Henry J. Haiser ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gene Cluster ◽  
Gut Bacteria ◽  
Functional Gene ◽  
Metagenomic Data ◽  
Human Gut ◽  
Bacterial Gene ◽  
Human Gut Microbiota ◽  
Choline Metabolism

ABSTRACTElucidation of the molecular mechanisms underlying the human gut microbiota's effects on health and disease has been complicated by difficulties in linking metabolic functions associated with the gut community as a whole to individual microorganisms and activities. Anaerobic microbial choline metabolism, a disease-associated metabolic pathway, exemplifies this challenge, as the specific human gut microorganisms responsible for this transformation have not yet been clearly identified. In this study, we established the link between a bacterial gene cluster, the choline utilization (cut) cluster, and anaerobic choline metabolism in human gut isolates by combining transcriptional, biochemical, bioinformatic, and cultivation-based approaches. Quantitative reverse transcription-PCR analysis andin vitrobiochemical characterization of twocutgene products linked the entire cluster to growth on choline and supported a model for this pathway. Analyses of sequenced bacterial genomes revealed that thecutcluster is present in many human gut bacteria, is predictive of choline utilization in sequenced isolates, and is widely but discontinuously distributed across multiple bacterial phyla. Given that bacterial phylogeny is a poor marker for choline utilization, we were prompted to develop a degenerate PCR-based method for detecting the key functional gene choline TMA-lyase (cutC) in genomic and metagenomic DNA. Using this tool, we found that new choline-metabolizing gut isolates universally possessedcutC. We also demonstrated that this gene is widespread in stool metagenomic data sets. Overall, this work represents a crucial step toward understanding anaerobic choline metabolism in the human gut microbiota and underscores the importance of examining this microbial community from a function-oriented perspective.IMPORTANCEAnaerobic choline utilization is a bacterial metabolic activity that occurs in the human gut and is linked to multiple diseases. While bacterial genes responsible for choline fermentation (thecutgene cluster) have been recently identified, there has been no characterization of these genes in human gut isolates and microbial communities. In this work, we use multiple approaches to demonstrate that the pathway encoded by thecutgenes is present and functional in a diverse range of human gut bacteria and is also widespread in stool metagenomes. We also developed a PCR-based strategy to detect a key functional gene (cutC) involved in this pathway and applied it to characterize newly isolated choline-utilizing strains. Both our analyses of thecutgene cluster and this molecular tool will aid efforts to further understand the role of choline metabolism in the human gut microbiota and its link to disease.

Model Characterization of Pulmonary Arterial Hypertension: Analysis of Lung Pathology with Respect to Human Disease

2020 ◽  
Author(s):  
◽  
Eptisam lambu
Keyword(s):  
Pulmonary Arterial Hypertension ◽  
Arterial Hypertension ◽  
Human Disease ◽  
Vascular Remodeling ◽  
Vascular Wall ◽  
Lung Pathology ◽  
Pulmonary Arterial ◽  
Lung Pathogenesis ◽  
Arterial Endothelial Cells

Pulmonary arterial hypertension (PAH) is a rare multifactorial disease characterized by abnormal high blood pressure in the pulmonary artery, or increased pulmonary vascular resistance (PVR), caused by obstruction in the small arteries of the lung. Increased PVR is also thought to be caused by abnormal vascular remodeling, due to thickening of the pulmonary vascular wall resulting from significant hypertrophy of pulmonary arterial smooth-muscle cells (PASMCs) and increased proliferation/impaired apoptosis of pulmonary arterial endothelial cells (PAECs). Herein, we investigated the mechanisms and explored molecular pathways mediating the lung pathogenesis in two PAH rat models: Monocrotaline (MCT) and Sugen5416/Hypoxia (SuHx). We analyzed these disease models to determine where the vasculature shows the most severe PAH pathology and which model best recapitulates the human disease. We investigated the role vascular remodeling, hypoxia, cell proliferation, apoptosis, DNA damage and inflammation play in the pathogenesis of PAH. Neither model recapitulated all features of the human disease, however each model presented with some of the pathology seen in PAH patients.

scholarly journals Characterization of symbiotic and associated bacteria from entomopathogenic nematode Heterorhabditis sp. (nematode: Heterorhabditidae) isolated from India

2020 ◽  
Vol 30 (1) ◽  
Author(s):  
Rashid Pervez ◽  
Showkat Ahmad Lone ◽  
Sasmita Pattnaik
Keyword(s):  
Insect Pests ◽  
Entomopathogenic Nematode ◽  
Alcaligenes Faecalis ◽  
Symbiotic Bacteria ◽  
Rrna Gene ◽  
Main Body ◽  
Associated Bacteria ◽  
Molecular Approaches

Abstract Background Entomopathogenic nematodes (EPNs) harboring symbiotic bacteria are one of the safest alternatives to the chemical insecticides for the control of various insect pests. Infective juveniles of EPNs locate a target insect, enter through the openings, and reach the hemocoel, where they release the symbiotic bacteria and the target gets killed by the virulence factors of the bacteria. Photorhabdus with Heterorhabditis spp. are well documented; little is known about the associated bacteria. Main body In this study, we explored the presence of symbiotic and associated bacteria from Heterorhabditis sp. (IISR-EPN 09) and characterized by phenotypic, biochemical, and molecular approaches. Six bacterial isolates, belonging to four different genera, were recovered and identified as follows: Photorhabdus luminescens, one each strain of Providencia vermicola, Pseudomonas entomophila, Alcaligenes aquatilis, and two strains of Alcaligenes faecalis based on the phenotypic, biochemical criteria and the sequencing of 16S rRNA gene. Conclusion P. luminescens is symbiotically associated with Heterorhabditis sp. (IISR-EPN 09), whereas P. vermicola, P. entomophila, A. aquatilis, and A. faecalis are the associated bacteria. Further studies are needed to determine the exact role of the bacterial associates with the Heterorhabditis sp.

scholarly journals Isolation and Characterization of Euglena gracilis-Associated Bacteria, Enterobacter sp. CA3 and Emticicia sp. CN5, Capable of Promoting the Growth and Paramylon Production of E. gracilis under Mixotrophic Cultivation

2021 ◽  
Vol 9 (7) ◽  
pp. 1496
Author(s):  
Rubiyatno ◽  
Kazuhiro Mori ◽  
Daisuke Inoue ◽  
Sunah Kim ◽  
Jaecheul Yu ◽  
...  
Keyword(s):  
Euglena Gracilis ◽  
Functional Foods ◽  
Mixotrophic Culture ◽  
Associated Bacteria ◽  
Isolation And Characterization ◽  
Growth Promoting ◽  
Value Functional ◽  
Mixotrophic Conditions ◽  
Microalgae Growth

Euglena gracilis produces paramylon, which is a feedstock for high-value functional foods and nutritional supplements. The enhancement of paramylon productivity is a critical challenge. Microalgae growth-promoting bacteria (MGPB) can improve microalgal productivity; however, the MGPB for E. gracilis remain unclear. This study isolated bacteria capable of enhancing E. gracilis growth and paramylon production under mixotrophic conditions. Enterobacter sp. CA3 and Emticicia sp. CN5 were isolated from E. gracilis grown with sewage-effluent bacteria under mixotrophic conditions at pH 4.5 or 7.5, respectively. In a 7-day E. gracilis mixotrophic culture with glucose, CA3 increased E. gracilis biomass and paramylon production 1.8-fold and 3.5-fold, respectively (at pH 4.5), or 1.9-fold and 3.5-fold, respectively (at pH 7.5). CN5 increased E. gracilis biomass and paramylon production 2.0-fold and 4.1-fold, respectively (at pH 7.5). However, the strains did not show such effects on E. gracilis under autotrophic conditions without glucose. The results suggest that CA3 and CN5 promoted both E. gracilis growth and paramylon production under mixotrophic conditions with glucose at pH 4.5 and 7.5 (CA3) or pH 7.5 (CN5). This study also provides an isolation method for E. gracilis MGPB that enables the construction of an effective E. gracilis–MGPB-association system for increasing the paramylon yield of E. gracilis.

scholarly journals Sequencing and characterization of the ntp gene cluster for vacuolar-type Na(+)-translocating ATPase of Enterococcus hirae

1994 ◽  
Vol 269 (15) ◽  
pp. 11037-11044
Author(s):  
K. Takase ◽  
S. Kakinuma ◽  
I. Yamato ◽  
K. Konishi ◽  
K. Igarashi ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Enterococcus Hirae

scholarly journals Transcriptome-based identification and characterization of genes responding to imidacloprid in Myzus persicae

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jianyu Meng ◽  
Xingjiang Chen ◽  
Changyu Zhang
Keyword(s):  
Genetic Basis ◽  
Expression Profiles ◽  
Control Measure ◽  
Effective Control ◽  
Agricultural Pest ◽  
Functional Classification ◽  
Quantitative Real Time Pcr ◽  
Underlying Mechanisms ◽  
Identification And Characterization

Abstract Myzus persicae is a serious and widespread agricultural pest, against which, imidacloprid remains an effective control measure. However, recent reports indicate that this aphid has evolved and developed resistance to imidacloprid. This study aimed to elucidate the underlying mechanisms and genetic basis of this resistance by conducting comparative transcriptomics studies on both imidacloprid-resistant (IR) and imidacloprid-susceptible (IS) M. persicae. The comparative analysis identified 252 differentially expressed genes (DEGs) among the IR and IS M. persicae transcriptomes. These candidate genes included 160 and 92 genes that were down- and up-regulated, respectively, in the imidacloprid-resistant strain. Using functional classification in the GO and KEGG databases, 187 DEGs were assigned to 303 functional subcategories and 100 DEGs were classified into 45 pathway groups. Moreover, several genes were associated with known insecticide targets, cuticle, metabolic processes, and oxidative phosphorylation. Quantitative real-time PCR of 10 DEGs confirmed the trends observed in the RNA sequencing expression profiles. These findings provide a valuable basis for further investigation into the complicated mechanisms of imidacloprid resistance in M. persicae.

Sign in / Sign up

Export Citation Format

Share Document