A gene cluster for taurine sulfur assimilation in an anaerobic human gut bacterium

2019 ◽  
Vol 476 (15) ◽  
pp. 2271-2279 ◽  
Author(s):  
Meining Xing ◽  
Yifeng Wei ◽  
Gaoqun Hua ◽  
Mengya Li ◽  
Ankanahalli N. Nanjaraj Urs ◽  
...  
Keyword(s):  
Biochemical Characterization ◽  
Anaerobic Bacteria ◽  
Aerobic Bacteria ◽  
Sulfur Source ◽  
Sulfur Assimilation ◽  
Human Gut ◽  
Fermenting Bacteria ◽  
Facultative Anaerobic Bacteria ◽  
Reducing Bacteria

Abstract Aminoethylsulfonate (taurine) is widespread in the environment and highly abundant in the human body. Taurine and other aliphatic sulfonates serve as sulfur sources for diverse aerobic bacteria, which carry out cleavage of the inert sulfonate C–S bond through various O2-dependent mechanisms. Taurine also serves as a sulfur source for certain strict anaerobic fermenting bacteria. However, the mechanism of C–S cleavage by these bacteria has long been a mystery. Here we report the biochemical characterization of an anaerobic pathway for taurine sulfur assimilation in a strain of Clostridium butyricum from the human gut. In this pathway, taurine is first converted to hydroxyethylsulfonate (isethionate), followed by C–S cleavage by the O2-sensitive isethionate sulfo-lyase IseG, recently identified in sulfate- and sulfite-reducing bacteria. Homologs of the enzymes described in this study have a sporadic distribution in diverse strict and facultative anaerobic bacteria, from both the environment and the taurine-rich human gut, and may enable sulfonate sulfur acquisition in certain nutrient limiting conditions.

scholarly journals Two radical-dependent mechanisms for anaerobic degradation of the globally abundant organosulfur compound dihydroxypropanesulfonate

2020 ◽  
Vol 117 (27) ◽  
pp. 15599-15608 ◽  
Author(s):  
Jiayi Liu ◽  
Yifeng Wei ◽  
Lianyun Lin ◽  
Lin Teng ◽  
Jinyu Yin ◽  
...  
Keyword(s):  
Anaerobic Degradation ◽  
Organosulfur Compound ◽  
Sulfur Cycle ◽  
Marine Phytoplankton ◽  
Human Gut ◽  
Terminal Electron Acceptor ◽  
Glycyl Radical ◽  
Fermenting Bacteria ◽  
Reducing Bacteria

2(S)-dihydroxypropanesulfonate (DHPS) is a microbial degradation product of 6-deoxy-6-sulfo-d-glucopyranose (sulfoquinovose), a component of plant sulfolipid with an estimated annual production of 1010tons. DHPS is also at millimolar levels in highly abundant marine phytoplankton. Its degradation and sulfur recycling by microbes, thus, play important roles in the biogeochemical sulfur cycle. However, DHPS degradative pathways in the anaerobic biosphere are not well understood. Here, we report the discovery and characterization of two O2-sensitive glycyl radical enzymes that use distinct mechanisms for DHPS degradation. DHPS-sulfolyase (HpsG) in sulfate- and sulfite-reducing bacteria catalyzes C–S cleavage to release sulfite for use as a terminal electron acceptor in respiration, producing H2S. DHPS-dehydratase (HpfG), in fermenting bacteria, catalyzes C–O cleavage to generate 3-sulfopropionaldehyde, subsequently reduced by the NADH-dependent sulfopropionaldehyde reductase (HpfD). Both enzymes are present in bacteria from diverse environments including human gut, suggesting the contribution of enzymatic radical chemistry to sulfur flux in various anaerobic niches.

scholarly journals Identification and characterization of a new sulfoacetaldehyde reductase from the human gut bacterium Bifidobacterium kashiwanohense

2019 ◽  
Vol 39 (6) ◽  
Author(s):  
Yan Zhou ◽  
Yifeng Wei ◽  
Ankanahalli N. Nanjaraj Urs ◽  
Lianyun Lin ◽  
Tong Xu ◽  
...  
Keyword(s):  
Nitrogen Assimilation ◽  
Biochemical Characterization ◽  
Anaerobic Bacteria ◽  
Binary Complex ◽  
Active Site Residues ◽  
Human Gut ◽  
Mammalian Tissues ◽  
Environmental Bacteria ◽  
Identification And Characterization

AbstractHydroxyethylsulfonate (isethionate (Ise)) present in mammalian tissues is thought to be derived from aminoethylsulfonate (taurine), as a byproduct of taurine nitrogen assimilation by certain anaerobic bacteria inhabiting the taurine-rich mammalian gut. In previously studied pathways occurring in environmental bacteria, isethionate is generated by the enzyme sulfoacetaldehyde reductase IsfD, belonging to the short-chain dehydrogenase/reductase (SDR) family. An unrelated sulfoacetaldehyde reductase SarD, belonging to the metal-dependent alcohol dehydrogenase superfamily (M-ADH), was recently discovered in the human gut sulfite-reducing bacterium Bilophila wadsworthia (BwSarD). Here we report the structural and biochemical characterization of a sulfoacetaldehyde reductase from the human gut fermenting bacterium Bifidobacterium kashiwanohense (BkTauF). BkTauF belongs to the M-ADH family, but is distantly related to BwSarD (28% sequence identity). The crystal structures of BkTauF in the apo form and in a binary complex with NAD+ were determined at 1.9 and 3.0 Å resolution, respectively. Mutagenesis studies were carried out to investigate the involvement of active site residues in binding the sulfonate substrate. Our studies demonstrate the presence of sulfoacetaldehyde reductase in Bifidobacteria, with a possible role in isethionate production as a byproduct of taurine nitrogen assimilation.

Activation of Acetone and Other Simple Ketones in Anaerobic Bacteria

2016 ◽  
Vol 26 (1-3) ◽  
pp. 152-164 ◽  
Author(s):  
Johann Heider ◽  
Karola Schühle ◽  
Jasmin Frey ◽  
Bernhard Schink
Keyword(s):  
Energy Supply ◽  
Anaerobic Bacteria ◽  
Aerobic Bacteria ◽  
Metabolic Intermediate ◽  
Present Evidence ◽  
Sulfate Reducing ◽  
Different Types ◽  
Subsequent Degradation ◽  
Reducing Bacteria ◽  
Hydrolysis Of

Acetone and other ketones are activated for subsequent degradation through carboxylation by many nitrate-reducing, phototrophic, and obligately aerobic bacteria. Acetone carboxylation leads to acetoacetate, which is subsequently activated to a thioester and degraded via thiolysis. Two different types of acetone carboxylases have been described, which require either 2 or 4 ATP equivalents as an energy supply for the carboxylation reaction. Both enzymes appear to combine acetone enolphosphate with carbonic phosphate to form acetoacetate. A similar but more complex enzyme is known to carboxylate the aromatic ketone acetophenone, a metabolic intermediate in anaerobic ethylbenzene metabolism in denitrifying bacteria, with simultaneous hydrolysis of 2 ATP to 2 ADP. Obligately anaerobic sulfate-reducing bacteria activate acetone to a four-carbon compound as well, but via a different process than bicarbonate- or CO<sub>2</sub>-dependent carboxylation. The present evidence indicates that either carbon monoxide or a formyl residue is used as a cosubstrate, and that the overall ATP expenditure of this pathway is substantially lower than in the known acetone carboxylase reactions.

scholarly journals Characterization of a novel multidomain CE15-GH8 enzyme encoded by a polysaccharide utilization locus in the human gut bacterium Bacteroides eggerthii

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Cathleen Kmezik ◽  
Daniel Krska ◽  
Scott Mazurkewich ◽  
Johan Larsbrink
Keyword(s):  
Biochemical Characterization ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Active Enzymes ◽  
Human Gut ◽  
Glucuronoyl Esterase ◽  
Cob Biomass ◽  
Polysaccharide Utilization Loci ◽  
Hydrolase Family ◽  
Discrete Functions

AbstractBacteroidetes are efficient degraders of complex carbohydrates, much thanks to their use of polysaccharide utilization loci (PULs). An integral part of PULs are highly specialized carbohydrate-active enzymes, sometimes composed of multiple linked domains with discrete functions—multicatalytic enzymes. We present the biochemical characterization of a multicatalytic enzyme from a large PUL encoded by the gut bacterium Bacteroides eggerthii. The enzyme, BeCE15A-Rex8A, has a rare and novel architecture, with an N-terminal carbohydrate esterase family 15 (CE15) domain and a C-terminal glycoside hydrolase family 8 (GH8) domain. The CE15 domain was identified as a glucuronoyl esterase (GE), though with relatively poor activity on GE model substrates, attributed to key amino acid substitutions in the active site compared to previously studied GEs. The GH8 domain was shown to be a reducing-end xylose-releasing exo-oligoxylanase (Rex), based on having activity on xylooligosaccharides but not on longer xylan chains. The full-length BeCE15A-Rex8A enzyme and the Rex domain were capable of boosting the activity of a commercially available GH11 xylanase on corn cob biomass. Our research adds to the understanding of multicatalytic enzyme architectures and showcases the potential of discovering novel and atypical carbohydrate-active enzymes from mining PULs.

scholarly journals Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Nitzan Koppel ◽  
Jordan E Bisanz ◽  
Maria-Eirini Pandelia ◽  
Peter J Turnbaugh ◽  
Emily P Balskus
Keyword(s):  
Human Population ◽  
Biochemical Characterization ◽  
Human Gut ◽  
Plant Toxins ◽  
Bacterial Enzyme ◽  
Strict Specificity ◽  
Close Relatives ◽  
Cardiac Medication

Although the human gut microbiome plays a prominent role in xenobiotic transformation, most of the genes and enzymes responsible for this metabolism are unknown. Recently, we linked the two-gene ‘cardiac glycoside reductase’ (cgr) operon encoded by the gut Actinobacterium Eggerthella lenta to inactivation of the cardiac medication and plant natural product digoxin. Here, we compared the genomes of 25 E. lenta strains and close relatives, revealing an expanded 8-gene cgr-associated gene cluster present in all digoxin metabolizers and absent in non-metabolizers. Using heterologous expression and in vitro biochemical characterization, we discovered that a single flavin- and [4Fe-4S] cluster-dependent reductase, Cgr2, is sufficient for digoxin inactivation. Unexpectedly, Cgr2 displayed strict specificity for digoxin and other cardenolides. Quantification of cgr2 in gut microbiomes revealed that this gene is widespread and conserved in the human population. Together, these results demonstrate that human-associated gut bacteria maintain specialized enzymes that protect against ingested plant toxins.

Isolation and Characterization of Paraquat-Degrading Extracellular Humus-Reducing Bacteria from Vegetable Field

2013 ◽  
Vol 807-809 ◽  
pp. 1026-1030 ◽  
Author(s):  
Chun Yuan Wu ◽  
Jin Kun Liu ◽  
Shan Shan Chen ◽  
Xiao Deng ◽  
Qin Fen Li
Keyword(s):  
Electron Acceptor ◽  
Anaerobic Degradation ◽  
Anaerobic Bacteria ◽  
Organic Substrate ◽  
Isolation And Characterization ◽  
Vegetable Soil ◽  
Pure Cultures ◽  
Degradation Activity ◽  
Facultative Anaerobic Bacteria ◽  
Reducing Bacteria

The aim of this paper is to isolate pure cultures that are capable of degrading paraquat (PQ) anaerobically with humic substances (humus) as the sole electron acceptor. Three facultative anaerobic bacteria (PQ-1, PQ-2, and PQ-3) were successively isolated from vegetable soil in Sanya city, China, via enrichment procedure with PQ and anthraquinone-2,6-disulphonate (AQDS) under anaerobic conditions. Batch experiments were conducted to investigate isolates PQ anaerobic degradation activity. Results showed that three strains were all capable of degrading PQ directly with AQDS as the sole electron acceptor (18.6% removal within 48h), and the microbial process might be AQDS dependent. The addition of low molecular weight organic substrate, such as sucrose, could enhance the anaerobic degradation of PQ from 18.6% to 34.2%, and the degradation rate reached 100% after 5-day incubation. This study was the first paper reporting that pure cultures have the ability to anaerobically degrade PQ with AQDS as the sole electron acceptor.

Formation and structure of granulated microbial aggregates used in aerobic wastewater treatment

2005 ◽  
Vol 52 (7) ◽  
pp. 13-19 ◽  
Author(s):  
V. Ivanov ◽  
S.T.-L. Tay ◽  
Q.-S. Liu ◽  
X.-H. Wang ◽  
Z.-W. Wang ◽  
...  
Keyword(s):  
Microbial Biomass ◽  
Anaerobic Bacteria ◽  
Cell Surface Hydrophobicity ◽  
Surface Hydrophobicity ◽  
Aerobic Bacteria ◽  
Structural Elements ◽  
Aerobic Wastewater Treatment ◽  
Obligate Anaerobic ◽  
Facultative Anaerobic Bacteria ◽  
Self Aggregation

Granular microbial aggregates are used in aerobic treatment of wastewater. The granules have diverse microbial community and complex spatial structure. The structural elements are radial sub-aggregates, concentric layers, channels, pores, polysaccharide plugs, and an anaerobic core of lysed cells. Aerobic bacteria, consisting of 69–84% of microbial biomass, were concentrated in a layer to the depth of 550 μm from the surface of the granule. Facultative anaerobic bacteria, consisting of 9–13% of microbial biomass, dominated in a layer at a depth from 550 μm to 850 μm from the surface of the granule. Obligate anaerobic bacteria, consisting of 2% of microbial biomass, dominated in a layer on the depth from 850 μm to 1,000 μm from the surface of the granule. A core of dead and lysed cells was at a depth greater than 1,000 μm from the surface of the granule. The depth of the anaerobic layer correlated with the appearance of polysaccharide plugs in the pores. Enrichment cultures of microorganisms with high cell surface hydrophobicity or self-aggregation ability can be used to facilitate the formation of microbial granules.

scholarly journals A ferredoxin-dependent dihydropyrimidine dehydrogenase in Clostridium chromiireducens

2020 ◽  
Vol 40 (7) ◽  
Author(s):  
Feifei Wang ◽  
Yifeng Wei ◽  
Qiang Lu ◽  
Ee Lui Ang ◽  
Huimin Zhao ◽  
...  
Keyword(s):  
Anaerobic Bacterium ◽  
Methyl Viologen ◽  
Flavin Adenine Dinucleotide ◽  
Biochemical Characterization ◽  
Dihydropyrimidine Dehydrogenase ◽  
Anaerobic Bacteria ◽  
Gene Clusters ◽  
Flavin Mononucleotide ◽  
Pyrimidine Degradation

Abstract Dihydropyrimidine dehydrogenase (PydA) catalyzes the first step of the reductive pyrimidine degradation (Pyd) pathway in bacteria and eukaryotes, enabling pyrimidines to be utilized as substrates for growth. PydA homologs studied to date catalyze the reduction of uracil to dihydrouracil, coupled to the oxidation of NAD(P)H. Uracil reduction occurs at a flavin mononucleotide (FMN) site, and NAD(P)H oxidation occurs at a flavin adenine dinucleotide (FAD) site, with two ferredoxin domains thought to mediate inter-site electron transfer. Here, we report the biochemical characterization of a Clostridial PydA homolog (PydAc) from a Pyd gene cluster in the strict anaerobic bacterium Clostridium chromiireducens. PydAc lacks the FAD domain, and instead is able to catalyze uracil reduction using reduced methyl viologen or reduced ferredoxin as the electron source. Homologs of PydAc are present in Pyd gene clusters in many strict anaerobic bacteria, which use reduced ferredoxin as an intermediate in their energy metabolism.

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