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Hunter SM, Blanco E, Borrion A. Expanding the anaerobic digestion map: A review of intermediates in the digestion of food waste. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 767:144265. [PMID: 33422959 DOI: 10.1016/j.scitotenv.2020.144265] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Anaerobic digestion is a promising technology as a renewable source of energy products, but these products have low economic value and process control is challenging. Identifying intermediates formed throughout the process could enhance understanding and offer opportunities for improved monitoring, control, and valorisation. In this review, intermediates present in the anaerobic digestion process are identified and discussed, including the following: volatile fatty acids, carboxylic acid, amino acids, furans, terpenes and phytochemicals. The key limitations associated with exploiting these intermediates are also addressed including challenging mixed cultures of microbiology, complex feedstocks, and difficult extraction and separation techniques.
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Affiliation(s)
- Sarah M Hunter
- Department of Civil, Environmental and Geomatic Engineering, University College London, UK
| | - Edgar Blanco
- Anaero Technology Limited, Cowley Road, Cambridge, UK
| | - Aiduan Borrion
- Department of Civil, Environmental and Geomatic Engineering, University College London, UK.
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Qiang W, Xuan H, Yu S, Hailun P, Yueli Z, Zhiguo P, Lei S. Impact of the gut microbiota on heat stroke rat mediated by Xuebijing metabolism. Microb Pathog 2021; 155:104861. [PMID: 33864878 DOI: 10.1016/j.micpath.2021.104861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 12/17/2022]
Abstract
The goal of the present study was to evaluate the fecal microbiome and serum metabolites in Xuebijing (XBJ)-injected rats after heat stroke using 16S rRNA gene sequencing and gas chromatography-mass spectrometry (GC-MS) metabolomics. Eighteen rats were divided into the control group (CON), heat stroke group (HS), and XBJ group. The 16S rRNA gene sequencing results revealed that the abundance of Bacteroidetes was overrepresented in the XBJ group compared to the HS group, while Actinobacteria was underrepresented. Metabolomic profiling showed that the pyrimidine metabolism pathway, pentose phosphate pathway, and glycerophospholipid metabolism pathway were upregulated in the XBJ group compared to the HS group. Taken together, these results demonstrated that heat stroke not only altered the gut microbiome community structure of rats but also greatly affected metabolic functions, leading to gut microbiome toxicity.
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Affiliation(s)
- Wen Qiang
- The First Clinical Medical College, Southern Medical University, Guangzhou, China; Department of Critical Care Medicine, General Hospital of Guangzhou Military Command, Guangzhou, China
| | - He Xuan
- Department of Critical Care Medicine, General Hospital of Guangzhou Military Command, Guangzhou, China
| | - Shao Yu
- Second Department of Internal Medicine for Cadres, General Hospital of Guangzhou Military Command, China
| | - Peng Hailun
- The First Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Zhao Yueli
- Graduate School, Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Pan Zhiguo
- The First Clinical Medical College, Southern Medical University, Guangzhou, China; Department of Critical Care Medicine, General Hospital of Guangzhou Military Command, Guangzhou, China.
| | - Su Lei
- The First Clinical Medical College, Southern Medical University, Guangzhou, China; Department of Critical Care Medicine, General Hospital of Guangzhou Military Command, Guangzhou, China.
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Metabolomics analysis of gut barrier dysfunction in a trauma-hemorrhagic shock rat model. Biosci Rep 2019; 39:BSR20181215. [PMID: 30393232 PMCID: PMC6328858 DOI: 10.1042/bsr20181215] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 09/30/2018] [Accepted: 10/10/2018] [Indexed: 12/12/2022] Open
Abstract
Intestinal barrier dysfunction has been implicated in the development of multiorgan dysfunction syndrome caused by the trauma-hemorrhagic shock (THS). However, the mechanisms underlying THS-induced gut barrier injury are still poorly understood. In the present study, we used the metabolomics analysis to test the hypothesis that altered metabolites might be related to the development of THS-induced barrier dysfunction in the large intestine. Under the induction of THS, gut barrier failure was characterized by injury of permeability and mucus layer, which were companied by the decreased expression of zonula occludens-1 in the colon and increased levels of inflammatory factors including tumor necrosis factor-α, interferon-γ, interleukin (IL)-6, and IL-1β in the serum. A total of 16 differential metabolites were identified in colonic tissues from THS-treated rats compared with control rats. These altered metabolites included dihydroxy acetone phosphate, ribose-5-phosphate, fructose, glyceric acid, succinic acid, and adenosine, which are critical intermediates or end products that are involved in pentose phosphate pathway, glycolysis, and tricarboxylic acid cycle as well as mitochondrial adenosine triphosphate biosynthesis. These findings may offer important insight into the metabolic alterations in THS-treated gut injury, which will be helpful for developing effective metabolites-based strategies to prevent THS-induced gut barrier dysfunction.
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Wang Y, Brown CA, Chen R. Industrial production, application, microbial biosynthesis and degradation of furanic compound, hydroxymethylfurfural (HMF). AIMS Microbiol 2018; 4:261-273. [PMID: 31294214 PMCID: PMC6604932 DOI: 10.3934/microbiol.2018.2.261] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/12/2018] [Indexed: 12/20/2022] Open
Abstract
Biorefinery is increasingly embraced as an environmentally friendly approach that has the potential to shift current petroleum-based chemical and material manufacture to renewable sources. Furanic compounds, particularly hydroxymethylfurfurals (HMFs) are platform chemicals, from which a variety of value-added chemicals can be derived. Their biomanufacture and biodegradation therefore will have a large impact. Here, we first review the potential industrial production of 4-HMF and 5-HMF, then we summarize the known microbial biosynthesis and biodegradation pathways of furanic compounds with emphasis on the enzymes in each pathway. We especially focus on the structure, function and catalytic mechanism of MfnB (4-(hydroxymethyl)-2-furancarboxyaldehyde-phosphate synthase) and hmfH (HMF oxidase), which catalyze the formation of phosphorylated 4-HMF and the oxidation of 5-HMF to furandicarboxylic acid (2,5-FDCA), respectively. Understanding the structure-function relationship of these enzymes will provide important insights in enzyme engineering, which eventually will find industry applications in mass-production of biobased polymers and other bulk chemicals in future.
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Affiliation(s)
- Yu Wang
- Department of Chemistry and Biochemistry, University of North Georgia-Dahlonega, Dahlonega, GA, 30597, USA
| | - Caroline A Brown
- Department of Chemistry and Biochemistry, University of North Georgia-Dahlonega, Dahlonega, GA, 30597, USA
| | - Rachel Chen
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2017; 2017:9763848. [PMID: 28133437 PMCID: PMC5241448 DOI: 10.1155/2017/9763848] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/17/2016] [Accepted: 11/01/2016] [Indexed: 02/07/2023]
Abstract
Decades of biochemical, bioinformatic, and sequencing data are currently being systematically compiled into genome-scale metabolic reconstructions (GEMs). Such reconstructions are knowledge-bases useful for engineering, modeling, and comparative analysis. Here we review the fifteen GEMs of archaeal species that have been constructed to date. They represent primarily members of the Euryarchaeota with three-quarters comprising representative of methanogens. Unlike other reviews on GEMs, we specially focus on archaea. We briefly review the GEM construction process and the genealogy of the archaeal models. The major insights gained during the construction of these models are then reviewed with specific focus on novel metabolic pathway predictions and growth characteristics. Metabolic pathway usage is discussed in the context of the composition of each organism's biomass and their specific energy and growth requirements. We show how the metabolic models can be used to study the evolution of metabolism in archaea. Conservation of particular metabolic pathways can be studied by comparing reactions using the genes associated with their enzymes. This demonstrates the utility of GEMs to evolutionary studies, far beyond their original purpose of metabolic modeling; however, much needs to be done before archaeal models are as extensively complete as those for bacteria.
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Peterson JR, Thor S, Kohler L, Kohler PR, Metcalf WW, Luthey-Schulten Z. Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans. BMC Genomics 2016; 17:924. [PMID: 27852217 PMCID: PMC5112694 DOI: 10.1186/s12864-016-3219-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/26/2016] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND While a few studies on the variations in mRNA expression and half-lives measured under different growth conditions have been used to predict patterns of regulation in bacterial organisms, the extent to which this information can also play a role in defining metabolic phenotypes has yet to be examined systematically. Here we present the first comprehensive study for a model methanogen. RESULTS We use expression and half-life data for the methanogen Methanosarcina acetivorans growing on fast- and slow-growth substrates to examine the regulation of its genes. Unlike Escherichia coli where only small shifts in half-lives were observed, we found that most mRNA have significantly longer half-lives for slow growth on acetate compared to fast growth on methanol or trimethylamine. Interestingly, half-life shifts are not uniform across functional classes of enzymes, suggesting the existence of a selective stabilization mechanism for mRNAs. Using the transcriptomics data we determined whether transcription or degradation rate controls the change in transcript abundance. Degradation was found to control abundance for about half of the metabolic genes underscoring its role in regulating metabolism. Genes involved in half of the metabolic reactions were found to be differentially expressed among the substrates suggesting the existence of drastically different metabolic phenotypes that extend beyond just the methanogenesis pathways. By integrating expression data with an updated metabolic model of the organism (iST807) significant differences in pathway flux and production of metabolites were predicted for the three growth substrates. CONCLUSIONS This study provides the first global picture of differential expression and half-lives for a class II methanogen, as well as provides the first evidence in a single organism that drastic genome-wide shifts in RNA half-lives can be modulated by growth substrate. We determined which genes in each metabolic pathway control the flux and classified them as regulated by transcription (e.g. transcription factor) or degradation (e.g. post-transcriptional modification). We found that more than half of genes in metabolism were controlled by degradation. Our results suggest that M. acetivorans employs extensive post-transcriptional regulation to optimize key metabolic steps, and more generally that degradation could play a much greater role in optimizing an organism's metabolism than previously thought.
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Affiliation(s)
- Joseph R. Peterson
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 S Mathews Ave, Urbana, 60801 IL USA
| | - ShengShee Thor
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, 60801 IL USA
| | - Lars Kohler
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 S Mathews Ave, Urbana, 60801 IL USA
| | - Petra R.A. Kohler
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S Goodwin AveIL, Urbana, 60801 USA
| | - William W. Metcalf
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S Goodwin AveIL, Urbana, 60801 USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory DrIL, Urbana, 60801 USA
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 S Mathews Ave, Urbana, 60801 IL USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, 60801 IL USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory DrIL, Urbana, 60801 USA
- Beckman Institute, University of Illinois at Urbana-Champaign, 405 N Mathews Ave, Urbana, 60801 IL USA
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Identification of the Final Two Genes Functioning in Methanofuran Biosynthesis in Methanocaldococcus jannaschii. J Bacteriol 2015; 197:2850-8. [PMID: 26100040 DOI: 10.1128/jb.00401-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 06/15/2015] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED All methanofuran structural variants contain a basic core structure of 4-[N-(γ-l-glutamyl)-p-(β-aminoethyl)phenoxymethyl]-(aminomethyl)furan (APMF-Glu) but have different side chains depending on the source organism. Recently, we identified four genes (MfnA, MfnB, MfnC, and MfnD) that are responsible for the biosynthesis of the methanofuran precursor γ-glutamyltyramine and 5-(aminomethyl)-3-furanmethanol-phosphate (F1-P) from tyrosine, glutamate, glyceraldehyde-3-P, and alanine in Methanocaldococcus jannaschii. How γ-glutamyltyramine and F1-P couple together to form the core structure of methanofuran was previously unknown. Here, we report the identification of two enzymes encoded by the genes mj0458 and mj0840 that catalyze the formation of F1-PP from ATP and F1-P and the condensation of F1-PP with γ-glutamyltyramine, respectively, to form APMF-Glu. We have annotated these enzymes as MfnE and MfnF, respectively, representing the fifth and sixth enzymes in the methanofuran biosynthetic pathway to be identified. Although MfnE was previously reported as an archaeal adenylate kinase, our present results show that MfnE is a promiscuous enzyme and that its possible physiological role is to produce F1-PP. Unlike other enzymes catalyzing coupling reactions involving pyrophosphate as the leaving group, MfnF exhibits a distinctive α/β two-layer sandwich structure. By comparing MfnF with thiamine synthase and dihydropteroate synthase, a substitution nucleophilic unimolecular (SN-1) reaction mechanism is proposed for MfnF. With the identification of MfnE and MfnF, the biosynthetic pathway for the methanofuran core structure APMF-Glu is complete. IMPORTANCE This work describes the identification of the final two enzymes responsible for catalyzing the biosynthesis of the core structure of methanofuran. The gene products of mj0458 and mj0840 catalyze the formation of F1-PP and the coupling of F1-PP with γ-glutamyltyramine, respectively, to form APMF-Glu. Although the chemistry of such a coupling reaction is widespread in biochemistry, we provide here the first evidence that such a mechanism is used in methanofuran biosynthesis. MfnF belongs to the hydantoinase A family (PF01968) and exhibits a unique α/β two-layer sandwich structure that is different from the enzymes catalyzing similar reactions. Our results show that MfnF catalyzes the formation of an ether bond during methanofuran biosynthesis. Therefore, this work further expands the functionality of this enzyme family.
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