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Fan L, Li M, Li Y, Fan X, Liu Y, Lv Y. Draft Genome Sequence of Thermophilic Bacillus sp. TYF-LIM-B05 Directly Producing Ethanol from Various Carbon Sources Including Lignocellulose. Curr Microbiol 2019; 77:491-499. [PMID: 31832840 DOI: 10.1007/s00284-019-01833-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/29/2019] [Indexed: 12/01/2022]
Abstract
Bacillus sp. TYF-LIM-B05, which is isolated from spoilage vinegar, is resistant to high temperature, high concentrated alcohol, acid, and salt, and can produce ethanol from mono-, di-, polysaccharide, and complex biomass as the sole carbon source. Thus, this strain is a potential candidate for consolidated bioprocessing (CBP) of fermenting lignocellulose to ethanol in a single step. To provide insight into the key enzymes involved in lignocellulose degradation and ethanol production, a draft genome of TYF-LIM-B05 was developed in this study. The results indicated that 348 genes are related to carbohydrate transport and metabolism according to the clusters of orthologous groups of proteins and annotated 187 CAZy domains from a total of 61 different families. The presence of genes encoding laccases, quinone oxidoreductases/reductases, and aryl-alcohol dehydrogenases further implies that TYF-LIM-B05 has the potential to degrade lignin. Remarkably, this strain has the ability to catalyze the oxidative decarboxylation of pyruvate to acetyl-CoA by pyruvate dehydrogenase complexes. The genomic information provided in this study will help researchers to better understand the mechanisms of the lignocellulose degradation and ethanol production pathway in thermophiles.
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Affiliation(s)
- Lulu Fan
- College of Environmental Science and Engineering, Taiyuan University of Technology, No. 209 of University Street, Yuci District, Jinzhong, 030600, Shanxi, China
| | - Min Li
- College of Biomedical Engineering, Taiyuan University of Technology, No. 209 of University Street, Yuci District, Jinzhong, 030600, Shanxi, China
| | - Yao Li
- College of Biomedical Engineering, Taiyuan University of Technology, No. 209 of University Street, Yuci District, Jinzhong, 030600, Shanxi, China
| | - Xiaojun Fan
- College of Environmental Science and Engineering, Taiyuan University of Technology, No. 209 of University Street, Yuci District, Jinzhong, 030600, Shanxi, China. .,Innovation Institute of Environmental Industry, Taiyuan University of Technology, No. 209 of University Street, Yuci District, Jinzhong, 030600, Shanxi, China.
| | - Yuxiang Liu
- College of Environmental Science and Engineering, Taiyuan University of Technology, No. 209 of University Street, Yuci District, Jinzhong, 030600, Shanxi, China.
| | - Yongkang Lv
- Key Laboratory of Coal Science and Technology, Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan, 030024, Shanxi, China
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Engineering acetyl coenzyme A supply: functional expression of a bacterial pyruvate dehydrogenase complex in the cytosol of Saccharomyces cerevisiae. mBio 2014; 5:e01696-14. [PMID: 25336454 PMCID: PMC4212835 DOI: 10.1128/mbio.01696-14] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The energetic (ATP) cost of biochemical pathways critically determines the maximum yield of metabolites of vital or commercial relevance. Cytosolic acetyl coenzyme A (acetyl-CoA) is a key precursor for biosynthesis in eukaryotes and for many industrially relevant product pathways that have been introduced into Saccharomyces cerevisiae, such as isoprenoids or lipids. In this yeast, synthesis of cytosolic acetyl-CoA via acetyl-CoA synthetase (ACS) involves hydrolysis of ATP to AMP and pyrophosphate. Here, we demonstrate that expression and assembly in the yeast cytosol of an ATP-independent pyruvate dehydrogenase complex (PDH) from Enterococcus faecalis can fully replace the ACS-dependent pathway for cytosolic acetyl-CoA synthesis. In vivo activity of E. faecalis PDH required simultaneous expression of E. faecalis genes encoding its E1α, E1β, E2, and E3 subunits, as well as genes involved in lipoylation of E2, and addition of lipoate to growth media. A strain lacking ACS that expressed these E. faecalis genes grew at near-wild-type rates on glucose synthetic medium supplemented with lipoate, under aerobic and anaerobic conditions. A physiological comparison of the engineered strain and an isogenic Acs(+) reference strain showed small differences in biomass yields and metabolic fluxes. Cellular fractionation and gel filtration studies revealed that the E. faecalis PDH subunits were assembled in the yeast cytosol, with a subunit ratio and enzyme activity similar to values reported for PDH purified from E. faecalis. This study indicates that cytosolic expression and assembly of PDH in eukaryotic industrial microorganisms is a promising option for minimizing the energy costs of precursor supply in acetyl-CoA-dependent product pathways. Importance: Genetically engineered microorganisms are intensively investigated and applied for production of biofuels and chemicals from renewable sugars. To make such processes economically and environmentally sustainable, the energy (ATP) costs for product formation from sugar must be minimized. Here, we focus on an important ATP-requiring process in baker's yeast (Saccharomyces cerevisiae): synthesis of cytosolic acetyl coenzyme A, a key precursor for many industrially important products, ranging from biofuels to fragrances. We demonstrate that pyruvate dehydrogenase from the bacterium Enterococcus faecalis, a huge enzyme complex with a size similar to that of a ribosome, can be functionally expressed and assembled in the cytosol of baker's yeast. Moreover, we show that this ATP-independent mechanism for cytosolic acetyl-CoA synthesis can entirely replace the ATP-costly native yeast pathway. This work provides metabolic engineers with a new option to optimize the performance of baker's yeast as a "cell factory" for sustainable production of fuels and chemicals.
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Krutsakorn B, Honda K, Ye X, Imagawa T, Bei X, Okano K, Ohtake H. In vitro production of n-butanol from glucose. Metab Eng 2013; 20:84-91. [DOI: 10.1016/j.ymben.2013.09.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 07/23/2013] [Accepted: 09/11/2013] [Indexed: 11/25/2022]
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Eram MS, Ma K. Decarboxylation of pyruvate to acetaldehyde for ethanol production by hyperthermophiles. Biomolecules 2013; 3:578-96. [PMID: 24970182 PMCID: PMC4030962 DOI: 10.3390/biom3030578] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/02/2013] [Accepted: 08/15/2013] [Indexed: 11/16/2022] Open
Abstract
Pyruvate decarboxylase (PDC encoded by pdc) is a thiamine pyrophosphate (TPP)-containing enzyme responsible for the conversion of pyruvate to acetaldehyde in many mesophilic organisms. However, no pdc/PDC homolog has yet been found in fully sequenced genomes and proteomes of hyper/thermophiles. The only PDC activity reported in hyperthermophiles was a bifunctional, TPP- and CoA-dependent pyruvate ferredoxin oxidoreductase (POR)/PDC enzyme from the hyperthermophilic archaeon Pyrococcus furiosus. Another enzyme known to be involved in catalysis of acetaldehyde production from pyruvate is CoA-acetylating acetaldehyde dehydrogenase (AcDH encoded by mhpF and adhE). Pyruvate is oxidized into acetyl-CoA by either POR or pyruvate formate lyase (PFL), and AcDH catalyzes the reduction of acetyl-CoA to acetaldehyde in mesophilic organisms. AcDH is present in some mesophilic (such as clostridia) and thermophilic bacteria (e.g., Geobacillus and Thermoanaerobacter). However, no AcDH gene or protein homologs could be found in the released genomes and proteomes of hyperthermophiles. Moreover, no such activity was detectable from the cell-free extracts of different hyperthermophiles under different assay conditions. In conclusion, no commonly-known PDCs was found in hyperthermophiles. Instead of the commonly-known PDC, it appears that at least one multifunctional enzyme is responsible for catalyzing the non-oxidative decarboxylation of pyruvate to acetaldehyde in hyperthermophiles.
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Affiliation(s)
- Mohammad S Eram
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada.
| | - Kesen Ma
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada.
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Hirani TA, Tovar-Méndez A, Miernyk JA, Randall DD. Asp295 stabilizes the active-site loop structure of pyruvate dehydrogenase, facilitating phosphorylation of ser292 by pyruvate dehydrogenase-kinase. Enzyme Res 2011; 2011:939068. [PMID: 21318135 PMCID: PMC3034952 DOI: 10.4061/2011/939068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 11/05/2010] [Indexed: 01/22/2023] Open
Abstract
We have developed an in vitro system for detailed analysis of reversible phosphorylation of the plant mitochondrial pyruvate dehydrogenase complex, comprising recombinant Arabidopsis thalianaα2β2-heterotetrameric pyruvate dehydrogenase (E1) plus A. thaliana E1-kinase (AtPDK). Upon addition of MgATP, Ser292, which is located within the active-site loop structure of E1α, is phosphorylated. In addition to Ser292, Asp295 and Gly297 are highly conserved in the E1α active-site loop sequences. Mutation of Asp295 to Ala, Asn, or Leu greatly reduced phosphorylation of Ser292, while mutation of Gly297 had relatively little effect. Quantitative two-hybrid analysis was used to show that mutation of Asp295 did not substantially affect binding of AtPDK to E1α. When using pyruvate as a variable substrate, the Asp295 mutant proteins had modest changes in kcat, Km, and kcat/Km values. Therefore, we propose that Asp295 plays an important role in stabilizing the active-site loop structure, facilitating transfer of the γ-phosphate from ATP to the Ser residue at regulatory site one of E1α.
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Affiliation(s)
- Tripty A Hirani
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
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Methanocaldococcus jannaschii adenylosuccinate synthetase: Studies on temperature dependence of catalytic activity and structural stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:2019-28. [DOI: 10.1016/j.bbapap.2008.08.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 07/30/2008] [Accepted: 08/12/2008] [Indexed: 11/19/2022]
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Lower BH, Kennelly PJ. Open reading frame sso2387 from the archaeon Sulfolobus solfataricus encodes a polypeptide with protein-serine kinase activity. J Bacteriol 2003; 185:3436-45. [PMID: 12754243 PMCID: PMC155377 DOI: 10.1128/jb.185.11.3436-3445.2003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2002] [Accepted: 03/21/2003] [Indexed: 11/20/2022] Open
Abstract
The predicted polypeptide product of open reading frame sso2387 from the archaeon Sulfolobus solfataricus, SsoPK2, displayed several of the sequence features conserved among the members of the "eukaryotic" protein kinase superfamily. sso2387 was cloned, and its polypeptide product was expressed in Escherichia coli. The recombinant protein, rSsoPK2, was recovered in insoluble aggregates that could be dispersed by using high concentrations (5 M) of urea. The solubilized polypeptide displayed the ability to phosphorylate itself as well as several exogenous proteins, including mixed histones, casein, bovine serum albumin, and reduced carboxyamidomethylated and maleylated lysozyme, on serine residues. The source of this activity resided in that portion of the protein displaying homology to the catalytic domain of eukaryotic protein kinases. By use of mass spectrometry, the sites of autophosphorylation were found to be located in two areas, one immediately N terminal to the region corresponding to subdomain I of eukaryotic protein kinases, and the second N terminal to the presumed activation loop located between subdomains VII and VIII. Autophosphorylation of rSsoPK2 could be uncoupled from the phosphorylation of exogenous proteins by manipulation of the temperature or mutagenic alteration of the enzyme. Autophosphorylation was detected only at temperatures >or=60 degrees C, whereas phosphorylation of exogenous proteins was detectable at 37 degrees C. Similarly, replacement of one of the potential sites of autophosphorylation, Ser(548), with alanine blocked autophosphorylation but not phosphorylation of an exogenous protein, casein.
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Affiliation(s)
- Brian H Lower
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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