1
|
Integrated rational and evolutionary engineering of genome-reduced Pseudomonas putida strains promotes synthetic formate assimilation. Metab Eng 2022; 74:191-205. [DOI: 10.1016/j.ymben.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/05/2022] [Accepted: 10/23/2022] [Indexed: 11/07/2022]
|
2
|
Volke DC, Martino RA, Kozaeva E, Smania AM, Nikel PI. Modular (de)construction of complex bacterial phenotypes by CRISPR/nCas9-assisted, multiplex cytidine base-editing. Nat Commun 2022; 13:3026. [PMID: 35641501 PMCID: PMC9156665 DOI: 10.1038/s41467-022-30780-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 05/19/2022] [Indexed: 01/01/2023] Open
Abstract
CRISPR/Cas technologies constitute a powerful tool for genome engineering, yet their use in non-traditional bacteria depends on host factors or exogenous recombinases, which limits both efficiency and throughput. Here we mitigate these practical constraints by developing a widely-applicable genome engineering toolset for Gram-negative bacteria. The challenge is addressed by tailoring a CRISPR base editor that enables single-nucleotide resolution manipulations (C·G → T·A) with >90% efficiency. Furthermore, incorporating Cas6-mediated processing of guide RNAs in a streamlined protocol for plasmid assembly supports multiplex base editing with >85% efficiency. The toolset is adopted to construct and deconstruct complex phenotypes in the soil bacterium Pseudomonas putida. Single-step engineering of an aromatic-compound production phenotype and multi-step deconstruction of the intricate redox metabolism illustrate the versatility of multiplex base editing afforded by our toolbox. Hence, this approach overcomes typical limitations of previous technologies and empowers engineering programs in Gram-negative bacteria that were out of reach thus far. Rapid engineering of bacterial genomes is a requisite for both fundamental and applied studies. Here the authors develop an enhanced, broad-host-range cytidine base editor that enables multiplexed and efficient genome editing of Gram-negative bacteria.
Collapse
Affiliation(s)
- Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Román A Martino
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.,Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Ekaterina Kozaeva
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Andrea M Smania
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.,Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
| |
Collapse
|
3
|
Lee S, Jung YJ, Park SJ, Ryu MH, Kim JE, Song HM, Kang KH, Song BK, Sung BH, Kim YH, Kim HT, Joo JC. Microbial production of 2-pyrone-4,6-dicarboxylic acid from lignin derivatives in an engineered Pseudomonas putida and its application for the synthesis of bio-based polyester. BIORESOURCE TECHNOLOGY 2022; 352:127106. [PMID: 35378283 DOI: 10.1016/j.biortech.2022.127106] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Lignin valorization depends on microbial upcycling of various aromatic compounds in the form of a complex mixture, including p-coumaric acid and ferulic acid. In this study, an engineered Pseudomonas putida strain utilizing lignin-derived monomeric compounds via biological funneling was developed to produce 2-pyrone-4,6-dicarboxylic acid (PDC), which has been considered a promising building block for bioplastics. The biosynthetic pathway for PDC production was established by introducing the heterologous ligABC genes under the promoter Ptac in a strain lacking pcaGH genes to accumulate a precursor of PDC, i.e., protocatechuic acid. Based on the culture optimization, fed-batch fermentation of the final strain resulted in 22.7 g/L PDC with a molar yield of 1.0 mol/mol and productivity of 0.21 g/L/h. Subsequent purification of PDC at high purity was successfully implemented, which was consequently applied for the novel polyester.
Collapse
Affiliation(s)
- Siseon Lee
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si, Gyeonggi-do 14662, Republic of Korea
| | - Ye Jean Jung
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si, Gyeonggi-do 14662, Republic of Korea
| | - Si Jae Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science & Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Mi-Hee Ryu
- Green Carbon Research Center, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Joo Eon Kim
- Research Center for Bio-based Chemicals, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Hye Min Song
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science & Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Kyoung Hee Kang
- Research Center for Bio-based Chemicals, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Bong Keun Song
- Research Center for Bio-based Chemicals, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Bong Hyun Sung
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Yong Hwan Kim
- Department of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Hee Taek Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jeong Chan Joo
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si, Gyeonggi-do 14662, Republic of Korea; Research Center for Bio-based Chemicals, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea.
| |
Collapse
|
4
|
Lee JA, Stolyar S, Marx CJ. Aerobic Methoxydotrophy: Growth on Methoxylated Aromatic Compounds by Methylobacteriaceae. Front Microbiol 2022; 13:849573. [PMID: 35359736 PMCID: PMC8963497 DOI: 10.3389/fmicb.2022.849573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/16/2022] [Indexed: 11/18/2022] Open
Abstract
Pink-pigmented facultative methylotrophs have long been studied for their ability to grow on reduced single-carbon (C1) compounds. The C1 groups that support methylotrophic growth may come from a variety of sources. Here, we describe a group of Methylobacterium strains that can engage in methoxydotrophy: they can metabolize the methoxy groups from several aromatic compounds that are commonly the product of lignin depolymerization. Furthermore, these organisms can utilize the full aromatic ring as a growth substrate, a phenotype that has rarely been described in Methylobacterium. We demonstrated growth on p-hydroxybenzoate, protocatechuate, vanillate, and ferulate in laboratory culture conditions. We also used comparative genomics to explore the evolutionary history of this trait, finding that the capacity for aromatic catabolism is likely ancestral to two clades of Methylobacterium, but has also been acquired horizontally by closely related organisms. In addition, we surveyed the published metagenome data to find that the most abundant group of aromatic-degrading Methylobacterium in the environment is likely the group related to Methylobacterium nodulans, and they are especially common in soil and root environments. The demethoxylation of lignin-derived aromatic monomers in aerobic environments releases formaldehyde, a metabolite that is a potent cellular toxin but that is also a growth substrate for methylotrophs. We found that, whereas some known lignin-degrading organisms excrete formaldehyde as a byproduct during growth on vanillate, Methylobacterium do not. This observation is especially relevant to our understanding of the ecology and the bioengineering of lignin degradation.
Collapse
Affiliation(s)
- Jessica A. Lee
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, United States
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, United States
- Space Biosciences Research Branch, NASA Ames Research Center, Moffett Field, CA, United States
| | - Sergey Stolyar
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, United States
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, United States
| | - Christopher J. Marx
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, United States
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, United States
| |
Collapse
|
5
|
Henson WR, Meyers AW, Jayakody LN, DeCapite A, Black BA, Michener WE, Johnson CW, Beckham GT. Biological upgrading of pyrolysis-derived wastewater: Engineering Pseudomonas putida for alkylphenol, furfural, and acetone catabolism and (methyl)muconic acid production. Metab Eng 2021; 68:14-25. [PMID: 34438073 DOI: 10.1016/j.ymben.2021.08.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/18/2021] [Accepted: 08/22/2021] [Indexed: 10/20/2022]
Abstract
While biomass-derived carbohydrates have been predominant substrates for biological production of renewable fuels, chemicals, and materials, organic waste streams are growing in prominence as potential alternative feedstocks to improve the sustainability of manufacturing processes. Catalytic fast pyrolysis (CFP) is a promising approach to generate biofuels from lignocellulosic biomass, but it generates a complex, carbon-rich, and toxic wastewater stream that is challenging to process catalytically but could be biologically upgraded to valuable co-products. In this work, we implemented modular, heterologous catabolic pathways in the Pseudomonas putida KT2440-derived EM42 strain along with the overexpression of native toxicity tolerance machinery to enable utilization of 89% (w/w) of carbon in CFP wastewater. The dmp monooxygenase and meta-cleavage pathway from Pseudomonas putida CF600 were constitutively expressed to enable utilization of phenol, cresols, 2- and 3-ethyl phenol, and methyl catechols, and the native chaperones clpB, groES, and groEL were overexpressed to improve toxicity tolerance to diverse aromatic substrates. Next, heterologous furfural and acetone utilization pathways were incorporated, and a native alcohol dehydrogenase was overexpressed to improve methanol utilization, generating reducing equivalents. All pathways (encoded by genes totaling ~30 kilobases of DNA) were combined into a single strain that can catabolize a mock CFP wastewater stream as a sole carbon source. Further engineering enabled conversion of all aromatic compounds in the mock wastewater stream to (methyl)muconates with a ~90% (mol/mol) yield. Biological upgrading of CFP wastewater as outlined in this work provides a roadmap for future applications in valorizing other heterogeneous waste streams.
Collapse
Affiliation(s)
- William R Henson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Alex W Meyers
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Lahiru N Jayakody
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Annette DeCapite
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Brenna A Black
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - William E Michener
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Christopher W Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
| |
Collapse
|
6
|
Tong C, Hu H, Chen G, Li Z, Li A, Zhang J. Disinfectant resistance in bacteria: Mechanisms, spread, and resolution strategies. ENVIRONMENTAL RESEARCH 2021; 195:110897. [PMID: 33617866 DOI: 10.1016/j.envres.2021.110897] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/02/2021] [Accepted: 02/15/2021] [Indexed: 05/19/2023]
Abstract
Disinfectants are widely acknowledged for removing microorganisms from the surface of the objects and transmission media. However, the emergence of disinfectant resistance has become a severe threat to the safety of life and health and the rational allocation of resources due to the reduced disinfectant effectiveness. The horizontal gene transfer (HGT) of disinfectant resistance genes has also expanded the resistant flora, making the situation worse. This review focused on the resistance mechanisms of disinfectant resistant bacteria on biofilms, cell membrane permeability, efflux pumps, degradable enzymes, and disinfectant targets. Efflux can be the fastest and most effective resistance mechanism for bacteria to respond to stress. The qac genes, located on some plasmids which can transmit resistance through conjugative transfer, are the most commonly reported in the study of disinfectant resistance genes. Whether the qac genes can be transferred through transformation or transduction is still unclear. Studying the factors affecting the resistance of bacteria to disinfectants can find breakthrough methods to more adequately deal with the problem of reduced disinfectant effectiveness. It has been confirmed that the interaction of probiotics and bacteria or the addition of 4-oxazolidinone can inhibit the formation of biofilms. Chemicals such as eugenol and indole derivatives can increase bacterial sensitivity by reducing the expression of efflux pumps. The role of these findings in anti-disinfectant resistance has proved invaluable.
Collapse
Affiliation(s)
- Chaoyu Tong
- Collage of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China.
| | - Hong Hu
- Collage of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China.
| | - Gang Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Zhengyan Li
- Collage of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China.
| | - Aifeng Li
- Collage of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China.
| | - Jianye Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| |
Collapse
|
7
|
Whole-genome sequencing, genome mining, metabolic reconstruction and evolution of pentachlorophenol and other xenobiotic degradation pathways in Bacillus tropicus strain AOA-CPS1. Funct Integr Genomics 2021; 21:171-193. [PMID: 33547987 DOI: 10.1007/s10142-021-00768-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 09/30/2020] [Accepted: 01/19/2021] [Indexed: 12/11/2022]
Abstract
A pentachlorophenol degrading bacterium was isolated from effluent of a wastewater treatment plant in Durban, South Africa, and identified as Bacillus tropicus strain AOA-CPS1 (BtAOA). The isolate degraded 29% of pentachlorophenol (PCP) within 9 days at an initial PCP concentration of 100 mg L-1 and 62% of PCP when the initial concentration was set at 350 mg L-1. The whole-genome of BtAOA was sequenced using Pacific Biosciences RS II sequencer with the Single Molecule, Real-Time (SMRT) Link (version 7.0.1.66975) and analysed using the HGAP4-de-novo assembly application. The contigs were annotated at NCBI, RASTtk and PROKKA prokaryotic genome annotation pipelines. The BtAOA genome is comprised of a 5,246,860-bp chromosome and a 58,449-bp plasmid with a GC content of 35.4%. The metabolic reconstruction for BtAOA showed that the organism has been naturally exposed to various chlorophenolic compounds including PCP and other xenobiotics. The chromosome encodes genes for core processes, stress response and PCP catabolic genes. Analogues of PCP catabolic gene (cpsBDCAE, and p450) sequences were identified from the NCBI annotation data, PCR-amplified from the whole genome of BtAOA, cloned into pET15b expression vector, overexpressed in E. coli BL21 (DE3) expression host, purified and characterized. Sequence mining and comparative analysis of the metabolic reconstruction of the BtAOA genome with closely related strains suggests that the operon encoding the first two enzymes in the PCP degradation pathway were acquired from a pre-existing pterin-carbinolamine dehydratase subsystem. The other two enzymes were recruited via horizontal gene transfer (HGT) from the pool of hypothetical proteins with no previous specific function, while the last enzyme was recruited from pre-existing enzymes from the TCA or serine-glyoxalase cycle via HGT events. This study provides a comprehensive understanding of the role of BtAOA in PCP degradation and its potential exploitation for bioremediation of other xenobiotic compounds.
Collapse
|
8
|
Lee JA, Baugh AC, Shevalier NJ, Strand B, Stolyar S, Marx CJ. Cross-Feeding of a Toxic Metabolite in a Synthetic Lignocellulose-Degrading Microbial Community. Microorganisms 2021; 9:321. [PMID: 33557371 PMCID: PMC7914493 DOI: 10.3390/microorganisms9020321] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/27/2021] [Accepted: 02/01/2021] [Indexed: 11/25/2022] Open
Abstract
The recalcitrance of complex organic polymers such as lignocellulose is one of the major obstacles to sustainable energy production from plant biomass, and the generation of toxic intermediates can negatively impact the efficiency of microbial lignocellulose degradation. Here, we describe the development of a model microbial consortium for studying lignocellulose degradation, with the specific goal of mitigating the production of the toxin formaldehyde during the breakdown of methoxylated aromatic compounds. Included are Pseudomonas putida, a lignin degrader; Cellulomonas fimi, a cellulose degrader; and sometimes Yarrowia lipolytica, an oleaginous yeast. Unique to our system is the inclusion of Methylorubrum extorquens, a methylotroph capable of using formaldehyde for growth. We developed a defined minimal "Model Lignocellulose" growth medium for reproducible coculture experiments. We demonstrated that the formaldehyde produced by P. putida growing on vanillic acid can exceed the minimum inhibitory concentration for C. fimi, and, furthermore, that the presence of M. extorquens lowers those concentrations. We also uncovered unexpected ecological dynamics, including resource competition, and interspecies differences in growth requirements and toxin sensitivities. Finally, we introduced the possibility for a mutualistic interaction between C. fimi and M. extorquens through metabolite exchange. This study lays the foundation to enable future work incorporating metabolomic analysis and modeling, genetic engineering, and laboratory evolution, on a model system that is appropriate both for fundamental eco-evolutionary studies and for the optimization of efficiency and yield in microbially-mediated biomass transformation.
Collapse
Affiliation(s)
- Jessica A. Lee
- NASA Ames Research Center, Moffett Field, CA 94035, USA
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (A.C.B.); (N.J.S.); (B.S.); (S.S.)
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83844, USA
| | - Alyssa C. Baugh
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (A.C.B.); (N.J.S.); (B.S.); (S.S.)
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Nicholas J. Shevalier
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (A.C.B.); (N.J.S.); (B.S.); (S.S.)
| | - Brandi Strand
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (A.C.B.); (N.J.S.); (B.S.); (S.S.)
| | - Sergey Stolyar
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (A.C.B.); (N.J.S.); (B.S.); (S.S.)
| | - Christopher J. Marx
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (A.C.B.); (N.J.S.); (B.S.); (S.S.)
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83844, USA
| |
Collapse
|
9
|
Riveros-Rosas H, Julián-Sánchez A, Moreno-Hagelsieb G, Muñoz-Clares RA. Aldehyde dehydrogenase diversity in bacteria of the Pseudomonas genus. Chem Biol Interact 2019; 304:83-87. [PMID: 30862475 DOI: 10.1016/j.cbi.2019.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/07/2019] [Indexed: 10/27/2022]
Abstract
Aldehyde dehydrogenases (ALDHs) comprise one of the most ancient protein superfamilies widely distributed in the three domains of life. Their members have been extensively studied in animals and plants, sorted out in different ALDH protein families and their participation in a broad variety of metabolic pathways has been documented. Paradoxically, no systematic studies comprising ALDHs from bacteria have been performed so far. Among bacteria, the genus Pseudomonas occupies numerous ecological niches, and is one of the most complex bacterial genera with the largest number of known species. For these reasons, we selected Pseudomonas as a paradigm to analyze the diversity of ALDHs in bacteria. With this aim, complete Pseudomonas genome sequences and annotations were retrieved from NCBI's RefSeq genome database. The 258 Pseudomonas strains belong to 46 different species, along with 23 with no species designation. The genomes of these Pseudomonas contain from 3,315 to 6,825 annotated protein coding genes. A total of 6,510 ALDH sequences were found in the selected Pseudomonas, with a median of 24 ALDH-coding genes per strain (by comparison humans possess only 19 different ALDH loci). Pseudomonas saudiphocaensis possesses the lowest number of aldh genes (9), while Pseudomonas pseudoalcaligenes KF707 NBRC110670 possesses the maximum number of aldh genes (49). The ALDHs found in Pseudomonas can be sorted out into 42 protein families, with a predominance of 14 families, which contained 76% of all ALDHs found. In this regard, it is important to note that many Pseudomonas genomes have multiple aldh genes coding for proteins belonging to the same family. Given that all strains contained members of families ALDH4, ALDH5, ALDH6, ALDH14, ALDH18 and ALDH27, we consider these families to be part of the core Pseudomonas genome.
Collapse
Affiliation(s)
- Héctor Riveros-Rosas
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, CdMx, 04510, México; Department of Biology, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada.
| | - Adriana Julián-Sánchez
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, CdMx, 04510, México
| | | | - Rosario A Muñoz-Clares
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, CdMx, 04510, México
| |
Collapse
|
10
|
Zobel S, Kuepper J, Ebert B, Wierckx N, Blank LM. Metabolic response of Pseudomonas putida to increased NADH regeneration rates. Eng Life Sci 2016; 17:47-57. [PMID: 32624728 DOI: 10.1002/elsc.201600072] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 07/19/2016] [Accepted: 08/10/2016] [Indexed: 11/08/2022] Open
Abstract
Pseudomonas putida efficiently utilizes many different carbon sources without the formation of byproducts even under conditions of stress. This implies a high degree of flexibility to cope with conditions that require a significantly altered distribution of carbon to either biomass or energy in the form of NADH. In the literature, co-feeding of the reduced C1 compound formate to Escherichia coli heterologously expressing the NAD+-dependent formate dehydrogenase of the yeast Candida boidinii was demonstrated to boost various NADH-demanding applications. Pseudomonas putida as emerging biotechnological workhorse is inherently equipped with an NAD+-dependent formate dehydrogenase encouraging us to investigate the use of formate and its effect on P. putida's metabolism. Hence, this study provides a detailed insight into the co-utilization of formate and glucose by P. putida. Our results show that the addition of formate leads to a high increase in the NADH regeneration rate resulting in a very high biomass yield on glucose. Metabolic flux analysis revealed a significant flux rerouting from catabolism to anabolism. These metabolic insights argue further for P. putida as a host for redox cofactor demanding bioprocesses.
Collapse
Affiliation(s)
- Sebastian Zobel
- Institute of Applied Microbiology - iAMB RWTH Aachen University - ABBt Aachen Germany
| | - Jannis Kuepper
- Institute of Applied Microbiology - iAMB RWTH Aachen University - ABBt Aachen Germany
| | - Birgitta Ebert
- Institute of Applied Microbiology - iAMB RWTH Aachen University - ABBt Aachen Germany
| | - Nick Wierckx
- Institute of Applied Microbiology - iAMB RWTH Aachen University - ABBt Aachen Germany
| | - Lars M Blank
- Institute of Applied Microbiology - iAMB RWTH Aachen University - ABBt Aachen Germany
| |
Collapse
|
11
|
Kuepper J, Zobel S, Wierckx N, Blank LM. A rapid method to estimate NADH regeneration rates in living cells. J Microbiol Methods 2016; 130:92-94. [PMID: 27592588 DOI: 10.1016/j.mimet.2016.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 09/01/2016] [Indexed: 02/05/2023]
Abstract
We introduce a rapid whole cell assay for the estimation of NADH regeneration rates based on the fluorescent dye resazurin. A co-feed of formate and glucose, known to increase the intrinsic NADH regeneration rate of P. putida KT2440, was chosen as model system for the validation of this assay.
Collapse
Affiliation(s)
- Jannis Kuepper
- Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Sebastian Zobel
- Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Nick Wierckx
- Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
| | - Lars M Blank
- Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| |
Collapse
|
12
|
Production of glucaric acid from myo-inositol in engineered Pichia pastoris. Enzyme Microb Technol 2016; 91:8-16. [DOI: 10.1016/j.enzmictec.2016.05.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/11/2016] [Accepted: 05/22/2016] [Indexed: 02/02/2023]
|
13
|
|
14
|
Roca A, Ramos JL. In vivo role of FdhD and FdmE in formate metabolism in Pseudomonas putida: Redundancy and expression in the stationary phase. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:208-213. [PMID: 23765795 DOI: 10.1111/j.1758-2229.2009.00032.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In Pseudomonas putida two open reading frames (ORFs) PP0257 and PP0492 were originally annotated as accessory formate dehydrogenase proteins. The ORF PP0492 (fdmD) is at the 3' end of the ORF PP0489 through PP0491 operon that encodes one of the formate dehydrogenases of P. putida and it is transcribed with this operon preferentially at the stationary phase. The ORF PP0257 (fdhD) is unlinked to formate dehydrogenase clusters and, as to multi-component formate dehydrogenases, PP0257 is also preferentially expressed in the stationary phase, although transcription can be mediated by either RpoD or RpoS. The transcriptional level of expression of fdhD increased in response to formaldehyde/formate or chemicals that yield these cited C1 compounds through their metabolism. In spite of these correlations, inactivation of PP0257 does not produce a significant effect on in vivo formate dehydrogenase activity, while inactivation of PP0492 leads to a 60% decrease in in vivo activity. These results suggest that redundancy in formaldehyde/formate metabolism in P. putida extends to the proteins involved in maturation/location of formate dehydrogenase complexes.
Collapse
Affiliation(s)
- Amalia Roca
- Department of Environmental Protection, Consejo Superior de Investigaciones científicas, Estación Experimental del Zaidín, Granada, Spain
| | | |
Collapse
|