1
|
Ren Y, Eronen V, Blomster Andberg M, Koivula A, Hakulinen N. Structure and function of aldopentose catabolism enzymes involved in oxidative non-phosphorylative pathways. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:147. [PMID: 36578086 PMCID: PMC9795676 DOI: 10.1186/s13068-022-02252-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/19/2022] [Indexed: 12/29/2022]
Abstract
Platform chemicals and polymer precursors can be produced via enzymatic pathways starting from lignocellulosic waste materials. The hemicellulose fraction of lignocellulose contains aldopentose sugars, such as D-xylose and L-arabinose, which can be enzymatically converted into various biobased products by microbial non-phosphorylated oxidative pathways. The Weimberg and Dahms pathways convert pentose sugars into α-ketoglutarate, or pyruvate and glycolaldehyde, respectively, which then serve as precursors for further conversion into a wide range of industrial products. In this review, we summarize the known three-dimensional structures of the enzymes involved in oxidative non-phosphorylative pathways of pentose catabolism. Key structural features and reaction mechanisms of a diverse set of enzymes responsible for the catalytic steps in the reactions are analysed and discussed.
Collapse
Affiliation(s)
- Yaxin Ren
- grid.9668.10000 0001 0726 2490Department of Chemistry, University of Eastern Finland, 111, 80101 Joensuu, Finland
| | - Veikko Eronen
- grid.9668.10000 0001 0726 2490Department of Chemistry, University of Eastern Finland, 111, 80101 Joensuu, Finland
| | | | - Anu Koivula
- grid.6324.30000 0004 0400 1852VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Nina Hakulinen
- grid.9668.10000 0001 0726 2490Department of Chemistry, University of Eastern Finland, 111, 80101 Joensuu, Finland
| |
Collapse
|
2
|
Valdehuesa KNG, Ramos KRM, Nisola GM, Bañares AB, Cabulong RB, Lee WK, Liu H, Chung WJ. Everyone loves an underdog: metabolic engineering of the xylose oxidative pathway in recombinant microorganisms. Appl Microbiol Biotechnol 2018; 102:7703-7716. [PMID: 30003296 DOI: 10.1007/s00253-018-9186-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 11/25/2022]
Abstract
The D-xylose oxidative pathway (XOP) has recently been employed in several recombinant microorganisms for growth or for the production of several valuable compounds. The XOP is initiated by D-xylose oxidation to D-xylonolactone, which is then hydrolyzed into D-xylonic acid. D-Xylonic acid is then dehydrated to form 2-keto-3-deoxy-D-xylonic acid, which may be further dehydrated then oxidized into α-ketoglutarate or undergo aldol cleavage to form pyruvate and glycolaldehyde. This review introduces a brief discussion about XOP and its discovery in bacteria and archaea, such as Caulobacter crescentus and Haloferax volcanii. Furthermore, the current advances in the metabolic engineering of recombinant strains employing the XOP are discussed. This includes utilization of XOP for the production of diols, triols, and short-chain organic acids in Escherichia coli, Saccharomyces cerevisiae, and Corynebacterium glutamicum. Improving the D-xylose uptake, growth yields, and product titer through several metabolic engineering techniques bring some of these recombinant strains close to industrial viability. However, more developments are still needed to optimize the XOP pathway in the host strains, particularly in the minimization of by-product formation.
Collapse
Affiliation(s)
- Kris Niño G Valdehuesa
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Kristine Rose M Ramos
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Grace M Nisola
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Angelo B Bañares
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Rhudith B Cabulong
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Won-Keun Lee
- Division of Bioscience and Bioinformatics, Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Huaiwei Liu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, 266237, People's Republic of China.
| | - Wook-Jin Chung
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 17058, Republic of Korea.
| |
Collapse
|
3
|
Peleg Y, Unger T. Application of the Restriction-Free (RF) cloning for multicomponents assembly. Methods Mol Biol 2014; 1116:73-87. [PMID: 24395358 DOI: 10.1007/978-1-62703-764-8_6] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Molecular manipulations, including DNA cloning and mutagenesis, are currently employed on a routine basis in all life science disciplines. Over the last decade new methodologies have emerged that expanded and facilitated the applications for DNA cloning. The classical Ligation-Dependent Cloning (LDC) is gradually replaced by Ligation-Independent Cloning (LIC) techniques. The Restriction-Free (RF) cloning was originally developed for introduction of a foreign DNA into a plasmid at any desired position. The RF methodology is based on generation of a PCR product, which serves as a set of mega-primers for subsequent incorporation into any desired position within a circular plasmid. We have expanded the applications of the RF methodology for multiple simultaneous alterations of a target DNA and for multicomponents assembly. In the current manuscript we describe a step-by-step protocol for application of the RF methodology for simultaneous multiple DNA fragments assembly in tandem and at distinct positions within an expression vector.
Collapse
Affiliation(s)
- Yoav Peleg
- Israel Structural Proteomics Center (ISPC), Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
| | | |
Collapse
|
4
|
Bhaskar V, Kumar M, Manicka S, Tripathi S, Venkatraman A, Krishnaswamy S. Identification of biochemical and putative biological role of a xenolog from Escherichia coli using structural analysis. Proteins 2011; 79:1132-42. [DOI: 10.1002/prot.22949] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Revised: 11/10/2010] [Accepted: 11/19/2010] [Indexed: 11/10/2022]
|