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Title: Genomics and biochemistry investigation on the metabolic pathway of milled wood and alkali lignin-derived aromatic metabolites of Comamonas serinivorans SP-35

Abstract

Background: The efficient depolymerization and utilization of lignin are one of the most important goals for the renewable use of lignocelluloses. The degradation and complete mineralization of lignin by bacteria represent a key step for carbon recycling in land ecosystems as well. However, many aspects of this process remain unclear, for example, the complex network of metabolic pathways involved in the degradation of lignin and the catabolic pathway of intermediate aromatic metabolites. To address these subjects, we characterized the deconstruction and mineralization of lignin with milled wood lignin (MWL, the most representative molecule of lignin in its native state) and alkali lignin (AL), and elucidated metabolic pathways of their intermediate metabolites by a bacterium named Comamonas serinivorans SP-35. Results: The degradation rate of MWL reached 30.9%, and its particle size range was decreased from 6 to 30 µm to 2–4 µm—when cultured with C. serinivorans SP35 over 7 days. FTIR analysis showed that the C–C and C–O–C bonds between the phenyl propane structures of lignin were oxidized and cleaved and the side chain structure was modi- fied. More than twenty intermediate aromatic metabolites were identified in the MWL and AL cultures based on GC–MS analysis. Through genome sequencing and annotation,more » and from GC–MS analysis, 93 genes encoding 33 enzymes and 5 regulatory factors that may be involved in lignin degradation were identified and more than nine metabolic pathways of lignin and its intermediates were predicted. Of particular note is that the metabolic pathway to form the powerful antioxidant 3,4-dihydroxyphenylglycol is described for the first time in bacteria. Conclusion: Elucidation of the ß-aryl ether cleavage pathway in the strain SP-35 indicates that the ß-aryl ether catabolic system is not only present in the family of Sphingomonadaceae, but also other species of bacteria kingdom. These newly elucidated catabolic pathways of lignin in strain SP-35 and the enzymes responsible for them provide exciting biotechnological opportunities for lignin valorization in future.« less

Authors:
ORCiD logo [1];  [2];  [2];  [2];  [3];  [4];  [5];  [2];  [2]
  1. Jiangsu University, Zhenjiang (China); Guangdong Institute of Microbiology, Guangzhou (China)
  2. Jiangsu University, Zhenjiang (China)
  3. Guangdong Institute of Microbiology, Guangzhou (China)
  4. Washington State University, Richland, WA (United States)
  5. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1497063
Report Number(s):
PNNL-SA-140577
Journal ID: ISSN 1754-6834
Grant/Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Biotechnology for Biofuels
Additional Journal Information:
Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 1754-6834
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Comamonas serinivorans SP-35; Metabolic pathway; Lignin; Whole genome sequencing; Aromatic metabolites

Citation Formats

Zhu, Daochen, Si, Haibing, Zhang, Peipei, Geng, Alei, Zhang, Weimin, Yang, Bin, Qian, Wei-Jun, Gabriel, Murillo, and Sun, Jianzhong. Genomics and biochemistry investigation on the metabolic pathway of milled wood and alkali lignin-derived aromatic metabolites of Comamonas serinivorans SP-35. United States: N. p., 2018. Web. doi:10.1186/s13068-018-1341-3.
Zhu, Daochen, Si, Haibing, Zhang, Peipei, Geng, Alei, Zhang, Weimin, Yang, Bin, Qian, Wei-Jun, Gabriel, Murillo, & Sun, Jianzhong. Genomics and biochemistry investigation on the metabolic pathway of milled wood and alkali lignin-derived aromatic metabolites of Comamonas serinivorans SP-35. United States. doi:10.1186/s13068-018-1341-3.
Zhu, Daochen, Si, Haibing, Zhang, Peipei, Geng, Alei, Zhang, Weimin, Yang, Bin, Qian, Wei-Jun, Gabriel, Murillo, and Sun, Jianzhong. Thu . "Genomics and biochemistry investigation on the metabolic pathway of milled wood and alkali lignin-derived aromatic metabolites of Comamonas serinivorans SP-35". United States. doi:10.1186/s13068-018-1341-3. https://www.osti.gov/servlets/purl/1497063.
@article{osti_1497063,
title = {Genomics and biochemistry investigation on the metabolic pathway of milled wood and alkali lignin-derived aromatic metabolites of Comamonas serinivorans SP-35},
author = {Zhu, Daochen and Si, Haibing and Zhang, Peipei and Geng, Alei and Zhang, Weimin and Yang, Bin and Qian, Wei-Jun and Gabriel, Murillo and Sun, Jianzhong},
abstractNote = {Background: The efficient depolymerization and utilization of lignin are one of the most important goals for the renewable use of lignocelluloses. The degradation and complete mineralization of lignin by bacteria represent a key step for carbon recycling in land ecosystems as well. However, many aspects of this process remain unclear, for example, the complex network of metabolic pathways involved in the degradation of lignin and the catabolic pathway of intermediate aromatic metabolites. To address these subjects, we characterized the deconstruction and mineralization of lignin with milled wood lignin (MWL, the most representative molecule of lignin in its native state) and alkali lignin (AL), and elucidated metabolic pathways of their intermediate metabolites by a bacterium named Comamonas serinivorans SP-35. Results: The degradation rate of MWL reached 30.9%, and its particle size range was decreased from 6 to 30 µm to 2–4 µm—when cultured with C. serinivorans SP35 over 7 days. FTIR analysis showed that the C–C and C–O–C bonds between the phenyl propane structures of lignin were oxidized and cleaved and the side chain structure was modi- fied. More than twenty intermediate aromatic metabolites were identified in the MWL and AL cultures based on GC–MS analysis. Through genome sequencing and annotation, and from GC–MS analysis, 93 genes encoding 33 enzymes and 5 regulatory factors that may be involved in lignin degradation were identified and more than nine metabolic pathways of lignin and its intermediates were predicted. Of particular note is that the metabolic pathway to form the powerful antioxidant 3,4-dihydroxyphenylglycol is described for the first time in bacteria. Conclusion: Elucidation of the ß-aryl ether cleavage pathway in the strain SP-35 indicates that the ß-aryl ether catabolic system is not only present in the family of Sphingomonadaceae, but also other species of bacteria kingdom. These newly elucidated catabolic pathways of lignin in strain SP-35 and the enzymes responsible for them provide exciting biotechnological opportunities for lignin valorization in future.},
doi = {10.1186/s13068-018-1341-3},
journal = {Biotechnology for Biofuels},
issn = {1754-6834},
number = 1,
volume = 11,
place = {United States},
year = {2018},
month = {12}
}

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