Genomics analysis and degradation characteristics of lignin by Streptomyces thermocarboxydus strain DF3-3

Fangyun Tan; Jun Cheng; Yu Zhang; Xingfu Jiang; Yueqiu Liu

doi:10.1186/s13068-022-02175-1

Genomics analysis and degradation characteristics of lignin by Streptomyces thermocarboxydus strain DF3-3

Biotechnol Biofuels Bioprod. 2022 Jul 12;15(1):78. doi: 10.1186/s13068-022-02175-1.

Authors

Fangyun Tan^#¹, Jun Cheng^#², Yu Zhang¹, Xingfu Jiang³, Yueqiu Liu⁴

Affiliations

¹ School of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China.
² School of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, People's Republic of China.
³ Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
⁴ School of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China. liuyueqiu@bua.edu.cn.

^# Contributed equally.

Abstract

Background: Lignocellulose is an important raw material for biomass-to-energy conversion, and it exhibits a complex but inefficient degradation mechanism. Microbial degradation is promising due to its environmental adaptability and biochemical versatility, but the pathways used by microbes for lignin degradation have not been fully studied. Degradation intermediates and complex metabolic pathways require more study.

Results: A novel actinomycete DF3-3, with the potential for lignin degradation, was screened and isolated. After morphological and molecular identification, DF3-3 was determined to be Streptomyces thermocarboxydus. The degradation of alkali lignin reached 31% within 15 days. Manganese peroxidase and laccase demonstrated their greatest activity levels, 1821.66 UL^-1 and 1265.58 UL^-1, respectively, on the sixth day. The highest lignin peroxidase activity was 480.33 UL^-1 on the fourth day. A total of 19 lignin degradation intermediates were identified by gas chromatography-mass spectrometry (GC-MS), including 9 aromatic compounds. Genome sequencing and annotation identified 107 lignin-degrading enzyme-coding genes containing three core enzymatic systems for lignin depolymerization: laccases, peroxidases and manganese peroxidase. In total, 7 lignin metabolic pathways were predicted.

Conclusions: Streptomyces thermocarboxydus strain DF3-3 has good lignin degradation ability. Degradation products and genomics analyses of DF3-3 show that it has a relatively complete lignin degradation pathway, including the β-ketoadipate pathway and peripheral reactions, gentisate pathway, anthranilate pathway, homogentisic pathway, and catabolic pathway for resorcinol. Two other pathways, the phenylacetate-CoA pathway and the 2,3-dihydroxyphenylpropionic acid pathway, are predicted based on genome data alone. This study provides the basis for future characterization of potential biotransformation enzyme systems for biomass energy conversion.

Keywords: Alkali lignin; Enzyme activity; Genomics; Metabolic pathways; Streptomyces thermocarboxydus strain DF3-3.

Abstract

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