Lignin bioconversion based on genome mining for ligninolytic genes in Erwinia billingiae QL-Z3
Abstract Background Bioconversion of plant biomass into biofuels and bio-products produces large amounts of lignin. The aromatic biopolymers need to be degraded before being converted into value-added bio-products. Microbes can be environment-friendly and efficiently degrade lignin. Compared to fung...
| Main Authors: | , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2024-02-01
|
| Series: | Biotechnology for Biofuels and Bioproducts |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13068-024-02470-z |
| _version_ | 1797275491580772352 |
|---|---|
| author | Shuting Zhao Dongtao Deng Tianzheng Wan Jie Feng Lei Deng Qianyi Tian Jiayu Wang Umm E. Aiman Balym Mukhaddi Xiaofeng Hu Shaolin Chen Ling Qiu Lili Huang Yahong Wei |
| author_facet | Shuting Zhao Dongtao Deng Tianzheng Wan Jie Feng Lei Deng Qianyi Tian Jiayu Wang Umm E. Aiman Balym Mukhaddi Xiaofeng Hu Shaolin Chen Ling Qiu Lili Huang Yahong Wei |
| author_sort | Shuting Zhao |
| collection | DOAJ |
| description | Abstract Background Bioconversion of plant biomass into biofuels and bio-products produces large amounts of lignin. The aromatic biopolymers need to be degraded before being converted into value-added bio-products. Microbes can be environment-friendly and efficiently degrade lignin. Compared to fungi, bacteria have some advantages in lignin degradation, including broad tolerance to pH, temperature, and oxygen and the toolkit for genetic manipulation. Results Our previous study isolated a novel ligninolytic bacterial strain Erwinia billingiae QL-Z3. Under optimized conditions, its rate of lignin degradation was 25.24% at 1.5 g/L lignin as the sole carbon source. Whole genome sequencing revealed 4556 genes in the genome of QL-Z3. Among 4428 protein-coding genes are 139 CAZyme genes, including 54 glycoside hydrolase (GH) and 16 auxiliary activity (AA) genes. In addition, 74 genes encoding extracellular enzymes are potentially involved in lignin degradation. Real-time PCR quantification demonstrated that the expression of potential ligninolytic genes were significantly induced by lignin. 8 knock-out mutants and complementary strains were constructed. Disruption of the gene for ELAC_205 (laccase) as well as EDYP_48 (Dyp-type peroxidase), ESOD_1236 (superoxide dismutase), EDIO_858 (dioxygenase), EMON_3330 (monooxygenase), or EMCAT_3587 (manganese catalase) significantly reduced the lignin-degrading activity of QL-Z3 by 47–69%. Heterologously expressed and purified enzymes further confirmed their role in lignin degradation. Fourier transform infrared spectroscopy (FTIR) results indicated that the lignin structure was damaged, the benzene ring structure and groups of macromolecules were opened, and the chemical bond was broken under the action of six enzymes encoded by genes. The abundant enzymatic metabolic products by EDYP_48, ELAC_205 and ESOD_1236 were systematically analyzed via liquid chromatography–mass spectrometry (LC–MS) analysis, and then provide a speculative pathway for lignin biodegradation. Finally, The activities of ligninolytic enzymes from fermentation supernatant, namely, LiP, MnP and Lac were 367.50 U/L, 839.50 U/L, and 219.00 U/L by orthogonal optimization. Conclusions Our findings provide that QL-Z3 and its enzymes have the potential for industrial application and hold great promise for the bioconversion of lignin into bioproducts in lignin valorization. |
| first_indexed | 2024-03-07T15:15:07Z |
| format | Article |
| id | doaj.art-8b12c5ea2b7f486296e732306ee9cba2 |
| institution | Directory Open Access Journal |
| issn | 2731-3654 |
| language | English |
| last_indexed | 2024-03-07T15:15:07Z |
| publishDate | 2024-02-01 |
| publisher | BMC |
| record_format | Article |
| series | Biotechnology for Biofuels and Bioproducts |
| spelling | doaj.art-8b12c5ea2b7f486296e732306ee9cba22024-03-05T17:57:57ZengBMCBiotechnology for Biofuels and Bioproducts2731-36542024-02-0117111810.1186/s13068-024-02470-zLignin bioconversion based on genome mining for ligninolytic genes in Erwinia billingiae QL-Z3Shuting Zhao0Dongtao Deng1Tianzheng Wan2Jie Feng3Lei Deng4Qianyi Tian5Jiayu Wang6Umm E. Aiman7Balym Mukhaddi8Xiaofeng Hu9Shaolin Chen10Ling Qiu11Lili Huang12Yahong Wei13State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F UniversityVrije University AmsterdamState Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F UniversityShanghai Personal Biotechnology Co., LtdState Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F UniversityCollege of Mechanical and Electronic Engineering, The West Scientific Observing and Experimental Station of Rural Renewable Energy Exploitation and Utilization of the Ministry of Agriculture, Northwest A&F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F UniversityAbstract Background Bioconversion of plant biomass into biofuels and bio-products produces large amounts of lignin. The aromatic biopolymers need to be degraded before being converted into value-added bio-products. Microbes can be environment-friendly and efficiently degrade lignin. Compared to fungi, bacteria have some advantages in lignin degradation, including broad tolerance to pH, temperature, and oxygen and the toolkit for genetic manipulation. Results Our previous study isolated a novel ligninolytic bacterial strain Erwinia billingiae QL-Z3. Under optimized conditions, its rate of lignin degradation was 25.24% at 1.5 g/L lignin as the sole carbon source. Whole genome sequencing revealed 4556 genes in the genome of QL-Z3. Among 4428 protein-coding genes are 139 CAZyme genes, including 54 glycoside hydrolase (GH) and 16 auxiliary activity (AA) genes. In addition, 74 genes encoding extracellular enzymes are potentially involved in lignin degradation. Real-time PCR quantification demonstrated that the expression of potential ligninolytic genes were significantly induced by lignin. 8 knock-out mutants and complementary strains were constructed. Disruption of the gene for ELAC_205 (laccase) as well as EDYP_48 (Dyp-type peroxidase), ESOD_1236 (superoxide dismutase), EDIO_858 (dioxygenase), EMON_3330 (monooxygenase), or EMCAT_3587 (manganese catalase) significantly reduced the lignin-degrading activity of QL-Z3 by 47–69%. Heterologously expressed and purified enzymes further confirmed their role in lignin degradation. Fourier transform infrared spectroscopy (FTIR) results indicated that the lignin structure was damaged, the benzene ring structure and groups of macromolecules were opened, and the chemical bond was broken under the action of six enzymes encoded by genes. The abundant enzymatic metabolic products by EDYP_48, ELAC_205 and ESOD_1236 were systematically analyzed via liquid chromatography–mass spectrometry (LC–MS) analysis, and then provide a speculative pathway for lignin biodegradation. Finally, The activities of ligninolytic enzymes from fermentation supernatant, namely, LiP, MnP and Lac were 367.50 U/L, 839.50 U/L, and 219.00 U/L by orthogonal optimization. Conclusions Our findings provide that QL-Z3 and its enzymes have the potential for industrial application and hold great promise for the bioconversion of lignin into bioproducts in lignin valorization.https://doi.org/10.1186/s13068-024-02470-zBiomass utilizationLigninolytic geneGenetic modificationLignin degradation productDegradation mechanism |
| spellingShingle | Shuting Zhao Dongtao Deng Tianzheng Wan Jie Feng Lei Deng Qianyi Tian Jiayu Wang Umm E. Aiman Balym Mukhaddi Xiaofeng Hu Shaolin Chen Ling Qiu Lili Huang Yahong Wei Lignin bioconversion based on genome mining for ligninolytic genes in Erwinia billingiae QL-Z3 Biotechnology for Biofuels and Bioproducts Biomass utilization Ligninolytic gene Genetic modification Lignin degradation product Degradation mechanism |
| title | Lignin bioconversion based on genome mining for ligninolytic genes in Erwinia billingiae QL-Z3 |
| title_full | Lignin bioconversion based on genome mining for ligninolytic genes in Erwinia billingiae QL-Z3 |
| title_fullStr | Lignin bioconversion based on genome mining for ligninolytic genes in Erwinia billingiae QL-Z3 |
| title_full_unstemmed | Lignin bioconversion based on genome mining for ligninolytic genes in Erwinia billingiae QL-Z3 |
| title_short | Lignin bioconversion based on genome mining for ligninolytic genes in Erwinia billingiae QL-Z3 |
| title_sort | lignin bioconversion based on genome mining for ligninolytic genes in erwinia billingiae ql z3 |
| topic | Biomass utilization Ligninolytic gene Genetic modification Lignin degradation product Degradation mechanism |
| url | https://doi.org/10.1186/s13068-024-02470-z |
| work_keys_str_mv | AT shutingzhao ligninbioconversionbasedongenomeminingforligninolyticgenesinerwiniabillingiaeqlz3 AT dongtaodeng ligninbioconversionbasedongenomeminingforligninolyticgenesinerwiniabillingiaeqlz3 AT tianzhengwan ligninbioconversionbasedongenomeminingforligninolyticgenesinerwiniabillingiaeqlz3 AT jiefeng ligninbioconversionbasedongenomeminingforligninolyticgenesinerwiniabillingiaeqlz3 AT leideng ligninbioconversionbasedongenomeminingforligninolyticgenesinerwiniabillingiaeqlz3 AT qianyitian ligninbioconversionbasedongenomeminingforligninolyticgenesinerwiniabillingiaeqlz3 AT jiayuwang ligninbioconversionbasedongenomeminingforligninolyticgenesinerwiniabillingiaeqlz3 AT ummeaiman ligninbioconversionbasedongenomeminingforligninolyticgenesinerwiniabillingiaeqlz3 AT balymmukhaddi ligninbioconversionbasedongenomeminingforligninolyticgenesinerwiniabillingiaeqlz3 AT xiaofenghu ligninbioconversionbasedongenomeminingforligninolyticgenesinerwiniabillingiaeqlz3 AT shaolinchen ligninbioconversionbasedongenomeminingforligninolyticgenesinerwiniabillingiaeqlz3 AT lingqiu ligninbioconversionbasedongenomeminingforligninolyticgenesinerwiniabillingiaeqlz3 AT lilihuang ligninbioconversionbasedongenomeminingforligninolyticgenesinerwiniabillingiaeqlz3 AT yahongwei ligninbioconversionbasedongenomeminingforligninolyticgenesinerwiniabillingiaeqlz3 |