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Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating beta-proteobacterium Pandoraea sp ISTKB

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Title Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating beta-proteobacterium Pandoraea sp ISTKB
 
Creator Kumar, Madan
Verma, Sandhya
Gazara, Rajesh Kumar
Kumar, Manish
Pandey, Ashok
Verma, Praveen K.
Thakur, Indu Shekhar
 
Subject Genomics
Vanillic acid
Lignin
Polyhydroxyalkanoate
Gene cluster
Label-free quantification
 
Description Accepted date: 17 May 2018
Background: Lignin is a major component of plant biomass and is recalcitrant to degradation due to its complex and heterogeneous aromatic structure. The biomass-based research mainly focuses on polysaccharides component of biomass and lignin is discarded as waste with very limited usage. The sustainability and success of plant polysaccharide-based biorefinery can be possible if lignin is utilized in improved ways and with minimal waste generation. Discovering new microbial strains and understanding their enzyme system for lignin degradation are necessary for its conversion into fuel and chemicals. The Pandoraea sp. ISTKB was previously characterized for lignin degradation and successfully applied for pretreatment of sugarcane bagasse and polyhydroxyalkanoate (PHA) production. In this study, genomic analysis and proteomics on aromatic polymer kraft lignin and vanillic acid are performed to find the important enzymes for polymer utilization.

Results: Genomic analysis of Pandoraea sp. ISTKB revealed the presence of strong lignin degradation machinery and identified various candidate genes responsible for lignin degradation and PHA production. We also applied label-free quantitative proteomic approach to identify the expression profile on monoaromatic compound vanillic acid (VA) and polyaromatic kraft lignin (KL). Genomic and proteomic analysis simultaneously discovered Dyp-type peroxidase, peroxidases, glycolate oxidase, aldehyde oxidase, GMC oxidoreductase, laccases, quinone oxidoreductase, dioxygenases, monooxygenases, glutathione-dependent etherases, dehydrogenases, reductases, and methyltransferases and various other recently reported enzyme systems such as superoxide dismutases or catalase-peroxidase for lignin degradation. A strong stress response and detoxification mechanism was discovered. The two important gene clusters for lignin degradation and three PHA polymerase spanning gene clusters were identified and all the clusters were functionally active on KL-VA

Conclusions: The unusual aerobic'-CoA'-mediated degradation pathway of phenylacetate and benzoate (reported only in 16 and 4-5% of total seguenced bacterial genomes), peroxidase-accessory enzyme system, and fenton chemistry based are the major pathways observed for lignin degradation. Both ortho and meta ring cleavage pathways for aromatic compound degradation were observed in expression profile. Genomic and proteomic approaches providedvalidation to this strain's robust machinery for the metabolism of recalcitrant compounds and PHA production and provide an opportunity to target important enzymes for lignin valorization in future.
Madan Kumar thanks Council of Scientifc and Industrial Research (CSIR), New
Delhi, India for providing Senior Research Fellowship. P.K.V. thanks the National
Institute of Plant Genome Research, New Delhi, for fnancial support. We thank
Shashi Shekhar Singh and Gagandeep Jhingan for their support in proteomics
work. We are grateful to Jawaharlal Nehru University, New Delhi, India, for
providing fnancial support.
 
Date 2018-06-18T11:47:34Z
2018-06-18T11:47:34Z
2018
 
Type Article
 
Identifier Biotechnology for Biofuels, 11: 154
1754-6834
http://223.31.159.10:8080/jspui/handle/123456789/861
https://biotechnologyforbiofuels.biomedcentral.com/articles/10.1186/s13068-018-1148-2
https://doi.org/10.1186/s13068-018-1148-2
 
Language en_US
 
Format application/pdf
 
Publisher BioMed Central Ltd