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

Abstract

BackgroundLignin 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.ResultsGenomic 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.ConclusionsThe unusual aerobic ‘-CoA’-mediated degradation pathway of phenylacetate and benzoate (reported only in 16 and 4–5% of total sequenced 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 provided validation 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.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1148-2) contains supplementary material, which is available to authorized users.

Public questions spur the discovery of new bacterial species associated with lignin bioconversion of industrial waste

“…Peroxdiases have also been shown to play a role in oxidative damage formed during metabolism of lignin and other aromatic compounds as well as being differentially expressed by Pandorawa sp. ISTKB in the presence of lignin-derived aromatics [14]. The proteomic analysis of the secretome of C. lapagei presented here represents an excellent starting point for identifying and characterizing enzymes that could be developed for applications in the bioenergy, wood and pulping, textiles and chemical production industries requiring lignocellulose degradation and depolymerization enzymes.…”

“…Proteomic analysis has been conducted on some lignin degrading strains including Pandoraea sp. ISTKB [14]. Lignin-degrading bacteria have also been analysed for use in product generation from black liquor [15].…”

Biotransformation of lignin: Mechanisms, applications and future work

“…To illustrate the details and metabolic pathways of lignin bioconver- and its presence could also increase the energy production efficiency. 139 With kraft lignin and vanillic acid as substrates, respectively, Kumar et al 140 analyzed the proteome and identified the differently expressed proteins between kraft lignin and vanillic acid as substrates.…”

Bioconversion of lignin and its derivatives into polyhydroxyalkanoates: Challenges and opportunities

“…ISTKB was identified during screening of rhizospheric soil samples taken from the coastal region and was found to be able to use kraft lignin as a sole carbon source for growth. This bacterium possesses lignin peroxidase and MnP enzymes showing both intracellular and extracellular laccase activities . It showed about 21–60% PHA accumulation, while growing on various lignin and related substrates.…”

“…Although such screening is helpful and used widely, one major challenge is our inability to culture the un‐culturable in laboratory conditions. Moreover, high‐throughput sequencing and related techniques have helped to pinpoint the untapped genome and potential enzymes that can have significant industrial applications . Besides this, the complex compounds released after deconstruction (by any method) are not naturally preferred substrate to the bacteria.…”