Abstract
BackgroundExploring microorganisms especially bacteria associated with the degradation of lignocellulosic biomass shows great potentials in biofuels production. The rice endophytic bacterium Pantoea ananatis Sd-1 with strong lignocellulose degradation capacity has been reported in our previous study. However, a comprehensive analysis of its corresponding degradative system has not yet been conducted. The aim of this work is to identify and characterize the lignocellulolytic enzymes of the bacterium to understand its mechanism of lignocellulose degradation and facilitate its application in sustainable energy production.ResultsThe genomic analysis revealed that there are 154 genes encoding putative carbohydrate-active enzymes (CAZy) in P. ananatis Sd-1. This number is higher than that of compared cellulolytic and ligninolytic bacteria as well as other eight P. ananatis strains. The CAZy in P. ananatis Sd-1 contains a complete repertoire of enzymes required for cellulose and hemicellulose degradation. In addition, P. ananatis Sd-1 also possesses plenty of genes encoding potential ligninolytic relevant enzymes, such as multicopper oxidase, catalase/hydroperoxidase, glutathione S-transferase, and quinone oxidoreductase. Quantitative real-time PCR analysis of parts of genes encoding lignocellulolytic enzymes revealed that they were significantly up-regulated (at least P < 0.05) in presence of rice straw. Further identification of secretome of P. ananatis Sd-1 by nano liquid chromatography–tandem mass spectrometry confirmed that considerable amounts of proteins involved in lignocellulose degradation were only detected in rice straw cultures. Rice straw saccharification levels by the secretome of P. ananatis Sd-1 reached 129.11 ± 2.7 mg/gds. Correspondingly, the assay of several lignocellulolytic enzymes including endoglucanase, exoglucanase, β-glucosidase, xylanase-like, lignin peroxidase-like, and laccase-like activities showed that these enzymes were more active in rice straw relative to glucose substrates. The high enzymes activities were not attributed to bacterial cell densities but to the difference of secreted protein contents.ConclusionOur results indicate that P. ananatis Sd-1 can produce considerable lignocellulolytic enzymes including cellulases, hemicellulases, and ligninolytic relevant enzymes. The high activities of those enzymes could be efficiently induced by lignocellulosic biomass. This identified degradative system is valuable for the lignocellulosic bioenergy industry.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0439-8) contains supplementary material, which is available to authorized users.
Highlights
Exploring microorganisms especially bacteria associated with the degradation of lignocellulosic biomass shows great potentials in biofuels production
To identify genes involved in lignocellulose degradation, coding sequences (CDS) were analyzed using dbCAN carbohydrate-active enzymes (CAZy) annotation algorithm
Results indicated that 154 genes have multiple domains assigned to CAZy families, including 59 glycoside hydrolases (GHs), 25 carbohydrate esterases (CEs), 2 polysaccharide lyases (PLs), 9 enzymes with auxillary activities (AAs), and 11 carbohydrate binding modules (CBMs); 28 of these proteins contain signal peptides and are predicted to be extracellular proteins (Additional file 2: Table S2)
Summary
Exploring microorganisms especially bacteria associated with the degradation of lignocellulosic biomass shows great potentials in biofuels production. The aim of this work is to identify and characterize the lignocellulolytic enzymes of the bacterium to understand its mechanism of lignocellulose degradation and facilitate its application in sustainable energy production. The main components of lignocellulose are polysaccharides and lignin. They are bound together in a matrix and the recalcitrance of structure gives rise to a major bottleneck in the efficient conversion of lignocellulosic biomass to biofuels [2]. Exploring highly efficient lignocellulose decomposition microorganisms has attracted significant research attention [3]. Only a limited number of microorganisms, such as various types of fungi, were found to breakdown the complex lignocellulose polymer structures [4]. Bacteria have great advantages over fungi due to their rapid growth, wide range of environmental adaptability, and facilitative genetic manipulations [5, 6]
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