Genomic and secretomic insight into lignocellulolytic system of an endophytic bacterium Pantoea ananatis Sd-1

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.

Pantoea ananatis: genomic insights into a versatile pathogen

“…All analysed P. ananatis strains have several CWDEs, including a putative xylanase, pectin acetylesterase, cellulase and two polygalacturonases (De Maayer et al ., ). The lignocellulose‐degrading strain P. ananatis Sd‐1 has an unusually high number of carbohydrate‐active enzymes among members of the species, including enzymes required for the degradation of cellulose and hemicellulose (Ma et al ., ). Included in its arsenal of CWDEs are 59 glycoside hydrolases, 25 carbohydrate esterases, 10 cellulases and two polysaccharide lyases (Ma et al ., ).…”

“…The lignocellulose‐degrading strain P. ananatis Sd‐1 has an unusually high number of carbohydrate‐active enzymes among members of the species, including enzymes required for the degradation of cellulose and hemicellulose (Ma et al ., ). Included in its arsenal of CWDEs are 59 glycoside hydrolases, 25 carbohydrate esterases, 10 cellulases and two polysaccharide lyases (Ma et al ., ). Pantoea ananatis is thus well equipped to degrade the integrity of the plant cell wall and cause disease in its host.…”

“…The secretome of P. ananatis Sd‐1 was analysed and found to encode 154 putative carbohydrate‐active enzymes. These enzymes are predominantly responsible for the degradation of cellulose and hemicellulose in plant cell wall polymers (Ma et al ., ). The secretome also revealed the presence of ligninolytic and lignocellulolytic enzymes and laccases, which have great potential in the lignocellulosic bioenergy industry for the production of biofuels, as well as the decolorization of synthetic dyes (Ma et al ., ; Shi et al ., ).…”

“…However, orthologues of other predicted pathogenicity determinants (Fig. ), such as flagella and fimbriae biosynthetic proteins, non‐fimbrial adhesins, amylovoran/stewartan‐like exopolysaccharide and potential cell wall‐degrading enzymes (CWDEs), are encoded on the genomes of many P. ananatis strains (De Maayer et al ., ; Ma et al ., ; Miller et al ., ). Recent genetic and mutagenic analyses have also contributed to our understanding of the mechanisms underlying P. ananatis phytopathogenesis.…”

Review on the current status of polymer degradation: a microbial approach

“…Fernandez-Fueyo et al (2016) reported lignin degradation with Pleurotus ostreatus. According to Ma et al (2016), P. ananatis Sd-1 produces ligninolytic relevant enzymes in addition to cellulases and hemicellulases. Pereira et al (2016) studied the catabolic pathway for β-aryl ether subunits of lignin.…”