Dataset Information

Genome Sequence of Pantoea ananatis Strain AMG 501, a Plant Growth-Promoting Bacterium Isolated from Rice Leaves Grown in Paddies of Southern Spain.

ABSTRACT: Pantoea ananatis AMG 501 is a plant growth-promoting bacterium isolated from rice leaves. Its genome was estimated at 5,102,640 bp with 4,994 coding sequences, encompassing genes related to the metabolism of carbohydrates, to the synthesis of auxins, siderophores, and homoserine lactones, and to the type I, II, III, IV, and VI secretion systems.

SUBMITTER: Megias E

PROVIDER: S-EPMC5571415 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Genome Sequence of <i>Pantoea ananatis</i> Strain AMG 501, a Plant Growth-Promoting Bacterium Isolated from Rice Leaves Grown in Paddies of Southern Spain.

Megías Esaú E Reis Junior Fábio Bueno FB Ribeiro Renan Augusto RA Ollero Francisco Javier FJ Megías Manuel M Hungria Mariangela M

Genome announcements 20170824 34

<i>Pantoea ananatis</i> AMG 501 is a plant growth-promoting bacterium isolated from rice leaves. Its genome was estimated at 5,102,640 bp with 4,994 coding sequences, encompassing genes related to the metabolism of carbohydrates, to the synthesis of auxins, siderophores, and homoserine lactones, and to the type I, II, III, IV, and VI secretion systems. ...[more]

PMID: 28839029

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Project description:BACKGROUND:Exploring 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. RESULTS:The 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, ?-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. CONCLUSION:Our 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.

Project description:Cysteine is a commercially important amino acid; however, it lacks an efficient fermentative production method. Due to its cytotoxicity, intracellular cysteine levels are stringently controlled via several regulatory modes. Managing its toxic effects as well as understanding and deregulating the complexities of regulation are crucial for establishing the fermentative production of cysteine. The regulatory modes include feedback inhibition of key metabolic enzymes, degradation, efflux pumps, and the transcriptional regulation of biosynthetic genes by a master cysteine regulator, CysB. These processes have been extensively studied using Escherichia coli for overproducing cysteine by fermentation. In this study, we genetically engineered Pantoea ananatis, an emerging host for the fermentative production of bio-based materials, to identify key factors required for cysteine production. According to this and our previous studies, we identified a major cysteine desulfhydrase gene, ccdA (formerly PAJ_0331), involved in cysteine degradation, and the cysteine efflux pump genes cefA and cefB (formerly PAJ_3026 and PAJ_p0018, respectively), which may be responsible for downregulating the intracellular cysteine level. Our findings revealed that ccdA deletion and cefA and cefB overexpression are crucial factors for establishing fermentative cysteine production in P. ananatis and for obtaining a higher cysteine yield when combined with genes in the cysteine biosynthetic pathway. To our knowledge, this is the first demonstration of cysteine production in P. ananatis, which has fundamental implications for establishing overproduction in this microbe.IMPORTANCE The efficient production of cysteine is a major challenge in the amino acid fermentation industry. In this study, we identified cysteine efflux pumps and degradation pathways as essential elements and genetically engineered Pantoea ananatis, an emerging host for the fermentative production of bio-based materials, to establish the fermentative production of cysteine. This study provides crucial insights into the design and construction of cysteine-producing strains, which may play central roles in realizing commercial basis production.

Dataset Information

Genome Sequence of Pantoea ananatis Strain AMG 501, a Plant Growth-Promoting Bacterium Isolated from Rice Leaves Grown in Paddies of Southern Spain.

Publications

Genome Sequence of <i>Pantoea ananatis</i> Strain AMG 501, a Plant Growth-Promoting Bacterium Isolated from Rice Leaves Grown in Paddies of Southern Spain.

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