A metagenomic approach for the identification and cloning of an endoglucanase from rice straw compost

Yeh, Yi-Fang; Chang, Samuel Chia-yu; Kuo, Hsion-Wen; Tong, C. C.; Yu, Su‐May; Ho, Tuan‐Hua David

doi:10.1016/j.gene.2012.07.076

Cited by 42 publications

(19 citation statements)

References 36 publications

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“…However, all enzymes displayed their maximum activities at a pH range of 5.4–6.2. Similar pH optima have been previously reported with other cellulases/endoglucanases of related GH-8 and GH-12 families and polygalacturonases/pectinases of related GH-28 family such as those reported by Yeh et al [ 72 ] for a GH-12 endoglucanase from rice straw compost, Lin et al [ 75 ] for a GH-8 cellulase from E. coli K12 strain, and Maisuria et al [ 83 ] and Maller et al [ 84 ] for GH-28 polygalacturonases from Pcc -BR1 and Aspergillus niveus , respectively. Figure 3 a also displays a similar decline in activity for each enzyme in the alkaline pH range, 7.0–10.…”

Section: Biochemical Characterization Of Recombinant Cel12b Cel8c Asupporting

confidence: 89%

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Molecular and biochemical characterization of recombinant cel12B, cel8C, and peh28 overexpressed in Escherichia coli and their potential in biofuel production

Ibrahim

Jones

Taylor

et al. 2017

Biotechnol Biofuels

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BackgroundThe high crystallinity of cellulosic biomass myofibrils as well as the complexity of their intermolecular structure is a significant impediment for biofuel production. Cloning of celB-, celC-encoded cellulases (cel12B and cel8C) and peh-encoded polygalacturonase (peh28) from Pectobacterium carotovorum subsp. carotovorum (Pcc) was carried out in our previous study using Escherichia coli as a host vector. The current study partially characterizes the enzymes’ molecular structures as well as their catalytic performance on different substrates which can be used to improve their potential for lignocellulosic biomass conversion.Resultsβ-Jelly roll topology, (α/α)6 antiparallel helices and right-handed β-helices were the folds identified for cel12B, cel8C, and peh28, respectively, in their corresponding protein model structures. Purifications of 17.4-, 6.2-, and 6.0-fold, compared to crude extract, were achieved for cel12B and cel8C, and peh28, respectively, using specific membrane ultrafiltrations and size-exclusion chromatography. Avicel and carboxymethyl cellulose (CMC) were substrates for cel12B, whereas for cel8C catalytic activity was only shown on CMC. The enzymes displayed significant synergy on CMC but not on Avicel when tested for 3 h at 45 °C. No observed β-glucosidase activities were identified for cel8C and cel12B when tested on p-nitrophenyl-β-d-glucopyranoside. Activity stimulation of 130% was observed when a recombinant β-glucosidase from Pcc was added to cel8C and cel12B as tested for 3 h at 45 °C. Optimum temperature and pH of 45 °C and 5.4, respectively, were identified for all three enzymes using various substrates. Catalytic efficiencies (k cat/K m) were calculated for cel12B and cel8C on CMC as 0.141 and 2.45 ml/mg/s respectively, at 45 °C and pH 5.0 and for peh28 on polygalacturonic acid as 4.87 ml/mg/s, at 40 °C and pH 5.0. Glucose and cellobiose were the end-products identified for cel8C, cel12B, and β-glucosidase acting together on Avicel or CMC, while galacturonic acid and other minor co-products were identified for peh28 action on pectin.ConclusionsThis study provides some insight into which parameters should be optimized when application of cel8C, cel12B, and peh28 to biomass conversion is the goal.

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Section: Biochemical Characterization Of Recombinant Cel12b Cel8c Asupporting

confidence: 89%

“…Table 3 shows that neither cel12B nor cel8C activities were detected on p -NPG and, thus, the enzymes’ β-glucosidase function can be dismissed. Similar findings have been reported for endoglucanases from different sources tested on p -NPG and cellobiose as substrates [ 72 , 73 ].…”

Section: Biochemical Characterization Of Recombinant Cel12b Cel8c Asupporting

confidence: 88%

Molecular and biochemical characterization of recombinant cel12B, cel8C, and peh28 overexpressed in Escherichia coli and their potential in biofuel production

Ibrahim

Jones

Taylor

et al. 2017

Biotechnol Biofuels

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“…Several studies showed that cellulose can be degraded by certain species within Micromonospora in thermophilic environments [ 13 , 36 , 37 ]. A prior study also showed that M. aurantiaca was stable over a wide temperature range (55–70 °C) [ 35 ]. In addition, Micromonospora spp .…”

Section: Discussionmentioning

confidence: 98%

“…Micromonosporaceae was the third largest contributor to dissimilarity between T1 and T6 for reactors R20 and R23 (Table 4 ) and it was the fourth largest contributor to dissimilarity for reactor R21. Two species, M. aurantiaca and M. carbonacea , have been identified in rice straw compost [ 34 , 35 ], and M. carbonacea was able to break down cellulose, hemicelluloses, and lignin in rice straw composted with chicken manure [ 34 ]. Several studies showed that cellulose can be degraded by certain species within Micromonospora in thermophilic environments [ 13 , 36 , 37 ].…”

Section: Discussionmentioning

confidence: 99%

Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions

Reddy

Simmons

et al. 2015

Biotechnol Biofuels

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BackgroundMicrobial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methods included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions.ResultsHigh-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms.ConclusionsA stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival under thermophilic and high-solid conditions. The results suggest that the presence of microorganisms may be more important than their relative abundance in retaining an active microbial community.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-015-0392-y) contains supplementary material, which is available to authorized users.

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“…Metagenomic investigations related to disease suppression with organic amendments have focused primarily on compost [174,175], with limited studies on compost tea. In a study designed to evaluate the impact of organic and conventional management on the phyllosphere microbial ecology of an apple crop, Ottesen et al [176] used clone library method to assess if increased biological food safety risks might be linked with the bacterial communities associated with either treatment.…”

Section: Research Approaches Traditionalmentioning

confidence: 99%

Potential of compost tea for suppressing plant diseases.

Martin¹

2015

CABI Reviews

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Numerous studies have demonstrated that water-based compost preparations, referred to as compost tea and compost-water extract, can suppress phytopathogens and plant diseases. Despite its potential, compost tea has generally been considered as inadequate for use as a biocontrol agent in conventional cropping systems but important to organic producers who have limited disease control options. The major impediments to the use of compost tea have been the lessthan-desirable and inconsistent levels of plant disease suppression as influenced by compost tea production and application factors including compost source and maturity, brewing time and aeration, dilution and application rate and application frequency. Although the mechanisms involved in disease suppression are not fully understood, sterilization of compost tea has generally resulted in a loss in disease suppressiveness. This indicates that the mechanisms of suppression are often, or predominantly, biological, although physico-chemical factors have also been implicated. Increasing the use of molecular approaches, such as metagenomics, metaproteomics, metatranscriptomics and metaproteogenomics should prove useful in better understanding the relationships between microbial abundance, diversity, functions and disease suppressive efficacy of compost tea. Such investigations are crucial in developing protocols for optimizing the compost tea production process so as to maximize disease suppressive effect without exposing the manufacturer or user to the risk of human pathogens. To this end, it is recommended that compost tea be used as part of an integrated disease management system.

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A metagenomic approach for the identification and cloning of an endoglucanase from rice straw compost

Cited by 42 publications

References 36 publications

Molecular and biochemical characterization of recombinant cel12B, cel8C, and peh28 overexpressed in Escherichia coli and their potential in biofuel production

Molecular and biochemical characterization of recombinant cel12B, cel8C, and peh28 overexpressed in Escherichia coli and their potential in biofuel production

Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions

Potential of compost tea for suppressing plant diseases.

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