Cloning and identification of novel cellulase genes from uncultured microorganisms in rabbit cecum and characterization of the expressed cellulases

Yue, Feng; Duan, Chengjie; Pang, Hao; Mo, Xin-Chun; Wu, Chunfeng; Yu, Yuan; Hu, Ya-Lin; Wei, Jie; Tang, Ji-Liang; Feng, Jia‐Xun

doi:10.1007/s00253-006-0820-9

Cited by 134 publications

(99 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Zheng et al (66) reported three main hypotheses explaining the enhancement of enzymatic cellulose hydrolysis in the presence of nonionic surfactants: (i) they stabilize the enzyme by reducing thermal and/or mechanical shear forces; (ii) they change the substrate structure, enhancing substrate accessibility; and (iii) they affect enzymesubstrate interaction, preventing enzyme inactivation due to nonproductive adsorption when, for example, lignocellulosic substrates are being hydrolyzed. This last hypothesis does not concern the substrate we used (CMC), and as, generally, no significant (positive or negative) effect of Triton X-100 has been observed on other bacterial cellulase activities characterized with CMC (9,54,63,67), the second hypothesis must not be the reason why Cell5.1_3 activity increases to 350% in the presence of Triton X-100. However, Cell5.1_3 is probably more stable, and therefore more active on CMC, in the presence of Triton X-100.…”

Section: Discussionmentioning

confidence: 99%

Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota

Martin

Biver

Steels

et al. 2014

Appl Environ Microbiol

View full text Add to dashboard Cite

A metagenomic library was constructed from microorganisms associated with the brown alga Ascophyllum nodosum. Functional screening of this library revealed 13 novel putative esterase loci and two glycoside hydrolase loci. Sequence and gene cluster analysis showed the wide diversity of the identified enzymes and gave an idea of the microbial populations present during the sample collection period. Lastly, an endo-␤-1,4-glucanase having less than 50% identity to sequences of known cellulases was purified and partially characterized, showing activity at low temperature and after prolonged incubation in concentrated salt solutions. Previous surveys have revealed that less than 1% of existing microorganisms can be studied by traditional culturing methods. This leaves most microorganisms and their by-products unknown and unexploited (1, 2) and explains why metagenomics, a culture-independent approach using total microbial genomes from environmental samples, has met with great success over the past decade (3, 4). Sequence-based metagenomics has already provided information about the composition, organization, function, and hierarchy of microbial communities in particular habitats (5). On the other hand, functional genomics applied to metagenomic libraries from diverse environments has led to the discovery of many new enzymes and bioactive compounds and to substantial enrichment of genome databases. To date, most of the enzymes brought to light through metagenomics have been derived from soil (6-9) and gut (10-13) samples.Marine microorganisms represent promising candidate sources of original biocatalysts, as they are exposed to extreme conditions of temperature, pressure, salinity, nutrient availability, etc. Hence, functional screening of marine microbial populations should yield new enzymes with specific and unique physiological and biochemical properties, produced by organisms far different from those usually described in terrestrial environments (14). New enzymes have already been identified in marine metagenomic libraries from seawater samples (15, 16) and from microorganisms in symbiosis with marine organisms such as sponges and corals (17). To our knowledge, however, nobody has yet performed functional screening of metagenomic libraries from algal microbial communities. As algal microbial biofilms are in constant interaction with algal biomass, they represent an interesting source of enzymes and other active compounds (18). Sequence-based studies have already revealed the importance and functions of microbial communities living on the surfaces of algae, showing tight interdependence between algae and their biofilms (19-21). Furthermore, many genes coding for enzymes involved in hydrolyzing algal biomass, such as cellulases, xylanases, ␣-amylases, and specific algal polysaccharidases (e.g., agarases, carrageenases, and alginate lyases), have been identified from cultivable marine bacteria (22,23). Only a few such enzymes have been found in marine metagenomes by functional screening. For example, no cellulase gene...

show abstract

Section: Discussionmentioning

confidence: 99%

Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota

Martin

Biver

Steels

et al. 2014

Appl Environ Microbiol

View full text Add to dashboard Cite

show abstract

“…Using this approach, several groups isolated novel enzymes from various environments (Ranjan et al, 2005;Rhee et al, 2005;Feng et al, 2007;Hardeman and Sjoling, 2007;Tirawongsaroj et al, 2008), and many of them were found to offer a good potential as new tools for industrial applications, because their biophysical properties arise from improved adaptations to the conditions met in the environment during the sampling process. Although such studies reported the characterization of metagenome-derived enzymes, insights into their physiological aspect are often lacking.…”

Section: Introductionmentioning

confidence: 99%

Insights into bacterial cellulose biosynthesis by functional metagenomics on Antarctic soil samples

et al. 2009

View full text Add to dashboard Cite

In this study, the mining of an Antarctic soil sample by functional metagenomics allowed the isolation of a cold-adapted protein (RBcel1) that hydrolyzes only carboxymethyl cellulose. The new enzyme is related to family 5 of the glycosyl hydrolase (GH5) protein from Pseudomonas stutzeri (Pst_2494) and does not possess a carbohydrate-binding domain. The protein was produced and purified to homogeneity. RBcel1 displayed an endoglucanase activity, producing cellobiose and cellotriose, using carboxymethyl cellulose as a substrate. Moreover, the study of pH and the thermal dependence of the hydrolytic activity shows that RBcel1 was active from pH 6 to pH 9 and remained significantly active when temperature decreased (18% of activity at 10 1C). It is interesting that RBcel1 was able to synthetize non-reticulated cellulose using cellobiose as a substrate. Moreover, by a combination of bioinformatics and enzyme analysis, the physiological relevance of the RBcel1 protein and its mesophilic homologous Pst_2494 protein from P. stutzeri, A1501, was established as the key enzymes involved in the production of cellulose by bacteria. In addition, RBcel1 and Pst_2494 are the two primary enzymes belonging to the GH5 family involved in this process.

show abstract

“…This can be addressed by functional screening of metagenomic libraries, in order to retrieve genes of interest. Numerous studies have provided conclusive evidence on the potential of such an approach for the identification of novel glycoside-hydrolases from various ecosystems such as soil (Rondon et al 2000;Richardson et al 2002;Voget et al 2003;Pang et al 2009), lakes (Rees et al 2003), hot springs (Tang et al 2006, rumen (Ferrer et al 2005;Guo et al 2008;Liu et al 2008;Duan et al 2009), rabbit (Feng et al 2007), and insect guts (Brennan et al 2004; for review, see Ferrer et al 2009;Li et al 2009;Simon and Daniel 2009;Uchiyama and Miyazaki 2009). In all cases, the identification of the gene responsible for the screened activity was carried out by sequencing only a few kilobases of metagenomic DNA.…”

mentioning

confidence: 99%

Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes

Tasse¹,

Bercovici²,

et al. 2010

View full text Add to dashboard Cite

The human gut microbiome is a complex ecosystem composed mainly of uncultured bacteria. It plays an essential role in the catabolism of dietary fibers, the part of plant material in our diet that is not metabolized in the upper digestive tract, because the human genome does not encode adequate carbohydrate active enzymes (CAZymes). We describe a multi-step functionally based approach to guide the in-depth pyrosequencing of specific regions of the human gut metagenome encoding the CAZymes involved in dietary fiber breakdown. High-throughput functional screens were first applied to a library covering 5.4 3 10 9 bp of metagenomic DNA, allowing the isolation of 310 clones showing beta-glucanase, hemicellulase, galactanase, amylase, or pectinase activities. Based on the results of refined secondary screens, sequencing efforts were reduced to 0.84 Mb of nonredundant metagenomic DNA, corresponding to 26 clones that were particularly efficient for the degradation of raw plant polysaccharides. Seventy-three CAZymes from 35 different families were discovered. This corresponds to a fivefold target-gene enrichment compared to random sequencing of the human gut metagenome. Thirty-three of these CAZy encoding genes are highly homologous to prevalent genes found in the gut microbiome of at least 20 individuals for whose metagenomic data are available. Moreover, 18 multigenic clusters encoding complementary enzyme activities for plant cell wall degradation were also identified. Gene taxonomic assignment is consistent with horizontal gene transfer events in dominant gut species and provides new insights into the human gut functional trophic chain.

show abstract

Cloning and identification of novel cellulase genes from uncultured microorganisms in rabbit cecum and characterization of the expressed cellulases

Cited by 134 publications

References 33 publications

Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota

Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota

Insights into bacterial cellulose biosynthesis by functional metagenomics on Antarctic soil samples

Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes

Contact Info

Product

Resources

About