Identification of novel enzymes with different hydrolytic activities by metagenome expression cloning

Lämmle, Katrin; Zipper, Hubert; Breuer, Michael; Hauer, Bernhard; Buta, Christiane; Brunner, Herwig; Rupp, Steffen

doi:10.1016/j.jbiotec.2006.07.036

Cited by 139 publications

(96 citation statements)

References 81 publications

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“…Liu et al (2010) and Syren et al (2010) employed rational design method for screening of lipases. Meta genomics approach, a molecular genomics approach was employed for the screening of non cultivated microbes (Steele et al, 2009;Lammle et al, 2007;Rondon et al, 2000;Henne et al, 2000;Yun and Ryu, 2005). This approach is now being widely employed to search novel industrial enzymes because of the availability of genetic material of most of the organisms (Lorenz and Eck, 2005;Kakirde et al, 2010;Kennedy et al, 2008;Jiang et al, 2010).…”

Section: Molecular Methods For Screening Of Lipasesmentioning

confidence: 99%

A Short Review on Various Screening Methods to Isolate Potential Lipase Producers: Lipases-the Present and Future Enzymes of Biotech Industry

Lanka¹,

Latha²

2015

International J. of Biological Chemistry

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The increased demand for microbial originated Industrial enzymes especially lipases which have received least priority till last one and half decades and gained lots of importance in recent days owing to their applications in wide variety of fields such as food, dairy, pharmaceutical, detergent, textile, oleo-chemical, perfume and cosmetic industries etc., has lead to the identification of novel enzymes from new sources with unique properties. The present review mainly focuses on various currently available screening methods for identification of lipase producers.

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Section: Molecular Methods For Screening Of Lipasesmentioning

confidence: 99%

A Short Review on Various Screening Methods to Isolate Potential Lipase Producers: Lipases-the Present and Future Enzymes of Biotech Industry

Lanka¹,

Latha²

2015

International J. of Biological Chemistry

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“…The cultureindependent approach used here also allowed the identification of other uncultured key microbes sustaining termite xylophagy that are potential producers of hydrolytic enzymes. These microorganisms can be exploited by metagenome expression cloning (Lämmle et al 2007). Reticulitermes lucifugus can be considered an acceptable source of hydrolytic enzymes for application in the conversion of lignocellulose into biofuels.…”

Section: Phylogenetic Analysis Of Cellulolytic Isolatesmentioning

confidence: 99%

The gut microbiota of the wood-feeding termite Reticulitermes lucifugus (Isoptera; Rhinotermitidae)

et al. 2015

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Termite gut is host to a complex microbial community consisting of prokaryotes, and in some cases flagellates, responsible for the degradation of lignocellulosic material. Here we report data concerning the analysis of the gut microbiota of Reticulitermes lucifugus (Rossi), a lower termite species that lives in underground environments and is widespread in Italy, where it causes damage to wood structures of historical and artistic monuments. A 16S rRNA gene clone library revealed that the R. lucifugus gut is colonized by members of five phyla in the domain Bacteria: Firmicutes (49 % of clones), Proteobacteria (24 %), Spirochaetes (14 %), the candidatus TG1 phylum (12 %), and Bacteroidetes (1 %). A collection of cellulolytic aerobic bacteria was isolated from the gut of R. lucifugus by enrichment cultures on different cellulose and lignocellulose substrates. Results showed that the largest amount of culturable cellulolytic bacteria of R. lucifugus belongs to Firmicutes in the genera Bacillus and Paenibacillus (67 %). These isolates are also able to grow on xylan and show the largest clear zone diameter in the Congo red test. Reticulitermes lucifugus hosts a diverse community of bacteria and could be considered an acceptable source of hydrolytic enzymes for biotechnological applications.

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“…Techniques such as quantitative PCR (qPCR) (5), microarrays (6), clone libraries (7), and stable-isotope probing (8) have been used successfully to identify organisms potentially involved in biodegradation. Substrate-induced gene expression (SIGEX) was proposed as a method for uncovering novel catabolic operons from metagenomes (9)(10)(11)(12).…”

mentioning

confidence: 99%

Use of Substrate-Induced Gene Expression in Metagenomic Analysis of an Aromatic Hydrocarbon-Contaminated Soil

Meier

Paterson

Lambert

2016

Appl Environ Microbiol

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Metagenomics allows the study of genes related to xenobiotic degradation in a culture-independent manner, but many of these studies are limited by the lack of genomic context for metagenomic sequences. This study combined a phenotypic screen known as substrate-induced gene expression (SIGEX) with whole-metagenome shotgun sequencing. SIGEX is a high-throughput promoter-trap method that relies on transcriptional activation of a green fluorescent protein (GFP) reporter gene in response to an inducing compound and subsequent fluorescence-activated cell sorting to isolate individual inducible clones from a metagenomic DNA library. We describe a SIGEX procedure with improved library construction from fragmented metagenomic DNA and improved flow cytometry sorting procedures. We used SIGEX to interrogate an aromatic hydrocarbon (AH)-contaminated soil metagenome. The recovered clones contained sequences with various degrees of similarity to genes (or partial genes) involved in aromatic metabolism, for example, nahG (salicylate oxygenase) family genes and their respective upstream nahR regulators. To obtain a broader context for the recovered fragments, clones were mapped to contigs derived from de novo assembly of shotgun-sequenced metagenomic DNA which, in most cases, contained complete operons involved in aromatic metabolism, providing greater insight into the origin of the metagenomic fragments. A comparable set of contigs was generated using a significantly less computationally intensive procedure in which assembly of shotgun-sequenced metagenomic DNA was directed by the SIGEX-recovered sequences. This methodology may have broad applicability in identifying biologically relevant subsets of metagenomes (including both novel and known sequences) that can be targeted computationally by in silico assembly and prediction tools.T he massive influx of novel sequence data derived from nextgeneration sequencing (NGS) technologies, in the context of both individual genomes (1) and metagenomes (2, 3), has far outstripped efforts to link those sequences to specific organisms and biological functions (4). Techniques such as quantitative PCR (qPCR) (5), microarrays (6), clone libraries (7), and stable-isotope probing (8) have been used successfully to identify organisms potentially involved in biodegradation. Substrate-induced gene expression (SIGEX) was proposed as a method for uncovering novel catabolic operons from metagenomes (9-12). SIGEX is a promoter trap method based on single-cell sorting of clones from a plasmid library using flow cytometry (FCM), where metagenomic clones of interest are identified by the increased expression of a downstream fluorescent reporter gene in the presence, but not in the absence, of an inducing compound. SIGEX was initially perceived as having great potential for mining genes from metagenomic samples in a high-throughput manner, without requiring prior knowledge of the sequences being screened for (13-15). However, SIGEX, and metagenomic promoter traps in general, has not lived up to this pote...

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Identification of novel enzymes with different hydrolytic activities by metagenome expression cloning

Cited by 139 publications

References 81 publications

A Short Review on Various Screening Methods to Isolate Potential Lipase Producers: Lipases-the Present and Future Enzymes of Biotech Industry

A Short Review on Various Screening Methods to Isolate Potential Lipase Producers: Lipases-the Present and Future Enzymes of Biotech Industry

The gut microbiota of the wood-feeding termite Reticulitermes lucifugus (Isoptera; Rhinotermitidae)

Use of Substrate-Induced Gene Expression in Metagenomic Analysis of an Aromatic Hydrocarbon-Contaminated Soil

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