Expanding functional spaces of enzymes by utilizing whole genome treasure for library construction

Oh, Hyo-Jeong; Cho, Kyoung Won; Jung, I J; Kim, Won‐Ho; Hur, Byung‐Ki; Kim, Geun-Joong

doi:10.1016/j.molcatb.2003.06.007

Cited by 7 publications

(6 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The potential for application of metagenomics to biotechnology seems endless. Functional screens have identified new enzymes (39,52,53,67,68,72,73,88,93,104,118,122,124,144) and antibiotics (22,23,39,61,69,91,110,118,146) and other reagents in libraries from diverse environments. A number of barriers have limited the discovery of new genes that provide insight into microbial community structure and function or that can be used to solve medical, agricultural, or industrial problems.…”

Section: Discussionmentioning

confidence: 99%

Metagenomics: Application of Genomics to Uncultured Microorganisms

Handelsman

2004

Microbiol Mol Biol Rev

1,993

1,038

View full text Add to dashboard Cite

Metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The development of metagenomics stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. This evidence was derived from analyses of 16S rRNA gene sequences amplified directly from the environment, an approach that avoided the bias imposed by culturing and led to the discovery of vast new lineages of microbial life. Although the portrait of the microbial world was revolutionized by analysis of 16S rRNA genes, such studies yielded only a phylogenetic description of community membership, providing little insight into the genetics, physiology, and biochemistry of the members. Metagenomics provides a second tier of technical innovation that facilitates study of the physiology and ecology of environmental microorganisms. Novel genes and gene products discovered through metagenomics include the first bacteriorhodopsin of bacterial origin; novel small molecules with antimicrobial activity; and new members of families of known proteins, such as an Na+(Li+)/H+ antiporter, RecA, DNA polymerase, and antibiotic resistance determinants. Reassembly of multiple genomes has provided insight into energy and nutrient cycling within the community, genome structure, gene function, population genetics and microheterogeneity, and lateral gene transfer among members of an uncultured community. The application of metagenomic sequence information will facilitate the design of better culturing strategies to link genomic analysis with pure culture studies

show abstract

Section: Discussionmentioning

confidence: 99%

Metagenomics: Application of Genomics to Uncultured Microorganisms

Handelsman

2004

Microbiol Mol Biol Rev

1,993

1,038

View full text Add to dashboard Cite

show abstract

“…Other terms have been used to describe the same method, including environmental DNA libraries (110), zoolibraries (55), soil DNA libraries (68), eDNA libraries (13), recombinant environmental libraries (22), whole genome treasures (77), community genome (114), whole genome shotgun sequencing (115), and probably others. In this review, we use metagenomics to describe work that has been presented with all of these names because it is the most commonly used term (15, 27, 35, 59-61, 65, 66, 82, 105, 107, 117, 118), was used for the title of the first international conference on the topic ("Metagenomics 2003" held in Darmstadt, Germany), and is the focus of an upcoming issue of the journal Environmental Microbiology.…”

Section: Metagenomics Definedmentioning

confidence: 99%

“…The uncultured microbiota must play pivotal roles in natural environmental processes and are a large untapped resource for biotechnology applications. Exploiting the rich microbial biodiversity for enzyme and natural product discovery is an active research area that has been reviewed elsewhere (39,45,46,65,66,77,97,104). This review discusses the application of culture-independent genomics-based approaches to understand the genetic diversity, population structure, and ecology of complex microbial assemblages (26,93,94).…”

Section: Introductionmentioning

confidence: 99%

Metagenomics: Genomic Analysis of Microbial Communities

2004

View full text Add to dashboard Cite

▪ Abstract Uncultured microorganisms comprise the majority of the planet's biological diversity. Microorganisms represent two of the three domains of life and contain vast diversity that is the product of an estimated 3.8 billion years of evolution. In many environments, as many as 99% of the microorganisms cannot be cultured by standard techniques, and the uncultured fraction includes diverse organisms that are only distantly related to the cultured ones. Therefore, culture-independent methods are essential to understand the genetic diversity, population structure, and ecological roles of the majority of microorganisms. Metagenomics, or the culture-independent genomic analysis of an assemblage of microorganisms, has potential to answer fundamental questions in microbial ecology. This review describes progress toward understanding the biology of uncultured Bacteria, Archaea, and viruses through metagenomic analyses.

show abstract

“…Functional metagenomics has helped us to identify new enzymes [33,49,50,51,52,53,32,54,55] and antibiotics [56,46,47,57,48]. Metagenomics may further enhance our understanding of many of the exotic and familiar habitats that are attracting the attention of microbial ecologists, including deep sea thermal vents; acidic hot springs; permafrost, temperate, desert, and cold soils; Antarctic frozen lakes; and eukaryotic host organs-the human mouth and gut, termite and caterpillar guts, plant rhizospheres, phyllospheres, and fungi in lichen symbioses [35].…”

Section: Metagenomicsmentioning

confidence: 99%