A perspective: metatranscriptomics as a tool for the discovery of novel biocatalysts.

In this mini-review, advantages and current bottlenecks of metatranscriptomic-sequencing for the discovery of novel enzymes for biotechnological applications will be discussed. Comparison of this innovative approach to traditional metagenomic-sequencing will illustrate that expression profiling has a promising future as a direct and very efficient method for the discovery of novel biocatalysts, even from complex microbial communities.

[1]  N. Pace.  A molecular view of microbial diversity and the biosphere. , 1997, Science.

[2]  Weidong Deng,et al.  The use of molecular techniques based on ribosomal RNA and DNA for rumen microbial ecosystem studies: a review , 2008, Molecular Biology Reports.

[3]  Ruifu Yang,et al.  DNA microarray-based global transcriptional profiling of Yersinia pestis in multicellularity , 2008, The Journal of Microbiology.

[4]  Philip Hugenholtz,et al.  A renaissance for the pioneering 16S rRNA gene. , 2008, Current opinion in microbiology.

[5]  L. Giver,et al.  Engineered enzymes for chemical production. , 2008, Biotechnology and bioengineering.

[6]  B. Ward,et al.  Sediment denitrifier community composition and nirS gene expression investigated with functional gene microarrays. , 2008, Environmental microbiology.

[7]  H. Winkler,et al.  DNA Microarray Analysis of the Heat Shock Transcriptome of the Obligate Intracytoplasmic Pathogen Rickettsia prowazekii , 2008, Applied and Environmental Microbiology.

[8]  D. Brady,et al.  A novel family VIII carboxylesterase derived from a leachate metagenome library exhibits promiscuous β-lactamase activity on nitrocefin , 2009, Applied Microbiology and Biotechnology.

[9]  P. Schenk,et al.  Isolation and analysis of mRNA from environmental microbial communities. , 2008, Journal of microbiological methods.

[10]  L. Øvreås,et al.  Prokaryotic Diversity--Magnitude, Dynamics, and Controlling Factors , 2002, Science.

[11]  Jürgen Eck,et al.  Metagenomics: An inexhaustible access to nature's diversity , 2006, Biotechnology journal.

[12]  Maureen L. Coleman,et al.  Microbial community gene expression in ocean surface waters , 2008, Proceedings of the National Academy of Sciences.

[13]  Mercedes Moreno-Paz,et al.  Analysis of environmental transcriptomes by DNA microarrays. , 2007, Environmental microbiology.

[14]  M. Moran,et al.  Analysis of Microbial Gene Transcripts in Environmental Samples , 2005, Applied and Environmental Microbiology.

[15]  Gabor T. Marth,et al.  Rapid whole-genome mutational profiling using next-generation sequencing technologies. , 2008, Genome research.

[16]  T. Urich,et al.  Archaea predominate among ammonia-oxidizing prokaryotes in soils , 2006, Nature.

[17]  Natalia N. Ivanova,et al.  Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite , 2007, Nature.

[18]  R. Amann,et al.  Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques , 2008, Nature Reviews Microbiology.

[19]  Michele Iacono,et al.  Whole-Genome Pyrosequencing of an Epidemic Multidrug-Resistant Acinetobacter baumannii Strain Belonging to the European Clone II Group , 2008, Antimicrobial Agents and Chemotherapy.

[20]  Susan M. Huse,et al.  Microbial diversity in the deep sea and the underexplored “rare biosphere” , 2006, Proceedings of the National Academy of Sciences.

[21]  Tao Zhang,et al.  Identification of ancient remains through genomic sequencing. , 2008, Genome research.

[22]  Julian Parkhill,et al.  Microbiology in the post-genomic era , 2008, Nature Reviews Microbiology.

[23]  Daniel H. Huson,et al.  Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome , 2008, PloS one.

[24]  Karl-Erich Jaeger,et al.  Prospecting for biocatalysts and drugs in the genomes of non-cultured microorganisms. , 2004, Current opinion in biotechnology.

[25]  N. Hall,et al.  Fast forward genetics , 2008, Nature Biotechnology.

[26]  K. Timmis,et al.  Metagenomics for Mining New Genetic Resources of Microbial Communities , 2008, Journal of Molecular Microbiology and Biotechnology.

[27]  M. Wésolowski-Louvel,et al.  Soil eukaryotic functional diversity, a metatranscriptomic approach , 2007, The ISME Journal.

[28]  J. Gilbert,et al.  Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities , 2008, PloS one.

[29]  Terry J. Gentry,et al.  Microarray-Based Analysis of Microbial Community RNAs by Whole-Community RNA Amplification , 2006, Applied and Environmental Microbiology.

[30]  Edward M. Rubin,et al.  Genomics of cellulosic biofuels , 2008, Nature.

[31]  Eugene V Koonin,et al.  Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation , 2003, Proceedings of the National Academy of Sciences of the United States of America.