G Model
ARTICLE IN PRESS
BIOTEC 6880 1
Journal of Biotechnology xxx (2014) xxx–xxx
Contents lists available at ScienceDirect
Journal of Biotechnology journal homepage: www.elsevier.com/locate/jbiotec
1
Editorial
2
The Genomics Revolution and its Impact on Future Biotechnology
3
4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50
The Center for Biotechnology (CeBiTec) of Bielefeld University, Germany, organizes annual symposia dealing with recent progress in biotechnological research. The 8th CeBiTec Symposium entitled “The Genomics Revolution and its Impact on Future Biotechnology” was held at Bielefeld University in October 2013. The topics of the conference were centered around all levels of -omics strategies or techniques, as well as analyses of high throughput data from such approaches. In particular, sessions were held on microbial, plant and animal genomics, metabolomics, bioinformatics, third-generation sequencing technologies, as well as systems- and synthetic biology. Current challenges and breakthroughs and their perspectives for and impact on future biotechnological developments were addressed. The present special issue of the Journal of Biotechnology entitled “The Genomics Revolution and its Impact on Future Biotechnology” is composed of 10 papers that are based on contributions of this conference. The first contribution by Becerra et al. deals with the analysis of ferric uptake and regulation in Pseudomonas pseudoalcaligenes. A possible link between iron and cyanide metabolism is discussed which may be relevant for possible biotechnological applications of this strain in biodegradation of cyanide-containing wastes. Kallnik et al. report on the characterization of a phosphotriesterase-like lactonase from the hyperthermoacidophilic crenarchaeon Vulcanisaeta moutnovskia, with special emphasis on its substrate specificity and stereoselectivity with lactone substrates. The next papers deal with metagenomic approaches to analyze complex microbial communities. Jacquiod et al. report on a high throughput DNA hybridization approach to identify novel genes in soil-derived large metagenomic libraries, and Dassi et al. analyzed the taxonomic composition and metabolic structure of human saliva microbiome samples and their variation upon shortterm probiotic intake by 16S rRNA profiling. Corynebacterium glutamicum is a workhorse of industrial production of amino acids and other compounds. Two reports focus on transcriptome analyses of this bacterium. Since its response to oxidative stress is biotechnologically relevant, Milse et al. examined the global transcriptional response of C. glutamicum to oxidative stress induced by hydrogen peroxide using whole genome DNA microarrays. Also, Neshat et al. report on a detailed analysis of existing RNA-seq data sets with respect to the organization of known transcriptional attenuators in amino acid synthesis pathways of C. glutamicum. Although the genomes and transcriptomes of the Chinese Hamster and Chinese hamster ovary (CHO) cells have been analyzed during the last years, the detailed structures of annotated genes are often in silico predictions and correctly annotated transcription
start sites are scarce. To address this issue, Jakobi et al. developed a modular bioinformatics pipeline to process a 5 -enriched RNA sequencing dataset, and identified transcription start sites to shed light on promoter landscapes in the Chinese hamster genome. In another study, one disadvantage of CHO cells, their low proliferation rate, has been addressed. In order to correlate microRNA transcription and cell-specific growth-rate, Hackl et al. used a transcriptomics approach to investigate the biological effect of deregulated miRNA biogenesis in different CHO cell lines with low to high specific growth rates. Actinoplanes sp. SE50/110 is the producer of the alphaglucosidase inhibitor acarviosyl-maltose (acarbose), which is used as potent drug in the treatment of type-2 diabetes mellitus. The paper by Schwientek et al. deals with the assignment of transcription start sites by sequencing and mapping enriched 5 -ends of primary transcripts to the genome of Actinoplanes sp. SE50/110. Since phosphate starvation often is applied to limit cell growth in microbial production processes, Schuhmacher et al. investigated the interplay of process-induced phosphate starvation and microbial performance in an l-tryptophan overproducing Escherichia coli strain as a model for highly ATP demanding processes. The comparison with an E. coli wild type strain was used to provide insights into metabolic flux distributions in conjunction with energy management. In conclusion, this special issue on the genomics revolution and its impact on future biotechnology presents a comprehensive overview about various aspects in this important research field and offers exciting applications for the future development of industrial biotechnology. Thus, we are confident that this collection of papers will attract the attention of the audience of the Journal of Biotechnology. Thomas Noll Q1 Alf Pühler Bernd Weisshaar Volker F. Wendisch Organizers of the 8th CeBiTec-Symposium, Center for Biotechnology, Bielefeld University, D-33594 Bielefeld, Germany E-mail addresses: [email protected] (T. Noll), [email protected] (A. Pühler), [email protected] (B. Weisshaar), [email protected] (V.F. Wendisch). Available online xxx
http://dx.doi.org/10.1016/j.jbiotec.2014.10.009 0168-1656/© 2014 Published by Elsevier B.V.
Please cite this article in press as: Noll, T., et al., The Genomics Revolution and its Impact on Future Biotechnology. J. Biotechnol. (2014), http://dx.doi.org/10.1016/j.jbiotec.2014.10.009
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ARTICLE IN PRESS
BIOTEC 6880 1
Journal of Biotechnology xxx (2014) xxx–xxx
Contents lists available at ScienceDirect
Journal of Biotechnology journal homepage: www.elsevier.com/locate/jbiotec
1
Editorial
2
The Genomics Revolution and its Impact on Future Biotechnology
3
4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50
The Center for Biotechnology (CeBiTec) of Bielefeld University, Germany, organizes annual symposia dealing with recent progress in biotechnological research. The 8th CeBiTec Symposium entitled “The Genomics Revolution and its Impact on Future Biotechnology” was held at Bielefeld University in October 2013. The topics of the conference were centered around all levels of -omics strategies or techniques, as well as analyses of high throughput data from such approaches. In particular, sessions were held on microbial, plant and animal genomics, metabolomics, bioinformatics, third-generation sequencing technologies, as well as systems- and synthetic biology. Current challenges and breakthroughs and their perspectives for and impact on future biotechnological developments were addressed. The present special issue of the Journal of Biotechnology entitled “The Genomics Revolution and its Impact on Future Biotechnology” is composed of 10 papers that are based on contributions of this conference. The first contribution by Becerra et al. deals with the analysis of ferric uptake and regulation in Pseudomonas pseudoalcaligenes. A possible link between iron and cyanide metabolism is discussed which may be relevant for possible biotechnological applications of this strain in biodegradation of cyanide-containing wastes. Kallnik et al. report on the characterization of a phosphotriesterase-like lactonase from the hyperthermoacidophilic crenarchaeon Vulcanisaeta moutnovskia, with special emphasis on its substrate specificity and stereoselectivity with lactone substrates. The next papers deal with metagenomic approaches to analyze complex microbial communities. Jacquiod et al. report on a high throughput DNA hybridization approach to identify novel genes in soil-derived large metagenomic libraries, and Dassi et al. analyzed the taxonomic composition and metabolic structure of human saliva microbiome samples and their variation upon shortterm probiotic intake by 16S rRNA profiling. Corynebacterium glutamicum is a workhorse of industrial production of amino acids and other compounds. Two reports focus on transcriptome analyses of this bacterium. Since its response to oxidative stress is biotechnologically relevant, Milse et al. examined the global transcriptional response of C. glutamicum to oxidative stress induced by hydrogen peroxide using whole genome DNA microarrays. Also, Neshat et al. report on a detailed analysis of existing RNA-seq data sets with respect to the organization of known transcriptional attenuators in amino acid synthesis pathways of C. glutamicum. Although the genomes and transcriptomes of the Chinese Hamster and Chinese hamster ovary (CHO) cells have been analyzed during the last years, the detailed structures of annotated genes are often in silico predictions and correctly annotated transcription
start sites are scarce. To address this issue, Jakobi et al. developed a modular bioinformatics pipeline to process a 5 -enriched RNA sequencing dataset, and identified transcription start sites to shed light on promoter landscapes in the Chinese hamster genome. In another study, one disadvantage of CHO cells, their low proliferation rate, has been addressed. In order to correlate microRNA transcription and cell-specific growth-rate, Hackl et al. used a transcriptomics approach to investigate the biological effect of deregulated miRNA biogenesis in different CHO cell lines with low to high specific growth rates. Actinoplanes sp. SE50/110 is the producer of the alphaglucosidase inhibitor acarviosyl-maltose (acarbose), which is used as potent drug in the treatment of type-2 diabetes mellitus. The paper by Schwientek et al. deals with the assignment of transcription start sites by sequencing and mapping enriched 5 -ends of primary transcripts to the genome of Actinoplanes sp. SE50/110. Since phosphate starvation often is applied to limit cell growth in microbial production processes, Schuhmacher et al. investigated the interplay of process-induced phosphate starvation and microbial performance in an l-tryptophan overproducing Escherichia coli strain as a model for highly ATP demanding processes. The comparison with an E. coli wild type strain was used to provide insights into metabolic flux distributions in conjunction with energy management. In conclusion, this special issue on the genomics revolution and its impact on future biotechnology presents a comprehensive overview about various aspects in this important research field and offers exciting applications for the future development of industrial biotechnology. Thus, we are confident that this collection of papers will attract the attention of the audience of the Journal of Biotechnology. Thomas Noll Q1 Alf Pühler Bernd Weisshaar Volker F. Wendisch Organizers of the 8th CeBiTec-Symposium, Center for Biotechnology, Bielefeld University, D-33594 Bielefeld, Germany E-mail addresses: [email protected] (T. Noll), [email protected] (A. Pühler), [email protected] (B. Weisshaar), [email protected] (V.F. Wendisch). Available online xxx
http://dx.doi.org/10.1016/j.jbiotec.2014.10.009 0168-1656/© 2014 Published by Elsevier B.V.
Please cite this article in press as: Noll, T., et al., The Genomics Revolution and its Impact on Future Biotechnology. J. Biotechnol. (2014), http://dx.doi.org/10.1016/j.jbiotec.2014.10.009
51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81
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