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Aspects of prokaryotic genome research
Journal of Biotechnology 126 (2006) 1–2
Editorial
Aspects of prokaryotic genome research This special issue of the Journal of Biotechnology is based on a selection of lectures presented at the 2nd European Conference on Prokaryotic Genomes—PROKAGEN, which was held in G¨ottingen, Germany, in September 2005. The PROKAGEN conference is a joint endeavour of the universities in G¨ottingen, Bielefeld and W¨urzburg. These universities host the co-ordinating centres of three German-wide competence networks focussing on bacterial genome research. The networks combine the expertise of more than 60 partners affiliated with universities, research institutes and companies. Each network devotes its research on specific groups of bacteria which play a role in biotechnological production processes, are relevant in the fields of agriculture, environment and biotechnology or are known as human pathogens. The research in these networks focusses on whole genome sequencing of prokaryotes and also on the development of cutting edge technologies to make use of the sequences for industrial production processes, for sustainable agriculture, and the control of infectious diseases.
1. Genome research of bacteria relevant for agriculture and environment The paper by Angelov and Liebl reviews on the genome analyses of Archaea, with special emphasis on thermoacidophily. The next review article by Simonato et al. is based on the genome studies of a deep-sea bacterium. It provides interesting information on highpressure adaptation and its potential importance for biotechnological applications, e.g., in food science and technology. The review by Dolla et al. gives an 0168-1656/$ – see front matter © 2006 Elsevier B.V. All rights reserved. doi:10.1016/j.jbiotec.2006.07.017
overview on the defense mechanisms against oxygen and its toxic derivatives in sulfate-reducing bacteria. For plant-interacting bacteria, the exchange of signals plays an important role in the bacteria–plant interaction. The two research papers in this field deal with secreted proteins, one of a symbiotic and the other of a pathogenic soil bacterium. Suess et al. report on the identification of genistein-inducible and type III-secreted proteins of the nitrogen fixing soybean symbiont Bradyrhizobium japonicum. The study contributes to the identification of novel extracellular proteins which are involved in the interaction of B. japonicum with its host plant. The research paper by Watt et al. reports the 2D-gel based analysis of the secretome of Xanthomonas campestris pv. campestris to demonstrate that secreted proteins have elicitor-potential for activating plant defense. The oxidative burst method was used to analyze eluted protein material that led to the identification of Xanthomonas SodM as elicitoractive compound.
2. Genome research of bacteria important for industry Silberbach and Burkovski provide an overview on the current knowledge of nitrogen regulation in the high GC Gram-positive bacterium Corynebacterium glutamicum. A special emphasis of this review article is the contribution of global or genome-scale analyses to the understanding of nitrogen regulation in this bacterium. This is followed by a research paper by Voget et al. who describe the cloning, sequencing and expression of a glycosyl hydrolase isolated from a soil
2
Editorial / Journal of Biotechnology 126 (2006) 1–2
metagenome. The biochemical characterization of this enzyme is reported, and its potential for biotechnological applications is discussed.
3. Genome research of bacteria relevant for medicine The genus Listeria consists of only six species including both pathogenic and non-pathogenic species. Since the genome sequences of representative strains of all six species are near to completion, the whole genetic code of an entire genus will soon be available and opens a wide field for comparative genomics. Thus, the review article by Hain et al. provides an overview on the whole field of Listeria comparative and functional genomics which will shed light on the pathogenicity mechanisms and improve the understanding of Listeria infection biology. Another pathogen, Helicobacter pylori, is the subject of the next review article. Pflock et al. give an overview on the processes involved in acidresponsive gene regulation in H. pylori which seems to be important for the pathogenicity since it is able to survive severe acid shocks and to grow under mildly acidic conditions. This is again followed by a research paper by Rachman et al. who describe the amplification of small amounts of bacterial mRNA for microarray analysis of prokaryotic organisms. This work dealt with mycobacteria, and a much higher amplification
factor is reported so that much smaller amounts of prokayotic RNA samples are sufficient than normally required. Funding of the networks by the German Ministry of Education and Research (BMBF) under the “GenoMik” guideline ended in the middle of 2006, however, future support will be provided under the “GenoMik-Plus” guideline which started in July 2006. Thus, this measure ensures that the 3rd European Conference on Prokaryotic Genomes will take place at G¨ottingen University in October 2007. G. Gottschalk Network Coordinator BiotechGenoMik, G¨ottingen University, Germany W. Goebel Network Coordinator PathoGenoMik, W¨urzburg University, Germany A. P¨uhler ∗ Network Coordinator Bacterial Genome Research, Bielefeld University, Faculty of Biology, 33594 Bielefeld, Germany ∗ Corresponding
author. Fax: +49 521 106 5626. E-mail addresses: [email protected] (G. Gottschalk), [email protected] (W. Goebel), [email protected] (A. P¨uhler) 25 July 2006
Editorial
Aspects of prokaryotic genome research This special issue of the Journal of Biotechnology is based on a selection of lectures presented at the 2nd European Conference on Prokaryotic Genomes—PROKAGEN, which was held in G¨ottingen, Germany, in September 2005. The PROKAGEN conference is a joint endeavour of the universities in G¨ottingen, Bielefeld and W¨urzburg. These universities host the co-ordinating centres of three German-wide competence networks focussing on bacterial genome research. The networks combine the expertise of more than 60 partners affiliated with universities, research institutes and companies. Each network devotes its research on specific groups of bacteria which play a role in biotechnological production processes, are relevant in the fields of agriculture, environment and biotechnology or are known as human pathogens. The research in these networks focusses on whole genome sequencing of prokaryotes and also on the development of cutting edge technologies to make use of the sequences for industrial production processes, for sustainable agriculture, and the control of infectious diseases.
1. Genome research of bacteria relevant for agriculture and environment The paper by Angelov and Liebl reviews on the genome analyses of Archaea, with special emphasis on thermoacidophily. The next review article by Simonato et al. is based on the genome studies of a deep-sea bacterium. It provides interesting information on highpressure adaptation and its potential importance for biotechnological applications, e.g., in food science and technology. The review by Dolla et al. gives an 0168-1656/$ – see front matter © 2006 Elsevier B.V. All rights reserved. doi:10.1016/j.jbiotec.2006.07.017
overview on the defense mechanisms against oxygen and its toxic derivatives in sulfate-reducing bacteria. For plant-interacting bacteria, the exchange of signals plays an important role in the bacteria–plant interaction. The two research papers in this field deal with secreted proteins, one of a symbiotic and the other of a pathogenic soil bacterium. Suess et al. report on the identification of genistein-inducible and type III-secreted proteins of the nitrogen fixing soybean symbiont Bradyrhizobium japonicum. The study contributes to the identification of novel extracellular proteins which are involved in the interaction of B. japonicum with its host plant. The research paper by Watt et al. reports the 2D-gel based analysis of the secretome of Xanthomonas campestris pv. campestris to demonstrate that secreted proteins have elicitor-potential for activating plant defense. The oxidative burst method was used to analyze eluted protein material that led to the identification of Xanthomonas SodM as elicitoractive compound.
2. Genome research of bacteria important for industry Silberbach and Burkovski provide an overview on the current knowledge of nitrogen regulation in the high GC Gram-positive bacterium Corynebacterium glutamicum. A special emphasis of this review article is the contribution of global or genome-scale analyses to the understanding of nitrogen regulation in this bacterium. This is followed by a research paper by Voget et al. who describe the cloning, sequencing and expression of a glycosyl hydrolase isolated from a soil
2
Editorial / Journal of Biotechnology 126 (2006) 1–2
metagenome. The biochemical characterization of this enzyme is reported, and its potential for biotechnological applications is discussed.
3. Genome research of bacteria relevant for medicine The genus Listeria consists of only six species including both pathogenic and non-pathogenic species. Since the genome sequences of representative strains of all six species are near to completion, the whole genetic code of an entire genus will soon be available and opens a wide field for comparative genomics. Thus, the review article by Hain et al. provides an overview on the whole field of Listeria comparative and functional genomics which will shed light on the pathogenicity mechanisms and improve the understanding of Listeria infection biology. Another pathogen, Helicobacter pylori, is the subject of the next review article. Pflock et al. give an overview on the processes involved in acidresponsive gene regulation in H. pylori which seems to be important for the pathogenicity since it is able to survive severe acid shocks and to grow under mildly acidic conditions. This is again followed by a research paper by Rachman et al. who describe the amplification of small amounts of bacterial mRNA for microarray analysis of prokaryotic organisms. This work dealt with mycobacteria, and a much higher amplification
factor is reported so that much smaller amounts of prokayotic RNA samples are sufficient than normally required. Funding of the networks by the German Ministry of Education and Research (BMBF) under the “GenoMik” guideline ended in the middle of 2006, however, future support will be provided under the “GenoMik-Plus” guideline which started in July 2006. Thus, this measure ensures that the 3rd European Conference on Prokaryotic Genomes will take place at G¨ottingen University in October 2007. G. Gottschalk Network Coordinator BiotechGenoMik, G¨ottingen University, Germany W. Goebel Network Coordinator PathoGenoMik, W¨urzburg University, Germany A. P¨uhler ∗ Network Coordinator Bacterial Genome Research, Bielefeld University, Faculty of Biology, 33594 Bielefeld, Germany ∗ Corresponding
author. Fax: +49 521 106 5626. E-mail addresses: [email protected] (G. Gottschalk), [email protected] (W. Goebel), [email protected] (A. P¨uhler) 25 July 2006