Journal ArticleDOI
The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1.
Ralf Rabus,Michael Kube,Johann Heider,Alfred Beck,Katja Heitmann,Friedrich Widdel,Richard Reinhardt +6 more
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TLDR
The first complete genome of a metabolically versatile representative, strain EbN1, which metabolizes various aromatic compounds, including hydrocarbons is presented, which indicates a finely tuned regulatory network able to respond to the fluctuating availability of organic substrates and electron acceptors in the environment.Abstract:
Recent research on microbial degradation of aromatic and other refractory compounds in anoxic waters and soils has revealed that nitrate-reducing bacteria belonging to the Betaproteobacteria contribute substantially to this process. Here we present the first complete genome of a metabolically versatile representative, strain EbN1, which metabolizes various aromatic compounds, including hydrocarbons. A circular chromosome (4.3 Mb) and two plasmids (0.21 and 0.22 Mb) encode 4603 predicted proteins. Ten anaerobic and four aerobic aromatic degradation pathways were recognized, with the encoding genes mostly forming clusters. The presence of paralogous gene clusters (e.g., for anaerobic phenylacetate oxidation), high sequence similarities to orthologs from other strains (e.g., for anaerobic phenol metabolism) and frequent mobile genetic elements (e.g., more than 200 genes for transposases) suggest high genome plasticity and extensive lateral gene transfer during metabolic evolution of strain EbN1. Metabolic versatility is also reflected by the presence of multiple respiratory complexes. A large number of regulators, including more than 30 two-component and several FNR-type regulators, indicate a finely tuned regulatory network able to respond to the fluctuating availability of organic substrates and electron acceptors in the environment. The absence of genes required for nitrogen fixation and specific interaction with plants separates strain EbN1 ecophysiologically from the closely related nitrogen-fixing plant symbionts of the Azoarcus cluster. Supplementary material on sequence and annotation are provided at the Web page http://www.micro-genomes.mpg.de/ebn1/.read more
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Journal ArticleDOI
Indole-3-acetic acid in microbial and microorganism-plant signaling.
TL;DR: The fact that bacteria use this phytohormone to interact with plants as part of their colonization strategy, including phyto-stimulation and circumvention of basal plant defense mechanisms, is highlighted.
Journal ArticleDOI
Marine microorganisms make a meal of oil
TL;DR: That the globe is not swamped with oil is testament to the efficiency and versatility of the networks of microorganisms that degrade hydrocarbons, some of which have recently begun to reveal the secrets of when and how they exploit Hydrocarbons as a source of carbon and energy.
Journal ArticleDOI
Microbial degradation of aromatic compounds — from one strategy to four
TL;DR: These strategies are based on different ring activation mechanisms that consist of either formation of a non-aromatic ring-epoxide under oxic conditions, or reduction of the aromatic ring under anoxic conditions using one of two completely different systems.
Book ChapterDOI
Geobacter: The Microbe Electric's Physiology, Ecology, and Practical Applications
Derek R. Lovley,Toshiyuki Ueki,Tian Zhang,Nikhil S. Malvankar,Pravin Malla Shrestha,Kelly A. Flanagan,Muktak Aklujkar,Jessica E. Butler,Ludovic Giloteaux,Amelia-Elena Rotaru,Dawn E. Holmes,Ashley E. Franks,Roberto Orellana,Carla Risso,Kelly P. Nevin +14 more
TL;DR: The study of Geobacter species has revealed a remarkable number of microbial physiological properties that had not previously been described in any microorganism, which might contribute to the field of bioelectronics.
Journal ArticleDOI
Anaerobic Catabolism of Aromatic Compounds: a Genetic and Genomic View
Manuel Carmona,María Teresa Zamarro,Blas Blázquez,Gonzalo Durante-Rodríguez,Javier F. Juárez,J. Andrés Valderrama,María J. López Barragán,José Luis García,Eduardo Díaz +8 more
TL;DR: This review focuses on the recent findings that standard molecular biology approaches together with new high-throughput technologies have provided regarding the genetics, regulation, ecophysiology, and evolution of anaerobic aromatic degradation pathways, revealing that the anaerobia catabolism of aromatic compounds is more diverse and widespread than previously thought.
References
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Journal ArticleDOI
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Journal ArticleDOI
Base-calling of automated sequencer traces using Phred. I. accuracy assessment
TL;DR: In this article, a base-calling program for automated sequencer traces, phred, with improved accuracy was proposed. But it was not shown to achieve a lower error rate than the ABI software, averaging 40%-50% fewer errors in the data sets examined independent of position in read, machine running conditions, or sequencing chemistry.
Journal ArticleDOI
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
TL;DR: A new method for the identification of signal peptides and their cleavage sites based on neural networks trained on separate sets of prokaryotic and eukaryotic sequence that performs significantly better than previous prediction schemes and can easily be applied on genome-wide data sets.
Journal ArticleDOI
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Brent Ewing,Philip Green +1 more
TL;DR: The ability to estimate a probability of error for each base-call, as a function of certain parameters computed from the trace data, is developed and implemented in the base-calling program.
SHORT COMMUNICATION Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
TL;DR: In this paper, a new method for the identification of in performance compared with the weight matrix method signal peptides and their cleavage sites based on neural (Arrigo et al., 1991; Ladunga et al, 1991; Schneider and networks trained on separate sets of prokaryotic and eukaryotic sequence.
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