MicroScope: a platform for microbial genome annotation and comparative genomics

Vallenet, David; Engelen, Stéfan; Mornico, Damien; Cruveiller, Stéphane; Fleury, Ludovic; Lajus, Aurélie; Rouy, Zoé; Roche, David; Salvignol, Grégory; Scarpelli, Claude; Médigue, Claudine

doi:10.1093/database/bap021

Cited by 263 publications

(270 citation statements)

References 46 publications

(63 reference statements)

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“…Bioinformatics, statistical analysis and phylogenomic approach Two-third of the metagenomic sequences were successfully organized in seven bins (Supplementary Information) and were then integrated into the MicroScope platform for the prediction of coding sequences, followed by automatic and expert annotation (Vallenet et al, 2009). The mean polymorphism frequency in the population was assessed using SNIPer (Ning et al, 2001).…”

Section: Methodsmentioning

confidence: 99%

Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics

et al. 2011

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By their metabolic activities, microorganisms have a crucial role in the biogeochemical cycles of elements. The complete understanding of these processes requires, however, the deciphering of both the structure and the function, including synecologic interactions, of microbial communities. Using a metagenomic approach, we demonstrated here that an acid mine drainage highly contaminated with arsenic is dominated by seven bacterial strains whose genomes were reconstructed. Five of them represent yet uncultivated bacteria and include two strains belonging to a novel bacterial phylum present in some similar ecosystems, and which was named 'Candidatus Fodinabacter communificans.' Metaproteomic data unravelled several microbial capabilities expressed in situ, such as iron, sulfur and arsenic oxidation that are key mechanisms in biomineralization, or organic nutrient, amino acid and vitamin metabolism involved in synthrophic associations. A statistical analysis of genomic and proteomic data and reverse transcriptase-PCR experiments allowed us to build an integrated model of the metabolic interactions that may be of prime importance in the natural attenuation of such anthropized ecosystems.

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Section: Methodsmentioning

confidence: 99%

Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics

et al. 2011

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“…Table 1 provides specific strain descriptions. Identification and analysis of the various allele homologies were conducted using keyword searches (terms: polymerase V, umuD, umuC, dinP, lexA) and BLAST analyses on the MaGe interface on the MicroScope platform of Genoscope (Vallenet et al, 2006(Vallenet et al, , 2009 (Table 1) for 24 h. All steps after UV exposure until handling the next day were performed in the dark to minimize possible photoreactivation, which has been observed for a few Acinetobacter species (Fernández Zenoff et al, 2006). Overnight cultures were plated onto agar media containing 100 mg rifampicin ml 21 or no rifampicin to calculate frequencies of rifampicin-resistant mutants.…”

Section: Methodsmentioning

confidence: 99%

Diverse responses to UV light exposure in Acinetobacter include the capacity for DNA damage-induced mutagenesis in the opportunistic pathogens Acinetobacter baumannii and Acinetobacter ursingii

et al. 2012

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Error-prone and error-free DNA damage repair responses that are induced in most bacteria after exposure to various chemicals, antibiotics or radiation sources were surveyed across the genus Acinetobacter. The error-prone SOS mutagenesis response occurs when DNA damage induces a cell's umuDC-or dinP-encoded error-prone polymerases. The model strain Acinetobacter baylyi ADP1 possesses an unusual, regulatory umuD allele (umuDAb) with an extended 59 region and only incomplete fragments of umuC. Diverse Acinetobacter species were investigated for the presence of umuDC and their ability to conduct UV-induced mutagenesis. Unlike ADP1, most Acinetobacter strains possessed multiple umuDC loci containing either umuDAb or a umuD allele resembling that of Escherichia coli. The nearly omnipresent umuDAb allele was the ancestral umuD in Acinetobacter, with horizontal gene transfer accounting for over half of the umuDC operons. Despite multiple umuD(Ab)C operons in many strains, only three species conducted UV-induced mutagenesis: Acinetobacter baumannii, Acinetobacter ursingii and Acinetobacter beijerinckii. The type of umuDC locus or mutagenesis phenotype a strain possessed was not correlated with its error-free response of survival after UV exposure, but similar diversity was apparent. The survival of 30 Acinetobacter strains after UV treatment ranged over five orders of magnitude, with the Acinetobacter calcoaceticus-A. baumannii (Acb) complex and haemolytic strains having lower survival than non-Acb or non-haemolytic strains. These observations demonstrate that a genus can possess a range of DNA damage response mechanisms, and suggest that DNA damage-induced mutation could be an important part of the evolution of the emerging pathogens A. baumannii and A. ursingii. INTRODUCTIONWhen bacteria are exposed to DNA-damaging agents, such as UV light or chemical mutagens, a wide variety of SOS response genes (genes that play critical roles in repairing damaged DNA) are specifically induced (Friedberg et al., 1995;Walker, 1996). In the model developed by experimentation in Escherichia coli, SOS genes are negatively regulated by the LexA repressor binding to the SOS box in the promoter (Mount et al., 1972). DNA damage causes the activation of RecA, which facilitates LexA self-cleavage and releases the repression of SOS genes such as umuDC (Little et al., 1980;1981). UmuD initially causes a pause in cell division while DNA repair and replication occurs (Opperman et al., 1999). However, within minutes, UmuD homodimerizes and carries out intermolecular self-cleavage, facilitated by activated RecA* interaction (Nohmi et al., 1988). Two cleaved UmuD9 molecules then associate with UmuC to form DNA polymerase V, which carries out error-prone, trans-lesion DNA replication (SOS mutagenesis) (Reuven et al., 1999;Tang et al., 1999). Another errorprone polymerase commonly involved in SOS mutagenesis as part of the DNA damage response is DinP (also called DinB), DNA polymerase IV, which can function either by itself (Kim et al., 1997) or with U...

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“…The contigs were annotated using the web interface Magnifying Genomes (MaGe) of the MicroScope platform from GenoScope (Vallenet et al, 2006(Vallenet et al, , 2009. The automatic annotations provided by MaGe were curated manually to validate the presence or absence of a particular gene involved in selected pathways of interest.…”

Section: Comparative Genome Analysismentioning

confidence: 99%

A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal

Kristiansen

Nguyen²,

Saunders³

et al. 2012

The ISME Journal

202

154

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Members of the genus Tetrasphaera are considered to be putative polyphosphate accumulating organisms (PAOs) in enhanced biological phosphorus removal (EBPR) from wastewater. Although abundant in Danish full-scale wastewater EBPR plants, how similar their ecophysiology is to 'Candidatus Accumulibacter phosphatis' is unclear, although they may occupy different ecological niches in EBPR communities. The genomes of four Tetrasphaera isolates (T. australiensis, T. japonica, T. elongata and T. jenkinsii) were sequenced and annotated, and the data used to construct metabolic models. These models incorporate central aspects of carbon and phosphorus metabolism critical to understanding their behavior under the alternating anaerobic/aerobic conditions encountered in EBPR systems. Key features of these metabolic pathways were investigated in pure cultures, although poor growth limited their analyses to T. japonica and T. elongata. Based on the models, we propose that under anaerobic conditions the Tetrasphaerarelated PAOs take up glucose and ferment this to succinate and other components. They also synthesize glycogen as a storage polymer, using energy generated from the degradation of stored polyphosphate and substrate fermentation. During the aerobic phase, the stored glycogen is catabolized to provide energy for growth and to replenish the intracellular polyphosphate reserves needed for subsequent anaerobic metabolism. They are also able to denitrify. This physiology is markedly different to that displayed by 'Candidatus Accumulibacter phosphatis', and reveals Tetrasphaera populations to be unusual and physiologically versatile PAOs carrying out denitrification, fermentation and polyphosphate accumulation.

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MicroScope: a platform for microbial genome annotation and comparative genomics

Cited by 263 publications

References 46 publications

Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics

Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics

Diverse responses to UV light exposure in Acinetobacter include the capacity for DNA damage-induced mutagenesis in the opportunistic pathogens Acinetobacter baumannii and Acinetobacter ursingii

A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal

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