Structure, Function, and Evolution of the Thiomonas spp. Genome

Arsène-Ploetze, Florence; Koechler, Sandrine; Marchal, Marie; Coppée, Jean‐Yves; Chandler, Michaël; Bonnefoy, Violaine; Brochier-Armanet, Céline; Barakat, Mohamed; Barbe, Valérie; Battaglia-Brunet, Fabienne; Bruneel, Odile; Bryan, Christopher G.; Cleiss-Arnold, Jessica; Cruveiller, Stéphane; Erhardt, Mathieu; Heinrich-Salmeron, Audrey; Hommais, Florence; Joulian, Catherine; Krin, Evelyne; Lieutaud, Aurélie; Lièvremont, Didier; Michel, Caroline; Müller, Daniel; Ortet, Philippe; Proux, Caroline; Siguier, Patricia; Roche, David; Rouy, Zoé; Salvignol, Grégory; Slyemi, Djamila; Talla, Emmanuel; Weiss, Stéphanie; Weissenbach, Jean; Médigue, Claudine; Bertin, Philippe

doi:10.1371/journal.pgen.1000859

Cited by 130 publications

(121 citation statements)

References 69 publications

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“…Finally, the presence at the sampling site of two subpopulations of 'Candidatus Fodinabacter communificans' (Supplementary Figures S1 and 2) is reminiscent to what has been observed in other environmental contexts (Simmons et al, 2008;Wilmes et al, 2008). Such ecotypes, which may reflect an important genetic variability resulting from gene gain or loss, has been recently described in Thiomonas strains (Arsène-Ploetze et al, 2010).…”

Section: Discussionsupporting

confidence: 62%

“…In the last few years, a huge amount of genomic sequences have been published in databases, including a complete characterization of several bacteria metabolizing arsenic (Muller et al, 2007;Arsène-Ploetze et al, 2010). In microbial ecology, the major challenge remains, however, to determine more precisely the role of microorganisms and their relationships with other members of the microbial community that result in an efficient functioning of the ecosystem.…”

Section: Discussionmentioning

confidence: 99%

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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: Discussionsupporting

confidence: 62%

Section: Discussionmentioning

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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“…Indeed, Thiomonas spp. isolated from Carnoulès carry genes involved in transport and degradation of glucose, fructose, glycerol, lactate and several amino acids, and are able to use fructose as a unique carbon source (Arsène-Ploetze et al, 2010;Slyemi et al, 2011). Interestingly, most of the secreted compounds contained nitrogen, which may have a key role in the ecosystems where E. mutabilis is found.…”

Section: Discussionmentioning

confidence: 99%

In situ proteo-metabolomics reveals metabolite secretion by the acid mine drainage bio-indicator, Euglena mutabilis

et al. 2012

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Euglena mutabilis is a photosynthetic protist found in acidic aquatic environments such as peat bogs, volcanic lakes and acid mine drainages (AMDs). Through its photosynthetic metabolism, this protist is supposed to have an important role in primary production in such oligotrophic ecosystems. Nevertheless, the exact contribution of E. mutabilis in organic matter synthesis remains unclear and no evidence of metabolite secretion by this protist has been established so far. Here we combined in situ proteo-metabolomic approaches to determine the nature of the metabolites accumulated by this protist or potentially secreted into an AMD. Our results revealed that the secreted metabolites are represented by a large number of amino acids, polyamine compounds, urea and some sugars but no fatty acids, suggesting a selective organic matter contribution in this ecosystem. Such a production may have a crucial impact on the bacterial community present on the study site, as it has been suggested previously that prokaryotes transport and recycle in situ most of the metabolites secreted by E. mutabilis. Consequently, this protist may have an indirect but important role in AMD ecosystems but also in other ecological niches often described as nitrogen-limited.

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“…As more genomes are sequenced, it has become increasingly apparent that many ars genes are reiterated, with some microorganisms containing two or more ars operons (18)(19)(20)(21)(22)(23)(24)(25)(26). The relative importance of such reiteration has been examined only sparingly.…”

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confidence: 99%

Regulatory Activities of Four ArsR Proteins in Agrobacterium tumefaciens 5A

Kang

Brame

Jetter

et al. 2016

Appl Environ Microbiol

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ArsR is a well-studied transcriptional repressor that regulates microbe-arsenic interactions. Most microorganisms have an arsR gene, but in cases where multiple copies exist, the respective roles or potential functional overlap have not been explored. We examined the repressors encoded by arsR1 and arsR2 (ars1 operon) and by arsR3 and arsR4 (ars2 operon) in Agrobacterium tumefaciens 5A. ArsR1 and ArsR4 are very similar in their primary sequences and diverge phylogenetically from ArsR2 and ArsR3, which are also quite similar to one another. Reporter constructs (lacZ) for arsR1, arsR2, and arsR4 were all inducible by As(III), but expression of arsR3 (monitored by reverse transcriptase PCR) was not influenced by As(III) and appeared to be linked transcriptionally to an upstream lysR-type gene. Experiments using a combination of deletion mutations and additional reporter assays illustrated that the encoded repressors (i) are not all autoregulatory as is typically known for ArsR proteins, (ii) exhibit variable control of each other's encoding genes, and (iii) exert variable control of other genes previously shown to be under the control of ArsR1. Furthermore, ArsR2, ArsR3, and ArsR4 appear to have an activator-like function for some genes otherwise repressed by ArsR1, which deviates from the well-studied repressor role of ArsR proteins. The differential regulatory activities suggest a complex regulatory network not previously observed in ArsR studies. The results indicate that fine-scale ArsR sequence deviations of the reiterated regulatory proteins apparently translate to different regulatory roles. IMPORTANCEGiven the significance of the ArsR repressor in regulating various aspects of microbe-arsenic interactions, it is important to assess potential regulatory overlap and/or interference when a microorganism carries multiple copies of arsR. This study explores this issue and shows that the four arsR genes in A. tumefaciens 5A, associated with two separate ars operons, encode proteins exhibiting various degrees of functional overlap with respect to autoregulation and cross-regulation, as well as control of other functional genes. In some cases, differences in regulatory activity are associated with only limited differences in protein primary structure. The experiments summarized herein also present evidence that ArsR proteins appear to have activator functions, representing novel regulatory activities for ArsR, previously known only to be a repressor. In reaction to arsenic in their environment, microorganisms orchestrate an organized response that may involve arsenite [As(III)] oxidation, arsenate [As(V)] reduction, or both. These redox reactions serve to detoxify or protect the organism or to generate energy, depending on the organism and the genes involved. Current models depict As(III) being taken up into the cell via aquaglyceroporins (e.g., reviewed in references 1, 2, and 3), where it then interacts with a DNA-binding repressor protein, ArsR, resulting in a conformational change in ArsR and causing it...

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Structure, Function, and Evolution of the Thiomonas spp. Genome

Cited by 130 publications

References 69 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

In situ proteo-metabolomics reveals metabolite secretion by the acid mine drainage bio-indicator, Euglena mutabilis

Regulatory Activities of Four ArsR Proteins in Agrobacterium tumefaciens 5A

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