Bionemo: molecular information on biodegradation metabolism

Carbajosa, Guillermo; Trigo, A Garrido; Valencia, Alfonso; Cases, Ildefonso

doi:10.1093/nar/gkn864

Cited by 56 publications

(39 citation statements)

References 19 publications

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“…Bionemo (http:// bionemo.bioinfo.cnio.es) is a database that includes structural information on proteins, regulatory elements, genes, etc. This database supports the aforementioned databases in a way that it provides regulatory perspective to the biochemical aspects of biodegradation [89].…”

Section: Desired Community and Its Performancementioning

confidence: 62%

Integrated Perspective for Effective Bioremediation

Paliwal

Puranik

Purohit

2011

Appl Biochem Biotechnol

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Identification of factors which can influence the natural attenuation process with available microbial genetic capacities can support the bioremediation which has been viewed as the safest procedure to combat with anthropogenic compounds in ecosystems. With the advent of molecular techniques, assimilatory capacity of an ecosystem can be defined with changing community dynamics, and if required, the essential genetic potential can be met through bioaugmentation. At the same time, intensification of microbial processes with nutrient balancing, expressing and enhancing the degradative capacities, could reduce the time frame of restoration of the ecosystem. The new concept of ecosystems biology has added greatly to conceptualize the networking of the evolving microbiota of the niche that helps in effective application of bioremediation tools to manage pollutants as additional carbon source.

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Section: Desired Community and Its Performancementioning

confidence: 62%

Integrated Perspective for Effective Bioremediation

Paliwal

Puranik

Purohit

2011

Appl Biochem Biotechnol

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“…Because the activity of the dioxygenase seems to be impervious to DNT whether DntR is present or not we concluded that (i) the regulator DntR does not stimulate directly or indirectly the first step of the DNT degradation, (ii) DNT does not control in any other way (e.g. riboswitches) expression of the genes that encode the leading biodegradation step and (iii) DntR does not repress either the P DNT promoter in the presence or absence of DNT, as is the case in other LysR‐type regulators when the inducer is missing (Maddocks and Oyston, 2008; Carbajosa et al ., 2009). While many TFs gratuitously respond to unrelated inducers (de Lorenzo and Perez‐Martin, 1996; Carbajosa et al ., 2009), that the regulatory system just examined allowed expression of the dntA genes independently of DNT presence suggested the second regulatory scenario discussed above i.e.…”

Section: Resultsmentioning

confidence: 99%

Association of dnt genes of Burkholderia sp. DNT with the substrate-blind regulator DntR draws the evolutionary itinerary of 2,4-dinitrotoluene biodegradation

Heras

Chavarría

2011

Molecular Microbiology

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SummaryThe regulation of the DNT pathway for biodegradation of 2,4-dinitrotoluene of Burkholderia sp. DNT has been examined by exporting each of its components to Pseudomonas putida KT2440. The cognate regulator DntR does not respond to the pathway substrate, but to the non-substrate salicylate. In order to examine whether such a response to an unrelated inducer was specific or rather a vestige of a previous evolutionary stage, the complete dnt complement or parts of it were expressed functionally for accumulation of various metabolic intermediates. Their effect on expression of dnt genes was then followed both biochemically and by means of a luminescent reporter engineered in the surrogate host. DntR was not only unresponsive to DNT biodegradation products, but it also failed to influence expression of dnt genes at all. Comparison of the dntR/dntA divergent promoter region with similar ones found in various catabolic systems indicated that the leading segment of the DNT biodegradation pathway evolved from a matching portion of naphthalene biodegradation routes existing in other bacteria. That a useless but still active transcriptional factor occurs along enzymes that have already evolved a new substrate specificity suggests that emergence of novel catalytic abilities precedes their submission to cognate regulatory devices, not vice versa.

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“…The list of chemically inducible TFs that can be exploited to the same or similar ends is very large (114,115) and likely to be expanded in the near future. An added bonus of these expression systems is that owing to being encoded by promiscuous plasmids, they are likely to be operative in a large variety of hosts.…”

Section: Expression Systemsmentioning

confidence: 99%

Mining Environmental Plasmids for Synthetic Biology Parts and Devices

2015

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The scientific and technical ambition of contemporary synthetic biology is the engineering of biological objects with a degree of predictability comparable to those made through electric and industrial manufacturing. To this end, biological parts with given specifications are sequence-edited, standardized, and combined into devices, which are assembled into complete systems. This goal, however, faces the customary context dependency of biological ingredients and their amenability to mutation. Biological orthogonality (i.e., the ability to run a function in a fashion minimally influenced by the host) is thus a desirable trait in any deeply engineered construct. Promiscuous conjugative plasmids found in environmental bacteria have evolved precisely to autonomously deploy their encoded activities in a variety of hosts, and thus they become excellent sources of basic building blocks for genetic and metabolic circuits. In this article we review a number of such reusable functions that originated in environmental plasmids and keep their properties and functional parameters in a variety of hosts. The properties encoded in the corresponding sequences include inter alia origins of replication, DNA transfer machineries, toxin-antitoxin systems, antibiotic selection markers, site-specific recombinases, effector-dependent transcriptional regulators (with their cognate promoters), and metabolic genes and operons. Several of these sequences have been standardized as BioBricks and/or as components of the SEVA (Standard European Vector Architecture) collection. Such formatting facilitates their physical composability, which is aimed at designing and deploying complex genetic constructs with new-to-nature properties.

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Bionemo: molecular information on biodegradation metabolism

Cited by 56 publications

References 19 publications

Integrated Perspective for Effective Bioremediation

Integrated Perspective for Effective Bioremediation

Association of dnt genes of Burkholderia sp. DNT with the substrate-blind regulator DntR draws the evolutionary itinerary of 2,4-dinitrotoluene biodegradation

Mining Environmental Plasmids for Synthetic Biology Parts and Devices

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