Bioremediation 3.0: Engineering Pollutant-Removing Bacteria in
the Times of Systemic Biology

J 2017

Bioremediation 3.0: Engineering Pollutant-Removing Bacteria in the Times of Systemic Biology

DVOŘÁK, Pavel, Pablo Ivan NIKEL, Jiří DAMBORSKÝ a Victor DE LORENZO

Základní údaje

Originální název

Bioremediation 3.0: Engineering Pollutant-Removing Bacteria in the Times of Systemic Biology

Autoři

DVOŘÁK, Pavel (203 Česká republika), Pablo Ivan NIKEL (32 Argentina), Jiří DAMBORSKÝ (203 Česká republika, garant, domácí) a Victor DE LORENZO (724 Španělsko)

Vydání

BIOTECHNOLOGY ADVANCES, Oxford, PERGAMON-ELSEVIER SCIENCE LTD, 2017, 0734-9750

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10606 Microbiology

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 11.452

Kód RIV

RIV/00216224:14310/17:00095406

Organizační jednotka

Přírodovědecká fakulta

DOI

http://dx.doi.org/10.1016/j.biotechadv.2017.08.001

UT WoS

000412254600001

Klíčová slova anglicky

Bioremediation; Biodegradation pathway engineering; Emerging pollutants; Environmental biotechnology; Systemic biology; Metabolic engineering; Systems biology; Synthetic biology

Štítky

NZ, rivok

Změněno: 29. 3. 2018 14:08, Ing. Nicole Zrilić

Anotace

V originále

Elimination or mitigation of the toxic effects of chemical waste released to the environment by industrial and urban activities relies largely on the catalytic activities of microorganisms—specifically bacteria. Given their capacity to evolve rapidly, they have the biochemical power to tackle a large number of molecules mobilized from their geological repositories through human action (e.g., hydrocarbons, heavy metals) or generated through chemical synthesis (e.g., xenobiotic compounds). Whereas naturally occurring microbes already have considerable ability to remove many environmental pollutants with no external intervention, the onset of genetic engineering in the 1980s allowed the possibility of rational design of bacteria to catabolize specific compounds, which could eventually be released into the environment as bioremediation agents. The complexity of this endeavour and the lack of fundamental knowledge nonetheless led to the virtual abandonment of such a recombinant DNA-based bioremediation only a decade later. In a twist of events, the last few years have witnessed the emergence of new systemic fields (including systems and synthetic biology, and metabolic engineering) that allow revisiting the same environmental pollution challenges through fresh and far more powerful approaches. The focus on contaminated sites and chemicals has been broadened by the phenomenal problems of anthropogenic emissions of greenhouse gases and the accumulation of plastic waste on a global scale. In this article, we analyze how contemporary systemic biology is helping to take the design of bioremediation agents back to the core of environmental biotechnology. We inspect a number of recent strategies for catabolic pathway construction and optimization and we bring them together by proposing an engineering workflow.

Návaznosti

GA16-06096S, projekt VaV

Název: Objasnění významu dynamických tunelů pro enzymatickou katalýzu: simulace a fluorescenční experimenty

Investor: Grantová agentura ČR, Objasnění významu dynamických tunelů pro enzymatickou katalýzu: simulace a fluorescenční experimenty

LM2015055, projekt VaV

Název: Centrum pro systémovou biologii (Akronym: C4SYS)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, The national infrastructure C4SYS - Centre for Systems Biology

LO1214, projekt VaV

Název: Centrum pro výzkum toxických látek v prostředí (Akronym: RECETOX)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Centrum pro výzkum toxických látek v prostředí

Citovat

DVOŘÁK, Pavel, Pablo Ivan NIKEL, Jiří DAMBORSKÝ a Victor DE LORENZO. Bioremediation 3.0: Engineering Pollutant-Removing Bacteria in the Times of Systemic Biology. BIOTECHNOLOGY ADVANCES. Oxford: PERGAMON-ELSEVIER SCIENCE LTD, 2017, roč. 35, č. 7, s. 845-866. ISSN 0734-9750. Dostupné z: https://dx.doi.org/10.1016/j.biotechadv.2017.08.001.

@article{1403829,
   author = {Dvořák, Pavel and Nikel, Pablo Ivan and Damborský, Jiří and de Lorenzo, Victor},
   article_location = {Oxford},
   article_number = {7},
   doi = {http://dx.doi.org/10.1016/j.biotechadv.2017.08.001},
   keywords = {Bioremediation; Biodegradation pathway engineering; Emerging pollutants; Environmental biotechnology; Systemic biology; Metabolic engineering; Systems biology; Synthetic biology},
   language = {eng},
   issn = {0734-9750},
   journal = {BIOTECHNOLOGY ADVANCES},
   title = {Bioremediation 3.0: Engineering Pollutant-Removing Bacteria in the Times of Systemic Biology},
   url = {https://loschmidt.chemi.muni.cz/peg/publications/bioremediation-3-0-engineering-pollutant-removing-agents-in-the-times-of-systemic-biology/},
   volume = {35},
   year = {2017}
}

TY  - JOUR
ID  - 1403829
AU  - Dvořák, Pavel - Nikel, Pablo Ivan - Damborský, Jiří - de Lorenzo, Victor
PY  - 2017
TI  - Bioremediation 3.0: Engineering Pollutant-Removing Bacteria in the Times of Systemic Biology
JF  - BIOTECHNOLOGY ADVANCES
VL  - 35
IS  - 7
SP  - 845-866
EP  - 845-866
PB  - PERGAMON-ELSEVIER SCIENCE LTD
SN  - 07349750
KW  - Bioremediation
KW  - Biodegradation pathway engineering
KW  - Emerging pollutants
KW  - Environmental biotechnology
KW  - Systemic biology
KW  - Metabolic engineering
KW  - Systems biology
KW  - Synthetic biology
UR  - https://loschmidt.chemi.muni.cz/peg/publications/bioremediation-3-0-engineering-pollutant-removing-agents-in-the-times-of-systemic-biology/
N2  - Elimination or mitigation of the toxic effects of chemical waste released to the environment by industrial and urban activities relies largely on the catalytic activities of microorganisms—specifically bacteria. Given their capacity to evolve rapidly, they have the biochemical power to tackle a large number of molecules mobilized from their geological repositories through human action (e.g., hydrocarbons, heavy metals) or generated through chemical synthesis (e.g., xenobiotic compounds). Whereas naturally occurring microbes already have considerable ability to remove many environmental pollutants with no external intervention, the onset of genetic engineering in the 1980s allowed the possibility of rational design of bacteria to catabolize specific compounds, which could eventually be released into the environment as bioremediation agents. The complexity of this endeavour and the lack of fundamental knowledge nonetheless led to the virtual abandonment of such a recombinant DNA-based bioremediation only a decade later. In a twist of events, the last few years have witnessed the emergence of new systemic fields (including systems and synthetic biology, and metabolic engineering) that allow revisiting the same environmental pollution challenges through fresh and far more powerful approaches. The focus on contaminated sites and chemicals has been broadened by the phenomenal problems of anthropogenic emissions of greenhouse gases and the accumulation of plastic waste on a global scale. In this article, we analyze how contemporary systemic biology is helping to take the design of bioremediation agents back to the core of environmental biotechnology. We inspect a number of recent strategies for catabolic pathway construction and optimization and we bring them together by proposing an engineering workflow.
ER  -

DVOŘÁK, Pavel, Pablo Ivan NIKEL, Jiří DAMBORSKÝ a Victor DE LORENZO. Bioremediation 3.0: Engineering Pollutant-Removing Bacteria in the Times of Systemic Biology. \textit{BIOTECHNOLOGY ADVANCES}. Oxford: PERGAMON-ELSEVIER SCIENCE LTD, 2017, roč.~35, č.~7, s.~845-866. ISSN~0734-9750. Dostupné z: https://dx.doi.org/10.1016/j.biotechadv.2017.08.001.

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