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 and Victor DE LORENZO

Basic information

Original name

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

Authors

DVOŘÁK, Pavel (203 Czech Republic), Pablo Ivan NIKEL (32 Argentina), Jiří DAMBORSKÝ (203 Czech Republic, guarantor, belonging to the institution) and Victor DE LORENZO (724 Spain)

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10606 Microbiology

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 11.452

RIV identification code

RIV/00216224:14310/17:00095406

Organization unit

Faculty of Science

DOI

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

UT WoS

000412254600001

Keywords in English

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

Abstract

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.

Links

GA16-06096S, research and development project

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

Investor: Czech Science Foundation

LM2015055, research and development project

Name: Centrum pro systémovou biologii (Acronym: C4SYS)

Investor: Ministry of Education, Youth and Sports of the CR

LO1214, research and development project

Name: Centrum pro výzkum toxických látek v prostředí (Acronym: RECETOX)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

DVOŘÁK, Pavel, Pablo Ivan NIKEL, Jiří DAMBORSKÝ and Victor DE LORENZO. Bioremediation 3.0: Engineering Pollutant-Removing Bacteria in the Times of Systemic Biology. BIOTECHNOLOGY ADVANCES. Oxford: PERGAMON-ELSEVIER SCIENCE LTD, 2017, vol. 35, No 7, p. 845-866. ISSN 0734-9750. Available from: 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 and 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, vol.~35, No~7, p.~845-866. ISSN~0734-9750. Available from: https://dx.doi.org/10.1016/j.biotechadv.2017.08.001.

Detailed Information on Publication Record