Catabolic Plasmids

Abstract

Catabolic plasmids are large (80→1100 kb) linear or circular, accessory deoxyribonucleic acid elements present in the cytoplasm of bacteria from virtually every ecological niche on Earth. Many have a broad host range and can be transferred by cell‐to‐cell contact to a wide range of bacteria. The large catabolic gene clusters carried by these plasmids play a central role in the Earth's carbon cycle, enabling their hosts to degrade and recycle complex naturally occurring molecules such as lignin, the second most abundant plant biopolymer on Earth after cellulose. More recently catabolic gene clusters have evolved the ability to degrade and recycle most man made molecules, including the most toxic and the most recalcitrant environmental pollutants, providing a biological solution to environmental pollution. Catabolic genes have been used to construct novel strains of bacteria which produce biopharmaceuticals such as antibiotics and anticancer agents, biofuels such as ethanol, industrial dyes such as indigo and biodegradable plastics. The very first patent for a genetically modified organism was for the use of catabolic plasmids to degrade oil.

Key Concepts:

  • Catabolic plasmids are giant bacterial plasmids that encode vast arrays of catabolic gene clusters. They play a central and indispensible role in the Earth's carbon cycle.

  • Catabolic plasmids are essential for the degradation and recycling of abundant, naturally occurring yet chemically complex plant materials such as lignin.

  • In addition, there are catabolic plasmids, which enable bacteria to degrade and recycle the most complex, most toxic and the most polluting man‐made molecules including most carcinogens, teratogens and mutagens.

  • Degradation and recycling of such complex molecules at room temperature and pressure, so called ‘green or eco‐friendly’ chemistry, requires many different enzymes encoded in large arrays of gene clusters. To accommodate these genes on catabolic plasmids they must be very large. Some are in excess of 1000 kb.

  • Many catabolic plasmids are transferable from one bacterial cell to another by cell‐to‐cell contact. They have an extraordinarily broad host range being able to rapidly confer their catabolic activities on large populations of soil bacteria.

  • Novel catabolic functions can be produced by rearranging existing pathway genes, combining genes from different pathways to form a new pathway and by fusing segments from a number of pre‐existing catabolic genes into a new catabolic gene.

  • The genes encoded by catabolic plasmids have been harnessed by humans to produce antibiotics and anticancer drugs, to synthesise biofuels such as ethanol from lignin and to degrade and recycle man‐made environmental pollutants.

  • The very first patent to be granted for a genetically modified organism was for catabolic plasmids that encoded the degradation of environmental oil spills.

Keywords: plasmid; gene; evolution; regulation; environmental pollution

Figure 1.

Plasmid‐encoded pathways for the degradation of natural and synthetic molecules. (a) The tfd regulon on pJP4. (b) The proposed pathway for 2,4‐dichlorophenoxyacetic acid degradation facilitated by the tfd regulon. (c) The xyl regulon on pWWD. (d) The proposed pathway for toluene degradation facilitated by the xyl regulon.

Figure 2.

Simplified plasmid map of a hypothetical biosensor construct. Regulator X is a transcriptional activator that responds to an environmental pollutant. Green fluorescent protein is a reporter gene activated by regulator X. ori is the origin of plasmid regulation. Ampicillin resistance is a selectable gene. In this model, regulator X responds to an environmental signal (e.g. polychlorinated biphenyl) and attaches to the promoter. Transcription from the promoter is activated and green fluorescent protein is produced. The level of fluorescence detected is proportional to the size of the signal and therefore to the concentration of the pollutant.

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Further Reading

van Belkum A, Scherer S, van Alphen L and Verbrugh H (1998) Short‐sequence DNA repeats in prokaryotic genomes. Microbiology and Molecular Biology Reviews 62: 275–293.

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Schmidt, Radomir, Ahmetagic, Adnan, Philip, Daniel S, and Pemberton, John M(Sep 2011) Catabolic Plasmids. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000471.pub3]