Members of some genera have been of particular interest, especially those known to cause disease in plants, animals and humans, notably the causative agent of tuberculosis, Mycobacterium tuberculosis. Actinobacteria inhabit a wide range of environments: they are found as endophytes in plants; symbionts in insects and marine invertebrates; are associated with animals and humans; and occur in various terrestrial and aqueous (fresh water and salt water) environments. Their biodiversity has been assessed through culture-dependent and culture independent methods through the use of selective isolation techniques and metagenomic studies, respectively.
Some actinobacteria are filamentous in nature and are typically referred to as the actinomycetes. They were initially classified as fungi, with the name “actinomyces” literally meaning “ray fungus”. It was only with the advent of 16S rRNA gene sequencing and analysis, that it was realized that actinomycetes are actually bacteria. Genome sequencing has allowed us to look deeper into the biosynthetic potential of these organisms and from this it has become clear that actinobacteria remain underexplored as a source of novel primary and secondary metabolites. Genome sizes typically range from 4 Mb to 10.5 Mb, with some genomes, especially those of Rhodococcus strains, containing multiple copies of genes encoding for enzymes involved in biodegradation.
One of the projects our research group is currently focusing on is looking at actinobacteria as a source of oxidative enzymes and relating genome sequence information to biosynthetic potential. Oxidative enzymes are highly sought after, particularly in view of the difficulties associated with oxidation reactions in conventional chemical catalysis, which include a lack of control and predictability of the product structures, as well as the expense of oxidizing reagents. In contrast, the generally high activity of oxidising enzymes confers some important advantages in developing oxidative bioprocesses such as the oxidation of compounds at specific positions.
"Oxidative enzymes" encompass a vast group of enzymes with varied catalytic abilities and among them, the enzymes laccase, peroxidase and tyrosinase are known for their ability to catalyse oligomerisation, depolymerisation and hydroxylation reactions. Some of these enzymes, notably laccase and tyrosinase, are often described as “green enzymes”: they only require molecular oxygen to catalyse their reactions and produce water as a by-product. As such, they are ideal candidates for the development of bioprocesses consistent with the bio-economy approach. Products can be manufactured or substrates degraded under conditions that are cost-effective and sustainable, with minimal impact on the environment.
Over the past few years, members of the Biocatalysis and Technical Biology (BTB) Research Group have isolated actinobacteria from a wide range of environments: marine invertebrates, soil samples from Antarctica, Namibia, New Zealand, South Africa and Zambia. In addition, we also have cultures from termite guts and selected deep-sea actinobacteria. This extensive culture collection of more than 1000 strains has been screened for potentially novel oxidative enzymes suitable for industrial application. The screening program involved functional screening on agar plates that contain the enzyme substrates, dye decolourisation and liquid assays in microtiter plate format. Induction and optimization of enzyme production from the native strains under various bioreactor conditions have been conducted: e.g. the production of a laccase-like protein from a novel marine actinomycete in an air-lift reactor. In addition, the involvement of a triphenylmethane reductase in the decolourisation and degradation of crystal violet by a deep-sea actinomycete have been shown. Oxidative enzymes produced by a range of actinobacterial strains are currently being applied in various biocatalysis reactions with the focus on the production of antioxidants and novel biomaterials.
This project is a collaborative project and is only possible due to the contributions of the following researchers (in no particular order): Dr Paul Meyers, Department of Molecular and Cell Biology, University of Cape Town; Dr Bronwyn Kirby, Department of Biotechnology, University of the Western Cape; Dr Jeffrey Rohland, Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape; Dr Nuraan Khan, Department of Biochemistry, Microbiology and Biotechnology, Rhodes University; Prof. Stephanie Burton, Vice-Principal: Research and Postgraduate studies, University of Pretoria; Prof. Don Cowan, Department of Genetics, University of Pretoria; Postgraduate students and work integrated learning students from the Cape Peninsula University of Technology (CPUT) Biotechnology program; and members of the BTB research group.
Author: Marilize Le Roes-Hill
Biocatalysis and Technical Biology (BTB) Research Group