A Microbial Biorealm page on the genus Mycobacterium vanbaalenii
Higher order taxa
Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Coyrnebacterineae; Mycobacteriaceae; Mycobacterium; Mycobacterium vanbaalenii PYR-1
Some members of the Mycobacterium genus are able to degrade various environmentally toxic chemicals. Mycobacterium vanbaalenii PYR-1 was first found in the Harbor Island oil tank farm in the watershed of Redfish Bay, Texas in 1986. It is notable for its ability to degrade polycyclic aromatic hydrocarbons (PAHs) such as pyrene, and use them as its sole carbon and energy source. PAH are common organic pollutants; some, i.e. pyrene, are found in incompletely combusted petroleum products. Some PAHs have been identified as carcinogens and pyrene itself is known to be toxic to the liver and kidneys. It has been proposed that the understanding of the genome sequence of the PYR-1 strain will allow an understanding of the PAH degradation pathway and may prove useful ecologically in bioremediation processes. (2)
Cultures of M. vanbaalenii grow in colonies of 0.5 - 1.0nm. The colonies are circular, smooth and convex with the surface of the plate. Individual cells are shaped typical of the Mycobacteria genus, slim and rod-shaped. They are 0.7 - 1.4μm in length and 0.4 - 0.7μm in width. Unlike some other Mycobacterium such as M. leprae it is considered a "fast-growing" bacteria, and not as difficult to culture as its cousin. (4)
The PYR-1 strain has a circular chromosome. It has 5,979 protein genes, and 58 RNA genes. It has 6,491,865 base pairs with a G+C content of 67.8%, 91% of these genes code for something (are functional). It contains 99 pseudogenes. These are genes which accumulate mutations at a higher rate, rendering them non-functional. (1)
Two genes nidA and nidB have been identified as the genes which code for the large and small subunits of a PAH dioxygenase. The dioxygenase is an enzyme that catalyzes both oxygen atoms in O_2 into a single substrate and has been shown to be involved in the PAH degradation pathway of M. vanbaalenii. The proteins of these genes are conserved homologues to proteins in other soil Mycobacterium species which indicate they may be important in PAH degradation.
An operon for the regulatory protein phtR and five genes closely located to each other; phtAa, phtAb, phtB, phtAc, and phtAd have been found close to the nidA and nidB genes. These genes are important for the degradation of phthalate, an intermediate in the degradation of three known PAH’s in M. vanbaalenii, and is currently being studied.
Further understanding of these genes and the enzymes they code may prove useful in the current studies of M. vanbaalenii and its relatives and their degradative properties of the harmful PAH compounds. (10)
Cell structure and metabolism
Mycobacteria are in the group of Actinobacteria, Gram-positive bacteria who live mostly in the soil and are involved in the degradation of organic materials. Like other Mycobacterium, M. vanbaalenii is an acid-fast, aerobic bacteria which stains Gram-positive which means it has only one inner cell membrane and a thick cell wall (unlike cells who stain Gram-negative which have two cell membranes and a thin cell wall in between). It is a rod-shaped, non-motile, and non-sporulating organism. Cells can grow singly, paired, or clustered with almost no pleomorphism, or variation in cell size and shape. It has only one layer of cell wall, which is hydrophobic, waxy, and thicker than the cell walls of most other bacteria. (3)
Research on similar relatives of M. vanbaalenii, M. bovis and M. tuberculosis, shows that the Mycobacterium cell walls are composed primarily of mycolic acids, arabinogalactan (made up mostly of arabinose, galactose, and rhamnose), and peptidoglycan (made up of various compounds such as alanine, glutamic acid, and galactosamine).  Mycolic acids are long saturated fatty acid chains composed of saturated alpha-alkyl, beta-hydroxy fatty acids chains 70-90 carbon atoms long. This structure is a key component in the pathogenic species of Mycobacterium in terms of antibiotic resistance and impermeability. For the genus as a whole, M. vanbaalenii included, the mycolic acid component of the cell wall protects it from dessication and allowing it to grow in conditions other microorganisms (such as some Gram-negatives) could not. (7) This key molecule which makes up so much of the cell wall is what gives the genus (Mycobacterium) its name. (3)
It has been deduced that the majority of M. vanbaalenii’s energy is derived from the metabolic degradation of PAHs for carbon and energy use. Due to its thick, waxy cell wall this genus of bacteria is very hardy. M. vanbaalenii's metabolic rates peak when it is in an environment of 24-30°C, suggesting that this is the optimal temperature for growth. There was no observable growth at 5°C or 42°C. (4)
Most Mycobacteria, excepting a few obligate, pathogenic bacteria, are found in the soil. M. vanbaalenii in particular is often found in contaminated soils or wells and plays an important role degrading toxic pollutants in the soil. There are at least 16 polycyclic aromatic hydrocarbons (PAHs) listed by the U.S. Environmental Protection Agency as priority pollutants due to toxicity and ubiquity.  PAH's are components of products such as crude oil used by humans and may enter into the environment through means such as combustion of fossil fuels. While PAH’s of low molecular density have been shown to degrade naturally, PAH’s of higher molecular density (molecules of four rings and more) are much harder to degrade and may persist in the environment. Different PAH’s have different effects, however, there have been proven toxic, mutagenic, and in some cases carcinogenic effects of some PAH’s which makes it important to find methods to degrade these compounds. M. vanbaalenii has already proven effective in degrading four-ring compounds such as pyrene, readily metabolizing pyrene into carbon dioxide. This is an important step towards bioremediation of polluted environmental sites. (8) M. vanbaalenii are one of the micro-organisms being studied now in the hopes of reducing the effects that these compounds have on (more immediately) aquatic animals and, potentially, humans. (4)
M. vanbaalenii comes from a diverse genus of bacteria. On the whole, most Mycobacteria are non-pathogenic soil bacteria and survive on their own. A few species, however, such as M. tuberculosis and M. leprae are obligate parasites and need hosts to survive. The mycolic acid layer that the single waxy layer of the cell wall characteristic in all the species in the Mycobacterium genus also contributes to the slow growth rate as well as the hardiness of the pathogenic strains such as M. tuberculosis, a pathogen which targets only humans. This makes the pathogenic strains very resistant to antibiotics. (7)
M. vanbaalenii is non-pathogenic and is currently characterized under risk group 1.  Like other Mycobacteria which uses the degradation of various compounds found in the soil (PAH for M. vanbaalenii) it is currently being studied for its potential to reduce environmental pollution, not its risk to the health of humans or animals. (2)
Application to Biotechnology
M. vanbaalenii is an ideal candidate for bioremediation in contaminated areas of the environment. First discovered in 1986 on contaminated sites it was the first known micro-organism to be able to degrade polycyclic aromatic hydrocarbons of more than three aromatic rings. (4) Studies are being conducted on how M. vanbaalenii may prove useful in the degradation of larger PAH molecules such as benzo[a]pyrene. Although there are no definite results on its effect to humans the Environmental Protection Agency (EPA) has shown BaP to be carcinogenic to various mammals including some primates. Exposure to drinking water contaminated with BaP resulted in tumors in various locations such as the forestomach and esophagus. As well as its proven carcinogenic effects BaP has also been shown to be genotoxic to various prokaryotic and mammalian DNA. (5) A terminal deoxygenase has been found to be an important factor in PAH degradation in M. vanbaalenii’s pathway to transform BaP into various metabolites. In studies, results showed that M. vanbaalenii was able to convert BaP into benzo[a]pyrene cis-4R,5S-dihydrodiol and benzo[a]pyrene cis-4S,5R-dihydrodiol both non-toxic and non-carcinogenic. Its regioselectivity in degrading compounds and forming others may also be studied for other pharmaceutical or industrial purposes. (8)
1. This paper studies the degradation of three particular polycyclic aromatic hydrocarbons, pyrene (PYR), benz[a]anthracene (BAA), and benzo[a]pyrene (BaP) by M. vanbaalenii. The studies focus on the degradative processes and identifies three metabolites formed in the study with PYR. Different cleavage products were identified for BAA and BaP and the possibility that the bacterium may be capable of attacking and degrading BAA and BaP from different sites of the compounds was explored. These reactions are believed to occur through dioxygenase enzymatic processes. (8)
2. This article studies the metabolic pathway of benzo[a]pyrene degradation by M. vanbaalenii PYR-1. More specifically it studies the reactions and the stereo and regio-selectivity of oxygenases, a class of enzymes that act in this pathway. The metabolites are separated and identified and the previously reported metabolic pathway is extended with the new evidence presented in this article. (9)
3. This article states that the study identified an operon within the M. vanbaalenii PYR-1 genome for putative phthalate dioxygenase. Phthalates are compounds commonly used as plasticizers which have known carcinogens in lab studies. This study is the first on a phthalate degradation operon in the M. vanbaalenii and includes brief notes on how it differs from those in other Gram-positive bacteria in terms of gene location and orientation. (10)
4. This article uses various methods to study and complete the metabolic path that M. vanbaalenii takes in the degradation of pyrene. In this study 1028 proteins and 27 enzymes are identified for the complete degradative process which is presented among the results. This study hopes to further elucidate the process involved in PAH degradation, especially that of high-molecular weight PAHs. (11)
4.  Heitkamp, M. A., Franklin, W., Cerniglia, C. E. Microbial metabolism of polycyclic aromatic hydrocarbons: isolation and characterization of a pyrene-degrading bacterium.
6.  Yuko Uenishi, Takashi Okada, Seiji Okabe and Makoto Sunagawa, “Study on the Cell Wall Skeleton Derived from Mycobacterium bovis BCG Tokyo 172 (SMP-105): Establishment of Preparation and Analytical Methods”, Chem. Pharm. Bull., Vol. 55, 843-852 (2007).
7.  Chih-chin Huang , Clare V. Smith , Michael S. Glickman§, William R. Jacobs Jr., and James C. Sacchettini “Crystal Structures of Mycolic Acid Cyclopropane Synthases from Mycobacterium tuberculosis” December 21, 2001.
8.  Joanne Schneider, Robert Grosser, Koka Jay Asimhulu, Weiling Xue, and David Warshawsky. "Degradation of Pyrene, Benz[a]anthracene, and Benz[a]pyrene by Mycobacterium sp. Strain RJGII-135, Isolated from a Former Coal Gasification Site". 1995.
9.  Joanna D. Moody,1 James P. Freeman,2 Peter P. Fu,3 and Carl E. Cerniglia1 "Degradation of Benzo[a]pyrene by Mycobacterium vanbaalenii PYR-1". Received July 28, 2003; Accepted October 6, 2003.
10.  Robin L. Stingley1, Barbara Brezna1,2, Ashraf A. Khan1 and Carl E. Cerniglia. "Novel organization of genes in a phthalate degradation operon of Mycobacterium vanbaalenii PYR-1".
11.  Seong-Jae Kim, Ohgew Kweon, Richard C. Jones, James P. Freeman, Ricky D. Edmondson, and Carl E. Cerniglia. "Complete and Integrated Pyrene Degradation Pathway in Mycobacterium vanbaalenii PYR-1 Based on Systems Biology". 2006