Bacillus subtilis

A Microbial Biorealm page on the genus Bacillus subtilis

Classification

Higher order taxa

Domain: Bacteria, phylum: Firmicutes, class: Bacilli, order: Bacillales, family: Bacillaceae (Entrez Genome Project)

Genus

Bacillus subtilis

NCBI: Taxonomy

Description and significance

Originally named Vibrio subtilis in 1835, this organism was renamed Bacillus subtilis in 1872. Other names for this bacteria also include Bacillus uniflagellatus, Bacillus globigii, and Bacillus natto. Bacillus subtilis bacteria were one of the first bacteria to be studied. These bacteria are a good model for cellular development and differentiation (Entrez Genome Project).

Bacillus subtilis cells are rod-shaped, Gram-positive bacteria that are naturally found in soil and vegetation. Bacillus subtilis grow in the mesophilic temperature range. The optimal temperature is 25-35 degrees Celsius. Stress and starvation is common in this environment, therefore, Bacillus subtilis has evolved a set of strategies that allow survival under these harsh conditions. One strategy, for example, is the formation of stress-resistant endospores. Another strategy is the uptake of external DNA, which allow the bacteria to adapt by recombination. However, these strategies are time-consuming. Bacillus subtilis can also gain protection more quickly against many stress situations such as acidic, alkaline, osmotic, or oxidative conditions, and heat or ethanol. The alternative sigma factor ςB is a global regulator of stress response. Heat, acid, or ethanol and glucose or phosphate starvation are all stimuli that activate ςB (Bandow 2002).

Genome structure

A total of 4,100 genes were identified in Bacillus subtilis, all of which are protein-coding genes. Only one DNA molecule is present in these cells. Bacillus subtilis has one circular chromosome. The total size of all the DNA is 4,214,814 bp (4.2 Mbp). 53% of the protein-coding genes are only seen once, while 25% of the genome relates to families of genes that have undergone gene duplication.

A great portion of the genome corresponds to carbon source applications. 192 of the 4,100 genes are considered indispensable, and an additional 79 were predicted to be essential genes. The majority of the essential genes are involved in metabolism. Half of the essential genes are responsible for processing information, one-fifth of them are responsible for cell wall synthesis, cell division and shape, and one-tenth of them were responsible for the energetics of the cell. The essential genes that code for functions that are not known are 4%. Bacillus subtilis bacteria are capable of secreting antibiotics in great numbers to the exterior of the cell. Five signal peptidase genes were found to be important for this secretion function. Many of Bacillus subtilis cells' genes are responsible for antibiotic synthesis.

Cell structure and metabolism

Bacillus subtilis are rod-shaped bacteria that are Gram-positive. The cell wall is a rigid structure outside the cell. It is composed of peptidoglycan, which is a polymer of sugars and amino acids. The peptidoglycan that is found in bacteria is known as murein. Other constituents that extend from the murein are teichoic acids, lipoteichoic acids, and proteins. The cell wall forms the barrier between the environment and the bacterial cell. It is also responsible for maintaining the shape of the cell and withstanding the cell's high internal turgor pressure.

Bacillus subtilis is a model organism for studying endospore formation in bacteria. Endospores in Bacillus subtilis bacteria are mostly formed in the tips of protuberances extending from liquid surface pellicles. Depletion of carbon, nitrogen, or phosphorous causes the process of sporulation to begin, however, the process needs to start before the entire exhaustion of nutrients. Otherwise, the spore formation cannot be completed due to the fact that the nutrients are too low for the energy-requiring sporulation process. This allows the cells to avoid being stuck in a vulnerable position.

The formation of the endospore occurs in several stages, denoted 0 through VI. Sporulation occurs in the following fashion. First the nucleoid lengthens, becoming an axial filament. Then, the cell forms a polar septum, one-fourth of the cell length from one end, and begins to divide. The smaller product of this division is called the forespore and the larger product is called the mother cell. The mother cell is responsible for nourishing the newly formed spore. When the septum forms, 30% of the chromosome is already on the forespore side. The remaining 70% of the chromosome enters the forespore in a fashion similar to DNA transfer during conjugation; it is pumped by a protein called spoIIIE (perez 2000). The mother cell then engulfs the forespore by acting like a phagocyte. This causes the forespore to have two cytoplasmic membranes with a thick murein layer, namely the cortex, between them. A protein spore coat and an exosporium, a membranous layer, form outside of the forespore membranes. At this time, the forespore undergoes internal changes. Lastly, the forespore leaves the mother cell upon lysis of the mother cell. A mature endospore has no metabolic activity; it is inert. It does not have any ATP or reduced pyridine nucleotides. The interior of the endospore, the core, is very dry and resistant to moisture.

Bacillus subtilis bacteria use their flagella for a swarming motility. This motility occurs on surfaces, for example on agar plates, rather than in liquids. Bacillus subtilis are arranged in singles or chains. Cells arranged next to each other can only swarm together, not individually. These arrangements of cells are called 'rafts'. In order for Bacillus subtilis bacteria to swarm, they need to secrete a slime layer which includes surfactin, a surface tension-reducing lipopeptide, as one of its components.

Bacillus subtilis bacteria have been considered strictly aerobic, meaning that they require oxygen to grow and they cannot undergo fermentation, however, recent studies show that they can indeed grow in anaerobic conditions. The bacteria can make ATP in anaerobic conditions via fermentation as well as nitrate ammonification. Bacillus subtilis can use nitrite or nitrate as a terminal acceptor of electrons. Bacillus subtilis contains two unique nitrate reductases. One is used for nitrate nitrogen assimilation and the other is used for nitrate respiration. However, there is only one nitrite reductase that serves both purposes. Nitrate reductase reduces nitrate to nitrite in nitrate respiration, which is then reduced to ammonia by nitrite reductase. Bacillus subtilis is different from other anaerobes in that it undergoes fermentation without external acceptors of electrons. During fermentation, the regeneration of NAD+ is chiefly mediated by lactate dehydrogenase, which is found in the cytoplasm. Lactate dehydrogenase converts pyruvate to lactate.

Bacillus subtilis contain catalase Kata and MrgA, an enzyme that is responsible in the catalysis of the decomposition of hydrogen peroxide to water and oxygen, and superoxide dismutase, an enzyme that catalyzes the breakdown of superoxide into oxygen and hydrogen peroxide (Bandow 2002).

References

[1] Ara, K., et al. "Bacillus minimum genome factory: effective utilization of microbial genome information." Biotechnol. Appl. Biochem.. 2007 March; 46(Pt 3):169-78.

[2] Bandow, J.E., H. Brötz, M. Hecker. "Bacillus subtilis Tolerance of Moderate Concentrations of Rifampin Involves the ςB-Dependent General and Multiple Stress Response". Journal of Bacteriology. 2002 January; 184(2): 459–467.

[3] Entrez Genome Project

[4] Kobayashi, K., et al. "Essential Bacillus subtilis genes". Proc Natl Acad Sci U S A. 2003 April 15; 100(8): 4678–4683.

[5] Kunst, F., et al. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis". Nature. 1997 November; 390, 249-256.

[6] Marino, M., et al. "Modulation of Anaerobic Energy Metabolism of Bacillus subtilis by arfM (ywiD)". J Bacteriol. 2001 December; 183(23): 6815–6821.

[7] Nakano, M.M., P. Zuber. "Anaerobic Growth of a 'Strict Aerobe' (Bacillus subtilis)". Annual Review of Microbiology. 1998 October; Vol. 52: 165-190.

[8] Perez, A.R., A. Abanes-De Mello, K. Pogliano. "SpoIIB Localizes to Active Sites of Septal Biogenesis and Spatially Regulates Septal Thinning during Engulfment in Bacillus subtilis". Journal of Bacteriology. 2000 February; 182(4): 1096–1108.

[9] The Institute for Genome Research, Comprehensive Microbial Resource (TIGR CMR).

Schaechter, M., J.L. Ingraham, F.C. Neidhardt. Microbe. (ASM Press, Washington, DC, 2006).

Edited by Margo Ucar, student of Rachel Larsen and Kit Pogliano