Rubrobacter Xylanophilus

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Classification

Domain (Bacteria); Phylum (Actinobacteria); Class (Actinobacteria); Subclass (Rubrobacteridae); Order (Rubrobacterales); Suborder (Rubrobacterineae); Family (Rubrobacteraceae); Genus (Rubrobacter) (7)

Species

Rubrobacter Xylanophilus

Figure 1.Rubrobacter Xylanophilus

Description and Significance

Rubrobacter xylanophilus was isolated from a thermally polluted effluent of a carpet factory in Wilton, Wiltshire, UK. This organism is one of the most gamma-radiation resistant organisms known, and the only truly radiation-resistant thermophile, with an optimum growth temperature of 60°C (3). R. xylanophilus is slightly halotolerant, capable of growth in 6-7% NaCl (1) and is the most thermophilic actinobacterium known. This organism is extremely tolerant to desiccation, and the isolation of DNA phylogenetically classified under the genus Rubrobacter found in deserts supports the hypothesis that gamma-radiation resistance is probably the consequence of adaptation to extreme arid or dehydration environments(3). As a result of the organism’s resistance to gamma irradiation, it is possible that genetically engineering this organism could lead to improved ways to clean up pollution and facilitate new industrial processes involving radiation technology- it could be a safe and inexpensive tool for difficult clean-up challenges, because this organism could function under conditions generated by industrial processes that most bacteria could not survive, such as those generated by nuclear wastes. Genes that encode functions for degradation of major pollutants that are commonly found in radioactive waste sites could be transformed into R. xylanophilus, facilitating clean-up processes at radioactive waste sites.


Rubrobacter xylanophilus has also been shown to degrade hemicellulose and xylan (1), and therefore could play a significant role in the environmental degradation of this material. Paper manufacture generates effluents from wood pulping and pulp processing that contain xylans, and agricultural residues also contain xylans. These wastes frequently pollute bodies of water, and because of its ability to degrade this material, R. xylanophilus could be helpful in cleaning up such polluted areas (4).Treatment with xylanase appears to loosen lignin surrounding cellulose fiber bundles and thereby reduces the need to utilize chlorine in paper pulp bleaching processes, which can be detrimental to the environment (9). Additionally, this organism's ability to thrive at temperatures above 50 degrees celsius is an especially desirable characteristic for pulp treatment in the paper industry (9). Xylan, along with cellulose, accounts for more than 50% of all plant biomass, and constitute an inexhaustable renewable resource as they are products of primary production. Combustion of biofuels derived from plant biomass is a carbon neutral process, and a major limitation is the recalcitrance of the plant cell wall, of which xylan is a constituent. Hydrolyzing xylan into xylose and arabinose for subsequent fermentation by ethanol producing microbes is necessary for the efficient use of plant biomass for production of biofuels(10). Through application of microbial fermentation technologies, the conversion of xylose into acetate, propionate, lactate, or succinate could provide a renewable resource of molecules for chemical and pharmaceutical industries(9).


This organism and its closely related relative Rubrobacter radiotolerans form a deep evolutionary line of descent within the gram positive bacteria. R. xylanophilus shares 90% sequence similarity to R. radiotolerans based on comparison of 16srRNA. Both are thermophilic, radiation-resistant, and posess unique branched-chain fatty acids. Major physiological differences between the two include the ability of R. xylanophilus to degrade xylan, utilize inisitol, and grows optimally at 60 degrees as opposed to 45 degrees Celsius, the optimal growth temperature for R. radiotolerans (1).

Genome Structure

Figure 3. Rooted dendrogram (based on pairwise 16s rRNA gene sequence comparisons) showing the derived phylogenetic relationships of R. Xylanophilus and reference strains of the gram-positive phylum. The scale bar indicates the average number of substitutions per nucleotide position. The root organism was E. coli.

R. xylanophilus has a 3.2 Mb circular chromosome, 3140 protein genes, and 64 RNA genes (5). Its GC content is 67.6% mol (1).

Cell Structure, Metabolism and Life Cycle

R. xylanophilus is a pink pigmented strain that forms pleomorphic short gram positive rods that are 0.9 to 1.0 um wide and 1 to 3 um long and coccoid cells. This organism thrives at 60 degrees Celsius, but cannot grow at temperatures below 40 degrees Celsius or above 70 degrees Celsius. The optimum pH for this organism is 7.5-8, and fails to grow at values below 6 or above 10. This organism is non-motile, fails to form endospores, and possesses unusual internal branched-chain fatty acids; mainly 12-methylhexadecanoic acid and 14-methyloctadecanoic acid are the major acyl chains of its lipids. R. xylanophilus possesses cytochrome oxidase, catalase, beta-galactosidase, and is capable of reducing nitrate to nitrite. It is unable to ferment carbohydrates, but grows very well on thermus basal salts medium containing only (NH4)2SO4 and a carbon source. Aside from differences in optimum temperature, the ability of R. xylanophilus to hydrolyze xylan and utilize Inositol are two major distinctions between this organism and its close relative, Rubrobacter radiotolerans. R. xylanophilus is an aerobic organism, incapable of growth in anaerobic conditions. As mentioned, this organism is slightly halophilic and survives in 6% NaCl. It can hydrolyze gelatin, hide powder azure, arbutin, esculin, and hippurate (1).


Interestingly, Rubrobacter xylanophilus is the only actinobacterium known to accumulate Mannosylglycerate (MG), and under all growth conditions tested (3) constitutively. Its pools of MG and Trehalose remain nearly constant regardless of many environmental stresses imposed on it, such as salt stress, oxidative stress, and nitrogen limitations (3). A number of other compatible solutes such as di-myo-inositol-phosphate and di-N-acetyl glucoasamine phosphate were detected in this organism. Compatible solutes may serve to protect cells from temperature extremes, dehydration, or oxygen radicals. Their protective roles may be useful for preserving cultures, and conserving tissues. The large and steady pools of organic solutes are believed to uphold a high internal turgor pressure essential to counteract mechanical properties of the thick peptidoglycan layer of high GC gram positive organisms (2). MG has been probed for the protection of cell macromolecules at high temperatures, and has been found to be a successful stabilizer of enzymes against thermal denaturation in vitro (8). Moreover, MG has been shown to prevent protein aggregation, and applications range from biotechnology to biomedicine and misfolding diseases. The applicability of MG as an inhibitor of soluble β-amyloid peptides aggregation in vitro, has been demonstrated, thus this molecule could be useful in the prevention of aggregation-related diseases (6). Meanwhile, MG is currently under study as a viable solution for a number of applications, from cosmetics to biotechnology, such as an enhancer of the quality of microarrays (3)

Figure 4. Structure of Mannosylglycerate

Ecology and Pathogenesis

R. xylanophilus was isolated from a thermally polluted industrial runoff. The natural habitat of this organism is not known (1). Microorganisms such as R. xylanophilus with xylan degrading capabilities could use this characteristic in symbiotic relationships with ruminant animals or wood consuming insects as xylan is a major component of plant material(9). However there is no such evidence of such symbioses in Rubobacter Xylanophilus, nor is there evidence of pathogenesis. If R. xylanophilus utilizes its xylan degradation capabilities in nature, it is possible the downstream products of this metabolism could be useful to other organisms.

References

1)Carreto, L., E. Moore, M. F. Nobre, R. Wait, P. W. Riley, R. J. Sharp, and M. S. Da Costa. "Rubrobacter xylanophilus sp. nov., a new thermophilic species isolated from a thermally polluted effluent." International Journal Of Systematic And Evolutionary Microbiology. 1996. Volume 46.2 p. 460-65.

2) Doyle, Ron J., and Robert E. Marquis. "Elastic, Flexible Peptidoglycan and Bacterial Cell Wall Properties." Trends in Microbiology 2.2 (1994): 57-60. Web. 10 Apr. 2011. <http://www.ncbi.nlm.nih.gov/pubmed/8162443>.

3) Empadinhas N, da Costa MS. “Diversity, biological roles and biosynthetic pathways for sugar-glycerate containing compatible solutes in bacteria and archaea.” Environmental Microbiology. 2010

4)Glazer, Alexander N., and Hiroshi Nikaido. "Degradation of Hemicelluloses." Microbial Biotechnology: Fundamentals of Applied Microbiology. 2nd ed. Cambridge: Cambridge UP, 2007. 453-56. Print.

5)"KEGG GENOME: Rubrobacter Xylanophilus." KEGG Genome. Web. 15 Apr. 2011. <http://www.genome.jp/kegg-bin/show_organism?org=T00368>.

6) Ryu, Jungki et al. "Inhibition of β-amyloid Peptide Aggregation and Neurotoxicity by α-d-mannosylglycerate, a Natural Extremolyte." Web. 10 Apr. 2011. <http://www.ncbi.nlm.nih.gov/pubmed/18304694>.

7) "Taxonomy Browser (root)." Taxonomy Browser. Web. 10 Apr. 2011. <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi>.

8) Tiago, Faria Q. et al. "Protein Stabilisation by Compatible Solutes: Effect of Mannosylglycerate on Unfolding Thermodynamics and Activity of Ribonuclease A - Faria - 2003 - ChemBioChem." Wiley Online Library. July-Aug. 2003. Web. 10 Apr. 2011. <http://onlinelibrary.wiley.com/doi/10.1002/cbic.200300574/abstract>.

9)Uffen, R. L. "Xylan Degradation: a Glimpse at Microbial Diversity." Journal of Industrial Microbiology and Biotechnology 19.1-6 (1997). Web.

10) Cann, ISAAC K.O., and Dylan Dodd. "Enzymatic Deconstruction of Xylan for Biofuel Production." Glob Change Biol Bioenergy 1.1 (2009): 2-17. Web. <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860967/>.

Author

Page authored by Ashley Konal and Cody Kurzer, students of Prof. Jay Lennon at Michigan State University.