Dictyoglomus thermophilum: Difference between revisions
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==Pathology== | ==Pathology== | ||
At this time, there are no known diseases caused by this organism. It has not been found to be pathogenic either [10]. | |||
==Application to Biotechnology== | ==Application to Biotechnology== | ||
Revision as of 06:49, 29 August 2007
A Microbial Biorealm page on the genus Dictyoglomus thermophilum
Classification
Higher order taxa
Bacteria; Dictyoglomi; Dictyoglomi; Dictyoglomales; Dictyoglomaceae
Species
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NCBI: Taxonomy |
Dictyoglomus thermophilum
Description and significance
Dictyoglomus thermophilum is light grey, anaerobic, extremely thermophilic, rod-shaped bacterium first isolated from a slightly alkaline hot spring (pH 7.2, 100% N2) in Japan, 1985. Since then, the organism has been found in hot spring beds located in New Zealand and Russia as well. Like other thermophiles, D. thermophilum, thrives in environments of high temperature (between 50 and 80˚C, with an optimal value of 78˚C) [7, 10, 12].
This bacterium is unique in that it is the only member of the phylum entitled Dictyoglomi. The properties of this strain do not fit those of any previously described genus, warranting its very own phylum. D. thermophilum only lives in aquatic environments and is not known to have any form of motility [10]. It is a chemoorganotorph, meaning it derives energy by metabolizing organic molecules. This mysterious and elusive bacterium has generated interest because it has the ability to express xylanase, an enzyme involved in the digestion of xylan (a heteropolymer of the pentose sugar xylose). By treating wood pulp with this enzyme, manufacturers can give paper its characteristic “whiteness” without the use of chlorine bleach [4, 8]. Scientists have attempted to sequence and study the genes which encode this unusual protein and many others, with the intention of understanding how this organism is able to thrive under such extreme conditions.
Dictyoglomus thermophilum is a fairly young organism, only discovered in the year 1985 by Saiki et al. in a tsuetate hot spring of Japan [3, 12].
Genome structure
The complete genome for D. thermophilum has yet to be fully sequenced. Since the year 2006, geneticists at The Institute for Genomic Research (TIGR), have been conducting “random” shotgun sequencing in an attempt to construct the organism’s entire genome. The lack of information has made it difficult for microbiologists to isolate numerous proteins and enzymes synthesized by this organism [10, 14].
The G+C content of D. thermophilum is around 29 mol% [6]. Thirteen nucleotide regions, which code for a total of 17 proteins have been sequenced from Dictyoglomus thermophilus’s genome [10]. These numbers are miniscule when compared to the thousands of coding regions that have been identified from genomes in other organisms. Of the 17 discovered coding regions, many of them code for amylase proteins, xylanse enzymes, DNA polymerase, multiple unnamed proteins, and various kinase and transferase proteins.
A total of three DNA sequences have been identified encoding three different Alpha-amylase enzymes (amyA, amyB, and amyC). Each of the sequences are 2649, 2496, and 2226 base pairs long. These enzymes are primarily involved in starch breakdown, providing the microbe with nutrients [6, 7, 9]. A 2639 base pair sequence was found to encode for DNA polymerase I [13]. Another internal 1507-bp fragment was sequenced and shown to code for a small, 352 amino acid long xylanase protein (XynA) [6]. This enzyme is involved in the degradation of heteropolymer, xylan. Another xylanase, xynB, is also coded in the genome of D. thermophilum. XynB also is involved in the breakdown of xylan, however, it is of greater interest than xynA because of its ability to bleach paper. Various nucleotide sequences such as these have been isolated and found to encode proteins primarily involved in hydrolysis of organic molecules.
The exact positioning of these genes on the chromosome is not yet known. Once the complete genome has been constructed, a lot more can be inferred about its genomic structure.
Cell structure and metabolism
D. thermophilum is a Gram negative (-) bacterium, meaning that it contains both an inner and outer cell membrane. Living in extremely warm environments, its cell membrane is fairly rigid, containing many saturated fatty acid chains, while its proteins contain many charged amino acids to prevent denaturation when subject to extreme heat. D. thermophilum typically resides in slightly alkaline mediums, with a pH around 7.2 [3]. Oddly enough, its amylase proteins function best at a pH between 5 and 5.5. It is possible that the internal environment of the bacterium is slightly acidic when compared to the medium in which it resides.
Being an organotroph, D thermophilum typically makes use of enzymes to degrade organic macromolecules for nutrients. The major food sources consumed are starch, galactomannan, and xylan. Due to its elusive nature, only a handful of enzymes involved in catabolic and anabolic pathways have been isolated from D. thermphilum. Three amylase enzymes have been purified from this strain, all of them thought to be involved in the hydrolysis of starch as a nutrient source. It was recently proved that the enzyme amylase A, has transglycosylation properties as well. Given this new development, it is possible that D. thermophilum also makes use of other saccharides as a nutrient source (see “Current Research”). In addition, it uses a beta-mannose enzyme to hydrolyze galactomannase into mannose, mannobiose and mannotriose [5]. D. thermophilum has generated significant interest given its ability to solubilize the heteropolymer xylan. Two xylanase enzymes, xynA and xynB, are thought to be involved in this process. Both enzymes function a similar temperatures and pH ranges. XynA, related to the family F group of xylanases, is capable of hydrolyzing xylan to xylotriose and xylobiose. Only xynB has proven useful in pulp bleaching [4].
The pfp gene from D. thermophilum encodes a pyrophosphate-dependent phosphofructokinase (PPi-PFK). A phylogenetic analysis of this enzyme indicates that it is closely related to another from the organism Thermoproteus tenax. It is known that ATP-dependent phosphofructokinase (PFK) is a vital enzyme in the glycolysis pathway. It is possible that PPi-PFK plays a role in the metabolism of glucose for energy in D. thermophilum. However, it was previously suggested that PPi-PFK represented an ancestral form of PFK during a time when pyrophosphate was the primary source of metabolic energy (before the advent of ATP) [2]. This sheds light on the idea that D. thermophilum may in fact be a fairly old organism, partially explaining its elusive nature.
Ecology
D. thermophilum resides in dilute mediums with a slightly basic pH (7.2) at temperatures around 78˚C. D. thermophilum is of the Bacterial domain, whereas most extremophiles are of the domain Archaea. It lives exclusively in aquatic environments and does not have any known method of locomotion. The medium from which D. thermophilum was discovered contained a mixture small quantities of ionic compounds such as Na2HPO4 x 12 H2O, ZnSO4, CaCl2 x 2 H2O, NH4Cl, KH2PO4, and Fe(NH4)2(SO4)2 x 6 H2O [3]. The medium also contained starch, glucose, and other polysaccharides. D. thermophilulm is a rod-shaped bacterium and can arrange itself in singles, pairs, chains and spherical bodies [10].
A thermophilic, chemoorganotrophic, and anaerobic strain of bacterium, similar to that of D. thermophilum was isolated from hot springs in New Zealand, 1996 [11]. Since its discovery, D. thermophilum, has been isolated in a few countries around the globe, including New Zealand. This indicates that the two bacteria might share similar characteristics in their genome. The strain discovered in New Zealand had a DNA base composition of 29.5% G+C [11], while D. thermophilum has a 29 mol% G+C composition. This new organism could be the second to join the Dictyoglomi phylum, which was created solely for D. thermophilum, upon its discovery.
Pathology
At this time, there are no known diseases caused by this organism. It has not been found to be pathogenic either [10].
Application to Biotechnology
Does this organism produce any useful compounds or enzymes? What are they and how are they used?
Current Research
Enter summaries of the most recent research here--at least three required
References
Edited by student of Rachel Larsen
