Survey of Genomes - Thermoplasma acidophilum
In this episode from the survey of genomes, Nikkia Schady from 2019 Hiram College Genetics course and the Women’s Volleyball team will introduce us to a member of the Archaea, the 3rd domain of life not recognized until 1977.
Hello my name is Nikkia Schady and today I will be talking to you about the organism Thermoplasma Acidophilum. Thermoplasma Acidophilum is a thermoacidophilic archaeon. It is classified as being in the archaea domain due to its membrane lipid composition, evolutionary ribosomal RNA and conserved proteins. (2) Thermoplasma Acidophilum is also in the subgroup Euryarchaeota and it’s strain is Thermoplasma acidophilum DSM 1728. (3) From here on out I will just call it Thermoplasma as a short name.
• This organism was first discovered when it was isolated from self-heated coal refuse piles. (1). It was first isolated by a man named Darland along with his colleagues in the late 1960’s at a Fair Tuck mine in southwestern Indiana in a pH environment of 1.96. They believed it represented a prokaryotic organism but noticed that unlike other bacterial cells it lacked a rigid cell wall and was only separated by a double membrane.
• The size of the genome was first discovered by Ruepp et. al. using a ‘shotgun primer walking’ method that used PCR amplifications and primer-walking strategies to fill in the missing gaps. Ruepp and his coworkers discovered that the genome of Thermoplasma was 1,564,905 base pairs (3).
• Thermoplasma is one of the smallest free-living organisms and Ruepp and his coworkers also found that the genome consisted of a single circular chromosome of the 1.56Mbp. There were no plasmids detected by biochemical or DNA sequencing methods (3). They also found that the Thermoplasma genome contained 1,509 ORF’s and 1/3 had homologs present in all 3 domains of life (3).
• The Thermoplasma is a typical archaeon with a fairly large protein complement of bacterial origin. By conservative search methods they were able to match 620 domains of 537 ORF’s (35.6%) to proteins of known structure. They discovered that Thermoplasma had 1,478 protein genes and 45 RNA genes. These proteins they found included degradation pathway proteins, putative proteins, chaperones, respiratory chain proteins, extracellular proteins and more. (3)
• While doing my research there were some findings I came across that I thought were interesting and worth noting, and I will discuss 3 of them.
• Ruepp et al found their evidence to indicate that there has been much lateral gene transfer between Thermoplasma and Sulfolobus Solfactaricus (a distinct crenarchaeon inhabiting the same environment). At least 252 ORF’s (17%), including protein degradation pathways and various transport proteins resemble Sulfolobus proteins most closely. (3) This first piece of evidence is interesting because it leads to an idea that organisms who live together can swap genes at higher frequencies.
• Thermoplasma can respire anaerobically using sulfur, but no sulfur-respiratory genes similar to those of other archaeon were found. Instead bacteria-like sulfur reducing proteins were identified and appear to be responsible for sulfur metabolism (2). Not all of the species that were found to share similarities with Thermoplasma were completely annotated at the time this article was published so it would be interesting to see the similarities between this organism and others if those sequences were up to date now to give more insight into it’s genome.
• The third piece of evidence was that Thermoplasma inhibits a hot and highly acidic environment, sometimes as low as pH 0.5 in which few organisms are viable. It has adapted to scavenging nutrients from the decomposition of organisms killed by the extreme acidity and requires yeast, bacterial or meat extract when grown in culture. (3). This information is important and useful because it could give insight into how other organisms similar to Thermoplasma can live in such conditions while missing some of the cell structure that other thermophilics have. The key point is that the proteins in this organism could tell us a lot about how it functions in these environments.
• Thermoplasma Acidophilum is an organism that could give us insight into how organisms in the same environment can transfer DNA to each other and serve as a lab tool to study how different organisms similar to this can live in extreme habitats which makes it worth understanding. That’s all I have for today, thanks for listening!
References:
1. Darland et. al., 1970. American Association for the Advancement of Science 170: 1416-1418.
A Thermophilic, Acidophilic Mycoplasma Isolated from a Coal Refuse Pile.
2. DeLong, E. 2000. Genome Biology. Extreme genome.
3. Ruepp et. al., 2000. Nature Research 407: 508-513. The genome sequence of their
thermoacidophilic scavenger Thermoplasma acidophilum.
• This organism was first discovered when it was isolated from self-heated coal refuse piles. (1). It was first isolated by a man named Darland along with his colleagues in the late 1960’s at a Fair Tuck mine in southwestern Indiana in a pH environment of 1.96. They believed it represented a prokaryotic organism but noticed that unlike other bacterial cells it lacked a rigid cell wall and was only separated by a double membrane.
• The size of the genome was first discovered by Ruepp et. al. using a ‘shotgun primer walking’ method that used PCR amplifications and primer-walking strategies to fill in the missing gaps. Ruepp and his coworkers discovered that the genome of Thermoplasma was 1,564,905 base pairs (3).
• Thermoplasma is one of the smallest free-living organisms and Ruepp and his coworkers also found that the genome consisted of a single circular chromosome of the 1.56Mbp. There were no plasmids detected by biochemical or DNA sequencing methods (3). They also found that the Thermoplasma genome contained 1,509 ORF’s and 1/3 had homologs present in all 3 domains of life (3).
• The Thermoplasma is a typical archaeon with a fairly large protein complement of bacterial origin. By conservative search methods they were able to match 620 domains of 537 ORF’s (35.6%) to proteins of known structure. They discovered that Thermoplasma had 1,478 protein genes and 45 RNA genes. These proteins they found included degradation pathway proteins, putative proteins, chaperones, respiratory chain proteins, extracellular proteins and more. (3)
• While doing my research there were some findings I came across that I thought were interesting and worth noting, and I will discuss 3 of them.
• Ruepp et al found their evidence to indicate that there has been much lateral gene transfer between Thermoplasma and Sulfolobus Solfactaricus (a distinct crenarchaeon inhabiting the same environment). At least 252 ORF’s (17%), including protein degradation pathways and various transport proteins resemble Sulfolobus proteins most closely. (3) This first piece of evidence is interesting because it leads to an idea that organisms who live together can swap genes at higher frequencies.
• Thermoplasma can respire anaerobically using sulfur, but no sulfur-respiratory genes similar to those of other archaeon were found. Instead bacteria-like sulfur reducing proteins were identified and appear to be responsible for sulfur metabolism (2). Not all of the species that were found to share similarities with Thermoplasma were completely annotated at the time this article was published so it would be interesting to see the similarities between this organism and others if those sequences were up to date now to give more insight into it’s genome.
• The third piece of evidence was that Thermoplasma inhibits a hot and highly acidic environment, sometimes as low as pH 0.5 in which few organisms are viable. It has adapted to scavenging nutrients from the decomposition of organisms killed by the extreme acidity and requires yeast, bacterial or meat extract when grown in culture. (3). This information is important and useful because it could give insight into how other organisms similar to Thermoplasma can live in such conditions while missing some of the cell structure that other thermophilics have. The key point is that the proteins in this organism could tell us a lot about how it functions in these environments.
• Thermoplasma Acidophilum is an organism that could give us insight into how organisms in the same environment can transfer DNA to each other and serve as a lab tool to study how different organisms similar to this can live in extreme habitats which makes it worth understanding. That’s all I have for today, thanks for listening!
References:
1. Darland et. al., 1970. American Association for the Advancement of Science 170: 1416-1418.
A Thermophilic, Acidophilic Mycoplasma Isolated from a Coal Refuse Pile.
2. DeLong, E. 2000. Genome Biology. Extreme genome.
3. Ruepp et. al., 2000. Nature Research 407: 508-513. The genome sequence of their
thermoacidophilic scavenger Thermoplasma acidophilum.