Survey of Genomes - Fusobacterium nucleatum ATCC 25586
Hunter Jenkins steps in to tell us about a microbial titan of human dental plaque - Fusobacterium nucleatum. It truly helps nucleate, or organize, the multi-microbial plaque biofilm.
Hey guys welcome to this guest podcast of Genomics Revolution hosted by yours truly Hunter Jenkins of the 2019 spring Genetics class of Hiram College. In this episode, we will be zeroing in on the specific strain Fusobacterium nucleatum ATCC 25586 which I will now refer to as F. Nucleatum. This strain is a subspecies of Fusobacterium nucleatum named nucleatum which can be found in the human oral cavity, (cough) your mouth. This organism is from a Genus of Fusobacterium, and family Fusobacteriaceae which I believe previously resided under the family of Bacteroidaceae. F. nucleatum is closely related to Fusobacterium necrophorum which is commonly found in the intestines of most animals especially mammals. This alone shows that Fusobacterium can range in many ways to survive and show wildly unique characteristics to those in its family.
F. nucleatum has been originally studied back in the early 1900’s however not our specific strain. With newer technology circa 2002, The F. nucleatum strain ATCC 25586 genome was assembled from shotgun sequences and analyzed using the ERGO bioinformatics pipeline. The genome is contained on a singular circular chromosome which holds 2.17 million base pairs encoding 2,046 proteins. On its own F. nucleatum is generally harmless to humans, however its ability to help form dental plaque and coaggregate with other bacteria can make it worrisome and lead to common disease such as gingivitis. F. nucleatum’s ability to coaggregate is due in large part to their outer membrane proteins. These outer membrane proteins were newly found as they previously would get stuck at the top of analytical gels. Due to this we previously only knew of one porin that could be created. However we now know that there are eleven ORFs encoding outer membrane proteins. We have also found several proteins that are closely related to the outer membrane protein family (omp)A-F. Given that the outer membrane proteins are typically correlated with pathogenesis we can hope to make vaccinations through closer evaluation and research of F. nucleatum (Kapatral et al). According to Rodrigues et al., F. nucleatum is proven to be more prevalent in the oral cavities of those whom have gingivitis and chronic periodontitis. However their study also shows that it is in high accordance with Aggregatibacter actinomycetemcomitans and that they work as a symbiotic relationship increasing their populations. In an experiment Bolstad et al attempted to create a model of the adherence created by F. nucleatum outer membrane proteins, specifically the 40kDa proteins. By ligating the ORF of each protein into vectors, they were capable of comparing it to the know structure of F. nucleatum strain Fev1 by looking at conserved sequences and variability of polypeptides. Their results show sixteen highly conserved polypeptide sequences which traverse the outer membrane and are highly variable amongst the strains ATCC 25586, Fev1, and ATCC 10953.
That’s all I have for you guys today I hope you enjoyed your time and make sure you have proper dental hygiene to prevent the build up of Fusobacterium nucleatum.
Erratum of podcast:
1) I said early 19th century instead of early 1900’s.
2) PCR does not tell about protein structure. My mistake.
3) If a mature protein sequence goes through a membrane one or more times, the correct term is that it traverses the membrane.
Works Cited:
Bolstad, Anne Isine, H. B. Jensen, and J. Tommassen. "Sequence variability of the 40-kDa outer membrane proteins of Fusobacterium nucleatum strains and a model for the topology of the proteins." Molecular and General Genetics MGG 244.1 (1994): 104-110.
Kapatral, Vinayak, et al. "Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586." Journal of bacteriology 184.7 (2002): 2005-2018.
Rodrigues, Viviane Aparecida Arenas, et al. "Qualitative, quantitative and genotypic evaluation of Aggregatibacter actinomycetemcomitans and Fusobacterium nucleatum isolated from individuals with different periodontal clinical conditions." Anaerobe 52 (2018): 50-58.
F. nucleatum has been originally studied back in the early 1900’s however not our specific strain. With newer technology circa 2002, The F. nucleatum strain ATCC 25586 genome was assembled from shotgun sequences and analyzed using the ERGO bioinformatics pipeline. The genome is contained on a singular circular chromosome which holds 2.17 million base pairs encoding 2,046 proteins. On its own F. nucleatum is generally harmless to humans, however its ability to help form dental plaque and coaggregate with other bacteria can make it worrisome and lead to common disease such as gingivitis. F. nucleatum’s ability to coaggregate is due in large part to their outer membrane proteins. These outer membrane proteins were newly found as they previously would get stuck at the top of analytical gels. Due to this we previously only knew of one porin that could be created. However we now know that there are eleven ORFs encoding outer membrane proteins. We have also found several proteins that are closely related to the outer membrane protein family (omp)A-F. Given that the outer membrane proteins are typically correlated with pathogenesis we can hope to make vaccinations through closer evaluation and research of F. nucleatum (Kapatral et al). According to Rodrigues et al., F. nucleatum is proven to be more prevalent in the oral cavities of those whom have gingivitis and chronic periodontitis. However their study also shows that it is in high accordance with Aggregatibacter actinomycetemcomitans and that they work as a symbiotic relationship increasing their populations. In an experiment Bolstad et al attempted to create a model of the adherence created by F. nucleatum outer membrane proteins, specifically the 40kDa proteins. By ligating the ORF of each protein into vectors, they were capable of comparing it to the know structure of F. nucleatum strain Fev1 by looking at conserved sequences and variability of polypeptides. Their results show sixteen highly conserved polypeptide sequences which traverse the outer membrane and are highly variable amongst the strains ATCC 25586, Fev1, and ATCC 10953.
That’s all I have for you guys today I hope you enjoyed your time and make sure you have proper dental hygiene to prevent the build up of Fusobacterium nucleatum.
Erratum of podcast:
1) I said early 19th century instead of early 1900’s.
2) PCR does not tell about protein structure. My mistake.
3) If a mature protein sequence goes through a membrane one or more times, the correct term is that it traverses the membrane.
Works Cited:
Bolstad, Anne Isine, H. B. Jensen, and J. Tommassen. "Sequence variability of the 40-kDa outer membrane proteins of Fusobacterium nucleatum strains and a model for the topology of the proteins." Molecular and General Genetics MGG 244.1 (1994): 104-110.
Kapatral, Vinayak, et al. "Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586." Journal of bacteriology 184.7 (2002): 2005-2018.
Rodrigues, Viviane Aparecida Arenas, et al. "Qualitative, quantitative and genotypic evaluation of Aggregatibacter actinomycetemcomitans and Fusobacterium nucleatum isolated from individuals with different periodontal clinical conditions." Anaerobe 52 (2018): 50-58.