Jclub 3 - Laura Daniels class PDF

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Oglethorpe University Biology Program

BIO 290L MICROBIOLOGY LAB

Spring 2021 Dr. Lea Alford

Paper: Fraser et al. 1998. Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science. 281:375-388. Additional reading: CDC website: US Public Health Service Syphilis Study at Tuskegee (https://www.cdc.gov/tuskegee/index.html) Terms:  Open reading frame  Catabolic  Virulence factor  Hemolysin  Latent asymptomatic infection  Penicillin  Genome  Obligate parasite

Discussion questions (Submit to Moodle by the start of lab; 20 pts. total): 1. (3 pts.) What is the significance of the authors mentioning that the T. pallidum “outer membrane is mostly lipid with a paucity of proteins?” (p. 375, middle column) This is significant because the lack of proteins limits the functionality of the membrane, meaning that materials are “hypothetically” transported in and out of the cell, or in this case scarcely. This makes it unclear what causes T. pallidum to be pathogenic, since there are no virulent factors moving it and out of the cell. 2. (6 pts.) How does the genome of T. pallidum compare to that of other prokaryotes with respect to size and number of protein-coding genes? Research, cite, and include the genome size of at least 2 additional prokaryotic organisms. T. pallidum has a genome that is made up of circular chromosomes that are composed of 1,138,006 base pairs and contains approximately is very small as a result. E. coli consists of about 4,600,000 base pairs and has 4,000 genes (NIH). This is more than four times larger than T. pallidum. On the other hand, Candidatus Carsonella ruddii has one of the smallest genomes, with a genome that is 173,904 base pairs long (NCBI). This is almost seven times smaller than the genome of T. pallidum.

3. (3 pts.) Genes for transcription, translation, and DNA replication were identified in the T. pallidum genome. Is the machinery (RNAs and proteins) for these three processes similar in T. pallidum to that in other bacteria? Briefly compare and contrast RNA polymerase, the ribosome, and DNA polymerase III from T. pallidum to those in other bacterial species.

Oglethorpe University Biology Program

BIO 290L MICROBIOLOGY LAB

Spring 2021 Dr. Lea Alford

The machinery is similar to those of other [minimal genomic] bacteria because most spirochete bacteria have the same processes. In terms of RNA polymerase, basic genes within the cell are similar to those of alpha, beta, and beta prime subunits of other bacteria. The only difference is that T. pallidum is missing important sigma factors that aid the stationary phase and the transcription of heat-shock proteins. The ribosome of this organism has rRNA operons that make up its genome that are also found in other bacteria. In terms of DNA polymerase III, the author states that the complement genes are alike in other minimal genomic organisms, such as B. burgdorferi and Mycoplasma genitalium. There are also orthologs of alpha, beta, gamma, epsilon, and tau subunits of E. coli present in DNA polymerase III. This is very significant because it indicates a shared common ancestor between the different bacterial species mentioned. 4. (2 pts.) Minimal genes that encode for proteins involved in biosynthetic pathways were identified in the T. pallidum genome. The authors mention this finding is consistent with the typical environment of T. pallidum. What is the typical environment of T. pallidum and from where does it acquire nutrients for survival and reproduction? T. pallidum is an obligate parasite that thrives in the human body. The typical environment of T. pallidum is a domain with small glucose concentrations with little oxygen being present. It acquires its nutrients from its host’s environment, specifically through a multiple sugar transport.

5. (1 pts.) How can the genome sequence of an organism such as T. pallidum inform us about its energy metabolism? The genome sequence informs us about its energy metabolism by confirming that these organisms depend on its host for almost all of its nutrients. The sequence identifies the genes that encode the important enzymes that aid glycolytic pathways. The genome sequence also confirms the similarity of metabolic pathways also observed in M. genitalium and B. burgdorferi.

6. (5 pts.) The Tuskegee Study was a 40+ year “experiment” to observe the pathology and progression of syphilis, which is caused by T. pallidum. In the 1930s, male persons of color were recruited as participants and were not informed—in fact they were deliberately misinformed—about the nature of the study in which they were participants. A basic guideline for human subject research, specified in both the Nuremberg Code and the Belmont Report is the requirement of informed consent. Based on your reading, what would have constituted informed consent in the case of the Tuskegee Study? Constituted informed consent would have consisted of information being told to them about the availability of treatments (that should have been offered), the nature of the tests being performed, and an option to withhold treatment or quit their involvement in the study. Overall, all of the important aspects and components of the study should have been mentioned to the participants to have obtained informed consent. How can one be informed if they are being lied to about the nature of the treatments?

Bonus question (+1 pt.) Why was the T. pallidum genome sequence published in such a high impact journal ( Science)? In other words, why is this research so important? The T. pallidum genome sequence research was so important because of its relevance to the syphilis study on black men conducted just a few years prior to its release. This research further informed the

Oglethorpe University Biology Program

BIO 290L MICROBIOLOGY LAB

Spring 2021 Dr. Lea Alford

public about the severity of the bacterium and the conditions in which it thrives. It also discussed the biological systems and compared it to similar bacteria, to further familiarize the nature of this pathogen that causes syphilis in the human body.

WORKS CITED FOR #2 Blattner, F.R., Plunkett, G. 3rd, Bloch, C.A., Perna, N.T., Burland, V., Riley, M., Collado-Vides, J., et al. The complete genome sequence of Escherichia coli K-12. Science, 277:1453-74. 1997. Katsir, L., Zhepu, R., Piasezky, A., Jiang, J., Sela, N., Freilich, S., & Bahar, O. (2018). Genome Sequence of "CandidatusCarsonella ruddii" Strain BT from the Psyllid Bactericera trigonica. Genome announcements, 6(4), e01466-17. https://doi.org/10.1128/genomeA.01466-17...