Gene Control

Third Edition

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Chapter 2: Transcription in Bacteria

As discussed in Chapter 1, transcription and translation are integral components of genetic information flow in living organisms. Both prokaryotes and eukaryotes employ many similar components and mechanisms to carry out these processes. For example, both pro- and eukaryotes synthesize and use messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA) as key components of the processes that convert the information encoded in DNA into proteins (see Chapter 1, Figure 1.1). The mRNA carries the information encoded in DNA to ribosomes, the machinery that synthesizes the proteins.

Multiple-choice questions

Questions for Discussion

  1. A unique feature of all living organisms is that they use DNA as their genetic material. However, the discovery of ribozymes (RNA with enzymatic activity) led to the RNA world hypothesis which suggests that self-replicating RNA molecules proliferated before the evolution of DNA and proteins. If RNA is capable of self-replicating and encoding enzymatic activity, why has RNA been replaced with DNA as genetic material of organisms.
  2. The monomer units of both RNA and DNA are nucleotides. Then why/how has RNA been used as an intermediate in protein biosynthesis rather than direct synthesis from the DNA?
  3. The discovery of introns in eukaryotic viruses contradicts the idea of the evolution of complex systems from simple ones because introns are absent in almost all of the bacterial genes. Based on this observation, discuss and formulate a model for the origin of intron-containing eukaryotic viruses.
  4. Coordinating gene expression with the rest of the cellular processes is critical for the survival of a living cell. How does bacterial RNA polymerase coordinate with other cellular processes during transcription? Discuss in detail.
  5. How does a basic understanding of bacterial transcription mechanism be useful in overcoming multidrug resistance, a leading public health problem.

Further Reading

Crick, F. H. C. The genetic code. Sci. Amer. 207 (October 1962): 66.

Holmes, S.F., T.J. Santangelo, C.K. Cunningham, J.W. Roberts, and D.A. Erie. 2006. Kinetic investigation of Escherichia coli RNA polymerase mutants that influence nucleotide discrimination and transcription fidelity. J. Biol. Chem. 281:18,677–18,683.

Landick, R. Shifting RNA polymerase into overdrive. Science 284 (1999): 598.

Mandell, Z. F., Zemba, D., & Babitzke, P. (2022). Factor-stimulated intrinsic termination: Getting by with a little help from some friends. Transcription, 13(4–5), 96–108. https://doi.org/10.1080/21541264.2022.2127602

Mohamed, A. A., Nunez, R. V., & Vos, S. M. (2022). Structural Advances in Transcription Elongation. Current Opinion in Structural Biology, 75, 102422. https://doi.org/10.1016/j.sbi.2022.102422

Mooney, R. A., S. A. Darst, and R. Landick. Sigma and RNA polymerase: An on-again, off-again relationship? Mol. Cell 20 (2005): 335.

Sarkar, S. Forty years under the central dogma. Trends Biochem. Sci. 23 (1998): 312.

Shapiro, L. (2022). A Half Century Defining the Logic of Cellular Life. Annual Review of Genetics, 56, 1–15. https://doi.org/10.1146/annurev-genet-071719-021436

Roberts, J. W., S. Shankar, and J. J. Filter. RNA polymerase elongation factors. Annu. Rev. Microbiol. 62 (2008): 211.

Young, B. A., T. M. Gruber, and C. A. Gross. Views of transcription initiation. Cell 109 (2002): 417. Young, B.A., T.M. Gruber, and C.A. Gross. 2004. Minimal machinery of RNA polymerase holoenzyme sufficient for promoter melting. Science 303:1382–1384.

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