Genome complexity: controlling rate of making RN A's (Introduction)

by David Turell , Monday, January 25, 2021, 23:51 (1179 days ago) @ David Turell

A special provision when food is scarce:

https://www.sciencedaily.com/releases/2021/01/210123091016.htm

"The enzyme that makes RNA from a DNA template is altered to slow the production of ribosomal RNA (rRNA), the most abundant type of RNA within cells, when resources are scarce and the bacteria Escherichia coli needs to slow its growth.

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"'RNA polymerase is an enzyme that produces a variety of RNAs using information encoded in DNA," said Katsuhiko Murakami, professor of biochemistry and molecular biology at Penn State and the leader of the research team. "This is one of the key steps in the central dogma of molecular biology: transferring genetic information from DNA to RNA, which in turn often codes for protein. It's required for life and the process is basically shared from bacteria to humans.

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"'When you talk about RNA, most people think about messenger RNA (mRNA), which is the template for making proteins," said Murakami. "But the most abundant type of RNA in cells doesn't actually code for protein. Ribosomal RNA is the major structural component of the ribosome, which is the cellular machinery that builds proteins using messenger RNAs as templates. Ribosomal RNA synthesis accounts for up to 70 percent of total RNA synthesis in E. coli cells."

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"'If you do some back-of-the-envelope calculations, an E. coli cell needs to make around 70,000 ribosomes every 20 minutes," said Murakami. "This means RNA polymerase starts ribosomal RNA synthesis every 1.7 seconds from each ribosomal RNA promoter. So, the polymerase has to bind the ribosomal RNA promoter transiently in order to quickly move onto the ribosomal RNA synthesis step. (my bold)

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"When E. coli needs to slow its growth due to limited resources, two molecules -- a global transcription regulator called DksA and a bacterial signaling molecule called ppGpp, bind directly with the polymerase to reduce production of ribosomal RNA. The research team investigated how the binding of these two factors alters the conformation of the polymerase and affects its activity in a promoter-specific manner.

"'DksA and ppGpp binding to the polymerase alters its conformation, which prevents the opening of a gate and therefor the polymerase has to follow an alternative pathway to form the open complex," said Murakami. "This is not an ideal pathway for the ribosomal RNA promoter and thus slow its activity. It's exciting to see these conformational changes to the polymerase that have direct functional consequences."

Comment: processes need speed controls and this is one of them. It reeks of design. Note my bold. The high speed of these processes is illustrated, from our knowledge that the bacteria replicating every 20 minutes. Occasional molecular mistakes must be expected.