Bacterial Intelligence? system analysis of bacteria (General)

by David Turell , Monday, August 13, 2018, 18:13 (2292 days ago) @ David Turell

Introducing Lucy Shapiro's studies:

https://www.the-scientist.com/profile/the-cells-integrated-circuit--a-profile-of-lucy-s...

"She saw the cell as a dynamic, three-dimensional entity with spatial features that were as important as its genetics and biochemistry. So she formulated two questions that continue to drive her research: How is information on the spatial positioning of the cell’s molecules encoded, and how are the events inside a cell coordinated to yield an integrated system?

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"Two postdocs in her lab, Janine Maddock and Dickon Alley, demonstrated that bacterial cells are highly organized. They showed that both in Caulobacter and in E. coli, the chemoreceptor proteins involved in chemotaxis—the movement of the bacterium in response to particular substances in its environment—are localized to one pole of the cell. The dogma in the field had been that bacterial cells were swimming pools of free-floating proteins with DNA, like an unorganized “ball of spaghetti,” Shapiro says. “It took the community five years to really believe our work that the cell’s proteins and other molecules are dynamically and highly regulated into subcellular domains.” Later, Shapiro and colleagues showed that a similar localization occurs with chromosomal loci on the single circular chromosome.

"In 1996, Shapiro’s graduate student, Kim Quon, was looking for mutations that prevented flagellum formation and discovered a master transcription factor, called CtrA, that controls an array of Caulobacter genes necessary to coordinate the cell cycle. “We knew this was big when we all swapped notes in the lab and realized that those working on chemoreceptor genes, flagella genes, DNA replication initiation, and other gene functions all had the same promoter sequence to which this transcription factor, CtrA, bound,” Shapiro explains. The discovery of a master gene regulator was among the first pieces of evidence showing that cells possess integrated genetic circuits, which orchestrate the complex set of cascading events that drive the cell cycle. The lab’s later work uncovered a hierarchical circuit in which one regulatory gene would turn on another set of genes, complete with feedback loops, and so on.

"Listening to Shapiro discuss the bacterial cell as a controlled circuit swayed her physicist husband, Harley McAdams, to join her in her research. Shapiro and McAdams opened a joint multidisciplinary lab in which biology students worked alongside engineering and physics students to address how the bacterial cell works as a complete system of genetic and spatial controls.

"Their collaborative efforts helped to launch the field of systems biology. In 1995, the pair proposed a model in which the genetic circuitry of the bacterial virus phage lambda parallels an electrical circuit. Five years later, Shapiro’s graduate student Mike Laub completed the first microarray experiment on the bacterial cell cycle, providing a comprehensive view of how all Caulobacter genes are transcriptionally controlled throughout the cycle. “That work told us that the bacterial cell doesn’t just turn genes on or off in response to its environment, but rather that there are hard-wired gene sets that are turned on in a temporal order as the bacterium progresses through the cell cycle,” Shapiro says.

"Her lab may be on the verge of yet another breakthrough. She and her students, along with collaborators, are among the first to study cytoplasm phase separations—non-membrane-bound cytoplasm regions that provide functional organization within the cell—in bacteria. “We’ve all missed this for years, thinking that membranous organelles provide the only structure within the cell,” Shapiro says. Instead, it appears that there are distinct and dynamic membraneless sections that carry out specific biochemical functions."

Comment: This is an editorial description of her work, and describes how highly organized and controlled are the systems in any bacteria. It reeks of intelligent design. No relation to James Shapiro.