Switching in bacterial gene expression networks

Koirala, Santosh

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https://hdl.handle.net/2142/89183 Copy

Description

Title

Switching in bacterial gene expression networks

Author(s)

Koirala, Santosh

Issue Date

2015-10-15

Director of Research (if dissertation) or Advisor (if thesis)

Rao, Christopher V.

Doctoral Committee Chair(s)

Rao, Christopher V.

Committee Member(s)

• Slauch, James M.
• Kraft, Mary L.
• Harley, Brendan A.

Department of Study

Chemical & Biomolecular Engineering

Discipline

Chemical Engineering

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

• Bistability
• Gene Expression

Abstract

An ability of a bacterium to appropriately respond to its environmental cues ultimately decides its fate. Bacteria deal with the fluctuating environment as a population instead of individual cells. By allowing individual cells to stochastically switch between multiple phenotypes, the cell population can make sure some cells are always fit for the environmental change. The underlying genetic circuitry plays a key role in eliciting multiple phenotypes by an isogenic population of bacteria. Understanding the underlying mechanism requires careful and systematic approach. In this study, we investigated two very well-known systems: the motility in Salmonella enterica serovar Typhimurium and the sugar utilization in Escherichia coli. Many bacteria are motile only when nutrients are scarce. By contrast, Salmonella enterica is motile only when nutrients are plentiful, suggesting this bacterium uses motility for purposes other than foraging, most likely host colonization. We investigated how nutrients affect motility in S. enterica and found that nutrients tune the fraction of motile cells. In particular, we observed co-existing populations of motile and non-motile cells, where the distribution was determined by the concentration of nutrients in the growth medium. Interestingly, S. enterica does not respond to a single nutrient but apparently a complex mixture of them. We investigated the mechanism governing this behavior and found that it results from two antagonizing regulatory proteins, FliZ and YdiV. We further demonstrated that the response is bistable: namely, that genetically identical cells can exhibit different phenotypes under identical growth conditions. We further characterized the differences within class 2 and class 3 gene expression and showed that a secretion-dependent feedback loop involving flagellar specific sigma factor, σ28, is responsible for partitioning cells into two fractions. Together, these results uncover a new facet to the regulation of the flagellar genes in S. enterica and further demonstrate how bacteria employ phenotypic diversity as general mechanism for adapting to change in their environment. We then investigated the sugar utilization system in E. coli. Glucose is known to inhibit the transport and metabolism of many sugars in Escherichia coli. This mechanism leads to its preferential consumption. Far less, however, is known about the preferential utilization of non-glucose sugars in E. coli. One notable exception is arabinose and xylose. Previous studies have shown that E. coli will consume arabinose ahead of xylose. Selective utilization results from arabinose-bound AraC binding to the promoter of the xylose metabolic genes and inhibiting their expression. This mechanisms, however, has not been explored in single cells. Both the arabinose and xylose utilization systems are known to exhibit a bimodal induction response to their cognate sugar, where mixed populations of cells either expressing the metabolic genes or not are observed at intermediate sugar concentrations. This suggests that arabinose can only inhibit xylose metabolism in arabinose-induced cells. To understand how crosstalk between these systems affects their response, we investigated E. coli during growth on mixtures of arabinose and xylose at single-cell resolution. Our results show that mixed, multimodal populations of arabinose and xylose-induced cells occur at some intermediate sugar concentrations. We also found that xylose can inhibit the expression of the arabinose metabolic genes and that this repression is due to XylR. We further found that xylose-bound XylR binds to the divergent promoter region of the regulator araC and the arabinose metabolic genes and inhibit expression. These results demonstrate that a strict hierarchy does not exist between arabinose and xylose as previously thought and this may aid in the design of E. coli strains capable of simultaneous sugar consumption.

Graduation Semester

2015-12

Type of Resource

text

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Copyright and License Information

Copyright 2015 Santosh Koirala

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