Real-Time Gene Expression Profiling of Live Shewanella Oneidensis Cells

Technical Report · Mon Mar 30 00:00:00 EDT 2009

DOI:https://doi.org/10.2172/950422· OSTI ID:950422

Xie, Xiaoliang Sunney

The overall objective of this proposal is to make real-time observations of gene expression in live Shewanella oneidensis cells with high sensitivity and high throughput. Gene expression, a central process to all life, is stochastic because most genes often exist in one or two copies per cell. Although the central dogma of molecular biology has been proven beyond doubt, due to insufficient sensitivity, stochastic protein production has not been visualized in real time in an individual cell at the single-molecule level. We report the first direct observation of single protein molecules as they are generated, one at a time in a single live E. coli cell, yielding quantitative information about gene expression [Science 2006; 311: 1600-1603]. We demonstrated a general strategy for live-cell single-molecule measurements: detection by localization. It is difficult to detect single fluorescence protein molecules inside cytoplasm - their fluorescence is spread by fast diffusion to the entire cell and overwhelmed by the strong autofluorescence. We achieved single-molecule sensitivity by immobilizing the fluorescence protein on the cell membrane, where the diffusion is much slowed. We learned that under the repressed condition protein molecules are produced in bursts, with each burst originating from a stochastically-transcribed single messenger RNA molecule, and that protein copy numbers in the bursts follow a geometric distribution. We also simultaneously published a paper reporting a different method using β-glactosidase as a reporter [Nature 440, 358 (2006)]. Many important proteins are expressed at low levels, inaccessible by previous proteomic techniques. Both papers allowed quantification of protein expression with unprecedented sensitivity and received overwhelming acclaim from the scientific community. The Nature paper has been identified as one of the most-cited papers in the past year [http://esi-topics.com/]. We have also an analytical framework describing the steady-state distribution of protein concentration in live cells, considering that protein production occurs in random bursts with an exponentially distributed number of molecules. This model allows for the extraction of kinetic parameters of gene expression from steady-state distributions of protein concentration in a cell population, which are available from single cell data obtained by fluorescence microscopy. [Phys. Rev. Lett. 97, 168302 (2006)]. A major objective in the Genome to Life (GtL) program is to monitor and understand the gene expression profile of a complete bacterial genome. We developed genetic and imaging methods for sensitive protein expression profiling in individual S. oneidensis cell. We have made good progress in constructing YFP-library with several hundred chromosomal fusion proteins and studied protein expression profiling in living Shewanella oneidensis cells. Fluorescence microscopy revealed the average abundance of specific proteins, as well as their noise in gene expression level across a population. We also explored ways to adapt our fluorescence measurement for other growth conditions, such as anaerobic growth.

• Research Organization: Harvard Univ., Cambridge, MA (United States)
• Sponsoring Organization: USDOE Office of Science (SC)
• DOE Contract Number: FG02-04ER63784
• OSTI ID: 950422
• Report Number(s): DOE/ER/63784-F; TRN: US201006%%841
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
ABUNDANCE
CELL MEMBRANES
CYTOPLASM
DETECTION
DIFFUSION
DISTRIBUTION
FLUORESCENCE
GENES
GENETICS
KINETICS
MESSENGER-RNA
MICROSCOPY
MOLECULAR BIOLOGY
MONITORS
PRODUCTION
PROTEINS
SENSITIVITY
live-cell single-molecule imaging
stochastic gene expression
fluorescence reporter library