Download What do colony patterns mean? - James A. Shapiro

What do colony patterns mean?
- A biologist’s view
James A. Shapiro, University of
Chicago
1. The colony as an organized, differentiated structure with a
complex morphogenesis, even laboratory E. coli.
2. Patterns that reflect the formation of adaptive structures: genetic
analysis.
3. A pattern that reflects the operation of adaptive systems under
defined conditions: environmental analysis and modeling (Proteus
mirabilis).
4. The dense-branching morphology of B. subtilis colonies under
nutritional restriction: a problem for modeling.
Clonal and Non-clonal Patterns in E. coli Colonies
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Initiation of E. coli colony development
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Morphogenesis and cellular
differentiation in E. coli
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Colony differentiation into
organized regions: E. coli
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Patterns
that reflect
the
formation of
adaptive
structures:
E. coli
Budrene EO,
Berg HC.
Dynamics of
formation of
symmetrical
patterns by
chemotactic
bacteria.
Nature. 1995
376(6535):4953.
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Patterns that reflect the formation of
adaptive structures: B. subtilis
Fruiting Body Formation by Bacillus subtilis Steven
S. Branda1†, José Eduardo González-Pastor2†, Sigal
Ben-Yehuda2, Richard Losick2 and Roberto Kolter.
Proc. Nat. Acad. Sci. USA, 98: 11621-11626
Patterns that reflect the formation of
adaptive structures: genetic analysis
Esteban Lombardía, Adrián J. Rovetto, Ana L. Arabolaza, and Roberto R. Grau. A LuxS-Dependent Cell-toCell Language Regulates Social Behavior and Development in Bacillus subtilis. Journal of Bacteriology, June
2006, p. 4442-4452, Vol. 188
A pattern that reflects the operation of adaptive
systems under defined conditions: Proteus mirabilis.
Where modeling matters most.
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Synchronous inoculation
Asynchronous inoculation (1 hr)
Proteus Crew
L-R: Todd Dupont,
Mitsugu Matsushita,
Bruce Ayati, Oliver
Rauprich, JAS, Sergei
Esipov & Sune Danø
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Different cell
types in
Proteus
swarming
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Distinct roles of glucose and amino acids in
growth and swarming
Dependence of swarming velocity on
amino acid, not glucose concentration
(above a threshold)
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Sune Danø
Robust Periodicity in Proteus Swarming
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20
b
a
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Lag
1st swarm
1st consol. 2nd swarm 2nd consol.
Lag
1st swarm 1st consol.2nd swarm 2nd consol.
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Hours at 32 C
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Rauprich O, Matsushita M, Weijer K,
Siegert F, Esipov S, Shapiro JA. 1996.
Periodic phenomena in Proteus mirabilis
swarm colony development. J. Bacteriol.
178:6525-38
Independence of swarm period from
swarming velocity (amino acids)
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Sune Danø
Interlocking Cell Cycles
d



max

Esipov, S. and J.A.Shapiro. 1998. Kinetic model of Proteus mirabilis swarm colony development. J. Math. Biol. 36, 249-268.
Kinetic Equations
Swarmer cell density
Diffusivity
Spatially Resolved Kinetics
Esipov, S. and J.A.Shapiro. 1998. Kinetic model of Proteus mirabilis swarm colony
development. J. Math. Biol. 36, 249-268.
Robust
periodicity
requires agedependent
dedifferentiation
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Bruce P. Ayati.
Modeling the role of
the cell cycle in
regulating Proteus
mirabilis swarm-colony
development. Applied
Mathematics Letters 20
(2007) 913–918
Experimental examination of
Proteus dedifferentiation
A. Liew & JAS
The dense-branching morphology of B. subtilis colonies
under nutritional restriction: a problem ripe for modeling.
Fujikawa H, and Matsushita M. 1989. Fractal growth of Bacillus subtilis on agar plates. J.
Phys. Soc. Japan 58:3875-78
Amino acid-dependent branching at different temperatures
Julkowska D, Obuchowski M, Holland IB, Séror SJ. 2004. Branched swarming patterns on a synthetic
medium formed by wild-type Bacillus subtilis strain 3610: detection of different cellular morphologies and
constellations of cells as the complex architecture develops. Microbiology 150:1839-49.
Motility occurs in a small “fingernail”
region at the tip of each dendrite
M. Matsushita
Observations and hypotheses for
modeling B. subtilis DBM
Observations:
1. Amino acids necessary (I.B. Holland, personal communication)
2. DBM limited to a special region of the nutritional-mobility space
3. DBM characterized by branches that do not grow in width
4. Tip-splitting occurs when branches separated by a critical distance
5. Increased cell activity in a limited zone at the tip of each dendrite
Hypotheses:
1. Tip expansion requires active cell movement inside front
2. Cell movement occurs only above a threshold amino acid level
3. Cell movement is the major sink for amino acid consumption
4. Glucose-based growth is not nutritionally limited