2,690 research outputs found
Phase resetting reveals network dynamics underlying a bacterial cell cycle
Genomic and proteomic methods yield networks of biological regulatory
interactions but do not provide direct insight into how those interactions are
organized into functional modules, or how information flows from one module to
another. In this work we introduce an approach that provides this complementary
information and apply it to the bacterium Caulobacter crescentus, a paradigm
for cell-cycle control. Operationally, we use an inducible promoter to express
the essential transcriptional regulatory gene ctrA in a periodic, pulsed
fashion. This chemical perturbation causes the population of cells to divide
synchronously, and we use the resulting advance or delay of the division times
of single cells to construct a phase resetting curve. We find that delay is
strongly favored over advance. This finding is surprising since it does not
follow from the temporal expression profile of CtrA and, in turn, simulations
of existing network models. We propose a phenomenological model that suggests
that the cell-cycle network comprises two distinct functional modules that
oscillate autonomously and couple in a highly asymmetric fashion. These
features collectively provide a new mechanism for tight temporal control of the
cell cycle in C. crescentus. We discuss how the procedure can serve as the
basis for a general approach for probing network dynamics, which we term
chemical perturbation spectroscopy (CPS)
Complex and unexpected dynamics in simple genetic regulatory networks
Peer reviewedPublisher PD
Periodic Cyclin-Cdk Activity Entrains an Autonomous Cdc14 Release Oscillator
SummaryOne oscillation of Cyclin-dependent kinase (Cdk) activity, largely driven by periodic synthesis and destruction of cyclins, is tightly coupled to a single complete eukaryotic cell division cycle. Tight linkage of different steps in diverse cell-cycle processes to Cdk activity has been proposed to explain this coupling. Here, we demonstrate an intrinsically oscillatory module controlling nucleolar release and resequestration of the Cdc14 phosphatase, which is essential for mitotic exit in budding yeast. We find that this Cdc14 release oscillator functions at constant and physiological cyclin-Cdk levels, and is therefore independent of the Cdk oscillator. However, the frequency of the release oscillator is regulated by cyclin-Cdk activity. This observation together with its mechanism suggests that the intrinsically autonomous Cdc14 release cycles are locked at once-per-cell-cycle through entrainment by the Cdk oscillator in wild-type cells. This concept may have broad implications for the structure and evolution of eukaryotic cell-cycle control
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Phase Resetting Reveals Network Dynamics Underlying a Bacterial Cell Cycle
Genomic and proteomic methods yield networks of biological regulatory interactions but do not provide direct insight into how those interactions are organized into functional modules, or how information flows from one module to another. In this work we introduce an approach that provides this complementary information and apply it to the bacterium Caulobacter crescentus, a paradigm for cell-cycle control. Operationally, we use an inducible promoter to express the essential transcriptional regulatory gene ctrA in a periodic, pulsed fashion. This chemical perturbation causes the population of cells to divide synchronously, and we use the resulting advance or delay of the division times of single cells to construct a phase resetting curve. We find that delay is strongly favored over advance. This finding is surprising since it does not follow from the temporal expression profile of CtrA and, in turn, simulations of existing network models. We propose a phenomenological model that suggests that the cell-cycle network comprises two distinct functional modules that oscillate autonomously and couple in a highly asymmetric fashion. These features collectively provide a new mechanism for tight temporal control of the cell cycle in C. crescentus. We discuss how the procedure can serve as the basis for a general approach for probing network dynamics, which we term chemical perturbation spectroscopy (CPS).</p
Omnipresent Maxwell’s demons orchestrate information management in living cells
The development of synthetic biology calls for accurate
understanding of the critical functions that allow
construction and operation of a living cell. Besides
coding for ubiquitous structures, minimal genomes
encode a wealth of functions that dissipate energy in
an unanticipated way. Analysis of these functions
shows that they are meant to manage information
under conditions when discrimination of substrates
in a noisy background is preferred over a simple
recognition process. We show here that many of
these functions, including transporters and the ribosome
construction machinery, behave as would
behave a material implementation of the informationmanaging
agent theorized by Maxwell almost
150 years ago and commonly known as Maxwell’s
demon (MxD). A core gene set encoding these functions belongs to the minimal genome required
to allow the construction of an autonomous cell.
These MxDs allow the cell to perform computations
in an energy-efficient way that is vastly better than
our contemporary computers
The compositional and evolutionary logic of metabolism
Metabolism displays striking and robust regularities in the forms of
modularity and hierarchy, whose composition may be compactly described. This
renders metabolic architecture comprehensible as a system, and suggests the
order in which layers of that system emerged. Metabolism also serves as the
foundation in other hierarchies, at least up to cellular integration including
bioenergetics and molecular replication, and trophic ecology. The
recapitulation of patterns first seen in metabolism, in these higher levels,
suggests metabolism as a source of causation or constraint on many forms of
organization in the biosphere.
We identify as modules widely reused subsets of chemicals, reactions, or
functions, each with a conserved internal structure. At the small molecule
substrate level, module boundaries are generally associated with the most
complex reaction mechanisms and the most conserved enzymes. Cofactors form a
structurally and functionally distinctive control layer over the small-molecule
substrate. Complex cofactors are often used at module boundaries of the
substrate level, while simpler ones participate in widely used reactions.
Cofactor functions thus act as "keys" that incorporate classes of organic
reactions within biochemistry.
The same modules that organize the compositional diversity of metabolism are
argued to have governed long-term evolution. Early evolution of core
metabolism, especially carbon-fixation, appears to have required few
innovations among a small number of conserved modules, to produce adaptations
to simple biogeochemical changes of environment. We demonstrate these features
of metabolism at several levels of hierarchy, beginning with the small-molecule
substrate and network architecture, continuing with cofactors and key conserved
reactions, and culminating in the aggregation of multiple diverse physical and
biochemical processes in cells.Comment: 56 pages, 28 figure
Molecular modeling of an antigenic complex between a viral peptide and a class I major histocompatibility glycoprotein
Computer simulation of the
conformations of short antigenic peptides (&lo
residues) either free or bound to their receptor,
the major histocompatibility complex (MHC)-
encoded glycoprotein H-2 Ld, was employed to
explain experimentally determined differences
in the antigenic activities within a set of related
peptides. Starting for each sequence from the
most probable conformations disclosed by a
pattern-recognition technique, several energyminimized
structures were subjected to molecular
dynamics simulations (MD) either in vacuo
or solvated by water molecules. Notably, antigenic
potencies were found to correlate to the
peptides propensity to form and maintain an
overall a-helical conformation through regular
i,i + 4 hydrogen bonds. Accordingly, less active
or inactive peptides showed a strong tendency
to form i,i+3 hydrogen bonds at their Nterminal
end. Experimental data documented
that the C-terminal residue is critical for interaction
of the peptide with H-2 Ld. This finding
could be satisfactorily explained by a 3-D
Q.S.A.R. analysis postulating interactions between
ligand and receptor by hydrophobic
forces. A 3-D model is proposed for the complex
between a high-affinity nonapeptide and the H-
2 Ld receptor. First, the H-2 Ld molecule was
built from X-ray coordinates of two homologous
proteins: HLA-A2 and HLA-Aw68, energyminimized
and studied by MD simulations. With
HLA-A2 as template, the only realistic simulation
was achieved for a solvated model with minor
deviations of the MD mean structure from
the X-ray conformation. Water simulation of the
H-2 Ld protein in complex with the antigenic
nonapeptide was then achieved with the template-
derived optimal parameters. The bound
peptide retains mainly its a-helical conformation
and binds to hydrophobic residues of H-2
Ld that correspond to highly polymorphic positions
of MHC proteins. The orientation of the
nonapeptide in the binding cleft is in accordance
with the experimentally determined distribution
of its MHC receptor-binding residues
(agretope residues). Thus, computer simulation was successfully employed to explain functional
data and predicts a-helical conformation
for the bound peptid
Bone Remodeling Monitor
The impact of bone loss due to different mechanical loadings in microgravity is a major concern for astronauts upon reintroduction to gravitational forces in exploration missions to the Moon and Mars. it has been shown that astronauts not only lose bone at differing rates, with levels up to 2% per month, but each astronaut will respond to bone loss treatments differently. Pre- and post-flight imaging techniques and frozen urine samples for post-flight laboratory immunoassays To develop a novel, non-invasive, highly . sensitive, portable, intuitive, and low-powered device to measure bone resorption levels in 'real time' to provide rapid and Individualized feedback to maximize the efficacy of bone loss countermeasures 1. Collect urine specimen and analyze the level of bone resorption marker, DPD (deoxypridinoline) excreted. 2. Antibodies specific to DPD conjugated with nanoshells and mixed with specimen, the change in absorbance from agglutination is measured by an optical device. 3. The concentration of DPD is displayed and recorded on a PD
Studies of the Kinetics of Cell Cycle Processes in S. Cerevisiae: The Molecular Basis of Start Irreversibility and Cyclin-Cdk Ordering of Mitotic Events
The cell cycle machinery of Saccharomyces cerevisiae consists of a central negative feedback oscillator comprising cyclin-CDK and its antagonist, APCCdc20. This oscillator is stabilized and tuned by positive feedback loops, and its frequency is modulated by checkpoint controls. Either by directly triggering events, or by entraining independent oscillators controlling events, the cyclin-CDK oscillator regulates the key events of the cell cycle. These events have an established order and timing within the overall cycle. The work I describe in this thesis concerns two fundamental questions: how is the order and timing of cell cycle events controlled, and what sets the intrinsic frequency of the cell cycle oscillator? I describe work on two major processes in the cell division cycle that reveals two very different modes of regulation. The first of these processes – Start – represents a pivotal commitment to divide. In collaboration with Gilles Charvin, I demonstrate that positive feedback in the molecular machinery underlying Start acts as a bistable switch that renders this regulatory transition irreversible. The second major process is Mitosis, a set of events all triggered by the same class of cyclin-CDKs and yet occurring in a set and reproducible order. I describe an ordering mechanism underlying this choreography that relies on the natural ramping-up of cyclin-CDK activity level. The observation that different events require different levels of cyclin-CDK activity leads to the question of how these thresholds are set. To begin to answer this, I discuss how mitotic cyclin-CDK triggers two different events – depolarization of growth and formation of the mitotic spindle – in two very different ways. The first relies on entrainment of an independent oscillator controlling growth polarization; the other may involve the simultaneous regulation of multiple targets. The observation that cyclin-CDK is rate-limiting for mitotic events suggests that increasing the level of this key cell cycle regulator above its endogenous range should accelerate Mitosis, and I show evidence that this is the case. Quite surprisingly, this increase in cyclin-CDK abundance also accelerates the frequency of the cell cycle oscillator as a whole through its effect on growth. This provides an intriguing new answer to the question of what sets the intrinsic frequency of the cell cycle oscillator. Together, this work underscores the central role of the mitotic cyclin-CDK regulator, which controls not only the relative timing of individual cell cycle events, but also the growth rate of the cell, and the overall frequency of the cell cycle oscillator
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