66,120 research outputs found
Fundamental Limits to Position Determination by Concentration Gradients
Position determination in biological systems is often achieved through
protein concentration gradients. Measuring the local concentration of such a
protein with a spatially-varying distribution allows the measurement of
position within the system. In order for these systems to work effectively,
position determination must be robust to noise. Here, we calculate fundamental
limits to the precision of position determination by concentration gradients
due to unavoidable biochemical noise perturbing the gradients. We focus on
gradient proteins with first order reaction kinetics. Systems of this type have
been experimentally characterised in both developmental and cell biology
settings. For a single gradient we show that, through time-averaging, great
precision can potentially be achieved even with very low protein copy numbers.
As a second example, we investigate the ability of a system with oppositely
directed gradients to find its centre. With this mechanism, positional
precision close to the centre improves more slowly with increasing averaging
time, and so longer averaging times or higher copy numbers are required for
high precision. For both single and double gradients, we demonstrate the
existence of optimal length scales for the gradients, where precision is
maximized, as well as analyzing how precision depends on the size of the
concentration measuring apparatus. Our results provide fundamental constraints
on the positional precision supplied by concentration gradients in various
contexts, including both in developmental biology and also within a single
cell.Comment: 24 pages, 2 figure
Optimal signal processing in small stochastic biochemical networks
We quantify the influence of the topology of a transcriptional regulatory
network on its ability to process environmental signals. By posing the problem
in terms of information theory, we may do this without specifying the function
performed by the network. Specifically, we study the maximum mutual information
between the input (chemical) signal and the output (genetic) response
attainable by the network in the context of an analytic model of particle
number fluctuations. We perform this analysis for all biochemical circuits,
including various feedback loops, that can be built out of 3 chemical species,
each under the control of one regulator. We find that a generic network,
constrained to low molecule numbers and reasonable response times, can
transduce more information than a simple binary switch and, in fact, manages to
achieve close to the optimal information transmission fidelity. These
high-information solutions are robust to tenfold changes in most of the
networks' biochemical parameters; moreover they are easier to achieve in
networks containing cycles with an odd number of negative regulators (overall
negative feedback) due to their decreased molecular noise (a result which we
derive analytically). Finally, we demonstrate that a single circuit can support
multiple high-information solutions. These findings suggest a potential
resolution of the "cross-talk" dilemma as well as the previously unexplained
observation that transcription factors which undergo proteolysis are more
likely to be auto-repressive.Comment: 41 pages 7 figures, 5 table
Environmental statistics and optimal regulation
Any organism is embedded in an environment that changes over time. The
timescale for and statistics of environmental change, the precision with which
the organism can detect its environment, and the costs and benefits of
particular protein expression levels all will affect the suitability of
different strategies-such as constitutive expression or graded response-for
regulating protein levels in response to environmental inputs. We propose a
general framework-here specifically applied to the enzymatic regulation of
metabolism in response to changing concentrations of a basic nutrient-to
predict the optimal regulatory strategy given the statistics of fluctuations in
the environment and measurement apparatus, respectively, and the costs
associated with enzyme production. We use this framework to address three
fundamental questions: (i) when a cell should prefer thresholding to a graded
response; (ii) when there is a fitness advantage to implementing a Bayesian
decision rule; and (iii) when retaining memory of the past provides a selective
advantage. We specifically find that: (i) relative convexity of enzyme
expression cost and benefit influences the fitness of thresholding or graded
responses; (ii) intermediate levels of measurement uncertainty call for a
sophisticated Bayesian decision rule; and (iii) in dynamic contexts,
intermediate levels of uncertainty call for retaining memory of the past.
Statistical properties of the environment, such as variability and correlation
times, set optimal biochemical parameters, such as thresholds and decay rates
in signaling pathways. Our framework provides a theoretical basis for
interpreting molecular signal processing algorithms and a classification scheme
that organizes known regulatory strategies and may help conceptualize
heretofore unknown ones.Comment: 21 pages, 7 figure
Regulatory control and the costs and benefits of biochemical noise
Experiments in recent years have vividly demonstrated that gene expression
can be highly stochastic. How protein concentration fluctuations affect the
growth rate of a population of cells, is, however, a wide open question. We
present a mathematical model that makes it possible to quantify the effect of
protein concentration fluctuations on the growth rate of a population of
genetically identical cells. The model predicts that the population's growth
rate depends on how the growth rate of a single cell varies with protein
concentration, the variance of the protein concentration fluctuations, and the
correlation time of these fluctuations. The model also predicts that when the
average concentration of a protein is close to the value that maximizes the
growth rate, fluctuations in its concentration always reduce the growth rate.
However, when the average protein concentration deviates sufficiently from the
optimal level, fluctuations can enhance the growth rate of the population, even
when the growth rate of a cell depends linearly on the protein concentration.
The model also shows that the ensemble or population average of a quantity,
such as the average protein expression level or its variance, is in general not
equal to its time average as obtained from tracing a single cell and its
descendants. We apply our model to perform a cost-benefit analysis of gene
regulatory control. Our analysis predicts that the optimal expression level of
a gene regulatory protein is determined by the trade-off between the cost of
synthesizing the regulatory protein and the benefit of minimizing the
fluctuations in the expression of its target gene. We discuss possible
experiments that could test our predictions.Comment: Revised manuscript;35 pages, 4 figures, REVTeX4; to appear in PLoS
Computational Biolog
Molecular Basis for poly(A) RNP Architecture and Recognition by the Pan2-Pan3 Deadenylase
The stability of eukaryotic mRNAs is dependent on a ribonucleoprotein (RNP) complex of poly(A)-binding proteins (PABPC1/Pab1) organized on the poly(A) tail. This poly(A) RNP not only protects mRNAs from premature degradation but also stimulates the Pan2-Pan3 deadenylase complex to catalyze the first step of poly(A) tail shortening. We reconstituted this process in vitro using recombinant proteins and show that Pan2-Pan3 associates with and degrades poly(A) RNPs containing two or more Pab1 molecules. The cryo-EM structure of Pan2-Pan3 in complex with a poly(A) RNP composed of 90 adenosines and three Pab1 protomers shows how the oligomerization interfaces of Pab1 are recognized by conserved features of the deadenylase and thread the poly(A) RNA substrate into the nuclease active site. The structure reveals the basis for the periodic repeating architecture at the 3' end of cytoplasmic mRNAs. This illustrates mechanistically how RNA-bound Pab1 oligomers act as rulers for poly(A) tail length over the mRNAs' lifetime.We would like to thank ... the MPIB cryo-EM, and core facilities ..
Localisation of the human hSuv3p helicase in the mitochondrial matrix and its preferential unwinding of dsDNA
We characterised the human hSuv3p protein belonging to the family of NTPases/helicases. In yeast mitochondria the hSUV3 orthologue is a component of the degradosome complex and participates in mtRNA turnover and processing, while in Caenorhabditis elegans the hSUV3 orthologue is necessary for viability of early embryos. Using immunofluorescence analysis, an in vitro mitochondrial uptake assay and sub‐fractionation of human mitochondria we show hSuv3p to be a soluble protein localised in the mitochondrial matrix. We expressed and purified recombinant hSuv3p protein from a bacterial expression system. The purified enzyme was capable of hydrolysing ATP with a Km of 41.9 µM and the activity was only modestly stimulated by polynucleotides. hSuv3p unwound partly hybridised dsRNA and dsDNA structures with a very strong preference for the latter. The presented analysis of the hSuv3p NTPase/helicase suggests that new functions of the protein have been acquired in the course of evolution
The Proteomics of N-terminal Methionine Cleavage
Methionine aminopeptidase (MAP) is a ubiquitous, essential enzyme involved in protein N-terminal methionine excision. According to the generally accepted cleavage rules for MAP, this enzyme cleaves all proteins with small side chains on the residue in the second position (P1′), but many exceptions are known. The substrate specificity of Escherichia coli MAP1 was studied in vitro with a large (\u3e120) coherent array of peptides mimicking the natural substrates and kinetically analyzed in detail. Peptides with Val or Thr at P1′ were much less efficiently cleaved than those with Ala, Cys, Gly, Pro, or Ser in this position. Certain residues at P2′, P3′, and P4′ strongly slowed the reaction, and some proteins with Val and Thr at P1′ could not undergo Met cleavage. These in vitro data were fully consistent with data for 862 E. coli proteins with known N-terminal sequences in vivo. The specificity sites were found to be identical to those for the other type of MAPs, MAP2s, and a dedicated prediction tool for Met cleavage is now available. Taking into account the rules of MAP cleavage and leader peptide removal, the N termini of all proteins were predicted from the annotated genome and compared with data obtained in vivo. This analysis showed that proteins displaying N-Met cleavage are overrepresented in vivo. We conclude that protein secretion involving leader peptide cleavage is more frequent than generally thought
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Genomics analysis on the responses of E. coli cells to varying environmental conditions
The natural living environments of E. coli cells are diverse, varying from
mammalian gastrointestinal tracts and soil. Each environment might require
distinct metabolic pathways and transporter systems, and long-term evolution
has established elaborate regulatory system for E. coli cells to quickly adapt to
the changing conditions. Sensing outside stresses and then adopting a different
phenotype enable them to take advantage of any possible nutrients and defend
against hostile environment. A lot of regulatory mechanisms have been identified
by genetic, biochemical and molecular biology methods, and our study aim to
build a systematic view on the response of the whole genome to four different
environmental conditions. We used statistical tests including Pearson’s tests and
Spearman’s tests and multiple testing adjustments to identify feature genes that
are induced or repressed significantly across treatment levels. The feature genes
identified were partially supported by previous literatures, and some of the novel
genes not found in any previous studies may infer a potential research blind spot.
Additionally, we compared the correlation tests to the implementation of machine
learning algorithms, and discussed the advantage and drawbacks of each
method.Statistic
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