Robert Karl Stonjek
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 Posted: Sat Nov 15, 2003 12:02 am Post subject: Research Updates] Towards an understanding of essential gene |
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Experimental Determination and System Level Analysis of Essential Genes in
Escherichia coli MG1655
Gerdes, S.Y. et al.
Journal of Bacteriology 2003 185(19):5673-5684
Commentary by Michael R Seringhaus
13 November 2003
Essentially conserved: towards an understanding of essential genes
Conceptually, essential genes are at once elusive and enticing. A gene
product cannot be deemed essential for life without some reference to
environment - typically, it>s that required for laboratory growth on rich
media - but the promise of killing an organism by disabling a single gene
product is an attractive one for drug discovery researchers.
In the October issue of the Journal of Bacteriology, Gerdes and coworkers
published the results of an extensive essentiality screen in Escherichia
coli MG1655. Although essentiality work has been underway in E. coli for
some time, most notably at the University of Wisconsin genome centre and the
Japanese Profiling of E. coli Chromosome site, this work represents an
interesting and informative step forward.
Gerdes et al. performed large-scale transposon mutagenesis, generating
insertions at 18 000 distinct locations. Mutants grew in rich media for 23
doublings before genomic DNA was harvested, and points of insertion were
identified with nested PCR. Because transposon insertions in essential genes
should cause a lethal phenotype, any gene free of transposon insertions
after the screen can be roughly characterized as essential - with some
caveats. A gene cannot be classified as essential unless transposon
insertion caused a lethal mutation; if the gene was simply missed, its
result in this screen will be the same. To circumvent this dilemma, the
authors compare insertion density in the gene of interest with its
surrounding region. If a gene yields no insertions but is situated in a
region of high insertion density, this gene is flagged as essential. The
authors need good coverage for this technique to work - and they have it,
with 3.2 inserts per kb of genomic sequence.
Read the rest at BioMedNet
http://tinyurl.com/v1k8
Experimental Models of Primitive Cellular Compartments: Encapsulation,
Growth and Division
Hanczyc, M.M. et al.
Science 2003 302(5645):618-622
11 November 2003
Commentary by Peter T Corbett and Jeremy K Sanders
Montmorillonite links prebiotic RNA chemistry and vesicle formation.
The lipid bilayers that surround modern cells are thought to have originated
from self-assembled vesicles made from simple amphiphillic molecules. Simple
amphiphiles have been generated under a wide range of prebiotic conditions
in the laboratory, and have been found in meteorites. Simple fatty acids
have been found to form membranes when the pH is close to the pKa of the
acid, and the resulting vesicles can be further stabilized by the addition
of fatty alcohols or fatty acid glycerol esters. In this paper, the authors
report the catalysis of vesicle formation by the clay montmorillonite, which
has previously been found to catalyse the formation of RNA from activated
nucleotides. They also study the prospects of vesicle growth and division.
In the study of the autocatalytic assembly of myristoleate (an unsaturated
C14 fatty acid) vesicles from myristoleate micelles, the addition of small
quantities of montmorillonite was found to increase the initial rate of
vesicle formation by a factor of 100. This acceleration was found to
increase linearly with added montmorillonite. The catalytic nature of the
effect is clear, as the membrane surface area generated is much greater than
the maximum possible surface area of the clay. Furthermore, the clay does
not affect the critical aggregate concentration, leaving the micelle/vesicle
equilibrium unaffected. The catalytic process was also found to work for
palmitoleic acid (C16), oleic acid (C18) and myristic acid (saturated C14).
Other charged surfaces were also substituted for the montmorillonite, with
some successes that demonstrated the importance of providing a negatively
charged surface. The vesicles produced using montmorillonite were often
found to contain particles of the clay used to produce them. Clay loaded
with fluorescent-labelled RNA could also become encapsulated, demonstrating
the delivery of RNA into vesicles. No leakage of RNA separately placed into
vesicles was observed over 24 hours. Vesicle growth was observed upon the
slow addition of micelles to preformed vesicles, and it was found that
vesicle division could be induced by extrusion through small-pore
polycarbonate membrane filters. Vesicles loaded with a fluorescent dye were
shown to lose only slightly more dye than might be expected from volume loss
upon division, even in repeated cycles of vesicle growth and division. No
loss of vesicle contents was observed on vesicle growth.
In summary, this system constitutes an intriguing link between prebiotic RNA
and membrane behaviour, and allows for the encapsulation of both RNA and the
catalyst for its synthesis. The system also acts as a proof-of-principle
demonstration of vesicle growth and division through simple physico-chemical
forces, although the authors do admit that their system of vesicle division
through extrusion is unlikely to possess any natural analogues.
[Full Text from BioMedNet reproduced above]
Comment:
Carboniferous meteorites are rich in amino acids. The Murchison meteorite
was found to have 70+ amino acids, many of which are novel to life on Earth.
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Kind Regards,
Robert Karl Stonjek. |
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