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Current
Genomics
ISSN: 1389-2029
Current Genomics
Volume 7, Number 4, June 2006
Contents
An Approach to Whole-Genome Identification of IRES
Elements Pp. 205-215
T.E. Graber, S.M. Lewis and M. Holcik
[Abstract]
Neuronal Genomics Using Mouse Cloning with the
Single Neuronal Nucleus Pp. 217-225
T. Osada and T. Yagi
[Abstract]
The Future of Data Analysis in Evolutionary Genomics
Pp. 227-234
A.L. Hughes, R. Friedman and N.L. Glenn
[Abstract]
Chloroplast Protein Import: Reverse Genetic Approaches
Pp. 235-244
M. Oreb, K. Reger and E. Schleiff
[Abstract]
Evolutional Divergence of the Metabotropic Glutamate
Receptor Genes: A New Receptor Belonging to the Metabotropic
Glutamate Receptor Family in Dictyostelium discoideum
Pp. 245-252
H. Taniura, N. Sanada, N. Kuramoto and Y. Yoneda
[Abstract]
Antigenic Differences Between Normal and Malignant
Cells as a Basis for Treatment of Intracerebral Neoplasms
Using a DNA Based Vaccine Pp. 253-261
T. Lichtor, R.P. Glick, I. O-Sullivan and E.P. Cohen
[Abstract]
The Anaphase Promoting Complex and Aging: The
APCs of Longevity Pp. 263-272
T.A.A. Harkness
[Abstract]
Abstracts
[Back to top]
An Approach to Whole-Genome Identification of IRES
Elements
T.E. Graber, S.M. Lewis and M. Holcik
Spatial and temporal control of proteome expression
is critical for cellular homeostasis. The ability to regulate
polypeptide synthesis allows the cell to rapidly respond to
changes in its environment. Under stress conditions, cap-dependent
translation initiation is downregulated and alternative mechanisms
of translation initiation are favoured for the production
of critical proteins that ultimately determine whether the
cell is able to overcome the stress. One such alternative
mechanism of translation initiation is mediated by sequence
elements located downstream of the 5’ cap structure
that are able to directly recruit ribosomes to a region proximal
to the translation start site. Identifying the eukaryotic
mRNAs that contain such internal ribosome entry sites (IRESes)
is an important first step in cataloguing the cellular complement
of proteins whose expression is translationally regulated
during cellular stress and understanding how cells regulate
translation under stress conditions. To date, no consensus
sequence motif or structure has been identified as a signature
of cellular IRES activity, making it difficult to identify
the full complement of eukaryotic IRESes. This review will
underscore the challenges faced in identifying IRESes on a
genomic scale and potential solutions will be presented.
[Back to top]
Neuronal Genomics Using Mouse Cloning with
the Single Neuronal Nucleus
T. Osada and T. Yagi
Brain system is composed of enormous numbers of
diversified single neurons. Therefore assessing epigenetic
and genetic regulation in the nucleus of single neurons is
a new challenge for understanding neuronal commitment, differentiation
and maturation. As differentiated neurons are, in nature,
postmitotic, neither the genome nor its epigenetic modifications
are easy to evaluate fully. The cloning of mammalian cells,
which has been used mainly in the fields of assisted reproduction
and regenerative medicine, can be applied to propagating the
entire genome of single neurons. In addition, embryonic stem
(ES) cells derived from embryos cloned from single neuronal
nuclei provide an “eternal” resource for assessing
the genetic content of individual neurons. Here, we discuss
the possible genetic/epigenetic regulation of gene expression
in the nuclei of single neurons, and the utility of cloning
by neuronal nuclear transfer to assess the genomic constitution
of the single nucleus of differentiated neurons during development.
This use of cloning technology may be a fruitful approach
for analyzing the entire genome of individual single neurons.
[Back to top]
The Future of Data Analysis in Evolutionary
Genomics
A.L. Hughes, R. Friedman and N.L. Glenn
Biology as a whole has entered a new era in which
data analysis plays a prominent role; but in the field of
evolutionary genomics, data analysis has so far yielded little
of value. This relative failure has been due in large part
to methodological problems. Frequently, researchers have not
sufficiently considered alternative hypotheses, leading to
a kind of “computer-assisted storytelling”. Moreover,
there has been widespread use of model-based statistical methods
that depend heavily on assumptions regarding evolutionary
processes of which we have little knowledge. The field of
evolutionary genomics would benefit from a greater use of
“sturdy statistics” that are model-free and make
few assumptions about processes we do not understand.
[Back to top]
Chloroplast Protein Import: Reverse Genetic
Approaches
M. Oreb, K. Reger and E. Schleiff
Most proteins required for chloroplast function
are encoded in the nuclear genome and have to be translocated
into the organelle upon synthesis on cytosolic ribosomes.
The translocation is facilitated by a proteinaceous machinery
located in the outer and inner chloroplast membrane, the Toc
and Tic complexes (translocon at the outer/inner chloroplast
membrane). In the past years, many components of these complexes
– including receptors, channels and regulatory proteins
– have been isolated and characterized biochemically.
Recently, the functional analysis of these proteins was complemented
by characterization of corresponding loss of function mutants
in Arabidopsis thaliana as a model system. Here,
we will discuss these in vivo data and the results
of expression profiling in the context of current biochemical
models.
[Back to top]
Evolutional Divergence of the Metabotropic
Glutamate Receptor Genes: A New Receptor Belonging to the
Metabotropic Glutamate Receptor Family in Dictyostelium
discoideum
H. Taniura, N. Sanada, N. Kuramoto and Y. Yoneda
Glutamate receptors are the principal neurotransmitter
receptors in the central nervous system and categorized into
ionotopic glutamate receptors (iGluRs) and metabotropic glutamate
receptors (mGluRs). iGluRs internally contain ligand-gated
ion-channels, and mGluRs are a class of G-protein coupled
receptors (GPCRs) that possess a seven transmembrane region.
iGluRs are considered to diverge as ligand-gated channel proteins
from ancestral potassium channels. A prokaryotic iGluR, GluR0,
has been found to bind glutamate, form potassium-selective
channels and be related in amino-acid sequence to both eukaryotic
iGluRs and potassium channels. While, the class III GPCRs
including the sensory receptors, the GABAB receptors
(GABABRs) and mGluRs are considered to diverge
from common ancestral GPCRs. mGluR orthologs have been identified
in Drosophila, C. elegans and higher organisms. We
have screened the Dictyostelium genome database using
ligand binding domain of rat mGluR1 as a bait, and identified
a receptor, DdmGluPR (Dictyostelium metabotropic
glutamate precursor receptor), belonging to the mGluR family.
The residues of mGluRs involved in the binding of the α-carboxylic
and α-amino
groups of glutamate are well conserved in DdmGluPR but the
residues interacting with the γ-carboxylic
group of glutamate are not. The phylogenetic analysis suggests
that DdmGluPR diverged after the mGluR family-GABAB
receptors split but before mGluR family divergence. GABA induces
but glutamate acts as a competitive inhibitor of GABA for
the efficient induction of encapsulation through DdmGluPR
in Dictyostelium. DdmGluPR has a hybrid structure
with extracellular region similar to mGluRs and transmembrane
region similar to GABABRs. We propose that DdmGluPR
is evolutionary precursor to mGluRs.
[Back to top]
Antigenic Differences Between Normal and
Malignant Cells as a Basis for Treatment of Intracerebral
Neoplasms Using a DNA Based Vaccine
T. Lichtor, R.P. Glick, I. O-Sullivan and E.P.
Cohen
Antigenic differences between normal and malignant
cells of the cancer patient form the rationale for clinical
immunotherapeutic strategies. Because the antigenic phenotype
of neoplastic cells varies widely among different cells within
the same malignant cell-population, immunization with a vaccine
that stimulates immunity to the broad array of tumor antigens
expressed by the cancer cells is likely to be more efficacious
than immunization with a vaccine for a single antigen. A vaccine
prepared by transfer of DNA from the tumor into a highly immunogenic
cell line can encompass the array of tumor antigens that characterize
the patient’s neoplasm. Poorly immunogenic tumor antigens,
characteristic of malignant cells, can become strongly antigenic
if they are expressed by highly immunogenic cells. A DNA-based
vaccine was prepared by transfer of genomic DNA from a breast
cancer that arose spontaneously in a C3H/He mouse into a highly
immunogenic mouse fibroblast cell line, where genes specifying
tumor-antigens were expressed. The fibroblasts were modified
in advance of DNA-transfer to secrete an immune augmenting
cytokine and to express allogeneic MHC class I-determinants.
In an animal model of breast cancer metastatic to the brain,
introduction of the vaccine directly into the tumor bed stimulated
a systemic cellular anti-tumor immune response measured by
two independent in vitro assays and prolonged the
lives of the tumor-bearing mice. Furthermore, using antibodies
against the various T-cell subsets, it was determined that
the systemic cellular anti-tumor immunity was mediated by
CD8+, CD4+ and NK/LAK cells. The application
of DNA-based genomic vaccines for the treatment of a variety
of brain tumors is being explored.
[Back to top]
The Anaphase Promoting Complex and Aging:
The APCs of Longevity
T.A.A. Harkness
The molecular biology of aging has always been of
extreme interest to researchers. Recent advances made through
studies of model systems have greatly increased efforts to
elucidate the mechanisms involved in aging. It now appears
that in yeast there are two pathways controlling aging: i)
the generation of extrachromosomal rDNA circles (ERCs) through
the antagonistic action of Sir2p and Fob1p; and ii) the stress
response pathway, regulated by the Sch9p and Tor1p kinases.
The stress response pathway in higher eukaryotes is inhibited
by the insulin-signaling pathway. Mutation to the AKT kinase
disrupts insulin signaling and increases longevity. Yeast
express orthologues of the insulin-signaling pathway, yet
insulin is not a natural substrate for yeast. The yeast Sch9p
is structurally and functionally related to the AKT kinase,
but the remainder of the putative yeast AKT pathways is uncharacterized.
Further mystery revolves around downstream targets that are
directly required for longevity. Yeast provide an opportunity
to investigate the function of the yeast AKT pathway at a
molecular level. A potential downstream target has been identified
in yeast that links the glucose and stress response pathways
with lifespan: the Anaphase Promoting Complex (APC). This
review will discuss the role the APC plays in established
aging pathways in yeast and the implications on higher eukaryotes.
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