Biology Reference
In-Depth Information
hybridization it was shown that the expression of a gene
downstream of SKN-1 becomes highly variable in the
mutants, with this variation propagating to an all-or-none
induction of the master intestine regulator ELT-2. Thus it
was argued that variation in gene expression underlies
incomplete penetrance
[134]
.
A second study addressed variation in the outcome of
a deletion of the gene tbx-9
[133]
. In this study, live
imaging of embryos expressing fluorescent protein reporter
constructs was used to relate early variation in gene
expression to later variation in the phenotypic outcome of
the mutation. Variation in two buffering systems was found
to partially predict the outcome of the mutation in each
individual. First, the compensatory upregulation of
a partially redundant gene, tbx-8, was found to vary among
individuals, with very strong upregulation masking the
effect of the inherited mutation in tbx-9. Second,
a surprising amount of variation in the induction of
molecular chaperones such as Hsp90 (DAF-21) was
observed among isogenic embryos, and this variation also
partially predicted the later outcome of the inherited
mutation. By simultaneously quantifying the variation in
both systems, more accurate predictions could be made
about the phenotypic outcome of the mutation in each
individual
[133]
. Chaperone activity is an important influ-
ence on the outcome of many mutations, so inter-individual
variation in chaperone expression may be quite a promis-
cuous determinant of mutation outcome
[149]
.
initiated to systematically map protein post-translational
modifications, with nearly 7000 phosphorylation sites
identified on 2400 proteins
[161]
. The C. elegans genome
encodes a large number of nematode-specific kinases, and
indeed the phosphoproteome was found to be rather distinct
from that of other higher eukaryotes, with different inferred
kinase substrate motifs and low conservation of the phos-
phorylated sites in other higher eukaryotes
[161]
.
C. elegans has been a leading model system for the
comprehensive mapping of protein
protein interactions,
primarily using the yeast two-hybrid system (see Chapter 3)
In this approach, two proteins (or protein domains) are
fused respectively to a DNA-binding domain and a tran-
scription activation domain, and are expressed in the yeast
nucleus. If the two proteins interact, then expression of
a reporter construct is activated. Early pioneering studies
systematically mapped protein interactions among proteins
implicated in regulating a common developmental process
e
e
among subunits of a protein
complex
[163]
, or among genes expressed in the germline
[164]
. Additional studies used protein interaction mapping
in combination with genetic perturbations to identify new
regulators of the DNA damage response
[165]
and TGF-
b
vulva development
[162]
e
signaling
[166]
. These efforts were extended to the scale
of a few thousand screens against cDNA libraries, identi-
fying
2000 high confidence two-hybrid interactions
[167]
. More recently, ~1800 yeast two-hybrid interactions
were reported from an experiment testing for interactions
among ~10 000 proteins
[168]
. Moreover, a strategy to
identify interaction domains has allowed the minimally
interacting regions to be identified for over 200 proteins
involved in early embryogenesis
[169]
. These datasets
provide a fantastic resource for the C. elegans community,
for example allowing researchers to identify new proteins
potentially involved in a process of interest. However, it is
important
>
Proteomics in C. elegans: Global Maps
of Protein Expression and Protein
Protein
e
Interactions
Compared, for example, to the situation in yeast, proteomic
approaches have not been very widely employed by the C.
elegans community. However, shotgun proteomics (see
Chapter 1) confirmed the expression of
protein
interactions in C. elegans (the 'interactome') are far from
complete: to date,
to note that efforts to map protein
e
10 000 proteins
(more than half of genes)
[156]
. Not surprisingly, the set of
identified proteins was biased against hydrophobic trans-
membrane proteins, short proteins and genes expressed in
only a small number of neurons, highlighting further
improvements that are needed in the approach. Comparing
mRNA and protein expression levels between C. elegans
and Drosophila melanogaster suggested that protein levels
might be more conserved during evolution than mRNA
expression
[156]
. Quantitative proteomics has also been
used to validate predicted miRNA targets
[157]
, and pro-
teomic approaches have been used to systematically iden-
tify sperm chromatin components
[158]
, targets of the
insulin-like signaling pathway
[159]
, and to identify several
hundred proteins that aggregate in old animals
[160]
. This
last study suggested that protein insolubility is an inherent
part of normal aging in C. elegans. Efforts have also been
>
5000 protein interactions have been
described, from an estimated total of
<
100 000 interactions
[168]
. Moreover, no large-scale studies have been initiated
to map protein interactions in C. elegans through the
isolatio
n of protein complexes, and more work is needed in
this area.
>
INTEGRATIVE AND DYNAMIC MODELING
TO LINK GENOTYPE TO PHENOTYPE
Data Integration and Genome-Scale
Networks to Connect Genes and Modules
to Phenotypic Variation
Aside from yeast, C. elegans is still the only eukaryote in
which systematic and comprehensive reverse genetic
