3 research outputs found
Kinase Substrate Profiling Using a Proteome-wide Serine-Oriented Human Peptide Library
The
human proteome encodes >500 protein kinases and hundreds of
thousands of potential phosphorylation sites. However, the identification
of kinase–substrate pairs remains an active area of research
because the relationships between individual kinases and these phosphorylation
sites remain largely unknown. Many techniques have been established
to discover kinase substrates but are often technically challenging
to perform. Moreover, these methods frequently rely on substrate reagent
pools that do not reflect human protein sequences or are biased by
human cell line protein expression profiles. Here, we describe a new
approach called SERIOHL-KILR (serine-oriented human library–kinase
library reactions) to profile kinase substrate specificity and to
identify candidate substrates for serine kinases. Using a purified
library of >100000 serine-oriented human peptides expressed heterologously
in <i>Escherichia coli</i>, we perform <i>in vitro</i> kinase reactions to identify phosphorylated human peptide sequences
by liquid chromatography and tandem mass spectrometry. We compare
our results for protein kinase A to those of a well-established positional
scanning peptide library method, certifying that SERIOHL-KILR can
identify the same predominant motif elements as traditional techniques.
We then interrogate a small panel of cancer-associated PKCβ
mutants using our profiling protocol and observe a shift in substrate
specificity likely attributable to the loss of key polar contacts
between the kinase and its substrates. Overall, we demonstrate that
SERIOHL-KILR can rapidly identify candidate kinase substrates that
can be directly mapped to human sequences for pathway analysis. Because
this technique can be adapted for various kinase studies, we believe
that SERIOHL-KILR will have many new victims in the future
Kinase Substrate Profiling Using a Proteome-wide Serine-Oriented Human Peptide Library
The
human proteome encodes >500 protein kinases and hundreds of
thousands of potential phosphorylation sites. However, the identification
of kinase–substrate pairs remains an active area of research
because the relationships between individual kinases and these phosphorylation
sites remain largely unknown. Many techniques have been established
to discover kinase substrates but are often technically challenging
to perform. Moreover, these methods frequently rely on substrate reagent
pools that do not reflect human protein sequences or are biased by
human cell line protein expression profiles. Here, we describe a new
approach called SERIOHL-KILR (serine-oriented human library–kinase
library reactions) to profile kinase substrate specificity and to
identify candidate substrates for serine kinases. Using a purified
library of >100000 serine-oriented human peptides expressed heterologously
in <i>Escherichia coli</i>, we perform <i>in vitro</i> kinase reactions to identify phosphorylated human peptide sequences
by liquid chromatography and tandem mass spectrometry. We compare
our results for protein kinase A to those of a well-established positional
scanning peptide library method, certifying that SERIOHL-KILR can
identify the same predominant motif elements as traditional techniques.
We then interrogate a small panel of cancer-associated PKCβ
mutants using our profiling protocol and observe a shift in substrate
specificity likely attributable to the loss of key polar contacts
between the kinase and its substrates. Overall, we demonstrate that
SERIOHL-KILR can rapidly identify candidate kinase substrates that
can be directly mapped to human sequences for pathway analysis. Because
this technique can be adapted for various kinase studies, we believe
that SERIOHL-KILR will have many new victims in the future
Comparative Proteomics Enables Identification of Nonannotated Cold Shock Proteins in <i>E. coli</i>
Recent advances in mass spectrometry-based
proteomics have revealed
translation of previously nonannotated microproteins from thousands
of small open reading frames (smORFs) in prokaryotic and eukaryotic
genomes. Facile methods to determine cellular functions of these newly
discovered microproteins are now needed. Here, we couple semiquantitative
comparative proteomics with whole-genome database searching to identify
two nonannotated, homologous cold shock-regulated microproteins in Escherichia coli K12 substr. MG1655, as well as two
additional constitutively expressed microproteins. We apply molecular
genetic approaches to confirm expression of these cold shock proteins
(YmcF and YnfQ) at reduced temperatures and identify the noncanonical
ATT start codons that initiate their translation. These proteins are
conserved in related Gram-negative bacteria and are predicted to be
structured, which, in combination with their cold shock upregulation,
suggests that they are likely to have biological roles in the cell.
These results reveal that previously unknown factors are involved
in the response of E. coli to lowered
temperatures and suggest that further nonannotated, stress-regulated E. coli microproteins may remain to be found. More
broadly, comparative proteomics may enable discovery of regulated,
and therefore potentially functional, products of smORF translation
across many different organisms and conditions