13 research outputs found
Comparative Analysis of the Endogenous Peptidomes Displayed by HLA-B*27 and Mamu-B*08: Two MHC Class I Alleles Associated with Elite Control of HIV/SIV Infection
Indian
rhesus macaques are arguably the most reliable animal models
in AIDS research. In this species the MHC class I allele Mamu-B*08,
among others, is associated with elite control of SIV replication.
A similar scenario is observed in humans where the expression of HLA-B*27
or HLA-B*57 has been linked to slow or no progression to AIDS after
HIV infection. Despite having large differences in their primary structure,
it has been reported that HLA-B*27 and Mamu-B*08 display peptides
with sequence similarity. To fine-map the Mamu-B*08 binding motif
and assess its similarities with that of HLA-B*27, we affinity purified
the peptidomes bound to these MHC class I molecules and analyzed them
by LC-MS, identifying several thousands of endogenous ligands. Sequence
analysis of both sets of peptides revealed a degree of similarity
in their binding motifs, especially at peptide position 2 (P2), where
arginine was present in the vast majority of ligands of both allotypes.
In addition, several differences emerged from this analysis: (i) ligands
displayed by Mamu-B*08 tended to be shorter and to have lower molecular
weight, (ii) Mamu-B*08 showed a higher preference for glutamine at
P2 as a suboptimal binding motif, and (iii) the second major anchor
position, found at PΩ, was much more restrictive in Mamu-B*08.
In this regard, HLA-B*27 bound efficiently peptides with aliphatic,
aromatic (including tyrosine), and basic C-terminal residues while
Mamu-B*08 preferred peptides with leucine and phenylalanine in this
position. Finally, in silico estimations of binding efficiency and
competitive binding assays to Mamu-B*08 of several selected peptides
revealed a good correlation between the characterized anchor motif
and binding affinity. These results deepen our understanding of the
molecular basis of the presentation of peptides by Mamu-B*08 and can
contribute to the detection of novel SIV epitopes restricted by this
allotype
New Copper Resistance Determinants in the Extremophile <i>Acidithiobacillus ferrooxidans</i>: A Quantitative Proteomic Analysis
<i>Acidithiobacillus ferrooxidans</i> is an extremophilic
bacterium used in biomining processes to recover metals. The presence
in <i>A. ferrooxidans</i> ATCC 23270 of canonical copper
resistance determinants does not entirely explain the extremely high
copper concentrations this microorganism is able to stand, suggesting
the existence of other efficient copper resistance mechanisms. New
possible copper resistance determinants were searched by using 2D-PAGE,
real time PCR (qRT-PCR) and quantitative proteomics with isotope-coded
protein labeling (ICPL). A total of 594 proteins were identified of
which 120 had altered levels in cells grown in the presence of copper.
Of this group of proteins, 76 were up-regulated and 44 down-regulated.
The up-regulation of RND-type Cus systems and different RND-type efflux
pumps was observed in response to copper, suggesting that these proteins
may be involved in copper resistance. An overexpression of most of
the genes involved in histidine synthesis and several of those annotated
as encoding for cysteine production was observed in the presence of
copper, suggesting a possible direct role for these metal-binding
amino acids in detoxification. Furthermore, the up-regulation of putative
periplasmic disulfide isomerases was also seen in the presence of
copper, suggesting that they restore copper-damaged disulfide bonds
to allow cell survival. Finally, the down-regulation of the major
outer membrane porin and some ionic transporters was seen in <i>A</i>. <i>ferrooxidans</i> grown in the presence of
copper, indicating a general decrease in the influx of the metal and
other cations into the cell. Thus, <i>A</i>. <i>ferrooxidans</i> most likely uses additional copper resistance strategies in which
cell envelope proteins are key components. This knowledge will not
only help to understand the mechanism of copper resistance in this
extreme acidophile but may help also to select the best fit members
of the biomining community to attain more efficient industrial metal
leaching processes
Proteogenomics Dashboard for the Human Proteome Project
<i>dasHPPboard</i> is a novel proteomics-based dashboard
that collects and reports the experiments produced by the Spanish
Human Proteome Project consortium (SpHPP) and aims to help HPP to
map the entire human proteome. We have followed the strategy of analog
genomics projects like the Encyclopedia of DNA Elements (ENCODE),
which provides a vast amount of data on human cell lines experiments.
The dashboard includes results of shotgun and selected reaction monitoring
proteomics experiments, post-translational modifications information,
as well as proteogenomics studies. We have also processed the transcriptomics
data from the ENCODE and Human Body Map (HBM) projects for the identification
of specific gene expression patterns in different cell lines and tissues,
taking special interest in those genes having little proteomic evidence
available (missing proteins). Peptide databases have been built using
single nucleotide variants and novel junctions derived from RNA-Seq
data that can be used in search engines for sample-specific protein
identifications on the same cell lines or tissues. The <i>dasHPPboard</i> has been designed as a tool that can be used to share and visualize
a combination of proteomic and transcriptomic data, providing at the
same time easy access to resources for proteogenomics analyses. The <i>dasHPPboard</i> can be freely accessed at: http://sphppdashboard.cnb.csic.es
PACOM: A Versatile Tool for Integrating, Filtering, Visualizing, and Comparing Multiple Large Mass Spectrometry Proteomics Data Sets
Mass-spectrometry-based
proteomics has evolved into a high-throughput
technology in which numerous large-scale data sets are generated from
diverse analytical platforms. Furthermore, several scientific journals
and funding agencies have emphasized the storage of proteomics data
in public repositories to facilitate its evaluation, inspection, and
reanalysis. As a consequence, public proteomics
data repositories are growing rapidly. However, tools are needed to
integrate multiple proteomics data sets to compare different experimental
features or to perform quality control analysis. Here, we present
a new Java stand-alone tool, Proteomics Assay COMparator (PACOM),
that is able to import, combine, and simultaneously compare numerous
proteomics experiments to check the integrity of the proteomic data
as well as verify data quality. With PACOM, the user can detect source
of errors that may have been introduced in any step of a proteomics
workflow and that influence the final results. Data sets can be easily
compared and integrated, and data quality and reproducibility can
be visually assessed through a rich set of graphical representations
of proteomics data features as well as a wide variety of data filters.
Its flexibility and easy-to-use interface make PACOM a unique tool
for daily use in a proteomics laboratory. PACOM is available at https://github.com/smdb21/pacom
Surfing Transcriptomic Landscapes. A Step beyond the Annotation of Chromosome 16 Proteome
The
Spanish team of the Human Proteome Project (SpHPP) marked the
annotation of Chr16 and data analysis as one of its priorities. Precise
annotation of Chromosome 16 proteins according to C-HPP criteria is
presented. Moreover, Human Body Map 2.0 RNA-Seq and Encyclopedia of
DNA Elements (ENCODE) data sets were used to obtain further information
relative to cell/tissue specific chromosome 16 coding gene expression
patterns and to infer the presence of missing proteins. Twenty-four
shotgun 2D-LC–MS/MS and gel/LC–MS/MS MIAPE compliant
experiments, representing 41% coverage of chromosome 16 proteins,
were performed. Furthermore, mapping of large-scale multicenter mass
spectrometry data sets from CCD18, MCF7, Jurkat, and Ramos cell lines
into RNA-Seq data allowed further insights relative to correlation
of chromosome 16 transcripts and proteins. Detection and quantification
of chromosome 16 proteins in biological matrices by SRM procedures
are also primary goals of the SpHPP. Two strategies were undertaken:
one focused on known proteins, taking advantage of MS data already
available, and the second, aimed at the detection of the missing proteins,
is based on the expression of recombinant proteins to gather MS information
and optimize SRM methods that will be used in real biological samples.
SRM methods for 49 known proteins and for recombinant forms of 24
missing proteins are reported in this study
Surfing Transcriptomic Landscapes. A Step beyond the Annotation of Chromosome 16 Proteome
The
Spanish team of the Human Proteome Project (SpHPP) marked the
annotation of Chr16 and data analysis as one of its priorities. Precise
annotation of Chromosome 16 proteins according to C-HPP criteria is
presented. Moreover, Human Body Map 2.0 RNA-Seq and Encyclopedia of
DNA Elements (ENCODE) data sets were used to obtain further information
relative to cell/tissue specific chromosome 16 coding gene expression
patterns and to infer the presence of missing proteins. Twenty-four
shotgun 2D-LC–MS/MS and gel/LC–MS/MS MIAPE compliant
experiments, representing 41% coverage of chromosome 16 proteins,
were performed. Furthermore, mapping of large-scale multicenter mass
spectrometry data sets from CCD18, MCF7, Jurkat, and Ramos cell lines
into RNA-Seq data allowed further insights relative to correlation
of chromosome 16 transcripts and proteins. Detection and quantification
of chromosome 16 proteins in biological matrices by SRM procedures
are also primary goals of the SpHPP. Two strategies were undertaken:
one focused on known proteins, taking advantage of MS data already
available, and the second, aimed at the detection of the missing proteins,
is based on the expression of recombinant proteins to gather MS information
and optimize SRM methods that will be used in real biological samples.
SRM methods for 49 known proteins and for recombinant forms of 24
missing proteins are reported in this study
Surfing Transcriptomic Landscapes. A Step beyond the Annotation of Chromosome 16 Proteome
The
Spanish team of the Human Proteome Project (SpHPP) marked the
annotation of Chr16 and data analysis as one of its priorities. Precise
annotation of Chromosome 16 proteins according to C-HPP criteria is
presented. Moreover, Human Body Map 2.0 RNA-Seq and Encyclopedia of
DNA Elements (ENCODE) data sets were used to obtain further information
relative to cell/tissue specific chromosome 16 coding gene expression
patterns and to infer the presence of missing proteins. Twenty-four
shotgun 2D-LC–MS/MS and gel/LC–MS/MS MIAPE compliant
experiments, representing 41% coverage of chromosome 16 proteins,
were performed. Furthermore, mapping of large-scale multicenter mass
spectrometry data sets from CCD18, MCF7, Jurkat, and Ramos cell lines
into RNA-Seq data allowed further insights relative to correlation
of chromosome 16 transcripts and proteins. Detection and quantification
of chromosome 16 proteins in biological matrices by SRM procedures
are also primary goals of the SpHPP. Two strategies were undertaken:
one focused on known proteins, taking advantage of MS data already
available, and the second, aimed at the detection of the missing proteins,
is based on the expression of recombinant proteins to gather MS information
and optimize SRM methods that will be used in real biological samples.
SRM methods for 49 known proteins and for recombinant forms of 24
missing proteins are reported in this study
Surfing Transcriptomic Landscapes. A Step beyond the Annotation of Chromosome 16 Proteome
The
Spanish team of the Human Proteome Project (SpHPP) marked the
annotation of Chr16 and data analysis as one of its priorities. Precise
annotation of Chromosome 16 proteins according to C-HPP criteria is
presented. Moreover, Human Body Map 2.0 RNA-Seq and Encyclopedia of
DNA Elements (ENCODE) data sets were used to obtain further information
relative to cell/tissue specific chromosome 16 coding gene expression
patterns and to infer the presence of missing proteins. Twenty-four
shotgun 2D-LC–MS/MS and gel/LC–MS/MS MIAPE compliant
experiments, representing 41% coverage of chromosome 16 proteins,
were performed. Furthermore, mapping of large-scale multicenter mass
spectrometry data sets from CCD18, MCF7, Jurkat, and Ramos cell lines
into RNA-Seq data allowed further insights relative to correlation
of chromosome 16 transcripts and proteins. Detection and quantification
of chromosome 16 proteins in biological matrices by SRM procedures
are also primary goals of the SpHPP. Two strategies were undertaken:
one focused on known proteins, taking advantage of MS data already
available, and the second, aimed at the detection of the missing proteins,
is based on the expression of recombinant proteins to gather MS information
and optimize SRM methods that will be used in real biological samples.
SRM methods for 49 known proteins and for recombinant forms of 24
missing proteins are reported in this study
Surfing Transcriptomic Landscapes. A Step beyond the Annotation of Chromosome 16 Proteome
The
Spanish team of the Human Proteome Project (SpHPP) marked the
annotation of Chr16 and data analysis as one of its priorities. Precise
annotation of Chromosome 16 proteins according to C-HPP criteria is
presented. Moreover, Human Body Map 2.0 RNA-Seq and Encyclopedia of
DNA Elements (ENCODE) data sets were used to obtain further information
relative to cell/tissue specific chromosome 16 coding gene expression
patterns and to infer the presence of missing proteins. Twenty-four
shotgun 2D-LC–MS/MS and gel/LC–MS/MS MIAPE compliant
experiments, representing 41% coverage of chromosome 16 proteins,
were performed. Furthermore, mapping of large-scale multicenter mass
spectrometry data sets from CCD18, MCF7, Jurkat, and Ramos cell lines
into RNA-Seq data allowed further insights relative to correlation
of chromosome 16 transcripts and proteins. Detection and quantification
of chromosome 16 proteins in biological matrices by SRM procedures
are also primary goals of the SpHPP. Two strategies were undertaken:
one focused on known proteins, taking advantage of MS data already
available, and the second, aimed at the detection of the missing proteins,
is based on the expression of recombinant proteins to gather MS information
and optimize SRM methods that will be used in real biological samples.
SRM methods for 49 known proteins and for recombinant forms of 24
missing proteins are reported in this study
Surfing Transcriptomic Landscapes. A Step beyond the Annotation of Chromosome 16 Proteome
The
Spanish team of the Human Proteome Project (SpHPP) marked the
annotation of Chr16 and data analysis as one of its priorities. Precise
annotation of Chromosome 16 proteins according to C-HPP criteria is
presented. Moreover, Human Body Map 2.0 RNA-Seq and Encyclopedia of
DNA Elements (ENCODE) data sets were used to obtain further information
relative to cell/tissue specific chromosome 16 coding gene expression
patterns and to infer the presence of missing proteins. Twenty-four
shotgun 2D-LC–MS/MS and gel/LC–MS/MS MIAPE compliant
experiments, representing 41% coverage of chromosome 16 proteins,
were performed. Furthermore, mapping of large-scale multicenter mass
spectrometry data sets from CCD18, MCF7, Jurkat, and Ramos cell lines
into RNA-Seq data allowed further insights relative to correlation
of chromosome 16 transcripts and proteins. Detection and quantification
of chromosome 16 proteins in biological matrices by SRM procedures
are also primary goals of the SpHPP. Two strategies were undertaken:
one focused on known proteins, taking advantage of MS data already
available, and the second, aimed at the detection of the missing proteins,
is based on the expression of recombinant proteins to gather MS information
and optimize SRM methods that will be used in real biological samples.
SRM methods for 49 known proteins and for recombinant forms of 24
missing proteins are reported in this study