7 research outputs found
Deciphering the Human Brain Proteome: Characterization of the Anterior Temporal Lobe and Corpus Callosum As Part of the Chromosome 15-centric Human Proteome Project
Defining
the proteomes encoded by each chromosome and characterizing
proteins related to human illnesses are among the goals of the Chromosome-centric
Human Proteome Project (C-HPP) and the Biology and Disease-driven
HPP. Following these objectives, we investigated the proteomes of
the human anterior temporal lobe (ATL) and corpus callosum (CC) collected
post-mortem from eight subjects. Using a label-free GeLCāMS/MS
approach, we identified 2454 proteins in the ATL and 1887 in the CC
through roughly 7500 and 5500 peptides, respectively. Considering
that the ATL is a gray-matter region while the CC is a white-matter
region, they presented proteomes specific to their functions. Besides,
38 proteins were found to be differentially expressed between the
two regions. Furthermore, the proteome data sets were classified according
to their chromosomal origin, and five proteins were evidenced at the
MS level for the first time. We identified 70 proteins of the chromosome
15 ā one of them for the first time by MS ā which were
submitted to an in silico pathway analysis. These revealed branch
point proteins associated with PraderāWilli and Angelman syndromes
and dyskeratosis congenita, which are chromosome-15-associated diseases.
Data presented here can be a useful for brain disorder studies as
well as for contributing to the C-HPP initiative. Our data are publicly
available as resource data to C-HPP participant groups at http://yoda.iq.ufrj.br/Daniel/chpp2013. Additionally, the mass spectrometry proteomics data have been deposited
to the ProteomeXchange with identifier PXD000547 for the corpus callosum
and PXD000548 for the anterior temporal lobe
Secretomic Survey of <i>Trichoderma harzianum</i> Grown on Plant Biomass Substrates
The present work
aims at characterizing <i>T. harzianum</i> secretome when
the fungus is grown in synthetic medium supplemented
with one of the four substrates: glucose, cellulose, xylan, and sugarcane
bagasse (SB). The characterization was done by enzymatic assays and
proteomic analysis using 2-DE/MALDI-TOF and gel-free shotgun LCāMS/MS.
The results showed that SB induced the highest cellulolytic and xylanolytic
activities when compared with the other substrates, while remarkable
differences in terms of number and distribution of protein spots in
2-DE gels were also observed among the samples. Additionally, treatment
of the secretomes with PNGase F revealed that most spot trails in
2-DE gels corresponded to N-glycosylated proteoforms. The LCāMS/MS
analysis of the samples identified 626 different protein groups, including
carbohydrate-active enzymes and accessory, noncatalytic, and cell-wall-associated
proteins. Although the SB-induced secretome displayed the highest
cellulolytic and xylanolytic activities, it did not correspond to
a higher proteome complexity because CM-cellulose-induced secretome
was significantly more diverse. Among the identified proteins, 73%
were exclusive to one condition, while only 5% were present in all
samples. Therefore, this study disclosed the variation of <i>T. harzianum</i> secretome in response to different substrates
and revealed the diversity of the fungus enzymatic toolbox
Proteome Analysis of Plastids from Developing Seeds of <i>Jatropha curcas</i> L.
In this study, we performed a proteomic
analysis of plastids isolated
from the endosperm of developing <i>Jatropha curcas</i> seeds
that were in the initial stage of deposition of protein and lipid
reserves. Proteins extracted from the plastids were digested with
trypsin, and the peptides were applied to an EASY-nano LC system coupled
inline to an ESI-LTQ-Orbitrap Velos mass spectrometer, and this led
to the identification of 1103 proteins representing 804 protein groups,
of which 923 proteins were considered as true identifications, and
this considerably expands the repertoire of <i>J. curcas</i> proteins identified so far. Of the identified proteins, only five
are encoded in the plastid genome, and none of them are involved in
photosynthesis, evidentiating the nonphotosynthetic nature of the
isolated plastids. Homologues for 824 out of 923 identified proteins
were present in PPDB, SUBA, or PlProt databases while homologues for
13 proteins were not found in any of the three plastid proteins databases
but were marked as plastidial by at least one of the three prediction
programs used. Functional classification showed that proteins belonging
to amino acids metabolism comprise the main functional class, followed
by carbohydrate, energy, and lipid metabolisms. The small and large
subunits of Rubisco were identified, and their presence in the plastids
is considered to be an adaptive feature counterbalancing for the loss
of one-third of the carbon as CO<sub>2</sub> as a result of the conversion
of carbohydrate to oil through glycolysis. While several enzymes involved
in the biosynthesis of several precursors of diterpenoids were identified,
we were unable to identify any terpene synthase/cyclase, which suggests
that the plastids isolated from the endosperm of developing seeds
do not synthesize phorbol esters. In conclusion, our study provides
insights into the major biosynthetic pathways and certain unique features
of the plastids from the endosperm of developing seeds at the whole
proteome level
Proteome Analysis of Plastids from Developing Seeds of <i>Jatropha curcas</i> L.
In this study, we performed a proteomic
analysis of plastids isolated
from the endosperm of developing <i>Jatropha curcas</i> seeds
that were in the initial stage of deposition of protein and lipid
reserves. Proteins extracted from the plastids were digested with
trypsin, and the peptides were applied to an EASY-nano LC system coupled
inline to an ESI-LTQ-Orbitrap Velos mass spectrometer, and this led
to the identification of 1103 proteins representing 804 protein groups,
of which 923 proteins were considered as true identifications, and
this considerably expands the repertoire of <i>J. curcas</i> proteins identified so far. Of the identified proteins, only five
are encoded in the plastid genome, and none of them are involved in
photosynthesis, evidentiating the nonphotosynthetic nature of the
isolated plastids. Homologues for 824 out of 923 identified proteins
were present in PPDB, SUBA, or PlProt databases while homologues for
13 proteins were not found in any of the three plastid proteins databases
but were marked as plastidial by at least one of the three prediction
programs used. Functional classification showed that proteins belonging
to amino acids metabolism comprise the main functional class, followed
by carbohydrate, energy, and lipid metabolisms. The small and large
subunits of Rubisco were identified, and their presence in the plastids
is considered to be an adaptive feature counterbalancing for the loss
of one-third of the carbon as CO<sub>2</sub> as a result of the conversion
of carbohydrate to oil through glycolysis. While several enzymes involved
in the biosynthesis of several precursors of diterpenoids were identified,
we were unable to identify any terpene synthase/cyclase, which suggests
that the plastids isolated from the endosperm of developing seeds
do not synthesize phorbol esters. In conclusion, our study provides
insights into the major biosynthetic pathways and certain unique features
of the plastids from the endosperm of developing seeds at the whole
proteome level
Proteome Analysis of Plastids from Developing Seeds of <i>Jatropha curcas</i> L.
In this study, we performed a proteomic
analysis of plastids isolated
from the endosperm of developing <i>Jatropha curcas</i> seeds
that were in the initial stage of deposition of protein and lipid
reserves. Proteins extracted from the plastids were digested with
trypsin, and the peptides were applied to an EASY-nano LC system coupled
inline to an ESI-LTQ-Orbitrap Velos mass spectrometer, and this led
to the identification of 1103 proteins representing 804 protein groups,
of which 923 proteins were considered as true identifications, and
this considerably expands the repertoire of <i>J. curcas</i> proteins identified so far. Of the identified proteins, only five
are encoded in the plastid genome, and none of them are involved in
photosynthesis, evidentiating the nonphotosynthetic nature of the
isolated plastids. Homologues for 824 out of 923 identified proteins
were present in PPDB, SUBA, or PlProt databases while homologues for
13 proteins were not found in any of the three plastid proteins databases
but were marked as plastidial by at least one of the three prediction
programs used. Functional classification showed that proteins belonging
to amino acids metabolism comprise the main functional class, followed
by carbohydrate, energy, and lipid metabolisms. The small and large
subunits of Rubisco were identified, and their presence in the plastids
is considered to be an adaptive feature counterbalancing for the loss
of one-third of the carbon as CO<sub>2</sub> as a result of the conversion
of carbohydrate to oil through glycolysis. While several enzymes involved
in the biosynthesis of several precursors of diterpenoids were identified,
we were unable to identify any terpene synthase/cyclase, which suggests
that the plastids isolated from the endosperm of developing seeds
do not synthesize phorbol esters. In conclusion, our study provides
insights into the major biosynthetic pathways and certain unique features
of the plastids from the endosperm of developing seeds at the whole
proteome level
Unraveling the Processing and Activation of Snake Venom Metalloproteinases
Snake
venom metalloproteinases (SVMPs) are zinc-dependent enzymes
responsible for most symptoms of human envenoming. Like matrix metalloproteinases
(MMPs) and a disintegrin and metalloproteinase (ADAM) proteins, SVMPs
are synthesized as zymogens, and enzyme activation is regulated by
hydrolysis of their prodomain, but the processing of SVMPs is still
unclear. In this study, we attempted to identify the presence of prodomain
in different compartments of snake venom glands as zymogens or in
the free form to elucidate some mechanism involved in SVMP activation.
Using antibodies obtained by immunization with a recombinant prodomain,
bands of zymogen molecular mass and prodomain peptides were detected
mostly in gland extracts all along the venom production cycle and
in the venom collected from the lumen at the peak of venom production.
Prodomain was detected in secretory cells mostly in the secretory
vesicles near the Golgi. We hypothesize that the processing of SVMPs
starts within secretory vesicles and continues in the lumen of the
venom gland just after enzyme secretion and involves different steps
compared to ADAMs and MMPs but can be used as a model for studying
the relevance of peptides resulting from prodomain processing and
degradation for controlling the activity of metalloproteinases
Unraveling the Processing and Activation of Snake Venom Metalloproteinases
Snake
venom metalloproteinases (SVMPs) are zinc-dependent enzymes
responsible for most symptoms of human envenoming. Like matrix metalloproteinases
(MMPs) and a disintegrin and metalloproteinase (ADAM) proteins, SVMPs
are synthesized as zymogens, and enzyme activation is regulated by
hydrolysis of their prodomain, but the processing of SVMPs is still
unclear. In this study, we attempted to identify the presence of prodomain
in different compartments of snake venom glands as zymogens or in
the free form to elucidate some mechanism involved in SVMP activation.
Using antibodies obtained by immunization with a recombinant prodomain,
bands of zymogen molecular mass and prodomain peptides were detected
mostly in gland extracts all along the venom production cycle and
in the venom collected from the lumen at the peak of venom production.
Prodomain was detected in secretory cells mostly in the secretory
vesicles near the Golgi. We hypothesize that the processing of SVMPs
starts within secretory vesicles and continues in the lumen of the
venom gland just after enzyme secretion and involves different steps
compared to ADAMs and MMPs but can be used as a model for studying
the relevance of peptides resulting from prodomain processing and
degradation for controlling the activity of metalloproteinases