9 research outputs found
Table_1_Common Features Between the Proteomes of Floral and Extrafloral Nectar From the Castor Plant (Ricinus Communis) and the Proteomes of Exudates From Carnivorous Plants.XLSX
<p>Label-free quantitative proteome analysis of extrafloral (EFN) and floral nectar (FN) from castor (Ricinus communis) plants resulted in the identification of 72 and 37 proteins, respectively. Thirty proteins were differentially accumulated between EFN and FN, and 24 of these were more abundant in the EFN. In addition to proteins involved in maintaining the nectar pathogen free such as chitinases and glucan 1,3-beta-glucosidase, both proteomes share an array of peptidases, lipases, carbohydrases, and nucleases. A total of 39 of the identified proteins, comprising different classes of hydrolases, were found to have biochemical matching partners in the exudates of at least five genera of carnivorous plants, indicating the EFN and FN possess a potential to digest biological material from microbial, animal or plant origin equivalent to the exudates of carnivorous plants.</p
Proteomic Analysis of the Endosperm Ontogeny of Jatropha curcas L. Seeds
Seeds
of Jatropha curcas L. represent
a potential source of raw material for the production of biodiesel.
However, this use is hampered by the lack of basic information on
the biosynthetic pathways associated with synthesis of toxic diterpenes,
fatty acids, and triacylglycerols, as well as the pattern of deposition
of storage proteins during seed development. In this study, we performed
an in-depth proteome analysis of the endosperm isolated from five
developmental stages which resulted in the identification of 1517,
1256, 1033, 752, and 307 proteins, respectively, summing up 1760 different
proteins. Proteins with similar label free quantitation expression
pattern were grouped into five clusters. The biological significance
of these identifications is discussed with special focus on the analysis
of seed storage proteins, proteins involved in the metabolism of fatty
acids, carbohydrates, toxic components and proteolytic processing.
Although several enzymes belonging to the biosynthesis of diterpenoid
precursors were identified, we were unable to find any terpene synthase/cyclase,
indicating that the synthesis of phorbol esters, the main toxic diterpenes,
does not occur in seeds. The strategy used enabled us to provide a
first in depth proteome analysis of the developing endosperm of this
biodiesel plant, providing an important glimpse into the enzymatic
machinery devoted to the production of C and N sources to sustain
seed development
Isotope Labeling-Based Quantitative Proteomics of Developing Seeds of Castor Oil Seed (<i>Ricinus communis</i> L.)
In
this study, we used a mass spectrometry-based quantification
approach employing isotopic (ICPL) and isobaric (iTRAQ) labeling to
investigate the pattern of protein deposition during castor oil seed
(<i>Ricinus communis</i> L.) development, including that
of proteins involved in fatty acid metabolism, seed-storage proteins
(SSPs), toxins, and allergens. Additionally, we have used off-line
hydrophilic interaction chromatography (HILIC) as a step of peptide
fractionation preceding the reverse-phase nanoLC coupled to a LTQ
Orbitrap. We were able to identify a total of 1875 proteins, and from
these 1748 could be mapped to extant castor gene models, considerably
expanding the number of proteins so far identified from developing
castor seeds. Cluster validation and statistical analysis resulted
in 975 protein trend patterns and the relative abundance of 618 proteins.
The results presented in this work give important insights into certain
aspects of the biology of castor oil seed development such as carbon
flow, anabolism, and catabolism of fatty acid and the pattern of deposition
of SSPs, toxins, and allergens such as ricin and 2S albumins. We also
found, for the first time, some genes of SSP that are differentially
expressed during seed development
Isotope Labeling-Based Quantitative Proteomics of Developing Seeds of Castor Oil Seed (<i>Ricinus communis</i> L.)
In
this study, we used a mass spectrometry-based quantification
approach employing isotopic (ICPL) and isobaric (iTRAQ) labeling to
investigate the pattern of protein deposition during castor oil seed
(<i>Ricinus communis</i> L.) development, including that
of proteins involved in fatty acid metabolism, seed-storage proteins
(SSPs), toxins, and allergens. Additionally, we have used off-line
hydrophilic interaction chromatography (HILIC) as a step of peptide
fractionation preceding the reverse-phase nanoLC coupled to a LTQ
Orbitrap. We were able to identify a total of 1875 proteins, and from
these 1748 could be mapped to extant castor gene models, considerably
expanding the number of proteins so far identified from developing
castor seeds. Cluster validation and statistical analysis resulted
in 975 protein trend patterns and the relative abundance of 618 proteins.
The results presented in this work give important insights into certain
aspects of the biology of castor oil seed development such as carbon
flow, anabolism, and catabolism of fatty acid and the pattern of deposition
of SSPs, toxins, and allergens such as ricin and 2S albumins. We also
found, for the first time, some genes of SSP that are differentially
expressed during seed development
Isotope Labeling-Based Quantitative Proteomics of Developing Seeds of Castor Oil Seed (<i>Ricinus communis</i> L.)
In
this study, we used a mass spectrometry-based quantification
approach employing isotopic (ICPL) and isobaric (iTRAQ) labeling to
investigate the pattern of protein deposition during castor oil seed
(<i>Ricinus communis</i> L.) development, including that
of proteins involved in fatty acid metabolism, seed-storage proteins
(SSPs), toxins, and allergens. Additionally, we have used off-line
hydrophilic interaction chromatography (HILIC) as a step of peptide
fractionation preceding the reverse-phase nanoLC coupled to a LTQ
Orbitrap. We were able to identify a total of 1875 proteins, and from
these 1748 could be mapped to extant castor gene models, considerably
expanding the number of proteins so far identified from developing
castor seeds. Cluster validation and statistical analysis resulted
in 975 protein trend patterns and the relative abundance of 618 proteins.
The results presented in this work give important insights into certain
aspects of the biology of castor oil seed development such as carbon
flow, anabolism, and catabolism of fatty acid and the pattern of deposition
of SSPs, toxins, and allergens such as ricin and 2S albumins. We also
found, for the first time, some genes of SSP that are differentially
expressed during seed development
Proteome Analysis of the Inner Integument from Developing <i>Jatropha curcas</i> L. Seeds
In
this study, we performed a systematic proteomic analysis of
the inner integument from developing seeds of <i>Jatropha curcas</i> and further explored the protein machinery responsible for generating
the carbon and nitrogen sources to feed the growing embryo and endosperm.
The inner integument of developing seeds was dissected into two sections
called distal and proximal, and proteins were extracted from these
sections and from the whole integument and analyzed using an EASY-nanoLC
system coupled to an ESI-LTQ-Orbitrap Velos mass spectrometer. We
identified 1526, 1192, and 1062 proteins from the proximal, distal,
and whole inner integuments, respectively. The identifications include
those of peptidases and other hydrolytic enzymes that play a key role
in developmental programmed cell death and proteins associated with
the cell-wall architecture and modification. Because many of these
proteins are differentially expressed within the integument cell layers,
these findings suggest that the cells mobilize an array of hydrolases
to produce carbon and nitrogen sources from proteins, carbohydrates,
and lipids available within the cells. Not least, the identification
of several classes of seed storage proteins in the inner integument
provides additional evidence of the role of the seed coat as a transient
source of reserves for the growing embryo and endosperm
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