Simple, efficient and thorough shotgun proteomic analysis with PatternLab V

Santos, Marlon D.M.; Lima, Diogo Borges; Fischer, Juliana de Saldanha da Gama; Clasen, Milan A; Kurt, Louise Ulrich; Camillo-Andrade, Amanda Caroline; Monteiro, Leandro C; Aquino, Priscila Ferreira de; Neves-Ferreira, Ana Gisele C.; Valente, Richard H.; Trugilho, Monique Ramos de Oliveira; Brunoro, Giselle Villa Flor; Souza, T.A.C.B.; Santos, Renata M.; Batista, Michel; Gozzo, Fábio C.; Durán, Rosario; Yates, John R.; Barbosa, Valmir C.; Carvalho, Paulo C.

doi:10.1038/s41596-022-00690-x

Cited by 33 publications

(26 citation statements)

References 58 publications

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“…When comparing salt-stressed against control plants, the pairwise differential expression analysis revealed 2728 differentially expressed (DE) proteins in the oil palm genome at False Discovery Rate (FDR) ≤ 0.05 in which 1138 were upregulated (Log 2 (FC) > 0) and 1590 were downregulated (Log 2 (FC) < 0) (Table 1, Supplementary Table S1). * Up = Proteins found exclusively in stressed samples + Proteins that attended to statistical criteria of PatternLab V software; Down = Proteins found exclusively in control samples + Proteins that attended to statistical criteria of PatternLab V software [17].…”

Section: Oil Palm Transcriptome Under Salinity Stressmentioning

confidence: 99%

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Insights from a Multi-Omics Integration (MOI) Study in Oil Palm (Elaeis guineensis Jacq.) Response to Abiotic Stresses: Part One—Salinity

Bittencourt

Silva

Neto

et al. 2022

Plants

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Oil palm (Elaeis guineensis Jacq.) is the number one source of consumed vegetable oil nowadays. It is cultivated in areas of tropical rainforest, where it meets its natural condition of high rainfall throughout the year. The palm oil industry faces criticism due to a series of practices that was considered not environmentally sustainable, and it finds itself under pressure to adopt new and innovative procedures to reverse this negative public perception. Cultivating this oilseed crop outside the rainforest zone is only possible using artificial irrigation. Close to 30% of the world’s irrigated agricultural lands also face problems due to salinity stress. Consequently, the research community must consider drought and salinity together when studying to empower breeding programs in order to develop superior genotypes adapted to those potential new areas for oil palm cultivation. Multi-Omics Integration (MOI) offers a new window of opportunity for the non-trivial challenge of unraveling the mechanisms behind multigenic traits, such as drought and salinity tolerance. The current study carried out a comprehensive, large-scale, single-omics analysis (SOA), and MOI study on the leaves of young oil palm plants submitted to very high salinity stress. Taken together, a total of 1239 proteins were positively regulated, and 1660 were negatively regulated in transcriptomics and proteomics analyses. Meanwhile, the metabolomics analysis revealed 37 metabolites that were upregulated and 92 that were downregulated. After performing SOA, 436 differentially expressed (DE) full-length transcripts, 74 DE proteins, and 19 DE metabolites underwent MOI analysis, revealing several pathways affected by this stress, with at least one DE molecule in all three omics platforms used. The Cysteine and methionine metabolism (map00270) and Glycolysis/Gluconeogenesis (map00010) pathways were the most affected ones, each one with 20 DE molecules.

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Section: Oil Palm Transcriptome Under Salinity Stressmentioning

confidence: 99%

“…All the transcriptomics analysis was performed with OmicsBox platform-version 2.0.36 [49], as previously described by [15,17]. The oil palm genome [19,20]-downloaded from NCBI (BioProject PRJNA268357; BioSample SAMN02981535) in September 2021-was the reference genome for RNA-Seq data alignment.…”

Section: Transcriptomics Data Analysismentioning

confidence: 99%

Insights from a Multi-Omics Integration (MOI) Study in Oil Palm (Elaeis guineensis Jacq.) Response to Abiotic Stresses: Part One—Salinity

Bittencourt

Silva

Neto

et al. 2022

Plants

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“…PatternLab for Proteomics software (http://www.patternlabforproteomics.org/) [22] was also used to identify the peptides and proteins. Briefly, the search was performed with the Comet search tool limited to fully tryptic candidate peptides, while cysteine carbamidomethylation and iTRAQ-4 (N-terminal and K) were defined as fixed modifications.…”

Section: Discussionmentioning

confidence: 99%

“…The quantitative analysis for protein expression was conducted with PatternLab for Proteomics software using the Isobaric Analyzer module [22]. In this module, iTRAQ reporter ion intensities were extracted, applied to purity correction (as indicated in the manufacturer's instructions), and then normalized by the signal from each isobaric marker according to the total ion current for that respective reporter ion mass.…”

Section: Quantitative Analysis Of Total Proteinsmentioning

confidence: 99%

Candidate proteins associated with popping expansion capacity of popcorn

Gemelli

Romani

Santos

et al. 2022

Preprint

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The mechanical resistance of the popcorn pericarp has a positive and direct relationship to its expansion volume. It allows enough time for the endosperm to gelatinize completely before its extravasation. Expansion is a polygenic trait that has been extensively studied. However, no records in the literature indicate proteins that directly affect pericarp thickness and integrity. Therefore, the present work aimed to identify candidate pericarp proteins associated with the expansion capacity of popcorn kernels using the shotgun proteomic approach. The analyses were carried out in the pericarp of two popcorn inbred lines, P11 (expansion volume of 30 mL g-1) and P16 (expansion volume of 14 mL g-1), in two developmental stages (15 and 25 DAP). A total of 803 non-redundant proteins were identified. Most of them were involved in key processes associated with pericarp development and thickening. Two candidate proteins stood out among the differentially abundant proteins. Peroxidase was up-accumulated in P11/25 DAP (high popping expansion) and was 1.498 times more abundant in this inbred line, while xyloglucan endotransglucosylase/hydrolase was more abundant in P16 (low popping expansion) in both developmental stages. Thus, the peroxidase protein increases expandability, whereas xyloglucan endotransglucosylase/hydrolase decreases it, even though its specific role has not been elucidated. These proteins should be further investigated, as they may be used to improve expansion capacity in popcorn breeding programs.

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“…To minimize cross-contamination, two blank injections were run before analyzing each biological replicate (i.e., different gel lanes). Proteins were identified by the peptide-spectrum matching (PSM) approach, using the PatternLab for Proteomics V (PLV) search and filtering algorithm [ 40 ] and a database containing the following sequences: (1) t-PA signal peptide + NS1 protein (DENV2-New Guinea strain. Both sequences were separated by the two amino acid residues coded by the restriction site used for cloning); (2) t-PA signal peptide + the first 80% amino acid residues of the envelope protein (DENV2–New Guinea strain.…”

Section: Methodsmentioning

confidence: 99%

Combination of E- and NS1-Derived DNA Vaccines: The Immune Response and Protection Elicited in Mice against DENV2

Pinto

Azamor

Lima

et al. 2022

Viruses

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The occurrence of dengue disease has increased radically in recent decades. Previously, we constructed the pE1D2 and pcTPANS1 DNA vaccines encoding the DENV2 envelope (E) and non-structural 1 (NS1) proteins, respectively. To decrease the number of plasmids in a tetravalent candidate vaccine, we constructed a bicistronic plasmid, pNS1/E/D2, encoding these two proteins simultaneously. We evaluated the protective immunity induced in mice vaccinated with the pNS1/E/D2 candidate and compared to the responses elicited by immunization with the former vaccines isolated or in combination. We transfected BHK-21 cells with the different plasmids and detected recombinant proteins by immunofluorescence and mass spectrometry assays to confirm antigen expression. BALB/c mice were inoculated with the DNA vaccines followed by a lethal DENV2 challenge. ELISA, PRNT50, and IFN-gamma ELISPOT assays were performed for the investigation of the humoral and cellular responses. We observed the concomitant expression of NS1 and E proteins in pNS1/E/D2-transfected cells. All E-based vaccines induced anti-E and neutralizing antibodies. However, anti-NS1 antibodies were only observed after immunization with the pcTPANS1 administered alone or combined with pE1D2. In contrast, splenocytes from pNS1/E/D2- or pcTPANS1 + pE1D2-vaccinated animals responded to NS1- and E-derived synthetic peptides. All the DNA vaccines conferred protection against DENV2.

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Simple, efficient and thorough shotgun proteomic analysis with PatternLab V

Cited by 33 publications

References 58 publications

Insights from a Multi-Omics Integration (MOI) Study in Oil Palm (Elaeis guineensis Jacq.) Response to Abiotic Stresses: Part One—Salinity

Insights from a Multi-Omics Integration (MOI) Study in Oil Palm (Elaeis guineensis Jacq.) Response to Abiotic Stresses: Part One—Salinity

Candidate proteins associated with popping expansion capacity of popcorn

Combination of E- and NS1-Derived DNA Vaccines: The Immune Response and Protection Elicited in Mice against DENV2

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