Proteomes

17 pages, 3013 KiB

Open AccessArticle

Comparative Proteomic Analysis Unveils Critical Pathways Underlying the Role of Nitrogen Fertilizer Treatment in American Elderberry

by Bo Yang, Andrew L. Thomas and C. Michael Greenlief

Proteomes 2019, 7(1), 10; https://doi.org/10.3390/proteomes7010010 - 20 Mar 2019

Cited by 1 | Viewed by 4315

Abstract

American elderberry (Sambucus nigra subsp. canadensis) is a rapidly growing specialty crop in Missouri and eastern North America. Nitrogen (N) is a major nutrient involved in plant growth and development. However, proteome changes for different genotypes of elder in response to [...] Read more.

American elderberry (Sambucus nigra subsp. canadensis) is a rapidly growing specialty crop in Missouri and eastern North America. Nitrogen (N) is a major nutrient involved in plant growth and development. However, proteome changes for different genotypes of elder in response to varying levels of N-treatment remain undefined. To reveal plant responses to N, comparative proteomic analyses were performed to determine consistent changes in three genotypes of elderberry leaves (Adams II, Bob Gordon and Wyldewood) grown under different N-fertilizer treatments. 165 proteins separated by two dimensional gel electrophoresis showed significant differences in abundance (p < 0.05 and greater than 2-fold). Principal component analysis of the abundance profiles of these proteins revealed Bob Gordon as a distinct genotype. The 165 proteins were identified by mass spectrometry and showed similar functional distributions in these genotypes underlying the N-treatment. Among the proteins identified, 23 are mainly involved in photosynthesis, protein metabolism and redox homeostasis. Their abundance profiles were not altered upon exposure to N or genotype. These results provide novel insights into plant responses to fertilizer treatment at the proteome level and could lead to a better understanding of molecular mechanisms of elderberry growth. Full article

► Show Figures

Graphical abstract

3 pages, 141 KiB

Open AccessEditorial

Editorial for Special Issue: Metaproteomics

by Jana Seifert and Thilo Muth

Proteomes 2019, 7(1), 9; https://doi.org/10.3390/proteomes7010009 - 05 Mar 2019

Cited by 2 | Viewed by 3334

Abstract

As the proteome-level counterpart of metagenomics, metaproteomics extends conventional single-organism proteomics and allows researchers to characterize the entire protein complement of complex microbiomes on a large scale [...] Full article

(This article belongs to the Special Issue Metaproteomics)

15 pages, 4673 KiB

Open AccessArticle

Comparative Proteome-Wide Analysis of Bone Marrow Microenvironment of β-Thalassemia/Hemoglobin E

by Saranyoo Ponnikorn, Rungrawee Mongkolrob, Suwit Klongthalay, Sittiruk Roytrakul, Kitima Srisanga, Sumalee Tungpradabkul and Suradej Hongeng

Proteomes 2019, 7(1), 8; https://doi.org/10.3390/proteomes7010008 - 23 Feb 2019

Cited by 6 | Viewed by 3715

Abstract

β-thalassemia/Hb E is a global health issue, which is characterized by a range of clinical symptoms from a mild and asymptomatic anemia to severe disorders that require transfusions from infancy. Pathological mechanisms of the disease involve the excess of unmatched alpha globin and [...] Read more.

β-thalassemia/Hb E is a global health issue, which is characterized by a range of clinical symptoms from a mild and asymptomatic anemia to severe disorders that require transfusions from infancy. Pathological mechanisms of the disease involve the excess of unmatched alpha globin and iron overload, leading to ineffective erythropoiesis and ultimately to the premature death of erythroid precursors in bone marrow (BM) and peripheral organs. However, it is unclear as to how BM microenvironment factors contribute to the defective erythropoiesis in β-thalassemia/Hb E patients. Here, we employed mass spectrometry-based comparative proteomics to analyze BM plasma that was collected from six β-thalassemia/Hb E patients and four healthy donors. We identified that the differentially expressed proteins are enriched in secretory or exosome-associated proteins, many of which have putative functions in the oxidative stress response. Using Western blot assay, we confirmed that atypical lipoprotein, Apolipoprotein D (APOD), belonging to the Lipocalin transporter superfamily, was significantly decreased in BM plasma of the tested pediatric β-thalassemia/Hb E patients. Our results highlight that the disease condition of ineffective erythropoiesis and oxidative stress found in BM microenvironment of β-thalassemia/Hb E patients is associated with the impaired expression of APOD protein. Full article

► Show Figures

Figure 1

1 pages, 139 KiB

Open AccessCorrection

Correction: Baucum II, Anthony J. et al. Proteomic Analysis of the Spinophilin Interactome in Rodent Striatum Following Psychostimulant Sensitization. Proteomes 2018, 6, 53

by Darryl S. Watkins, Jason D. True, Amber L. Mosley and Anthony J. Baucum

Proteomes 2019, 7(1), 7; https://doi.org/10.3390/proteomes7010007 - 13 Feb 2019

Cited by 1 | Viewed by 2243

Abstract

The author wishes to make the following corrections to the methods section of their paper [...] Full article

(This article belongs to the Special Issue Neuroproteomics)

18 pages, 1280 KiB

Open AccessArticle

A Novel Analysis of the Peptide Terminome Characterizes Dynamics of Proteolytic Regulation in Vertebrate Skeletal Muscle Under Severe Stress

by Yuri Kominami, Tatsuya Hayashi, Tetsuji Tokihiro and Hideki Ushio

Proteomes 2019, 7(1), 6; https://doi.org/10.3390/proteomes7010006 - 13 Feb 2019

Cited by 2 | Viewed by 3182

Abstract

In healthy cells, proteolysis is orderly executed to maintain basal homeostasis and normal physiology. Dyscontrol in proteolysis under severe stress condition induces cell death, but the dynamics of proteolytic regulation towards the critical phase remain unclear. Teleosts have been suggested an alternative model [...] Read more.

In healthy cells, proteolysis is orderly executed to maintain basal homeostasis and normal physiology. Dyscontrol in proteolysis under severe stress condition induces cell death, but the dynamics of proteolytic regulation towards the critical phase remain unclear. Teleosts have been suggested an alternative model for the study of proteolysis under severe stress. In this study, horse mackerel (Trachurus japonicus) was used and exacerbated under severe stress conditions due to air exposure. Although the complete genome for T. japonicus is not available, a transcriptomic analysis was performed to construct a reference protein database, and the expression of 72 proteases were confirmed. Quantitative peptidomic analysis revealed that proteins related to glycolysis and muscle contraction systems were highly cleaved into peptides immediately under the severe stress. Novel analysis of the peptide terminome using a multiple linear regression model demonstrated profiles of proteolysis under severe stress. The results indicated a phase transition towards dyscontrol in proteolysis in T. japonicus skeletal muscle during air exposure. Our novel approach will aid in investigating the dynamics of proteolytic regulation in skeletal muscle of non-model vertebrates. Full article

► Show Figures

Graphical abstract

17 pages, 12351 KiB

Open AccessArticle

Sex-Specific Proteomic Changes Induced by Genetic Deletion of Fibroblast Growth Factor 14 (FGF14), a Regulator of Neuronal Ion Channels

by Mark L. Sowers, Jessica Di Re, Paul A. Wadsworth, Alexander S. Shavkunov, Cheryl Lichti, Kangling Zhang and Fernanda Laezza

Proteomes 2019, 7(1), 5; https://doi.org/10.3390/proteomes7010005 - 23 Jan 2019

Cited by 9 | Viewed by 4973

Abstract

Fibroblast growth factor 14 (FGF14) is a member of the intracellular FGFs, which is a group of proteins involved in neuronal ion channel regulation and synaptic transmission. We previously demonstrated that male Fgf14^−/− mice recapitulate the salient endophenotypes of synaptic dysfunction and [...] Read more.

Fibroblast growth factor 14 (FGF14) is a member of the intracellular FGFs, which is a group of proteins involved in neuronal ion channel regulation and synaptic transmission. We previously demonstrated that male Fgf14^−/− mice recapitulate the salient endophenotypes of synaptic dysfunction and behaviors that are associated with schizophrenia (SZ). As the underlying etiology of SZ and its sex-specific onset remain elusive, the Fgf14^−/− model may provide a valuable tool to interrogate pathways related to disease mechanisms. Here, we performed label-free quantitative proteomics to identify enriched pathways in both male and female hippocampi from Fgf14^+/+ and Fgf14^−/− mice. We discovered that all of the differentially expressed proteins measured in Fgf14^−/− animals, relative to their same-sex wildtype counterparts, are associated with SZ based on genome-wide association data. In addition, measured changes in the proteome were predominantly sex-specific, with the male Fgf14^−/− mice distinctly enriched for pathways associated with neuropsychiatric disorders. In the male Fgf14^−/− mouse, we found molecular characteristics that, in part, may explain a previously described neurotransmission and behavioral phenotype. This includes decreased levels of ALDH1A1 and protein kinase A (PRKAR2B). ALDH1A1 has been shown to mediate an alternative pathway for gamma-aminobutyric acid (GABA) synthesis, while PRKAR2B is essential for dopamine 2 receptor signaling, which is the basis of current antipsychotics. Collectively, our results provide new insights in the role of FGF14 and support the use of the Fgf14^−/− mouse as a useful preclinical model of SZ for generating hypotheses on disease mechanisms, sex-specific manifestation, and therapy. Full article

(This article belongs to the Special Issue Neuroproteomics)

► Show Figures

Figure 1

15 pages, 2515 KiB

Open AccessFeature PaperArticle

Analysis of the Bacterial and Host Proteins along and across the Porcine Gastrointestinal Tract

by Johanna Tröscher-Mußotter, Bruno Tilocca, Volker Stefanski and Jana Seifert

Proteomes 2019, 7(1), 4; https://doi.org/10.3390/proteomes7010004 - 10 Jan 2019

Cited by 22 | Viewed by 4155

Abstract

Pigs are among the most important farm animals worldwide and research to optimize their feed efficiency and improve their welfare is still in progress. The porcine intestinal microbiome is so far mainly known from sequencing-based studies. Digesta and mucosa samples from five different [...] Read more.

Pigs are among the most important farm animals worldwide and research to optimize their feed efficiency and improve their welfare is still in progress. The porcine intestinal microbiome is so far mainly known from sequencing-based studies. Digesta and mucosa samples from five different porcine gastrointestinal tract sections were analyzed by metaproteomics to obtain a deeper insight into the functions of bacterial groups with concomitant analyses of host proteins. Firmicutes (Prevotellaceae) dominated mucosa and digesta samples, followed by Bacteroidetes. Actinobacteria and Proteobacteria were much higher in abundance in mucosa compared to digesta samples. Functional profiling reveals the presence of core functions shared between digesta and mucosa samples. Protein abundances of energy production and conversion were higher in mucosa samples, whereas in digesta samples more proteins were involved in lipid transport and metabolism; short-chain fatty acids production were detected. Differences were also highlighted between sections, with the small intestine appearing more involved in carbohydrate transport and metabolism than the large intestine. Thus, this study produced the first functional analyses of the porcine GIT biology, discussing the findings in relation to expected bacterial and host functions. Full article

(This article belongs to the Special Issue Metaproteomics)

► Show Figures

Figure 1

2 pages, 209 KiB

Open AccessEditorial

Acknowledgement to Reviewers of Proteomes in 2018

by Proteomes Editorial Office

Proteomes 2019, 7(1), 3; https://doi.org/10.3390/proteomes7010003 - 08 Jan 2019

Viewed by 1830

Abstract

Rigorous peer-review is the corner-stone of high-quality academic publishing [...] Full article

19 pages, 4993 KiB

Open AccessArticle

Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae

by Julia Rechenberger, Patroklos Samaras, Anna Jarzab, Juergen Behr, Martin Frejno, Ana Djukovic, Jaime Sanz, Eva M. González-Barberá, Miguel Salavert, Jose Luis López-Hontangas, Karina B. Xavier, Laurent Debrauwer, Jean-Marc Rolain, Miguel Sanz, Marc Garcia-Garcera, Mathias Wilhelm, Carles Ubeda and Bernhard Kuster

Proteomes 2019, 7(1), 2; https://doi.org/10.3390/proteomes7010002 - 08 Jan 2019

Cited by 40 | Viewed by 6278

Abstract

The microbiome has a strong impact on human health and disease and is, therefore, increasingly studied in a clinical context. Metaproteomics is also attracting considerable attention, and such data can be efficiently generated today owing to improvements in mass spectrometry-based proteomics. As we [...] Read more.

The microbiome has a strong impact on human health and disease and is, therefore, increasingly studied in a clinical context. Metaproteomics is also attracting considerable attention, and such data can be efficiently generated today owing to improvements in mass spectrometry-based proteomics. As we will discuss in this study, there are still major challenges notably in data analysis that need to be overcome. Here, we analyzed 212 fecal samples from 56 hospitalized acute leukemia patients with multidrug-resistant Enterobactericeae (MRE) gut colonization using metagenomics and metaproteomics. This is one of the largest clinical metaproteomic studies to date, and the first metaproteomic study addressing the gut microbiome in MRE colonized acute leukemia patients. Based on this substantial data set, we discuss major current limitations in clinical metaproteomic data analysis to provide guidance to researchers in the field. Notably, the results show that public metagenome databases are incomplete and that sample-specific metagenomes improve results. Furthermore, biological variation is tremendous which challenges clinical study designs and argues that longitudinal measurements of individual patients are a valuable future addition to the analysis of patient cohorts. Full article

(This article belongs to the Special Issue Metaproteomics)

► Show Figures

Figure 1

10 pages, 962 KiB

Open AccessCommunication

Proteomic Profiling of Primary Human Acute Myeloid Leukemia Cells Does Not Reflect Their Constitutive Release of Soluble Mediators

by Elise Aasebø, Maria Hernandez-Valladares, Frode Selheim, Frode S. Berven, Annette K. Brenner and Øystein Bruserud

Proteomes 2019, 7(1), 1; https://doi.org/10.3390/proteomes7010001 - 20 Dec 2018

Cited by 8 | Viewed by 2762

Abstract

Acute myeloid leukemia (AML) is a heterogeneous disease, and communication between leukemic cells and their neighboring leukemia-supporting normal cells is involved in leukemogenesis. The bone marrow cytokine network is therefore important, and the mediator release profile seems more important than single mediators. It [...] Read more.

Acute myeloid leukemia (AML) is a heterogeneous disease, and communication between leukemic cells and their neighboring leukemia-supporting normal cells is involved in leukemogenesis. The bone marrow cytokine network is therefore important, and the mediator release profile seems more important than single mediators. It is not known whether the characterization of primary AML cell proteomes reflects the heterogeneity of the broad and dynamic constitutive mediator release profile by these cells. To address this, we compared the intracellular levels of 41 proteins in 19 AML patients with the constitutive extracellular release during in vitro culture, including chemokines, growth factors, proteases, and protease regulators. The constitutive release of most mediators showed a wide variation (up to 2000-fold differences) between patients. Detectable intracellular levels were seen for 10 of 41 mediators, but for most of these 10 mediators we could not detect significant correlations between the constitutive release during in vitro culture and their intracellular levels. Intracellular protein levels in primary human AML cells do not reflect the dynamics, capacity, and variation between patients in constitutive mediator release profiles. Measurements of these profiles thus add complementary information to proteomic detection/quantification regarding the heterogeneity of the AML cell contributions to the bone marrow cytokine network. Full article

(This article belongs to the Special Issue Cancer Proteomics 2018)

► Show Figures

Graphical abstract

Journal Menu

Journal Browser

Proteomes, Volume 7, Issue 1 (March 2019) – 10 articles

Further Information

Guidelines

MDPI Initiatives

Follow MDPI