scholarly journals Detecting differential protein abundance by combining peptide level P-values

2020 ◽  
Vol 16 (6) ◽  
pp. 554-562
Author(s):  
Bryan J. Killinger ◽  
Vladislav A. Petyuk ◽  
Aaron T. Wright
Keyword(s):  
Protein Abundance ◽  
P Values ◽  
Differential Protein ◽  
Peptide Level ◽  
Brown's Method ◽  
P Application ◽  
Differentially Abundant Proteins

Application of empirical Brown's method to peptide intensities from comparative LC-MS proteomics experiments accurately detects differentially abundant proteins.

Differential protein abundance during the first month of regeneration of the Caribbean star coral Montastraea cavernosa

Coral Reefs ◽  
2018 ◽  
Vol 38 (1) ◽  
pp. 45-61 ◽  
Author(s):  
Ryan A. Horricks ◽  
Christophe M. Herbinger ◽  
Brandon N. Lillie ◽  
Paul Taylor ◽  
John S. Lumsden
Keyword(s):  
Protein Abundance ◽  
Differential Protein ◽  
The Caribbean ◽  
Montastraea Cavernosa

scholarly journals Quantitative Proteomics and Differential Protein Abundance Analysis after the Depletion of PEX3 from Human Cells Identifies Additional Aspects of Protein Targeting to the ER

2021 ◽  
Vol 22 (23) ◽  
pp. 13028
Author(s):  
Richard Zimmermann ◽  
Sven Lang ◽  
Monika Lerner ◽  
Friedrich Förster ◽  
Duy Nguyen ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Protein Import ◽  
Protein Targeting ◽  
Human Cells ◽  
Protein Abundance ◽  
General Role ◽  
Differential Protein ◽  
Er Targeting ◽  
Dependent Pathway ◽  
Er Membrane

Protein import into the endoplasmic reticulum (ER) is the first step in the biogenesis of around 10,000 different soluble and membrane proteins in humans. It involves the co- or post-translational targeting of precursor polypeptides to the ER, and their subsequent membrane insertion or translocation. So far, three pathways for the ER targeting of precursor polypeptides and four pathways for the ER targeting of mRNAs have been described. Typically, these pathways deliver their substrates to the Sec61 polypeptide-conducting channel in the ER membrane. Next, the precursor polypeptides are inserted into the ER membrane or translocated into the ER lumen, which may involve auxiliary translocation components, such as the TRAP and Sec62/Sec63 complexes, or auxiliary membrane protein insertases, such as EMC and the TMCO1 complex. Recently, the PEX19/PEX3-dependent pathway, which has a well-known function in targeting and inserting various peroxisomal membrane proteins into pre-existent peroxisomal membranes, was also found to act in the targeting and, putatively, insertion of monotopic hairpin proteins into the ER. These either remain in the ER as resident ER membrane proteins, or are pinched off from the ER as components of new lipid droplets. Therefore, the question arose as to whether this pathway may play a more general role in ER protein targeting, i.e., whether it represents a fourth pathway for the ER targeting of precursor polypeptides. Thus, we addressed the client spectrum of the PEX19/PEX3-dependent pathway in both PEX3-depleted HeLa cells and PEX3-deficient Zellweger patient fibroblasts by an established approach which involved the label-free quantitative mass spectrometry of the total proteome of depleted or deficient cells, as well as differential protein abundance analysis. The negatively affected proteins included twelve peroxisomal proteins and two hairpin proteins of the ER, thus confirming two previously identified classes of putative PEX19/PEX3 clients in human cells. Interestingly, fourteen collagen-related proteins with signal peptides or N-terminal transmembrane helices belonging to the secretory pathway were also negatively affected by PEX3 deficiency, which may suggest compromised collagen biogenesis as a hitherto-unknown contributor to organ failures in the respective Zellweger patients.

Differential protein abundance associated with delayed regeneration of the scleractinian coral Montastraea cavernosa

Coral Reefs ◽  
2020 ◽  
Vol 39 (4) ◽  
pp. 1175-1186
Author(s):  
Ryan A. Horricks ◽  
Christophe M. Herbinger ◽  
Matthew K. Vickaryous ◽  
Paul Taylor ◽  
John S. Lumsden
Keyword(s):  
Scleractinian Coral ◽  
Protein Abundance ◽  
Differential Protein ◽  
Montastraea Cavernosa

Differential protein abundance in promastigotes of nitric oxide-sensitive and resistantLeishmania chagasistrains

2016 ◽  
Vol 10 (11) ◽  
pp. 1132-1146 ◽  
Author(s):  
Pedro J. Alcolea ◽  
Gabriel I. L. Tuñón ◽  
Ana Alonso ◽  
Francisco García-Tabares ◽  
Sergio Ciordia ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Protein Abundance ◽  
Differential Protein

scholarly journals Differential protein abundance and function of UT-B urea transporters in human colon

2010 ◽  
Vol 298 (3) ◽  
pp. G345-G351 ◽  
Author(s):  
D. Collins ◽  
D. C. Winter ◽  
A. M. Hogan ◽  
L. Schirmer ◽  
A. W. Baird ◽  
...  
Keyword(s):  
Intestinal Bacteria ◽  
Human Colon ◽  
Immunoblot Analysis ◽  
Cellular Level ◽  
Gut Bacteria ◽  
Protein Abundance ◽  
Urea Transport ◽  
Ascending Colon ◽  
Differential Protein ◽  
Descending Colon

Facilitative UT-B urea transporters enable the passage of urea across cell membranes. Gastrointestinal urea transporters are thought to play a significant role in the urea nitrogen salvaging process that occurs between mammalian hosts and their gut bacteria. This study investigated the expression of UT-B urea transporters in different segments of human colon. Immunoblot analysis showed that human colon expressed a 35-kDa glycosylated UT-B protein in the colonic mucosa. The 35-kDa UT-B transporter was predominantly located in plasma membrane-enriched samples ( P < 0.001; n = 6), and its expression was greater in the ascending colon compared with the descending colon ( P < 0.01; n = 3). At the cellular level, UT-B transporters were located throughout colonocytes situated in the upper portion of the colonic crypts. Bidirectional trans-epithelial urea transport was significantly greater in the ascending colon than the descending colon ( P < 0.05; n = 6). In addition, the facilitative urea transporter inhibitor 1,3,dimethylurea significantly reduced urea transport in the ascending colon ( P < 0.05; n = 6) but had no effect in the descending colon (NS; n = 6). These results illustrate differential protein abundance of functional UT-B protein in different sections of the human colon, strongly correlating to regions that contain the largest populations of intestinal bacteria. This study suggests an important role for UT-B urea transporters in maintaining the symbiotic relationship between humans and their gut bacteria.

Increased P application to lateritic soil in 1976 increased Colwell soil test P for P applied in 2000

Soil Research ◽  
2003 ◽  
Vol 41 (4) ◽  
pp. 645 ◽  
Author(s):  
M. D. A. Bolland ◽  
D. G. Allen
Keyword(s):  
Sodium Bicarbonate ◽  
Sandy Soil ◽  
Buffer Capacity ◽  
Lateritic Soil ◽  
Soil Test ◽  
P Values ◽  
Phosphate Retention ◽  
Subsequent Application ◽  
Soil Test P ◽  
P Application

In a field experiment, 6 amounts of superphosphate [0–800 kg phosphorus (P)/ha] were applied in July 2000 to an acidic lateritic ironstone gravel sandy soil treated 24 years previously (May 1976) with 6 amounts of superphosphate (0–599 kg P/ha). In October 2001, samples of the top 10 cm of soil were collected to measure the capacity of the soil to sorb P by the phosphate retention index (PRI) and P buffer capacity (PBC) methods, and to measure soil test P by the Colwell (sodium bicarbonate) procedure. The capacity of the soil to sorb P, as measured by both PRI and PBC, decreased with increased P application in 1976. For all amounts of P applied in 2000, Colwell soil test P increased with increased P application in 1976. We conclude that increasing amounts of P applied in 1976 decreased the capacity of the soil to sorb the subsequent application of P, thereby increasing soil test P values of soil treated with the subsequent P.

Identification of Putative Genes Involved in Bisphenol A Degradation Using Differential Protein Abundance Analysis of Sphingobium sp. BiD32

2015 ◽  
Vol 49 (20) ◽  
pp. 12232-12241 ◽  
Author(s):  
Nicolette A. Zhou ◽  
Henrik Kjeldal ◽  
Heidi L. Gough ◽  
Jeppe L. Nielsen
Keyword(s):  
Bisphenol A ◽  
Protein Abundance ◽  
Differential Protein

Differential protein abundance of a basolateral MCT1 transporter in the human gastrointestinal tract

2016 ◽  
Vol 40 (12) ◽  
pp. 1303-1312 ◽  
Author(s):  
Hashemeya Al-mosauwi ◽  
Elizabeth Ryan ◽  
Alison McGrane ◽  
Stefanie Riveros-Beltran ◽  
Caragh Walpole ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Protein Abundance ◽  
Human Gastrointestinal Tract ◽  
Differential Protein

scholarly journals Quantitative Proteomics and Differential Protein Abundance Analysis after Depletion of Putative mRNA Receptors in the ER Membrane of Human Cells Identifies Novel Aspects of mRNA Targeting to the ER

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3591
Author(s):  
Pratiti Bhadra ◽  
Stefan Schorr ◽  
Monika Lerner ◽  
Duy Nguyen ◽  
Johanna Dudek ◽  
...  
Keyword(s):  
Quantitative Proteomics ◽  
Secretory Pathway ◽  
Human Cells ◽  
Ribosome Profiling ◽  
Protein Abundance ◽  
Label Free ◽  
Differential Protein ◽  
Cellular Assays ◽  
Pros And Cons ◽  
Er Membrane

In human cells, one-third of all polypeptides enter the secretory pathway at the endoplasmic reticulum (ER). The specificity and efficiency of this process are guaranteed by targeting of mRNAs and/or polypeptides to the ER membrane. Cytosolic SRP and its receptor in the ER membrane facilitate the cotranslational targeting of most ribosome-nascent precursor polypeptide chain (RNC) complexes together with the respective mRNAs to the Sec61 complex in the ER membrane. Alternatively, fully synthesized precursor polypeptides are targeted to the ER membrane post-translationally by either the TRC, SND, or PEX19/3 pathway. Furthermore, there is targeting of mRNAs to the ER membrane, which does not involve SRP but involves mRNA- or RNC-binding proteins on the ER surface, such as RRBP1 or KTN1. Traditionally, the targeting reactions were studied in cell-free or cellular assays, which focus on a single precursor polypeptide and allow the conclusion of whether a certain precursor can use a certain pathway. Recently, cellular approaches such as proximity-based ribosome profiling or quantitative proteomics were employed to address the question of which precursors use certain pathways under physiological conditions. Here, we combined siRNA-mediated depletion of putative mRNA receptors in HeLa cells with label-free quantitative proteomics and differential protein abundance analysis to characterize RRBP1- or KTN1-involving precursors and to identify possible genetic interactions between the various targeting pathways. Furthermore, we discuss the possible implications on the so-called TIGER domains and critically discuss the pros and cons of this experimental approach.

scholarly journals Quantitative Proteomics and Differential Protein Abundance Analysis after Depletion of PEX3 from Human Cells Identifies Additional Aspects of Protein Targeting to the ER

2021 ◽  
Author(s):  
Richard Zimmermann ◽  
Sven Lang ◽  
Monika Lerner ◽  
Friedrich G Förster ◽  
Duy Nguyen ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Protein Import ◽  
Protein Targeting ◽  
Human Cells ◽  
Protein Abundance ◽  
General Role ◽  
Differential Protein ◽  
Er Targeting ◽  
Dependent Pathway ◽  
Er Membrane

Protein import into the endoplasmic reticulum (ER) is the first step in the biogenesis of about 10,000 different soluble and membrane proteins in humans. It involves co- or post-translational targeting of precursor polypeptides to the ER and their subsequent membrane insertion or translocation. So far, three pathways for ER targeting of precursor polypeptides plus four pathways for ER targeting of mRNAs were described. Typically, these pathways deliver their substrates to the Sec61 polypeptide-conducting channel in the ER membrane. Next, the precursor polypeptides are inserted into the ER membrane or translocated into the ER lumen, which may involve auxiliary translocation components, such as the TRAP and Sec62/Sec63 complexes, or auxiliary membrane protein insertases, such as EMC and the TMCO1 complex. Recently, the PEX19/PEX3-dependent pathway, which has a well-known function in targeting and inserting various peroxisomal membrane proteins into pre-existent peroxisomal membranes, was also found to act in targeting and, putatively, inserting monotopic hairpin proteins into the ER. These either remain in the ER as resident ER membrane proteins or are pinched off from the ER as components of new lipid droplets. Therefore, the question arose if this pathway may play a more general role in ER protein targeting, i.e. represents a fourth pathway for ER targeting of precursor polypeptides. Thus, we addressed the client spectrum of the PEX19/PEX3-dependent pathway in both PEX3-depleted HeLa cells and PEX3-deficient Zellweger patient fibroblasts by an established approach, which involves label-free quantitative mass spectrometry of the total proteome of depleted or deficient cells and differential protein abundance analysis. The negatively affected proteins included twelve peroxisomal proteins and two hairpin proteins of the ER, thus confirming two previously identified classes of putative PEX19/PEX3-clients in human cells. Interestingly, fourteen collagen-related proteins with signal peptides or N-terminal transmembrane helices and belonging to the secretory pathway were also negatively affected by PEX3-deficiency, which may suggest compromised collagen biogenesis as a hitherto unknown contributor to organ failures in the respective Zellweger patients.

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