Proteomic analysis of oilseed cake: a comparative study of species‐specific proteins and peptides extracted from ten seed species

2020 ◽  
Vol 101 (1) ◽  
pp. 297-306 ◽  
Author(s):  
Klaudia Kotecka‐Majchrzak ◽  
Agata Sumara ◽  
Emilia Fornal ◽  
Magdalena Montowska
Keyword(s):  
Comparative Study ◽  
Proteomic Analysis ◽  
Specific Proteins ◽  
Oilseed Cake ◽  
Species Specific ◽  
Proteins And Peptides

scholarly journals Signatures of conserved and unique molecular features in Afrotheria

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Arangasamy Yazhini ◽  
Narayanaswamy Srinivasan ◽  
Sankaran Sandhya
Keyword(s):  
Ribosomal Proteins ◽  
Individual Species ◽  
Functional Domain ◽  
Nucleic Acid Binding ◽  
Uncharacterized Protein ◽  
Homologous Proteins ◽  
Functional Roles ◽  
Molecular Features ◽  
Specific Proteins ◽  
Species Specific

AbstractAfrotheria is a clade of African-origin species with striking dissimilarities in appearance and habitat. In this study, we compared whole proteome sequences of six Afrotherian species to obtain a broad viewpoint of their underlying molecular make-up, to recognize potentially unique proteomic signatures. We find that 62% of the proteomes studied here, predominantly involved in metabolism, are orthologous, while the number of homologous proteins between individual species is as high as 99.5%. Further, we find that among Afrotheria, L. africana has several orphan proteins with 112 proteins showing < 30% sequence identity with their homologues. Rigorous sequence searches and complementary approaches were employed to annotate 156 uncharacterized protein sequences and 28 species-specific proteins. For 122 proteins we predicted potential functional roles, 43 of which we associated with protein- and nucleic-acid binding roles. Further, we analysed domain content and variations in their combinations within Afrotheria and identified 141 unique functional domain architectures, highlighting proteins with potential for specialized functions. Finally, we discuss the potential relevance of highly represented protein families such as MAGE-B2, olfactory receptor and ribosomal proteins in L. africana and E. edwardii, respectively. Taken together, our study reports the first comparative study of the Afrotherian proteomes and highlights salient molecular features.

scholarly journals Multispecies Identification of Oilseed- and Meat-Specific Proteins and Heat-Stable Peptide Markers in Food Products

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1577
Author(s):  
Klaudia Kotecka-Majchrzak ◽  
Natalia Kasałka-Czarna ◽  
Agata Sumara ◽  
Emilia Fornal ◽  
Magdalena Montowska
Keyword(s):  
Limit Of Detection ◽  
Raw Materials ◽  
Meat Products ◽  
Food Products ◽  
Plant Raw Materials ◽  
Heat Stable ◽  
2S Albumins ◽  
Specific Proteins ◽  
Meat Species ◽  
Species Specific

Consumer demand for both plant products and meat products enriched with plant raw materials is constantly increasing. Therefore, new versatile and reliable methods are needed to find and combat fraudulent practices in processed foods. The objective of this study was to identify oilseed species-specific peptide markers and meat-specific markers that were resistant to processing, for multispecies authentication of different meat and vegan food products using the proteomic LC-MS/MS method. To assess the limit of detection (LOD) for hemp proteins, cooked meatballs consisting of three meat species and hemp cake at a final concentration of up to 7.4% were examined. Hemp addition at a low concentration of below 1% was detected. The LOD for edestin subunits and albumin was 0.9% (w/w), whereas for 7S vicilin-like protein it was 4.2% (w/w). Specific heat-stable peptides unique to hemp seeds, flaxseed, nigella, pumpkin, sesame, and sunflower seeds, as well as guinea fowl, rabbit, pork, and chicken meat, were detected in different meat and vegan foods. Most of the oilseed-specific peptides were identified as processing-resistant markers belonging to 11S globulin subunits, namely conlinin, edestin, helianthinin, pumpkin vicilin-like or late embryogenesis proteins, and sesame legumin-like as well as 2S albumins and oleosin isoforms or selected enzymic proteins.

THU0021 Cartilage zone specific proteins: A quantitative proteomic analysis

2013 ◽  
Vol 71 (Suppl 3) ◽  
pp. 160.3-160
Author(s):  
P. Fernández-Puente ◽  
L. Lourido ◽  
V. Calamia ◽  
J. Mateos ◽  
C. Ruiz-Romero ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Quantitative Proteomic Analysis ◽  
Specific Proteins

scholarly journals Importance of serological cross-reactivity amongToxoplasma gondii, Hammondiaspp.,Neosporaspp.,Sarcocystisspp. andBesnoitia besnoiti

Parasitology ◽  
2017 ◽  
Vol 144 (7) ◽  
pp. 851-868 ◽  
Author(s):  
LUÍS F. P. GONDIM ◽  
JOSÉ R. MINEO ◽  
GEREON SCHARES
Keyword(s):  
Toxoplasma Gondii ◽  
Neospora Caninum ◽  
Cross Reactivity ◽  
Besnoitia Besnoiti ◽  
Cross Reactions ◽  
Epidemiological Surveys ◽  
Specific Proteins ◽  
Specific Antigens ◽  
Species Specific

SUMMARYToxoplasma gondii, Neosporaspp.,Sarcocystisspp.,Hammondiaspp. andBesnoitia besnoitiare genetically related cyst-forming coccidia. Serology is frequently used for the identification ofT. gondii, Neosporaspp. andB. besnoiti-exposed individuals. Serologic cross-reactions occur in different tests among animals infected withT. gondiiandH. hammondi,as well as among animals infected byT. gondiiandN. caninum. Infections caused byN. caninumandN. hughesiare almost indistinguishable by serology.Neospora caninum, B. besnoitiandSarcocystisspp. infections in cattle show some degree of serologic cross-reactivity. Antibody cross-reactivity betweenNeosporaspp. andH. heydorni-infected animals is suspected, but not proven to occur. We review serologic cross-reactivity among animals and/or humans infected withT. gondii, Neosporaspp.,Sarcocystisspp.,Hammondiaspp. andB. besnoiti. Emphasis is laid upon antigens and serological methods forN. caninumdiagnosis which were tested for cross-reactivity with related protozoa. Species-specific antigens, as well as stage-specific proteins have been identified in some of these parasites and have promising use for diagnosis and epidemiological surveys.

scholarly journals Cryo-EM reveals new species-specific proteins and symmetry elements in the Legionella pneumophila Dot/Icm T4SS

2021 ◽  
Author(s):  
Michael J Sheedlo ◽  
Clarissa L Durie ◽  
Jeong Min Chung ◽  
Louise Chang ◽  
Michele Swanson ◽  
...  
Keyword(s):  
Legionella Pneumophila ◽  
Genetic Locus ◽  
Opportunistic Pathogen ◽  
Effector Proteins ◽  
Large Set ◽  
Type Iv ◽  
Specific Proteins ◽  
Multiple Conformations ◽  
Membrane Spanning ◽  
Species Specific

Legionella pneumophila is an opportunistic pathogen that causes the potentially fatal pneumonia known as Legionnaires’ Disease. The pathology associated with infection depends on bacterial delivery of effector proteins into the host via the membrane spanning Dot/Icm type IV secretion system (T4SS). We have determined sub-3.0 Å resolution maps of the Dot/Icm T4SS core complex by single particle cryo-EM. The high-resolution structural analysis has allowed us to identify proteins encoded outside the Dot/Icm genetic locus that contribute to the core T4SS structure. We can also now define two distinct areas of symmetry mismatch, one that connects the C18 periplasmic ring (PR) and the C13 outer membrane cap (OMC) and one that connects the C13 OMC with a 16-fold symmetric dome. Unexpectedly the connection between the PR and OMC is DotH, with five copies sandwiched between the OMC and PR to accommodate the symmetry mismatch. Finally, we observe multiple conformations in the reconstructions that indicate flexibility within the structure. We hypothesize this conformational flexibility is likely to facilitate the Dot/Icm T4SS’s ability to translocate a remarkably large set of ~300 putative substrates across the inner and outer membranes of the bacterial cell.

scholarly journals P1457COMPARISON OF PEPTIDOMES BETWEEN URINE, PLASMA, AND HEMODIALYSIS FLUID INDICATES SELECTIVITY IN RENAL PEPTIDE PROCESSING

2020 ◽  
Vol 35 (Supplement_3) ◽  
Author(s):  
Tianlin He ◽  
Julia Raad ◽  
Joachim Beige ◽  
Harald Mischak
Keyword(s):  
Mass Spectrometry ◽  
Chronic Kidney Disease ◽  
Body Fluids ◽  
Tubular Reabsorption ◽  
Artificial Kidney ◽  
Advanced Stage ◽  
Specific Proteins ◽  
Spent Dialysate ◽  
Three Body ◽  
Proteins And Peptides

Abstract Background and Aims The physiological and related body fluids, urine, plasma and hemodialysis (HD) fluid spent dialysate (a mixture of technical HD fluid and patient´s ultrafiltrate) are rich biological sources of information especially in the context of kidney diseases. Of particular relevance are proteins and peptides, as they reflect essentially every biological process. Urine is produced as a result of glomerular plasma filtration and subsequent tubular reabsorption in the kidney. In analogy, HD spent dialysate is a result of ultrafiltration by an artificial kidney (dialysis membrane), but lacking tubular reabsorption and thereby accumulating in huge amounts of &gt; 100 L per session comparable to primary urine. A recent study suggested that tubular reabsorption may be selective for specific proteins, and this process may represent a major difference between “natural” and artificial kidney. In this study, we aim at gaining insight into the composition of the peptidome/proteome in these body fluids of renal significance in a comprehensive analysis, in order to shed light on the relevant pathophysiological processes that take place in kidney, which may help developing better strategy in advanced-stage chronic kidney disease and detoxification in renal replacement therapies (RRT). Method We collected 15 plasma, 15 urine and 13 HD filtrate (spent dialysate during the first 30min of RRT) from age and sex matched subjects with stage 4 or above chronic kidney disease. Peptide identification and quantification were performed with capillary-electrophoresis coupled mass spectrometry and tandem mass spectrometry (CE-MS). The abundance, overlap and differences of the peptidome/proteome of the three body fluids were evaluated. Results We were able to detect 6281 urinary peptides, 1750 plasma peptides and 1728 peptides from spent dialysate. Of these we could identify 1764, 452 and 374 sequenced peptides, respectively Among them, there are 318 peptides detectable in both urine and spent dialysate, 307 detectable in both plasma and urine and only 191 detectable in both plasma and spent dialysate. Among the most abundant peptides in plasma were Thymosine-ß4 and fragments from hemoglobin, fibrinogen and collagen. In dialysate, the most abundant proteins detected in these patients were ß-2-microglobuline, Thymosine-ß4, and fragments from fibrinogen, while in urine fragments derived from collagen, albumin, and from alpha-1-antitrypsin were of the highest abundance. When investigating proteins/peptides found in at least 2 body fluids, a strong correlation in peptide abundance between urine and spent dialysate (P=4.2e-27, Rho=0.56), and a moderately strong correlation between HD fluid and plasma (P=3.7e-5, Rho=0.29) were detected. However, there is no significant correlation between peptide abundance in urine and plasma (P=0.22, Rho=0.07). Collagen peptides are the most abundant peptides in all three body fluids. Conclusion This dataset will serve as a valid basis to define the protein and peptide contents in blood, urine, and spent dialysate. The data show, as expected, substantial similarity between plasma and spent dialysate, but, surprisingly, very little similarity between urine and plasma. This further supports the hypothesis that tubular reabsorption may be selective for specific proteins and peptides, possibly excluding collagen-derived peptides. A more detailed investigation into the process and relevance of tubular reabsorption appears warranted in the light of the data. The fact that the samples investigated in this study are derived from advanced stage CKD patients must be taken into account, significant differences exist in comparison to urine produced by healthy kidney. The identification of molecular differences between urine and dialysate spent may present an opportunity to design future “biologically adapted” removal devices.

scholarly journals Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution

2013 ◽  
Vol 368 (1632) ◽  
pp. 20130022 ◽  
Author(s):  
Noboru Jo Sakabe ◽  
Marcelo A. Nobrega
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Expression Patterns ◽  
Dna Interaction ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Genome Wide ◽  
Identify Transcription Factor ◽  
Specific Proteins ◽  
Species Specific

The complex expression patterns observed for many genes are often regulated by distal transcription enhancers. Changes in the nucleotide sequences of enhancers may therefore lead to changes in gene expression, representing a central mechanism by which organisms evolve. With the development of the experimental technique of chromatin immunoprecipitation (ChIP), in which discrete regions of the genome bound by specific proteins can be identified, it is now possible to identify transcription factor binding events (putative cis -regulatory elements) in entire genomes. Comparing protein–DNA binding maps allows us, for the first time, to attempt to identify regulatory differences and infer global patterns of change in gene expression across species. Here, we review studies that used genome-wide ChIP to study the evolution of enhancers. The trend is one of high divergence of cis -regulatory elements between species, possibly compensated by extensive creation and loss of regulatory elements and rewiring of their target genes. We speculate on the meaning of the differences observed and discuss that although ChIP experiments identify the biochemical event of protein–DNA interaction, it cannot determine whether the event results in a biological function, and therefore more studies are required to establish the effect of divergence of binding events on species-specific gene expression.

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