Biochemical Mapping of Pyrodinium bahamense Unveils Molecular Underpinnings behind Organismal Processes

Proteins, lipids, and carbohydrates from the harmful algal bloom (HAB)-causing organism Pyrodinium bahamense were characterized to obtain insights into the biochemical processes in this environmentally relevant dinoflagellate. Shotgun proteomics using label-free quantitation followed by proteome mapping using the P. bahamense transcriptome and translated protein databases of Marinovum algicola, Alexandrium sp., Cylindrospermopsis raciborskii, and Symbiodinium kawagutii for annotation enabled the characterization of the proteins in P. bahamense. The highest number of annotated hits were obtained from M. algicola and highlighted the contribution of microorganisms associated with P. bahamense. Proteins involved in dimethylsulfoniopropionate (DMSP) degradation such as propionyl CoA synthethase and acryloyl-CoA reductase were identified, suggesting the DMSP cleavage pathway as the preferred route in this dinoflagellate. Most of the annotated proteins were involved in amino acid biosynthesis and carbohydrate degradation and metabolism, indicating the active roles of these molecules in the vegetative stage of P. bahamense. This characterization provides baseline information on the cellular machinery and the molecular basis of the ecophysiology of P. bahamense.

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Growth Phase-Dependent Proteomes of the Malaysian IsolatedLactococcus lactisDairy Strain M4 Using Label-Free Qualitative Shotgun Proteomics Analysis

The Scientific World JOURNAL ◽

10.1155/2014/642891 ◽

2014 ◽

Vol 2014 ◽

pp. 1-14 ◽

Cited By ~ 3

Author(s):

Theresa Wan Chen Yap ◽

Amir Rabu ◽

Farah Diba Abu Bakar ◽

Raha Abdul Rahim ◽

Nor Muhammad Mahadi ◽

...

Keyword(s):

Stationary Phase ◽

Shotgun Proteomics ◽

Exponential Phase ◽

Metabolic Energy ◽

Cell Factory ◽

Label Free ◽

Growth Phases ◽

Sufficient Energy ◽

A Cell ◽

Cellular Machinery

Lactococcus lactisis the most studied mesophilic fermentative lactic acid bacterium. It is used extensively in the food industry and plays a pivotal role as a cell factory and also as vaccine delivery platforms. The proteome of the Malaysian isolatedL. lactisM4 dairy strain, obtained from the milk of locally bred cows, was studied to elucidate the physiological changes occurring between the growth phases of this bacterium. In this study, ultraperformance liquid chromatography nanoflow electrospray ionization tandem mass spectrometry (UPLC- nano-ESI-MSE) approach was used for qualitative proteomic analysis. A total of 100 and 121 proteins were identified from the midexponential and early stationary growth phases, respectively, of theL. lactisstrain M4. During the exponential phase, the most important reaction was the generation of sufficient energy, whereas, in the early stationary phase, the metabolic energy pathways decreased and the biosynthesis of proteins became more important. Thus, the metabolism of the cells shifted from energy production in the exponential phase to the synthesis of macromolecules in the stationary phase. The resultant proteomes are essential in providing an improved view of the cellular machinery ofL. lactisduring the transition of growth phases and hence provide insight into various biotechnological applications.

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sxtA4+ and sxtA4- Genotypes Occur Together within Natural Pyrodinium bahamense Sub-Populations from the Western Atlantic

Microorganisms ◽

10.3390/microorganisms9061128 ◽

2021 ◽

Vol 9 (6) ◽

pp. 1128

Author(s):

Kathleen Cusick ◽

Gabriel Duran

Keyword(s):

Molecular Mechanisms ◽

Harmful Algal Bloom ◽

Single Cells ◽

Natural Populations ◽

Indian River Lagoon ◽

Toxin Production ◽

Genotype Frequency ◽

Rrna Gene ◽

Western Atlantic ◽

Pyrodinium Bahamense

Saxitoxin (STX) is a secondary metabolite and potent neurotoxin produced by several genera of harmful algal bloom (HAB) marine dinoflagellates. The basis for variability in STX production within natural bloom populations is undefined as both toxic and non-toxic strains (of the same species) have been isolated from the same geographic locations. Pyrodinium bahamense is a STX-producing bioluminescent dinoflagellate that blooms along the east coast of Florida as well as the bioluminescent bays in Puerto Rico (PR), though no toxicity reports exist for PR populations. The core genes in the dinoflagellate STX biosynthetic pathway have been identified, and the sxtA4 gene is essential for toxin production. Using sxtA4 as a molecular proxy for the genetic capacity of STX production, we examined sxtA4+ and sxtA4- genotype frequency at the single cell level in P. bahamense populations from different locations in the Indian River Lagoon (IRL), FL, and Mosquito Bay (MB), a bioluminescent bay in PR. Multiplex PCR was performed on individual cells with Pyrodinium-specific primers targeting the 18S rRNA gene and sxtA4. The results reveal that within discrete natural populations of P. bahamense, both sxtA4+ and sxtA4- genotypes occur, and the sxtA4+ genotype dominates. In the IRL, the frequency of the sxtA4+ genotype ranged from ca. 80–100%. In MB, sxtA4+ genotype frequency ranged from ca 40–66%. To assess the extent of sxtA4 variation within individual cells, sxtA4 amplicons from single cells representative of the different sampling sites were cloned and sequenced. Overall, two variants were consistently obtained, one of which is likely a pseudogene based on alignment with cDNA sequences. These are the first data demonstrating the existence of both genotypes in natural P. bahamense sub-populations, as well as sxtA4 presence in P. bahamense from PR. These results provide insights on underlying genetic factors influencing the potential for toxin variability among natural sub-populations of HAB species and highlight the need to study the genetic diversity within HAB sub-populations at a fine level in order to identify the molecular mechanisms driving HAB evolution.

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Analysis of the Barley Malt Rootlet Proteome

International Journal of Molecular Sciences ◽

10.3390/ijms21010179 ◽

2019 ◽

Vol 21 (1) ◽

pp. 179 ◽

Cited By ~ 2

Author(s):

Ramamurthy Mahalingam

Keyword(s):

Animal Feed ◽

Protein Biosynthesis ◽

In Silico Analysis ◽

Shotgun Proteomics ◽

Label Free ◽

High Coverage ◽

Barley Malt ◽

Naturally Occurring ◽

Two Stages ◽

Silico Analysis

Barley seeds are one of the main ingredients of the malting industry for brewing beer. The barley rootlets that are separated from the kilned seeds at the end of the malting process and used as animal feed are one of the byproducts of this industry. In this study, the proteome of rootlets derived from two stages of the malting process, germination and kilning, from a popular malting barley variety were analyzed. A label-free shotgun proteomics strategy was used to identify more than 800 proteins from the barley rootlets. A high coverage and high confidence Gene Ontology annotations of the barley genome was used to facilitate the functional annotation of the proteins that were identified in the rootlets. An analysis of these proteins using Kellogg Encyclopedia of Genes and Genomes (KEGG) and Plant Reactome databases indicated the enrichment of pathways associated with phytohormones, protein biosynthesis, secondary metabolism, and antioxidants. Increased levels of jasmonic acid and auxin in the rootlets further supported the in silico analysis. As a rich source of proteins and amino acids use of these by-products of the malting industry for animal feed is validated. This study also indicates rootlets as a potential source of naturally occurring phenylpropanoids and antioxidants that can be further exploited in the development of functional foods.

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Proteomics in Diagnosis of Prostate Cancer/ Протеомика Во Дијагноза На Простатниот Карцином

PRILOZI ◽

10.1515/prilozi-2015-0027 ◽

2015 ◽

Vol 36 (1) ◽

pp. 5-36 ◽

Cited By ~ 3

Author(s):

Katarina Davalieva ◽

Momir Polenakovic

Keyword(s):

Prostate Cancer ◽

Tumor Tissue ◽

Biomarker Discovery ◽

Molecular Level ◽

Specific Antigen ◽

Shotgun Proteomics ◽

Comparative Proteomics ◽

Label Free ◽

The Past ◽

Proteomics Research

Abstract Prostate cancer (PCa) is the second most frequently diagnosed malignancy in men worldwide. The introduction of prostate specific antigen (PSA) has greatly increased the number of men diagnosed with PCa but at the same time, as a result of the low specificity, led to overdiagnosis, resulting to unnecessary biopsies and high medical cost treatments. The primary goal in PCa research today is to find a biomarker or biomarker set for clear and effecttive diagnosis of PCa as well as for distinction between aggressive and indolent cancers. Different proteomic technologies such as 2-D PAGE, 2-D DIGE, MALDI MS profiling, shotgun proteomics with label-based (ICAT, iTRAQ) and label-free (SWATH) quantification, MudPIT, CE-MS have been applied to the study of PCa in the past 15 years. Various biological samples, including tumor tissue, serum, plasma, urine, seminal plasma, prostatic secretions and prostatic-derived exosomes were analyzed with the aim of identifying diagnostic and prognostic biomarkers and developing a deeper understanding of the disease at the molecular level. This review is focused on the overall analysis of expression proteomics studies in the PCa field investigating all types of human samples in the search for diagnostics biomarkers. Emphasis is given on proteomics platforms used in biomarker discovery and characterization, explored sources for PCa biomarkers, proposed candidate biomarkers by comparative proteomics studies and the possible future clinical application of those candidate biomarkers in PCa screening and diagnosis. In addition, we review the specificity of the putative markers and existing challenges in the proteomics research of PCa.

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Peptide-level Robust Ridge Regression Improves Estimation, Sensitivity, and Specificity in Data-dependent Quantitative Label-free Shotgun Proteomics

Molecular & Cellular Proteomics ◽

10.1074/mcp.m115.055897 ◽

2015 ◽

Vol 15 (2) ◽

pp. 657-668 ◽

Cited By ~ 33

Author(s):

Ludger J. E. Goeminne ◽

Kris Gevaert ◽

Lieven Clement

Keyword(s):

Sensitivity And Specificity ◽

Ridge Regression ◽

Shotgun Proteomics ◽

Label Free ◽

Peptide Level

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Proteomic changes in the milk of water buffaloes (Bubalus bubalis) with subclinical mastitis due to intramammary infection by Staphylococcus aureus and by non-aureus staphylococci

Scientific Reports ◽

10.1038/s41598-019-52063-2 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 8

Author(s):

Salvatore Pisanu ◽

Carla Cacciotto ◽

Daniela Pagnozzi ◽

Giulia Maria Grazia Puggioni ◽

Sergio Uzzau ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Shotgun Proteomics ◽

Subclinical Mastitis ◽

Bubalus Bubalis ◽

Buffalo Milk ◽

Label Free ◽

Western Immunoblotting ◽

Differential Proteins ◽

Culture Negative ◽

Protein Dataset

Abstract Subclinical mastitis by Staphylococcus aureus (SAU) and by non-aureus staphylococci (NAS) is a major issue in the water buffalo. To understand its impact on milk, 6 quarter samples with >3,000,000 cells/mL (3 SAU-positive and 3 NAS-positive) and 6 culture-negative quarter samples with <50,000 cells/mL were investigated by shotgun proteomics and label-free quantitation. A total of 1530 proteins were identified, of which 152 were significantly changed. SAU was more impacting, with 162 vs 127 differential proteins and higher abundance changes (P < 0.0005). The 119 increased proteins had mostly structural (n = 43, 28.29%) or innate immune defence functions (n = 39, 25.66%) and included vimentin, cathelicidins, histones, S100 and neutrophil granule proteins, haptoglobin, and lysozyme. The 33 decreased proteins were mainly involved in lipid metabolism (n = 13, 59.10%) and included butyrophilin, xanthine dehydrogenase/oxidase, and lipid biosynthetic enzymes. The same biological processes were significantly affected also upon STRING analysis. Cathelicidins were the most increased family, as confirmed by western immunoblotting, with a stronger reactivity in SAU mastitis. S100A8 and haptoglobin were also validated by western immunoblotting. In conclusion, we generated a detailed buffalo milk protein dataset and defined the changes occurring in SAU and NAS mastitis, with potential for improving detection (ProteomeXchange identifier PXD012355).

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Naturally Produced Lovastatin Modifies the Histology and Proteome Profile of Goat Skeletal Muscle

Animals ◽

10.3390/ani10010072 ◽

2019 ◽

Vol 10 (1) ◽

pp. 72

Author(s):

Teik Kee Leo ◽

Sani Garba ◽

Danmaigoro Abubakar ◽

Awis Qurni Sazili ◽

Su Chui Len Candyrine ◽

...

Keyword(s):

Skeletal Muscle ◽

Expression Patterns ◽

Daily Intake ◽

Palm Kernel ◽

Label Free ◽

Intact Male ◽

Treatment Groups ◽

Biochemical Processes ◽

Development Processes ◽

Proteome Profile

This study was conducted to examine the effects of different levels of lovastatin on the histological and sarcoplasmic proteome profile of goat skeletal muscle. A total of 20 intact male Saanen goats were randomly assigned in equal numbers to four groups and fed a total mixed ration containing 50% rice straw, 22.8% concentrates and 27.2% of various proportions of untreated or treated palm kernel cake (PKC) to achieve the target daily intake levels of 0 (Control), 2 (Low), 4 (Medium) or 6 (High) mg lovastatin/kg BW. A histological examination discovered that the longissimus thoracis et lumborum muscle of animals from the Medium and High treatment groups showed abnormalities in terms of necrosis, degeneration, interstitial space and vacuolization. Our preliminary label-free proteomics analysis demonstrates that lovastatin supplementation induced complex modifications to the protein expression patterns of the skeletal muscle of the goat which were associated with the metabolism of carbohydrate and creatine, cell growth and development processes and other metabolic processes. The changes in these biochemical processes indicate perturbations in energy metabolism, which could play a major role in the development of myopathy. In conclusion, the present study suggests that supplementation of naturally produced lovastatin above 4 mg/kg BW could adversely affecting the health and wellbeing of treated animals.

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Characterization of the MDSC Proteome Associated with Metastatic Murine Mammary Tumors Using Label-Free Mass Spectrometry and Shotgun Proteomics

PLoS ONE ◽

10.1371/journal.pone.0022446 ◽

2011 ◽

Vol 6 (8) ◽

pp. e22446 ◽

Cited By ~ 21

Author(s):

Angela M. Boutté ◽

W. Hayes McDonald ◽

Yu Shyr ◽

Li Yang ◽

P. Charles Lin

Keyword(s):

Mass Spectrometry ◽

Shotgun Proteomics ◽

Mammary Tumors ◽

Label Free

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Staphylococcus aureus Induces Hypoxia and Cellular Damage in Porcine Dermal Explants

Infection and Immunity ◽

10.1128/iai.03075-14 ◽

2015 ◽

Vol 83 (6) ◽

pp. 2531-2541 ◽

Cited By ~ 27

Author(s):

Abdul G. Lone ◽

Erhan Atci ◽

Ryan Renslow ◽

Haluk Beyenal ◽

Susan Noh ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Cell Death ◽

Effective Diffusion ◽

Oxygen Demand ◽

Shotgun Proteomics ◽

Cellular Damage ◽

Label Free ◽

Content Type ◽

Dermal Tissue ◽

The Difference

We developed a porcine dermal explant model to determine the extent to whichStaphylococcus aureusbiofilm communities deplete oxygen, change pH, and produce damage in underlying tissue. Microelectrode measurements demonstrated that dissolved oxygen (DO) in biofilm-free dermal tissue was 4.45 ± 1.17 mg/liter, while DO levels for biofilm-infected tissue declined sharply from the surface, with no measurable oxygen detectable in the underlying dermal tissue. Magnetic resonance imaging demonstrated that biofilm-free dermal tissue had a significantly lower relative effective diffusion coefficient (0.26 ± 0.09 to 0.30 ± 0.12) than biofilm-infected dermal tissue (0.40 ± 0.12 to 0.48 ± 0.12;P< 0.0001). Thus, the difference in DO level was attributable to biofilm-induced oxygen demand rather than changes in oxygen diffusivity. Microelectrode measures showed that pH within biofilm-infected explants was more alkaline than in biofilm-free explants (8.0 ± 0.17 versus 7.5 ± 0.15, respectively;P< 0.002). Cellular and nuclear details were lost in the infected explants, consistent with cell death. Quantitative label-free shotgun proteomics demonstrated that both proapoptotic programmed cell death protein 5 and antiapoptotic macrophage migration inhibitory factor accumulated in the infected-explant spent medium, compared with uninfected-explant spent media (1,351-fold and 58-fold, respectively), consistent with the cooccurrence of apoptosis and necrosis in the explants. Biofilm-origin proteins reflected an extracellular matrix-adapted lifestyle ofS. aureus. S. aureusbiofilms deplete oxygen, increase pH, and induce cell death, all factors that contribute to impede wound healing.

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