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Teijeiro JM. Unveiling the role of protein kinase A (PKA) activity in bovine oviductal epithelial cells: implications on apoptotic signaling pathways during the estrous cycle. Cell Tissue Res 2024; 397:275-285. [PMID: 39105776 DOI: 10.1007/s00441-024-03911-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/26/2024] [Indexed: 08/07/2024]
Abstract
The complex interactome crucial for successful pregnancy is constituted by the intricate network of endocrine and paracrine signaling pathways, involving gametes, embryos, and the female reproductive tract. Specifically, the oviduct exhibits distinct responses to gametes and early embryos during particular phases of the estrus cycle, a process tightly regulated by reproductive hormones. Moreover, these hormones play a pivotal role in orchestrating cyclical changes within oviductal epithelial cells. To unravel the molecular mechanisms underlying these dynamic changes, our study aimed to investigate the involvement of protein kinase A (PKA) in oviductal epithelial cells throughout the estrus cycle and in advanced pregnancy, extending our studies to oviductal epithelial cell in primary culture. By a combination of 2D-gel electrophoresis, Western blotting, and mass spectrometry, we identified 17 proteins exhibiting differential phosphorylation status mediated by PKA. Among these proteins, we successfully validated the phosphorylation status of heat shock 70 kDa protein (HSP70), aconitase 2 (ACO2), and lamin B1 (LMNB1). Our findings unequivocally demonstrate the dynamic regulation of PKA throughout the estrus cycle in oviductal epithelial cells. Also, analysis by bioinformatics tools suggest its pivotal role in mediating cyclical changes possibly through modulation of apoptotic pathways. This research sheds light on the intricate molecular mechanisms underlying reproductive processes, with implications for understanding fertility and reproductive health.
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Affiliation(s)
- Juan Manuel Teijeiro
- Laboratorio de Medicina Reproductiva, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531. S2002LRK, Rosario, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rosario, Argentina.
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2
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Synthetic Data Generation for the Development of 2D Gel Electrophoresis Protein Spot Models. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12094393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Two-dimensional electrophoresis gels (2DE, 2DEG) are the result of the procedure of separating, based on two molecular properties, a protein mixture on gel. Separated similar proteins concentrate in groups, and these groups appear as dark spots in the captured gel image. Gel images are analyzed to detect distinct spots and determine their peak intensity, background, integrated intensity, and other attributes of interest. One of the approaches to parameterizing the protein spots is spot modeling. Spot parameters of interest are obtained after the spot is approximated by a mathematical model. The development of the modeling algorithm requires a rich, diverse, representative dataset. The primary goal of this research is to develop a method for generating a synthetic protein spot dataset that can be used to develop 2DEG image analysis algorithms. The secondary objective is to evaluate the usefulness of the created dataset by developing a neural-network-based protein spot reconstruction algorithm that provides parameterization and denoising functionalities. In this research, a spot modeling algorithm based on autoencoders is developed using only the created synthetic dataset. The algorithm is evaluated on real and synthetic data. Evaluation results show that the created synthetic dataset is effective for the development of protein spot models. The developed algorithm outperformed all baseline algorithms in all experimental cases.
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3
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Imbalances in the eye lens proteome are linked to cataract formation. Nat Struct Mol Biol 2021; 28:143-151. [PMID: 33432246 DOI: 10.1038/s41594-020-00543-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 11/04/2020] [Indexed: 01/29/2023]
Abstract
The prevalent model for cataract formation in the eye lens posits that damaged crystallin proteins form light-scattering aggregates. The α-crystallins are thought to counteract this process as chaperones by sequestering misfolded crystallin proteins. In this scenario, chaperone pool depletion would result in lens opacification. Here we analyze lenses from different mouse strains that develop early-onset cataract due to point mutations in α-, β-, or γ-crystallin proteins. We find that these mutant crystallins are unstable in vitro; in the lens, their levels are substantially reduced, and they do not accumulate in the water-insoluble fraction. Instead, all the other crystallin proteins, including the α-crystallins, are found to precipitate. The changes in protein composition and spatial organization of the crystallins observed in the mutant lenses suggest that the imbalance in the lenticular proteome and altered crystallin interactions are the bases for cataract formation, rather than the aggregation propensity of the mutant crystallins.
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Effects of Hexane on Protein Profile, Solubility and Foaming Properties of Defatted Proteins Extracted from Tenebrio molitor Larvae. Molecules 2021; 26:molecules26020351. [PMID: 33445507 PMCID: PMC7826597 DOI: 10.3390/molecules26020351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/08/2021] [Accepted: 01/09/2021] [Indexed: 12/05/2022] Open
Abstract
Inclusion of edible insects in human diets is increasingly promoted as a sustainable source of proteins with high nutritional value. While consumer acceptability remains the main challenge to their integration into Western food culture, the use of edible insects as meal and protein concentrate could decrease neophobia. The defatting of edible insects, mostly done with hexane, is the first step in producing protein ingredients. However, its impact on protein profiles and techno-functionality is still unclear. Consequently, this study compares the protein profiles of hexane-defatted and non-hexane-defatted yellow mealworm (Tenebrio molitor) meals and protein extracts, and evaluates the impact of hexane on protein solubility and foaming properties. Results showed that profiles for major proteins were similar between hexane-defatted and non-defatted samples, however some specific content differences (e.g., hexamerin 2) were observed and characterized using proteomic tools. Protein solubility was markedly lower for T. molitor meals compared to protein extracts. A large increase in the foaming capacity was observed for defatted fractions, whereas foam stability decreased similarly in all fractions. Consequently, although the hexane-defatting step was largely studied to produce edible insect protein ingredients, it is necessary to precisely understand its impact on their techno-functional properties for the development of food formulations.
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Molina-Mora JA, Chinchilla-Montero D, Castro-Peña C, García F. Two-dimensional gel electrophoresis (2D-GE) image analysis based on CellProfiler: Pseudomonas aeruginosa AG1 as model. Medicine (Baltimore) 2020; 99:e23373. [PMID: 33285719 PMCID: PMC7717798 DOI: 10.1097/md.0000000000023373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Two-dimensional gel electrophoresis (2D-GE) is an indispensable technique for the study of proteomes of biological systems, providing an assessment of changes in protein abundance under various experimental conditions. However, due to the complexity of 2D-GE gels, there is no systematic, automatic, and reproducible protocol for image analysis and specific implementations are required for each context. In addition, practically all available solutions are commercial, which implies high cost and little flexibility to modulate the parameters of the algorithms. Using the bacterial strain, Pseudomonas aeruginosaAG1 as a model, we obtained images from 2D-GE of periplasmic protein profiles when the strain was exposed to multiple conditions, including antibiotics. Then, we proceeded to implement and evaluate an image analysis protocol with open-source software, CellProfiler. First, a preprocessing step included a bUnwarpJ-Image pipeline for aligning 2D-GE images. Then, using CellProfiler, we standardized two pipelines for spots identification. Total spots recognition was achieved using segmentation by intensity, whose performance was evaluated when compared with a reference protocol. In a second pipeline with the same program, differential identification of spots was addressed when comparing pairs of protein profiles. Due to the characteristics of the programs used, our workflow can automatically analyze a large number of images and it is parallelizable, which is an advantage with respect to other implementations. Finally, we compared six experimental conditions of bacterial strain in the presence or absence of antibiotics, determining protein profiles relationships by applying clustering algorithms PCA (Principal Components Analysis) and HC (Hierarchical Clustering).
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Lin H, Fang F, Zang J, Su J, Tian Q, Kumar Kankala R, Lin X. A Fluorescent Sensor-Assisted Paper-Based Competitive Lateral Flow Immunoassay for the Rapid and Sensitive Detection of Ampicillin in Hospital Wastewater. MICROMACHINES 2020; 11:mi11040431. [PMID: 32326021 PMCID: PMC7231327 DOI: 10.3390/mi11040431] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/29/2020] [Accepted: 04/14/2020] [Indexed: 01/10/2023]
Abstract
In this study, a convenient assay method has been developed based on labeled functional nucleic acids (H-DNA) and a competitive fluorescent lateral flow immunoassay (CF-LFI) for ampicillin (AMP) detection. Herein, we designed the tunable AMP probes for AMP detection based on the AMP aptamer, and the secondary DNA fragment. The probes can generate tunable signals on the test line (T line) and control line (C line) according to the concentration of AMP. The accuracy of detection was improved by optimizing the tunable AMP probes. Under the optimal conditions, the linear concentration of AMP detection is ranged from 10 to 200 ng/L with a limit of quantitation (LOQ) value of 2.71 ng/L, and the recovery is higher than 80.5 %. Moreover, the developed method shows the potential application for AMP detection in the hospital wastewater.
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Affiliation(s)
- Honggui Lin
- Fujian Province Key Laboratory of Ship and Ocean Engineering, Marine Engineering College, Jimei University, Xiamen 361021, China; (H.L.); (Q.T.)
| | - Feixiang Fang
- Department of Chemical Engineering& Pharmaceutical Engineering, College of Chemical Engineering, Huaqiao University, Xiamen 361021, China; (F.F.); (J.Z.); (J.S.); (R.K.K.)
| | - Jiahui Zang
- Department of Chemical Engineering& Pharmaceutical Engineering, College of Chemical Engineering, Huaqiao University, Xiamen 361021, China; (F.F.); (J.Z.); (J.S.); (R.K.K.)
| | - Jianlong Su
- Department of Chemical Engineering& Pharmaceutical Engineering, College of Chemical Engineering, Huaqiao University, Xiamen 361021, China; (F.F.); (J.Z.); (J.S.); (R.K.K.)
| | - Qingyuan Tian
- Fujian Province Key Laboratory of Ship and Ocean Engineering, Marine Engineering College, Jimei University, Xiamen 361021, China; (H.L.); (Q.T.)
- Marine Engineering College, Dalian Maritime University, Dalian 116026, China
| | - Ranjith Kumar Kankala
- Department of Chemical Engineering& Pharmaceutical Engineering, College of Chemical Engineering, Huaqiao University, Xiamen 361021, China; (F.F.); (J.Z.); (J.S.); (R.K.K.)
| | - Xuexia Lin
- Department of Chemical Engineering& Pharmaceutical Engineering, College of Chemical Engineering, Huaqiao University, Xiamen 361021, China; (F.F.); (J.Z.); (J.S.); (R.K.K.)
- Correspondence:
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Teijeiro JM, Marini PE. Hormone-regulated PKA activity in porcine oviductal epithelial cells. Cell Tissue Res 2020; 380:657-667. [PMID: 32112257 DOI: 10.1007/s00441-020-03180-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/28/2020] [Indexed: 11/24/2022]
Abstract
The oviduct is a dynamic organ that suffers changes during the oestrous cycle and modulates gamete and embryo physiology. We analyse the possible existence of Protein kinase A (PKA)-dependent hormone-regulated pathways in porcine ampulla and primary cell cultures by 2D-electrophoresis/Western blot using anti-phospho PKA substrate antibodies. Differential phosphorylation was observed for ten proteins that were identified by mass spectrometry. The results were validated for five of the proteins: Annexin A5, Calumenin, Glyoxalase I and II and Enolase I. Immunofluorescence analyses show that Calumenin, Glyoxalase II and Enolase I change their localisation in the oviductal epithelium through the oestrus cycle. The results demonstrate the existence of PKA hormone-regulated pathways in the ampulla epithelium during the oestrus cycle.
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Affiliation(s)
- Juan Manuel Teijeiro
- Laboratorio de Medicina Reproductiva, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rosario, Argentina.
| | - Patricia Estela Marini
- Laboratorio de Medicina Reproductiva, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.,Consejo de Investigaciones de la Universidad Nacional de Rosario (CIUNR), Rosario, Argentina.,Instituto de Biología Molecular y Celular de Rosario, IBR-CONICET, Rosario, Argentina
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8
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Zang T, Cuttle L, Broszczak DA, Broadbent JA, Tanzer C, Parker TJ. Characterization of the Blister Fluid Proteome for Pediatric Burn Classification. J Proteome Res 2019; 18:69-85. [PMID: 30520305 DOI: 10.1021/acs.jproteome.8b00355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Blister fluid (BF) is a novel and viable research matrix for burn injury study, which can reflect both systemic and local microenvironmental responses. The protein abundance in BF from different burn severities were initially observed using a 2D SDS-PAGE approach. Subsequently, a quantitative data independent acquisition (DIA) method, SWATH, was employed to characterize the proteome of pediatric burn blister fluid. More than 600 proteins were quantitatively profiled in 87 BF samples from different pediatric burn patients. These data were correlated with clinically assessed burn depth and time until complete wound re-epithelialization through several different statistical analyses. Several proteins from these analyses exhibited significant abundance change between different burn depth or re-epithelialization groups, and can be considered as potential biomarker candidates. Further gene ontology (GO) enrichment analysis of the significant proteins revealed the most significant burn related biological processes (BP) that are altered with burn depth, including homeostasis and oxygen transport. However, for wounds with re-epithelialization times more or less than 21 days, the significant GO annotations were related to enzyme activity. This quantitative proteomics investigation of burn BF may enable objective classification of burn wound severity and assist with clinical decision-making. Data are available via ProteomeXchange with identifier PXD011102.
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Affiliation(s)
- Tuo Zang
- Tissue Repair and Translational Physiology Program , Institute of Health and Biomedical Innovation, Queensland University of Technology , Kelvin Grove , Queensland 4059 , Australia.,School of Biomedical Sciences, Faculty of Health , Queensland University of Technology , Brisbane , Queensland 4000 , Australia.,Wound Management Innovation Co-operative Research Centre , Brisbane , Queensland 4000 , Australia
| | - Leila Cuttle
- Tissue Repair and Translational Physiology Program , Institute of Health and Biomedical Innovation, Queensland University of Technology , Kelvin Grove , Queensland 4059 , Australia.,School of Biomedical Sciences, Faculty of Health , Queensland University of Technology , Brisbane , Queensland 4000 , Australia.,Centre for Children's Burns and Trauma Research, Queensland University of Technology , Institute of Health and Biomedical Innovation at the Centre for Children's Health Research , South Brisbane , Queensland 4101 , Australia
| | - Daniel A Broszczak
- Tissue Repair and Translational Physiology Program , Institute of Health and Biomedical Innovation, Queensland University of Technology , Kelvin Grove , Queensland 4059 , Australia.,School of Biomedical Sciences, Faculty of Health , Queensland University of Technology , Brisbane , Queensland 4000 , Australia.,School of Science, Faculty of Health Sciences , Australian Catholic University , Brisbane , Queensland 4014 , Australia
| | - James A Broadbent
- Tissue Repair and Translational Physiology Program , Institute of Health and Biomedical Innovation, Queensland University of Technology , Kelvin Grove , Queensland 4059 , Australia.,School of Biomedical Sciences, Faculty of Health , Queensland University of Technology , Brisbane , Queensland 4000 , Australia
| | - Catherine Tanzer
- Tissue Repair and Translational Physiology Program , Institute of Health and Biomedical Innovation, Queensland University of Technology , Kelvin Grove , Queensland 4059 , Australia.,Wound Management Innovation Co-operative Research Centre , Brisbane , Queensland 4000 , Australia.,Centre for Children's Burns and Trauma Research, Queensland University of Technology , Institute of Health and Biomedical Innovation at the Centre for Children's Health Research , South Brisbane , Queensland 4101 , Australia
| | - Tony J Parker
- Tissue Repair and Translational Physiology Program , Institute of Health and Biomedical Innovation, Queensland University of Technology , Kelvin Grove , Queensland 4059 , Australia.,School of Biomedical Sciences, Faculty of Health , Queensland University of Technology , Brisbane , Queensland 4000 , Australia
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9
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Gokalp S, Horton W, Jónsdóttir-Lewis EB, Foster M, Török M. Laboratory exercise for studying the morphology of heat-denatured and amyloid aggregates of lysozyme by atomic force microscopy. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 46:162-171. [PMID: 29219231 DOI: 10.1002/bmb.21101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/18/2017] [Accepted: 11/21/2017] [Indexed: 05/20/2023]
Abstract
To facilitate learning advanced instrumental techniques, essential tools for visualizing biomaterials, a simple and versatile laboratory exercise demonstrating the use of Atomic Force Microscopy (AFM) in biomedical applications was developed. In this experiment, the morphology of heat-denatured and amyloid-type aggregates formed from a low-cost and well-characterized model protein, hen egg white lysozyme (HEWL), are compared. Structural differences between the amorphous and ordered particles are quantified using ImageJ for the analysis of AFM images as a postlaboratory assignment. The laboratory exercise allows the direct observation of changes in the protein structure and helps students to understand the operation of AFM, as well as protein folding and misfolding related to many physiological and pathological processes. The described protocol stands alone, but also fits well into a larger module on protein structure and function or microscopic techniques as it can be linked easily to existing laboratory exercises on these topics. It can be easily adapted to the upper level undergraduate laboratory courses with limited lab hours as well as graduate level courses to improve students' research skills. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(2):162-171, 2018.
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Affiliation(s)
- Sumeyra Gokalp
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, 02125
| | - William Horton
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, 02125
| | | | - Michelle Foster
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, 02125
| | - Marianna Török
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, 02125
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10
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Zhalimov VK, Kukushkin NI, Gritsyna YV. A study of the nature of plasma protein adsorption on the surface of perfluorocarbon emulsions stabilized by different triblock copolymers. Biophysics (Nagoya-shi) 2017. [DOI: 10.1134/s0006350917010225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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11
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Bielczynski LW, Schansker G, Croce R. Effect of Light Acclimation on the Organization of Photosystem II Super- and Sub-Complexes in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2016; 7:105. [PMID: 26925068 PMCID: PMC4756287 DOI: 10.3389/fpls.2016.00105] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/20/2016] [Indexed: 05/18/2023]
Abstract
To survive under highly variable environmental conditions, higher plants have acquired a large variety of acclimation responses. Different strategies are used to cope with changes in light intensity with the common goal of modulating the functional antenna size of Photosystem II (PSII). Here we use a combination of biochemical and biophysical methods to study these changes in response to acclimation to high light (HL). After 2 h of exposure, a decrease in the amount of the large PSII supercomplexes is observed indicating that plants are already acclimating to HL at this stage. It is also shown that in HL the relative amount of antenna proteins decreases but this decrease is far less than the observed decrease of the functional antenna size, suggesting that part of the antenna present in the membranes in HL does not transfer energy efficiently to the reaction center. Finally, we observed LHCII monomers in all conditions. As the solubilization conditions used do not lead to monomerization of purified LHCII trimers, we should conclude that a population of LHCII monomers exists in the membrane. The relative amount of LHCII monomers strongly increases in plants acclimated to HL, while no changes in the trimer to monomer ratio are observed upon short exposure to stress.
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12
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A Novel Gaussian Extrapolation Approach for 2-D Gel Electrophoresis Saturated Protein Spots. Methods Mol Biol 2015; 1384:203-11. [PMID: 26611417 DOI: 10.1007/978-1-4939-3255-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Analysis of images obtained from two-dimensional gel electrophoresis (2-D GE) is a topic of utmost importance in bioinformatics research, since commercial and academic software currently available have proven to be neither completely effective nor fully automatic, often requiring manual revision and refinement of computer generated matches. In this chapter, we present an effective technique for the detection and the reconstruction of over-saturated protein spots. Firstly, the algorithm reveals overexposed areas, where spots may be truncated, and plateau regions caused by smeared and overlapping spots. Next, it reconstructs the correct distribution of pixel values in these overexposed areas and plateau regions, using a two-dimensional least-squares fitting based on a generalized Gaussian distribution. Pixel correction in saturated and smeared spots allows more accurate proteins quantification, providing more reliable image analysis results. The method is validated for processing highly exposed 2-D GE images, comparing reconstructed spots with the corresponding non-saturated image. The results demonstrate that the algorithm enables correct spot quantification.
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Weyda I, Lübeck M, Ahring BK, Lübeck PS. Point mutation of the xylose reductase (XR) gene reduces xylitol accumulation and increases citric acid production in Aspergillus carbonarius. J Ind Microbiol Biotechnol 2014; 41:733-9. [PMID: 24570325 PMCID: PMC3953602 DOI: 10.1007/s10295-014-1415-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 02/04/2014] [Indexed: 11/07/2022]
Abstract
Aspergillus carbonarius accumulates xylitol when it grows on D-xylose. In fungi, D-xylose is reduced to xylitol by the NAD(P)H-dependent xylose reductase (XR). Xylitol is then further oxidized by the NAD(+)-dependent xylitol dehydrogenase (XDH). The cofactor impairment between the XR and XDH can lead to the accumulation of xylitol under oxygen-limiting conditions. Most of the XRs are NADPH dependent and contain a conserved Ile-Pro-Lys-Ser motif. The only known naturally occurring NADH-dependent XR (from Candida parapsilosis) carries an arginine residue instead of the lysine in this motif. In order to overcome xylitol accumulation in A. carbonarius a Lys-274 to Arg point mutation was introduced into the XR with the aim of changing the specificity toward NADH. The effect of the genetic engineering was examined in fermentation for citric acid production and xylitol accumulation by using D-xylose as the sole carbon source. Fermentation with the mutant strain showed a 2.8-fold reduction in xylitol accumulation and 4.5-fold increase in citric acid production compared to the wild-type strain. The fact that the mutant strain shows decreased xylitol levels is assumed to be associated with the capability of the mutated XR to use the NADH generated by the XDH, thus preventing the inhibition of XDH by the high levels of NADH and ensuring the flux of xylose through the pathway. This work shows that enhanced production of citric acid can be achieved using xylose as the sole carbon source by reducing accumulation of other by-products, such as xylitol.
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Affiliation(s)
- István Weyda
- Section for Sustainable Biotechnology, Aalborg University Copenhagen, A. C. Meyers Vænge 15, 2450 Copenhagen SV, Denmark
| | - Mette Lübeck
- Section for Sustainable Biotechnology, Aalborg University Copenhagen, A. C. Meyers Vænge 15, 2450 Copenhagen SV, Denmark
| | - Birgitte K. Ahring
- Section for Sustainable Biotechnology, Aalborg University Copenhagen, A. C. Meyers Vænge 15, 2450 Copenhagen SV, Denmark
- Bioproducts, Sciences and Engineering Laboratory (BSEL), Washington State University Tri-Cities, 2710 Crimson Way, Richland, WA 99354 USA
| | - Peter S. Lübeck
- Section for Sustainable Biotechnology, Aalborg University Copenhagen, A. C. Meyers Vænge 15, 2450 Copenhagen SV, Denmark
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Aćimović JM, Penezić AZ, Pavićević ID, Jovanović VB, Mandić LM. The efficiency of compounds with α-amino-β-mercapto-ethane group in protection of human serum albumin carbonylation and cross-linking with methylglyoxal. ACTA ACUST UNITED AC 2014; 10:2166-75. [DOI: 10.1039/c4mb00217b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Substances containing an α-amino-β-mercapto-ethane pharmacophore may be used as effective methylglyoxal scavengers and inhibitors of protein carbonylation and cross-linking.
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Affiliation(s)
- Jelena M. Aćimović
- Department of Biochemistry
- Faculty of Chemistry
- University of Belgrade
- Belgrade, Serbia
| | - Ana Z. Penezić
- Department of Biochemistry
- Faculty of Chemistry
- University of Belgrade
- Belgrade, Serbia
| | - Ivan D. Pavićević
- Department of Biochemistry
- Faculty of Chemistry
- University of Belgrade
- Belgrade, Serbia
| | - Vesna B. Jovanović
- Department of Biochemistry
- Faculty of Chemistry
- University of Belgrade
- Belgrade, Serbia
| | - Ljuba M. Mandić
- Department of Biochemistry
- Faculty of Chemistry
- University of Belgrade
- Belgrade, Serbia
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15
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Yoshigi M, Pronovost SM, Kadrmas JL. Interactions by 2D Gel Electrophoresis Overlap (iGEO): a novel high fidelity approach to identify constituents of protein complexes. Proteome Sci 2013; 11:21. [PMID: 23663728 PMCID: PMC3688448 DOI: 10.1186/1477-5956-11-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 05/08/2013] [Indexed: 01/29/2023] Open
Abstract
Background Here we describe a novel approach used to identify the constituents of protein complexes with high fidelity, using the integrin-associated scaffolding protein PINCH as a test case. PINCH is comprised of five LIM domains, zinc-finger protein interaction modules. In Drosophila melanogaster, PINCH has two known high-affinity binding partners—Integrin-linked kinase (ILK) that binds to LIM1 and Ras Suppressor 1 (RSU1) that binds to LIM5—but has been postulated to bind additional proteins as well. Results To purify PINCH complexes, in parallel we fused different affinity tags (Protein A and Flag) to different locations within the PINCH sequence (N- and C-terminus). We expressed these tagged versions of PINCH both in cell culture (overexpressed in Drosophila S2 cell culture in the presence of endogenous PINCH) and in vivo (at native levels in Drosophila lacking endogenous PINCH). After affinity purification, we analyzed PINCH complexes by a novel 2D-gel electrophoresis analysis, iGEO (interactions by 2D Gel Electrophoresis Overlap), with mass spectrometric identification of individual spots of interest. iGEO allowed the identification of protein partners that associate with PINCH under two independent purification strategies, providing confidence in the significance of the interaction. Proteins identified by iGEO were validated against a highly inclusive list of candidate PINCH interacting proteins identified in previous analyses by MuDPIT mass spectrometry. Conclusions The iGEO strategy confirmed a core complex comprised of PINCH, RSU1, ILK, and ILK binding partner Parvin. Our iGEO method also identified five novel protein partners that specifically interacted with PINCH in Drosophila S2 cell culture. Because of the improved reproducibility of 2D-GE methodology and the increasing affordability of the required labeling reagents, iGEO is a method that is accessible to most moderately well-equipped biological laboratories. The biochemical co-purifications inherent in iGEO allow for rapid and unambiguous identification of the constituents of protein complexes, without the need for extensive follow-up experiments.
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Affiliation(s)
- Masaaki Yoshigi
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA.
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A novel Gaussian extrapolation approach for 2D gel electrophoresis saturated protein spots. GENOMICS PROTEOMICS & BIOINFORMATICS 2012; 10:336-44. [PMID: 23317701 PMCID: PMC5054705 DOI: 10.1016/j.gpb.2012.06.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 05/03/2012] [Accepted: 06/04/2012] [Indexed: 11/23/2022]
Abstract
Analysis of images obtained from two-dimensional gel electrophoresis (2D-GE) is a topic of utmost importance in bioinformatics research, since commercial and academic software available currently has proven to be neither completely effective nor fully automatic, often requiring manual revision and refinement of computer generated matches. In this work, we present an effective technique for the detection and the reconstruction of over-saturated protein spots. Firstly, the algorithm reveals overexposed areas, where spots may be truncated, and plateau regions caused by smeared and overlapping spots. Next, it reconstructs the correct distribution of pixel values in these overexposed areas and plateau regions, using a two-dimensional least-squares fitting based on a generalized Gaussian distribution. Pixel correction in saturated and smeared spots allows more accurate quantification, providing more reliable image analysis results. The method is validated for processing highly exposed 2D-GE images, comparing reconstructed spots with the corresponding non-saturated image, demonstrating that the algorithm enables correct spot quantification.
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