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van den Dungen MW, Boer R, Wilms LC, Efimova Y, Abbas HE. The safety of a Kluyveromyces lactis strain lineage for enzyme production. Regul Toxicol Pharmacol 2021; 126:105027. [PMID: 34428516 DOI: 10.1016/j.yrtph.2021.105027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 07/16/2021] [Accepted: 08/18/2021] [Indexed: 11/20/2022]
Abstract
Kluyveromyces lactis is broadly considered as a safe yeast in food and a suitable organism for the production of food enzymes. The K. lactis enzyme production strains of DSM are used to produce a variety of enzymes, for example beta-galactosidase (lactase), chymosin and esterase. All of these production strains are derived from the same lineage, meaning they all originate from the same ancestor strain after classical mutagenesis and/or genetic engineering. Four different enzyme preparations produced with strains within this lineage were toxicologically tested. These enzyme preparations were nontoxic in repeated-dose oral toxicity studies performed in rats and were non-genotoxic in vitro. These studies confirm the safety of the DSM K. lactis strains as a production platform for food enzymes, as well as the safety of the genetic modifications made to these strains through genetic engineering or classical mutagenesis. The outcome of the toxicity studies can be extended to other enzyme preparations produced by any strain from this lineage through read across. Therefore, no new toxicity studies are required for the safety evaluation, as long as the modifications made do not raise safety concerns. Consequently, this approach is in line with the public ambition to reduce animal toxicity studies.
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Affiliation(s)
| | - Rémon Boer
- DSM Food Specialties B.V, Alexander Fleminglaan 1, 2613 AX, Delft, the Netherlands
| | - Lonneke C Wilms
- DSM Food Specialties B.V, Alexander Fleminglaan 1, 2613 AX, Delft, the Netherlands
| | - Yulia Efimova
- DSM Food Specialties B.V, Alexander Fleminglaan 1, 2613 AX, Delft, the Netherlands
| | - Hanna E Abbas
- DSM Food Specialties B.V, Alexander Fleminglaan 1, 2613 AX, Delft, the Netherlands.
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2
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Abstract
RNA helicases are ubiquitous, highly conserved RNA-binding enzymes that use the energy derived from the hydrolysis of nucleoside triphosphate to modify the structure of RNA molecules and/or the functionality of ribonucleoprotein complexes. Ultimately, the action of RNA helicases results in changes in gene expression that allow the cell to perform crucial functions. In this chapter, we review established and emerging concepts for DEAD-box and DExH-box RNA helicases. We mention examples from both eukaryotic and prokaryotic systems, in order to highlight common themes and specific actions.
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Affiliation(s)
- Martina Valentini
- Faculty of Medicine, Department of Microbiology and Molecular Medicine, University of Geneva, Genève, Switzerland
| | - Patrick Linder
- Faculty of Medicine, Department of Microbiology and Molecular Medicine, University of Geneva, Genève, Switzerland.
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3
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Koebke KJ, Batelu S, Kandegedara A, Smith SR, Stemmler TL. Refinement of protein Fe(II) binding characteristics utilizing a competition assay exploiting small molecule ferrous chelators. J Inorg Biochem 2020; 203:110882. [PMID: 31683123 DOI: 10.1016/j.jinorgbio.2019.110882] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 12/20/2022]
Abstract
Iron is the most prevalent metal in biology. Its chemical and redox versatility allows it to direct activity of many Fe binding proteins. While iron's biological applications are diverse, challenges inherent in having Fe(II) present at high abundance means cells must ensure delivery to the correct recipient, while also ensuring its chemistry is regulated. Having a detailed understanding of the biophysical characteristics of a protein's iron binding characteristics allows us to understand general cellular metal homeostasis events. Unfortunately, most spectroscopic techniques available to measure metal binding affinity require protein be in a homogeneous state. Homogeneity creates an artificial environment when measuring metal binding since within cells numerous additional metal binding biomolecules compete with the target. Here we investigate commercially available Fe(II) chelators with spectral markers coupled to metal binding and release. Our goal was to determine their utility as competitors while measuring aspects of metal binding by apoproteins during a metal binding competition assay. Adding chelators during apoprotein metal binding mimics heterogeneous metal binding environments present in vivo, and provides a more realistic metal binding affinity measurement. Ferrous chelators explored within this report include: Rhod-5N, Magfura-2, Fura-4F, Fura-2, and TPA (Tris-(2-byridyl-methyl)amine; each forms a 1:1 complex with Fe(II) and combined cover a binding range of 5 orders of magnitude (micromolar to nanomolar Kd). These chelators were used to calibrate binding affinities for yeast and fly frataxin (Yfh1 and Dfh, respectively), involved in mitochondrial FeS cluster bioassembly.
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Affiliation(s)
- Karl J Koebke
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Sharon Batelu
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Ashoka Kandegedara
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Sheila R Smith
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI 48101, USA
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA.
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4
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Visnapuu T, Meldre A, Põšnograjeva K, Viigand K, Ernits K, Alamäe T. Characterization of a Maltase from an Early-Diverged Non-Conventional Yeast Blastobotrys adeninivorans. Int J Mol Sci 2019; 21:E297. [PMID: 31906253 PMCID: PMC6981392 DOI: 10.3390/ijms21010297] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/20/2019] [Accepted: 12/30/2019] [Indexed: 11/17/2022] Open
Abstract
Genome of an early-diverged yeast Blastobotrys (Arxula) adeninivorans (Ba) encodes 88 glycoside hydrolases (GHs) including two α-glucosidases of GH13 family. One of those, the rna_ARAD1D20130g-encoded protein (BaAG2; 581 aa) was overexpressed in Escherichia coli, purified and characterized. We showed that maltose, other maltose-like substrates (maltulose, turanose, maltotriose, melezitose, malto-oligosaccharides of DP 4‒7) and sucrose were hydrolyzed by BaAG2, whereas isomaltose and isomaltose-like substrates (palatinose, α-methylglucoside) were not, confirming that BaAG2 is a maltase. BaAG2 was competitively inhibited by a diabetes drug acarbose (Ki = 0.8 µM) and Tris (Ki = 70.5 µM). BaAG2 was competitively inhibited also by isomaltose-like sugars and a hydrolysis product-glucose. At high maltose concentrations, BaAG2 exhibited transglycosylating ability producing potentially prebiotic di- and trisaccharides. Atypically for yeast maltases, a low but clearly recordable exo-hydrolytic activity on amylose, amylopectin and glycogen was detected. Saccharomyces cerevisiae maltase MAL62, studied for comparison, had only minimal ability to hydrolyze these polymers, and its transglycosylating activity was about three times lower compared to BaAG2. Sequence identity of BaAG2 with other maltases was only moderate being the highest (51%) with the maltase MalT of Aspergillus oryzae.
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Affiliation(s)
| | | | | | | | | | - Tiina Alamäe
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia; (T.V.); (A.M.); (K.P.); (K.V.); (K.E.)
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5
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Ren S, Li K, Liu Z. Research on the Influences of Five Food-Borne Polyphenols on In Vitro Slow Starch Digestion and the Mechanism of Action. J Agric Food Chem 2019; 67:8617-8625. [PMID: 31293160 DOI: 10.1021/acs.jafc.9b01724] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Inhibiting starch digestion can effectively control postprandial blood sugar level. In this study, the in vitro digestion differences among the mixtures of five polyphenols (i.e., procyanidins [PAs], catechin [CA], tannic acid [TA], rutin [RU], and quercetin [QU]) and starch were analyzed through an in vitro simulation test of starch digestion. The interaction characteristics of these five polyphenols with α-amylase and α-glucosidase were investigated in terms of the inhibition effect, dynamics, fluorescence quenching, and circular dichroism (CD). The results revealed that the rapidly digestible starch (RDS) contents decreased, while the resistant starch (RS) contents increased. All five polyphenols inhibited the α-amylase activity through the noncompetitive approach but inhibited the α-glucosidase activity through the competitive approach. Five polyphenols combined with α-amylase spontaneously by using the hydrophobic effect. The interaction of PAs and QU with α-glucosidase were recognized as van der Waals forces and H bonding, whereas CA and TA interacted with α-glucosidase through the hydrophobic effect. All five polyphenols can cause conformational changes in enzymes.
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Affiliation(s)
- Shuncheng Ren
- School of Food Science and Technology , Henan University of Technology , Zhengzhou 450001 , P R China
| | - Keke Li
- School of Food Science and Technology , Henan University of Technology , Zhengzhou 450001 , P R China
| | - Zelong Liu
- School of Food Science and Technology , Henan University of Technology , Zhengzhou 450001 , P R China
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6
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Snyman C, Theron LW, Divol B. Understanding the regulation of extracellular protease gene expression in fungi: a key step towards their biotechnological applications. Appl Microbiol Biotechnol 2019; 103:5517-5532. [PMID: 31129742 DOI: 10.1007/s00253-019-09902-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/07/2019] [Accepted: 05/07/2019] [Indexed: 12/20/2022]
Abstract
The secretion of proteases by certain species of yeast and filamentous fungi is of importance not only for their biological function and survival, but also for their biotechnological application to various processes in the food, beverage, and bioprocessing industries. A key step towards understanding the role that these organisms play in their environment, and how their protease-secreting ability may be optimally utilised through industrial applications, involves an evaluation of those factors which influence protease production. The objective of this review is to provide an overview of the findings from investigations directed at elucidating the regulatory mechanisms underlying extracellular protease secretion in yeast and filamentous fungi, and the environmental stimuli that elicit these responses. The influence of nitrogen-, carbon-, and sulphur-containing compounds, as well as proteins, temperature, and pH, on extracellular protease regulation, which is frequently exerted at the transcriptional level, is discussed in particular depth. Protease-secreting organisms of biotechnological interest are also presented in this context, in an effort to explore the areas of industrial significance that could possibly benefit from such knowledge. In this way, the establishment of a platform of existing knowledge regarding fungal protease regulation is attempted, with the particular goal of aiding in the practical application of these organisms to processes that require secretion of this enzyme.
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Affiliation(s)
- C Snyman
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Private Bag X1, Matieland, 7602, South Africa
| | - L W Theron
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Private Bag X1, Matieland, 7602, South Africa
| | - B Divol
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Private Bag X1, Matieland, 7602, South Africa.
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7
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Tufegdzic Vidakovic A, Harreman M, Dirac-Svejstrup AB, Boeing S, Roy A, Encheva V, Neumann M, Wilson M, Snijders AP, Svejstrup JQ. Analysis of RNA polymerase II ubiquitylation and proteasomal degradation. Methods 2019; 159-160:146-156. [PMID: 30769100 PMCID: PMC6617506 DOI: 10.1016/j.ymeth.2019.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 12/19/2022] Open
Abstract
Transcribing RNA polymerase II (RNAPII) is decorated by a plethora of post-translational modifications that mark different stages of transcription. One important modification is RNAPII ubiquitylation, which occurs in response to numerous different stimuli that cause RNAPII stalling, such as DNA damaging agents, RNAPII inhibitors, or depletion of the nucleotide pool. Stalled RNAPII triggers a so-called "last resort pathway", which involves RNAPII poly-ubiquitylation and proteasome-mediated degradation. Different approaches have been described to study RNAPII poly-ubiquitylation and degradation, each method with its own advantages and caveats. Here, we describe optimised strategies for detecting ubiquitylated RNAPII and studying its degradation, but these protocols are suitable for studying other ubiquitylated proteins as well.
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Affiliation(s)
- Ana Tufegdzic Vidakovic
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Michelle Harreman
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - A Barbara Dirac-Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stefan Boeing
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Anindya Roy
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Vesela Encheva
- Protein Analysis and Proteomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Michelle Neumann
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Marcus Wilson
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ambrosius P Snijders
- Protein Analysis and Proteomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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8
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Oh J, Xu J, Chong J, Wang D. Structural and biochemical analysis of DNA lesion-induced RNA polymerase II arrest. Methods 2019; 159-160:29-34. [PMID: 30797902 DOI: 10.1016/j.ymeth.2019.02.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/30/2019] [Accepted: 02/19/2019] [Indexed: 11/16/2022] Open
Abstract
Transcription, catalyzed by RNA polymerase II (Pol II) in eukaryotes, is the first step in gene expression. RNA Pol II is a 12-subunit enzyme complex regulated by many different transcription factors during transcription initiation, elongation, and termination. During elongation, Pol II encounters various types of obstacles that can cause transcriptional pausing and arrest. Through decades of research on transcriptional pausing, it is widely known that Pol II can distinguish between different types of obstacles by its active site. A major class of obstacles is DNA lesions. While some DNA lesions can cause transient transcriptional pausing, which can be bypassed by Pol II itself or with the help from other elongation factors, bulky DNA damage can cause prolonged transcriptional pausing and arrest, which signals for transcription coupled repair. Using biochemical and structural biology approaches, the outcomes of many different types of DNA lesions, DNA modifications, and DNA binding molecules to transcription were studied. In this mini review, we will describe the in vitro transcription assays with Pol II to investigate the impacts of various DNA lesions on transcriptional outcomes and the crystallization method of lesion-arrested Pol II complex. These methods can provide a general platform for the structural and biochemical analysis of Pol II transcriptional pausing and bypass mechanisms.
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Affiliation(s)
- Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States
| | - Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States; Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, United States.
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9
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Lieser RM, Chen W, Sullivan MO. Controlled Epidermal Growth Factor Receptor Ligand Display on Cancer Suicide Enzymes via Unnatural Amino Acid Engineering for Enhanced Intracellular Delivery in Breast Cancer Cells. Bioconjug Chem 2019; 30:432-442. [PMID: 30615416 DOI: 10.1021/acs.bioconjchem.8b00783] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Proteins are ideal candidates for disease treatment because of their high specificity and potency. Despite this potential, delivery of proteins remains a significant challenge due to the intrinsic size, charge, and stability of proteins. Attempts to overcome these challenges have most commonly relied on direct conjugation of polymers and peptides to proteins via reactive groups on naturally occurring residues. While such approaches have shown some success, they allow limited control of the spacing and number of moieties coupled to proteins, which can hinder bioactivity and delivery capabilities of the therapeutic. Here, we describe a strategy to site-specifically conjugate delivery moieties to therapeutic proteins through unnatural amino acid (UAA) incorporation, in order to explore the effect of epidermal growth factor receptor (EGFR)-targeted ligand valency and spacing on internalization of proteins in EGFR-overexpressing inflammatory breast cancer (IBC) cells. Our results demonstrate the ability to enhance targeted protein delivery by tuning a small number of EGFR ligands per protein and clustering these ligands to promote multivalent ligand-receptor interactions. Furthermore, the tailorability of this simple approach was demonstrated through IBC-targeted cell death via the delivery of yeast cytosine deaminase (yCD), a prodrug converting enzyme.
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Affiliation(s)
- Rachel M Lieser
- Department of Chemical and Biomolecular Engineering , University of Delaware , 150 Academy Street , Newark , Delaware 19716 , United States
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering , University of Delaware , 150 Academy Street , Newark , Delaware 19716 , United States
| | - Millicent O Sullivan
- Department of Chemical and Biomolecular Engineering , University of Delaware , 150 Academy Street , Newark , Delaware 19716 , United States
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10
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Abstract
Gene therapy involves the introduction of genes (termed transgenes) into cells to compensate for a deficiency or to make a beneficial protein. Gene therapy can used as a form of cancer treatment. A particularly attractive paradigm in this regard involves the selective introduction of transgenes into cancer cells that converts inactive prodrugs into active chemotherapeutic agents, thereby triggering the death of cancer cells. Since prodrugs are inactive, they tend not to cause significant side-effects and are well-tolerated by patients relative to conventional chemotherapy. Several viral and nonviral vectors have been used as delivery tools for suicide gene therapy. Extracellular vesicles (EVs) are now recognized as a promising class of nonviral delivery vectors. Here, we describe a method in which a suicide fusion gene construct is loaded into EVs derived from a non-tumorigenic cell line. Delivery of these modified EVs to glioblastoma cell lines and spheroids decreases glioblastoma cell viability, induces apoptotic cell death, and inhibits tumor growth in vivo.
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Affiliation(s)
- Erdogan Pekcan Erkan
- Department of Medical Genetics, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Nurten Saydam
- Department of Neurosurgery and School of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Clark C Chen
- Department of Neurosurgery and School of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Okay Saydam
- Department of Neurosurgery and School of Medicine, University of Minnesota, Minneapolis, MN, USA.
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11
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Abstract
Exosomes derived from human mesenchymal stem cells (MSCs) engineered to express the suicide gene yeast cytosine deaminase::uracil phosphoribosyl transferase (yCD::UPRT) represent a new therapeutic approach for tumor-targeted innovative therapy. The yCD::UPRT-MSC-exosomes carry mRNA of the suicide gene in their cargo. Upon internalization by tumor cells, the exosomes inhibit the growth of broad types of cancer cells in vitro, in the presence of a prodrug. Here we describe the method leading to the production and testing of these therapeutic exosomes. The described steps include the preparation of replication-deficient retrovirus possessing the yCD::UPRT suicide gene, and the preparation and selection of MSCs transduced with yCD::UPRT suicide gene. We present procedures to obtain exosomes possessing the ability to induce the death of tumor cells. In addition, we highlight methods for the evaluation of the suicide gene activity of yCD::UPRT-MSC-exosomes.
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Affiliation(s)
- Cestmir Altaner
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia.
- Stem Cell Preparation Department, St. Elizabeth Cancer Institute, Bratislava, Slovakia.
| | - Ursula Altanerova
- Stem Cell Preparation Department, St. Elizabeth Cancer Institute, Bratislava, Slovakia
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12
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Komissarov AA, Kostrov SV, Demidyuk IV. In Vitro Assay for the Evaluation of Cytotoxic Effects Provided by a Combination of Suicide and Killer Genes in a Bicistronic Vector. Methods Mol Biol 2019; 1895:135-147. [PMID: 30539535 DOI: 10.1007/978-1-4939-8922-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
When using bicistronic expression constructs the issue arises concerning proper evaluation of the cytotoxic efficiency of a combination of therapeutic genes. For this purpose, an approach can be applied based on the transient transfection of cultured human cells with a specifically designed set of mono- and bicistronic expression constructs and on the comparison of their cytotoxic effects. Here the application of this approach is described using an example of the evaluation of the combined cytotoxic action of bifunctional yeast cytosine deaminase/uracil phosphoribosyltransferase fusion protein (FCU1) and hepatitis A virus 3C protease in a bicistronic plasmid construct.
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Affiliation(s)
- Alexey A Komissarov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Sergey V Kostrov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Ilya V Demidyuk
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.
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13
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Marangon M, Vegro M, Vincenzi S, Lomolino G, De Iseppi A, Curioni A. A Novel Method for the Quantification of White Wine Mannoproteins by a Competitive Indirect Enzyme-Linked Lectin Sorbent Assay (CI-ELLSA). Molecules 2018; 23:molecules23123070. [PMID: 30477183 PMCID: PMC6321203 DOI: 10.3390/molecules23123070] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/12/2018] [Accepted: 11/20/2018] [Indexed: 11/16/2022] Open
Abstract
Mannoproteins (MPs) are cell wall proteoglycans released in wine by yeast during fermentation and ageing on lees, a procedure used for the production of several wines to enrich them in these components with consequences from both a technological and sensory point of view. Given the significance that wine MPs have for wine quality, winemakers would welcome a simple and accurate method for their quantification, as this would allow them to have a better control of this aspect at different winemaking stages. This study develops and validates a novel, simple and accurate method for MPs quantification in white wines based on a competitive indirect enzyme-linked lectin sorbent assay (CI-ELLSA), using the highly mannosylated yeast invertase as the standard. The method utilizes the lectin concanavalin A (ConA) as the immobilized ligand for MPs, and peroxidase, an enzyme rich in mannose, as the competitor for ConA. After addition of the peroxidase substrate, the intensity of the signal produced by the activity of this enzyme (absorbance at 450 nm) is inversely proportional to the amount of mannosylated proteins in the sample. Results have been validated on several wine styles including still, sparkling and sweet wines.
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Affiliation(s)
- Matteo Marangon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Padova, Italy.
| | - Mara Vegro
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Padova, Italy.
| | - Simone Vincenzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Padova, Italy.
- Centre for Research in Viticulture and Enology (CIRVE), Viale XXVIII Aprile 14, 31015 Conegliano, Italy.
| | - Giovanna Lomolino
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Padova, Italy.
| | - Alberto De Iseppi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Padova, Italy.
| | - Andrea Curioni
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Padova, Italy.
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14
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Abstract
Covering: up to mid of 2018 Type I fatty acid synthases (FASs) are giant multienzymes catalyzing all steps of the biosynthesis of fatty acids from acetyl- and malonyl-CoA by iterative precursor extension. Two strikingly different architectures of FAS evolved in yeast (as well as in other fungi and some bacteria) and metazoans. Yeast-type FAS (yFAS) assembles into a barrel-shaped structure of more than 2 MDa molecular weight. Catalytic domains of yFAS are embedded in an extensive scaffolding matrix and arranged around two enclosed reaction chambers. Metazoan FAS (mFAS) is a 540 kDa X-shaped dimer, with lateral reaction clefts, minimal scaffolding and pronounced conformational variability. All naturally occurring yFAS are strictly specialized for the production of saturated fatty acids. The yFAS architecture is not used for the biosynthesis of any other secondary metabolite. On the contrary, mFAS is related at the domain organization level to major classes of polyketide synthases (PKSs). PKSs produce a variety of complex and potent secondary metabolites; they either act iteratively (iPKS), or are linked via directed substrate transfer into modular assembly lines (modPKSs). Here, we review the architectures of yFAS, mFAS, and iPKSs. We rationalize the evolution of the yFAS assembly, and provide examples for re-engineering of yFAS. Recent studies have provided novel insights into the organization of iPKS. A hybrid crystallographic model of a mycocerosic acid synthase-like Pks5 yielded a comprehensive visualization of the organization and dynamics of fully-reducing iPKS. Deconstruction experiments, structural and functional studies of specialized enzymatic domains, such as the product template (PT) and the starter-unit acyltransferase (SAT) domain have revealed functional principles of non-reducing iterative PKS (NR-PKSs). Most recently, a six-domain loading region of an NR-PKS has been visualized at high-resolution together with cryo-EM studies of a trapped loading intermediate. Altogether, these data reveal the related, yet divergent architectures of mFAS, iPKS and also modPKSs. The new insights highlight extensive dynamics, and conformational coupling as key features of mFAS and iPKS and are an important step towards collection of a comprehensive series of snapshots of PKS action.
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Affiliation(s)
- Dominik A Herbst
- Department Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland.
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15
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Nishii K, Wright F, Chen YY, Möller M. Tangled history of a multigene family: The evolution of ISOPENTENYLTRANSFERASE genes. PLoS One 2018; 13:e0201198. [PMID: 30070990 PMCID: PMC6071968 DOI: 10.1371/journal.pone.0201198] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 07/10/2018] [Indexed: 01/07/2023] Open
Abstract
ISOPENTENYLTRANSFERASE (IPT) genes play important roles in the initial steps of cytokinin synthesis, exist in plant and pathogenic bacteria, and form a multigene family in plants. Protein domain searches revealed that bacteria and plant IPT proteins were to assigned to different protein domains families in the Pfam database, namely Pfam IPT (IPTPfam) and Pfam IPPT (IPPTPfam) families, both are closely related in the P-loop NTPase clan. To understand the origin and evolution of the genes, a species matrix was assembled across the tree of life and intensively in plant lineages. The IPTPfam domain was only found in few bacteria lineages, whereas IPPTPfam is common except in Archaea and Mycoplasma bacteria. The bacterial IPPTPfam domain miaA genes were shown as ancestral of eukaryotic IPPTPfam domain genes. Plant IPTs diversified into class I, class II tRNA-IPTs, and Adenosine-phosphate IPTs; the class I tRNA-IPTs appeared to represent direct successors of miaA genes were found in all plant genomes, whereas class II tRNA-IPTs originated from eukaryotic genes, and were found in prasinophyte algae and in euphyllophytes. Adenosine-phosphate IPTs were only found in angiosperms. Gene duplications resulted in gene redundancies with ubiquitous expression or diversification in expression. In conclusion, it is shown that IPT genes have a complex history prior to the protein family split, and might have experienced losses or HGTs, and gene duplications that are to be likely correlated with the rise in morphological complexity involved in fine tuning cytokinin production.
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Affiliation(s)
- Kanae Nishii
- Royal Botanic Garden Edinburgh, Scotland, United Kingdom
- Tokyo Gakugei University, Koganei, Tokyo, Japan
- * E-mail: (KN); (MM)
| | - Frank Wright
- Biomathematics and Statistics Scotland, Edinburgh, Scotland, United Kingdom
| | - Yun-Yu Chen
- Royal Botanic Garden Edinburgh, Scotland, United Kingdom
- University of Edinburgh, Edinburgh, United Kingdom
| | - Michael Möller
- Royal Botanic Garden Edinburgh, Scotland, United Kingdom
- * E-mail: (KN); (MM)
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16
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Abstract
Met80, one of the heme iron ligands in cytochrome c (cyt c), is readily oxidized to Met sulfoxide (Met-SO) by several biologically relevant oxidants. The modification has been suggested to affect both the electron-transfer (ET) and apoptotic functions of this metalloprotein. The coordination of the heme iron in Met-oxidized cyt c (Met-SO cyt c) is critical for both of these functions but has remained poorly defined. We present electronic absorption, NMR, and EPR spectroscopic investigations as well as kinetic studies and mutational analyses to identify the heme iron ligands in yeast iso-1 Met-SO cyt c. Similar to the alkaline form of native cyt c, Lys73 and Lys79 ligate to the ferric heme iron in the Met80-oxidized protein, but this coordination takes place at much lower pH. The ferrous heme iron is ligated by Met-SO, implying the redox-linked ligand switch in the modified protein. Binding studies with the model peptide microperoxidase-8 provide a rationale for alterations in ligation and for the role of the polypeptide packing in native and Met-SO cyt c. Imidazole binding experiments have revealed that Lys dissociation from the ferric heme in K73A/K79G/M80K (M80K#) and Met-SO is more than 3 orders of magnitude slower than the opening of the heme pocket that limits Met80 replacement in native cyt c. The Lys-to-Met-SO ligand substitution gates ET of ferric Met-SO cyt c with Co(terpy)22+. Owing to the slow Lys dissociation step, ET reaction is slow but possible, which is not the case for nonswitchable M80A and M80K#. Acidic conditions cause Lys replacement by a water ligand in Met-SO cyt c (p Ka = 6.3 ± 0.1), increasing the intrinsic peroxidase activity of the protein. This pH-driven ligand switch may be a mechanism to boost peroxidase function of cyt c specifically in apoptotic cells.
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Affiliation(s)
- Fangfang Zhong
- Department of Chemistry, Dartmouth College, Hanover, NH 03755
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17
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Irazusta V, Bernal AR, Estévez MC, de Figueroa LIC. Proteomic and enzymatic response under Cr(VI) overload in yeast isolated from textile-dye industry effluent. Ecotoxicol Environ Saf 2018; 148:490-500. [PMID: 29121591 DOI: 10.1016/j.ecoenv.2017.10.076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/18/2017] [Accepted: 10/31/2017] [Indexed: 06/07/2023]
Abstract
Cyberlindnera jadinii M9 and Wickerhamomyces anomalus M10 isolated from textile-dye liquid effluents has shown capacity for chromium detoxification via Cr(VI) biological reduction. The aim of the study was to evaluate the effect of hexavalent chromium on synthesis of novel and/or specific proteins involved in chromium tolerance and reduction in response to chromium overload in two indigenous yeasts. A study was carried out following a proteomic approach with W. anomalus M10 and Cy. jadinii M9 strains. For this, proteins extracts belonging to total cell extracts, membranes and mitochondria were analyzed. When Cr(VI) was added to culture medium there was an over-synthesis of 39 proteins involved in different metabolic pathways. In both strains, chromium supplementation changed protein biosynthesis by upregulating proteins involved in stress response, methionine metabolism, energy production, protein degradation and novel oxide-reductase enzymes. Moreover, we observed that Cy. jadinii M9 and W. anomalus M10 displayed ability to activate superoxide dismutase, catalase and chromate reductase activity. Two enzymes from the total cell extracts, type II nitroreductase (Frm2) and flavoprotein wrbA (Ycp4), were identified as possibly responsible for inducing crude chromate-reductase activity in cytoplasm of W. anomalus M10 under chromium overload. In Cy.jadinii M9, mitochondrial Ferredoxine-NADP reductase (Yah1) and membrane FAD flavoprotein (Lpd1) were identified as probably involved in Cr(VI) reduction. To our knowledge, this is the first study proposing chromate reductase activity of these four enzymes in yeast and reporting a relationship between protein synthesis, enzymatic response and chromium biospeciation in Cy. jadinii and W. anomalus.
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Affiliation(s)
- Verónica Irazusta
- PROIMI-CONICET, Av. Belgrano y Pje. Caseros, Tucumán T4001MVB, Argentina; Facultad de Ciencias Naturales, Universidad Nacional de Salta, Salta, Argentina; INIQUI-CONICET, Av. Bolivia 5150, Salta 4400, Argentina.
| | | | - María Cristina Estévez
- PROIMI-CONICET, Av. Belgrano y Pje. Caseros, Tucumán T4001MVB, Argentina; Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Lucía I C de Figueroa
- PROIMI-CONICET, Av. Belgrano y Pje. Caseros, Tucumán T4001MVB, Argentina; Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
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18
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Rodrigues JMP, Pereira CS, Fontes N, Gerós H, Côrte-Real M. Flow Cytometry and Fluorescence Microscopy as Tools for Structural and Functional Analysis of Vacuoles Isolated from Yeast and Plant Cells. Methods Mol Biol 2018; 1789:101-115. [PMID: 29916074 DOI: 10.1007/978-1-4939-7856-4_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A series of optimized protocols to isolate vacuoles from both yeast and plant cells, and to characterize the purified organelles at a functional and structural level, are described. For this purpose, we took advantage of the combined use of cell fractionation techniques with different fluorescence-based approaches namely flow cytometry, fluorescence microscopy and spectrofluorimetry. These protocols altogether constitute valuable tools for the study of vacuole structure and function, as well as for the high-throughput screening of drug libraries to identify new molecules that target the vacuole.
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Affiliation(s)
- Jorge M P Rodrigues
- Centre of Molecular and Environmental Biology, CBMA, University of Minho, Braga, Portugal
| | - Cátia S Pereira
- Centre of Molecular and Environmental Biology, CBMA, University of Minho, Braga, Portugal
- Centre of Biological Engineering, CEB, University of Minho, Braga, Portugal
| | - Natacha Fontes
- Sogrape Vinhos, S.A., Research and Development Department, Aldeia Nova, Avintes, Portugal
| | - Hernâni Gerós
- Centre of Molecular and Environmental Biology, CBMA, University of Minho, Braga, Portugal.
- Centre of Biological Engineering, CEB, University of Minho, Braga, Portugal.
- Centre for the Research and Technology of Agro-environmental and Biological Sciences, CITAB-UMinho Pole, University of Minho, Braga, Portugal.
| | - Manuela Côrte-Real
- Centre of Molecular and Environmental Biology, CBMA, University of Minho, Braga, Portugal
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19
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Abstract
Free thiol-containing proteins are suggested to work as antioxidants in beer, but the majority of thiols in wort are present in their oxidized form as disulfides and are therefore not active as antioxidants. Thioredoxin, a disulfide-reducing protein, is released into the wort from some yeast strains during fermentation. The capacity of the thioredoxin enzyme system (thioredoxin, thioredoxin reductase, NADPH) to reduce oxidized thiols in boiled wort under fermentation-like conditions was studied. Free thiols were quantitated in boiled wort samples by derivatization with ThioGlo1 and fluorescence detection of thiol-derivatives. When boiled wort was incubated with all components of the thioredoxin system at pH 7.0 and 25 °C for 60 min under anaerobic conditions, the free thiol concentration increased from 25 to 224 μM. At pH values similar to wort (pH 5.7) and beer (pH 4.5), the thioredoxin system was also capable of increasing the free thiol concentration, although with lower efficiency to 187 and 170 μM, respectively. The presence of sulfite, an important antioxidant in beer secreted by the yeast during fermentation, was found to inactivate thioredoxin by sulfitolysis. Reduction of oxidized thiols by the thioredoxin system was therefore only found to be efficient in the absence of sulfite.
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Affiliation(s)
- Anne N Murmann
- Department of Food Science, Faculty of Science, University of Copenhagen , Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Per Hägglund
- Department of Biotechnology and Biomedicine, Technical University of Denmark , Søltofts Plads, Building 224, DK-2800 Kongens Lyngby, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen , Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark , Søltofts Plads, Building 224, DK-2800 Kongens Lyngby, Denmark
| | - Marianne N Lund
- Department of Food Science, Faculty of Science, University of Copenhagen , Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen , Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
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20
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Souza LTDA, Moreno-Perez S, Fernández Lorente G, Cipolatti EP, de Oliveira D, Resende RR, Pessela BC. Immobilization of Moniliella spathulata R25L270 Lipase on Ionic, Hydrophobic and Covalent Supports: Functional Properties and Hydrolysis of Sardine Oil. Molecules 2017; 22:molecules22101508. [PMID: 28946698 PMCID: PMC6151709 DOI: 10.3390/molecules22101508] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 08/27/2017] [Accepted: 09/04/2017] [Indexed: 11/18/2022] Open
Abstract
The oleaginous yeast Moniliella spathulata R25L270 was the first yeast able to grow and produce extracellular lipase using Macaúba (Acrocomia aculeate) cake as substrate. The novel lipase was recently identified, and presented promising features for biotechnological applications. The M. spathulata R25L270 lipase efficiently hydrolyzed vegetable and animal oils, and showed selectivity for generating cis-5,8,11,15,17-eicosapentaenoic acid from sardine oil. The enzyme can act in a wide range of temperatures (25–48 °C) and pH (6.5–8.4). The present study deals with the immobilization of M. spathulata R25L270 lipase on hydrophobic, covalent and ionic supports to select the most active biocatalyst capable to obtain omega-3 fatty acids (PUFA) from sardine oil. Nine immobilized agarose derivatives were prepared and biochemically characterized for thermostability, pH stability and catalytic properties (KM and Vmax). Ionic supports improved the enzyme–substrate affinity; however, it was not an effective strategy to increase the M. spathulata R25L270 lipase stability against pH and temperature. Covalent support resulted in a biocatalyst with decreased activity, but high thermostability. The enzyme was most stabilized when immobilized on hydrophobic supports, especially Octyl-Sepharose. Compared with the free enzyme, the half-life of the Octyl-Sepharose derivative at 60 °C increased 10-fold, and lipase stability under acidic conditions was achieved. The Octyl-Sepharose derivative was selected to obtain omega-3 fatty acids from sardine oil, and the maximal enzyme selectivity was achieved at pH 5.0.
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Affiliation(s)
- Lívia T de A Souza
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Presidente Antônio Carlos, 6627, Caixa Postal 486, Belo Horizonte MG 31270-901, Brazil.
| | - Sonia Moreno-Perez
- Pharmacy and Biotechnology Department, School of Biomedical Sciences, Universidad Europea, Villaviciosa de Odón, 28670 Madrid, Spain.
| | - Gloria Fernández Lorente
- Departamento de Biotecnología y Microbiología de Alimentos, Instituto de Investigación en Ciencias de la Alimentación CIAL (CSIC-UAM), Campus de la Universidad Autónoma de Madrid, Nicolás Cabrera 9, 28049 Madrid, Spain.
| | - Eliane P Cipolatti
- Departamento de Engenharia Química e Engenharia de Alimentos, Universidade Federal de Santa Catarina (UFSC), P.O. Box 476, Florianópolis SC 88040-900, Brazil.
| | - Débora de Oliveira
- Departamento de Engenharia Química e Engenharia de Alimentos, Universidade Federal de Santa Catarina (UFSC), P.O. Box 476, Florianópolis SC 88040-900, Brazil.
| | - Rodrigo R Resende
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Presidente Antônio Carlos, 6627, Caixa Postal 486, Belo Horizonte MG 31270-901, Brazil.
- Instituto Nanocell, Divinópolis MG 35500-041, Brazil.
| | - Benevides C Pessela
- Departamento de Biotecnología y Microbiología de Alimentos, Instituto de Investigación en Ciencias de la Alimentación CIAL (CSIC-UAM), Campus de la Universidad Autónoma de Madrid, Nicolás Cabrera 9, 28049 Madrid, Spain.
- Departamento de Engenharia e Tecnologías, Instituto Superior Politécnico de Tecnologías e Ciências (ISPTEC) Av. Luanda Sul, Rua Lateral Via S10, P.O. Box 1316, Talatona-Luanda Sul, Angola.
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21
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Abstract
Directed evolution is a useful method for the discovery of nucleic acids, peptides, or proteins that have desired binding abilities or functions. Because of the abundance and importance of glycosylation in nature, directed evolution of glycopeptides and glycoproteins is also highly desirable. However, common directed evolution platforms such as phage-, yeast-, or mammalian-cell display are limited for these applications by several factors. Glycan structure at each glycosylation site is not genetically encoded, and yeast and mammalian cells produce a heterogeneous mixture of glycoforms at each site on the protein. Although yeast, mammalian and Escherichia coli cells can be engineered to produce a homogenous glycoform at all glycosylation sites, there are just a few specific glycan structures that can readily be accessed in this manner. Recently, we reported a novel system for the directed evolution of glycopeptide libraries, which could in principle be decorated with any desired glycan. Our method combines in vitro peptide selection by mRNA display with unnatural amino acid incorporation and chemical attachment of synthetic oligosaccharides. Here, we provide an updated and optimized protocol for this method, which is designed to create glycopeptide mRNA display libraries containing ~1013 sequences and select them for target binding. The target described here is the HIV broadly neutralizing monoclonal antibody 2G12; 2G12 binds to cluster of high-mannose oligosaccharides on the HIV envelope glycoprotein gp120; and glycopeptides that mimic this epitope may be useful in HIV vaccine applications. This method is expected to be readily applicable for other types of glycans and targets of interest in glycobiology.
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22
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Ali SS, Wu J, Xie R, Zhou F, Sun J, Huang M. Screening and characterizing of xylanolytic and xylose-fermenting yeasts isolated from the wood-feeding termite, Reticulitermes chinensis. PLoS One 2017; 12:e0181141. [PMID: 28704553 PMCID: PMC5509302 DOI: 10.1371/journal.pone.0181141] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/21/2017] [Indexed: 11/20/2022] Open
Abstract
The effective fermentation of xylose remains an intractable challenge in bioethanol industry. The relevant xylanase enzyme is also in a high demand from industry for several biotechnological applications that inevitably in recent times led to many efforts for screening some novel microorganisms for better xylanase production and fermentation performance. Recently, it seems that wood-feeding termites can truly be considered as highly efficient natural bioreactors. The highly specialized gut systems of such insects are not yet fully realized, particularly, in xylose fermentation and xylanase production to advance industrial bioethanol technology as well as industrial applications of xylanases. A total of 92 strains from 18 yeast species were successfully isolated and identified from the gut of wood-feeding termite, Reticulitermes chinensis. Of these yeasts and strains, seven were identified for new species: Candida gotoi, Candida pseudorhagii, Hamamotoa lignophila, Meyerozyma guilliermondii, Sugiyamaella sp.1, Sugiyamaella sp. 2, and Sugiyamaella sp.3. Based on the phylogenetic and phenotypic characterization, the type strain of C. pseudorhagii sp. nov., which was originally designated strain SSA-1542T, was the most frequently occurred yeast from termite gut samples, showed the highly xylanolytic activity as well as D-xylose fermentation. The highest xylanase activity was recorded as 1.73 and 0.98 U/mL with xylan or D-xylose substrate, respectively, from SSA-1542T. Among xylanase-producing yeasts, four novel species were identified as D-xylose-fermenting yeasts, where the yeast, C. pseudorhagii SSA-1542T, showed the highest ethanol yield (0.31 g/g), ethanol productivity (0.31 g/L·h), and its fermentation efficiency (60.7%) in 48 h. Clearly, the symbiotic yeasts isolated from termite guts have demonstrated a competitive capability to produce xylanase and ferment xylose, suggesting that the wood-feeding termite gut is a promising reservoir for novel xylanases-producing and xylose-fermenting yeasts that are potentially valued for biorefinery industry.
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Affiliation(s)
- Sameh Samir Ali
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- Botany Department, Faculty of Science, Tanta University, Tanta, Egypt
| | - Jian Wu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Rongrong Xie
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Feng Zhou
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- * E-mail:
| | - Miao Huang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
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23
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Tükenmez H, Magnussen HM, Kovermann M, Byström A, Wolf-Watz M. Linkage between Fitness of Yeast Cells and Adenylate Kinase Catalysis. PLoS One 2016; 11:e0163115. [PMID: 27642758 PMCID: PMC5028032 DOI: 10.1371/journal.pone.0163115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 09/03/2016] [Indexed: 01/08/2023] Open
Abstract
Enzymes have evolved with highly specific values of their catalytic parameters kcat and KM. This poses fundamental biological questions about the selection pressures responsible for evolutionary tuning of these parameters. Here we are address these questions for the enzyme adenylate kinase (Adk) in eukaryotic yeast cells. A plasmid shuffling system was developed to allow quantification of relative fitness (calculated from growth rates) of yeast in response to perturbations of Adk activity introduced through mutations. Biophysical characterization verified that all variants studied were properly folded and that the mutations did not cause any substantial differences to thermal stability. We found that cytosolic Adk is essential for yeast viability in our strain background and that viability could not be restored with a catalytically dead, although properly folded Adk variant. There exist a massive overcapacity of Adk catalytic activity and only 12% of the wild type kcat is required for optimal growth at the stress condition 20°C. In summary, the approach developed here has provided new insights into the evolutionary tuning of kcat for Adk in a eukaryotic organism. The developed methodology may also become useful for uncovering new aspects of active site dynamics and also in enzyme design since a large library of enzyme variants can be screened rapidly by identifying viable colonies.
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Affiliation(s)
- Hasan Tükenmez
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
| | | | | | - Anders Byström
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
- * E-mail: (MWW); (AB)
| | - Magnus Wolf-Watz
- Department of Chemistry, Umeå University, SE-901 87, Umeå, Sweden
- * E-mail: (MWW); (AB)
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Wemhoff S, Klassen R, Beetz A, Meinhardt F. DNA Damage Responses Are Induced by tRNA Anticodon Nucleases and Hygromycin B. PLoS One 2016; 11:e0157611. [PMID: 27472060 PMCID: PMC4966947 DOI: 10.1371/journal.pone.0157611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 06/01/2016] [Indexed: 12/26/2022] Open
Abstract
Previous studies revealed DNA damage to occur during the toxic action of PaT, a fungal anticodon ribonuclease (ACNase) targeting the translation machinery via tRNA cleavage. Here, we demonstrate that other translational stressors induce DNA damage-like responses in yeast as well: not only zymocin, another ACNase from the dairy yeast Kluyveromyces lactis, but also translational antibiotics, most pronouncedly hygromycin B (HygB). Specifically, DNA repair mechanisms BER (base excision repair), HR (homologous recombination) and PRR (post replication repair) provided protection, whereas NHEJ (non-homologous end-joining) aggravated toxicity of all translational inhibitors. Analysis of specific BER mutants disclosed a strong HygB, zymocin and PaT protective effect of the endonucleases acting on apurinic sites. In cells defective in AP endonucleases, inactivation of the DNA glycosylase Ung1 increased tolerance to ACNases and HygB. In addition, Mag1 specifically contributes to the repair of DNA lesions caused by HygB. Consistent with DNA damage provoked by translation inhibitors, mutation frequencies were elevated upon exposure to both fungal ACNases and HygB. Since polymerase ζ contributed to toxicity in all instances, error-prone lesion-bypass probably accounts for the mutagenic effects. The finding that differently acting inhibitors of protein biosynthesis induce alike cellular responses in DNA repair mutants is novel and suggests the dependency of genome stability on translational fidelity.
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Affiliation(s)
- Sabrina Wemhoff
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Roland Klassen
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Anja Beetz
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Friedhelm Meinhardt
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
- * E-mail:
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25
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Mudalkar S, Sreeharsha RV, Reddy AR. A novel aldo-keto reductase from Jatropha curcas L. (JcAKR) plays a crucial role in the detoxification of methylglyoxal, a potent electrophile. J Plant Physiol 2016; 195:39-49. [PMID: 26995646 DOI: 10.1016/j.jplph.2016.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 03/09/2016] [Accepted: 03/09/2016] [Indexed: 06/05/2023]
Abstract
Abiotic stress leads to the generation of reactive oxygen species (ROS) which further results in the production of reactive carbonyls (RCs) including methylglyoxal (MG). MG, an α, β-dicarbonyl aldehyde, is highly toxic to plants and the mechanism behind its detoxification is not well understood. Aldo-keto reductases (AKRs) play a role in detoxification of reactive aldehydes and ketones. In the present study, we cloned and characterised a putative AKR from Jatropha curcas (JcAKR). Phylogenetically, it forms a small clade with AKRs of Glycine max and Rauwolfia serpentina. JcAKR was heterologously expressed in Escherichia coli BL-21(DE3) cells and the identity of the purified protein was confirmed through MALDI-TOF analysis. The recombinant protein had high enzyme activity and catalytic efficiency in assays containing MG as the substrate. Protein modelling and docking studies revealed MG was efficiently bound to JcAKR. Under progressive drought and salinity stress, the enzyme and transcript levels of JcAKR were higher in leaves compared to roots. Further, the bacterial and yeast cells expressing JcAKR showed more tolerance towards PEG (5%), NaCl (200mM) and MG (5mM) treatments compared to controls. In conclusion, our results project JcAKR as a possible and potential target in crop improvement for abiotic stress tolerance.
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Affiliation(s)
- Shalini Mudalkar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
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26
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Dagher SF, Bruno-Bárcena JM. A novel N-terminal region of the membrane β-hexosyltransferase: its role in secretion of soluble protein by Pichia pastoris. Microbiology (Reading) 2016; 162:23-34. [PMID: 26552922 PMCID: PMC5974927 DOI: 10.1099/mic.0.000211] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/05/2015] [Indexed: 11/18/2022]
Abstract
The β-hexosyltransferase (BHT) from Sporobolomyces singularis is a membrane-bound enzyme that catalyses transgalactosylation reactions to synthesize galacto-oligosaccharides (GOSs). To increase the secretion of the active soluble version of this protein, we examined the uncharacterized novel N-terminal region (amino acids 1-110), which included two predicted endogenous structural domains. The first domain (amino acids 1-22) may act as a classical leader while a non-classical signal was located within the remaining region (amino acids 23-110). A functional analysis of these domains was performed by evaluating the amounts of the rBHT forms secreted by recombinant P. pastoris strains carrying combinations of the predicted structural domains and the α mating factor (MFα) from Saccharomyces cerevisiae as positive control. Upon replacement of the leader domain (amino acids 1-22) by MFα (MFα-rBht(23-594)), protein secretion increased and activity of both soluble and membrane-bound enzymes was improved 53- and 14-fold, respectively. Leader interference was demonstrated when MFα preceded the putative classical rBHT(1-22) leader (amino acids 1-22), explaining the limited secretion of soluble protein by P. pastoris (GS115 : : MFα-rBht(1-594)). To validate the role of the N-terminal domains in promoting protein secretion, we tested the domains using a non-secreted protein, the anti-β-galactosidase single-chain variable antibody fragment scFv13R4. The recombinants carrying chimeras of the N-terminal 1-110 regions of rBHT preceding scFv13R4 correlated with the secretion strength of soluble protein observed with the rBHT recombinants. Finally, soluble bioactive HIS-tagged and non-tagged rBHT (purified to homogeneity) obtained from the most efficient recombinants (GS115 : : MFα-rBht(23-594)-HIS and GS115 : : MFα-rBht(23-594)) showed comparable activity rates of GOS generation.
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Affiliation(s)
- Suzanne F. Dagher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695-7615, USA
| | - José M. Bruno-Bárcena
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695-7615, USA
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Abstract
The peroxiredoxins (Prxs) constitute a very large and highly conserved family of thiol-based peroxidases that has been discovered only very recently. We consider here these enzymes through the angle of their discovery, and of some features of their molecular and physiological functions, focusing on complex phenotypes of the gene mutations of the 2-Cys Prxs subtype in yeast. As scavengers of the low levels of H2O2 and as H2O2 receptors and transducers, 2-Cys Prxs have been highly instrumental to understand the biological impact of H2O2, and in particular its signaling function. 2-Cys Prxs can also become potent chaperone holdases, and unveiling the in vivo relevance of this function, which is still not established, should further increase our knowledge of the biological impact and toxicity of H2O2. The diverse molecular functions of 2-Cys Prx explain the often-hard task of relating them to peroxiredoxin genes phenotypes, which underscores the pleiotropic physiological role of these enzymes and complex biologic impact of H2O2.
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Affiliation(s)
- Michel B. Toledano
- CEA, DSV, IBITECS, SBIGEM, Laboratoire Stress Oxydant et Cancer (LSOC), CEA-Saclay, 91191 Gif-sur-Yvette,
France
| | - Bo Huang
- CEA, DSV, IBITECS, SBIGEM, Laboratoire Stress Oxydant et Cancer (LSOC), CEA-Saclay, 91191 Gif-sur-Yvette,
France
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Laszlo KJ, Bush MF. Analysis of Native-Like Proteins and Protein Complexes Using Cation to Anion Proton Transfer Reactions (CAPTR). J Am Soc Mass Spectrom 2015; 26:2152-61. [PMID: 26323617 PMCID: PMC4655144 DOI: 10.1007/s13361-015-1245-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/23/2015] [Accepted: 08/01/2015] [Indexed: 05/08/2023]
Abstract
Mass spectra of native-like protein complexes often exhibit narrow charge-state distributions, broad peaks, and contributions from multiple, coexisting species. These factors can make it challenging to interpret those spectra, particularly for mixtures with significant heterogeneity. Here we demonstrate the use of ion/ion proton transfer reactions to reduce the charge states of m/z-selected, native-like ions of proteins and protein complexes, a technique that we refer to as cation to anion proton transfer reactions (CAPTR). We then demonstrate that CAPTR can increase the accuracy of charge state assignments and the resolution of interfering species in native mass spectrometry. The CAPTR product ion spectra for pyruvate kinase exhibit ~30 peaks and enable unambiguous determination of the charge state of each peak, whereas the corresponding precursor spectra exhibit ~6 peaks and the assigned charge states have an uncertainty of ±3%. 15+ bovine serum albumin and 21+ yeast enolase dimer both appear near m/z 4450 and are completely unresolved in a mixture. After a single CAPTR event, the resulting product ions are baseline resolved. The separation of the product ions increases dramatically after each subsequent CAPTR event; 12 events resulted in a 3000-fold improvement in separation relative to the precursor ions. Finally, we introduce a framework for interpreting and predicting the figures of merit for CAPTR experiments. More generally, these results suggest that CAPTR strongly complements other mass spectrometry tools for analyzing proteins and protein complexes, particularly those in mixtures. Graphical Abstract ᅟ.
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Affiliation(s)
- Kenneth J Laszlo
- Department of Chemistry, University of Washington, Seattle, WA, 98195-1700, USA
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Seattle, WA, 98195-1700, USA.
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Chen CY, Huang YC, Yang TY, Jian JY, Chen WL, Yang CH. Degradation of konjac glucomannan by Thermobifida fusca thermostable β-mannanase from yeast transformant. Int J Biol Macromol 2015; 82:1-6. [PMID: 26476245 DOI: 10.1016/j.ijbiomac.2015.10.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 10/01/2015] [Accepted: 10/03/2015] [Indexed: 11/19/2022]
Abstract
Native konjac glucomannan was used as the substrate for thermophilic actinomycetes, Thermobifida fusca BCRC19214, to produce β-mannanase. The β-mannanase was purified and five internal amino acid sequences were determined by LC-MS/MS. These sequences had high homology with the β-mannanase from T. fusca YX. The tfm gene which encoded the β-mannanase was cloned, sequenced and heterologous expressed in Yarrowia lipolytica P01 g expression system. Recombinant heterologous expression resulted in extracellular β-mannanase production at levels as high as 3.16 U/ml in the culture broth within 48 h cultivation. The recombinant β-mannanase from Y. lipolytica transformant had superior thermal property. The optimal temperature of the recombinant β-mannanase from Y. lipolytica transformant (pYLSC1-tfm) was 80°C. When native konjac glucomannan was incubated with the recombinant β-mannanase from Y. lipolytica transformant (pYLSC1-tfm) at 50°C, there was a fast decrease of viscosity happen during the initial phase of reaction. This viscosity reduction was accompanied by an increase of reducing sugars. The surface of konjac glucomannan film became smooth. After 24h of treatment, the DPw of native konjac glucomannan decreased from 6,435,139 to 3089.
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Affiliation(s)
- Cheng-Yu Chen
- Department of Cosmetic Science, Providence University, Taichung 43301, Taiwan; Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yu-Chun Huang
- Department of Cosmetic Science, Providence University, Taichung 43301, Taiwan
| | - Ting-Ya Yang
- Department of Cosmetic Science, Providence University, Taichung 43301, Taiwan
| | - Jhen-Yi Jian
- Department of Cosmetic Science, Providence University, Taichung 43301, Taiwan
| | - Wei-Lin Chen
- Department of Cosmetic Science, Providence University, Taichung 43301, Taiwan; Department of Applied Chemistry, Providence University, Taichung 43301, Taiwan
| | - Chao-Hsun Yang
- Department of Cosmetic Science, Providence University, Taichung 43301, Taiwan; Department of Applied Chemistry, Providence University, Taichung 43301, Taiwan.
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Greppi A, Krych Ł, Costantini A, Rantsiou K, Hounhouigan DJ, Arneborg N, Cocolin L, Jespersen L. Phytase-producing capacity of yeasts isolated from traditional African fermented food products and PHYPk gene expression of Pichia kudriavzevii strains. Int J Food Microbiol 2015; 205:81-9. [PMID: 25910031 DOI: 10.1016/j.ijfoodmicro.2015.04.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/19/2015] [Accepted: 04/06/2015] [Indexed: 12/22/2022]
Abstract
Phytate is known as a strong chelate of minerals causing their reduced uptake by the human intestine. Ninety-three yeast isolates from traditional African fermented food products, belonging to nine species (Pichia kudriavzevii, Saccharomyces cerevisiae, Clavispora lusitaniae, Kluyveromyces marxianus, Millerozyma farinosa, Candida glabrata, Wickerhamomyces anomalus, Hanseniaspora guilliermondii and Debaryomyces nepalensis) were screened for phytase production on solid and liquid media. 95% were able to grow in the presence of phytate as sole phosphate source, P. kudriavzevii being the best growing species. A phytase coding gene of P. kudriavzevii (PHYPk) was identified and its expression was studied during growth by RT-qPCR. The expression level of PHYPk was significantly higher in phytate-medium, compared to phosphate-medium. In phytate-medium expression was seen in the lag phase. Significant differences in gene expression were detected among the strains as well as between the media. A correlation was found between the PHYPk expression and phytase extracellular activity.
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Affiliation(s)
- Anna Greppi
- Università di Torino, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Grugliasco, Torino, Italy.
| | - Łukasz Krych
- Department of Food Science, Food Microbiology, Faculty of Science, University of Copenhagen, Denmark
| | - Antonella Costantini
- Università di Torino, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Grugliasco, Torino, Italy
| | - Kalliopi Rantsiou
- Università di Torino, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Grugliasco, Torino, Italy
| | - D Joseph Hounhouigan
- Département de Nutrition et Sciences Alimentaires, Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, Benin
| | - Nils Arneborg
- Department of Food Science, Food Microbiology, Faculty of Science, University of Copenhagen, Denmark
| | - Luca Cocolin
- Università di Torino, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Grugliasco, Torino, Italy
| | - Lene Jespersen
- Department of Food Science, Food Microbiology, Faculty of Science, University of Copenhagen, Denmark
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Mondal A, Guria T, Maity TK. A new ester of fatty acid from a methanol extract of the whole plant of Amaranthus spinosus and its α-glucosidase inhibitory activity. Pharm Biol 2015; 53:600-604. [PMID: 25339411 DOI: 10.3109/13880209.2014.935863] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
CONTEXT Amaranthus spinosus Linn. (Amaranthaceae), commonly known as "spiny pigweed", is used both in the Indian traditional system and in folk medicine to treat diabetes. OBJECTIVE The present study evaluates the scientific basis of antidiabetic activity of chloroform fraction of methanol extract of A. spinosus and of an isolated constituent of A. spinosus. MATERIALS AND METHODS HPLC analysis was performed to determine the purity and the amount of the constituent present in the plant extract. The yeast α-glucosidase inhibition technique was used to determine the antidiabetic activity of A. spinosus. Acarbose was used as a standard. An appropriate therapeutic approach for preventing diabetes mellitus and obesity is to retard the absorption of glucose by inhibition of α-glucosidase. RESULTS One novel fatty acid with strong α-glucosidase inhibitory activity - (14E, 18E, 22E, 26E) - methyl nonacosa-14, 18, 22, 26 tetraenoate [1] (IC50 value 6.52 µM/mL) and β-sitosterol [2] were purified. Compound 1 was found to be more potent than the methanol extract. HPLC quantitative analysis revealed that 0.15% of compound 1 and 0.06% of compound 2 were present in the plant extract. CONCLUSION This novel fatty acid can potentially be developed as a novel natural nutraceutical for the management of diabetes.
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Affiliation(s)
- Arijit Mondal
- Drug Development Diagnostics & Biotechnology Division, CSIR - Indian Institute of Chemical Biology , Kolkata, West Bengal , India and
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Jin HH, Jiang JG. Phosphatidic acid phosphatase and diacylglycerol acyltransferase: potential targets for metabolic engineering of microorganism oil. J Agric Food Chem 2015; 63:3067-77. [PMID: 25672855 DOI: 10.1021/jf505975k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Oleaginous microorganism is becoming one of the most promising oil feedstocks for biodiesel production due to its great advantages in triglyceride (TAG) accumulation. Previous studies have shown that de novo TAG biosynthesis can be divided into two parts: the fatty acid biosynthesis pathway (the upstream part which generates acyl-CoAs) and the glycerol-3-phosphate acylation pathway (the downstream part in which three acyl groups are sequentially added onto a glycerol backbone). This review mainly focuses on two enzymes in the G3P pathway, phosphatidic acid phosphatase (PAP) and diacylglycerol acyltransferase (DGAT). The former catalyzes a dephosphorylation reaction, and the latter catalyzes a subsequent acylation reaction. Genes, functional motifs, transmembrane domains, action mechanism, and new studies of the two enzymes are discussed in detail. Furthermore, this review also covers diacylglycerol kinase, an enzyme that catalyzes the reverse reaction of diacylglycerol formation. In addition, PAP and DGAT are the conjunction points of the G3P pathway, the Kennedy pathway, and the CDP-diacylglycerol pathway (CDP-DAG pathway), and the mutual transformation between TAGs and phospholipids is discussed as well. Given that both the Kennedy and CDP-diacylglycerol pathways are in metabolic interlock (MI) with the G3P pathway, it is suggested that, via metabolic engineering, TAG accumulation can be improved by the two pathways based on the pivotal function of PAP and DGAT.
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Affiliation(s)
- Hong-Hao Jin
- College of Food and Bioengineering, South China University of Technology, Guangzhou, 510640, China
| | - Jian-Guo Jiang
- College of Food and Bioengineering, South China University of Technology, Guangzhou, 510640, China
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Abstract
Cell growth and progression through the cell cycle is finely tuned by nutrient availability and stress in eukaryotic cells. In yeast, the Sch9 protein kinase has been identified as a central regulator of longevity and stress resistance. Recent work revealed that Sch9 plays critical roles in transcriptional activation dependent on the environmental conditions. Favorable growth conditions stimulate the expression of genes related to ribosomal function by direct targeting of Sch9 by the TOR kinase, whereas under osmostress conditions, Sch9 plays a direct role in the activation of stress defense genes. At least upon stress, Sch9 seems to activate transcription directly at the chromatin structure. Therefore we speculate that targeting of the kinase to chromatin might coordinate transcription dependent on environmental stimuli and be responsible for the functions of Sch9 in life span regulation and adaptation to stress.
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Affiliation(s)
- Amparo Pascual-Ahuir
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica Valencia, Valencia, Spain
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Sharapov MG, Ravin VK, Novoselov VI. [Peroxyredoxins as multifunctional enzymes]. Mol Biol (Mosk) 2014; 48:600-628. [PMID: 25842845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Peroxiredoxins are evolutionarily ancient, but relatively recently discovered group of seleniumindependent peroxidases. Peroxiredoxins protect cells from various peroxides and play an important role in maintaining the oxidation-reduction homeostasis. Moreover, they are involved in many cellular processes that are not related to peroxidase activity. Here, recent data on the structure and function of peroxiredoxins, regulation of gene expression and activity of different peroxiredoxins are considered.
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Molodtsov V, Anikin M, McAllister WT. The presence of an RNA:DNA hybrid that is prone to slippage promotes termination by T7 RNA polymerase. J Mol Biol 2014; 426:3095-3107. [PMID: 24976131 DOI: 10.1016/j.jmb.2014.06.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 06/20/2014] [Accepted: 06/23/2014] [Indexed: 11/17/2022]
Abstract
Intrinsic termination signals for multisubunit bacterial RNA polymerases (RNAPs) encode a GC-rich stem-loop structure followed by a polyuridine [poly(U)] tract, and it has been proposed that steric clash of the stem-loop with the exit pore of the RNAP imposes a shearing force on the RNA in the downstream RNA:DNA hybrid, resulting in misalignment of the active site. The structurally unrelated T7 RNAP terminates at a similar type of signal (TΦ), suggesting a common mechanism for termination. In the absence of a hairpin (passive conditions), T7 RNAP slips efficiently in both homopolymeric A and U tracts, and we have found that replacement of the U tract in TΦ with a slippage-prone A tract still allows efficient termination. Under passive conditions, incorporation of a single G residue following a poly(U) tract (which is the situation during termination at TΦ) results in a "locked" complex that is unable to extend the transcript. Our results support a model in which transmission of the shearing force generated by steric clash of the hairpin with the exit pore is promoted by the presence of a slippery tracts downstream, resulting in alterations in the active site and the formation of a locked complex that represents an early step in the termination pathway.
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Affiliation(s)
- Vadim Molodtsov
- Graduate Program in Cell and Molecular Biology, Rowan University School of Osteopathic Medicine, 42 East Laurel Road, UDP 2200, Stratford, NJ 08084, USA; Department of Cell Biology, Rowan University School of Osteopathic Medicine, 42 East Laurel Road, UDP 2200, Stratford, NJ 08084, USA
| | - Michael Anikin
- Department of Cell Biology, Rowan University School of Osteopathic Medicine, 42 East Laurel Road, UDP 2200, Stratford, NJ 08084, USA
| | - William T McAllister
- Department of Cell Biology, Rowan University School of Osteopathic Medicine, 42 East Laurel Road, UDP 2200, Stratford, NJ 08084, USA.
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Rovati JI, Pajot HF, Ruberto L, Mac Cormack W, Figueroa LIC. Polyphenolic substrates and dyes degradation by yeasts from 25 de Mayo/King George Island (Antarctica). Yeast 2014; 30:459-70. [PMID: 24298603 DOI: 10.1002/yea.2982] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Antarctica offers a range of extreme climatic conditions, such as low temperatures, high solar radiation and low nutrient availability, and constitutes one of the harshest environments on Earth. Despite that, it has been successfully colonized by ’cold-loving’ fungi, which play a key role in decomposition cycles in cold ecosystems. However, knowledge about the ecological role of yeasts in nutrient or organic matter recycling/mineralization remains highly fragmentary. The aim of this work was to study the yeast microbiota in samples collected on 25 de Mayo/King George Island regarding the scope of their ability to degrade polyphenolic substrates such as lignin and azo dyes. Sixty-one yeast isolates were obtained from 37 samples, including soil, rocks, wood and bones. Molecular analyses based on rDNA sequences revealed that 35 yeasts could be identified at the species level and could be classified in the genera Leucosporidiella, Rhodotorula, Cryptococcus, Bullera and Candida. Cryptococcus victoriae was by far the most ubiquitous species. In total, 33% of the yeast isolates examined showed significant activity for dye decolorization, 25% for laccase activity and 38% for ligninolytic activity. Eleven yeasts did not show positive activity in any of the assays performed and no isolates showed positive activity across all tested substrates. A high diversity of yeasts were isolated in this work, possibly including undescribed species and conspicuous Antarctic yeasts, most of them belonging to oligotrophic, slow-growing and metabolically diverse basidiomycetous genera.
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Yu XH, Prakash RR, Sweet M, Shanklin J. Coexpressing Escherichia coli cyclopropane synthase with Sterculia foetida Lysophosphatidic acid acyltransferase enhances cyclopropane fatty acid accumulation. Plant Physiol 2014; 164:455-65. [PMID: 24204024 PMCID: PMC3875821 DOI: 10.1104/pp.113.230953] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 11/05/2013] [Indexed: 05/18/2023]
Abstract
Cyclopropane fatty acids (CPAs) are desirable as renewable chemical feedstocks for the production of paints, plastics, and lubricants. Toward our goal of creating a CPA-accumulating crop, we expressed nine higher plant cyclopropane synthase (CPS) enzymes in the seeds of fad2fae1 Arabidopsis (Arabidopsis thaliana) and observed accumulation of less than 1% CPA. Surprisingly, expression of the Escherichia coli CPS gene resulted in the accumulation of up to 9.1% CPA in the seed. Coexpression of a Sterculia foetida lysophosphatidic acid acyltransferase (SfLPAT) increases CPA accumulation up to 35% in individual T1 seeds. However, seeds with more than 9% CPA exhibit wrinkled seed morphology and reduced size and oil accumulation. Seeds with more than 11% CPA exhibit strongly decreased seed germination and establishment, and no seeds with CPA more than 15% germinated. That previous reports suggest that plant CPS prefers the stereospecific numbering (sn)-1 position whereas E. coli CPS acts on sn-2 of phospholipids prompted us to investigate the preferred positions of CPS on phosphatidylcholine (PC) and triacylglycerol. Unexpectedly, in planta, E. coli CPS acts primarily on the sn-1 position of PC; coexpression of SfLPAT results in the incorporation of CPA at the sn-2 position of lysophosphatidic acid. This enables a cycle that enriches CPA at both sn-1 and sn-2 positions of PC and results in increased accumulation of CPA. These data provide proof of principle that CPA can accumulate to high levels in transgenic seeds and sets the stage for the identification of factors that will facilitate the movement of CPA from PC into triacylglycerol to produce viable seeds with additional CPA accumulation.
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Rengasamy KRR, Aderogba MA, Amoo SO, Stirk WA, Van Staden J. Potential antiradical and alpha-glucosidase inhibitors from Ecklonia maxima (Osbeck) Papenfuss. Food Chem 2013; 141:1412-5. [PMID: 23790932 DOI: 10.1016/j.foodchem.2013.04.019] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 04/03/2013] [Accepted: 04/06/2013] [Indexed: 12/19/2022]
Abstract
Alpha-glucosidase inhibitors play a potential role in the treatment of type 2 diabetes by delaying glucose absorption in the small intestine. Ecklonia maxima, a brown alga which grows abundantly on the west coast of South Africa, is used to produce alginate, animal feed, nutritional supplements and fertilizer. The crude aqueous methanol extract, four solvent fractions and three phlorotannins: 1,3,5-trihydroxybenezene (phloroglucinol) (1), dibenzo [1,4] dioxine-2,4,7,9-tetraol (2) and hexahydroxyphenoxydibenzo [1,4] dioxine (eckol) (3) isolated from E. maxima were evaluated for antiradical and alpha-glucosidase inhibitory activities. All the phlorotannins tested had strong antioxidant activities on DPPH free radicals with EC50 values ranging from 0.008 to 0.128μM. Compounds 2 and 3 demonstrated stronger antioxidant activity and an alpha-glucosidase inhibitory property than positive controls. These results suggest that E. maxima could be a natural source of potent antioxidants and alpha-glucosidase inhibitors. This study could facilitate effective utilization of E. maxima as an oral antidiabetic drug or functional food ingredient with a promising role in the formulation of medicines and nutrition supplements.
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Affiliation(s)
- Kannan R R Rengasamy
- Research Centre for Plant Growth and Development, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, Private Bag X01, Scottsville 3209, South Africa
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Yan Y, Li Z, Dong M, Zhou Q, Jin F, Yang L, Li S. [Yeasts from Yangzonghai Lake in Yunnan (China): diversity and extracellular enzymes]. Wei Sheng Wu Xue Bao 2013; 53:1205-1212. [PMID: 24617262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
OBJECTIVE The aims of this study were to investigate yeast diversity in Yangzonghai Lake, and to explore the value of these yeasts in such ecological environment, and at the same time, to analyze biological factors and abiotic factors on the influence of the yeast diversity. METHODS Water was filtered through cellulose acetate membrane, serial dilutions of soil and sediment; The D1/D2 domain of 26S rRNA gene of all yeast strains have been sequenced and analyzed. The ability of the yeast strains to produce various enzymes was tested by enzyme screening plates. RESULTS In total of 201 yeast strains were isolated,these strains were identified as 48 species in 15 genera, including 10 presumed new species or variety; 15.9% showed at least one extracellular enzymatic activity, mainly the lipases and amylases. CONCLUSION The yeast community from Yangzonghai Lake showed high species richness, and anthropogenical influenced is an important factor for the yeast count and distribution, at same time, conductivity and turbidity are also important factors for yeast distribution; Some yeasts produced at least one extracellular enzymatic activity, which suggested that these microorganisms are participating in nature cycle and are metabolically active in the lake.
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Gómez-Llorente Y, Malik R, Jain R, Choudhury JR, Johnson RE, Prakash L, Prakash S, Ubarretxena-Belandia I, Aggarwal AK. The architecture of yeast DNA polymerase ζ. Cell Rep 2013; 5:79-86. [PMID: 24120860 DOI: 10.1016/j.celrep.2013.08.046] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/11/2013] [Accepted: 08/29/2013] [Indexed: 02/06/2023] Open
Abstract
DNA polymerase ζ (Polζ) is specialized for the extension step of translesion DNA synthesis (TLS). Despite its central role in maintaining genome integrity, little is known about its overall architecture. Initially identified as a heterodimer of the catalytic subunit Rev3 and the accessory subunit Rev7, yeast Polζ has recently been shown to form a stable four-subunit enzyme (Polζ-d) upon the incorporation of Pol31 and Pol32, the accessory subunits of yeast Polδ. To understand the 3D architecture and assembly of Polζ and Polζ-d, we employed electron microscopy. We show here how the catalytic and accessory subunits of Polζ and Polζ-d are organized relative to each other. In particular, we show that Polζ-d has a bilobal architecture resembling the replicative polymerases and that Pol32 lies in proximity to Rev7. Collectively, our study provides views of Polζ and Polζ-d and a structural framework for understanding their roles in DNA damage bypass.
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Affiliation(s)
- Yacob Gómez-Llorente
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA
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Vanwetswinkel S, van Nuland NAJ, Volkov AN. Paramagnetic properties of the low- and high-spin states of yeast cytochrome c peroxidase. J Biomol NMR 2013; 57:21-26. [PMID: 23832496 DOI: 10.1007/s10858-013-9760-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 06/26/2013] [Indexed: 06/02/2023]
Abstract
Here we describe paramagnetic NMR analysis of the low- and high-spin forms of yeast cytochrome c peroxidase (CcP), a 34 kDa heme enzyme involved in hydroperoxide reduction in mitochondria. Starting from the assigned NMR spectra of a low-spin CN-bound CcP and using a strategy based on paramagnetic pseudocontact shifts, we have obtained backbone resonance assignments for the diamagnetic, iron-free protein and the high-spin, resting-state enzyme. The derived chemical shifts were further used to determine low- and high-spin magnetic susceptibility tensors and the zero-field splitting constant (D) for the high-spin CcP. The D value indicates that the latter contains a hexacoordinate heme species with a weak field ligand, such as water, in the axial position. Being one of the very few high-spin heme proteins analyzed in this fashion, the resting state CcP expands our knowledge of the heme coordination chemistry in biological systems.
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Affiliation(s)
- Sophie Vanwetswinkel
- Jean Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
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Johanson KE, Watt TJ, McIntyre NR, Thompson M. Purification and characterization of enzymes from yeast: an extended undergraduate laboratory sequence for large classes. Biochem Mol Biol Educ 2013; 41:251-261. [PMID: 23868379 DOI: 10.1002/bmb.20704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 04/15/2013] [Indexed: 06/02/2023]
Abstract
Providing a project-based experience in an undergraduate biochemistry laboratory class can be complex with large class sizes and limited resources. We have designed a 6-week curriculum during which students purify and characterize the enzymes invertase and phosphatase from bakers yeast. Purification is performed in two stages via ethanol precipitation and anion exchange chromatography, and students perform both direct and coupled enzyme assays. By completion of the experimental series, students are able to identify which enzymes they have purified and have obtained kinetic parameters for one. This experimental series requires minimal instructor preparation time, is cost effective, and works with multiple sections of large groups of students. Students participating in this sequence showed increases in conceptual understanding of biochemical concepts as measured through in-class assessments and anonymous surveys.
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Affiliation(s)
- Kelly E Johanson
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel. Dr, New Orleans, LA 70125, USA.
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Abstract
A fundamental question in cell biology is how cells determine membrane compartment identity and the directionality with which cargoes pass through the secretory and endocytic pathways. The discovery of so-called 'Rab cascades' provides a satisfying molecular mechanism that helps to resolve this paradox. One Rab GTPase has the ability to template the localization of the subsequent acting Rab GTPase along a given transport pathway. Thus, in addition to determining compartment identity and functionality, Rab GTPases are likely able to order the events of membrane trafficking. This review will highlight recent advances in our understanding of Rabs and Rab cascades.
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Affiliation(s)
- Suzanne R Pfeffer
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive B400, Stanford, CA 94305-5307, USA.
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Abstract
This review focuses on organellar AAA/FtsH proteases, whose proteolytic and chaperone-like activity is a crucial component of the protein quality control systems of mitochondrial and chloroplast membranes. We compare the AAA/FtsH proteases from yeast, mammals and plants. The nature of the complexes formed by AAA/FtsH proteases and the current view on their involvement in degradation of non-native organellar proteins or assembly of membrane complexes are discussed. Additional functions of AAA proteases not directly connected with protein quality control found in yeast and mammals but not yet in plants are also described shortly. Following an overview of the molecular functions of the AAA/FtsH proteases we discuss physiological consequences of their inactivation in yeast, mammals and plants. The molecular basis of phenotypes associated with inactivation of the AAA/FtsH proteases is not fully understood yet, with the notable exception of those observed in m-AAA protease-deficient yeast cells, which are caused by impaired maturation of mitochondrial ribosomal protein. Finally, examples of cytosolic events affecting protein quality control in mitochondria and chloroplasts are given. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
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Affiliation(s)
- Hanna Janska
- Department of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland.
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Abstract
A new adaptive strategy was developed for the ex vivo assembly of a functional tetravalent designer cellulosome on the yeast cell surface. The design is based on the use of (1) a surface-bound anchoring scaffoldin composed of two divergent cohesin domains, (2) two dockerin-tagged adaptor scaffoldins to amplify the number of enzyme loading sites based on the specific dockerin-cohesin interaction with the anchoring scaffoldin, and (3) two dockerin-tagged enzymatic subunits (the endoglucanse Gt and the β-glucosidase Bglf) for cellulose hydrolysis. Cells displaying the tetravalent cellulosome on the surface exhibited a 4.2-fold enhancement in the hydrolysis of phosphoric acid swollen cellulose (PASC) compared with free enzymes. More importantly, cells displaying the tetravalent celluosome also exhibited an ~2-fold increase in ethanol production compared with cells displaying a divalent cellulosome using a similar enzyme loading. These results clearly indicate the more crucial role of enzyme proximity than just simply increasing the enzyme loading on the overall cellulosomal synergy. To the best of our knowledge, this is the first report that exploits the natural adaptive assembly strategy in creating artificial cellulosome structures. The unique feature of the anchoring and the adaptor scaffoldin strategy to amplify the number of enzymatic subunits can be easily extended to more complex cellulosomal structures to achieve an even higher level of enzyme synergy.
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Affiliation(s)
- Shen-Long Tsai
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
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Abstract
Telomerase adds simple-sequence repeats to the ends of linear chromosomes to counteract the loss of end sequence inherent in conventional DNA replication. Catalytic activity for repeat synthesis results from the cooperation of the telomerase reverse transcriptase protein (TERT) and the template-containing telomerase RNA (TER). TERs vary widely in sequence and structure but share a set of motifs required for TERT binding and catalytic activity. Species-specific TER motifs play essential roles in RNP biogenesis, stability, trafficking, and regulation. Remarkably, the biogenesis pathways that generate mature TER differ across eukaryotes. Furthermore, the cellular processes that direct the assembly of a biologically functional telomerase holoenzyme and its engagement with telomeres are evolutionarily varied and regulated. This review highlights the diversity of strategies for telomerase RNP biogenesis, RNP assembly, and telomere recruitment among ciliates, yeasts, and vertebrates and suggests common themes in these pathways and their regulation.
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Affiliation(s)
- Emily D. Egan
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720-3200, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720-3200, USA
- Corresponding authorE-mail
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Lundquist PK, Davis JI, van Wijk KJ. ABC1K atypical kinases in plants: filling the organellar kinase void. Trends Plant Sci 2012; 17:546-55. [PMID: 22694836 PMCID: PMC3926664 DOI: 10.1016/j.tplants.2012.05.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 05/10/2012] [Accepted: 05/12/2012] [Indexed: 05/20/2023]
Abstract
Surprisingly few protein kinases have been demonstrated in chloroplasts or mitochondria. Here, we discuss the activity of bc(1) complex kinase (ABC1K) protein family, which we suggest locate in mitochondria and plastids, thus filling the kinase void. The ABC1Ks are atypical protein kinases and their ancestral function is the regulation of quinone synthesis. ABC1Ks have proliferated from one or two members in non-photosynthetic organisms to more than 16 members in algae and higher plants. In this review, we reconstruct the evolutionary history of the ABC1K family, provide a functional domain analysis for angiosperms and a nomenclature for ABC1Ks in Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and maize (Zea mays). Finally, we hypothesize that targets of ABC1Ks include enzymes of prenyl-lipid metabolism as well as components of the organellar gene expression machineries.
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Affiliation(s)
- Peter K Lundquist
- Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
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Affiliation(s)
- Paul Nurse
- The Royal Society, 6-9 Carlton House, London, SW1Y 5AG, UK.
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Wang F, Li RH, Yin GR. [Research progress in phosphoglycerate mutase]. Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi 2012; 24:353-357. [PMID: 23012968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Phosphoglycerate mutase (PGAM) is one of glycolytic enzymes, concerning with the transport of carbohydrates, metabolism, catalytic activity and growth development. PGAM was discovered in yeast firstly, and with its amino acid sequence and crystal structure determined, this protein was found in varies organism, such as human, Escherichia coli, Schistosoma japonicum and Toxoplasma gondii. This article reviews the physico-chemical property and research progress of PGAM of vertebrate, invertebrate and protozoa.
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Affiliation(s)
- Fen Wang
- Department of Parasitology, Shanxi Medical University, Taiyuan 030001, China
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Kondrák M, Marincs F, Antal F, Juhász Z, Bánfalvi Z. Effects of yeast trehalose-6-phosphate synthase 1 on gene expression and carbohydrate contents of potato leaves under drought stress conditions. BMC Plant Biol 2012; 12:74. [PMID: 22646706 PMCID: PMC3459809 DOI: 10.1186/1471-2229-12-74] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 04/30/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND The development of drought-tolerant, elite varieties of potato (Solanum tuberosum L.) is a challenging task, which might be achieved by introducing transgenic lines into breeding. We previously demonstrated that strains of the White Lady potato cultivar that express the yeast trehalose-6-phosphate synthase (TPS1) gene exhibit improved drought tolerance. RESULTS We investigated the responses of the drought-sensitive potato cultivar White Lady and the drought-tolerant TPS1 transgenic variant to prolonged drought stress at both the transcriptional and metabolic levels. Leaf mRNA expression profiles were compared using the POCI microarray, which contains 42,034 potato unigene probes. We identified 379 genes of known function that showed at least a 2-fold change in expression across genotypes, stress levels or the interaction between these factors. Wild-type leaves had twice as many genes with altered expression in response to stress than TPS1 transgenic leaves, but 112 genes were differentially expressed in both strains. We identified 42 transcription factor genes with altered expression, of which four were uniquely up-regulated in TPS1 transgenic leaves. The majority of the genes with altered expression that have been implicated in photosynthesis and carbohydrate metabolism were down-regulated in both the wild-type and TPS1 transgenic plants. In agreement with this finding, the starch concentration of the stressed leaves was very low. At the metabolic level, the contents of fructose, galactose and glucose were increased and decreased in the wild-type and TPS1 transgenic leaves, respectively, while the amounts of proline, inositol and raffinose were highly increased in both the wild-type and TPS1 transgenic leaves under drought conditions. CONCLUSIONS To our knowledge, this study is the most extensive transcriptional and metabolic analysis of a transgenic, drought-tolerant potato line. We identified four genes that were previously reported as drought-responsive in non-transgenic Andean potato cultivars. The substantial increases in proline, inositol and raffinose contents detected in both the wild-type and TPS1 transgenic leaves appears to be a general response of potatoes to drought stress. The four transcription factors uniquely up-regulated in TPS1 transgenic leaves are good candidates for future functional analyses aimed at understanding the regulation of the 57 genes with differential expression in TPS1 transgenic leaves.
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MESH Headings
- Adaptation, Physiological
- Carbohydrate Metabolism
- Carbohydrates/analysis
- Carbohydrates/genetics
- Droughts
- Gene Expression Regulation, Plant
- Genes, Plant
- Glucosyltransferases/genetics
- Glucosyltransferases/metabolism
- Linear Models
- Metabolomics/methods
- Oligonucleotide Array Sequence Analysis
- Photosynthesis
- Plant Leaves/genetics
- Plant Leaves/metabolism
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Solanum tuberosum/genetics
- Solanum tuberosum/metabolism
- Stress, Physiological
- Time Factors
- Transcriptome
- Yeasts/enzymology
- Yeasts/genetics
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Affiliation(s)
- Mihály Kondrák
- Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, Gödöllő, Hungary
| | - Ferenc Marincs
- Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, Gödöllő, Hungary
| | - Ferenc Antal
- Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, Gödöllő, Hungary
| | - Zsófia Juhász
- Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, Gödöllő, Hungary
| | - Zsófia Bánfalvi
- Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, Gödöllő, Hungary
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