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Öhman T, Tamene F, Göös H, Loukovaara S, Varjosalo M. Systems pathology analysis identifies neurodegenerative nature of age-related vitreoretinal interface diseases. Aging Cell 2018; 17:e12809. [PMID: 29963742 PMCID: PMC6156470 DOI: 10.1111/acel.12809] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/11/2018] [Accepted: 06/01/2018] [Indexed: 12/14/2022] Open
Abstract
Aging is a phenomenon that is associated with profound medical implications. Idiopathic epiretinal membrane (iEMR) and macular hole (MH) are the major vision-threatening vitreoretinal diseases affecting millions of aging people globally, making these conditions an important public health issue. iERM is characterized by fibrous tissue developing on the surface of the macula, which leads to biomechanical and biochemical macular damage. MH is a small breakage in the macula and is associated with many ocular conditions. Although several individual factors and pathways are suggested, a systems pathology level understanding of the molecular mechanisms underlying these disorders is lacking. Therefore, we performed mass spectrometry-based label-free quantitative proteomics analysis of the vitreous proteomes from patients with iERM and MH to identify the key proteins, as well as the multiple interconnected biochemical pathways, contributing to the development of these diseases. We identified a total of 1,014 unique proteins, many of which are linked to inflammation and the complement cascade, revealing the inflammation processes in retinal diseases. Additionally, we detected a profound difference in the proteomes of iEMR and MH compared to those of diabetic retinopathy with macular edema and rhegmatogenous retinal detachment. A large number of neuronal proteins were present at higher levels in the iERM and MH vitreous, including neuronal adhesion molecules, nervous system development proteins, and signaling molecules, pointing toward the important role of neurodegenerative component in the pathogenesis of age-related vitreoretinal diseases. Despite them having marked similarities, several unique vitreous proteins were identified in both iERM and MH, from which candidate targets for new diagnostic and therapeutic approaches can be provided.
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Affiliation(s)
- Tiina Öhman
- Institute of Biotechnology and Helsinki Institute of Life Science; University of Helsinki; Helsinki Finland
| | - Fitsum Tamene
- Institute of Biotechnology and Helsinki Institute of Life Science; University of Helsinki; Helsinki Finland
| | - Helka Göös
- Institute of Biotechnology and Helsinki Institute of Life Science; University of Helsinki; Helsinki Finland
| | - Sirpa Loukovaara
- Unit of Vitreoretinal Surgery, Department of Ophthalmology; University of Helsinki and Helsinki University Hospital; Helsinki Finland
| | - Markku Varjosalo
- Institute of Biotechnology and Helsinki Institute of Life Science; University of Helsinki; Helsinki Finland
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Liu X, Salokas K, Tamene F, Jiu Y, Weldatsadik RG, Öhman T, Varjosalo M. An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations. Nat Commun 2018; 9:1188. [PMID: 29568061 PMCID: PMC5864832 DOI: 10.1038/s41467-018-03523-2] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 02/21/2018] [Indexed: 11/09/2022] Open
Abstract
Protein-protein interactions govern almost all cellular functions. These complex networks of stable and transient associations can be mapped by affinity purification mass spectrometry (AP-MS) and complementary proximity-based labeling methods such as BioID. To exploit the advantages of both strategies, we here design and optimize an integrated approach combining AP-MS and BioID in a single construct, which we term MAC-tag. We systematically apply the MAC-tag approach to 18 subcellular and 3 sub-organelle localization markers, generating a molecular context database, which can be used to define a protein’s molecular location. In addition, we show that combining the AP-MS and BioID results makes it possible to obtain interaction distances within a protein complex. Taken together, our integrated strategy enables the comprehensive mapping of the physical and functional interactions of proteins, defining their molecular context and improving our understanding of the cellular interactome. AP-MS and BioID provide complementary insights into cellular protein interaction networks. To facilitate their combined use, the authors here present an AP-MS- and BioID-compatible affinity tag, enabling efficient determination of cellular protein locations and interaction distances.
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Affiliation(s)
- Xiaonan Liu
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland
| | - Kari Salokas
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland
| | - Fitsum Tamene
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland.,Proteomics Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Yaming Jiu
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland
| | - Rigbe G Weldatsadik
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland.,Proteomics Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Tiina Öhman
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland.,Proteomics Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland. .,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland. .,Proteomics Unit, University of Helsinki, Helsinki, 00014, Finland.
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Yadav L, Tamene F, Göös H, van Drogen A, Katainen R, Aebersold R, Gstaiger M, Varjosalo M. Systematic Analysis of Human Protein Phosphatase Interactions and Dynamics. Cell Syst 2017; 4:430-444.e5. [PMID: 28330616 DOI: 10.1016/j.cels.2017.02.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/10/2017] [Accepted: 02/15/2017] [Indexed: 10/19/2022]
Abstract
Coordinated activities of protein kinases and phosphatases ensure phosphorylation homeostasis, which, when perturbed, can instigate diseases, including cancer. Yet, in contrast to kinases, much less is known about protein phosphatase functions and their interactions and complexes. Here, we used quantitative affinity proteomics to assay protein-protein interactions for 54 phosphatases distributed across the three major protein phosphatase families, with additional analysis of their 12 co-factors. We identified 838 high-confidence interactions, of which 631, to our knowledge, have not been reported before. We show that inhibiting the activity of phosphatases PP1 and PP2A by okadaic acid disrupts their specific interactions, supporting the potential of therapeutics that target these proteins. Additional analyses revealed candidate physical and functional interaction links to phosphatase-based regulation of several signaling pathways and to human cancer. Our study provides an initial glimpse of the protein interaction landscape of phosphatases and their functions in cellular regulation.
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Affiliation(s)
- Leena Yadav
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Fitsum Tamene
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Helka Göös
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Audrey van Drogen
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Riku Katainen
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki 00014, Finland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Matthias Gstaiger
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland.
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Kaustio M, Haapaniemi E, Göös H, Hautala T, Park G, Syrjänen J, Einarsdottir E, Sahu B, Kilpinen S, Rounioja S, Fogarty CL, Glumoff V, Kulmala P, Katayama S, Tamene F, Trotta L, Morgunova E, Krjutškov K, Nurmi K, Eklund K, Lagerstedt A, Helminen M, Martelius T, Mustjoki S, Taipale J, Saarela J, Kere J, Varjosalo M, Seppänen M. Damaging heterozygous mutations in NFKB1 lead to diverse immunologic phenotypes. J Allergy Clin Immunol 2017; 140:782-796. [PMID: 28115215 DOI: 10.1016/j.jaci.2016.10.054] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 09/02/2016] [Accepted: 10/07/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND The nuclear factor κ light-chain enhancer of activated B cells (NF-κB) signaling pathway is a key regulator of immune responses. Accordingly, mutations in several NF-κB pathway genes cause immunodeficiency. OBJECTIVE We sought to identify the cause of disease in 3 unrelated Finnish kindreds with variable symptoms of immunodeficiency and autoinflammation. METHODS We applied genetic linkage analysis and next-generation sequencing and functional analyses of NFKB1 and its mutated alleles. RESULTS In all affected subjects we detected novel heterozygous variants in NFKB1, encoding for p50/p105. Symptoms in variant carriers differed depending on the mutation. Patients harboring a p.I553M variant presented with antibody deficiency, infection susceptibility, and multiorgan autoimmunity. Patients with a p.H67R substitution had antibody deficiency and experienced autoinflammatory episodes, including aphthae, gastrointestinal disease, febrile attacks, and small-vessel vasculitis characteristic of Behçet disease. Patients with a p.R157X stop-gain experienced hyperinflammatory responses to surgery and showed enhanced inflammasome activation. In functional analyses the p.R157X variant caused proteasome-dependent degradation of both the truncated and wild-type proteins, leading to a dramatic loss of p50/p105. The p.H67R variant reduced nuclear entry of p50 and showed decreased transcriptional activity in luciferase reporter assays. The p.I553M mutation in turn showed no change in p50 function but exhibited reduced p105 phosphorylation and stability. Affinity purification mass spectrometry also demonstrated that both missense variants led to altered protein-protein interactions. CONCLUSION Our findings broaden the scope of phenotypes caused by mutations in NFKB1 and suggest that a subset of autoinflammatory diseases, such as Behçet disease, can be caused by rare monogenic variants in genes of the NF-κB pathway.
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Affiliation(s)
- Meri Kaustio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Emma Haapaniemi
- Folkhälsan Institute of Genetics, Helsinki, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Helka Göös
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Timo Hautala
- Department of Internal Medicine, Oulu University Hospital, Oulu, Finland
| | - Giljun Park
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Jaana Syrjänen
- Department of Internal Medicine, Tampere University Hospital, Tampere, Finland
| | - Elisabet Einarsdottir
- Folkhälsan Institute of Genetics, Helsinki, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden; Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Biswajyoti Sahu
- Research Programs Unit, Genome-scale Biology Program, University of Helsinki, Helsinki, Finland
| | - Sanna Kilpinen
- Department of Internal Medicine, Jyväskylä Central Hospital, Jyväskylä, Finland
| | - Samuli Rounioja
- Fimlab Laboratories, Tampere University Hospital, Tampere, Finland; Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Christopher L Fogarty
- Folkhälsan Institute of Genetics, Helsinki, Finland; Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Virpi Glumoff
- Research Unit of Biomedicine, University of Oulu, Oulu, Finland
| | - Petri Kulmala
- Research Unit of Biomedicine, University of Oulu, Oulu, Finland; Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology (PEDEGO) and MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Fitsum Tamene
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Luca Trotta
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Ekaterina Morgunova
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Kaarel Krjutškov
- Folkhälsan Institute of Genetics, Helsinki, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden; Competence Centre on Health Technologies, Tartu, Estonia
| | - Katariina Nurmi
- Department of Rheumatology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kari Eklund
- Department of Rheumatology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Anssi Lagerstedt
- Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Merja Helminen
- Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Timi Martelius
- Adult Immunodeficiency Unit, Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland; Comprehensive Cancer Center, Helsinki University Central Hospital, Helsinki, Finland
| | - Jussi Taipale
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Janna Saarela
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Juha Kere
- Folkhälsan Institute of Genetics, Helsinki, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden; Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland.
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Mikko Seppänen
- Adult Immunodeficiency Unit, Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Rare Diseases Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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Kuuskeri J, Häkkinen M, Laine P, Smolander OP, Tamene F, Miettinen S, Nousiainen P, Kemell M, Auvinen P, Lundell T. Time-scale dynamics of proteome and transcriptome of the white-rot fungus Phlebia radiata: growth on spruce wood and decay effect on lignocellulose. Biotechnol Biofuels 2016; 9:192. [PMID: 27602055 PMCID: PMC5011852 DOI: 10.1186/s13068-016-0608-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 08/30/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND The white-rot Agaricomycetes species Phlebia radiata is an efficient wood-decaying fungus degrading all wood components, including cellulose, hemicellulose, and lignin. We cultivated P. radiata in solid state cultures on spruce wood, and extended the experiment to 6 weeks to gain more knowledge on the time-scale dynamics of protein expression upon growth and wood decay. Total proteome and transcriptome of P. radiata were analyzed by peptide LC-MS/MS and RNA sequencing at specific time points to study the enzymatic machinery on the fungus' natural growth substrate. RESULTS According to proteomics analyses, several CAZy oxidoreductase class-II peroxidases with glyoxal and alcohol oxidases were the most abundant proteins produced on wood together with enzymes important for cellulose utilization, such as GH7 and GH6 cellobiohydrolases. Transcriptome additionally displayed expression of multiple AA9 lytic polysaccharide monooxygenases indicative of oxidative cleavage of wood carbohydrate polymers. Large differences were observed for individual protein quantities at specific time points, with a tendency of enhanced production of specific peroxidases on the first 2 weeks of growth on wood. Among the 10 class-II peroxidases, new MnP1-long, characterized MnP2-long and LiP3 were produced in high protein abundances, while LiP2 and LiP1 were upregulated at highest level as transcripts on wood together with the oxidases and one acetyl xylan esterase, implying their necessity as primary enzymes to function against coniferous wood lignin to gain carbohydrate accessibility and fungal growth. Majority of the CAZy encoding transcripts upregulated on spruce wood represented activities against plant cell wall and were identified in the proteome, comprising main activities of white-rot decay. CONCLUSIONS Our data indicate significant changes in carbohydrate-active enzyme expression during the six-week surveillance of P. radiata growing on wood. Response to wood substrate is seen already during the first weeks. The immediate oxidative enzyme action on lignin and wood cell walls is supported by detected lignin substructure sidechain cleavages, release of phenolic units, and visual changes in xylem cell wall ultrastructure. This study contributes to increasing knowledge on fungal genetics and lignocellulose bioconversion pathways, allowing us to head for systems biology, development of biofuel production, and industrial applications on plant biomass utilizing wood-decay fungi.
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Affiliation(s)
- Jaana Kuuskeri
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, P.O.Box 56, Viikki Biocenter 1, 00014 Helsinki, Finland
| | - Mari Häkkinen
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, P.O.Box 56, Viikki Biocenter 1, 00014 Helsinki, Finland
| | - Pia Laine
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Olli-Pekka Smolander
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Fitsum Tamene
- Proteomics Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Sini Miettinen
- Proteomics Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Paula Nousiainen
- Laboratory of Organic Chemistry, Department of Chemistry, University of Helsinki, Helsinki, Finland
| | - Marianna Kemell
- Laboratory of Inorganic Chemistry, Department of Chemistry, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Taina Lundell
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, P.O.Box 56, Viikki Biocenter 1, 00014 Helsinki, Finland
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Loukovaara S, Nurkkala H, Tamene F, Gucciardo E, Liu X, Repo P, Lehti K, Varjosalo M. Quantitative Proteomics Analysis of Vitreous Humor from Diabetic Retinopathy Patients. J Proteome Res 2015; 14:5131-43. [PMID: 26490944 DOI: 10.1021/acs.jproteome.5b00900] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Initial triggers for diabetic retinopathy (DR) are hyperglycemia-induced oxidative stress and advanced glycation end-products. The most pathological structural changes occur in retinal microvasculature, but the overall development of DR is multifactorial, with a complex interplay of microvascular, neurodegenerative, genetic/epigenetic, immunological, and secondary inflammation-related factors. Although several individual factors and pathways have been associated with retinopathy, a systems level understanding of the disease is lacking. To address this, we performed mass spectrometry based label-free quantitative proteomics analysis of 138 vitreous humor samples from patients with nonproliferative DR or the more severe proliferative form of the disease. Additionally, we analyzed samples from anti-VEGF (vascular endothelial growth factor) (bevacizumab)-treated patients from both groups. In our study, we identified 2482 and quantified the abundancy of 1351 vitreous proteins. Of these, the abundancy of 230 proteins was significantly higher in proliferative retinopathy compared with nonproliferative retinopathy. This specific subset of proteins was linked to inflammation, complement, and coagulation cascade proteins, protease inhibitors, apolipoproteins, immunoglobulins, and cellular adhesion molecules, reflecting the multifactorial nature of the disease. The identification of the key molecules of the disease is critical for the development of new therapeutic molecules and for the new use of existing drugs.
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Affiliation(s)
- Sirpa Loukovaara
- Unit of Vitreoretinal Surgery, Department of Ophthalmology, University of Helsinki and Helsinki University Hospital , FI-00029 Helsinki, Finland
| | - Helka Nurkkala
- Molecular Systems Biology Research Group, Institute of Biotechnology, University of Helsinki , FI-00014 Helsinki, Finland.,Proteomics Unit, Institute of Biotechnology, University of Helsinki , FI-00014 Helsinki, Finland
| | - Fitsum Tamene
- Molecular Systems Biology Research Group, Institute of Biotechnology, University of Helsinki , FI-00014 Helsinki, Finland.,Proteomics Unit, Institute of Biotechnology, University of Helsinki , FI-00014 Helsinki, Finland
| | - Erika Gucciardo
- Research Programs Unit, Genome-Scale Biology and Haartman Institute, Biomedicum Helsinki, University of Helsinki , FI-00014 Helsinki, Finland
| | - Xiaonan Liu
- Molecular Systems Biology Research Group, Institute of Biotechnology, University of Helsinki , FI-00014 Helsinki, Finland.,Proteomics Unit, Institute of Biotechnology, University of Helsinki , FI-00014 Helsinki, Finland
| | - Pauliina Repo
- Research Programs Unit, Genome-Scale Biology and Haartman Institute, Biomedicum Helsinki, University of Helsinki , FI-00014 Helsinki, Finland
| | - Kaisa Lehti
- Research Programs Unit, Genome-Scale Biology and Haartman Institute, Biomedicum Helsinki, University of Helsinki , FI-00014 Helsinki, Finland
| | - Markku Varjosalo
- Molecular Systems Biology Research Group, Institute of Biotechnology, University of Helsinki , FI-00014 Helsinki, Finland.,Proteomics Unit, Institute of Biotechnology, University of Helsinki , FI-00014 Helsinki, Finland
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Koskinen P, Deptula P, Smolander OP, Tamene F, Kammonen J, Savijoki K, Paulin L, Piironen V, Auvinen P, Varmanen P. Complete genome sequence of Propionibacterium freudenreichii DSM 20271(T). Stand Genomic Sci 2015; 10:83. [PMID: 26500719 PMCID: PMC4619572 DOI: 10.1186/s40793-015-0082-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 10/15/2015] [Indexed: 11/10/2022] Open
Abstract
Propionibacterium freudenreichii subsp. freudenreichii DSM 20271T is the type strain of species Propionibacterium freudenreichii that has a long history of safe use in the production dairy products and B12 vitamin. P. freudenreichii is the type species of the genus Propionibacterium which contains Gram-positive, non-motile and non-sporeforming bacteria with a high G + C content. We describe the genome of P. freudenreichii subsp. freudenreichii DSM 20271T consisting of a 2,649,166 bp chromosome containing 2320 protein-coding genes and 50 RNA-only encoding genes.
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Affiliation(s)
- Patrik Koskinen
- Institute of Biotechnology, University of Helsinki, PO Box 56 (Viikinkaari 9), 00014 Helsinki, Finland
| | - Paulina Deptula
- Department of Food and Environmental Sciences, University of Helsinki, PO Box 66 (Agnes Sjöbergin katu 2), 00014 Helsinki, Finland
| | - Olli-Pekka Smolander
- Institute of Biotechnology, University of Helsinki, PO Box 56 (Viikinkaari 9), 00014 Helsinki, Finland
| | - Fitsum Tamene
- Institute of Biotechnology, University of Helsinki, PO Box 56 (Viikinkaari 9), 00014 Helsinki, Finland
| | - Juhana Kammonen
- Institute of Biotechnology, University of Helsinki, PO Box 56 (Viikinkaari 9), 00014 Helsinki, Finland
| | - Kirsi Savijoki
- Department of Food and Environmental Sciences, University of Helsinki, PO Box 66 (Agnes Sjöbergin katu 2), 00014 Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, PO Box 56 (Viikinkaari 9), 00014 Helsinki, Finland
| | - Vieno Piironen
- Department of Food and Environmental Sciences, University of Helsinki, PO Box 66 (Agnes Sjöbergin katu 2), 00014 Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, PO Box 56 (Viikinkaari 9), 00014 Helsinki, Finland
| | - Pekka Varmanen
- Department of Food and Environmental Sciences, University of Helsinki, PO Box 66 (Agnes Sjöbergin katu 2), 00014 Helsinki, Finland
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