801
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Lovell JT, Schwartz S, Lowry DB, Shakirov EV, Bonnette JE, Weng X, Wang M, Johnson J, Sreedasyam A, Plott C, Jenkins J, Schmutz J, Juenger TE. Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C4 grass. Genome Res 2016; 26:510-8. [PMID: 26953271 PMCID: PMC4817774 DOI: 10.1101/gr.198135.115] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/26/2016] [Indexed: 01/18/2023]
Abstract
Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C4 grass,Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. While less well-represented, we observe 1294 genes (7.8%) with transeffects.Trans-by-environment interactions are weaker and much less common than cis G×E, occurring in only 0.7% oft rans-regulated genes. Finally, gene expression heterosis is highly enriched in expression phenotypes with significant G×E. As such, modes of inheritance that drive heterosis, such as dominance or overdominance, may be common among G×E genes. Interestingly, motifs specific to drought-responsive transcription factors are highly enriched in the promoters of genes exhibiting G×E and transregulation, indicating that expression G×E and heterosis may result from the evolution of transcription factors or their binding sites.P. hallii serves as the genomic model for its close relative and emerging biofuel crop, switchgrass (Panicum virgatum). Accordingly, the results here not only aid in the discovery of the genetic mechanisms that underlie local adaptation but also provide a foundation to improve switchgrass yield under water-limited conditions.
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Affiliation(s)
- John T Lovell
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Scott Schwartz
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - David B Lowry
- Department of Plant Sciences, Michigan State University, East Lansing, Michigan 48824, USA
| | - Eugene V Shakirov
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 42008, Republic of Tatarstan, Russia
| | - Jason E Bonnette
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Xiaoyu Weng
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Mei Wang
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jenifer Johnson
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | | | - Christopher Plott
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
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802
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Bruender NA, Wilcoxen J, Britt RD, Bandarian V. Biochemical and Spectroscopic Characterization of a Radical S-Adenosyl-L-methionine Enzyme Involved in the Formation of a Peptide Thioether Cross-Link. Biochemistry 2016; 55:2122-34. [PMID: 27007615 DOI: 10.1021/acs.biochem.6b00145] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide-derived natural products are a class of metabolites that afford the producing organism a selective advantage over other organisms in their biological niche. While the polypeptide antibiotics produced by the nonribosomal polypeptide synthetases (NRPS) are the most widely recognized, the ribosomally synthesized and post-translationally modified peptides (RiPPs) are an emerging group of natural products with diverse structures and biological functions. Both the NRPS derived peptides and the RiPPs undergo extensive post-translational modifications to produce structural diversity. Here we report the first characterization of the six cysteines in forty-five (SCIFF) [Haft, D. H. and Basu M. K. (2011) J. Bacteriol. 193, 2745-2755] peptide maturase Tte1186, which is a member of the radical S-adenosyl-l-methionine (SAM) superfamily. Tte1186 catalyzes the formation of a thioether cross-link in the peptide Tte1186a encoded by an orf located upstream of the maturase, under reducing conditions in the presence of SAM. Tte1186 contains three [4Fe-4S] clusters that are indispensable for thioether cross-link formation; however, only one cluster catalyzes the reductive cleavage of SAM. Mechanistic imperatives for the reaction catalyzed by the thioether forming radical SAM maturases will be discussed.
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Affiliation(s)
- Nathan A Bruender
- Chemistry Department, University of Utah , Salt Lake City, Utah 84112, United States
| | - Jarett Wilcoxen
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - R David Britt
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Vahe Bandarian
- Chemistry Department, University of Utah , Salt Lake City, Utah 84112, United States
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803
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Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SRS, Purushothaman K, Saju JM, Jiang J, Mbandi SK, Jonas M, Hin Yan Tong A, Mwangi S, Lau D, Ngoh SY, Liew WC, Shen X, Hon LS, Drake JP, Boitano M, Hall R, Chin CS, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck FJ, Vurture GW, Gopalapillai G, Kumar Katneni V, Noble TH, Scaria V, Sivasubbu S, Jerry DR, O'Brien SJ, Schatz MC, Dalmay T, Turner SW, Lok S, Christoffels A, Orbán L. Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet 2016; 12:e1005954. [PMID: 27082250 PMCID: PMC4833346 DOI: 10.1371/journal.pgen.1005954] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 03/03/2016] [Indexed: 11/18/2022] Open
Abstract
We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics.
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Affiliation(s)
- Shubha Vij
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Inna S. Kuznetsova
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
- Laboratory of Chromosome Structure and Function, Department of Cytology and Histology, Biological Faculty, Saint Petersburg State University, St. Petersburg, Russia
| | - Aleksey Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| | - Andrey A. Yurchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| | - Peter Van Heusden
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Siddharth Singh
- Pacific Biosciences, Menlo Park, California, United States of America
| | | | | | | | - Jolly M. Saju
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Junhui Jiang
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Stanley Kimbung Mbandi
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Mario Jonas
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Amy Hin Yan Tong
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Sarah Mwangi
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Doreen Lau
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Si Yan Ngoh
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Woei Chang Liew
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Xueyan Shen
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Lawrence S. Hon
- Pacific Biosciences, Menlo Park, California, United States of America
| | - James P. Drake
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Matthew Boitano
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Richard Hall
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Chen-Shan Chin
- Pacific Biosciences, Menlo Park, California, United States of America
| | | | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Vladimir Trifonov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Marsel Kabilov
- Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey Tupikin
- Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Darrell Green
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Simon Moxon
- The Genome Analysis Centre, Norwich, United Kingdom
| | - Tyler Garvin
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America
| | - Fritz J. Sedlazeck
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Gregory W. Vurture
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America
| | - Gopikrishna Gopalapillai
- Nutrition, Genetics & Biotechnology Division, ICAR-Central Institute of Brackishwater Aquaculture, Tamil Nadu, India
| | - Vinaya Kumar Katneni
- Nutrition, Genetics & Biotechnology Division, ICAR-Central Institute of Brackishwater Aquaculture, Tamil Nadu, India
| | - Tansyn H. Noble
- College of Marine and Environmental Sciences and Center for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Dean R. Jerry
- College of Marine and Environmental Sciences and Center for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
| | - Stephen J. O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
- Oceanographic Center, Nova Southeastern University Ft. Lauderdale, Ft. Lauderdale, Florida, United States of America
| | - Michael C. Schatz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tamás Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Stephen W. Turner
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Si Lok
- The Centre for Applied Genomics, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Alan Christoffels
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - László Orbán
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
- Department of Animal Sciences and Animal Husbandry, Georgikon Faculty, University of Pannonia, Keszthely, Hungary
- Centre for Comparative Genomics, Murdoch University, Murdoch, Australia
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804
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Svensk E, Devkota R, Ståhlman M, Ranji P, Rauthan M, Magnusson F, Hammarsten S, Johansson M, Borén J, Pilon M. Caenorhabditis elegans PAQR-2 and IGLR-2 Protect against Glucose Toxicity by Modulating Membrane Lipid Composition. PLoS Genet 2016; 12:e1005982. [PMID: 27082444 PMCID: PMC4833288 DOI: 10.1371/journal.pgen.1005982] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 03/16/2016] [Indexed: 12/19/2022] Open
Abstract
In spite of the worldwide impact of diabetes on human health, the mechanisms behind glucose toxicity remain elusive. Here we show that C. elegans mutants lacking paqr-2, the worm homolog of the adiponectin receptors AdipoR1/2, or its newly identified functional partner iglr-2, are glucose intolerant and die in the presence of as little as 20 mM glucose. Using FRAP (Fluorescence Recovery After Photobleaching) on living worms, we found that cultivation in the presence of glucose causes a decrease in membrane fluidity in paqr-2 and iglr-2 mutants and that genetic suppressors of this sensitivity act to restore membrane fluidity by promoting fatty acid desaturation. The essential roles of paqr-2 and iglr-2 in the presence of glucose are completely independent from daf-2 and daf-16, the C. elegans homologs of the insulin receptor and its downstream target FoxO, respectively. Using bimolecular fluorescence complementation, we also show that PAQR-2 and IGLR-2 interact on plasma membranes and thus may act together as a fluidity sensor that controls membrane lipid composition.
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Affiliation(s)
- Emma Svensk
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Ranjan Devkota
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Marcus Ståhlman
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Parmida Ranji
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Manish Rauthan
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Magnusson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Sofia Hammarsten
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Maja Johansson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jan Borén
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Marc Pilon
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
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805
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Attwood MM, Krishnan A, Pivotti V, Yazdi S, Almén MS, Schiöth HB. Topology based identification and comprehensive classification of four-transmembrane helix containing proteins (4TMs) in the human genome. BMC Genomics 2016; 17:268. [PMID: 27030248 PMCID: PMC4815072 DOI: 10.1186/s12864-016-2592-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 03/16/2016] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Membrane proteins are key components in a large spectrum of diverse functions and thus account for the major proportion of the drug-targeted portion of the genome. From a structural perspective, the α-helical transmembrane proteins can be categorized into major groups based on the number of transmembrane helices and these groups are often associated with specific functions. When compared to the well-characterized seven-transmembrane containing proteins (7TM), other TM groups are less explored and in particular the 4TM group. In this study, we identify the complete 4TM complement from the latest release of the human genome and assess the 4TM structure group as a whole. We functionally characterize this dataset and evaluate the resulting groups and ubiquitous functions, and furthermore describe disease and drug target involvement. RESULTS We classified 373 proteins, which represents ~7 % of the human membrane proteome, and includes 69 more proteins than our previous estimate. We have characterized the 4TM dataset based on functional, structural, and/or evolutionary similarities. Proteins that are involved in transport activity constitute 37 % of the dataset, 23 % are receptor-related, and 13 % have enzymatic functions. Intriguingly, proteins involved in transport are more than double the 15 % of transporters in the entire human membrane proteome, which might suggest that the 4TM topological architecture is more favored for transporting molecules over other functions. Moreover, we found an interesting exception to the ubiquitous intracellular N- and C-termini localization that is found throughout the entire membrane proteome and 4TM dataset in the neurotransmitter gated ion channel families. Overall, we estimate that 58 % of the dataset has a known association to disease conditions with 19 % of the genes possibly involved in different types of cancer. CONCLUSIONS We provide here the most robust and updated classification of the 4TM complement of the human genome as a platform to further understand the characteristics of 4TM functions and to explore pharmacological opportunities.
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Affiliation(s)
- Misty M. Attwood
- />Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Arunkumar Krishnan
- />Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Valentina Pivotti
- />Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Samira Yazdi
- />Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Markus Sällman Almén
- />Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Helgi B. Schiöth
- />Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
- />Institutionen för neurovetenskap, BMC, Box 593, 751 24 Uppsala, Sweden
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806
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Ligand-binding specificity and promiscuity of the main lignocellulolytic enzyme families as revealed by active-site architecture analysis. Sci Rep 2016; 6:23605. [PMID: 27009476 PMCID: PMC4806347 DOI: 10.1038/srep23605] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/09/2016] [Indexed: 02/02/2023] Open
Abstract
Biomass can be converted into sugars by a series of lignocellulolytic enzymes, which belong to the glycoside hydrolase (GH) families summarized in CAZy databases. Here, using a structural bioinformatics method, we analyzed the active site architecture of the main lignocellulolytic enzyme families. The aromatic amino acids Trp/Tyr and polar amino acids Glu/Asp/Asn/Gln/Arg occurred at higher frequencies in the active site architecture than in the whole enzyme structure. And the number of potential subsites was significantly different among different families. In the cellulase and xylanase families, the conserved amino acids in the active site architecture were mostly found at the −2 to +1 subsites, while in β-glucosidase they were mainly concentrated at the −1 subsite. Families with more conserved binding amino acid residues displayed strong selectivity for their ligands, while those with fewer conserved binding amino acid residues often exhibited promiscuity when recognizing ligands. Enzymes with different activities also tended to bind different hydroxyl oxygen atoms on the ligand. These results may help us to better understand the common and unique structural bases of enzyme-ligand recognition from different families and provide a theoretical basis for the functional evolution and rational design of major lignocellulolytic enzymes.
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807
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Hugo W, Zaretsky JM, Sun L, Song C, Moreno BH, Hu-Lieskovan S, Berent-Maoz B, Pang J, Chmielowski B, Cherry G, Seja E, Lomeli S, Kong X, Kelley MC, Sosman JA, Johnson DB, Ribas A, Lo RS. Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma. Cell 2016. [PMID: 26997480 DOI: 10.1016/j.cell.2016.02.065.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
PD-1 immune checkpoint blockade provides significant clinical benefits for melanoma patients. We analyzed the somatic mutanomes and transcriptomes of pretreatment melanoma biopsies to identify factors that may influence innate sensitivity or resistance to anti-PD-1 therapy. We find that overall high mutational loads associate with improved survival, and tumors from responding patients are enriched for mutations in the DNA repair gene BRCA2. Innately resistant tumors display a transcriptional signature (referred to as the IPRES, or innate anti-PD-1 resistance), indicating concurrent up-expression of genes involved in the regulation of mesenchymal transition, cell adhesion, extracellular matrix remodeling, angiogenesis, and wound healing. Notably, mitogen-activated protein kinase (MAPK)-targeted therapy (MAPK inhibitor) induces similar signatures in melanoma, suggesting that a non-genomic form of MAPK inhibitor resistance mediates cross-resistance to anti-PD-1 therapy. Validation of the IPRES in other independent tumor cohorts defines a transcriptomic subset across distinct types of advanced cancer. These findings suggest that attenuating the biological processes that underlie IPRES may improve anti-PD-1 response in melanoma and other cancer types.
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Affiliation(s)
- Willy Hugo
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Jesse M Zaretsky
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Lu Sun
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Chunying Song
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Blanca Homet Moreno
- Division of Hematology & Oncology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Siwen Hu-Lieskovan
- Division of Hematology & Oncology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Beata Berent-Maoz
- Division of Hematology & Oncology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Jia Pang
- Division of Hematology & Oncology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Bartosz Chmielowski
- Division of Hematology & Oncology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Grace Cherry
- Division of Hematology & Oncology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Elizabeth Seja
- Division of Hematology & Oncology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Shirley Lomeli
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Xiangju Kong
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Mark C Kelley
- Department of Surgery, Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA
| | - Jeffrey A Sosman
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA
| | - Douglas B Johnson
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA
| | - Antoni Ribas
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095-1662, USA; Division of Hematology & Oncology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA; Division of Surgical Oncology, Department of Surgery, University of California, Los Angeles, CA 90095-1662, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Roger S Lo
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA; Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095-1662, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1662, USA.
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808
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Njamkepo E, Fawal N, Tran-Dien A, Hawkey J, Strockbine N, Jenkins C, Talukder KA, Bercion R, Kuleshov K, Kolínská R, Russell JE, Kaftyreva L, Accou-Demartin M, Karas A, Vandenberg O, Mather AE, Mason CJ, Page AJ, Ramamurthy T, Bizet C, Gamian A, Carle I, Sow AG, Bouchier C, Wester AL, Lejay-Collin M, Fonkoua MC, Le Hello S, Blaser MJ, Jernberg C, Ruckly C, Mérens A, Page AL, Aslett M, Roggentin P, Fruth A, Denamur E, Venkatesan M, Bercovier H, Bodhidatta L, Chiou CS, Clermont D, Colonna B, Egorova S, Pazhani GP, Ezernitchi AV, Guigon G, Harris SR, Izumiya H, Korzeniowska-Kowal A, Lutyńska A, Gouali M, Grimont F, Langendorf C, Marejková M, Peterson LAM, Perez-Perez G, Ngandjio A, Podkolzin A, Souche E, Makarova M, Shipulin GA, Ye C, Žemličková H, Herpay M, Grimont PAD, Parkhill J, Sansonetti P, Holt KE, Brisse S, Thomson NR, Weill FX. Global phylogeography and evolutionary history of Shigella dysenteriae type 1. Nat Microbiol 2016; 1:16027. [PMID: 27572446 DOI: 10.1038/nmicrobiol.2016.27] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 02/03/2016] [Indexed: 11/09/2022]
Abstract
Together with plague, smallpox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries(1). A previous genomic study concluded that Shigella dysenteriae type 1 (Sd1), the epidemic dysentery bacillus, emerged and spread worldwide after the First World War, with no clear pattern of transmission(2). This is not consistent with the massive cyclic dysentery epidemics reported in Europe during the eighteenth and nineteenth centuries(1,3,4) and the first isolation of Sd1 in Japan in 1897(5). Here, we report a whole-genome analysis of 331 Sd1 isolates from around the world, collected between 1915 and 2011, providing us with unprecedented insight into the historical spread of this pathogen. We show here that Sd1 has existed since at least the eighteenth century and that it swept the globe at the end of the nineteenth century, diversifying into distinct lineages associated with the First World War, Second World War and various conflicts or natural disasters across Africa, Asia and Central America. We also provide a unique historical perspective on the evolution of antibiotic resistance over a 100-year period, beginning decades before the antibiotic era, and identify a prevalent multiple antibiotic-resistant lineage in South Asia that was transmitted in several waves to Africa, where it caused severe outbreaks of disease.
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Affiliation(s)
- Elisabeth Njamkepo
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | - Nizar Fawal
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | - Alicia Tran-Dien
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | - Jane Hawkey
- Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.,School of Agriculture and Veterinary Science, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nancy Strockbine
- Centers for Disease Control and Prevention, Escherichia and Shigella Reference Unit, Atlanta, Georgia 30333, USA
| | - Claire Jenkins
- Public Health England, Gastrointestinal Bacteria Reference Unit, Colindale NW9 5HT, UK
| | - Kaisar A Talukder
- icddr,b, Enteric and Food Microbiology Laboratory, Dhaka 1212, Bangladesh
| | - Raymond Bercion
- Institut Pasteur de Bangui, BP 923, Bangui, République Centrafricaine.,Institut Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Konstantin Kuleshov
- Federal Budget Institute of Science, Central Research Institute for Epidemiology, Moscow 111123, Russia
| | - Renáta Kolínská
- Czech National Collection of Type Cultures (CNCTC), National Institute of Public Health, Prague 10, Czech Republic
| | - Julie E Russell
- Public Health England, National Collection of Type Cultures, Porton Down SP4 0JG, UK
| | - Lidia Kaftyreva
- Pasteur Institute of St Petersburg, St Petersburg 197101, Russia
| | - Marie Accou-Demartin
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | - Andreas Karas
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Olivier Vandenberg
- Department of Microbiology, LHUB-ULB, Brussels University Hospitals Laboratory, 1000 Brussels, Belgium.,Environmental Health Research Centre, Public Health School, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Alison E Mather
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Carl J Mason
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok 10400, Thailand
| | - Andrew J Page
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | | | - Chantal Bizet
- Institut Pasteur, Collection de l'Institut Pasteur (CIP), 75724 Paris Cedex 15, France
| | - Andrzej Gamian
- Polish Collection of Microorganisms, Institute of Immunology and Experimental Therapy, 53-114 Wroclaw, Poland
| | - Isabelle Carle
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | | | | | - Astrid Louise Wester
- Department of Foodborne Infections, Norwegian Institute of Public Health, Nydalen 0403, Oslo, Norway
| | - Monique Lejay-Collin
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | | | - Simon Le Hello
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | - Martin J Blaser
- Departments of Medicine and Microbiology, New York University Langone Medical Center, New York, New York 10016, USA
| | | | - Corinne Ruckly
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | - Audrey Mérens
- Biology Department and Infection Control Unit, Bégin Military Hospital, 94160 Saint-Mandé, France
| | | | - Martin Aslett
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | | | - Angelika Fruth
- Divison of Enteropathogenic Bacteria and Legionella, Robert Koch Institut, 38855 Wernigerode, Germany
| | - Erick Denamur
- INSERM, IAME, UMR 1137, Univ. Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, 75018 Paris, France
| | - Malabi Venkatesan
- Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, USA
| | - Hervé Bercovier
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Ladaporn Bodhidatta
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok 10400, Thailand
| | - Chien-Shun Chiou
- Center of Research and Diagnostics, Centers for Disease Control, Taichung 40855, Taiwan
| | - Dominique Clermont
- Institut Pasteur, Collection de l'Institut Pasteur (CIP), 75724 Paris Cedex 15, France
| | - Bianca Colonna
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie C Darwin, Sapienza Università di Roma, 00185, Roma, Italy
| | - Svetlana Egorova
- Pasteur Institute of St Petersburg, St Petersburg 197101, Russia
| | - Gururaja P Pazhani
- National Institute of Cholera and Enteric Diseases (NICED), Kolkata, West Bengal 700010, India
| | | | - Ghislaine Guigon
- Institut Pasteur, Genotyping of Pathogens and Public Health Platform, 75724 Paris Cedex 15, France
| | | | - Hidemasa Izumiya
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | | | - Anna Lutyńska
- Department of Sera and Vaccines Evaluation, National Institute of Public Health-National Institute of Hygiene, 00-791 Warsaw, Poland
| | - Malika Gouali
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | - Francine Grimont
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | | | - Monika Marejková
- National Reference Laboratory for E. coli and Shigella, National Institute of Public Health, Prague 10, Czech Republic
| | - Lorea A M Peterson
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Guillermo Perez-Perez
- Departments of Medicine and Microbiology, New York University Langone Medical Center, New York, New York 10016, USA
| | | | - Alexander Podkolzin
- Federal Budget Institute of Science, Central Research Institute for Epidemiology, Moscow 111123, Russia
| | - Erika Souche
- Institut Pasteur, Bioinformatics platform, 75724 Paris Cedex 15, France
| | - Mariia Makarova
- Pasteur Institute of St Petersburg, St Petersburg 197101, Russia
| | - German A Shipulin
- Federal Budget Institute of Science, Central Research Institute for Epidemiology, Moscow 111123, Russia
| | - Changyun Ye
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing 102206, China
| | - Helena Žemličková
- Czech National Collection of Type Cultures (CNCTC), National Institute of Public Health, Prague 10, Czech Republic.,Department of Clinical Microbiology, Faculty of Medicine and University Hospital, Charles University, 500 05, Hradec Kralove, Czech Republic
| | - Mária Herpay
- Hungarian National Collection of Medical Bacteria, National Center for Epidemiology, H-1097 Budapest, Hungary
| | - Patrick A D Grimont
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | | | - Philippe Sansonetti
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 75724 Paris Cedex 15, France
| | - Kathryn E Holt
- Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Sylvain Brisse
- Institut Pasteur, Genotyping of Pathogens and Public Health Platform, 75724 Paris Cedex 15, France.,Institut Pasteur, Microbial Evolutionary Genomics Unit, 75724 Paris Cedex 15, France.,CNRS, UMR 3525, 75015 Paris, France
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK.,London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - François-Xavier Weill
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France.,Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
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809
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Sangrador-Vegas A, Mitchell AL, Chang HY, Yong SY, Finn RD. GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw027. [PMID: 26994912 PMCID: PMC4799721 DOI: 10.1093/database/baw027] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 02/19/2016] [Indexed: 11/17/2022]
Abstract
The removal of annotation from biological databases is often perceived as an indicator of erroneous annotation. As a corollary, annotation stability is considered to be a measure of reliability. However, diverse data-driven events can affect the stability of annotations in both primary protein sequence databases and the protein family databases that are built upon the sequence databases and used to help annotate them. Here, we describe some of these events and their consequences for the InterPro database, and demonstrate that annotation removal or reassignment is not always linked to incorrect annotation by the curator. Database URL:http://www.ebi.ac.uk/interpro
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Affiliation(s)
- Amaia Sangrador-Vegas
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Alex L Mitchell
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Hsin-Yu Chang
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Siew-Yit Yong
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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810
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Chen YA, Tripathi LP, Mizuguchi K. An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw009. [PMID: 26989145 PMCID: PMC4795931 DOI: 10.1093/database/baw009] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 01/21/2016] [Indexed: 12/30/2022]
Abstract
Data analysis is one of the most critical and challenging steps in drug discovery and disease biology. A user-friendly resource to visualize and analyse high-throughput data provides a powerful medium for both experimental and computational biologists to understand vastly different biological data types and obtain a concise, simplified and meaningful output for better knowledge discovery. We have previously developed TargetMine, an integrated data warehouse optimized for target prioritization. Here we describe how upgraded and newly modelled data types in TargetMine can now survey the wider biological and chemical data space, relevant to drug discovery and development. To enhance the scope of TargetMine from target prioritization to broad-based knowledge discovery, we have also developed a new auxiliary toolkit to assist with data analysis and visualization in TargetMine. This toolkit features interactive data analysis tools to query and analyse the biological data compiled within the TargetMine data warehouse. The enhanced system enables users to discover new hypotheses interactively by performing complicated searches with no programming and obtaining the results in an easy to comprehend output format. Database URL:http://targetmine.mizuguchilab.org
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Affiliation(s)
- Yi-An Chen
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Lokesh P Tripathi
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Kenji Mizuguchi
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
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811
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Jaiteh M, Taly A, Hénin J. Evolution of Pentameric Ligand-Gated Ion Channels: Pro-Loop Receptors. PLoS One 2016; 11:e0151934. [PMID: 26986966 PMCID: PMC4795631 DOI: 10.1371/journal.pone.0151934] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 03/07/2016] [Indexed: 01/27/2023] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) are ubiquitous neurotransmitter receptors in Bilateria, with a small number of known prokaryotic homologues. Here we describe a new inventory and phylogenetic analysis of pLGIC genes across all kingdoms of life. Our main finding is a set of pLGIC genes in unicellular eukaryotes, some of which are metazoan-like Cys-loop receptors, and others devoid of Cys-loop cysteines, like their prokaryotic relatives. A number of such “Cys-less” receptors also appears in invertebrate metazoans. Together, those findings draw a new distribution of pLGICs in eukaryotes. A broader distribution of prokaryotic channels also emerges, including a major new archaeal taxon, Thaumarchaeota. More generally, pLGICs now appear nearly ubiquitous in major taxonomic groups except multicellular plants and fungi. However, pLGICs are sparsely present in unicellular taxa, suggesting a high rate of gene loss and a non-essential character, contrasting with their essential role as synaptic receptors of the bilaterian nervous system. Multiple alignments of these highly divergent sequences reveal a small number of conserved residues clustered at the interface between the extracellular and transmembrane domains. Only the “Cys-loop” proline is absolutely conserved, suggesting the more fitting name “Pro loop” for that motif, and “Pro-loop receptors” for the superfamily. The infered molecular phylogeny shows a Cys-loop and a Cys-less clade in eukaryotes, both containing metazoans and unicellular members. This suggests new hypotheses on the evolutionary history of the superfamily, such as a possible origin of the Cys-loop cysteines in an ancient unicellular eukaryote. Deeper phylogenetic relationships remain uncertain, particularly around the split between bacteria, archaea, and eukaryotes.
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Affiliation(s)
- Mariama Jaiteh
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, CNRS and Université Paris Diderot, Paris, France
| | - Antoine Taly
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, CNRS and Université Paris Diderot, Paris, France
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, CNRS and Université Paris Diderot, Paris, France
- * E-mail:
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812
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Hugo W, Zaretsky JM, Sun L, Song C, Moreno BH, Hu-Lieskovan S, Berent-Maoz B, Pang J, Chmielowski B, Cherry G, Seja E, Lomeli S, Kong X, Kelley MC, Sosman JA, Johnson DB, Ribas A, Lo RS. Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma. Cell 2016; 165:35-44. [PMID: 26997480 DOI: 10.1016/j.cell.2016.02.065] [Citation(s) in RCA: 2179] [Impact Index Per Article: 272.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 01/30/2016] [Accepted: 02/29/2016] [Indexed: 12/14/2022]
Abstract
PD-1 immune checkpoint blockade provides significant clinical benefits for melanoma patients. We analyzed the somatic mutanomes and transcriptomes of pretreatment melanoma biopsies to identify factors that may influence innate sensitivity or resistance to anti-PD-1 therapy. We find that overall high mutational loads associate with improved survival, and tumors from responding patients are enriched for mutations in the DNA repair gene BRCA2. Innately resistant tumors display a transcriptional signature (referred to as the IPRES, or innate anti-PD-1 resistance), indicating concurrent up-expression of genes involved in the regulation of mesenchymal transition, cell adhesion, extracellular matrix remodeling, angiogenesis, and wound healing. Notably, mitogen-activated protein kinase (MAPK)-targeted therapy (MAPK inhibitor) induces similar signatures in melanoma, suggesting that a non-genomic form of MAPK inhibitor resistance mediates cross-resistance to anti-PD-1 therapy. Validation of the IPRES in other independent tumor cohorts defines a transcriptomic subset across distinct types of advanced cancer. These findings suggest that attenuating the biological processes that underlie IPRES may improve anti-PD-1 response in melanoma and other cancer types.
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Affiliation(s)
- Willy Hugo
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Jesse M Zaretsky
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Lu Sun
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Chunying Song
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Blanca Homet Moreno
- Division of Hematology & Oncology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Siwen Hu-Lieskovan
- Division of Hematology & Oncology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Beata Berent-Maoz
- Division of Hematology & Oncology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Jia Pang
- Division of Hematology & Oncology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Bartosz Chmielowski
- Division of Hematology & Oncology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Grace Cherry
- Division of Hematology & Oncology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Elizabeth Seja
- Division of Hematology & Oncology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Shirley Lomeli
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Xiangju Kong
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Mark C Kelley
- Department of Surgery, Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA
| | - Jeffrey A Sosman
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA
| | - Douglas B Johnson
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA
| | - Antoni Ribas
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095-1662, USA; Division of Hematology & Oncology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA; Division of Surgical Oncology, Department of Surgery, University of California, Los Angeles, CA 90095-1662, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1662, USA
| | - Roger S Lo
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, CA 90095-1662, USA; Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095-1662, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1662, USA.
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813
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Cromar GL, Zhao A, Xiong X, Swapna LS, Loughran N, Song H, Parkinson J. PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw013. [PMID: 26980519 PMCID: PMC4792532 DOI: 10.1093/database/baw013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/29/2016] [Indexed: 11/13/2022]
Abstract
PhyloPro is a database and accompanying web-based application for the construction and exploration of phylogenetic profiles across the Eukarya. In this update article, we present six major new developments in PhyloPro: (i) integration of Pfam-A domain predictions for all proteins; (ii) new summary heatmaps and detailed level views of domain conservation; (iii) an interactive, network-based visualization tool for exploration of domain architectures and their conservation; (iv) ability to browse based on protein functional categories (GOSlim); (v) improvements to the web interface to enhance drill down capability from the heatmap view; and (vi) improved coverage including 164 eukaryotes and 12 reference species. In addition, we provide improved support for downloading data and images in a variety of formats. Among the existing tools available for phylogenetic profiles, PhyloPro provides several innovative domain-based features including a novel domain adjacency visualization tool. These are designed to allow the user to identify and compare proteins with similar domain architectures across species and thus develop hypotheses about the evolution of lineage-specific trajectories. Database URL: http://www.compsysbio.org/phylopro/.
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Affiliation(s)
- Graham L Cromar
- Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and
| | - Anthony Zhao
- Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and
| | - Xuejian Xiong
- Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and
| | - Lakshmipuram S Swapna
- Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and
| | - Noeleen Loughran
- Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and
| | - Hongyan Song
- Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and
| | - John Parkinson
- Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON M5G 0A4, Canada and Departments of Biochemistry, Computer Science and Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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814
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Glantz ST, Carpenter EJ, Melkonian M, Gardner KH, Boyden ES, Wong GKS, Chow BY. Functional and topological diversity of LOV domain photoreceptors. Proc Natl Acad Sci U S A 2016; 113:E1442-51. [PMID: 26929367 PMCID: PMC4801262 DOI: 10.1073/pnas.1509428113] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Light-oxygen-voltage sensitive (LOV) flavoproteins are ubiquitous photoreceptors that mediate responses to environmental cues. Photosensory inputs are transduced into signaling outputs via structural rearrangements in sensor domains that consequently modulate the activity of an effector domain or multidomain clusters. Establishing the diversity in effector function and sensor-effector topology will inform what signaling mechanisms govern light-responsive behaviors across multiple kingdoms of life and how these signals are transduced. Here, we report the bioinformatics identification of over 6,700 candidate LOV domains (including over 4,000 previously unidentified sequences from plants and protists), and insights from their annotations for ontological function and structural arrangements. Motif analysis identified the sensors from ∼42 million ORFs, with strong statistical separation from other flavoproteins and non-LOV members of the structurally related Per-aryl hydrocarbon receptor nuclear translocator (ARNT)-Sim family. Conserved-domain analysis determined putative light-regulated function and multidomain topologies. We found that for certain effectors, sensor-effector linker length is discretized based on both phylogeny and the preservation of α-helical heptad repeats within an extended coiled-coil linker structure. This finding suggests that preserving sensor-effector orientation is a key determinant of linker length, in addition to ancestry, in LOV signaling structure-function. We found a surprisingly high prevalence of effectors with functions previously thought to be rare among LOV proteins, such as regulators of G protein signaling, and discovered several previously unidentified effectors, such as lipases. This work highlights the value of applying genomic and transcriptomic technologies to diverse organisms to capture the structural and functional variation in photosensory proteins that are vastly important in adaptation, photobiology, and optogenetics.
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Affiliation(s)
- Spencer T Glantz
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Eric J Carpenter
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | - Michael Melkonian
- Institute of Botany, Cologne Biocenter, University of Cologne, 50674 Cologne, Germany
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, City College of New York, New York, NY 10031; Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031; Biochemistry, Chemistry and Biology Programs, Graduate Center, The City University of New York, New York, NY 10031
| | - Edward S Boyden
- The Media Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139; McGovern Institute for Brain Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9; Department of Medicine, University of Alberta, Edmonton, AB, Canada T6G 2E1; BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Brian Y Chow
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104;
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815
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Karaki L, Da Silva P, Rizk F, Chouabe C, Chantret N, Eyraud V, Gressent F, Sivignon C, Rahioui I, Kahn D, Brochier-Armanet C, Rahbé Y, Royer C. Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula. BMC PLANT BIOLOGY 2016; 16:63. [PMID: 26964738 PMCID: PMC4785745 DOI: 10.1186/s12870-016-0745-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 02/25/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND Albumin 1b peptides (A1b) are small disulfide-knotted insecticidal peptides produced by Fabaceae (also called Leguminosae). To date, their diversity among this plant family has been essentially investigated through biochemical and PCR-based approaches. The availability of high-quality genomic resources for several fabaceae species, among which the model species Medicago truncatula (Mtr), allowed for a genomic analysis of this protein family aimed at i) deciphering the evolutionary history of A1b proteins and their links with A1b-nodulins that are short non-insecticidal disulfide-bonded peptides involved in root nodule signaling and ii) exploring the functional diversity of A1b for novel bioactive molecules. RESULTS Investigating the Mtr genome revealed a remarkable expansion, mainly through tandem duplications, of albumin1 (A1) genes, retaining nearly all of the same canonical structure at both gene and protein levels. Phylogenetic analysis revealed that the ancestral molecule was most probably insecticidal giving rise to, among others, A1b-nodulins. Expression meta-analysis revealed that many A1b coding genes are silent and a wide tissue distribution of the A1 transcripts/peptides within plant organs. Evolutionary rate analyses highlighted branches and sites with positive selection signatures, including two sites shown to be critical for insecticidal activity. Seven peptides were chemically synthesized and folded in vitro, then assayed for their biological activity. Among these, AG41 (aka MtrA1013 isoform, encoded by the orphan TA24778 contig.), showed an unexpectedly high insecticidal activity. The study highlights the unique burst of diversity of A1 peptides within the Medicago genus compared to the other taxa for which full-genomes are available: no A1 member in Lotus, or in red clover to date, while only a few are present in chick pea, soybean or pigeon pea genomes. CONCLUSION The expansion of the A1 family in the Medicago genus is reminiscent of the situation described for another disulfide-rich peptide family, the "Nodule-specific Cysteine-Rich" (NCR), discovered within the same species. The oldest insecticidal A1b toxin was described from the Sophorae, dating the birth of this seed-defense function to more than 58 million years, and making this model of plant/insect toxin/receptor (A1b/insect v-ATPase) one of the oldest known.
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Affiliation(s)
- L. Karaki
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />ER030-EDST; Department of Life and Earth Sciences, Faculty of Sciences II, Lebanese University, Beirut, Lebanon
- />Université de Lyon, F-69000 Lyon, France
| | - P. Da Silva
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - F. Rizk
- />ER030-EDST; Department of Life and Earth Sciences, Faculty of Sciences II, Lebanese University, Beirut, Lebanon
| | - C. Chouabe
- />Université de Lyon, F-69000 Lyon, France
- />UCBL, CarMeN Laboratory, INSERM UMR-1060, Cardioprotection Team, Faculté de Médecine, Univ Lyon-1, Université Claude Bernard Lyon1, 8 Avenue Rockefeller, 69373 Lyon Cedex 08, France
| | - N. Chantret
- />INRA, UMR1334 AGAP, 2 Place Pierre Viala, 34060 Montpellier, France
- />Supagro Montpellier, 2 Place Pierre Viala, 34060 Montpellier, France
| | - V. Eyraud
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - F. Gressent
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - C. Sivignon
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - I. Rahioui
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - D. Kahn
- />Université de Lyon, F-69000 Lyon, France
- />Université Claude Bernard Lyon 1; CNRS; INRA; UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne, France
| | - C. Brochier-Armanet
- />Université de Lyon, F-69000 Lyon, France
- />Université Claude Bernard Lyon 1; CNRS; INRA; UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Y. Rahbé
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - C. Royer
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
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816
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Alves JMP, de Oliveira AL, Sandberg TOM, Moreno-Gallego JL, de Toledo MAF, de Moura EMM, Oliveira LS, Durham AM, Mehnert DU, Zanotto PMDA, Reyes A, Gruber A. GenSeed-HMM: A Tool for Progressive Assembly Using Profile HMMs as Seeds and its Application in Alpavirinae Viral Discovery from Metagenomic Data. Front Microbiol 2016; 7:269. [PMID: 26973638 PMCID: PMC4777721 DOI: 10.3389/fmicb.2016.00269] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/19/2016] [Indexed: 01/01/2023] Open
Abstract
This work reports the development of GenSeed-HMM, a program that implements seed-driven progressive assembly, an approach to reconstruct specific sequences from unassembled data, starting from short nucleotide or protein seed sequences or profile Hidden Markov Models (HMM). The program can use any one of a number of sequence assemblers. Assembly is performed in multiple steps and relatively few reads are used in each cycle, consequently the program demands low computational resources. As a proof-of-concept and to demonstrate the power of HMM-driven progressive assemblies, GenSeed-HMM was applied to metagenomic datasets in the search for diverse ssDNA bacteriophages from the recently described Alpavirinae subfamily. Profile HMMs were built using Alpavirinae-specific regions from multiple sequence alignments (MSA) using either the viral protein 1 (VP1; major capsid protein) or VP4 (genome replication initiation protein). These profile HMMs were used by GenSeed-HMM (running Newbler assembler) as seeds to reconstruct viral genomes from sequencing datasets of human fecal samples. All contigs obtained were annotated and taxonomically classified using similarity searches and phylogenetic analyses. The most specific profile HMM seed enabled the reconstruction of 45 partial or complete Alpavirinae genomic sequences. A comparison with conventional (global) assembly of the same original dataset, using Newbler in a standalone execution, revealed that GenSeed-HMM outperformed global genomic assembly in several metrics employed. This approach is capable of detecting organisms that have not been used in the construction of the profile HMM, which opens up the possibility of diagnosing novel viruses, without previous specific information, constituting a de novo diagnosis. Additional applications include, but are not limited to, the specific assembly of extrachromosomal elements such as plastid and mitochondrial genomes from metagenomic data. Profile HMM seeds can also be used to reconstruct specific protein coding genes for gene diversity studies, and to determine all possible gene variants present in a metagenomic sample. Such surveys could be useful to detect the emergence of drug-resistance variants in sensitive environments such as hospitals and animal production facilities, where antibiotics are regularly used. Finally, GenSeed-HMM can be used as an adjunct for gap closure on assembly finishing projects, by using multiple contig ends as anchored seeds.
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Affiliation(s)
- João M P Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - André L de Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Tatiana O M Sandberg
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | | | - Marcelo A F de Toledo
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Elisabeth M M de Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Liliane S Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São PauloSão Paulo, Brazil; Department of Computer Science, Institute of Mathematics and Statistics, University of São PauloSão Paulo, Brazil
| | - Alan M Durham
- Department of Computer Science, Institute of Mathematics and Statistics, University of São Paulo São Paulo, Brazil
| | - Dolores U Mehnert
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Paolo M de A Zanotto
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Alejandro Reyes
- Department of Biological Sciences, Universidad de los AndesBogotá, Colombia; Center for Genome Sciences and Systems Biology, Department of Pathology and Immunology, Washington University in Saint LouisMO, USA
| | - Arthur Gruber
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
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817
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Kerkhoven EJ, Pomraning KR, Baker SE, Nielsen J. Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica. NPJ Syst Biol Appl 2016; 2:16005. [PMID: 28725468 PMCID: PMC5516929 DOI: 10.1038/npjsba.2016.5] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/23/2015] [Accepted: 12/07/2015] [Indexed: 01/01/2023] Open
Abstract
Yarrowia lipolytica is a promising microbial cell factory for the production of lipids to be used as fuels and chemicals, but there are few studies on regulation of its metabolism. Here we performed the first integrated data analysis of Y. lipolytica grown in carbon and nitrogen limited chemostat cultures. We first reconstructed a genome-scale metabolic model and used this for integrative analysis of multilevel omics data. Metabolite profiling and lipidomics was used to quantify the cellular physiology, while regulatory changes were measured using RNAseq. Analysis of the data showed that lipid accumulation in Y. lipolytica does not involve transcriptional regulation of lipid metabolism but is associated with regulation of amino-acid biosynthesis, resulting in redirection of carbon flux during nitrogen limitation from amino acids to lipids. Lipid accumulation in Y. lipolytica at nitrogen limitation is similar to the overflow metabolism observed in many other microorganisms, e.g. ethanol production by Sacchromyces cerevisiae at nitrogen limitation.
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Affiliation(s)
- Eduard J Kerkhoven
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Kyle R Pomraning
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Scott E Baker
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jens Nielsen
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
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818
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Laurino P, Tóth-Petróczy Á, Meana-Pañeda R, Lin W, Truhlar DG, Tawfik DS. An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors. PLoS Biol 2016; 14:e1002396. [PMID: 26938925 PMCID: PMC4777477 DOI: 10.1371/journal.pbio.1002396] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 01/29/2016] [Indexed: 01/30/2023] Open
Abstract
Nucleoside-based cofactors are presumed to have preceded proteins. The Rossmann fold is one of the most ancient and functionally diverse protein folds, and most Rossmann enzymes utilize nucleoside-based cofactors. We analyzed an omnipresent Rossmann ribose-binding interaction: a carboxylate side chain at the tip of the second β-strand (β2-Asp/Glu). We identified a canonical motif, defined by the β2-topology and unique geometry. The latter relates to the interaction being bidentate (both ribose hydroxyls interacting with the carboxylate oxygens), to the angle between the carboxylate and the ribose, and to the ribose's ring configuration. We found that this canonical motif exhibits hallmarks of divergence rather than convergence. It is uniquely found in Rossmann enzymes that use different cofactors, primarily SAM (S-adenosyl methionine), NAD (nicotinamide adenine dinucleotide), and FAD (flavin adenine dinucleotide). Ribose-carboxylate bidentate interactions in other folds are not only rare but also have a different topology and geometry. We further show that the canonical geometry is not dictated by a physical constraint--geometries found in noncanonical interactions have similar calculated bond energies. Overall, these data indicate the divergence of several major Rossmann-fold enzyme classes, with different cofactors and catalytic chemistries, from a common pre-LUCA (last universal common ancestor) ancestor that possessed the β2-Asp/Glu motif.
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Affiliation(s)
- Paola Laurino
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Ágnes Tóth-Petróczy
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Rubén Meana-Pañeda
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Wei Lin
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Dan S. Tawfik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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819
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Morton KJ, Jia S, Zhang C, Holding DR. Proteomic profiling of maize opaque endosperm mutants reveals selective accumulation of lysine-enriched proteins. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1381-96. [PMID: 26712829 PMCID: PMC4762381 DOI: 10.1093/jxb/erv532] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Reduced prolamin (zein) accumulation and defective endoplasmic reticulum (ER) body formation occurs in maize opaque endosperm mutants opaque2 (o2), floury2 (fl2), defective endosperm*B30 (DeB30), and Mucronate (Mc), whereas other opaque mutants such as opaque1 (o1) and floury1 (fl1) are normal in these regards. This suggests that other factors contribute to kernel texture. A liquid chromatography approach coupled with tandem mass spectrometry (LC-MS/MS) proteomics was used to compare non-zein proteins of nearly isogenic opaque endosperm mutants. In total, 2762 proteins were identified that were enriched for biological processes such as protein transport and folding, amino acid biosynthesis, and proteolysis. Principal component analysis and pathway enrichment suggested that the mutants partitioned into three groups: (i) Mc, DeB30, fl2 and o2; (ii) o1; and (iii) fl1. Indicator species analysis revealed mutant-specific proteins, and highlighted ER secretory pathway components that were enriched in selected groups of mutants. The most significantly changed proteins were related to stress or defense and zein partitioning into the soluble fraction for Mc, DeB30, o1, and fl1 specifically. In silico dissection of the most significantly changed proteins revealed novel qualitative changes in lysine abundance contributing to the overall lysine increase and the nutritional rebalancing of the o2 and fl2 endosperm.
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Affiliation(s)
- Kyla J Morton
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, 1901 Vine Street, PO Box 880665, University of Nebraska, Lincoln, NE 68588-0665, USA
| | - Shangang Jia
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, 1901 Vine Street, PO Box 880665, University of Nebraska, Lincoln, NE 68588-0665, USA
| | - Chi Zhang
- School of Biological Sciences, Center for Plant Science Innovation, Beadle Center for Biotechnology, 1901 Vine Street, PO Box 880665, University of Nebraska, Lincoln, NE 68588-0665, USA
| | - David R Holding
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, 1901 Vine Street, PO Box 880665, University of Nebraska, Lincoln, NE 68588-0665, USA
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820
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Schmoll M, Dattenböck C, Carreras-Villaseñor N, Mendoza-Mendoza A, Tisch D, Alemán MI, Baker SE, Brown C, Cervantes-Badillo MG, Cetz-Chel J, Cristobal-Mondragon GR, Delaye L, Esquivel-Naranjo EU, Frischmann A, Gallardo-Negrete JDJ, García-Esquivel M, Gomez-Rodriguez EY, Greenwood DR, Hernández-Oñate M, Kruszewska JS, Lawry R, Mora-Montes HM, Muñoz-Centeno T, Nieto-Jacobo MF, Nogueira Lopez G, Olmedo-Monfil V, Osorio-Concepcion M, Piłsyk S, Pomraning KR, Rodriguez-Iglesias A, Rosales-Saavedra MT, Sánchez-Arreguín JA, Seidl-Seiboth V, Stewart A, Uresti-Rivera EE, Wang CL, Wang TF, Zeilinger S, Casas-Flores S, Herrera-Estrella A. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. Microbiol Mol Biol Rev 2016; 80:205-327. [PMID: 26864432 PMCID: PMC4771370 DOI: 10.1128/mmbr.00040-15] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.
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Affiliation(s)
- Monika Schmoll
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | - Christoph Dattenböck
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Doris Tisch
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Mario Ivan Alemán
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | - Scott E Baker
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher Brown
- University of Otago, Department of Biochemistry and Genetics, Dunedin, New Zealand
| | | | - José Cetz-Chel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - Luis Delaye
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | | | - Alexa Frischmann
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | - Monica García-Esquivel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - David R Greenwood
- The University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Miguel Hernández-Oñate
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | - Joanna S Kruszewska
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Robert Lawry
- Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand
| | | | | | | | | | | | | | - Sebastian Piłsyk
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aroa Rodriguez-Iglesias
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | | | - Chih-Li Wang
- National Chung-Hsing University, Department of Plant Pathology, Taichung, Taiwan
| | - Ting-Fang Wang
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan
| | - Susanne Zeilinger
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria University of Innsbruck, Institute of Microbiology, Innsbruck, Austria
| | | | - Alfredo Herrera-Estrella
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
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821
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Schilmiller AL, Gilgallon K, Ghosh B, Jones AD, Last RL. Acylsugar Acylhydrolases: Carboxylesterase-Catalyzed Hydrolysis of Acylsugars in Tomato Trichomes. PLANT PHYSIOLOGY 2016; 170:1331-44. [PMID: 26811191 PMCID: PMC4775116 DOI: 10.1104/pp.15.01348] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 01/23/2016] [Indexed: 05/05/2023]
Abstract
Glandular trichomes of cultivated tomato (Solanum lycopersicum) and many other species throughout the Solanaceae produce and secrete mixtures of sugar esters (acylsugars) on the plant aerial surfaces. In wild and cultivated tomato, these metabolites consist of a sugar backbone, typically glucose or sucrose, and two to five acyl chains esterified to various positions on the sugar core. The aliphatic acyl chains vary in length and branching and are transferred to the sugar by a series of reactions catalyzed by acylsugar acyltransferases. A phenotypic screen of a set of S. lycopersicum M82 × Solanum pennellii LA0716 introgression lines identified a dominant genetic locus on chromosome 5 from the wild relative that affected total acylsugar levels. Genetic mapping revealed that the reduction in acylsugar levels was consistent with the presence and increased expression of two S. pennellii genes (Sopen05g030120 and Sopen05g030130) encoding putative carboxylesterase enzymes of the α/β-hydrolase superfamily. These two enzymes, named ACYLSUGAR ACYLHYDROLASE1 (ASH1) and ASH2, were shown to remove acyl chains from specific positions of certain types of acylsugars in vitro. A survey of related genes in M82 and LA0716 identified another trichome-expressed ASH gene on chromosome 9 (M82, Solyc09g075710; LA0716, Sopen09g030520) encoding a protein with similar activity. Characterization of the in vitro activities of the SpASH enzymes showed reduced activities with acylsugars produced by LA0716, presumably contributing to the high-level production of acylsugars in the presence of highly expressed SpASH genes.
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Affiliation(s)
- Anthony L Schilmiller
- Department of Biochemistry and Molecular Biology (A.L.S, K.G., B.G., A.D.J., R.L.L.), Department of Chemistry (A.D.J.), and Department of Plant Biology (R.L.L.), Michigan State University, East Lansing, Michigan 48824-1319
| | - Karin Gilgallon
- Department of Biochemistry and Molecular Biology (A.L.S, K.G., B.G., A.D.J., R.L.L.), Department of Chemistry (A.D.J.), and Department of Plant Biology (R.L.L.), Michigan State University, East Lansing, Michigan 48824-1319
| | - Banibrata Ghosh
- Department of Biochemistry and Molecular Biology (A.L.S, K.G., B.G., A.D.J., R.L.L.), Department of Chemistry (A.D.J.), and Department of Plant Biology (R.L.L.), Michigan State University, East Lansing, Michigan 48824-1319
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology (A.L.S, K.G., B.G., A.D.J., R.L.L.), Department of Chemistry (A.D.J.), and Department of Plant Biology (R.L.L.), Michigan State University, East Lansing, Michigan 48824-1319
| | - Robert L Last
- Department of Biochemistry and Molecular Biology (A.L.S, K.G., B.G., A.D.J., R.L.L.), Department of Chemistry (A.D.J.), and Department of Plant Biology (R.L.L.), Michigan State University, East Lansing, Michigan 48824-1319
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822
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Agarwal A, Bertolla RP, Samanta L. Sperm proteomics: potential impact on male infertility treatment. Expert Rev Proteomics 2016; 13:285-96. [DOI: 10.1586/14789450.2016.1151357] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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823
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Hunt VL, Tsai IJ, Coghlan A, Reid AJ, Holroyd N, Foth BJ, Tracey A, Cotton JA, Stanley EJ, Beasley H, Bennett HM, Brooks K, Harsha B, Kajitani R, Kulkarni A, Harbecke D, Nagayasu E, Nichol S, Ogura Y, Quail MA, Randle N, Xia D, Brattig NW, Soblik H, Ribeiro DM, Sanchez-Flores A, Hayashi T, Itoh T, Denver DR, Grant W, Stoltzfus JD, Lok JB, Murayama H, Wastling J, Streit A, Kikuchi T, Viney M, Berriman M. The genomic basis of parasitism in the Strongyloides clade of nematodes. Nat Genet 2016; 48:299-307. [PMID: 26829753 PMCID: PMC4948059 DOI: 10.1038/ng.3495] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 12/23/2015] [Indexed: 12/19/2022]
Abstract
Soil-transmitted nematodes, including the Strongyloides genus, cause one of the most prevalent neglected tropical diseases. Here we compare the genomes of four Strongyloides species, including the human pathogen Strongyloides stercoralis, and their close relatives that are facultatively parasitic (Parastrongyloides trichosuri) and free-living (Rhabditophanes sp. KR3021). A significant paralogous expansion of key gene families--families encoding astacin-like and SCP/TAPS proteins--is associated with the evolution of parasitism in this clade. Exploiting the unique Strongyloides life cycle, we compare the transcriptomes of the parasitic and free-living stages and find that these same gene families are upregulated in the parasitic stages, underscoring their role in nematode parasitism.
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Affiliation(s)
- Vicky L. Hunt
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Isheng J. Tsai
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Avril Coghlan
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Adam J. Reid
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Nancy Holroyd
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Bernardo J. Foth
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Alan Tracey
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - James A. Cotton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Eleanor J. Stanley
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Helen Beasley
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Hayley M. Bennett
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Karen Brooks
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Bhavana Harsha
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Rei Kajitani
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Arpita Kulkarni
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | - Eiji Nagayasu
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Sarah Nichol
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Michael A. Quail
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Nadine Randle
- Department of Infection Biology, Institute of Infection and Global Health and School of Veterinary Science, University of Liverpool, Liverpool, UK
| | - Dong Xia
- Department of Infection Biology, Institute of Infection and Global Health and School of Veterinary Science, University of Liverpool, Liverpool, UK
| | - Norbert W. Brattig
- Department of Molecular Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Hanns Soblik
- Department of Molecular Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Diogo M. Ribeiro
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Alejandro Sanchez-Flores
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Unidad de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México, 62210
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takehiko Itoh
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Dee R. Denver
- Department of Intergrative Biology, Oregon State University, Corvallis, Oregon, USA
| | - Warwick Grant
- Department of Animal, Plant and Soil Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Jonathan D. Stoltzfus
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia 19104, PA, USA
| | - James B. Lok
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia 19104, PA, USA
| | - Haruhiko Murayama
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Jonathan Wastling
- Department of Infection Biology, Institute of Infection and Global Health and School of Veterinary Science, University of Liverpool, Liverpool, UK
- Faculty of Natural Sciences, University of Keele, Keele, Staffordshire, ST5 5BG, UK
| | - Adrian Streit
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Taisei Kikuchi
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Mark Viney
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
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824
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Venom gland transcriptome analyses of two freshwater stingrays (Myliobatiformes: Potamotrygonidae) from Brazil. Sci Rep 2016; 6:21935. [PMID: 26916342 PMCID: PMC4768133 DOI: 10.1038/srep21935] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 02/03/2016] [Indexed: 01/17/2023] Open
Abstract
Stingrays commonly cause human envenoming related accidents in populations of the sea, near rivers and lakes. Transcriptomic profiles have been used to elucidate components of animal venom, since they are capable of providing molecular information on the biology of the animal and could have biomedical applications. In this study, we elucidated the transcriptomic profile of the venom glands from two different freshwater stingray species that are endemic to the Paraná-Paraguay basin in Brazil, Potamotrygon amandae and Potamotrygon falkneri. Using RNA-Seq, we identified species-specific transcripts and overlapping proteins in the venom gland of both species. Among the transcripts related with envenoming, high abundance of hyaluronidases was observed in both species. In addition, we built three-dimensional homology models based on several venom transcripts identified. Our study represents a significant improvement in the information about the venoms employed by these two species and their molecular characteristics. Moreover, the information generated by our group helps in a better understanding of the biology of freshwater cartilaginous fishes and offers clues for the development of clinical treatments for stingray envenoming in Brazil and around the world. Finally, our results might have biomedical implications in developing treatments for complex diseases.
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825
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Jeong CS, Kim D. Structure-based Markov random field model for representing evolutionary constraints on functional sites. BMC Bioinformatics 2016; 17:99. [PMID: 26911566 PMCID: PMC4765150 DOI: 10.1186/s12859-016-0948-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 02/15/2016] [Indexed: 11/10/2022] Open
Abstract
Background Elucidating the cooperative mechanism of interconnected residues is an important component toward understanding the biological function of a protein. Coevolution analysis has been developed to model the coevolutionary information reflecting structural and functional constraints. Recently, several methods have been developed based on a probabilistic graphical model called the Markov random field (MRF), which have led to significant improvements for coevolution analysis; however, thus far, the performance of these models has mainly been assessed by focusing on the aspect of protein structure. Results In this study, we built an MRF model whose graphical topology is determined by the residue proximity in the protein structure, and derived a novel positional coevolution estimate utilizing the node weight of the MRF model. This structure-based MRF method was evaluated for three data sets, each of which annotates catalytic site, allosteric site, and comprehensively determined functional site information. We demonstrate that the structure-based MRF architecture can encode the evolutionary information associated with biological function. Furthermore, we show that the node weight can more accurately represent positional coevolution information compared to the edge weight. Lastly, we demonstrate that the structure-based MRF model can be reliably built with only a few aligned sequences in linear time. Conclusions The results show that adoption of a structure-based architecture could be an acceptable approximation for coevolution modeling with efficient computation complexity.
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Affiliation(s)
- Chan-Seok Jeong
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Dongsup Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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826
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Identification of repetitive units in protein structures with ReUPred. Amino Acids 2016; 48:1391-400. [PMID: 26898549 DOI: 10.1007/s00726-016-2187-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 01/23/2016] [Indexed: 01/02/2023]
Abstract
Over the last decade, numerous studies have demonstrated the fundamental importance of tandem repeat (TR) proteins in many biological processes. A plethora of new repeat structures have also been solved. The recently published RepeatsDB provides information on TR proteins. However, a detailed structural characterization of repetitive elements is largely missing, as repeat unit annotation is manually curated and currently covers only 3 % of the bona fide TR proteins. Repeat Protein Unit Predictor (ReUPred) is a novel method for the fast automatic prediction of repeat units and repeat classification using an extensive Structure Repeat Unit Library (SRUL) derived from RepeatsDB. ReUPred uses an iterative structural search against the SRUL to find repetitive units. On a test set of solenoid proteins, ReUPred is able to correctly detect 92 % of the proteins. Unlike previous methods, it is also able to correctly classify solenoid repeats in 89 % of cases. It also outperforms two recent state-of-the-art methods for the repeat unit identification problem. The accurate prediction of repeat units increases the number of annotated repeat units by an order of magnitude compared to the sequence-based Pfam classification. ReUPred is implemented in Python for Linux and freely available from the URL: http://protein.bio.unipd.it/reupred/ .
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827
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Bohne AV, Schwenkert S, Grimm B, Nickelsen J. Roles of Tetratricopeptide Repeat Proteins in Biogenesis of the Photosynthetic Apparatus. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 324:187-227. [PMID: 27017009 DOI: 10.1016/bs.ircmb.2016.01.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Biosynthesis of the photosynthetic apparatus is a complex operation, which includes the concerted synthesis and assembly of lipids, pigments and metal cofactors, and dozens of proteins. Research conducted in recent years has shown that these processes, as well as the stabilization and repair of this molecular machinery, are facilitated by transiently acting regulatory proteins, many of which belong to the superfamily of helical repeat proteins. Here, we focus on one of its families in photoautotrophic model organisms, the tetratricopeptide repeat (TPR) proteins, which participate in almost all of these steps and are crucial for biogenesis of the thylakoid membrane.
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Affiliation(s)
- A-V Bohne
- Molecular Plant Sciences, Ludwig-Maximilians-University, Munich, Germany
| | - S Schwenkert
- Botany, Ludwig-Maximilians-University, Munich, Germany
| | - B Grimm
- Institute of Biology/Plant Physiology, Humboldt University, Berlin, Germany
| | - J Nickelsen
- Molecular Plant Sciences, Ludwig-Maximilians-University, Munich, Germany.
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828
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Shore R, Covill L, Pettigrew KA, Brandler WM, Diaz R, Xu Y, Tello JA, Talcott JB, Newbury DF, Stein J, Monaco AP, Paracchini S. The handedness-associated PCSK6 locus spans an intronic promoter regulating novel transcripts. Hum Mol Genet 2016; 25:1771-9. [PMID: 26908617 PMCID: PMC4986331 DOI: 10.1093/hmg/ddw047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 02/15/2016] [Indexed: 12/12/2022] Open
Abstract
We recently reported the association of the PCSK6 gene with handedness through a quantitative genome-wide association study (GWAS; P < 0.5 × 10−8) for a relative hand skill measure in individuals with dyslexia. PCSK6 activates Nodal, a morphogen involved in regulating left–right body axis determination. Therefore, the GWAS data suggest that the biology underlying the patterning of structural asymmetries may also contribute to behavioural laterality, e.g. handedness. The association is further supported by an independent study reporting a variable number tandem repeat (VNTR) within the same PCSK6 locus to be associated with degree of handedness in a general population cohort. Here, we have conducted a functional analysis of the PCSK6 locus combining further genetic analysis, in silico predictions and molecular assays. We have shown that the previous GWAS signal was not tagging a VNTR effect, suggesting that the two markers have independent effects. We demonstrated experimentally that one of the top GWAS-associated markers, rs11855145, directly alters the binding site for a nuclear factor. Furthermore, we have shown that the predicted regulatory region adjacent to rs11855415 acts as a bidirectional promoter controlling the expression of novel RNA transcripts. These include both an antisense long non-coding RNA (lncRNA) and a short PCSK6 isoform predicted to be coding. This is the first molecular characterization of a handedness-associated locus that supports the role of common variants in non-coding sequences in influencing complex phenotypes through gene expression regulation.
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Affiliation(s)
- Robert Shore
- School of Medicine, University of St Andrews, St Andrews KY169TF, UK
| | - Laura Covill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kerry A Pettigrew
- School of Medicine, University of St Andrews, St Andrews KY169TF, UK
| | - William M Brandler
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Rebeca Diaz
- School of Medicine, University of St Andrews, St Andrews KY169TF, UK
| | - Yiwang Xu
- School of Medicine, University of St Andrews, St Andrews KY169TF, UK
| | - Javier A Tello
- School of Medicine, University of St Andrews, St Andrews KY169TF, UK
| | - Joel B Talcott
- School of Life and Health Sciences, Aston University, Birmingham, UK and
| | - Dianne F Newbury
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - John Stein
- Department of Physiology, Anatomy & Genetics, Parks Rd., Oxford OX1 3PT, UK
| | - Anthony P Monaco
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Silvia Paracchini
- School of Medicine, University of St Andrews, St Andrews KY169TF, UK,
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829
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The Genetic Basis of Haploid Induction in Maize Identified with a Novel Genome-Wide Association Method. Genetics 2016; 202:1267-76. [PMID: 26896330 DOI: 10.1534/genetics.115.184234] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 02/16/2016] [Indexed: 11/18/2022] Open
Abstract
In vivo haploid induction (HI) triggered by pollination with special intraspecific genotypes, called inducers, is unique to Zea maysL. within the plant kingdom and has revolutionized maize breeding during the last decade. However, the molecular mechanisms underlying HI in maize are still unclear. To investigate the genetic basis of HI, we developed a new approach for genome-wide association studies (GWAS), termed conditional haplotype extension (CHE) test that allows detection of selective sweeps even under almost perfect confounding of population structure and trait expression. Here, we applied this test to identify genomic regions required for HI expression and dissected the combined support interval (50.34 Mb) of the QTL qhir1, detected in a previous study, into two closely linked genomic segments relevant for HI expression. The first, termed qhir11(0.54 Mb), comprises an already fine-mapped region but was not diagnostic for differentiating inducers and noninducers. The second segment, termed qhir12(3.97 Mb), had a haplotype allele common to all 53 inducer lines but not found in any of the 1482 noninducers. By comparing resequencing data of one inducer with 14 noninducers, we detected in the qhir12 region three candidate genes involved in DNA or amino acid binding, however, none for qhir11 We propose that the CHE test can be utilized in introgression breeding and different fields of genetics to detect selective sweeps in heterogeneous genetic backgrounds.
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830
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Wang R, Xiong J, Wang W, Miao W, Liang A. High frequency of +1 programmed ribosomal frameshifting in Euplotes octocarinatus. Sci Rep 2016; 6:21139. [PMID: 26891713 PMCID: PMC4759687 DOI: 10.1038/srep21139] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 01/18/2016] [Indexed: 01/25/2023] Open
Abstract
Programmed -1 ribosomal frameshifting (-1 PRF) has been identified as a mechanism to regulate the expression of many viral genes and some cellular genes. The slippery site of -1 PRF has been well characterized, whereas the +1 PRF signal and the mechanism involved in +1 PRF remain poorly understood. Previous study confirmed that +1 PRF is required for the synthesis of protein products in several genes of ciliates from the genus Euplotes. To accurately assess the frequency of genes requiring frameshift in Euplotes, the macronuclear genome and transcriptome of Euplotes octocarinatus were analyzed in this study. A total of 3,700 +1 PRF candidate genes were identified from 32,353 transcripts, and the gene products of these putative +1 PRFs were mainly identified as protein kinases. Furthermore, we reported a putative suppressor tRNA of UAA which may provide new insights into the mechanism of +1 PRF in euplotids. For the first time, our transcriptome-wide survey of +1 PRF in E. octocarinatus provided a dataset which serves as a valuable resource for the future understanding of the mechanism underlying +1 PRF.
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Affiliation(s)
- Ruanlin Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Aihua Liang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
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831
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Dos Santos Castro L, de Paula RG, Antoniêto ACC, Persinoti GF, Silva-Rocha R, Silva RN. Understanding the Role of the Master Regulator XYR1 in Trichoderma reesei by Global Transcriptional Analysis. Front Microbiol 2016; 7:175. [PMID: 26909077 PMCID: PMC4754417 DOI: 10.3389/fmicb.2016.00175] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 02/01/2016] [Indexed: 11/13/2022] Open
Abstract
We defined the role of the transcriptional factor—XYR1—in the filamentous fungus Trichoderma reesei during cellulosic material degradation. In this regard, we performed a global transcriptome analysis using RNA-Seq of the Δxyr1 mutant strain of T. reesei compared with the parental strain QM9414 grown in the presence of cellulose, sophorose, and glucose as sole carbon sources. We found that 5885 genes were expressed differentially under the three tested carbon sources. Of these, 322 genes were upregulated in the presence of cellulose, while 367 and 188 were upregulated in sophorose and glucose, respectively. With respect to genes under the direct regulation of XYR1, 30 and 33 are exclusive to cellulose and sophorose, respectively. The most modulated genes in the Δxyr1 belong to Carbohydrate-Active Enzymes (CAZymes), transcription factors, and transporters families. Moreover, we highlight the downregulation of transporters belonging to the MFS and ABC transporter families. Of these, MFS members were mostly downregulated in the presence of cellulose. In sophorose and glucose, the expression of these transporters was mainly upregulated. Our results revealed that MFS and ABC transporters could be new players in cellulose degradation and their role was shown to be carbon source-dependent. Our findings contribute to a better understanding of the regulatory mechanisms of XYR1 to control cellulase gene expression in T. reesei in the presence of cellulosic material, thereby potentially enhancing its application in several biotechnology fields.
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Affiliation(s)
- Lilian Dos Santos Castro
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
| | - Renato G de Paula
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
| | - Amanda C C Antoniêto
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
| | - Gabriela F Persinoti
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais Campinas, Brazil
| | - Rafael Silva-Rocha
- Systems and Synthetic Biology Laboratory, Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
| | - Roberto N Silva
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
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832
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Martínez-Montiel N, Morales-Lara L, Hernández-Pérez JM, Martínez-Contreras RD. In Silico Analysis of the Structural and Biochemical Features of the NMD Factor UPF1 in Ustilago maydis. PLoS One 2016; 11:e0148191. [PMID: 26863136 PMCID: PMC4749658 DOI: 10.1371/journal.pone.0148191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/14/2016] [Indexed: 11/23/2022] Open
Abstract
The molecular mechanisms regulating the accuracy of gene expression are still not fully understood. Among these mechanisms, Nonsense-mediated Decay (NMD) is a quality control process that detects post-transcriptionally abnormal transcripts and leads them to degradation. The UPF1 protein lays at the heart of NMD as shown by several structural and functional features reported for this factor mainly for Homo sapiens and Saccharomyces cerevisiae. This process is highly conserved in eukaryotes but functional diversity can be observed in various species. Ustilago maydis is a basidiomycete and the best-known smut, which has become a model to study molecular and cellular eukaryotic mechanisms. In this study, we performed in silico analysis to investigate the structural and biochemical properties of the putative UPF1 homolog in Ustilago maydis. The putative homolog for UPF1 was recognized in the annotated genome for the basidiomycete, exhibiting 66% identity with its human counterpart at the protein level. The known structural and functional domains characteristic of UPF1 homologs were also found. Based on the crystal structures available for UPF1, we constructed different three-dimensional models for umUPF1 in order to analyze the secondary and tertiary structural features of this factor. Using these models, we studied the spatial arrangement of umUPF1 and its capability to interact with UPF2. Moreover, we identified the critical amino acids that mediate the interaction of umUPF1 with UPF2, ATP, RNA and with UPF1 itself. Mutating these amino acids in silico showed an important effect over the native structure. Finally, we performed molecular dynamic simulations for UPF1 proteins from H. sapiens and U. maydis and the results obtained show a similar behavior and physicochemical properties for the protein in both organisms. Overall, our results indicate that the putative UPF1 identified in U. maydis shows a very similar sequence, structural organization, mechanical stability, physicochemical properties and spatial organization in comparison to the NMD factor depicted for Homo sapiens. These observations strongly support the notion that human and fungal UPF1 could perform equivalent biological activities.
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Affiliation(s)
- Nancy Martínez-Montiel
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Laura Morales-Lara
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | | | - Rebeca D. Martínez-Contreras
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, México
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833
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Gray KA, Seal RL, Tweedie S, Wright MW, Bruford EA. A review of the new HGNC gene family resource. Hum Genomics 2016; 10:6. [PMID: 26842383 PMCID: PMC4739092 DOI: 10.1186/s40246-016-0062-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 01/25/2016] [Indexed: 11/28/2022] Open
Abstract
The HUGO Gene Nomenclature Committee (HGNC) approves unique gene symbols and names for human loci. As well as naming genomic loci, we manually curate genes into family sets based on shared characteristics such as function, homology or phenotype. Each HGNC gene family has its own dedicated gene family report on our website, www.genenames.org. We have recently redesigned these reports to support the visualisation and browsing of complex relationships between families and to provide extra curated information such as family descriptions, protein domain graphics and gene family aliases. Here, we review how our gene families are curated and explain how to view, search and download the gene family data.
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Affiliation(s)
- Kristian A Gray
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
| | - Ruth L Seal
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
| | - Susan Tweedie
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
| | - Mathew W Wright
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK. .,Department of Genetics, Stanford University, Palo Alto, CA, 94304, USA.
| | - Elspeth A Bruford
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
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834
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Song A, Wu D, Fan Q, Tian C, Chen S, Guan Z, Xin J, Zhao K, Chen F. Transcriptome-Wide Identification and Expression Profiling Analysis of Chrysanthemum Trihelix Transcription Factors. Int J Mol Sci 2016; 17:ijms17020198. [PMID: 26848650 PMCID: PMC4783932 DOI: 10.3390/ijms17020198] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 12/19/2015] [Accepted: 01/28/2016] [Indexed: 12/23/2022] Open
Abstract
Trihelix transcription factors are thought to feature a typical DNA-binding trihelix (helix-loop-helix-loop-helix) domain that binds specifically to the GT motif, a light-responsive DNA element. Members of the trihelix family are known to function in a number of processes in plants. Here, we characterize 20 trihelix family genes in the important ornamental plant chrysanthemum (Chrysanthemum morifolium). Based on transcriptomic data, 20 distinct sequences distributed across four of five groups revealed by a phylogenetic tree were isolated and amplified. The phylogenetic analysis also identified four pairs of orthologous proteins shared by Arabidopsis and chrysanthemum and five pairs of paralogous proteins in chrysanthemum. Conserved motifs in the trihelix proteins shared by Arabidopsis and chrysanthemum were analyzed using MEME, and further bioinformatic analysis revealed that 16 CmTHs can be targeted by 20 miRNA families and that miR414 can target 9 CmTHs. qPCR results displayed that most chrysanthemum trihelix genes were highly expressed in inflorescences, while 20 CmTH genes were in response to phytohormone treatments and abiotic stresses. This work improves our understanding of the various functions of trihelix gene family members in response to hormonal stimuli and stress.
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Affiliation(s)
- Aiping Song
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Dan Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Qingqing Fan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Chang Tian
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jingjing Xin
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Kunkun Zhao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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835
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Banerjee S, De RK. Structural disorder: a tool for housekeeping proteins performing tissue-specific interactions. J Biomol Struct Dyn 2016; 34:1930-45. [DOI: 10.1080/07391102.2015.1095115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Sanghita Banerjee
- Machine Intelligence Unit, Indian Statistical Institute, 203 Barrackpore Trunk Road, Kolkata 700108, India
| | - Rajat K. De
- Machine Intelligence Unit, Indian Statistical Institute, 203 Barrackpore Trunk Road, Kolkata 700108, India
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836
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Horton ER, Humphries JD, Stutchbury B, Jacquemet G, Ballestrem C, Barry ST, Humphries MJ. Modulation of FAK and Src adhesion signaling occurs independently of adhesion complex composition. J Cell Biol 2016; 212:349-64. [PMID: 26833789 PMCID: PMC4739608 DOI: 10.1083/jcb.201508080] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 01/06/2016] [Indexed: 01/15/2023] Open
Abstract
Integrin adhesion complexes (IACs) form mechanochemical connections between the extracellular matrix and actin cytoskeleton and mediate phenotypic responses via posttranslational modifications. Here, we investigate the modularity and robustness of the IAC network to pharmacological perturbation of the key IAC signaling components focal adhesion kinase (FAK) and Src. FAK inhibition using AZ13256675 blocked FAK(Y397) phosphorylation but did not alter IAC composition, as reported by mass spectrometry. IAC composition was also insensitive to Src inhibition using AZD0530 alone or in combination with FAK inhibition. In contrast, kinase inhibition substantially reduced phosphorylation within IACs, cell migration and proliferation. Furthermore using fluorescence recovery after photobleaching, we found that FAK inhibition increased the exchange rate of a phosphotyrosine (pY) reporter (dSH2) at IACs. These data demonstrate that kinase-dependent signal propagation through IACs is independent of gross changes in IAC composition. Together, these findings demonstrate a general separation between the composition of IACs and their ability to relay pY-dependent signals.
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Affiliation(s)
- Edward R Horton
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, England, UK
| | - Jonathan D Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, England, UK
| | - Ben Stutchbury
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, England, UK
| | - Guillaume Jacquemet
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, England, UK
| | - Christoph Ballestrem
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, England, UK
| | - Simon T Barry
- Oncology iMed, AstraZeneca, Cheshire SK10 4TG, England, UK
| | - Martin J Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, England, UK
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837
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The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Nature 2016; 530:331-5. [PMID: 26814964 DOI: 10.1038/nature16548] [Citation(s) in RCA: 287] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 12/18/2015] [Indexed: 11/09/2022]
Abstract
Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants.
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838
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Abd-Alla AMM, Kariithi HM, Cousserans F, Parker NJ, İnce İA, Scully ED, Boeren S, Geib SM, Mekonnen S, Vlak JM, Parker AG, Vreysen MJB, Bergoin M. Comprehensive annotation of Glossina pallidipes salivary gland hypertrophy virus from Ethiopian tsetse flies: a proteogenomics approach. J Gen Virol 2016; 97:1010-1031. [PMID: 26801744 DOI: 10.1099/jgv.0.000409] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Glossina pallidipes salivary gland hypertrophy virus (GpSGHV; family Hytrosaviridae) can establish asymptomatic and symptomatic infection in its tsetse fly host. Here, we present a comprehensive annotation of the genome of an Ethiopian GpSGHV isolate (GpSGHV-Eth) compared with the reference Ugandan GpSGHV isolate (GpSGHV-Uga; GenBank accession number EF568108). GpSGHV-Eth has higher salivary gland hypertrophy syndrome prevalence than GpSGHV-Uga. We show that the GpSGHV-Eth genome has 190 291 nt, a low G+C content (27.9 %) and encodes 174 putative ORFs. Using proteogenomic and transcriptome mapping, 141 and 86 ORFs were mapped by transcripts and peptides, respectively. Furthermore, of the 174 ORFs, 132 had putative transcriptional signals [TATA-like box and poly(A) signals]. Sixty ORFs had both TATA-like box promoter and poly(A) signals, and mapped by both transcripts and peptides, implying that these ORFs encode functional proteins. Of the 60 ORFs, 10 ORFs are homologues to baculovirus and nudivirus core genes, including three per os infectivity factors and four RNA polymerase subunits (LEF4, 5, 8 and 9). Whereas GpSGHV-Eth and GpSGHV-Uga are 98.1 % similar at the nucleotide level, 37 ORFs in the GpSGHV-Eth genome had nucleotide insertions (n = 17) and deletions (n = 20) compared with their homologues in GpSGHV-Uga. Furthermore, compared with the GpSGHV-Uga genome, 11 and 24 GpSGHV ORFs were deleted and novel, respectively. Further, 13 GpSGHV-Eth ORFs were non-canonical; they had either CTG or TTG start codons instead of ATG. Taken together, these data suggest that GpSGHV-Eth and GpSGHV-Uga represent two different lineages of the same virus. Genetic differences combined with host and environmental factors possibly explain the differential GpSGHV pathogenesis observed in different G. pallidipes colonies.
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Affiliation(s)
- Adly M M Abd-Alla
- Insect Pest Control Laboratories, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
| | - Henry M Kariithi
- Insect Pest Control Laboratories, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria.,Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, PO Box 57811, Loresho, Nairobi, Kenya.,Laboratory of Virology, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - François Cousserans
- Laboratoire de Pathologie Comparée, Faculté des Sciences, Université de Montpellier, 34095 Montpellier, France
| | | | - İkbal Agah İnce
- Department of Medical Microbiology, School of Medicine, Acibadem University, 34752 Atas¸ehir, Istanbul, Turkey
| | - Erin D Scully
- Grain, Forage and Bioenergy Research Unit, USDA-ARS, University of Nebraska East Campus, Lincoln, NE 68583, USA
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands
| | - Scott M Geib
- Tropical Crop and Commodity Protection Research Unit, USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Centre, Hilo, HI 96720, USA
| | - Solomon Mekonnen
- National Institute for Control and Eradication of Tsetse and Trypanosomosis (NICETT), Addis Ababa, Ethiopia
| | - Just M Vlak
- Laboratory of Virology, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Andrew G Parker
- Insect Pest Control Laboratories, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
| | - Marc J B Vreysen
- Insect Pest Control Laboratories, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
| | - Max Bergoin
- Laboratoire de Pathologie Comparée, Faculté des Sciences, Université de Montpellier, 34095 Montpellier, France
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839
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Xiao Y, Wu Y, Sun K, Wang H, Jiang T, Lin A, Huang X, Yue X, Shi L, Feng J. Gene expression and adaptive evolution of ZBED1 in the hibernating greater horseshoe bat (Rhinolophus ferrumequinum). ACTA ACUST UNITED AC 2016; 219:834-43. [PMID: 26787476 DOI: 10.1242/jeb.133272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/08/2016] [Indexed: 01/11/2023]
Abstract
Mammalian hibernators experience physiological extremes, e.g. ischemia, muscle disuse and hypothermia, which are lethal to non-hibernators, implying the existence of underlying mechanisms that allow hibernators to withstand these physiological extremes. Increased cell proliferation is suggested to be such a strategy, but its molecular basis remains unknown. In this study, we characterized the expression pattern of ZBED1 (zinc finger, BED-type containing 1), a transcription factor that plays a crucial role in regulating cell proliferation, in five tissues of the greater horseshoe bat (Rhinolophus ferrumequinum) during pre-hibernation, deep hibernation and post-hibernation. Moreover, we investigated the ZBED1 genetic divergence from individuals with variable hibernation phenotypes that cover all three known mtDNA lineages of the species. Expression analyses showed that ZBED1 is overexpressed only in brain and skeletal muscle, not in the other three tissues, suggesting an increased cell proliferation in these two tissues during deep hibernation. Evolutionary analyses showed that ZBED1 sequences were clustered into two well-supported clades with each one dominated by hibernating and non-hibernating individuals, respectively. Positive selection analyses further showed some positively selected sites and a divergent selection pressure among hibernating and non-hibernating groups of R. ferrumequinum. Our results suggest that ZBED1 as a potential candidate gene that regulates cell proliferation for hibernators to face physiological extremes during hibernation.
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Affiliation(s)
- Yanhong Xiao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun 130117, China
| | - Yonghua Wu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun 130117, China School of Life Sciences, Northeast Normal University, 5268 Renmin Street, Changchun 130024, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun 130117, China
| | - Hui Wang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun 130117, China
| | - Tinglei Jiang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun 130117, China
| | - Aiqing Lin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun 130117, China
| | - Xiaobin Huang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun 130117, China
| | - Xinke Yue
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun 130117, China
| | - Limin Shi
- School of Life Science, Yunnan Normal University, Chenggong District, Kunming 650500, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun 130117, China
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840
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Gonzalez-Perez A. Circuits of cancer drivers revealed by convergent misregulation of transcription factor targets across tumor types. Genome Med 2016; 8:6. [PMID: 26792175 PMCID: PMC4719577 DOI: 10.1186/s13073-015-0260-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/29/2015] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Large tumor genome sequencing projects have now uncovered a few hundred genes involved in the onset of tumorigenesis, or drivers, in some two dozen malignancies. One of the main challenges emerging from this catalog of drivers is how to make sense of their heterogeneity in most cancer types. This is key not only to understand how carcinogenesis appears and develops in these malignancies to be able to early diagnose them, but also to open up the possibility to employ therapeutic strategies targeting a driver protein to counteract the alteration of another connected driver. METHODS Here, I focus on driver transcription factors and their connection to tumorigensis in several tumor types through the alteration of the expression of their targets. First, I explore their involvement in tumorigenesis as mutational drivers in 28 different tumor types. Then, I collect a list of downstream targets of the all driver transcription factors (TFs), and identify which of them exhibit a differential expression upon alterations of driver transcription factors. RESULTS I identify the subset of targets of each TF most likely mediating the tumorigenic effect of their driver alterations in each tumor type, and explore their overlap. Furthermore, I am able to identify other driver genes that cause tumorigenesis through the alteration of very similar sets of targets. CONCLUSIONS I thus uncover these circuits of connected drivers which cause tumorigenesis through the perturbation of overlapping cellular pathways in a pan-cancer manner across 15 malignancies. The systematic detection of these circuits may be key to propose novel therapeutic strategies indirectly targeting driver alterations in tumors.
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Affiliation(s)
- Abel Gonzalez-Perez
- Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003, Barcelona, Spain.
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841
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Hyndman KA, Arguello AM, Morsing SKH, Pollock JS. Dynamin-2 is a novel NOS1β interacting protein and negative regulator in the collecting duct. Am J Physiol Regul Integr Comp Physiol 2016; 310:R570-7. [PMID: 26791826 DOI: 10.1152/ajpregu.00008.2015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 01/19/2016] [Indexed: 12/19/2022]
Abstract
Nitric oxide synthase 1 (NOS1)-derived nitric oxide (NO) production in collecting ducts is critical for maintaining fluid-electrolyte balance. Rat collecting ducts express both the full-length NOS1α and its truncated variant NOS1β, while NOS1β predominates in mouse collecting ducts. We reported that dynamin-2 (DNM2), a protein involved in excising vesicles from the plasma membrane, and NOS1α form a protein-protein interaction that promotes NO production in rat collecting ducts. NOS1β was found to be highly expressed in human renal cortical/medullary samples; hence, we tested the hypothesis that DNM2 is a positive regulator of NOS1β-derived NO production. COS7 and mouse inner medullary collecting duct-3 (mIMCD3) cells were transfected with NOS1β and/or DNM2. Coimmunoprecipitation experiments show that NOS1β and DNM2 formed a protein-protein interaction. DNM2 overexpression decreased nitrite production (index of NO) in both COS7 and mIMCD-3 cells by 50-75%. mIMCD-3 cells treated with a panel of dynamin inhibitors or DNM2 siRNA displayed increased nitrite production. To elucidate the physiological significance of IMCD DNM2/NOS1β regulation in vivo, flox control and CDNOS1 knockout mice were placed on a high-salt diet, and freshly isolated IMCDs were treated acutely with a dynamin inhibitor. Dynamin inhibition increased nitrite production by IMCDs from flox mice. This response was blunted (but not abolished) in collecting duct-specific NOS1 knockout mice, suggesting that DNM2 also negatively regulates NOS3 in the mouse IMCD. We conclude that DNM2 is a novel negative regulator of NO production in mouse collecting ducts. We propose that DNM2 acts as a "break" to prevent excess or potentially toxic NO levels under high-salt conditions.
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Affiliation(s)
- Kelly A Hyndman
- Section of Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Alexandra M Arguello
- Section of Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Sofia K H Morsing
- Section of Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jennifer S Pollock
- Section of Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
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842
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Preisitsch M, Heiden SE, Beerbaum M, Niedermeyer THJ, Schneefeld M, Herrmann J, Kumpfmüller J, Thürmer A, Neidhardt I, Wiesner C, Daniel R, Müller R, Bange FC, Schmieder P, Schweder T, Mundt S. Effects of Halide Ions on the Carbamidocyclophane Biosynthesis in Nostoc sp. CAVN2. Mar Drugs 2016; 14:21. [PMID: 26805858 PMCID: PMC4728517 DOI: 10.3390/md14010021] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/09/2015] [Accepted: 12/21/2015] [Indexed: 01/28/2023] Open
Abstract
In this study, the influence of halide ions on [7.7]paracyclophane biosynthesis in the cyanobacterium Nostoc sp. CAVN2 was investigated. In contrast to KI and KF, supplementation of the culture medium with KCl or KBr resulted not only in an increase of growth but also in an up-regulation of carbamidocyclophane production. LC-MS analysis indicated the presence of chlorinated, brominated, but also non-halogenated derivatives. In addition to 22 known cylindrocyclophanes and carbamidocyclophanes, 27 putative congeners have been detected. Nine compounds, carbamidocyclophanes M-U, were isolated, and their structural elucidation by 1D and 2D NMR experiments in combination with HRMS and ECD analysis revealed that they are brominated analogues of chlorinated carbamidocyclophanes. Quantification of the carbamidocyclophanes showed that chloride is the preferably utilized halide, but incorporation is reduced in the presence of bromide. Evaluation of the antibacterial activity of 30 [7.7]paracyclophanes and related derivatives against selected pathogenic Gram-positive and Gram-negative bacteria exhibited remarkable effects especially against methicillin- and vancomycin-resistant staphylococci and Mycobacterium tuberculosis. For deeper insights into the mechanisms of biosynthesis, the carbamidocyclophane biosynthetic gene cluster in Nostoc sp. CAVN2 was studied. The gene putatively coding for the carbamoyltransferase has been identified. Based on bioinformatic analyses, a possible biosynthetic assembly is discussed.
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Affiliation(s)
- Michael Preisitsch
- Institute of Pharmacy, Department of Pharmaceutical Biology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Straße 17, 17489 Greifswald, Germany.
| | - Stefan E Heiden
- Institute of Pharmacy, Department of Pharmaceutical Biotechnology, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Straße 3, 17489 Greifswald, Germany.
| | - Monika Beerbaum
- Leibniz Institute for Molecular Pharmacology (FMP), Robert-Rössle-Straße 10, 13125 Berlin, Germany.
| | - Timo H J Niedermeyer
- Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
- German Centre for Infection Research (DZIF), Partner Site Tübingen (T.H.J.N.) and Partner Site Hannover-Braunschweig, Germany.
| | - Marie Schneefeld
- German Centre for Infection Research (DZIF), Partner Site Tübingen (T.H.J.N.) and Partner Site Hannover-Braunschweig, Germany.
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany.
| | - Jennifer Herrmann
- German Centre for Infection Research (DZIF), Partner Site Tübingen (T.H.J.N.) and Partner Site Hannover-Braunschweig, Germany.
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
| | - Jana Kumpfmüller
- Institute of Pharmacy, Department of Pharmaceutical Biotechnology, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Straße 3, 17489 Greifswald, Germany.
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Department of Biomolecular Chemistry, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Andrea Thürmer
- Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University, Grisebachstraße 8, 37077 Göttingen, Germany.
| | - Inga Neidhardt
- Institute of Pharmacy, Department of Pharmaceutical Biology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Straße 17, 17489 Greifswald, Germany.
- Institute of Technology, Department of Pharmacology, Toxicology and Clinical Pharmacy, Technical University of Braunschweig, Mendelssohnstraße 1, 38106 Braunschweig, Germany.
| | | | - Rolf Daniel
- Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University, Grisebachstraße 8, 37077 Göttingen, Germany.
| | - Rolf Müller
- German Centre for Infection Research (DZIF), Partner Site Tübingen (T.H.J.N.) and Partner Site Hannover-Braunschweig, Germany.
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
| | - Franz-Christoph Bange
- German Centre for Infection Research (DZIF), Partner Site Tübingen (T.H.J.N.) and Partner Site Hannover-Braunschweig, Germany.
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany.
| | - Peter Schmieder
- Leibniz Institute for Molecular Pharmacology (FMP), Robert-Rössle-Straße 10, 13125 Berlin, Germany.
| | - Thomas Schweder
- Institute of Pharmacy, Department of Pharmaceutical Biotechnology, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Straße 3, 17489 Greifswald, Germany.
| | - Sabine Mundt
- Institute of Pharmacy, Department of Pharmaceutical Biology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Straße 17, 17489 Greifswald, Germany.
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843
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Zheng L, Abhyankar W, Ouwerling N, Dekker HL, van Veen H, van der Wel NN, Roseboom W, de Koning LJ, Brul S, de Koster CG. Bacillus subtilis Spore Inner Membrane Proteome. J Proteome Res 2016; 15:585-94. [PMID: 26731423 DOI: 10.1021/acs.jproteome.5b00976] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The endospore is the dormant form of Bacillus subtilis and many other Firmicutes. By sporulation, these spore formers can survive very harsh physical and chemical conditions. Yet, they need to go through germination to return to their growing form. The spore inner membrane (IM) has been shown to play an essential role in triggering the initiation of germination. In this study, we isolated the IM of bacterial spores, in parallel with the isolation of the membrane of vegetative cells. With the use of GeLC-MS/MS, over 900 proteins were identified from the B. subtilis spore IM preparations. By bioinformatics-based membrane protein predictions, ca. one-third could be predicted to be membrane-localized. A large number of unique proteins as well as proteins common to the two membrane proteomes were identified. In addition to previously known IM proteins, a number of IM proteins were newly identified, at least some of which are likely to provide new insights into IM physiology, unveiling proteins putatively involved in spore germination machinery and hence putative germination inhibition targets.
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Affiliation(s)
| | | | | | | | - Henk van Veen
- Electron Microscopy Centre Amsterdam, Department of Cell Biology and Histology, Academic Medical Center , 1105 AZ Amsterdam, The Netherlands
| | - Nicole N van der Wel
- Electron Microscopy Centre Amsterdam, Department of Cell Biology and Histology, Academic Medical Center , 1105 AZ Amsterdam, The Netherlands
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844
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Surujon D, Ratner DI. Use of a Probabilistic Motif Search to Identify Histidine Phosphotransfer Domain-Containing Proteins. PLoS One 2016; 11:e0146577. [PMID: 26751210 PMCID: PMC4709007 DOI: 10.1371/journal.pone.0146577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/18/2015] [Indexed: 11/18/2022] Open
Abstract
The wealth of newly obtained proteomic information affords researchers the possibility of searching for proteins of a given structure or function. Here we describe a general method for the detection of a protein domain of interest in any species for which a complete proteome exists. In particular, we apply this approach to identify histidine phosphotransfer (HPt) domain-containing proteins across a range of eukaryotic species. From the sequences of known HPt domains, we created an amino acid occurrence matrix which we then used to define a conserved, probabilistic motif. Examination of various organisms either known to contain (plant and fungal species) or believed to lack (mammals) HPt domains established criteria by which new HPt candidates were identified and ranked. Search results using a probabilistic motif matrix compare favorably with data to be found in several commonly used protein structure/function databases: our method identified all known HPt proteins in the Arabidopsis thaliana proteome, confirmed the absence of such motifs in mice and humans, and suggests new candidate HPts in several organisms. Moreover, probabilistic motif searching can be applied more generally, in a manner both readily customized and computationally compact, to other protein domains; this utility is demonstrated by our identification of histones in a range of eukaryotic organisms.
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Affiliation(s)
- Defne Surujon
- Program in Biochemistry and Biophysics, Amherst College, Amherst, Massachusetts, United States of America
| | - David I. Ratner
- Program in Biochemistry and Biophysics, Amherst College, Amherst, Massachusetts, United States of America
- Department of Biology, Amherst College, Amherst, Massachusetts, United States of America
- * E-mail:
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845
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Moreton J, Izquierdo A, Emes RD. Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes. Front Genet 2016; 6:361. [PMID: 26793234 PMCID: PMC4707302 DOI: 10.3389/fgene.2015.00361] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 12/19/2015] [Indexed: 11/13/2022] Open
Abstract
De novo assembly of a complete transcriptome without the need for a guiding reference genome is attractive, particularly where the cost and complexity of generating a eukaryote genome is prohibitive. The transcriptome should not however be seen as just a quick and cheap alternative to building a complete genome. Transcriptomics allows the understanding and comparison of spatial and temporal samples within an organism, and allows surveying of multiple individuals or closely related species. De novo assembly in theory allows the building of a complete transcriptome without any prior knowledge of the genome. It also allows the discovery of alternate splice forms of coding RNAs and also non-coding RNAs, which are often missed by proteomic approaches, or are incompletely annotated in genome studies. The limitations of the method are that the generation of a truly complete assembly is unlikely, and so we require some methods for the assessment of the quality and appropriateness of a generated transcriptome. Whilst no single consensus pipeline or tool is agreed as optimal, various algorithms, and easy to use software do exist making transcriptome generation a more common approach. With this expansion of data, questions still exist relating to how do we make these datasets fully discoverable, comparable and most useful to understand complex biological systems?
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Affiliation(s)
- Joanna Moreton
- Advanced Data Analysis Centre, Sutton Bonington Campus, University of NottinghamLeicestershire, UK
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of NottinghamLeicestershire, UK
| | - Abril Izquierdo
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of NottinghamLeicestershire, UK
| | - Richard D. Emes
- Advanced Data Analysis Centre, Sutton Bonington Campus, University of NottinghamLeicestershire, UK
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of NottinghamLeicestershire, UK
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846
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Calderan-Rodrigues MJ, Jamet E, Douché T, Bonassi MBR, Cataldi TR, Fonseca JG, San Clemente H, Pont-Lezica R, Labate CA. Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases. BMC PLANT BIOLOGY 2016; 16:14. [PMID: 26754199 PMCID: PMC4709929 DOI: 10.1186/s12870-015-0677-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/05/2015] [Indexed: 05/25/2023]
Abstract
BACKGROUND Sugarcane has been used as the main crop for ethanol production for more than 40 years in Brazil. Recently, the production of bioethanol from bagasse and straw, also called second generation (2G) ethanol, became a reality with the first commercial plants started in the USA and Brazil. However, the industrial processes still need to be improved to generate a low cost fuel. One possibility is the remodeling of cell walls, by means of genetic improvement or transgenesis, in order to make the bagasse more accessible to hydrolytic enzymes. We aimed at characterizing the cell wall proteome of young sugarcane culms, to identify proteins involved in cell wall biogenesis. Proteins were extracted from the cell walls of 2-month-old culms using two protocols, non-destructive by vacuum infiltration vs destructive. The proteins were identified by mass spectrometry and bioinformatics. RESULTS A predicted signal peptide was found in 84 different proteins, called cell wall proteins (CWPs). As expected, the non-destructive method showed a lower percentage of proteins predicted to be intracellular than the destructive one (33% vs 44%). About 19% of CWPs were identified with both methods, whilst the infiltration protocol could lead to the identification of 75% more CWPs. In both cases, the most populated protein functional classes were those of proteins related to lipid metabolism and oxido-reductases. Curiously, a single glycoside hydrolase (GH) was identified using the non-destructive method whereas 10 GHs were found with the destructive one. Quantitative data analysis allowed the identification of the most abundant proteins. CONCLUSIONS The results highlighted the importance of using different protocols to extract proteins from cell walls to expand the coverage of the cell wall proteome. Ten GHs were indicated as possible targets for further studies in order to obtain cell walls less recalcitrant to deconstruction. Therefore, this work contributed to two goals: enlarge the coverage of the sugarcane cell wall proteome, and provide target proteins that could be used in future research to facilitate 2G ethanol production.
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Affiliation(s)
- Maria Juliana Calderan-Rodrigues
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil.
| | - Elisabeth Jamet
- Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France.
- CNRS; UMR 5546, BP 42617, F-31326, Castanet-Tolosan, France.
| | - Thibaut Douché
- Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France.
- CNRS; UMR 5546, BP 42617, F-31326, Castanet-Tolosan, France.
| | - Maria Beatriz Rodrigues Bonassi
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil.
| | - Thaís Regiani Cataldi
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil.
| | - Juliana Guimarães Fonseca
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil.
| | - Hélène San Clemente
- Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France.
- CNRS; UMR 5546, BP 42617, F-31326, Castanet-Tolosan, France.
| | - Rafael Pont-Lezica
- Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France
- CNRS; UMR 5546, BP 42617, F-31326, Castanet-Tolosan, France
| | - Carlos Alberto Labate
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil.
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847
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Hakenberg J, Cheng WY, Thomas P, Wang YC, Uzilov AV, Chen R. Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts. BMC Bioinformatics 2016; 17:24. [PMID: 26746786 PMCID: PMC4706706 DOI: 10.1186/s12859-015-0865-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 12/17/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Data from a plethora of high-throughput sequencing studies is readily available to researchers, providing genetic variants detected in a variety of healthy and disease populations. While each individual cohort helps gain insights into polymorphic and disease-associated variants, a joint perspective can be more powerful in identifying polymorphisms, rare variants, disease-associations, genetic burden, somatic variants, and disease mechanisms. DESCRIPTION We have set up a Reference Variant Store (RVS) containing variants observed in a number of large-scale sequencing efforts, such as 1000 Genomes, ExAC, Scripps Wellderly, UK10K; various genotyping studies; and disease association databases. RVS holds extensive annotations pertaining to affected genes, functional impacts, disease associations, and population frequencies. RVS currently stores 400 million distinct variants observed in more than 80,000 human samples. CONCLUSIONS RVS facilitates cross-study analysis to discover novel genetic risk factors, gene-disease associations, potential disease mechanisms, and actionable variants. Due to its large reference populations, RVS can also be employed for variant filtration and gene prioritization. AVAILABILITY A web interface to public datasets and annotations in RVS is available at https://rvs.u.hpc.mssm.edu/.
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Affiliation(s)
- Jörg Hakenberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Box 1498, New York, 10029, USA.
| | - Wei-Yi Cheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Box 1498, New York, 10029, USA.
- Current affiliation: Illumina, Inc., 451 El Camino Real, Suite 210, Santa Clara, 95050, USA.
| | - Philippe Thomas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Box 1498, New York, 10029, USA.
- Current affiliation: Roche Parma Research and Early Development, Informatics, Roche Innovation Center New York, 430 East 29th St, New York, 10016, USA.
| | - Ying-Chih Wang
- Department of Computer Science, Humboldt-Universität zu Berlin, Unter den Linden 6, Berlin, 10099, Germany.
- Current affiliation: German Research Centre for Artificial Intelligence (DFKI), Alt Moabit 91c, Berlin, 10559, Germany.
| | - Andrew V Uzilov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Box 1498, New York, 10029, USA.
| | - Rong Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Box 1498, New York, 10029, USA.
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848
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Li S, Li K, Ju Z, Cao D, Fu D, Zhu H, Zhu B, Luo Y. Genome-wide analysis of tomato NF-Y factors and their role in fruit ripening. BMC Genomics 2016; 17:36. [PMID: 26742635 PMCID: PMC4705811 DOI: 10.1186/s12864-015-2334-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/18/2015] [Indexed: 11/10/2022] Open
Abstract
Background Fruit ripening is a complex developmental process that depends on a coordinated regulation of numerous genes, including ripening-related transcription factors (TFs), fruit-related microRNAs, DNA methylation and chromatin remodeling. It is known that various TFs, such as MADS-domain, MYB, AP2/ERF and SBP/SPL family proteins play key roles in modulating ripening. However, little attention has been given to members of the large NF-Y TF family in this regard, although genes in this family are known to have important functions in regulating plant growth, development, and abiotic or biotic stress responses. Results In this study, the evolutionary relationship between Arabidopsis thaliana and tomato (Solanum lycopersicum) NF-Y genes was examined to predict similarities in function. Furthermore, through gene expression analysis, 13 tomato NF-Y genes were identified as candidate regulators of fruit ripening. Functional studies involving suppression of NF-Y gene expression using virus induced gene silencing (VIGS) indicated that five NF-Y genes, including two members of the NF-YB subgroup (Solyc06g069310, Solyc07g065500) and three members of the NF-YA subgroup (Solyc01g087240, Solyc08g062210, Solyc11g065700), influence ripening. In addition, subcellular localization analyses using NF-Y proteins fused to a green fluorescent protein (GFP) reporter showed that the three NF-YA proteins accumulated in the nucleus, while the two NF-YB proteins were observed in both the nucleus and cytoplasm. Conclusions In this study, we identified tomato NF-Y genes by analyzing the tomato genome sequence using bioinformatics approaches, and characterized their chromosomal distribution, gene structures, phylogenetic relationship and expression patterns. We also examined their biological functions in regulating tomato fruit via VIGS and subcellular localization analyses. The results indicated that five NF-Y transcription factors play roles in tomato fruit ripening. This information provides a platform for further investigation of their biological functions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2334-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China.
| | - Ka Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China.
| | - Zheng Ju
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China.
| | - Dongyan Cao
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China.
| | - Daqi Fu
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China.
| | - Hongliang Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China.
| | - Benzhong Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China.
| | - Yunbo Luo
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China.
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849
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Segura J, Sanchez-Garcia R, Tabas-Madrid D, Cuenca-Alba J, Sorzano COS, Carazo JM. 3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling. Biophys J 2016; 110:766-75. [PMID: 26772592 PMCID: PMC4775853 DOI: 10.1016/j.bpj.2015.11.3519] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 11/27/2015] [Accepted: 11/30/2015] [Indexed: 11/19/2022] Open
Abstract
Electron microscopy (EM) is experiencing a revolution with the advent of a new generation of Direct Electron Detectors, enabling a broad range of large and flexible structures to be resolved well below 1 nm resolution. Although EM techniques are evolving to the point of directly obtaining structural data at near-atomic resolution, for many molecules the attainable resolution might not be enough to propose high-resolution structural models. However, accessing information on atomic coordinates is a necessary step toward a deeper understanding of the molecular mechanisms that allow proteins to perform specific tasks. For that reason, methods for the integration of EM three-dimensional maps with x-ray and NMR structural data are being developed, a modeling task that is normally referred to as fitting, resulting in the so called hybrid models. In this work, we present a novel application—3DIANA—specially targeted to those cases in which the EM map resolution is medium or low and additional experimental structural information is scarce or even lacking. In this way, 3DIANA statistically evaluates proposed/potential contacts between protein domains, presents a complete catalog of both structurally resolved and predicted interacting regions involving these domains and, finally, suggests structural templates to model the interaction between them. The evaluation of the proposed interactions is computed with DIMERO, a new method that scores physical binding sites based on the topology of protein interaction networks, which has recently shown the capability to increase by 200% the number of domain-domain interactions predicted in interactomes as compared to previous approaches. The new application displays the information at a sequence and structural level and is accessible through a web browser or as a Chimera plugin at http://3diana.cnb.csic.es.
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Affiliation(s)
- Joan Segura
- GN7, Spanish National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC)/Instruct Image Processing Center, Madrid, Spain.
| | - Ruben Sanchez-Garcia
- GN7, Spanish National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC)/Instruct Image Processing Center, Madrid, Spain
| | - Daniel Tabas-Madrid
- GN7, Spanish National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC)/Instruct Image Processing Center, Madrid, Spain
| | - Jesus Cuenca-Alba
- GN7, Spanish National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC)/Instruct Image Processing Center, Madrid, Spain
| | - Carlos Oscar S Sorzano
- GN7, Spanish National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC)/Instruct Image Processing Center, Madrid, Spain
| | - Jose Maria Carazo
- GN7, Spanish National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC)/Instruct Image Processing Center, Madrid, Spain
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850
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Brozovic M, Martin C, Dantec C, Dauga D, Mendez M, Simion P, Percher M, Laporte B, Scornavacca C, Di Gregorio A, Fujiwara S, Gineste M, Lowe EK, Piette J, Racioppi C, Ristoratore F, Sasakura Y, Takatori N, Brown TC, Delsuc F, Douzery E, Gissi C, McDougall A, Nishida H, Sawada H, Swalla BJ, Yasuo H, Lemaire P. ANISEED 2015: a digital framework for the comparative developmental biology of ascidians. Nucleic Acids Res 2016; 44:D808-18. [PMID: 26420834 PMCID: PMC4702943 DOI: 10.1093/nar/gkv966] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 09/14/2015] [Indexed: 11/24/2022] Open
Abstract
Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Over the past five years, we refactored the system from an initial custom schema to an extended version of the Chado schema and redesigned all user and back end interfaces. This new architecture was used to improve and enrich the description of Ciona intestinalis embryonic development, based on an improved genome assembly and gene model set, refined functional gene annotation, and anatomical ontologies, and a new collection of full ORF cDNAs. The genomes of nine ascidian species have been sequenced since the release of the C. intestinalis genome. In ANISEED 2015, all nine new ascidian species can be explored via dedicated genome browsers, and searched by Blast. In addition, ANISEED provides full functional gene annotation, anatomical ontologies and some gene expression data for the six species with highest quality genomes. ANISEED is publicly available at: http://www.aniseed.cnrs.fr.
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Affiliation(s)
- Matija Brozovic
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Cyril Martin
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Christelle Dantec
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Delphine Dauga
- Institut de Biologie du Développement de Marseille (IBDM), UMR7288 CNRS-Aix Marseille Université, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France Bioself Communication, 28 rue de la Bibliothèque, F-13001 Marseille, France
| | - Mickaël Mendez
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Paul Simion
- Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS-IRD-Université de Montpellier, F-34090 Montpellier, France
| | - Madeline Percher
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Baptiste Laporte
- Institut de Biologie du Développement de Marseille (IBDM), UMR7288 CNRS-Aix Marseille Université, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France
| | - Céline Scornavacca
- Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS-IRD-Université de Montpellier, F-34090 Montpellier, France
| | - Anna Di Gregorio
- Department of Basic Science and Craniofacial Biology New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Shigeki Fujiwara
- Department of Applied Science, Kochi University, Kochi-shi, Kochi 780-8520, Japan
| | - Mathieu Gineste
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Elijah K Lowe
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA
| | - Jacques Piette
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Claudia Racioppi
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
| | - Filomena Ristoratore
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan
| | - Naohito Takatori
- Developmental Biology Laboratory, Department of Biological Sciences, School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamioosawa, Hachiooji, Tokyo 192-0397, Japan Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Titus C Brown
- Population Health and Reproduction, UC Davis, Davis, CA 95616, USA
| | - Frédéric Delsuc
- Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS-IRD-Université de Montpellier, F-34090 Montpellier, France
| | - Emmanuel Douzery
- Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS-IRD-Université de Montpellier, F-34090 Montpellier, France
| | - Carmela Gissi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy
| | - Alex McDougall
- Sorbonne Universités, Université Pierre et Marie Curie, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Hitoshi Sawada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, 429-63 Sugashima, Toba 517-0004, Japan
| | - Billie J Swalla
- Friday Harbor Laboratories, 620 University Road, Friday Harbor, WA 98250-9299, USA
| | - Hitoyoshi Yasuo
- Sorbonne Universités, Université Pierre et Marie Curie, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Patrick Lemaire
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France Institut de Biologie du Développement de Marseille (IBDM), UMR7288 CNRS-Aix Marseille Université, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France
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