401
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Calvete O, Martinez P, Garcia-Pavia P, Benitez-Buelga C, Paumard-Hernández B, Fernandez V, Dominguez F, Salas C, Romero-Laorden N, Garcia-Donas J, Carrillo J, Perona R, Triviño JC, Andrés R, Cano JM, Rivera B, Alonso-Pulpon L, Setien F, Esteller M, Rodriguez-Perales S, Bougeard G, Frebourg T, Urioste M, Blasco MA, Benítez J. A mutation in the POT1 gene is responsible for cardiac angiosarcoma in TP53-negative Li-Fraumeni-like families. Nat Commun 2015; 6:8383. [PMID: 26403419 DOI: 10.1038/ncomms9383] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 08/14/2015] [Indexed: 12/30/2022] Open
Abstract
Cardiac angiosarcoma (CAS) is a rare malignant tumour whose genetic basis is unknown. Here we show, by whole-exome sequencing of a TP53-negative Li-Fraumeni-like (LFL) family including CAS cases, that a missense variant (p.R117C) in POT1 (protection of telomeres 1) gene is responsible for CAS. The same gene alteration is found in two other LFL families with CAS, supporting the causal effect of the identified mutation. We extend the analysis to TP53-negative LFL families with no CAS and find the same mutation in a breast AS family. The mutation is recently found once in 121,324 studied alleles in ExAC server but it is not described in any other database or found in 1,520 Spanish controls. In silico structural analysis suggests how the mutation disrupts POT1 structure. Functional and in vitro studies demonstrate that carriers of the mutation show reduced telomere-bound POT1 levels, abnormally long telomeres and increased telomere fragility.
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Affiliation(s)
- Oriol Calvete
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, Madrid 28029, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid 28029, Spain
| | - Paula Martinez
- Telomeres and Telomerase Group, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain
| | - Pablo Garcia-Pavia
- Department of Cardiology. Hospital Universitario Puerta de Hierro, Mahadahonda, Madrid 28222, Spain.,Department of Cardiovascular Development and Repair, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Carlos Benitez-Buelga
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, Madrid 28029, Spain
| | - Beatriz Paumard-Hernández
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, Madrid 28029, Spain
| | - Victoria Fernandez
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, Madrid 28029, Spain
| | - Fernando Dominguez
- Department of Cardiology. Hospital Universitario Puerta de Hierro, Mahadahonda, Madrid 28222, Spain
| | - Clara Salas
- Department of Pathology. Hospital Universitario Puerta de Hierro Majadahonda, Madrid 28222, Spain
| | - Nuria Romero-Laorden
- Oncology Department, Clara Campal Comprehensive Cancer Center, Sanchinarro, Madrid 28050, Spain
| | - Jesus Garcia-Donas
- Oncology Department, Clara Campal Comprehensive Cancer Center, Sanchinarro, Madrid 28050, Spain
| | - Jaime Carrillo
- Department of Experimental Models of Human Disease. Instituto Investigaciones Biomédicas (CSIC/UAM), Madrid 28029, Spain
| | - Rosario Perona
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid 28029, Spain.,Department of Experimental Models of Human Disease. Instituto Investigaciones Biomédicas (CSIC/UAM), Madrid 28029, Spain
| | | | - Raquel Andrés
- Medical Oncology Service, Hospital Universitario Lozano Blesa, Zaragoza 50009, Spain
| | - Juana María Cano
- Medical Oncology Service, Hospital General de Ciudad Real, Ciudad Real 13005, Spain
| | - Bárbara Rivera
- Familial Cancer Clinical Unit, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain
| | - Luis Alonso-Pulpon
- Department of Cardiology. Hospital Universitario Puerta de Hierro, Mahadahonda, Madrid 28222, Spain
| | - Fernando Setien
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona 08908, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona 08908, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona 08007, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | | | - Gaelle Bougeard
- Genetics Department, Rouen University Hospital, Rouen 76000, France
| | - Tierry Frebourg
- Genetics Department, Rouen University Hospital, Rouen 76000, France
| | - Miguel Urioste
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid 28029, Spain.,Familial Cancer Clinical Unit, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain
| | - Maria A Blasco
- Telomeres and Telomerase Group, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain
| | - Javier Benítez
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, Madrid 28029, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid 28029, Spain
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402
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Architecture of the mammalian mechanosensitive Piezo1 channel. Nature 2015; 527:64-9. [PMID: 26390154 DOI: 10.1038/nature15247] [Citation(s) in RCA: 308] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/24/2015] [Indexed: 12/12/2022]
Abstract
Piezo proteins are evolutionarily conserved and functionally diverse mechanosensitive cation channels. However, the overall structural architecture and gating mechanisms of Piezo channels have remained unknown. Here we determine the cryo-electron microscopy structure of the full-length (2,547 amino acids) mouse Piezo1 (Piezo1) at a resolution of 4.8 Å. Piezo1 forms a trimeric propeller-like structure (about 900 kilodalton), with the extracellular domains resembling three distal blades and a central cap. The transmembrane region has 14 apparently resolved segments per subunit. These segments form three peripheral wings and a central pore module that encloses a potential ion-conducting pore. The rather flexible extracellular blade domains are connected to the central intracellular domain by three long beam-like structures. This trimeric architecture suggests that Piezo1 may use its peripheral regions as force sensors to gate the central ion-conducting pore.
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403
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Tompa P, Schad E, Tantos A, Kalmar L. Intrinsically disordered proteins: emerging interaction specialists. Curr Opin Struct Biol 2015; 35:49-59. [PMID: 26402567 DOI: 10.1016/j.sbi.2015.08.009] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/23/2015] [Accepted: 08/28/2015] [Indexed: 12/22/2022]
Abstract
Intrinsically disordered proteins or regions of proteins (IDPs/IDRs) most often function through protein-protein interactions, when they permanently or transiently bind partner molecules with diverse functional consequences. There is a rapid advance in our understanding of the ensuing functional modes, obtained from describing atomic details of individual complexes, proteome-wide studies of interactomes and characterizing loosely assembled hydrogels and tightly packed amyloids. Here we briefly survey the most important recent methodological developments and structural-functional observations, with the aim of increasing the general appreciation of IDPs/IDRs as 'interaction specialists'.
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Affiliation(s)
- Peter Tompa
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium; Vrije Universiteit Brussel, Brussels, Belgium; Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.
| | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Lajos Kalmar
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
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404
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Gee JA, Frausto RF, Chung DWD, Tangmonkongvoragul C, Le DJ, Wang C, Han J, Aldave AJ. Identification of novel PIKFYVE gene mutations associated with Fleck corneal dystrophy. Mol Vis 2015; 21:1093-100. [PMID: 26396486 PMCID: PMC4575904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 09/15/2015] [Indexed: 10/27/2022] Open
Abstract
PURPOSE To report the identification of a novel frameshift mutation and copy number variation (CNV) in PIKFYVE in two probands with fleck corneal dystrophy (FCD). METHODS Slit-lamp examination was performed to identify characteristic features of FCD. After genomic DNA was collected, PCR amplification and automated sequencing of all 41 exons of PIKFYVE was performed. Using genomic DNA, quantitative PCR (qPCR) was performed to detect CNVs within PIKFYVE. RESULTS In the first FCD proband, numerous panstromal punctate opacities were observed in each of the proband's corneas, consistent with the diagnosis of FCD. Screening of PIKFYVE demonstrated a novel heterozygous frameshift mutation in exon 19, c.3151dupA, which is predicted to encode for a truncated PIKFYVE protein, p.(Asp1052Argfs*18). This variant was identified in an affected sister but not in the proband's unaffected mother or brother or 200 control chromosomes. The second FCD proband presented with bilateral, discrete, punctate, grayish-white stromal opacities. Exonic screening of PIKFYVE revealed no causative variant. However, CNV analysis demonstrated the hemizygous deletion of exons 15 and 16. CONCLUSIONS We report a novel heterozygous frameshift mutation (c.3151dupA) and a CNV in PIKFYVE, representing the first CNV and the fifth frameshift mutation associated with FCD.
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405
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Evidence for an Ancestral Association of Human Coronavirus 229E with Bats. J Virol 2015; 89:11858-70. [PMID: 26378164 DOI: 10.1128/jvi.01755-15] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/07/2015] [Indexed: 12/11/2022] Open
Abstract
UNLABELLED We previously showed that close relatives of human coronavirus 229E (HCoV-229E) exist in African bats. The small sample and limited genomic characterizations have prevented further analyses so far. Here, we tested 2,087 fecal specimens from 11 bat species sampled in Ghana for HCoV-229E-related viruses by reverse transcription-PCR (RT-PCR). Only hipposiderid bats tested positive. To compare the genetic diversity of bat viruses and HCoV-229E, we tested historical isolates and diagnostic specimens sampled globally over 10 years. Bat viruses were 5- and 6-fold more diversified than HCoV-229E in the RNA-dependent RNA polymerase (RdRp) and spike genes. In phylogenetic analyses, HCoV-229E strains were monophyletic and not intermixed with animal viruses. Bat viruses formed three large clades in close and more distant sister relationships. A recently described 229E-related alpaca virus occupied an intermediate phylogenetic position between bat and human viruses. According to taxonomic criteria, human, alpaca, and bat viruses form a single CoV species showing evidence for multiple recombination events. HCoV-229E and the alpaca virus showed a major deletion in the spike S1 region compared to all bat viruses. Analyses of four full genomes from 229E-related bat CoVs revealed an eighth open reading frame (ORF8) located at the genomic 3' end. ORF8 also existed in the 229E-related alpaca virus. Reanalysis of HCoV-229E sequences showed a conserved transcription regulatory sequence preceding remnants of this ORF, suggesting its loss after acquisition of a 229E-related CoV by humans. These data suggested an evolutionary origin of 229E-related CoVs in hipposiderid bats, hypothetically with camelids as intermediate hosts preceding the establishment of HCoV-229E. IMPORTANCE The ancestral origins of major human coronaviruses (HCoVs) likely involve bat hosts. Here, we provide conclusive genetic evidence for an evolutionary origin of the common cold virus HCoV-229E in hipposiderid bats by analyzing a large sample of African bats and characterizing several bat viruses on a full-genome level. Our evolutionary analyses show that animal and human viruses are genetically closely related, can exchange genetic material, and form a single viral species. We show that the putative host switches leading to the formation of HCoV-229E were accompanied by major genomic changes, including deletions in the viral spike glycoprotein gene and loss of an open reading frame. We reanalyze a previously described genetically related alpaca virus and discuss the role of camelids as potential intermediate hosts between bat and human viruses. The evolutionary history of HCoV-229E likely shares important characteristics with that of the recently emerged highly pathogenic Middle East respiratory syndrome (MERS) coronavirus.
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406
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Functional and structural properties of a novel cellulosome-like multienzyme complex: efficient glycoside hydrolysis of water-insoluble 7-xylosyl-10-deacetylpaclitaxel. Sci Rep 2015; 5:13768. [PMID: 26347949 PMCID: PMC4562250 DOI: 10.1038/srep13768] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 08/05/2015] [Indexed: 11/09/2022] Open
Abstract
Cellulosome is a kind of multienzyme complex that displays high activity, selectivity, and stability. Here, we report a novel, non-cellulolytic, cellulosome-like multienzyme complex that produced by the Cellulosimicrobium cellulans wild-type strain F16 isolated from soil microflora. This multienzyme complex, with excellent catalytic efficiency of kcat 13.2 s(-1) to remove the C-7 xylosyl group from 7-xylosyl-10-deacetylpaclitaxel (10-DAXP), has an outstanding tolerance against organic solvents and an excellent general stability, with the long half-life of 214 hours. This cellulosome-like multienzyme complex has a novel structure distinct from the well-documented ones. The key catalytic subunit responsible for the β-xylosidase activity against 10-DAXP is identified to be a novel protein, indicating a new glycoside hydrolase (GH) family. The pioneering work described here offers a novel nanoscale biocatalyst for the production of biofuels and chemicals from renewable plant-based natural resources.
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407
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Chakravorty D, Gookin TE, Milner MJ, Yu Y, Assmann SM. Extra-Large G Proteins Expand the Repertoire of Subunits in Arabidopsis Heterotrimeric G Protein Signaling. PLANT PHYSIOLOGY 2015; 169:512-29. [PMID: 26157115 PMCID: PMC4577375 DOI: 10.1104/pp.15.00251] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 07/06/2015] [Indexed: 05/21/2023]
Abstract
Heterotrimeric G proteins, consisting of Gα, Gβ, and Gγ subunits, are a conserved signal transduction mechanism in eukaryotes. However, G protein subunit numbers in diploid plant genomes are greatly reduced as compared with animals and do not correlate with the diversity of functions and phenotypes in which heterotrimeric G proteins have been implicated. In addition to GPA1, the sole canonical Arabidopsis (Arabidopsis thaliana) Gα subunit, Arabidopsis has three related proteins: the extra-large GTP-binding proteins XLG1, XLG2, and XLG3. We demonstrate that the XLGs can bind Gβγ dimers (AGB1 plus a Gγ subunit: AGG1, AGG2, or AGG3) with differing specificity in yeast (Saccharomyces cerevisiae) three-hybrid assays. Our in silico structural analysis shows that XLG3 aligns closely to the crystal structure of GPA1, and XLG3 also competes with GPA1 for Gβγ binding in yeast. We observed interaction of the XLGs with all three Gβγ dimers at the plasma membrane in planta by bimolecular fluorescence complementation. Bioinformatic and localization studies identified and confirmed nuclear localization signals in XLG2 and XLG3 and a nuclear export signal in XLG3, which may facilitate intracellular shuttling. We found that tunicamycin, salt, and glucose hypersensitivity and increased stomatal density are agb1-specific phenotypes that are not observed in gpa1 mutants but are recapitulated in xlg mutants. Thus, XLG-Gβγ heterotrimers provide additional signaling modalities for tuning plant G protein responses and increase the repertoire of G protein heterotrimer combinations from three to 12. The potential for signal partitioning and competition between the XLGs and GPA1 is a new paradigm for plant-specific cell signaling.
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Affiliation(s)
- David Chakravorty
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Timothy E Gookin
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Matthew J Milner
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Yunqing Yu
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Sarah M Assmann
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
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408
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Koberg S, Mohamed MDA, Faulhaber K, Neve H, Heller KJ. Identification and characterization of cis- and trans-acting elements involved in prophage induction in Streptococcus thermophilus J34. Mol Microbiol 2015; 98:535-52. [PMID: 26193959 DOI: 10.1111/mmi.13140] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2015] [Indexed: 11/29/2022]
Abstract
The genetic switch region of temperate Streptococcus thermophilus phage TP-J34 contains two divergently oriented promoters and several predicted operator sites. It separates lytic cycle-promoting genes from those promoting lysogeny. A polycistronic transcript comprises the genes coding for repressor Crh, metalloproteinase-motif protein Rir and superinfection exclusion lipoprotein Ltp. Weak promoters effecting monocistronic transcripts were localized for ltp and int (encoding integrase) by Northern blot and 5'-RACE-PCR. These transcripts appeared in lysogenic as well as lytic state. A polycistronic transcript comprising genes coh (encoding Cro homolog), ant (encoding putative antirepressor), orf7, orf8 and orf9 was only detected in the lytic state. Four operator sites, of which three were located in the intergenic regions between crh and coh, and one between coh and ant, were identified by competition electromobility shift assays. Cooperative binding of Crh to two operator sites immediately upstream of coh could be demonstrated. Coh was shown to bind to the operator closest to crh only. Oligomerization was proven by cross-linking Crh by glutaraldehyde. Knock-out of rir revealed a key role in prophage induction. Rir and Crh were shown to form a complex in solution and Rir prevented binding of Crh to its operator sites.
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Affiliation(s)
- Sabrina Koberg
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food), Kiel, Germany
| | - Mazhar Desouki Ali Mohamed
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food), Kiel, Germany
| | - Katharina Faulhaber
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food), Kiel, Germany
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food), Kiel, Germany
| | - Knut J Heller
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food), Kiel, Germany
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409
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Volpato V, Alshomrani B, Pollastri G. Accurate Ab Initio and Template-Based Prediction of Short Intrinsically-Disordered Regions by Bidirectional Recurrent Neural Networks Trained on Large-Scale Datasets. Int J Mol Sci 2015; 16:19868-85. [PMID: 26307973 PMCID: PMC4581330 DOI: 10.3390/ijms160819868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/28/2015] [Accepted: 07/29/2015] [Indexed: 12/02/2022] Open
Abstract
Intrinsically-disordered regions lack a well-defined 3D structure, but play key roles in determining the function of many proteins. Although predictors of disorder have been shown to achieve relatively high rates of correct classification of these segments, improvements over the the years have been slow, and accurate methods are needed that are capable of accommodating the ever-increasing amount of structurally-determined protein sequences to try to boost predictive performances. In this paper, we propose a predictor for short disordered regions based on bidirectional recurrent neural networks and tested by rigorous five-fold cross-validation on a large, non-redundant dataset collected from MobiDB, a new comprehensive source of protein disorder annotations. The system exploits sequence and structural information in the forms of frequency profiles, predicted secondary structure and solvent accessibility and direct disorder annotations from homologous protein structures (templates) deposited in the Protein Data Bank. The contributions of sequence, structure and homology information result in large improvements in predictive accuracy. Additionally, the large scale of the training set leads to low false positive rates, making our systems a robust and efficient way to address high-throughput disorder prediction.
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Affiliation(s)
- Viola Volpato
- School of Computer Science, University College Dublin, Belfield, Dublin 4, Ireland.
- Adaptive and Complex Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Badr Alshomrani
- School of Computer Science, University College Dublin, Belfield, Dublin 4, Ireland.
- Adaptive and Complex Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Gianluca Pollastri
- School of Computer Science, University College Dublin, Belfield, Dublin 4, Ireland.
- Adaptive and Complex Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland.
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410
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Rockah-Shmuel L, Tóth-Petróczy Á, Tawfik DS. Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations. PLoS Comput Biol 2015; 11:e1004421. [PMID: 26274323 PMCID: PMC4537296 DOI: 10.1371/journal.pcbi.1004421] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 06/30/2015] [Indexed: 11/18/2022] Open
Abstract
Systematic mappings of the effects of protein mutations are becoming increasingly popular. Unexpectedly, these experiments often find that proteins are tolerant to most amino acid substitutions, including substitutions in positions that are highly conserved in nature. To obtain a more realistic distribution of the effects of protein mutations, we applied a laboratory drift comprising 17 rounds of random mutagenesis and selection of M.HaeIII, a DNA methyltransferase. During this drift, multiple mutations gradually accumulated. Deep sequencing of the drifted gene ensembles allowed determination of the relative effects of all possible single nucleotide mutations. Despite being averaged across many different genetic backgrounds, about 67% of all nonsynonymous, missense mutations were evidently deleterious, and an additional 16% were likely to be deleterious. In the early generations, the frequency of most deleterious mutations remained high. However, by the 17th generation, their frequency was consistently reduced, and those remaining were accepted alongside compensatory mutations. The tolerance to mutations measured in this laboratory drift correlated with sequence exchanges seen in M.HaeIII’s natural orthologs. The biophysical constraints dictating purging in nature and in this laboratory drift also seemed to overlap. Our experiment therefore provides an improved method for measuring the effects of protein mutations that more closely replicates the natural evolutionary forces, and thereby a more realistic view of the mutational space of proteins. Understanding and predicting the effects of single nucleotide polymorphisms (SNPs) is of fundamental importance in many fields. Systematic experimental mappings of the effects of such mutations within a given gene/protein comprise an essential experimental tool for determining protein function and for refining models of protein evolution, as well as an important resource for improving prediction algorithms. Here, we present the results of a laboratory system that mimics the manner by which protein sequences diverge in nature: a prolonged process of gradually accumulating random mutations that retain the protein’s structure and function. The change in frequencies of mutations over generations, as obtained by deep sequencing, enabled us to assess the relative effects of all possible SNPs at the background of an accumulating number of mutations. Compared to previous reports, we found that > 80% of all possible amino acid exchanges have potential deleterious effects, with 67% being clearly deleterious. Tolerance vs. purging of mutations in our prolonged drift also showed better correlation with natural diversity. Overall, our experimental setup provides a better understanding of how protein sequences diverge in nature, plus a new basis for improving the prediction accuracy of the effects of protein mutations, and specifically of SNPs.
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Affiliation(s)
- Liat Rockah-Shmuel
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Ágnes Tóth-Petróczy
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Dan S. Tawfik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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411
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de Diego Puente T, Gallego-Jara J, Castaño-Cerezo S, Bernal Sánchez V, Fernández Espín V, García de la Torre J, Manjón Rubio A, Cánovas Díaz M. The Protein Acetyltransferase PatZ from Escherichia coli Is Regulated by Autoacetylation-induced Oligomerization. J Biol Chem 2015; 290:23077-93. [PMID: 26251518 DOI: 10.1074/jbc.m115.649806] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Indexed: 01/31/2023] Open
Abstract
Lysine acetylation is an important post-translational modification in the metabolic regulation of both prokaryotes and eukaryotes. In Escherichia coli, PatZ (formerly YfiQ) is the only known acetyltransferase protein and is responsible for acetyl-CoA synthetase acetylation. In this study, we demonstrated PatZ-positive cooperativity in response to acetyl-CoA and the regulation of acetyl-CoA synthetase activity by the acetylation level. Furthermore, functional analysis of an E809A mutant showed that the conserved glutamate residue is not relevant for the PatZ catalytic mechanism. Biophysical studies demonstrated that PatZ is a stable tetramer in solution and is transformed to its octameric form by autoacetylation. Moreover, this modification is reversed by the sirtuin CobB. Finally, an in silico PatZ tetramerization model based on hydrophobic and electrostatic interactions is proposed and validated by three-dimensional hydrodynamic analysis. These data reveal, for the first time, the structural regulation of an acetyltransferase by autoacetylation in a prokaryotic organism.
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Affiliation(s)
| | - Julia Gallego-Jara
- From the Departments of Biochemistry and Molecular Biology and Immunology (B) and
| | - Sara Castaño-Cerezo
- From the Departments of Biochemistry and Molecular Biology and Immunology (B) and
| | | | - Vanesa Fernández Espín
- Physical Chemistry, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum," P. O. Box 4021, Murcia E-30100, Spain
| | - José García de la Torre
- Physical Chemistry, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum," P. O. Box 4021, Murcia E-30100, Spain
| | - Arturo Manjón Rubio
- From the Departments of Biochemistry and Molecular Biology and Immunology (B) and
| | - Manuel Cánovas Díaz
- From the Departments of Biochemistry and Molecular Biology and Immunology (B) and
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412
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Heimer G, Marek-Yagel D, Eyal E, Barel O, Oz Levi D, Hoffmann C, Ruzzo EK, Ganelin-Cohen E, Lancet D, Pras E, Rechavi G, Nissenkorn A, Anikster Y, Goldstein DB, Ben Zeev B. SLC1A4 mutations cause a novel disorder of intellectual disability, progressive microcephaly, spasticity and thin corpus callosum. Clin Genet 2015; 88:327-35. [PMID: 26138499 DOI: 10.1111/cge.12637] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 06/25/2015] [Accepted: 06/30/2015] [Indexed: 12/30/2022]
Abstract
Two unrelated patients, presenting with significant global developmental delay, severe progressive microcephaly, seizures, spasticity and thin corpus callosum (CC) underwent trio whole-exome sequencing. No candidate variant was found in any known genes related to the phenotype. However, crossing the data of the patients illustrated that they both manifested pathogenic variants in the SLC1A4 gene which codes the ASCT1 transporter of serine and other neutral amino acids. The Ashkenazi patient is homozygous for a deleterious missense c.766G>A, p.(E256K) mutation whereas the Ashkenazi-Iraqi patient is compound heterozygous for this mutation and a nonsense c.945delTT, p.(Leu315Hisfs*42) mutation. Structural prediction demonstrates truncation of significant portion of the protein by the nonsense mutation and speculates functional disruption by the missense mutation. Both mutations are extremely rare in general population databases, however, the missense mutation was found in heterozygous mode in 1:100 Jewish Ashkenazi controls suggesting a higher carrier rate among Ashkenazi Jews. We conclude that SLC1A4 is the disease causing gene of a novel neurologic disorder manifesting with significant intellectual disability, severe postnatal microcephaly, spasticity and thin CC. The role of SLC1A4 in the serine transport from astrocytes to neurons suggests a possible pathomechanism for this disease and implies a potential therapeutic approach.
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Affiliation(s)
- G Heimer
- Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Ramat Gan, Israel.,The Pinchas Borenstein Talpiot Medical Leadership Program, Ramat Gan, Israel
| | - D Marek-Yagel
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Ramat Gan, Israel
| | - E Eyal
- Cancer Research Center, Pediatric Hemato/oncology Unit, Edmond and Lily Safra Children's Hospital, The Chaim Sheba Medical Center, Ramat Gan, Israel
| | - O Barel
- Cancer Research Center, Pediatric Hemato/oncology Unit, Edmond and Lily Safra Children's Hospital, The Chaim Sheba Medical Center, Ramat Gan, Israel
| | - D Oz Levi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - C Hoffmann
- Diagnostic Imaging Unit, The Chaim Sheba Medical Center, Ramat Gan, Israel
| | - E K Ruzzo
- Center for Human Genome Variation, Duke University School of Medicine, Durham, NC, USA
| | - E Ganelin-Cohen
- Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Ramat Gan, Israel
| | - D Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - E Pras
- Danek Gertner Institute of Human Genetics, Sheba Medical Center, Ramat Gan, Israel.,The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - G Rechavi
- Cancer Research Center, Pediatric Hemato/oncology Unit, Edmond and Lily Safra Children's Hospital, The Chaim Sheba Medical Center, Ramat Gan, Israel.,The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - A Nissenkorn
- Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Ramat Gan, Israel.,The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Y Anikster
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Ramat Gan, Israel.,The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - D B Goldstein
- Institute for Genomic Medicine, Columbia University Medical School, Columbia University Medical Center, New York, NY, USA
| | - B Ben Zeev
- Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Ramat Gan, Israel.,The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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413
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Crystal structure of the Ego1-Ego2-Ego3 complex and its role in promoting Rag GTPase-dependent TORC1 signaling. Cell Res 2015. [PMID: 26206314 DOI: 10.1038/cr.2015.86] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The target of rapamycin complex 1 (TORC1) integrates various hormonal and nutrient signals to regulate cell growth, proliferation, and differentiation. Amino acid-dependent activation of TORC1 is mediated via the yeast EGO complex (EGOC) consisting of Gtr1, Gtr2, Ego1, and Ego3. Here, we identify the previously uncharacterized Ycr075w-a/Ego2 protein as an additional EGOC component that is required for the integrity and localization of the heterodimeric Gtr1-Gtr2 GTPases, equivalent to mammalian Rag GTPases. We also report the crystal structure of the Ego1-Ego2-Ego3 ternary complex (EGO-TC) at 2.4 Å resolution, in which Ego2 and Ego3 form a heterodimer flanked along one side by Ego1. Structural data also reveal the structural conservation of protein components between the yeast EGO-TC and the human Ragulator, which acts as a GEF for Rag GTPases. Interestingly, however, artificial tethering of Gtr1-Gtr2 to the vacuolar membrane is sufficient to activate TORC1 in response to amino acids even in the absence of the EGO-TC. Our structural and functional data therefore support a model in which the EGO-TC acts as a scaffold for Rag GTPases in TORC1 signaling.
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414
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Yachdav G, Goldberg T, Wilzbach S, Dao D, Shih I, Choudhary S, Crouch S, Franz M, García A, García LJ, Grüning BA, Inupakutika D, Sillitoe I, Thanki AS, Vieira B, Villaveces JM, Schneider MV, Lewis S, Pettifer S, Rost B, Corpas M. Anatomy of BioJS, an open source community for the life sciences. eLife 2015; 4. [PMID: 26153621 PMCID: PMC4495654 DOI: 10.7554/elife.07009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 06/20/2015] [Indexed: 01/12/2023] Open
Abstract
BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source software projects. DOI:http://dx.doi.org/10.7554/eLife.07009.001
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Affiliation(s)
- Guy Yachdav
- Bioinformatik, Biosof LLC, Garching, Germany
| | - Tatyana Goldberg
- Bioinformatik, Technische Universität München, Garching, Germany
| | | | - David Dao
- Bioinformatik, Technische Universität München, Garching, Germany
| | - Iris Shih
- Bioinformatik, Technische Universität München, Garching, Germany
| | - Saket Choudhary
- Molecular and Computational Biology, University of Southern California, Los Angeles, United States
| | - Steve Crouch
- Web and Internet Science, University of Southampton, Southampton, United Kingdom
| | - Max Franz
- Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | | | - Leyla J García
- European Molecular Biology Laboratory-European Bioinformatics Institute, Cambridge, United Kingdom
| | - Björn A Grüning
- Bioinformatics Group, Department of Computer Science and Centre for Biological Systems Analysis, University of Freiburg, Freiburg, Germany
| | - Devasena Inupakutika
- Web and Internet Science, University of Southampton, Southampton, United Kingdom
| | - Ian Sillitoe
- Institute of Structure and Molecular Biology, University College London, London, United Kingdom
| | | | - Bruno Vieira
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | | | | | - Suzanna Lewis
- Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Steve Pettifer
- School of Computer Science, The University of Manchester, Manchester, United Kingdom
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415
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Ofer D, Linial M. ProFET: Feature engineering captures high-level protein functions. Bioinformatics 2015; 31:3429-36. [DOI: 10.1093/bioinformatics/btv345] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 05/29/2015] [Indexed: 11/13/2022] Open
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416
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Two Proteins Form a Heteromeric Bacterial Self-Recognition Complex in Which Variable Subdomains Determine Allele-Restricted Binding. mBio 2015; 6:e00251. [PMID: 26060269 PMCID: PMC4471559 DOI: 10.1128/mbio.00251-15] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
UNLABELLED Self- versus nonself-recognition in bacteria has been described recently through genetic analyses in multiple systems; however, understanding of the biochemical properties and mechanisms of recognition-determinant proteins remains limited. Here we extend the molecular and biochemical understanding of two recognition-determinant proteins in bacteria. We have found that a heterotypic complex is formed between two bacterial self-recognition proteins, IdsD and IdsE, the genes of which have been shown to genetically encode the determinants for strain-specific identity in the opportunistic bacterial pathogen Proteus mirabilis. This IdsD-IdsE complex forms independently of other P. mirabilis-encoded self-recognition proteins. We have also shown that the binding between IdsD and IdsE is strain- and allele-specific. The specificity for interactions is encoded within a predicted membrane-spanning subdomain within each protein that contains stretches of unique amino acids in each P. mirabilis variant. Finally, we have demonstrated that this in vitro IdsD-IdsE binding interaction correlates to in vivo population identity, suggesting that the binding interactions between IdsD and IdsE are part of a cellular pathway that underpins self-recognition behavior in P. mirabilis and drives bacterial population sociality. IMPORTANCE Here we demonstrate that two proteins, the genes of which were genetically shown to encode determinants of self-identity in bacteria, bind in vitro in an allele-restricted interaction, suggesting that molecular recognition between these two proteins is a mechanism underpinning self-recognition behaviors in P. mirabilis. Binding specificity in each protein is encapsulated in a variable region subdomain that is predicted to span the membrane, suggesting that the interaction occurs in the cell envelope. Furthermore, conversion of binding affinities in vitro correlates with conversion of self-identity in vivo, suggesting that this molecular recognition might help to drive population behaviors.
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417
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Shi X, Li L, Guo C, Lin X, Li M, Lin S. Rhodopsin gene expression regulated by the light dark cycle, light spectrum and light intensity in the dinoflagellate Prorocentrum. Front Microbiol 2015; 6:555. [PMID: 26082770 PMCID: PMC4451421 DOI: 10.3389/fmicb.2015.00555] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 05/20/2015] [Indexed: 12/13/2022] Open
Abstract
The proton pump rhodopsin is widely found in marine bacteria and archaea, where it functions to capture light energy and convert it to ATP. While found in several lineages of dinoflagellates, this gene has not been studied in Prorocentrales species and whether it functionally tunes to light spectra and intensities as in bacteria remains unclear. Here we identified and characterized this gene in the bloom-forming Prorocentrum donghaiense. It is a 7-helix transmembrane polypeptide containing conserved domains and critical amino acid residues of PPR. This gene is phylogenetically affiliated to the xanthorhodopsin clade, but seems to have a distinct evolutionary origin. Quantitative reverse transcription PCR showed that in regular cultures, the transcript abundance of the gene exhibited a clear diel pattern, high abundance in the light period and low in the dark. The same diel pattern was observed for protein abundance with a Western blot using specific antiserum. The rhythm was dampened when the cultures were shifted to continuous dark or light condition, suggesting that this gene is not under circadian clock control. Rhodopsin transcript and protein abundances varied with light intensity, both being highest at a moderate illumination level. Furthermore, the expression of this gene responded to different light spectra, with slightly higher transcript abundance under green than blue light, and lowest abundance under red light. Transformed Escherichia coli over-expressing this rhodopsin gene also exhibited an absorption maximum in the blue–green region with slightly higher absorption in the green. These rhodopsin-promoting light conditions are similar to the relatively turbid marine habitat where the species forms blooms, suggesting that this gene may function to compensate for the light-limited photosynthesis in the dim environment.
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Affiliation(s)
- Xinguo Shi
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University Xiamen, China ; College of the Environment and Ecology, Xiamen University Xiamen, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University Xiamen, China
| | - Chentao Guo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University Xiamen, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University Xiamen, China
| | - Meizhen Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University Xiamen, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University Xiamen, China ; Department of Marine Sciences, University of Connecticut Groton, CT, USA
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418
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Suwansa-ard S, Thongbuakaew T, Wang T, Zhao M, Elizur A, Hanna PJ, Sretarugsa P, Cummins SF, Sobhon P. In silico Neuropeptidome of Female Macrobrachium rosenbergii Based on Transcriptome and Peptide Mining of Eyestalk, Central Nervous System and Ovary. PLoS One 2015; 10:e0123848. [PMID: 26023789 PMCID: PMC4449106 DOI: 10.1371/journal.pone.0123848] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 03/08/2015] [Indexed: 01/13/2023] Open
Abstract
Macrobrachium rosenbergii is the most economically important of the cultured freshwater crustacean species, yet there is currently a deficiency in genomic and transcriptomic information for research requirements. In this study, we present an in silico analysis of neuropeptide genes within the female M. rosenbergii eyestalk, central nervous system, and ovary. We could confidently predict 37 preproneuropeptide transcripts, including those that encode bursicons, crustacean cardioactive peptide, crustacean hyperglycemic hormones, eclosion hormone, pigment-dispersing hormones, diuretic hormones, neuropeptide F, neuroparsins, SIFamide, and sulfakinin. These transcripts are most prominent within the eyestalk and central nervous system. Transcript tissue distribution as determined by reverse transcription-polymerase chain reaction revealed the presence of selected neuropeptide genes of interest mainly in the nervous tissues while others were additionally present in the non-nervous tissues. Liquid chromatography-mass spectrometry analysis of eyestalk peptides confirmed the presence of the crustacean hyperglycemic hormone precursor. This data set provides a strong foundation for further studies into the functional roles of neuropeptides in M. rosenbergii, and will be especially helpful for developing methods to improve crustacean aquaculture.
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Affiliation(s)
- Saowaros Suwansa-ard
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Tipsuda Thongbuakaew
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Tianfang Wang
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Min Zhao
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Abigail Elizur
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Peter J. Hanna
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
- Pro Vice-Chancellor’s Office, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong, Victoria, Australia
| | - Prapee Sretarugsa
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Scott F. Cummins
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
- * E-mail: (SFC); (P. Sobhon)
| | - Prasert Sobhon
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
- * E-mail: (SFC); (P. Sobhon)
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419
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Identification of a mitochondrial-binding site on the N-terminal end of hexokinase II. Biosci Rep 2015; 35:BSR20150047. [PMID: 26182367 PMCID: PMC4613670 DOI: 10.1042/bsr20150047] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 04/23/2015] [Indexed: 11/17/2022] Open
Abstract
Hexokinase II (HKII) is responsible for the first step in the glycolysis pathway by adding a phosphate on to the glucose molecule so it can proceed down the pathway to produce the energy for continuous cancer cell growth. Tumour cells overexpress the HKII enzyme. In fact, it is the overexpression of the HKII enzyme that makes the diagnosis of cancer possible when imaged by positron emission tomography (PET). HKII binds to the voltage-dependent anion channel (VDAC) located on the mitochondrial outer membrane (MOM). When bound to the MOM, HKII is blocking a major cell death pathway. Thus, HKII is responsible for two characteristics of cancer cells, rapid tumour growth and inability of cancer cells to undergo apoptosis. One method to identify novel compounds that may interfere with the HKII-VDAC-binding site is to create a molecular model using the crystal structure of HKII. However, the amino acid(s) responsible for HKII binding to VDAC are not known. Therefore, a series of truncations and point mutations were made to the N-terminal end of HKII to identify the binding site to VDAC. Deletions of the first 10 and 20 amino acids indicated that important amino acid(s) for binding were located within the first 10 amino acids. Next, a series of point mutations were made within the first 10 amino acids. It is clear from the immunofluorescence images and immunoblot results that mutating the fifth amino acid from histidine to proline completely abolished binding to the MOM.
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420
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Drozdetskiy A, Cole C, Procter J, Barton GJ. JPred4: a protein secondary structure prediction server. Nucleic Acids Res 2015; 43:W389-94. [PMID: 25883141 PMCID: PMC4489285 DOI: 10.1093/nar/gkv332] [Citation(s) in RCA: 1241] [Impact Index Per Article: 137.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/28/2015] [Indexed: 11/13/2022] Open
Abstract
JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 94 000 jobs per month and has carried out over 1.5 million predictions in total for users in 179 countries. The JPred4 web server has been re-implemented in the Bootstrap framework and JavaScript to improve its design, usability and accessibility from mobile devices. JPred4 features higher accuracy, with a blind three-state (α-helix, β-strand and coil) secondary structure prediction accuracy of 82.0% while solvent accessibility prediction accuracy has been raised to 90% for residues <5% accessible. Reporting of results is enhanced both on the website and through the optional email summaries and batch submission results. Predictions are now presented in SVG format with options to view full multiple sequence alignments with and without gaps and insertions. Finally, the help-pages have been updated and tool-tips added as well as step-by-step tutorials.
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Affiliation(s)
- Alexey Drozdetskiy
- Division of Computational Biology, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Christian Cole
- Division of Computational Biology, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - James Procter
- Division of Computational Biology, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Geoffrey J Barton
- Division of Computational Biology, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
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421
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Wuertenberger S, Groemping Y. A single PXXP motif in the C-terminal region of srGAP3 mediates binding to multiple SH3 domains. FEBS Lett 2015; 589:1156-63. [PMID: 25819436 DOI: 10.1016/j.febslet.2015.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 03/18/2015] [Accepted: 03/18/2015] [Indexed: 11/17/2022]
Abstract
The Slit-Robo GTPase-activating protein 3 (srGAP3) has been implicated in different critical aspects of neuronal development. These findings have mainly been based on the characterisation of the three conserved globular N-terminal domains, while the function of the C-terminal region (CTR) is still unknown. We show that this predicted unstructured region acts as an adaptor by binding to the endocytic proteins Amphiphysin, Endophilin-A2, Endophilin-A1, as well as the Ras signalling protein Grb2. All these interactions depend on a single proline-rich motif in the CTR and the Src-homology 3 domains of the binding partners. Via these interactions srGAP3 could link receptor signalling events to the endocytic machinery.
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Affiliation(s)
- Silvia Wuertenberger
- Max Planck Institute for Developmental Biology, Department of Protein Evolution, Spemannstr. 35, D-72076 Tübingen, Germany
| | - Yvonne Groemping
- Max Planck Institute for Developmental Biology, Department of Protein Evolution, Spemannstr. 35, D-72076 Tübingen, Germany.
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422
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Mahalingam M, Fessenden JD. Methods for labeling skeletal muscle ion channels site-specifically with fluorophores suitable for FRET-based structural analysis. Methods Enzymol 2015; 556:455-74. [PMID: 25857795 DOI: 10.1016/bs.mie.2014.11.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Skeletal muscle excitation-contraction coupling is triggered by the concerted action of two enormous Ca(2+) channel complexes, the dihydropyridine receptor and the type 1 ryanodine receptor. Recent advances in our understanding of the structure of these large Ca(2+) channels have been driven by fluorescence resonance energy transfer (FRET)-based analysis. A methodological challenge in conducting these FRET measurements is the ability to site-specifically label these huge ion channels with donor and acceptor fluorophores capable of undergoing energy transfer. In this chapter, we detail specific protocols for tagging large membrane proteins with these fluorescent probes using three orthogonal labeling methods: fluorescent protein fusions, biarsenical reagents directed to engineered tetracysteine tags, and Cy3/5 nitrilotriacetic acid conjugates that bind to poly-histidine tags.
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Affiliation(s)
- Mohana Mahalingam
- Department of Anesthesia, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - James D Fessenden
- Department of Anesthesia, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.
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423
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Calvete O, Reyes J, Zuñiga S, Paumard-Hernández B, Fernández V, Bujanda L, Rodriguez-Pinilla MS, Palacios J, Heine-Suñer D, Banka S, Newman WG, Cañamero M, Pritchard DM, Benítez J. Exome sequencing identifies ATP4A gene as responsible of an atypical familial type I gastric neuroendocrine tumour. Hum Mol Genet 2015; 24:2914-22. [PMID: 25678551 DOI: 10.1093/hmg/ddv054] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 02/06/2015] [Indexed: 02/06/2023] Open
Abstract
Gastric neuroendocrine tumours (NETs) arise from enterochromaffin-like cells, which are located in oxyntic glands within the stomach. Type I tumours represent 70-80% of gastric NETs and are associated with hypergastrinaemia, chronic atrophic gastritis and achlorhydria. Gastrin is involved in the endocrine regulation of gastric acid production. Most type I gastric NETs are sporadic, have a good prognosis and their genetic basis are unknown. We performed an exome sequencing study in a family with consanguineous parents and 10 children, five of whom were affected by type I gastric NET. Atypical clinical traits included an earlier age of onset (around 30 years), aggressiveness (three had nodal infiltration requiring total gastrectomy and one an adenocarcinoma) and iron-deficiency rather than megaloblastic anaemia. We identified a homozygous missense mutation in the 14th exon of the ATP4A gene (c.2107C>T), which encodes the proton pump responsible for acid secretion by gastric parietal cells. The amino acid p.Arg703Cys is highly conserved across species and originates a change of one of the transmembrane domains that avoids the liberation of protons from cells to stomach. This is consistent with the achlorhydria that was observed in the affected individuals. No germline or somatic mutations in the ATP4A gene were found in sporadic gastric NET patients. Based on the results of this large family, it seems that this atypical form of gastric NET has an earlier age of onset, behaves more aggressively and has atypical clinical traits that differentiated from other studied cases.
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Affiliation(s)
- Oriol Calvete
- Human Genetics Group and Network of Research on Rare Diseases (CIBERER), Madrid 28029, Spain
| | - Jose Reyes
- Department of Gastroenterology, Hospital INCA, Majorca 07300, Spain
| | - Sheila Zuñiga
- Department of Bioinformatics, Sistemas Genómicos, Valencia 46980, Spain
| | | | | | - Luís Bujanda
- Department of Gastroenterology, Hospital Donostia/Instituto Biodonostia, Biomedical Research Center, and CIBEREHD, Universidad del País Vasco, San Sebastián 20080, Spain
| | | | - Jose Palacios
- Pathology Department, Hospital Ramón y Cajal. Madrid 28034, Spain
| | - Damian Heine-Suñer
- Genetics Department, Hospital Universitario Son Espases, Majorca 07120, Spain
| | - Siddharth Banka
- Centre for Genomic Medicine, University of Manchester and Central Manchester University Hospital NHS Foundation Trust, Manchester M13 9WL, UK and
| | - William G Newman
- Centre for Genomic Medicine, University of Manchester and Central Manchester University Hospital NHS Foundation Trust, Manchester M13 9WL, UK and
| | - Marta Cañamero
- Histopathology Unit, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain
| | - D Mark Pritchard
- Department of Gastroenterology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK
| | - Javier Benítez
- Human Genetics Group and Network of Research on Rare Diseases (CIBERER), Madrid 28029, Spain,
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424
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Kaiser ML, Römisch K. Proteasome 19S RP binding to the Sec61 channel plays a key role in ERAD. PLoS One 2015; 10:e0117260. [PMID: 25658429 PMCID: PMC4319758 DOI: 10.1371/journal.pone.0117260] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 12/20/2014] [Indexed: 11/24/2022] Open
Abstract
Import of secretory proteins into the Endoplasmic Reticulum (ER) is an established function of the Sec61 channel. The contribution of the Sec61 channel to export of misfolded proteins from the ER for degradation by proteasomes is still controversial, but the proteasome 19S regulatory particle (RP) is necessary and sufficient for extraction of specific misfolded proteins from the ER, and binds directly to the Sec61 channel. In this work we have identified an import-competent sec61 mutant, S353C, carrying a point mutation in ER-lumenal loop 7 which reduces affinity of the cytoplasmic face of the Sec61 channel for the 19S RP. This indicates that the interaction between the 19S RP and the Sec61 channel is dependent on conformational changes in Sec61p hinging on loop 7. The sec61-S353C mutant had no measurable ER import defects and did not cause ER stress in intact cells, but reduced ER-export of a 19S RP-dependent misfolded protein when proteasomes were limiting in a cell-free assay. Our data suggest that the interaction between the 19S RP and the Sec61 channel is essential for the export of specific substrates from the ER to the cytosol for proteasomal degradation.
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Affiliation(s)
- Marie-Luise Kaiser
- Department of Microbiology, Faculty of Natural Sciences and Technology VIII, Saarland University, 66123, Saarbrücken, Germany
| | - Karin Römisch
- Department of Microbiology, Faculty of Natural Sciences and Technology VIII, Saarland University, 66123, Saarbrücken, Germany
- * E-mail:
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425
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Hamp T, Rost B. Evolutionary profiles improve protein–protein interaction prediction from sequence. Bioinformatics 2015; 31:1945-50. [DOI: 10.1093/bioinformatics/btv077] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 02/02/2015] [Indexed: 11/14/2022] Open
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426
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Regulation of human adenovirus alternative RNA splicing by the adenoviral L4-33K and L4-22K proteins. Int J Mol Sci 2015; 16:2893-912. [PMID: 25636034 PMCID: PMC4346872 DOI: 10.3390/ijms16022893] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 01/06/2015] [Accepted: 01/22/2015] [Indexed: 01/12/2023] Open
Abstract
Adenovirus makes extensive use of alternative RNA splicing to produce a complex set of spliced viral mRNAs. Studies aimed at characterizing the interactions between the virus and the host cell RNA splicing machinery have identified three viral proteins of special significance for the control of late viral gene expression: L4-33K, L4-22K, and E4-ORF4. L4-33K is a viral alternative RNA splicing factor that controls L1 alternative splicing via an interaction with the cellular protein kinases Protein Kinase A (PKA) and DNA-dependent protein kinase (DNA-PK). L4-22K is a viral transcription factor that also has been implicated in the splicing of a subset of late viral mRNAs. E4-ORF4 is a viral protein that binds the cellular protein phosphatase IIA (PP2A) and controls Serine/Arginine (SR)-rich protein activity by inducing SR protein dephosphorylation. The L4-33K, and most likely also the L4-22K protein, are highly phosphorylated in vivo. Here we will review the function of these viral proteins in the post-transcriptional control of adenoviral gene expression and further discuss the significance of potential protein kinases phosphorylating the L4-33K and/or L4-22K proteins.
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427
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Reeb J, Kloppmann E, Bernhofer M, Rost B. Evaluation of transmembrane helix predictions in 2014. Proteins 2015; 83:473-84. [PMID: 25546441 DOI: 10.1002/prot.24749] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/02/2014] [Accepted: 12/13/2014] [Indexed: 11/05/2022]
Abstract
Experimental structure determination continues to be challenging for membrane proteins. Computational prediction methods are therefore needed and widely used to supplement experimental data. Here, we re-examined the state of the art in transmembrane helix prediction based on a nonredundant dataset with 190 high-resolution structures. Analyzing 12 widely-used and well-known methods using a stringent performance measure, we largely confirmed the expected high level of performance. On the other hand, all methods performed worse for proteins that could not have been used for development. A few results stood out: First, all methods predicted proteins in eukaryotes better than those in bacteria. Second, methods worked less well for proteins with many transmembrane helices. Third, most methods correctly discriminated between soluble and transmembrane proteins. However, several older methods often mistook signal peptides for transmembrane helices. Some newer methods have overcome this shortcoming. In our hands, PolyPhobius and MEMSAT-SVM outperformed other methods.
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Affiliation(s)
- Jonas Reeb
- Department of Informatics & Center for Bioinformatics & Computational Biology-i12, Technische Universität München (TUM), Garching/Munich, 85748, Germany
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428
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Gallaher WR, Garry RF. Modeling of the Ebola virus delta peptide reveals a potential lytic sequence motif. Viruses 2015; 7:285-305. [PMID: 25609303 PMCID: PMC4306839 DOI: 10.3390/v7010285] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/12/2015] [Accepted: 01/16/2015] [Indexed: 12/24/2022] Open
Abstract
Filoviruses, such as Ebola and Marburg viruses, cause severe outbreaks of human infection, including the extensive epidemic of Ebola virus disease (EVD) in West Africa in 2014. In the course of examining mutations in the glycoprotein gene associated with 2014 Ebola virus (EBOV) sequences, a differential level of conservation was noted between the soluble form of glycoprotein (sGP) and the full length glycoprotein (GP), which are both encoded by the GP gene via RNA editing. In the region of the proteins encoded after the RNA editing site sGP was more conserved than the overlapping region of GP when compared to a distant outlier species, Tai Forest ebolavirus. Half of the amino acids comprising the “delta peptide”, a 40 amino acid carboxy-terminal fragment of sGP, were identical between otherwise widely divergent species. A lysine-rich amphipathic peptide motif was noted at the carboxyl terminus of delta peptide with high structural relatedness to the cytolytic peptide of the non-structural protein 4 (NSP4) of rotavirus. EBOV delta peptide is a candidate viroporin, a cationic pore-forming peptide, and may contribute to EBOV pathogenesis.
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Affiliation(s)
- William R Gallaher
- Mockingbird Nature Research Group, PO Box 568, Pearl River, LA 70452, USA.
| | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University Medical Center, 1430 Tulane Avenue, New Orleans, LA 70112, USA.
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429
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YANG MINGCHANG, LOH JOONKHIM, LI YIYANG, HUANG WENSHENG, CHOU CHIAHUA, CHENG JIINTSUEY, WANG YENGTSENG, LIEU ANNSHUNG, HOWNG SHENLONG, HONG YIREN, CHOU ANKUO. Bcl2L12 with a BH3-like domain in regulating apoptosis and TMZ-induced autophagy: A prospective combination of ABT-737 and TMZ for treating glioma. Int J Oncol 2015; 46:1304-16. [DOI: 10.3892/ijo.2015.2838] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 12/29/2014] [Indexed: 11/06/2022] Open
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430
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Abstract
Immunoinformatics focuses on modeling immune responses for better understanding of the immune system and in many cases for proposing agents able to modify the immune system. The most classical of these agents are vaccines derived from living organisms such as smallpox or polio. More modern vaccines comprise recombinant proteins, protein domains, and in some cases peptides. Generating a vaccine from peptides however requires technologies and concepts very different from classical vaccinology. Immunoinformatics therefore provides the computational tools to propose peptides suitable for formulation into vaccines. This chapter introduces the essential biological concepts affecting design and efficacy of peptide vaccines and discusses current methods and workflows applied to design successful peptide vaccines using computers.
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Affiliation(s)
- Johannes Söllner
- Emergentec Biodevelopment GmbH, Gersthofer Straße 29-31, 1180, Vienna, Austria,
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431
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Li L, Yu S, Xiao W, Li Y, Hu W, Huang L, Zheng X, Zhou S, Yang H. Protein submitochondrial localization from integrated sequence representation and SVM-based backward feature extraction. MOLECULAR BIOSYSTEMS 2015; 11:170-7. [PMID: 25335193 DOI: 10.1039/c4mb00340c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Mitochondrion, a tiny energy factory, plays an important role in various biological processes of most eukaryotic cells.
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Affiliation(s)
- Liqi Li
- Department of General Surgery
- Xinqiao Hospital
- Third Military Medical University
- Chongqing 400037
- China
| | - Sanjiu Yu
- Institute of Cardiovascular Diseases of PLA
- Xinqiao Hospital
- Third Military Medical University
- Chongqing 400037
- China
| | - Weidong Xiao
- Department of General Surgery
- Xinqiao Hospital
- Third Military Medical University
- Chongqing 400037
- China
| | - Yongsheng Li
- Institute of Cancer
- Xinqiao Hospital
- Third Military Medical University
- Chongqing 400037
- China
| | - Wenjuan Hu
- Department of Pathophysiology and High Altitude Pathology
- College of High Altitude Military Medicine
- Third Military Medical University
- Chongqing 400038
- China
| | - Lan Huang
- Institute of Cardiovascular Diseases of PLA
- Xinqiao Hospital
- Third Military Medical University
- Chongqing 400037
- China
| | - Xiaoqi Zheng
- Department of Mathematics
- Shanghai Normal University
- Shanghai 200234
- China
| | - Shiwen Zhou
- National Drug Clinical Trial Institution
- Xinqiao Hospital
- Third Military Medical University
- Chongqing 400037
- China
| | - Hua Yang
- Department of General Surgery
- Xinqiao Hospital
- Third Military Medical University
- Chongqing 400037
- China
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432
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Duro N, Miskei M, Fuxreiter M. Fuzziness endows viral motif-mimicry. MOLECULAR BIOSYSTEMS 2015; 11:2821-9. [DOI: 10.1039/c5mb00301f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The local dynamics of host and viral peptide motifs suggests a different scenario for partner recognition. Host peptide motifs serve as molecular recognition elements, while viral motifs preserve the structural heterogeneity and remain fuzzy when bound to the host.
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Affiliation(s)
- Norbert Duro
- MTA-DE Momentum
- Laboratory of Protein Dynamics
- Department of Biochemistry and Molecular Biology
- University of Debrecen
- Hungary
| | - Marton Miskei
- MTA-DE Momentum
- Laboratory of Protein Dynamics
- Department of Biochemistry and Molecular Biology
- University of Debrecen
- Hungary
| | - Monika Fuxreiter
- MTA-DE Momentum
- Laboratory of Protein Dynamics
- Department of Biochemistry and Molecular Biology
- University of Debrecen
- Hungary
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433
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Sormanni P, Camilloni C, Fariselli P, Vendruscolo M. The s2D method: simultaneous sequence-based prediction of the statistical populations of ordered and disordered regions in proteins. J Mol Biol 2014; 427:982-996. [PMID: 25534081 DOI: 10.1016/j.jmb.2014.12.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/10/2014] [Accepted: 12/12/2014] [Indexed: 11/18/2022]
Abstract
Extensive amounts of information about protein sequences are becoming available, as demonstrated by the over 79 million entries in the UniProt database. Yet, it is still challenging to obtain proteome-wide experimental information on the structural properties associated with these sequences. Fast computational predictors of secondary structure and of intrinsic disorder of proteins have been developed in order to bridge this gap. These two types of predictions, however, have remained largely separated, often preventing a clear characterization of the structure and dynamics of proteins. Here, we introduce a computational method to predict secondary-structure populations from amino acid sequences, which simultaneously characterizes structure and disorder in a unified statistical mechanics framework. To develop this method, called s2D, we exploited recent advances made in the analysis of NMR chemical shifts that provide quantitative information about the probability distributions of secondary-structure elements in disordered states. The results that we discuss show that the s2D method predicts secondary-structure populations with an average error of about 14%. A validation on three datasets of mostly disordered, mostly structured and partly structured proteins, respectively, shows that its performance is comparable to or better than that of existing predictors of intrinsic disorder and of secondary structure. These results indicate that it is possible to perform rapid and quantitative sequence-based characterizations of the structure and dynamics of proteins through the predictions of the statistical distributions of their ordered and disordered regions.
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Affiliation(s)
- Pietro Sormanni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Piero Fariselli
- Department of Computer Science, University of Bologna, 40127 Bologna, Italy
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434
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Ma C, Zhang HH, Wang X. Machine learning for Big Data analytics in plants. TRENDS IN PLANT SCIENCE 2014; 19:798-808. [PMID: 25223304 DOI: 10.1016/j.tplants.2014.08.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/30/2014] [Accepted: 08/20/2014] [Indexed: 05/19/2023]
Abstract
Rapid advances in high-throughput genomic technology have enabled biology to enter the era of 'Big Data' (large datasets). The plant science community not only needs to build its own Big-Data-compatible parallel computing and data management infrastructures, but also to seek novel analytical paradigms to extract information from the overwhelming amounts of data. Machine learning offers promising computational and analytical solutions for the integrative analysis of large, heterogeneous and unstructured datasets on the Big-Data scale, and is gradually gaining popularity in biology. This review introduces the basic concepts and procedures of machine-learning applications and envisages how machine learning could interface with Big Data technology to facilitate basic research and biotechnology in the plant sciences.
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Affiliation(s)
- Chuang Ma
- School of Plant Sciences, University of Arizona, 1140 E. South Campus Drive, Tucson, AZ 85721, USA
| | - Hao Helen Zhang
- Department of Mathematics, University of Arizona, 617 North Santa Rita Ave, Tucson, AZ 85721, USA
| | - Xiangfeng Wang
- School of Plant Sciences, University of Arizona, 1140 E. South Campus Drive, Tucson, AZ 85721, USA; Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
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435
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Wiwanitkit V. Binding site prediction within Ebola virus VP40 protein: clue for further drug development. Asian Pac J Trop Biomed 2014. [DOI: 10.12980/apjtb.4.2014apjtb-2014-0431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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436
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Lysophospholipid-containing membranes modulate the fibril formation of the repeat domain of a human functional amyloid, pmel17. J Mol Biol 2014; 426:4074-4086. [PMID: 25451784 DOI: 10.1016/j.jmb.2014.10.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 09/23/2014] [Accepted: 10/08/2014] [Indexed: 11/23/2022]
Abstract
Pmel17 is an important protein for pigmentation in human skin and eyes. Proteolytic fragments from Pmel17 form fibrils upon which melanin is deposited in melanosomes. The repeat domain (RPT) derived from Pmel17 only forms fibrils under acidic melanosomal conditions. Here, we examined the effects of lipids on RPT aggregation to explore whether intramelanosomal vesicles can facilitate fibrillogenesis. Using transmission electron microscopy, circular dichroism, and fluorescence spectroscopy, we monitored fibril formation at the ultrastructural, secondary conformational, and local levels, respectively. Phospholipid vesicles and lysophospholipid (lysolipid) micelles were employed as membrane mimics. The surfactant-like lysolipids are particularly pertinent due to their high content in melanosomal membranes. Interestingly, RPT aggregation kinetics were influenced only by lysolipid-containing phospholipid vesicles. While both vesicles containing either anionic lysophosphatidylglycerol (LPG) or zwitterionic lysophosphatidylcholine (LPC) stimulate aggregation, LPG exerted a greater effect on reducing the apparent nucleation time. A detailed comparison showed distinct behaviors of LPG versus LPC monomers and micelles plausibly originating from their headgroup hydrogen bonding capabilities. Acceleration and retardation of aggregation were observed for LPG monomers and micelles, respectively. Because a specific interaction between LPG and RPT was identified by intrinsic W423 fluorescence and induced α-helical structure, it is inferred that binding of LPG near the C-terminal amyloid core initiates intermolecular association, whereas stabilization of α-helical conformation inhibits β-sheet formation. Contrastingly, LPC promotes RPT aggregation at both submicellar and micellar concentrations via non-specific binding with undetectable secondary structural change. Our findings suggest that protein-lysolipid interactions within melanosomes may regulate amyloid formation in vivo.
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437
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Bacterial and algal orthologs of prostaglandin H₂synthase: novel insights into the evolution of an integral membrane protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:83-94. [PMID: 25281773 DOI: 10.1016/j.bbamem.2014.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 09/09/2014] [Accepted: 09/23/2014] [Indexed: 01/01/2023]
Abstract
Prostaglandin H₂synthase (PGHS; EC 1.14.99.1), a bi-functional heme enzyme that contains cyclooxygenase and peroxidase activities, plays a central role in the inflammatory response, pain, and blood clotting in higher eukaryotes. In this review, we discuss the progenitors of the mammalian enzyme by using modern bioinformatics and homology modeling to draw comparisons between this well-studied system and its orthologs from algae and bacterial sources. A clade of bacterial and algal orthologs is described that have salient structural features distinct from eukaryotic counterparts, including the lack of a dimerization and EGF-like domains, the absence of gene duplicates, and minimal membrane-binding domains. The functional implications of shared and variant features are discussed.
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438
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Vaccinia virus mutations in the L4R gene encoding a virion structural protein produce abnormal mature particles lacking a nucleocapsid. J Virol 2014; 88:14017-29. [PMID: 25253347 DOI: 10.1128/jvi.02126-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
UNLABELLED Electron micrographs from the 1960s revealed the presence of an S-shaped tubular structure in the center of the vaccinia virion core. Recently, we showed that packaging of virus transcription enzymes is necessary for the formation of the tubular structure, suggesting that the structure is equivalent to a nucleocapsid. Based on this study and on what is known about nucleocapsids of other viruses, we hypothesized that in addition to transcription enzymes, the tubular structure also contains the viral DNA and a structural protein as a scaffold. The vaccinia virion structural protein L4 stands out as the best candidate for the role of a nucleocapsid structural protein because it is abundant, it is localized in the center of the virion core, and it binds DNA. In order to gain more insight into the structure and relevance of the nucleocapsid, we analyzed thermosensitive and inducible mutants in the L4R gene. Using a cryo-fixation method for electron microscopy (high-pressure freezing followed by freeze-substitution) to preserve labile structures like the nucleocapsid, we were able to demonstrate that in the absence of functional L4, mature particles with defective internal structures are produced under nonpermissive conditions. These particles do not contain a nucleocapsid. In addition, the core wall of these virions is abnormal. This suggests that the nucleocapsid interacts with the core wall and that the nucleocapsid structure might be more complex than originally assumed. IMPORTANCE The vaccinia virus nucleocapsid has been neglected since the 1960s due to a lack of electron microscopy techniques to preserve this labile structure. With the advent of cryo-fixation techniques, like high-pressure freezing/freeze-substitution, we are now able to consistently preserve and visualize the nucleocapsid. Because vaccinia virus early transcription is coupled to the viral core structure, detailing the structure of the nucleocapsid is indispensable for determining the mechanisms of vaccinia virus core-directed transcription. The present study represents our second attempt to understand the structure and biological significance of the nucleocapsid. We demonstrate the importance of the protein L4 for the formation of the nucleocapsid and reveal in addition that the nucleocapsid and the core wall may be associated, suggesting a higher level of complexity of the nucleocapsid than predicted. In addition, we prove the utility of high-pressure freezing in preserving the vaccinia virus nucleocapsid.
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439
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Biggar KK, Storey KB. New Approaches to Comparative and Animal Stress Biology Research in the Post-genomic Era: A Contextual Overview. Comput Struct Biotechnol J 2014; 11:138-46. [PMID: 25408848 PMCID: PMC4232569 DOI: 10.1016/j.csbj.2014.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/07/2014] [Accepted: 09/11/2014] [Indexed: 02/06/2023] Open
Abstract
Although much is known about the physiological responses of many environmental stresses in tolerant animals, studies evaluating the regulation of stress-induced mechanisms that regulate the transitions to and from this state are beginning to explore new and fascinating areas of molecular research. Current findings have developed a general, but refined, view of the important molecular pathways contributing to stress-survival. However, studies utilizing newly developed technologies that broadly focus on genomic and proteomic screening are beginning to identify many new targets for future study. This minireview will provide a contextual overview on the use of DNA/RNA sequencing, microRNA annotation and prediction software, protein structure and function prediction tools, as well as methods of high-throughput protein expression analysis. We will also use select examples to highlight the existing use of these technologies in stress biology research. Such tools can be used in comparative stress biology in the characterization of animal responses to environmental challenges. Although there are many areas of study left to be explored, research in comparative stress biology will always be continuing as new technologies allow the further analysis of cell function, and new paradigms in gene regulation and regulatory molecules (such as microRNAs) are continuing to be discovered. Building upon the findings of past research, while utilizing new technologies in the appropriate manner, future studies can be carried out in new and exciting areas still unexplored. Proper use of rapidly developing technologies will help to create a complete understanding of the animal stress response and survival mechanisms utilized by many diverse organisms.
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Affiliation(s)
| | - Kenneth B. Storey
- Institute of Biochemistry, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
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440
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Cloning and expression characteristics of the pig Stra8 gene. Int J Mol Sci 2014; 15:12480-94. [PMID: 25029539 PMCID: PMC4139855 DOI: 10.3390/ijms150712480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 06/16/2014] [Accepted: 06/16/2014] [Indexed: 01/04/2023] Open
Abstract
Stra8 (Stimulated by Retinoic Acid 8) is considered a meiotic gatekeeper gene. Using reverse transcriptase PCR and rapid amplification of cDNA ends (RACE), the complete sequence of the pig Stra8 gene was cloned. Bioinformatics analyses of this sequence were performed. Using semi-quantitative methods, the expression characteristics of Stra8 in Testis, cauda epididymis, body epididymis, caput epididymis, seminal vesicles, prostate gland, Cowper's gland, heart, liver, spleen, lung, kidney, stomach, hypothalamus, pituitary gland, cerebrum, cerebellum, and hippocampus of adult Meishan boar and sow tissues were examined. The expression pattern in the testis of 2-, 30-, 60-, 90-, and 150-day old Meishan boars were analyzed using real-time PCR. We constructed a eukaryotic expression vector for the Stra8 gene and used it to transfect NIH-3T3 cells and third generation pig spermatogonial stem cells (SSCs) cultured in vitro. Testes weight and sperm count in the cauda epididymis were evaluated at various time points. The results showed that the length of the pig Stra8 gene cDNA was 1444 bp encoding 366 amino acids with one typical helix-loop-helix (HLH) domain. It is testes-specific expression. Expression was first detected in boar testis starting at day 2, and its expression significantly (p<0.05) increased with age and body weight. When NIH-3T3 cells and pig SSCs were transfected with the eukaryotic expression vector EGFP (enhanced green fluorescent protein)-N1-pStra8, it was expressed in the cytoplasm of NIH-3T3 cells. However, in SSCs, Stra8 was expressed predominantly in cytoplasm and few in nucleus. Our data suggest that perhaps Stra8 acts as a transcription factor to initiate meiosis in young boar.
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441
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Goldberg T, Hecht M, Hamp T, Karl T, Yachdav G, Ahmed N, Altermann U, Angerer P, Ansorge S, Balasz K, Bernhofer M, Betz A, Cizmadija L, Do KT, Gerke J, Greil R, Joerdens V, Hastreiter M, Hembach K, Herzog M, Kalemanov M, Kluge M, Meier A, Nasir H, Neumaier U, Prade V, Reeb J, Sorokoumov A, Troshani I, Vorberg S, Waldraff S, Zierer J, Nielsen H, Rost B. LocTree3 prediction of localization. Nucleic Acids Res 2014; 42:W350-5. [PMID: 24848019 PMCID: PMC4086075 DOI: 10.1093/nar/gku396] [Citation(s) in RCA: 196] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The prediction of protein sub-cellular localization is an important step toward elucidating protein function. For each query protein sequence, LocTree2 applies machine learning (profile kernel SVM) to predict the native sub-cellular localization in 18 classes for eukaryotes, in six for bacteria and in three for archaea. The method outputs a score that reflects the reliability of each prediction. LocTree2 has performed on par with or better than any other state-of-the-art method. Here, we report the availability of LocTree3 as a public web server. The server includes the machine learning-based LocTree2 and improves over it through the addition of homology-based inference. Assessed on sequence-unique data, LocTree3 reached an 18-state accuracy Q18 = 80 ± 3% for eukaryotes and a six-state accuracy Q6 = 89 ± 4% for bacteria. The server accepts submissions ranging from single protein sequences to entire proteomes. Response time of the unloaded server is about 90 s for a 300-residue eukaryotic protein and a few hours for an entire eukaryotic proteome not considering the generation of the alignments. For over 1000 entirely sequenced organisms, the predictions are directly available as downloads. The web server is available at http://www.rostlab.org/services/loctree3.
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Affiliation(s)
- Tatyana Goldberg
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), 85748 Garching, Germany
| | - Maximilian Hecht
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Tobias Hamp
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Timothy Karl
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Guy Yachdav
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany Biosof LLC, New York, NY 10001, USA
| | - Nadeem Ahmed
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Uwe Altermann
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Philipp Angerer
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Sonja Ansorge
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Kinga Balasz
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Michael Bernhofer
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Alexander Betz
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Laura Cizmadija
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Kieu Trinh Do
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Julia Gerke
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Robert Greil
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Vadim Joerdens
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | | | - Katharina Hembach
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Max Herzog
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Maria Kalemanov
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Michael Kluge
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Alice Meier
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Hassan Nasir
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Ulrich Neumaier
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Verena Prade
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Jonas Reeb
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | | | - Ilira Troshani
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Susann Vorberg
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Sonja Waldraff
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Jonas Zierer
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany
| | - Henrik Nielsen
- Center for Biological Sequence Analysis, Department of Systems Biology, DTU, 2800 Lyngby, Denmark
| | - Burkhard Rost
- Department of Informatics, Bioinformatics-I12, TUM, 85748 Garching, Germany Biosof LLC, New York, NY 10001, USA Institute for Advanced Study (TUM-IAS), 85748 Garching, Germany New York Consortium on Membrane Protein Structure (NYCOMPS) & Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA Institute for Food and Plant Sciences WZW - Weihenstephan, 85350 Freising, Germany
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Sanchez-Pulido L, Andrade-Navarro MA. The FTO (fat mass and obesity associated) gene codes for a novel member of the non-heme dioxygenase superfamily. BMC BIOCHEMISTRY 2007; 8:23. [PMID: 17996046 PMCID: PMC2241624 DOI: 10.1186/1471-2091-8-23] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 11/08/2007] [Indexed: 11/10/2022]
Abstract
BACKGROUND Genetic variants in the FTO (fat mass and obesity associated) gene have been associated with an increased risk of obesity. However, the function of its protein product has not been experimentally studied and previously reported sequence similarity analyses suggested the absence of homologs in existing protein databases. Here, we present the first detailed computational analysis of the sequence and predicted structure of the protein encoded by FTO. RESULTS We performed a sequence similarity search using the human FTO protein as query and then generated a profile using the multiple sequence alignment of the homologous sequences. Profile-to-sequence and profile-to-profile based comparisons identified remote homologs of the non-heme dioxygenase family. CONCLUSION Our analysis suggests that human FTO is a member of the non-heme dioxygenase (Fe(II)- and 2-oxoglutarate-dependent dioxygenases) superfamily. Amino acid conservation patterns support this hypothesis and indicate that both 2-oxoglutarate and iron should be important for FTO function. This computational prediction of the function of FTO should suggest further steps for its experimental characterization and help to formulate hypothesis about the mechanisms by which it relates to obesity in humans.
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Affiliation(s)
| | - Miguel A Andrade-Navarro
- Molecular Medicine, Ottawa Health Research Institute, Ottawa, Canada
- Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
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