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Li J, Zhao Y, Liang R, Mao Y, Zuo H, Hopkins DL, Yang X, Luo X, Zhu L, Zhang Y. Effects of different protein phosphorylation levels on the tenderness of different ultimate pH beef. Food Res Int 2023; 174:113512. [PMID: 37986506 DOI: 10.1016/j.foodres.2023.113512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/26/2023] [Accepted: 09/24/2023] [Indexed: 11/22/2023]
Abstract
This study investigated the relationship between tenderness and protein phosphorylation levels of normal ultimate pH (pHu, 5.4-5.8, NpHu), intermediate pHu (5.8-6.2, IpHu) and high pHu (≥6.2, HpHu) Longissimus lumborum from beef. During 21 d of ageing, the HpHu group had the lowest Warner-Bratzler shear force (WBSF) values, while the IpHu group showed the highest and even after 21 days of ageing still had high levels. In the late stage of the 24 h post-mortem period the faster degradation rate of troponin T and earlier activation of caspase 9 in the HpHu group were the key reasons for the lower WBSF compared with the NpHu and IpHu groups. The activity of caspase 3 cannot explain the tenderness differences between IpHu and HpHu groups, since their activities did not show any difference. At 24 h post-mortem, 17 common differential phosphorylated peptides were detected among pHu groups, of which nine were associated with pHu and WBSF. The higher phosphorylation level of glycogen synthase may have caused the delay of meat tenderization in the IpHu group.
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Affiliation(s)
- Jiqiang Li
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong 271018, PR China.
| | - Yan Zhao
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong 271018, PR China.
| | - Rongrong Liang
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong 271018, PR China.
| | - Yanwei Mao
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong 271018, PR China.
| | - Huixin Zuo
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong 271018, PR China.
| | - David L Hopkins
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong 271018, PR China; Canberra ACT, 2903, Australia.
| | - Xiaoyin Yang
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong 271018, PR China.
| | - Xin Luo
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong 271018, PR China.
| | - Lixian Zhu
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong 271018, PR China.
| | - Yimin Zhang
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong 271018, PR China.
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Darbinian N, Gallia GL, Darbinyan A, Vadachkoria E, Merabova N, Moore A, Goetzl L, Amini S, Selzer ME. Effects of In Utero EtOH Exposure on 18S Ribosomal RNA Processing: Contribution to Fetal Alcohol Spectrum Disorder. Int J Mol Sci 2023; 24:13714. [PMID: 37762017 PMCID: PMC10531167 DOI: 10.3390/ijms241813714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Fetal alcohol spectrum disorders (FASD) are leading causes of neurodevelopmental disability. The mechanisms by which alcohol (EtOH) disrupts fetal brain development are incompletely understood, as are the genetic factors that modify individual vulnerability. Because the phenotype abnormalities of FASD are so varied and widespread, we investigated whether fetal exposure to EtOH disrupts ribosome biogenesis and the processing of pre-ribosomal RNAs and ribosome assembly, by determining the effect of exposure to EtOH on the developmental expression of 18S rRNA and its cleaved forms, members of a novel class of short non-coding RNAs (srRNAs). In vitro neuronal cultures and fetal brains (11-22 weeks) were collected according to an IRB-approved protocol. Twenty EtOH-exposed brains from the first and second trimester were compared with ten unexposed controls matched for gestational age and fetal gender. Twenty fetal-brain-derived exosomes (FB-Es) were isolated from matching maternal blood. RNA was isolated using Qiagen RNA isolation kits. Fetal brain srRNA expression was quantified by ddPCR. srRNAs were expressed in the human brain and FB-Es during fetal development. EtOH exposure slightly decreased srRNA expression (1.1-fold; p = 0.03). Addition of srRNAs to in vitro neuronal cultures inhibited EtOH-induced caspase-3 activation (1.6-fold, p = 0.002) and increased cell survival (4.7%, p = 0.034). The addition of exogenous srRNAs reversed the EtOH-mediated downregulation of srRNAs (2-fold, p = 0.002). EtOH exposure suppressed expression of srRNAs in the developing brain, increased activity of caspase-3, and inhibited neuronal survival. Exogenous srRNAs reversed this effect, possibly by stabilizing endogenous srRNAs, or by increasing the association of cellular proteins with srRNAs, modifying gene transcription. Finally, the reduction in 18S rRNA levels correlated closely with the reduction in fetal eye diameter, an anatomical hallmark of FASD. The findings suggest a potential mechanism for EtOH-mediated neurotoxicity via alterations in 18S rRNA processing and the use of FB-Es for early diagnosis of FASD. Ribosome biogenesis may be a novel target to ameliorate FASD in utero or after birth. These findings are consistent with observations that gene-environment interactions contribute to FASD vulnerability.
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Affiliation(s)
- Nune Darbinian
- Center for Neural Repair and Rehabilitation Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (E.V.); (N.M.); (A.M.)
| | - Gary L. Gallia
- Department of Neurosurgery, Johns Hopkins Hospital, Baltimore, MD 21287, USA;
| | - Armine Darbinyan
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA;
| | - Ekaterina Vadachkoria
- Center for Neural Repair and Rehabilitation Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (E.V.); (N.M.); (A.M.)
| | - Nana Merabova
- Center for Neural Repair and Rehabilitation Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (E.V.); (N.M.); (A.M.)
- Medical College of Wisconsin-Prevea Health, Green Bay, WI 54304, USA
| | - Amos Moore
- Center for Neural Repair and Rehabilitation Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (E.V.); (N.M.); (A.M.)
| | - Laura Goetzl
- Department of Obstetrics & Gynecology, University of Texas, Houston, TX 77030, USA;
| | - Shohreh Amini
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA;
| | - Michael E. Selzer
- Center for Neural Repair and Rehabilitation Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (E.V.); (N.M.); (A.M.)
- Departments of Neurology and Neural Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
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3
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Rappoport D, Jinich A. Enzyme Substrate Prediction from Three-Dimensional Feature Representations Using Space-Filling Curves. J Chem Inf Model 2023; 63:1637-1648. [PMID: 36802628 DOI: 10.1021/acs.jcim.3c00005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Compact and interpretable structural feature representations are required for accurately predicting properties and function of proteins. In this work, we construct and evaluate three-dimensional feature representations of protein structures based on space-filling curves (SFCs). We focus on the problem of enzyme substrate prediction, using two ubiquitous enzyme families as case studies: the short-chain dehydrogenase/reductases (SDRs) and the S-adenosylmethionine-dependent methyltransferases (SAM-MTases). Space-filling curves such as the Hilbert curve and the Morton curve generate a reversible mapping from discretized three-dimensional to one-dimensional representations and thus help to encode three-dimensional molecular structures in a system-independent way and with only a few adjustable parameters. Using three-dimensional structures of SDRs and SAM-MTases generated using AlphaFold2, we assess the performance of the SFC-based feature representations in predictions on a new benchmark database of enzyme classification tasks including their cofactor and substrate selectivity. Gradient-boosted tree classifiers yield binary prediction accuracy of 0.77-0.91 and area under curve (AUC) characteristics of 0.83-0.92 for the classification tasks. We investigate the effects of amino acid encoding, spatial orientation, and (the few) parameters of SFC-based encodings on the accuracy of the predictions. Our results suggest that geometry-based approaches such as SFCs are promising for generating protein structural representations and are complementary to the existing protein feature representations such as evolutionary scale modeling (ESM) sequence embeddings.
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Affiliation(s)
- Dmitrij Rappoport
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, California 92697, United States
| | - Adrian Jinich
- Weill Cornell Medicine, 1300 York Avenue, Box 65, New York, New York 10065, United States
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4
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Duša F, Moravcová D, Šlais K. Low-molecular-mass colored compounds for fine tracing of pH gradient on broad and narrow scale in isoelectric focusing. Anal Chim Acta 2022; 1221:340035. [DOI: 10.1016/j.aca.2022.340035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/27/2022] [Accepted: 06/02/2022] [Indexed: 11/28/2022]
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5
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Heinzinger M, Littmann M, Sillitoe I, Bordin N, Orengo C, Rost B. Contrastive learning on protein embeddings enlightens midnight zone. NAR Genom Bioinform 2022; 4:lqac043. [PMID: 35702380 PMCID: PMC9188115 DOI: 10.1093/nargab/lqac043] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 03/25/2022] [Accepted: 05/17/2022] [Indexed: 12/23/2022] Open
Abstract
Experimental structures are leveraged through multiple sequence alignments, or more generally through homology-based inference (HBI), facilitating the transfer of information from a protein with known annotation to a query without any annotation. A recent alternative expands the concept of HBI from sequence-distance lookup to embedding-based annotation transfer (EAT). These embeddings are derived from protein Language Models (pLMs). Here, we introduce using single protein representations from pLMs for contrastive learning. This learning procedure creates a new set of embeddings that optimizes constraints captured by hierarchical classifications of protein 3D structures defined by the CATH resource. The approach, dubbed ProtTucker, has an improved ability to recognize distant homologous relationships than more traditional techniques such as threading or fold recognition. Thus, these embeddings have allowed sequence comparison to step into the 'midnight zone' of protein similarity, i.e. the region in which distantly related sequences have a seemingly random pairwise sequence similarity. The novelty of this work is in the particular combination of tools and sampling techniques that ascertained good performance comparable or better to existing state-of-the-art sequence comparison methods. Additionally, since this method does not need to generate alignments it is also orders of magnitudes faster. The code is available at https://github.com/Rostlab/EAT.
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Affiliation(s)
- Michael Heinzinger
- TUM (Technical University of Munich) Dept Informatics, Bioinformatics & Computational Biology - i12, Boltzmannstr. 3, 85748 Garching/Munich, Germany
- TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Boltzmannstr. 11, 85748 Garching, Germany
| | - Maria Littmann
- TUM (Technical University of Munich) Dept Informatics, Bioinformatics & Computational Biology - i12, Boltzmannstr. 3, 85748 Garching/Munich, Germany
| | - Ian Sillitoe
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Nicola Bordin
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Christine Orengo
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Burkhard Rost
- TUM (Technical University of Munich) Dept Informatics, Bioinformatics & Computational Biology - i12, Boltzmannstr. 3, 85748 Garching/Munich, Germany
- Institute for Advanced Study (TUM-IAS), Lichtenbergstr. 2a, 85748 Garching, Germany & TUM School of Life Sciences Weihenstephan (WZW), Alte Akademie 8, Freising, Germany
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6
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Pathak A, Jayaram B. Seq2Enz: An application of mask BLAST methodology with a new chemical logic of amino acids for improved enzyme function prediction. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140721. [PMID: 34624539 DOI: 10.1016/j.bbapap.2021.140721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Seq2Enz method is a new way to identify whether a query protein sequence is an enzyme and to assign an enzyme class to the protein sequence. The method is based on mask BLAST fortified with some novel structural-chemical properties (NCL) of the building blocks of proteins. All available reviewed enyme sequences (267,276 in number) in Uniprot/SwissProt and most recent depositions (7062) not used for training in ECPred, a state of the art software for enzyme class prediction, are taken for assessment and the results are compared with those from conventional BLAST and ECPred respectively. Seq2Enz is seen to perform consistently better for all the enzyme classes to all the four levels. Seq2Enz methodology is converted into an easy to use web-server and made freely accessible at http://www.scfbio-iitd.res.in Seq2Enz/.
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Affiliation(s)
- Amita Pathak
- Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India; Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - B Jayaram
- Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India; Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India; Kusuma School of Biological Sciences, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India.
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7
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Zhang Y, Wierbowski SD, Yu H. Combining views for newly sequenced organisms. NAT MACH INTELL 2021. [DOI: 10.1038/s42256-021-00426-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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8
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Wollenberg Valero KC, Garcia-Porta J, Irisarri I, Feugere L, Bates A, Kirchhof S, Jovanović Glavaš O, Pafilis P, Samuel SF, Müller J, Vences M, Turner AP, Beltran-Alvarez P, Storey KB. Functional genomics of abiotic environmental adaptation in lacertid lizards and other vertebrates. J Anim Ecol 2021; 91:1163-1179. [PMID: 34695234 DOI: 10.1111/1365-2656.13617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/27/2021] [Indexed: 11/27/2022]
Abstract
Understanding the genomic basis of adaptation to different abiotic environments is important in the context of climate change and resulting short-term environmental fluctuations. Using functional and comparative genomics approaches, we here investigated whether signatures of genomic adaptation to a set of environmental parameters are concentrated in specific subsets of genes and functions in lacertid lizards and other vertebrates. We first identify 200 genes with signatures of positive diversifying selection from transcriptomes of 24 species of lacertid lizards and demonstrate their involvement in physiological and morphological adaptations to climate. To understand how functionally similar these genes are to previously predicted candidate functions for climate adaptation and to compare them with other vertebrate species, we then performed a meta-analysis of 1,100 genes under selection obtained from -omics studies in vertebrate species adapted to different abiotic factors. We found that the vertebrate gene set formed a tightly connected interactome, which was to 23% enriched in previously predicted functions of adaptation to climate, and to a large part (18%) involved in organismal stress response. We found a much higher degree of identical genes being repeatedly selected among different animal groups (43.6%), and of functional similarity and post-translational modifications than expected by chance, and no clear functional division between genes used for ectotherm and endotherm physiological strategies. In total, 171 out of 200 genes of Lacertidae were part of this network. These results highlight an important role of a comparatively small set of genes and their functions in environmental adaptation and narrow the set of candidate pathways and markers to be used in future research on adaptation and stress response related to climate change.
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Affiliation(s)
| | - Joan Garcia-Porta
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Iker Irisarri
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Göttingen, Göttingen, Germany.,Campus Institut Data Science (CIDAS), Göttingen, Germany
| | - Lauric Feugere
- Department of Biological and Marine Sciences, University of Hull, Kingston-Upon-Hull, UK
| | - Adam Bates
- Department of Biological and Marine Sciences, University of Hull, Kingston-Upon-Hull, UK
| | - Sebastian Kirchhof
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.,New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | | | - Panayiotis Pafilis
- Section of Zoology and Marine Biology, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Sabrina F Samuel
- Department of Biomedical Sciences, University of Hull, Kingston-Upon-Hull, UK
| | - Johannes Müller
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Miguel Vences
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Alexander P Turner
- Department of Computer Science, University of Nottingham, Nottingham, UK
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9
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An integrated deep learning and dynamic programming method for predicting tumor suppressor genes, oncogenes, and fusion from PDB structures. Comput Biol Med 2021; 133:104323. [PMID: 33934067 DOI: 10.1016/j.compbiomed.2021.104323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 02/18/2021] [Accepted: 03/07/2021] [Indexed: 11/20/2022]
Abstract
Mutations in proto-oncogenes (ONGO) and the loss of regulatory function of tumor suppression genes (TSG) are the common underlying mechanism for uncontrolled tumor growth. While cancer is a heterogeneous complex of distinct diseases, finding the potentiality of the genes related functionality to ONGO or TSG through computational studies can help develop drugs that target the disease. This paper proposes a classification method that starts with a preprocessing stage to extract the feature map sets from the input 3D protein structural information. The next stage is a deep convolutional neural network stage (DCNN) that outputs the probability of functional classification of genes. We explored and tested two approaches: in Approach 1, all filtered and cleaned 3D-protein-structures (PDB) are pooled together, whereas in Approach 2, the primary structures and their corresponding PDBs are separated according to the genes' primary structural information. Following the DCNN stage, a dynamic programming-based method is used to determine the final prediction of the primary structures' functionality. We validated our proposed method using the COSMIC online database. For the ONGO vs TSG classification problem the AUROC of the DCNN stage for Approach 1 and Approach 2 DCNN are 0.978 and 0.765, respectively. The AUROCs of the final genes' primary structure functionality classification for Approach 1 and Approach 2 are 0.989, and 0.879, respectively. For comparison, the current state-of-the-art reported AUROC is 0.924. Our results warrant further study to apply the deep learning models to humans' (GRCh38) genes, for predicting their corresponding probabilities of functionality in the cancer drivers.
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10
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Sirén K, Millard A, Petersen B, Gilbert M, Clokie MRJ, Sicheritz-Pontén T. Rapid discovery of novel prophages using biological feature engineering and machine learning. NAR Genom Bioinform 2021; 3:lqaa109. [PMID: 33575651 PMCID: PMC7787355 DOI: 10.1093/nargab/lqaa109] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 01/10/2023] Open
Abstract
Prophages are phages that are integrated into bacterial genomes and which are key to understanding many aspects of bacterial biology. Their extreme diversity means they are challenging to detect using sequence similarity, yet this remains the paradigm and thus many phages remain unidentified. We present a novel, fast and generalizing machine learning method based on feature space to facilitate novel prophage discovery. To validate the approach, we reanalyzed publicly available marine viromes and single-cell genomes using our feature-based approaches and found consistently more phages than were detected using current state-of-the-art tools while being notably faster. This demonstrates that our approach significantly enhances bacteriophage discovery and thus provides a new starting point for exploring new biologies.
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Affiliation(s)
- Kimmo Sirén
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen,1353 Denmark
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, LE1 7RH Leicester, UK
| | - Bent Petersen
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen,1353 Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University,08100 Kedah, Malaysia
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen,1353 Denmark
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen,1353 Copenhagen, Denmark
- University Museum, NTNU, 7012 Trondheim, Norway
| | - Martha R J Clokie
- Department of Genetics and Genome Biology, University of Leicester, LE1 7RH Leicester, UK
| | - Thomas Sicheritz-Pontén
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen,1353 Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University,08100 Kedah, Malaysia
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11
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Anis Ahamed N, Panneerselvam A, Arif IA, Syed Abuthakir MH, Jeyam M, Ambikapathy V, Mostafa AA. Identification of potential drug targets in human pathogen Bacillus cereus and insight for finding inhibitor through subtractive proteome and molecular docking studies. J Infect Public Health 2021; 14:160-168. [PMID: 33422858 DOI: 10.1016/j.jiph.2020.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/28/2020] [Accepted: 12/02/2020] [Indexed: 11/19/2022] Open
Abstract
Bacillus cereus is a gram-positive, anaerobic, spore-forming bacterium related to food poisoning in humans. Vomit and diarrhea are the symptoms of foodborne B. cereus infection caused by emetic toxins and three enterotoxins, respectively. This bacterium is broadly present in soil and foods such as vegetables, spices, milk, and meat. The antibiotics impenem, vancomycin, chloramphenicol, gentamicin, and ciprofloxacin are used for all susceptible strains of B. cereus. But these antibiotics cause side effects in the host due to the drug-host interaction; because the targeted proteins by the drugs are not pathogen specific proteins, they are similar to human proteins also. To overcome this problem, this study focused on identifying putative drug targets in the pathogen B. cereus and finding new drugs to inhibit the function of the pathogen. The identification of drug targets is a pipeline process, starting with the identification of targets non-homologous to human and gutmicrobiota proteins, finding essential proteins, finding other proteins that highly interact with these essential proteins that are also highly important for protein network stability, finding cytoplasmic proteins with a clear pathway and known molecular function, and finding non-druggable proteins. Through this process, two novel drug targets were identified in B. cereus. Among the various antibiotics, Gentamicin had showed good binding affinity with the identified novel targets through molecular modeling and docking studies using Prime and GLIDE module of Schrödinger. Hence, this study suggest that the identified novel drug targets may very useful in drug therapeutic field for finding inhibitors which are similar to Gentamicin and designing new formulation of drug molecules to control the function of the foodborne illness causing pathogen B. cereus.
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Affiliation(s)
- N Anis Ahamed
- Prince Sultan Research Chair for Environment and Wildlife, Department of Botany and Microbiology, College of Sciences, King Saud University (KSU), Riyadh, Saudi Arabia; Department of Botany and Microbiology, College of Sciences, King Saud University (KSU), Riyadh, Saudi Arabia; Department of Botany and Microbiology, A.V.V.M. Sri Pushpam College (Autonomous), Poondi, Affiliated to Bharathidasan University, Thanjavur 620024, India.
| | - A Panneerselvam
- Department of Botany and Microbiology, A.V.V.M. Sri Pushpam College (Autonomous), Poondi, Affiliated to Bharathidasan University, Thanjavur 620024, India
| | - Ibrahim A Arif
- Prince Sultan Research Chair for Environment and Wildlife, Department of Botany and Microbiology, College of Sciences, King Saud University (KSU), Riyadh, Saudi Arabia; Department of Botany and Microbiology, College of Sciences, King Saud University (KSU), Riyadh, Saudi Arabia
| | | | - Muthusamy Jeyam
- Biochematics Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, India
| | - V Ambikapathy
- Department of Botany and Microbiology, A.V.V.M. Sri Pushpam College (Autonomous), Poondi, Affiliated to Bharathidasan University, Thanjavur 620024, India
| | - Ashraf A Mostafa
- Department of Botany and Microbiology, College of Sciences, King Saud University (KSU), Riyadh, Saudi Arabia
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12
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Li X, Zhang D, Ren C, Bai Y, Ijaz M, Hou C, Chen L. Effects of protein posttranslational modifications on meat quality: A review. Compr Rev Food Sci Food Saf 2020; 20:289-331. [PMID: 33443799 DOI: 10.1111/1541-4337.12668] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/14/2020] [Accepted: 10/20/2020] [Indexed: 02/06/2023]
Abstract
Meat quality plays an important role in the purchase decision of consumers, affecting producers and retailers. The formation mechanisms determining meat quality are intricate, as several endogenous and exogenous factors contribute during antemortem and postmortem periods. Abundant research has been performed on meat quality; however, unexpected variation in meat quality remains an issue in the meat industry. Protein posttranslational modifications (PTMs) regulate structures and functions of proteins in living tissues, and recent reports confirmed their importance in meat quality. The objective of this review was to provide a summary of the research on the effects of PTMs on meat quality. The effects of four common PTMs, namely, protein phosphorylation, acetylation, S-nitrosylation, and ubiquitination, on meat quality were discussed, with emphasis on the effects of protein phosphorylation on meat tenderness, color, and water holding capacity. The mechanisms and factors that may affect the function of protein phosphorylation are also discussed. The current research confirms that meat quality traits are regulated by multiple PTMs. Cross talk between different PTMs and interactions of PTMs with postmortem biochemical processes need to be explored to improve our understanding on factors affecting meat quality.
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Affiliation(s)
- Xin Li
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dequan Zhang
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chi Ren
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuqiang Bai
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muawuz Ijaz
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chengli Hou
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Chen
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
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13
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Fan K, Zhang Y. Pseudo2GO: A Graph-Based Deep Learning Method for Pseudogene Function Prediction by Borrowing Information From Coding Genes. Front Genet 2020; 11:807. [PMID: 33014009 PMCID: PMC7461887 DOI: 10.3389/fgene.2020.00807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/06/2020] [Indexed: 12/16/2022] Open
Abstract
Pseudogenes are indicating more and more functional potentials recently, though historically were regarded as relics of evolution. Computational methods for predicting pseudogene functions on Gene Ontology is important for directing experimental discovery. However, no pseudogene-specific computational methods have been proposed to directly predict their Gene Ontology (GO) terms. The biggest challenge for pseudogene function prediction is the lack of enough features and functional annotations, making training a predictive model difficult. Considering the close functional similarity between pseudogenes and their parent coding genes that share great amount of DNA sequence, as well as that coding genes have rich annotations, we aim to predict pseudogene functions by borrowing information from coding genes in a graph-based way. Here we propose Pseudo2GO, a graph-based deep learning semi-supervised model for pseudogene function prediction. A sequence similarity graph is first constructed to connect pseudogenes and coding genes. Multiple features are incorporated into the model as the node attributes to enable the graph an attributed graph, including expression profiles, interactions with microRNAs, protein-protein interactions (PPIs), and genetic interactions. Graph convolutional networks are used to propagate node attributes across the graph to make classifications on pseudogenes. Comparing Pseudo2GO with other frameworks adapted from popular protein function prediction methods, we demonstrated that our method has achieved state-of-the-art performance, significantly outperforming other methods in terms of the M-AUPR metric.
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Affiliation(s)
- Kunjie Fan
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Yan Zhang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, United States
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
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14
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Fan K, Guan Y, Zhang Y. Graph2GO: a multi-modal attributed network embedding method for inferring protein functions. Gigascience 2020; 9:giaa081. [PMID: 32770210 PMCID: PMC7414417 DOI: 10.1093/gigascience/giaa081] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 04/30/2020] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Identifying protein functions is important for many biological applications. Since experimental functional characterization of proteins is time-consuming and costly, accurate and efficient computational methods for predicting protein functions are in great demand for generating the testable hypotheses guiding large-scale experiments." RESULTS Here, we propose Graph2GO, a multi-modal graph-based representation learning model that can integrate heterogeneous information, including multiple types of interaction networks (sequence similarity network and protein-protein interaction network) and protein features (amino acid sequence, subcellular location, and protein domains) to predict protein functions on gene ontology. Comparing Graph2GO to BLAST, as a baseline model, and to two popular protein function prediction methods (Mashup and deepNF), we demonstrated that our model can achieve state-of-the-art performance. We show the robustness of our model by testing on multiple species. We also provide a web server supporting function query and downstream analysis on-the-fly. CONCLUSIONS Graph2GO is the first model that has utilized attributed network representation learning methods to model both interaction networks and protein features for predicting protein functions, and achieved promising performance. Our model can be easily extended to include more protein features to further improve the performance. Besides, Graph2GO is also applicable to other application scenarios involving biological networks, and the learned latent representations can be used as feature inputs for machine learning tasks in various downstream analyses.
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Affiliation(s)
- Kunjie Fan
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yan Zhang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center (OSUCCC - James), Columbus, OH 43210, USA
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15
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Saviola AJ, Negrão F, Yates JR. Proteomics of Select Neglected Tropical Diseases. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:315-336. [PMID: 32109150 DOI: 10.1146/annurev-anchem-091619-093003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Technological advances in mass spectrometry have enabled the extensive identification, characterization, and quantification of proteins in any biological system. In disease processes proteins are often altered in response to external stimuli; therefore, proteomics, the large-scale study of proteins and their functions, represents an invaluable tool for understanding the molecular basis of disease. This review highlights the use of mass spectrometry-based proteomics to study the pathogenesis, etiology, and pathology of several neglected tropical diseases (NTDs), a diverse group of disabling diseases primarily associated with poverty in tropical and subtropical regions of the world. While numerous NTDs have been the subject of proteomic studies, this review focuses on Buruli ulcer, dengue, leishmaniasis, and snakebite envenoming. The proteomic studies highlighted provide substantial information on the pathogenic mechanisms driving these diseases; they also identify molecular targets for drug discovery and development and uncover promising biomarkers that can assist in early diagnosis.
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Affiliation(s)
- Anthony J Saviola
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, California 92037, USA;
| | - Fernanda Negrão
- Department of Biosciences and Technology of Bioactive Products, Institute of Biology, University of Campinas, São Paulo 13083-862, Brazil
| | - John R Yates
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, California 92037, USA;
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16
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Parthasarathy A, Kalesh K. Defeating the trypanosomatid trio: proteomics of the protozoan parasites causing neglected tropical diseases. RSC Med Chem 2020; 11:625-645. [PMID: 33479664 PMCID: PMC7549140 DOI: 10.1039/d0md00122h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/12/2020] [Indexed: 12/20/2022] Open
Abstract
Mass spectrometry-based proteomics enables accurate measurement of the modulations of proteins on a large scale upon perturbation and facilitates the understanding of the functional roles of proteins in biological systems. It is a particularly relevant methodology for studying Leishmania spp., Trypanosoma cruzi and Trypanosoma brucei, as the gene expression in these parasites is primarily regulated by posttranscriptional mechanisms. Large-scale proteomics studies have revealed a plethora of information regarding modulated proteins and their molecular interactions during various life processes of the protozoans, including stress adaptation, life cycle changes and interactions with the host. Important molecular processes within the parasite that regulate the activity and subcellular localisation of its proteins, including several co- and post-translational modifications, are also accurately captured by modern proteomics mass spectrometry techniques. Finally, in combination with synthetic chemistry, proteomic techniques facilitate unbiased profiling of targets and off-targets of pharmacologically active compounds in the parasites. This provides important data sets for their mechanism of action studies, thereby aiding drug development programmes.
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Affiliation(s)
- Anutthaman Parthasarathy
- Rochester Institute of Technology , Thomas H. Gosnell School of Life Sciences , 85 Lomb Memorial Dr , Rochester , NY 14623 , USA
| | - Karunakaran Kalesh
- Department of Chemistry , Durham University , Lower Mount Joy, South Road , Durham DH1 3LE , UK .
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17
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Chen K, Tian Z, Chen P, He H, Jiang F, Long CA. Genome-wide identification, characterization and expression analysis of lineage-specific genes within Hanseniaspora yeasts. FEMS Microbiol Lett 2020; 367:5837084. [PMID: 32407480 DOI: 10.1093/femsle/fnaa077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
Lineage-specific genes (LSGs) are defined as genes with sequences that are not significantly similar to those in any other lineage. LSGs have been proposed, and sometimes shown, to have significant effects in the evolution of biological function. In this study, two sets of Hanseniaspora spp. LSGs were identified by comparing the sequences of the Kloeckera apiculata genome and of 80 other yeast genomes. This study identified 344 Hanseniaspora-specific genes (HSGs) and 109 genes ('orphan genes') specific to K. apiculata. Three thousand three hundred thirty-one K. apiculata genes that showed significant similarity to at least one sequence outside the Hanseniaspora were classified into evolutionarily conserved genes. We analyzed their sequence features, functional categories, gene origin, gene structure and gene expression. We also investigated the predicted cellular roles and Gene Ontology categories of the LSGs using functional inference. The patterns of the functions of LSGs do not deviate significantly from genome-wide average. The results showed that a few LSGs were formed by gene duplication, followed by rapid sequence divergence. Many of the HSGs and orphan genes exhibited altered expression in response to abiotic stress. Studying these LSGs might be helpful for understanding the molecular mechanism of yeast adaption.
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Affiliation(s)
- Kai Chen
- School of Biological Engineering and Food, Hubei University of Technology, Wuhan 430068, China
| | - Zhonghuan Tian
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, National Centre of Citrus Breeding, Huazhong Agricultural University, Wuhan 430070, China
| | - Ping Chen
- Department of Pediatric Hematology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Hua He
- School of Landscape Architecture and Horticulture, Wuhan Institute of Bioengineering, Wuhan 430415, China
| | - Fatang Jiang
- School of Biological Engineering and Food, Hubei University of Technology, Wuhan 430068, China
| | - Chao-An Long
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, National Centre of Citrus Breeding, Huazhong Agricultural University, Wuhan 430070, China
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18
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Koo DCE, Bonneau R. Towards region-specific propagation of protein functions. Bioinformatics 2020; 35:1737-1744. [PMID: 30304483 PMCID: PMC6513163 DOI: 10.1093/bioinformatics/bty834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 08/23/2018] [Accepted: 10/08/2018] [Indexed: 01/06/2023] Open
Abstract
MOTIVATION Due to the nature of experimental annotation, most protein function prediction methods operate at the protein-level, where functions are assigned to full-length proteins based on overall similarities. However, most proteins function by interacting with other proteins or molecules, and many functional associations should be limited to specific regions rather than the entire protein length. Most domain-centric function prediction methods depend on accurate domain family assignments to infer relationships between domains and functions, with regions that are unassigned to a known domain-family left out of functional evaluation. Given the abundance of residue-level annotations currently available, we present a function prediction methodology that automatically infers function labels of specific protein regions using protein-level annotations and multiple types of region-specific features. RESULTS We apply this method to local features obtained from InterPro, UniProtKB and amino acid sequences and show that this method improves both the accuracy and region-specificity of protein function transfer and prediction. We compare region-level predictive performance of our method against that of a whole-protein baseline method using proteins with structurally verified binding sites and also compare protein-level temporal holdout predictive performances to expand the variety and specificity of GO terms we could evaluate. Our results can also serve as a starting point to categorize GO terms into region-specific and whole-protein terms and select prediction methods for different classes of GO terms. AVAILABILITY AND IMPLEMENTATION The code and features are freely available at: https://github.com/ek1203/rsfp. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Da Chen Emily Koo
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Richard Bonneau
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA.,Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.,Center for Data Science, New York University, New York, NY, USA
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19
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García-Reina A, Rodríguez-García MJ, Cuello F, Galián J. Immune transcriptome analysis in predatory beetles reveals two cecropin genes overexpressed in mandibles. J Invertebr Pathol 2020; 171:107346. [PMID: 32067979 DOI: 10.1016/j.jip.2020.107346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 12/22/2022]
Abstract
The great complexity and variety of the innate immune system and the production of antimicrobial peptides in insects is correlated with their evolutionary success and adaptation to different environments. Tiger beetles are an example of non-pest species with a cosmopolitan distribution, but the immune system is barely known and its study could provide useful information about the humoral immunity of predatory insects. Suppression subtractive hybridization (SSH) was performed in Calomera littoralis beetles to obtain a screening of those genes that were overexpressed after an injection with Escherichia coli lipopolysaccharide (LPS). Several genes were identified to be related to immune defense. Among those genes, two members of the cecropin antimicrobial peptides were characterized and identified as CliCec-A and CliCec-B2. Both protein sequences showed cecropin characteristics including 37 and 38 residue mature peptides, composed by two α-helices structures with amphipathic and hydrophobic nature, as shown in their predicted three-dimensional structure. Chemically synthesized CliCec-B2 confirmed cecropin antimicrobial activity against some Gram (+) and Gram (-) bacteria, but not against yeast. Expression of both cecropin genes was assessed by qPCR and showed increases after a LPS injection and highlighted their overexpression in adult beetle mandibles, which could be related to their alimentary habits.
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Affiliation(s)
- Andrés García-Reina
- University of Murcia Department of Zoology and Physical Anthropology, Faculty of Veterinary, Campus Mare Nostrum, E-30100 Murcia, Spain.
| | - María Juliana Rodríguez-García
- University of Murcia Department of Zoology and Physical Anthropology, Faculty of Veterinary, Campus Mare Nostrum, E-30100 Murcia, Spain
| | - Francisco Cuello
- University of Murcia, Departament of Animal Health, Faculty of Veterinary, Campus Mare Nostrum, E-30100 Murcia, Spain
| | - José Galián
- University of Murcia Department of Zoology and Physical Anthropology, Faculty of Veterinary, Campus Mare Nostrum, E-30100 Murcia, Spain
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20
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Nielsen H, Petsalaki EI, Zhao L, Stühler K. Predicting eukaryotic protein secretion without signals. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140174. [DOI: 10.1016/j.bbapap.2018.11.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 10/30/2018] [Accepted: 11/29/2018] [Indexed: 10/27/2022]
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21
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Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang JM, Liao WH, Liu YW, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Björne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Šmuc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O'Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biol 2019; 20:244. [PMID: 31744546 PMCID: PMC6864930 DOI: 10.1186/s13059-019-1835-8] [Citation(s) in RCA: 202] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/24/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. RESULTS Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. CONCLUSION We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.
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Affiliation(s)
- Naihui Zhou
- Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.,Program in Bioinformatics and Computational Biology, Ames, IA, USA
| | - Yuxiang Jiang
- Indiana University Bloomington, Bloomington, Indiana, USA
| | - Timothy R Bergquist
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Alexandra J Lee
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Balint Z Kacsoh
- Geisel School of Medicine at Dartmouth, Hanover, NH, USA.,Department of Molecular and Systems Biology, Hanover, NH, USA
| | - Alex W Crocker
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Kimberley A Lewis
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - George Georghiou
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
| | - Huy N Nguyen
- Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.,Program in Computer Science, Ames, IA, USA
| | - Md Nafiz Hamid
- Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.,Program in Bioinformatics and Computational Biology, Ames, IA, USA
| | - Larry Davis
- Program in Bioinformatics and Computational Biology, Ames, IA, USA
| | - Tunca Dogan
- Department of Computer Engineering, Hacettepe University, Ankara, Turkey.,European Molecular Biolo gy Labora tory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Volkan Atalay
- Department of Computer Engineering, Middle East Technical University (METU), Ankara, Turkey
| | - Ahmet S Rifaioglu
- Department of Computer Engineering, Middle East Technical University (METU), Ankara, Turkey.,Department of Computer Engineering, Iskenderun Technical University, Hatay, Turkey
| | - Alperen Dalkıran
- Department of Computer Engineering, Middle East Technical University (METU), Ankara, Turkey
| | - Rengul Cetin Atalay
- CanSyL, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Rebecca L Hurto
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Peter L Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | | | - Fran Supek
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - José M Fernández
- INB Coordination Unit, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, Spain.,(former) INB GN2, Structural and Computational Biology Programme, Spanish National Cancer Research Centre, Barcelona, Catalonia, Spain
| | - Branislava Gemovic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade, Serbia
| | - Vladimir R Perovic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade, Serbia
| | - Radoslav S Davidović
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade, Serbia
| | - Neven Sumonja
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade, Serbia
| | - Nevena Veljkovic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade, Serbia
| | - Ehsaneddin Asgari
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering, University of California Berkeley, Berkeley, CA, USA.,Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Berkeley, CA, USA
| | | | - Giuseppe Profiti
- Bologna Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.,National Research Council, IBIOM, Bologna, Italy
| | - Castrense Savojardo
- Bologna Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Pier Luigi Martelli
- Bologna Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Rita Casadio
- Bologna Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Florian Boecker
- University of Bonn: INRES Crop Bioinformatics, Bonn, North Rhine-Westphalia, Germany
| | - Heiko Schoof
- INRES Crop Bioinformatics, University of Bonn, Bonn, Germany
| | - Indika Kahanda
- Gianforte School of Computing, Montana State University, Bozeman, Montana, USA
| | - Natalie Thurlby
- University of Bristol, Computer Science, Bristol, Bristol, United Kingdom
| | - Alice C McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Brunswick, Germany.,RESIST, DFG Cluster of Excellence 2155, Brunswick, Germany
| | - Alexandre Renaux
- Interuniversity Institute of Bioinformatics in Brussels, Université libre de Bruxelles - Vrije Universiteit Brussel, Brussels, Belgium.,Machine Learning Group, Université libre de Bruxelles, Brussels, Belgium.,Artificial Intelligence lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Rabie Saidi
- European Molecular Biolo gy Labora tory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Julian Gough
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Alex A Freitas
- University of Kent, School of Computing, Canterbury, United Kingdom
| | - Magdalena Antczak
- School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | - Fabio Fabris
- University of Kent, School of Computing, Canterbury, United Kingdom
| | - Mark N Wass
- School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | - Jie Hou
- University of Missouri, Computer Science, Columbia, Missouri, USA.,Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Zheng Wang
- University of Miami, Coral Gables, Florida, USA
| | - Alfonso E Romero
- Centre for Systems and Synthetic Biology, Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, United Kingdom
| | - Alberto Paccanaro
- Centre for Systems and Synthetic Biology, Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, United Kingdom
| | - Haixuan Yang
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Galway, Ireland.,Technical University of Munich, Garching, Germany
| | - Tatyana Goldberg
- Department of Informatics, Bioinformatics & Computational Biology-i12, Technische Universitat Munchen, Munich, Germany
| | - Chenguang Zhao
- Faculty for Informatics, Garching, Germany.,Department for Bioinformatics and Computational Biology, Garching, Germany.,School of Computing Sciences and Computer Engineering, Hattiesburg, Mississippi, USA
| | - Liisa Holm
- Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Finland, Helsinki, Finland
| | - Petri Törönen
- Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Finland, Helsinki, Finland
| | - Alan J Medlar
- Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Finland, Helsinki, Finland
| | - Elaine Zosa
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Ilya Novikov
- Baylor College of Medicine, Department of Biochemistry and Molecular Biology, Houston, TX, USA
| | - Angela Wilkins
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX, USA
| | - Olivier Lichtarge
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX, USA
| | - Po-Han Chi
- National TsingHua University, Hsinchu, Taiwan
| | - Wei-Cheng Tseng
- Department of Electrical Engineering in National Tsing Hua University, Hsinchu City, Taiwan
| | - Michal Linial
- The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Peter W Rose
- University of California San Diego, San Diego Supercomputer Center, La Jolla, California, USA
| | - Christophe Dessimoz
- Department of Computational Biology and Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Genetics, Evolution & Environment, and Department of Computer Science, University College London, London, UK.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Vedrana Vidulin
- Department of Knowledge Technologies, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Saso Dzeroski
- Jozef Stefan Institute, Ljubljana, Slovenia.,Jozef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Ian Sillitoe
- Research Department of Structural and Molecular Biology, University College London, London, England
| | - Sayoni Das
- Research Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Jonathan Gill Lees
- Research Department of Structural and Molecular Biology, University College London, London, United Kingdom.,Department of Health and Life Sciences, Oxford Brookes University, London, UK
| | - David T Jones
- The Francis Crick Institute, Biomedical Data Science Laboratory, London, United Kingdom.,Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Cen Wan
- Department of Computer Science, University College London, London, United Kingdom.,The Francis Crick Institute, Biomedical Data Science Laboratory, London, United Kingdom
| | - Domenico Cozzetto
- Department of Computer Science, University College London, London, United Kingdom.,The Francis Crick Institute, Biomedical Data Science Laboratory, London, United Kingdom
| | - Rui Fa
- Department of Computer Science, University College London, London, United Kingdom.,The Francis Crick Institute, Biomedical Data Science Laboratory, London, United Kingdom
| | - Mateo Torres
- Centre for Systems and Synthetic Biology, Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, United Kingdom
| | - Alex Warwick Vesztrocy
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, United Kingdom.,SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Jose Manuel Rodriguez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Michael L Tress
- Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Marco Frasca
- Università degli Studi di Milano - Computer Science Department - AnacletoLab, Milan, Milan, Italy
| | - Marco Notaro
- Università degli Studi di Milano - Computer Science Department - AnacletoLab, Milan, Milan, Italy
| | - Giuliano Grossi
- Università degli Studi di Milano - Computer Science Department - AnacletoLab, Milan, Milan, Italy
| | - Alessandro Petrini
- Università degli Studi di Milano - Computer Science Department - AnacletoLab, Milan, Milan, Italy
| | - Matteo Re
- Università degli Studi di Milano - Computer Science Department - AnacletoLab, Milan, Milan, Italy
| | - Giorgio Valentini
- Università degli Studi di Milano - Computer Science Department - AnacletoLab, Milan, Milan, Italy
| | - Marco Mesiti
- Università degli Studi di Milano - Computer Science Department - AnacletoLab, Milan, Milan, Italy.,Institut de Biologie Computationnelle, LIRMM, CNRS-UMR 5506, Universite de Montpellier, Montpellier, France
| | - Daniel B Roche
- Department of Informatics, Bioinformatics and Computational Biology-i12, Technische Universitat Munchen, Munich, Germany
| | - Jonas Reeb
- Department of Informatics, Bioinformatics and Computational Biology-i12, Technische Universitat Munchen, Munich, Germany
| | - David W Ritchie
- University of Lorraine, CNRS, Inria, LORIA, Nancy, 54000, France
| | - Sabeur Aridhi
- University of Lorraine, CNRS, Inria, LORIA, Nancy, 54000, France
| | | | - Marie-Dominique Devignes
- University of Lorraine, CNRS, Inria, LORIA, Nancy, 54000, France.,University of Lorraine, Nancy, Lorraine, France.,Inria, Nancy, France
| | | | - Richard Bonneau
- NYU Center for Data Science, New York, 10010, NY, USA.,Flatiron Institute, CCB, New York, 10010, NY, USA
| | - Vladimir Gligorijević
- Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation, New York, New York, USA
| | - Meet Barot
- Center for Data Science, New York University, New York, 10011, NY, USA
| | - Hai Fang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Marco Falda
- Department of Biology, University of Padova, Padova, Italy
| | - Michele Berselli
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Silvio C E Tosatto
- CNR Institute of Neuroscience, Padova, Italy.,Department of Biomedical Sciences, University of Padua, Padova, Italy
| | - Marco Carraro
- Department of Biomedical Sciences, University of Padua, Padova, Italy
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padua, Padova, Italy
| | - Hafeez Ur Rehman
- Department of Computer Science, National University of Computer and Emerging Sciences, Peshawar, Khyber Pakhtoonkhwa, Pakistan
| | - Qizhong Mao
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA, USA.,University of California, Riverside, Philadelphia, PA, USA
| | - Shanshan Zhang
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA, USA
| | - Slobodan Vucetic
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA, USA
| | - Gage S Black
- Department of Biology, Brigham Young University, Provo, UT, USA.,Bioinformatics Research Group, Provo, UT, USA
| | - Dane Jo
- Department of Biology, Brigham Young University, Provo, UT, USA.,Bioinformatics Research Group, Provo, UT, USA
| | - Erica Suh
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Jonathan B Dayton
- Department of Biology, Brigham Young University, Provo, UT, USA.,Bioinformatics Research Group, Provo, UT, USA
| | - Dallas J Larsen
- Department of Biology, Brigham Young University, Provo, UT, USA.,Bioinformatics Research Group, Provo, UT, USA
| | - Ashton R Omdahl
- Department of Biology, Brigham Young University, Provo, UT, USA.,Bioinformatics Research Group, Provo, UT, USA
| | - Liam J McGuffin
- School of Biological Sciences, University of Reading, Reading, England, United Kingdom
| | | | - Patricia C Babbitt
- Department of Pharmaceutical Chemistry, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 94158, CA, USA
| | - Jeffrey M Yunes
- UC Berkeley - UCSF Graduate Program in Bioengineering, University of California, San Francisco, 94158, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 94158, CA, USA
| | - Paolo Fontana
- Research and Innovation Center, Edmund Mach Foundation, San Michele all'Adige, Italy
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, Shanghai, China.,Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, Shanghai, China
| | - Shanfeng Zhu
- School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China.,Institute of Science and Technology for Brain-Inspired Intelligence and Shanghai Institute of Artificial Intelligence Algorithms, Fudan University, Shanghai, China.,Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China
| | - Ronghui You
- School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China.,Institute of Science and Technology for Brain-Inspired Intelligence and Shanghai Institute of Artificial Intelligence Algorithms, Fudan University, Shanghai, China.,Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China
| | - Zihan Zhang
- School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China.,Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China
| | - Suyang Dai
- School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China.,Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China
| | - Shuwei Yao
- School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China.,Institute of Science and Technology for Brain-Inspired Intelligence and Shanghai Institute of Artificial Intelligence Algorithms, Fudan University, Shanghai, China
| | - Weidong Tian
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, Shanghai, China.,Department of Pediatrics, Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Renzhi Cao
- Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA
| | - Caleb Chandler
- Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA
| | - Miguel Amezola
- Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA
| | - Devon Johnson
- Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA
| | - Jia-Ming Chang
- Department of Computer Science, National Chengchi University, Taipei, Taiwan
| | - Wen-Hung Liao
- Department of Computer Science, National Chengchi University, Taipei, Taiwan
| | - Yi-Wei Liu
- Department of Computer Science, National Chengchi University, Taipei, Taiwan
| | | | | | - Robert Hoehndorf
- Computer, Electrical and Mathematical Sciences & Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Jeddah, Saudi Arabia
| | - Maxat Kulmanov
- Computer, Electrical and Mathematical Sciences & Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Jeddah, Saudi Arabia
| | - Imane Boudellioua
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Computer, Electrical and Mathematical Sciences Engineering Division (CEMSE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Gianfranco Politano
- Control and Computer Engineering Department, Politecnico di Torino, Torino, TO, Italy
| | - Stefano Di Carlo
- Control and Computer Engineering Department, Politecnico di Torino, Torino, TO, Italy
| | - Alfredo Benso
- Control and Computer Engineering Department, Politecnico di Torino, Torino, TO, Italy
| | - Kai Hakala
- Department of Future Technologies, Turku NLP Group, University of Turku, Turku, Finland.,University of Turku Graduate School (UTUGS), Turku, Finland
| | - Filip Ginter
- Department of Future Technologies, Turku NLP Group, University of Turku, Turku, Finland.,University of Turku, Turku, Finland
| | - Farrokh Mehryary
- Department of Future Technologies, Turku NLP Group, University of Turku, Turku, Finland.,University of Turku Graduate School (UTUGS), Turku, Finland
| | - Suwisa Kaewphan
- Department of Future Technologies, Turku NLP Group, University of Turku, Turku, Finland.,University of Turku Graduate School (UTUGS), Turku, Finland.,Turku Centre for Computer Science (TUCS), Turku, Finland
| | - Jari Björne
- Department of Future Technologies, Faculty of Science and Engineering, University of Turku, Turku, FI-20014, Finland.,Turku Centre for Computer Science (TUCS), Agora, Vesilinnantie 3, Turku, FI-20500, Finland
| | | | | | - Tapio Salakoski
- Department of Future Technologies, Faculty of Science and Engineering, University of Turku, Turku, FI-20014, Finland.,Turku Centre for Computer Science (TUCS), Agora, Vesilinnantie 3, Turku, FI-20500, Finland
| | - Daisuke Kihara
- Department of Biological Sciences, Department of Computer Science, Purdue University, 47907, IN, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, 45229, OH, USA
| | - Aashish Jain
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Tomislav Šmuc
- Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia
| | - Adrian Altenhoff
- Department of Computer Science, ETH Zurich, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Asa Ben-Hur
- Department of Computer Science, Colorado State University, Fort Collins, CO, USA
| | - Burkhard Rost
- Department of Informatics, Bioinformatics & Computational Biology-i12, Technische Universitat Munchen, Munich, Germany.,Institute for Food and Plant Sciences WZW, Technische Universität München, Freising, Germany
| | | | - Christine A Orengo
- Research Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Constance J Jeffery
- Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Giovanni Bosco
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Deborah A Hogan
- Geisel School of Medicine at Dartmouth, Hanover, NH, USA.,Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Maria J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Philadelphia, Pennsylvania, USA
| | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
| | - Iddo Friedberg
- Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.
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22
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Concu R, Cordeiro MNDS. Alignment-Free Method to Predict Enzyme Classes and Subclasses. Int J Mol Sci 2019; 20:ijms20215389. [PMID: 31671806 PMCID: PMC6862210 DOI: 10.3390/ijms20215389] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 01/03/2023] Open
Abstract
The Enzyme Classification (EC) number is a numerical classification scheme for enzymes, established using the chemical reactions they catalyze. This classification is based on the recommendation of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology. Six enzyme classes were recognised in the first Enzyme Classification and Nomenclature List, reported by the International Union of Biochemistry in 1961. However, a new enzyme group was recently added as the six existing EC classes could not describe enzymes involved in the movement of ions or molecules across membranes. Such enzymes are now classified in the new EC class of translocases (EC 7). Several computational methods have been developed in order to predict the EC number. However, due to this new change, all such methods are now outdated and need updating. In this work, we developed a new multi-task quantitative structure-activity relationship (QSAR) method aimed at predicting all 7 EC classes and subclasses. In so doing, we developed an alignment-free model based on artificial neural networks that proved to be very successful.
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Affiliation(s)
- Riccardo Concu
- LAQV@REQUIMTE/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal.
| | - M Natália D S Cordeiro
- LAQV@REQUIMTE/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal.
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23
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Zhan FB, Tan K, Song X, Yu J, Wang WM. Isolation and expression of four Megalobrama amblycephala toll-like receptor genes in response to a bacterial infection. FISH & SHELLFISH IMMUNOLOGY 2019; 93:1028-1040. [PMID: 31430559 DOI: 10.1016/j.fsi.2019.08.051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/24/2019] [Accepted: 08/16/2019] [Indexed: 06/10/2023]
Abstract
Toll-like receptors (TLRs) are a category of pattern recognition receptors (PRRs), which recognize pathogen associated molecular patterns (PAMPs) and participate in the immune responses. We identified tlr5a, tlr5b, tlr9 and tlr21 from the genome of blunt snout bream (Megalobrama amblycephala). All four tlrs were constitutively expressed in all examined tissues. After an immune bacterial challenge with Aeromonas hydrophila, their expressionwas up-regulated in lymphoid organs and tissues. Recombinant eukaryotic plasmid pEGFP-N1 was transfected into the common carp (Cyprinus carpio) EPC (epithelioma papulosum cyprini) cells for the purpose of subcellular localization. pcDNA3.1(+) recombinant eukaryotic plasmid was used to investigate the effects of overexpression of tlrs on the expression of downstream interferon-associated immune factors. The four Tlrs were distributed in the cytoplasm of transfected cells and appeared as filamentous or reticular. The expression of irf3, irf7, isg15, mx1, pkr and viperin at 0, 6, 12, 18, 24, 36, 48 and 72 h post-transfection in transfected EPC cells was quantified by qPCR. Overexpression of tlrs upregulated the expression of viperin, isg15, irf3, irf7, mx1 and pkr (in that order of magnitude). We also cloned the following promoters of irfs: Irf1-p, irf2-p, irf6-p, irf7-p, irf8-p and irf9-p. Results of the dual luciferase reporter assay suggested that tlr5a, tlr5b and tlr9 enhanced the activities of irf7-p, while tlr5b enhanced the activities of irf1-p and irf7-p. This suggests that they all play a role in the innate immunity. The experiments also indicated that TLRs activate irf3 or irf7 signaling to induce IFN secretion and subsequent upregulation of IFN-stimulated genes. These results indicate that tlrs and irfs play an important immune role in response to A. hydrophila infection in blunt snout bream, and pave the way for further studies of immune mechanisms mediated by TLRs in fish.
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Affiliation(s)
- Fan-Bin Zhan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kianann Tan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoran Song
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiongying Yu
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wei-Min Wang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China.
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24
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Leng F, Li Y, Luo W, Wei Q, Jing Y, Wang X, Yang M, Wang Y. Cloning, Expression, and Bioinformatics Analysis of Heavy Metal Resistance Gene afe_1862 from Acidithiobacillus ferrooxidans L1 in Escherichia coli. Biol Trace Elem Res 2019; 189:291-300. [PMID: 30117047 DOI: 10.1007/s12011-018-1462-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 07/25/2018] [Indexed: 11/28/2022]
Abstract
Molecular studies of copper and cadmium resistances in acidophilic bacteria are significant in biomining. In this study, afe_1862, which encodes a heavy metal-binding protein in Acidithiobacillus ferrooxidans L1, was amplified using PCR, cloned into the pET32a plasmid, and sequenced. Following SDS-PAGE analysis, optimization of the expression conditions and heterologous overexpression of afe_1862 in Escherichia coli BL21 in the presence of Cu2+ and Cd2+ were studied as well. The results indicated that AFE_1862 has higher resistance to Cu2+ than Cd2+. Bioinformatics analysis illustrated that AFE_1862 has a conserved HMA domain containing heavy metal-binding sites, which may play a role in transporting or detoxifying heavy metals.
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Affiliation(s)
- Feifan Leng
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China.
| | - Yuanli Li
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Wen Luo
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Qingwei Wei
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Yanjun Jing
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Xiaoli Wang
- Lanzhou Institute of Husbandry and Pharmaceutical Science of CAAS, Lanzhou, 730050, China
| | - Mingjun Yang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Yonggang Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China.
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25
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Bi X, Xu M, Li J, Huang T, Jiang B, Shen L, Luo L, Liu S, Yin Z. Heat shock protein 27 inhibits HMGB1 translocation by regulating CBP acetyltransferase activity and ubiquitination. Mol Immunol 2019; 108:45-55. [DOI: 10.1016/j.molimm.2019.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 01/31/2019] [Accepted: 02/03/2019] [Indexed: 11/28/2022]
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26
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Squires KE, Montañez-Miranda C, Pandya RR, Torres MP, Hepler JR. Genetic Analysis of Rare Human Variants of Regulators of G Protein Signaling Proteins and Their Role in Human Physiology and Disease. Pharmacol Rev 2018; 70:446-474. [PMID: 29871944 DOI: 10.1124/pr.117.015354] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Regulators of G protein signaling (RGS) proteins modulate the physiologic actions of many neurotransmitters, hormones, and other signaling molecules. Human RGS proteins comprise a family of 20 canonical proteins that bind directly to G protein-coupled receptors/G protein complexes to limit the lifetime of their signaling events, which regulate all aspects of cell and organ physiology. Genetic variations account for diverse human traits and individual predispositions to disease. RGS proteins contribute to many complex polygenic human traits and pathologies such as hypertension, atherosclerosis, schizophrenia, depression, addiction, cancers, and many others. Recent analysis indicates that most human diseases are due to extremely rare genetic variants. In this study, we summarize physiologic roles for RGS proteins and links to human diseases/traits and report rare variants found within each human RGS protein exome sequence derived from global population studies. Each RGS sequence is analyzed using recently described bioinformatics and proteomic tools for measures of missense tolerance ratio paired with combined annotation-dependent depletion scores, and protein post-translational modification (PTM) alignment cluster analysis. We highlight selected variants within the well-studied RGS domain that likely disrupt RGS protein functions and provide comprehensive variant and PTM data for each RGS protein for future study. We propose that rare variants in functionally sensitive regions of RGS proteins confer profound change-of-function phenotypes that may contribute, in newly appreciated ways, to complex human diseases and/or traits. This information provides investigators with a valuable database to explore variation in RGS protein function, and for targeting RGS proteins as future therapeutic targets.
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Affiliation(s)
- Katherine E Squires
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia (K.E.S., C.M.-M., J.R.H.); and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia (R.R.P., M.P.T.)
| | - Carolina Montañez-Miranda
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia (K.E.S., C.M.-M., J.R.H.); and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia (R.R.P., M.P.T.)
| | - Rushika R Pandya
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia (K.E.S., C.M.-M., J.R.H.); and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia (R.R.P., M.P.T.)
| | - Matthew P Torres
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia (K.E.S., C.M.-M., J.R.H.); and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia (R.R.P., M.P.T.)
| | - John R Hepler
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia (K.E.S., C.M.-M., J.R.H.); and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia (R.R.P., M.P.T.)
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27
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Le NQK, Sandag GA, Ou YY. Incorporating post translational modification information for enhancing the predictive performance of membrane transport proteins. Comput Biol Chem 2018; 77:251-260. [DOI: 10.1016/j.compbiolchem.2018.10.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 08/01/2018] [Accepted: 10/14/2018] [Indexed: 10/28/2022]
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28
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Dalkiran A, Rifaioglu AS, Martin MJ, Cetin-Atalay R, Atalay V, Doğan T. ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature. BMC Bioinformatics 2018; 19:334. [PMID: 30241466 PMCID: PMC6150975 DOI: 10.1186/s12859-018-2368-y] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/10/2018] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The automated prediction of the enzymatic functions of uncharacterized proteins is a crucial topic in bioinformatics. Although several methods and tools have been proposed to classify enzymes, most of these studies are limited to specific functional classes and levels of the Enzyme Commission (EC) number hierarchy. Besides, most of the previous methods incorporated only a single input feature type, which limits the applicability to the wide functional space. Here, we proposed a novel enzymatic function prediction tool, ECPred, based on ensemble of machine learning classifiers. RESULTS In ECPred, each EC number constituted an individual class and therefore, had an independent learning model. Enzyme vs. non-enzyme classification is incorporated into ECPred along with a hierarchical prediction approach exploiting the tree structure of the EC nomenclature. ECPred provides predictions for 858 EC numbers in total including 6 main classes, 55 subclass classes, 163 sub-subclass classes and 634 substrate classes. The proposed method is tested and compared with the state-of-the-art enzyme function prediction tools by using independent temporal hold-out and no-Pfam datasets constructed during this study. CONCLUSIONS ECPred is presented both as a stand-alone and a web based tool to provide probabilistic enzymatic function predictions (at all five levels of EC) for uncharacterized protein sequences. Also, the datasets of this study will be a valuable resource for future benchmarking studies. ECPred is available for download, together with all of the datasets used in this study, at: https://github.com/cansyl/ECPred . ECPred webserver can be accessed through http://cansyl.metu.edu.tr/ECPred.html .
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Affiliation(s)
- Alperen Dalkiran
- Department of Computer Engineering, Middle East Technical University, 06800 Ankara, Turkey
- Department of Computer Engineering, Adana Science and Technology University, 01250 Adana, Turkey
| | - Ahmet Sureyya Rifaioglu
- Department of Computer Engineering, Middle East Technical University, 06800 Ankara, Turkey
- Department of Computer Engineering, Iskenderun Technical University, Hatay, 31200 İskenderun, Turkey
| | - Maria Jesus Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD UK
| | - Rengul Cetin-Atalay
- KanSiL, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey
- Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | - Volkan Atalay
- Department of Computer Engineering, Middle East Technical University, 06800 Ankara, Turkey
- KanSiL, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | - Tunca Doğan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD UK
- KanSiL, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey
- Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey
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29
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Abstract
Since the 1980s, deep learning and biomedical data have been coevolving and feeding each other. The breadth, complexity, and rapidly expanding size of biomedical data have stimulated the development of novel deep learning methods, and application of these methods to biomedical data have led to scientific discoveries and practical solutions. This overview provides technical and historical pointers to the field, and surveys current applications of deep learning to biomedical data organized around five subareas, roughly of increasing spatial scale: chemoinformatics, proteomics, genomics and transcriptomics, biomedical imaging, and health care. The black box problem of deep learning methods is also briefly discussed.
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Affiliation(s)
- Pierre Baldi
- Department of Computer Science, Institute for Genomics and Bioinformatics, and Center for Machine Learning and Intelligent Systems, University of California, Irvine, California 92697, USA
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30
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Cho Y, Ross RS. A mini review: Proteomics approaches to understand disused vs. exercised human skeletal muscle. Physiol Genomics 2018; 50:746-757. [PMID: 29958080 DOI: 10.1152/physiolgenomics.00043.2018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Immobilization, bed rest, or denervation leads to muscle disuse and subsequent skeletal muscle atrophy. Muscle atrophy can also occur as a component of various chronic diseases such as cancer, AIDS, sepsis, diabetes, and chronic heart failure or as a direct result of genetic muscle disorders. In addition to this atrophic loss of muscle mass, metabolic deregulation of muscle also occurs. In contrast, physical exercise plays a beneficial role in counteracting disuse-induced atrophy by increasing muscle mass and strength. Along with this, exercise can also reduce mitochondrial dysfunction and metabolic deregulation. Still, while exercise causes valuable metabolic and functional adaptations in skeletal muscle, the mechanisms and effectors that lead to these changes such as increased mitochondria content or enhanced protein synthesis are not fully understood. Therefore, mechanistic insights may ultimately provide novel ways to treat disuse induced atrophy and metabolic deregulation. Mass spectrometry (MS)-based proteomics offers enormous promise for investigating the molecular mechanisms underlying disuse and exercise-induced changes in skeletal muscle. This review will focus on initial findings uncovered by using proteomics approaches with human skeletal muscle specimens and discuss their potential for the future study.
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Affiliation(s)
- Yoshitake Cho
- Division of Cardiology, Department of Medicine, University of California San Diego , La Jolla, California
| | - Robert S Ross
- Division of Cardiology, Department of Medicine, University of California San Diego , La Jolla, California.,Cardiology Section, Department of Medicine, Veterans Administration Healthcare , San Diego, California
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31
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Weber M, Wunderer J, Lengerer B, Pjeta R, Rodrigues M, Schärer L, Ladurner P, Ramm SA. A targeted in situ hybridization screen identifies putative seminal fluid proteins in a simultaneously hermaphroditic flatworm. BMC Evol Biol 2018; 18:81. [PMID: 29848299 PMCID: PMC5977470 DOI: 10.1186/s12862-018-1187-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/30/2018] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Along with sperm, in many taxa ejaculates also contain large numbers of seminal fluid proteins (SFPs). SFPs and sperm are transferred to the mating partner, where they are thought to play key roles in mediating post-mating sexual selection. They modulate the partner's behavior and physiology in ways that influence the reproductive success of both partners, thus potentially leading to sexual conflict. Despite the presumed general functional and evolutionary significance of SFPs, their identification and characterization has to date focused on just a few animal groups, predominantly insects and mammals. Moreover, until now seminal fluid profiling has mainly focused on species with separate sexes. Here we report a comprehensive screen for putative SFPs in the simultaneously hermaphroditic flatworm Macrostomum lignano. RESULTS Based on existing transcriptomic data, we selected 150 transcripts known to be (a) predominantly expressed in the tail region of the worms, where the seminal fluid-producing prostate gland cells are located, and (b) differentially expressed in social environments differing in sperm competition level, strongly implying that they represent a phenotypically plastic aspect of male reproductive allocation in this species. For these SFP candidates, we then performed whole-mount in situ hybridization (ISH) experiments to characterize tissue-specific expression. In total, we identified 98 transcripts that exhibited prostate-specific expression, 76 of which we found to be expressed exclusively in the prostate gland cells; additional sites of expression for the remaining 22 included the testis or other gland cells. Bioinformatics analyses of the prostate-limited candidates revealed that at least 64 are predicted to be secretory proteins, making these especially strong candidates to be SFPs that are transferred during copulation. CONCLUSIONS Our study represents a first comprehensive analysis using a combination of transcriptomic and ISH screen data to identify SFPs based on transcript expression in seminal fluid-producing tissues. We thereby extend the range of taxa for which seminal fluid has been characterized to a flatworm species with a sequenced genome and for which several methods such as antibody staining, transgenesis and RNA interference have been established. Our data provide a basis for testing the functional and evolutionary significance of SFPs.
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Affiliation(s)
- Michael Weber
- Evolutionary Biology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany
| | - Julia Wunderer
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Birgit Lengerer
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Robert Pjeta
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Marcelo Rodrigues
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Current address: School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne, England NE1 7RU UK
| | - Lukas Schärer
- Evolutionary Biology, Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Peter Ladurner
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Steven A. Ramm
- Evolutionary Biology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany
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32
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Pan X, Gong D, Gao F, Sangild PT. Diet-dependent changes in the intestinal DNA methylome after introduction of enteral feeding in preterm pigs. Epigenomics 2018; 10:395-408. [PMID: 29587528 DOI: 10.2217/epi-2017-0122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
AIM To examine how enteral feeding affects the intestinal epigenome and gene expression just after preterm birth. MATERIALS & METHODS Intestinal tissue from preterm pigs, modeling preterm infants, was collected at birth and 5 days after gradual introduction of infant formula or bovine colostrum. The intestinal tissue was analyzed by reduced representation bisulfite sequencing and real-time qPCR. RESULTS Relative to colostrum, formula increased bacterial epithelial adherence and lipopolysaccharide binding protein (LBP) expression, which was regulated by promoter methylation. Diet-dependent changes in DNA methylation and/or mRNA expression were related to innate immune response, hypoxia, angiogenesis and epithelial-mesenchymal transition pathways (e.g., TTC38, IL8, C3, HIF1A and VEGFR1). CONCLUSION Epigenetic changes may mediate important effects of the first feeding on intestinal development in preterm neonates.
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Affiliation(s)
- Xiaoyu Pan
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg DK 1870 C, Denmark
| | - Desheng Gong
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, PR China
| | - Fei Gao
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, PR China
| | - Per Torp Sangild
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg DK 1870 C, Denmark
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33
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Zhou Y, Cao X, Yang Y, Wang J, Yang W, Ben P, Shen L, Cao P, Luo L, Yin Z. Glutathione S-Transferase Pi Prevents Sepsis-Related High Mobility Group Box-1 Protein Translocation and Release. Front Immunol 2018. [PMID: 29520271 PMCID: PMC5827551 DOI: 10.3389/fimmu.2018.00268] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Glutathione S-transferase Pi (GSTP) was originally identified as one of cytosolic phase II detoxification enzymes and also was considered to function via its non-catalytic, ligand-binding activity. We have reported that GSTP played an anti-inflammatory role in macrophages, suggesting that GSTP may have a protective role in inflammation. In this study, we deleted the murine Gstp gene cluster and found that GSTP significantly decreased the mortality of experimental sepsis and reduced related serum level of high mobility group box-1 protein (HMGB1). As HMGB1 is the key cytokine involved in septic death, we further studied the effect of GSTP on HMGB1 release. The results demonstrated that a classic protein kinase C (cPKC) dependent phosphorylation of cytoplasmic GSTP at Ser184 occurred in macrophages in response to lipopolysaccharide (LPS) stimulation. Phosphorylated GSTP was then translocated to the nucleus. In the nucleus, GSTP bound to HMGB1 and suppressed LPS-triggered and cPKC-mediated HMGB1 phosphorylation. Consequently, GSTP prevented the translocation of HMGB1 to cytoplasm and release. Our findings provide the new evidence that GSTP inhibited HMGB1 release via binding to HMGB1 in the nucleus independent of its transferase activity. cPKC-mediated GSTP phosphorylation was essential for GSTP to translocate from cytoplasm to nucleus. To our knowledge, we are the first to report that nuclear GSTP functions as a negative regulator to control HMGB1 release from macrophages and decreases the mortality of sepsis.
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Affiliation(s)
- Yi Zhou
- Jiangsu Province Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Xiang Cao
- Jiangsu Province Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Yang Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.,Laboratory of Cellular and Molecular Biology, Jiangsu Province Institute of Traditional Chinese Medicine, Nanjing, China
| | - Jing Wang
- Jiangsu Province Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Weidong Yang
- Jiangsu Province Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Peiling Ben
- Jiangsu Province Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Lei Shen
- Jiangsu Province Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Peng Cao
- Laboratory of Cellular and Molecular Biology, Jiangsu Province Institute of Traditional Chinese Medicine, Nanjing, China
| | - Lan Luo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zhimin Yin
- Jiangsu Province Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
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34
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Rodrigues V, Fernandez B, Vercoutere A, Chamayou L, Andersen A, Vigy O, Demettre E, Seveno M, Aprelon R, Giraud-Girard K, Stachurski F, Loire E, Vachiéry N, Holzmuller P. Immunomodulatory Effects of Amblyomma variegatum Saliva on Bovine Cells: Characterization of Cellular Responses and Identification of Molecular Determinants. Front Cell Infect Microbiol 2018; 7:521. [PMID: 29354598 PMCID: PMC5759025 DOI: 10.3389/fcimb.2017.00521] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 12/07/2017] [Indexed: 12/25/2022] Open
Abstract
The tropical bont tick, Amblyomma variegatum, is a tick species of veterinary importance and is considered as one of major pest of ruminants in Africa and in the Caribbean. It causes direct skin lesions, transmits heartwater, and reactivates bovine dermatophilosis. Tick saliva is reported to affect overall host responses through immunomodulatory and anti-inflammatory molecules, among other bioactive molecules. The general objective of this study was to better understand the role of saliva in interaction between the Amblyomma tick and the host using cellular biology approaches and proteomics, and to discuss its impact on disease transmission and/or activation. We first focused on the immuno-modulating effects of semi-fed A. variegatum female saliva on bovine peripheral blood mononuclear cells (PBMC) and monocyte-derived macrophages in vitro. We analyzed its immuno-suppressive properties by measuring the effect of saliva on PBMC proliferation, and observed a significant decrease in ConA-stimulated PBMC lymphoproliferation. We then studied the effect of saliva on bovine macrophages using flow cytometry to analyze the expression of MHC-II and co-stimulation molecules (CD40, CD80, and CD86) and by measuring the production of nitric oxide (NO) and pro- or anti-inflammatory cytokines. We observed a significant decrease in the expression of MHC-II, CD40, and CD80 molecules, associated with decreased levels of IL-12-p40 and TNF-α and increased level of IL-10, which could explain the saliva-induced modulation of NO. To elucidate these immunomodulatory effects, crude saliva proteins were analyzed using proteomics with an Orbitrap Elite mass spectrometer. Among the 336 proteins identified in A. variegatum saliva, we evidenced bioactive molecules exhibiting anti-inflammatory, immuno-modulatory, and anti-oxidant properties (e.g., serpins, phospholipases A2, heme lipoprotein). We also characterized an intriguing ubiquitination complex that could be involved in saliva-induced immune modulation of the host. We propose a model for the interaction between A. variegatum saliva and host immune cells that could have an effect during tick feeding by favoring pathogen dissemination or activation by reducing the efficiency of host immune response to the corresponding tick-borne diseases.
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Affiliation(s)
- Valérie Rodrigues
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,ASTRE, Université de Montpellier (I-MUSE), CIRAD, Institut National de la Recherche Agronomique, Montpellier, France
| | - Bernard Fernandez
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,ASTRE, Université de Montpellier (I-MUSE), CIRAD, Institut National de la Recherche Agronomique, Montpellier, France
| | - Arthur Vercoutere
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,ASTRE, Université de Montpellier (I-MUSE), CIRAD, Institut National de la Recherche Agronomique, Montpellier, France
| | - Léo Chamayou
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,ASTRE, Université de Montpellier (I-MUSE), CIRAD, Institut National de la Recherche Agronomique, Montpellier, France
| | - Alexandre Andersen
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,ASTRE, Université de Montpellier (I-MUSE), CIRAD, Institut National de la Recherche Agronomique, Montpellier, France
| | - Oana Vigy
- Institut de Génomique Fonctionnelle, Centre Nationnal de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Edith Demettre
- BioCampus Montpellier, Centre Nationnal de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Martial Seveno
- BioCampus Montpellier, Centre Nationnal de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Rosalie Aprelon
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,CIRAD, UMR ASTRE, Petit-Bourg, Guadeloupe, France
| | - Ken Giraud-Girard
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,CIRAD, UMR ASTRE, Petit-Bourg, Guadeloupe, France
| | - Frédéric Stachurski
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,ASTRE, Université de Montpellier (I-MUSE), CIRAD, Institut National de la Recherche Agronomique, Montpellier, France
| | - Etienne Loire
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,ASTRE, Université de Montpellier (I-MUSE), CIRAD, Institut National de la Recherche Agronomique, Montpellier, France
| | - Nathalie Vachiéry
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,ASTRE, Université de Montpellier (I-MUSE), CIRAD, Institut National de la Recherche Agronomique, Montpellier, France.,CIRAD, UMR ASTRE, Petit-Bourg, Guadeloupe, France
| | - Philippe Holzmuller
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,ASTRE, Université de Montpellier (I-MUSE), CIRAD, Institut National de la Recherche Agronomique, Montpellier, France
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35
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Ellens KW, Christian N, Singh C, Satagopam VP, May P, Linster CL. Confronting the catalytic dark matter encoded by sequenced genomes. Nucleic Acids Res 2017; 45:11495-11514. [PMID: 29059321 PMCID: PMC5714238 DOI: 10.1093/nar/gkx937] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 10/03/2017] [Indexed: 01/02/2023] Open
Abstract
The post-genomic era has provided researchers with a deluge of protein sequences. However, a significant fraction of the proteins encoded by sequenced genomes remains without an identified function. Here, we aim at determining how many enzymes of uncertain or unknown function are still present in the Saccharomyces cerevisiae and human proteomes. Using information available in the Swiss-Prot, BRENDA and KEGG databases in combination with a Hidden Markov Model-based method, we estimate that >600 yeast and 2000 human proteins (>30% of their proteins of unknown function) are enzymes whose precise function(s) remain(s) to be determined. This illustrates the impressive scale of the ‘unknown enzyme problem’. We extensively review classical biochemical as well as more recent systematic experimental and computational approaches that can be used to support enzyme function discovery research. Finally, we discuss the possible roles of the elusive catalysts in light of recent developments in the fields of enzymology and metabolism as well as the significance of the unknown enzyme problem in the context of metabolic modeling, metabolic engineering and rare disease research.
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Affiliation(s)
- Kenneth W Ellens
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Nils Christian
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Charandeep Singh
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Venkata P Satagopam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
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36
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Cryar A, Groves K, Quaglia M. Online Hydrogen-Deuterium Exchange Traveling Wave Ion Mobility Mass Spectrometry (HDX-IM-MS): a Systematic Evaluation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1192-1202. [PMID: 28374315 PMCID: PMC5438439 DOI: 10.1007/s13361-017-1633-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/17/2017] [Accepted: 02/18/2017] [Indexed: 05/11/2023]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is an important tool for measuring and monitoring protein structure. A bottom-up approach to HDX-MS provides peptide level deuterium uptake values and a more refined localization of deuterium incorporation compared with global HDX-MS measurements. The degree of localization provided by HDX-MS is proportional to the number of peptides that can be identified and monitored across an exchange experiment. Ion mobility spectrometry (IMS) has been shown to improve MS-based peptide analysis of biological samples through increased separation capacity. The integration of IMS within HDX-MS workflows has been commercialized but presently its adoption has not been widespread. The potential benefits of IMS, therefore, have not yet been fully explored. We herein describe a comprehensive evaluation of traveling wave ion mobility integrated within an online-HDX-MS system and present the first reported example of UDMSE acquisition for HDX analysis. Instrument settings required for optimal peptide identifications are described and the effects of detector saturation due to peak compression are discussed. A model system is utilized to confirm the comparability of HDX-IM-MS and HDX-MS uptake values prior to an evaluation of the benefits of IMS at increasing sample complexity. Interestingly, MS and IM-MS acquisitions were found to identify distinct populations of peptides that were unique to the respective methods, a property that can be utilized to increase the spatial resolution of HDX-MS experiments by >60%. Graphical Abstract ᅟ.
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Affiliation(s)
- Adam Cryar
- LGC, Queens Road, Teddington, London, TW11 0LY, UK.
| | - Kate Groves
- LGC, Queens Road, Teddington, London, TW11 0LY, UK
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37
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Wang H, Yan L, Huang H, Ding C. From Protein Sequence to Protein Function via Multi-Label Linear Discriminant Analysis. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017; 14:503-513. [PMID: 27429445 DOI: 10.1109/tcbb.2016.2591529] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Sequence describes the primary structure of a protein, which contains important structural, characteristic, and genetic information and thereby motivates many sequence-based computational approaches to infer protein function. Among them, feature-base approaches attract increased attention because they make prediction from a set of transformed and more biologically meaningful sequence features. However, original features extracted from sequence are usually of high dimensionality and often compromised by irrelevant patterns, therefore dimension reduction is necessary prior to classification for efficient and effective protein function prediction. A protein usually performs several different functions within an organism, which makes protein function prediction a multi-label classification problem. In machine learning, multi-label classification deals with problems where each object may belong to more than one class. As a well-known feature reduction method, linear discriminant analysis (LDA) has been successfully applied in many practical applications. It, however, by nature is designed for single-label classification, in which each object can belong to exactly one class. Because directly applying LDA in multi-label classification causes ambiguity when computing scatters matrices, we apply a new Multi-label Linear Discriminant Analysis (MLDA) approach to address this problem and meanwhile preserve powerful classification capability inherited from classical LDA. We further extend MLDA by l1-normalization to overcome the problem of over-counting data points with multiple labels. In addition, we incorporate biological network data using Laplacian embedding into our method, and assess the reliability of predicted putative functions. Extensive empirical evaluations demonstrate promising results of our methods.
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38
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Kim KJ, Kim YW, Park HG, Hwang CH, Park IY, Choi KY, Yang YH, Kim YH, Kim YG. A MALDI-MS-based quantitative glycoprofiling method on a 96-well plate platform. J IND ENG CHEM 2017. [DOI: 10.1016/j.jiec.2016.10.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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39
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Sharma A, Sharma D, Verma SK. Proteome wide identification of iron binding proteins of Xanthomonas translucens pv. undulosa: focus on secretory virulent proteins. Biometals 2017; 30:127-141. [DOI: 10.1007/s10534-017-9991-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 01/08/2017] [Indexed: 12/19/2022]
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40
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In-silico prediction of dual function of DksA like hypothetical protein in V. cholerae O395 genome. Microbiol Res 2017; 195:60-70. [DOI: 10.1016/j.micres.2016.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 11/04/2016] [Accepted: 11/05/2016] [Indexed: 11/20/2022]
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41
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Abstract
Surveys of public sequence resources show that experimentally supported functional information is still completely missing for a considerable fraction of known proteins and is clearly incomplete for an even larger portion. Bioinformatics methods have long made use of very diverse data sources alone or in combination to predict protein function, with the understanding that different data types help elucidate complementary biological roles. This chapter focuses on methods accepting amino acid sequences as input and producing GO term assignments directly as outputs; the relevant biological and computational concepts are presented along with the advantages and limitations of individual approaches.
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Affiliation(s)
- Domenico Cozzetto
- Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK
| | - David T Jones
- Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK.
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42
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Abstract
Protein function is a concept that can have different interpretations in different biological contexts, and the number and diversity of novel proteins identified by large-scale "omics" technologies poses increasingly new challenges. In this review we explore current strategies used to predict protein function focused on high-throughput sequence analysis, as for example, inference based on sequence similarity, sequence composition, structure, and protein-protein interaction. Various prediction strategies are discussed together with illustrative workflows highlighting the use of some benchmark tools and knowledge bases in the field.
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Affiliation(s)
- Leonardo Magalhães Cruz
- Department of Biochemistry and Molecular Biology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil.
- Sector of Professional and Technological Education, Federal University of Paraná (UFPR), Curitiba, PR, Brazil.
| | - Sheyla Trefflich
- Sector of Professional and Technological Education, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Vinícius Almir Weiss
- Sector of Professional and Technological Education, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Mauro Antônio Alves Castro
- Sector of Professional and Technological Education, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
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Wang L, Fu H, Nanayakkara G, Li Y, Shao Y, Johnson C, Cheng J, Yang WY, Yang F, Lavallee M, Xu Y, Cheng X, Xi H, Yi J, Yu J, Choi ET, Wang H, Yang X. Novel extracellular and nuclear caspase-1 and inflammasomes propagate inflammation and regulate gene expression: a comprehensive database mining study. J Hematol Oncol 2016; 9:122. [PMID: 27842563 PMCID: PMC5109738 DOI: 10.1186/s13045-016-0351-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/03/2016] [Indexed: 12/19/2022] Open
Abstract
Background Caspase-1 is present in the cytosol as an inactive zymogen and requires the protein complexes named “inflammasomes” for proteolytic activation. However, it remains unclear whether the proteolytic activity of caspase-1 is confined only to the cytosol where inflammasomes are assembled to convert inactive pro-caspase-1 to active caspase-1. Methods We conducted meticulous data analysis methods on proteomic, protein interaction, protein intracellular localization, and gene expressions of 114 experimentally identified caspase-1 substrates and 38 caspase-1 interaction proteins in normal physiological conditions and in various pathologies. Results We made the following important findings: (1) Caspase-1 substrates and interaction proteins are localized in various intracellular organelles including nucleus and secreted extracellularly; (2) Caspase-1 may get activated in situ in the nucleus in response to intra-nuclear danger signals; (3) Caspase-1 cleaves its substrates in exocytotic secretory pathways including exosomes to propagate inflammation to neighboring and remote cells; (4) Most of caspase-1 substrates are upregulated in coronary artery disease regardless of their subcellular localization but the majority of metabolic diseases cause no significant expression changes in caspase-1 nuclear substrates; and (5) In coronary artery disease, majority of upregulated caspase-1 extracellular substrate-related pathways are involved in induction of inflammation; and in contrast, upregulated caspase-1 nuclear substrate-related pathways are more involved in regulating cell death and chromatin regulation. Conclusions Our identification of novel caspase-1 trafficking sites, nuclear and extracellular inflammasomes, and extracellular caspase-1-based inflammation propagation model provides a list of targets for the future development of new therapeutics to treat cardiovascular diseases, inflammatory diseases, and inflammatory cancers. Electronic supplementary material The online version of this article (doi:10.1186/s13045-016-0351-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luqiao Wang
- Centers for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA.,Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, Jiangxi, 330006, China
| | - Hangfei Fu
- Centers for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA
| | - Gayani Nanayakkara
- Centers for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA
| | - Yafeng Li
- Centers for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA
| | - Ying Shao
- Centers for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA
| | - Candice Johnson
- Centers for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA
| | - Jiali Cheng
- Centers for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA
| | - William Y Yang
- Centers for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA
| | - Fan Yang
- Centers for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA
| | - Muriel Lavallee
- Centers for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA
| | - Yanjie Xu
- Centers for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA.,Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, Jiangxi, 330006, China
| | - Xiaoshu Cheng
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, Jiangxi, 330006, China
| | - Hang Xi
- Centers for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA
| | - Jonathan Yi
- Centers for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA
| | - Jun Yu
- Centers for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA.,Department of Pharmacology, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA
| | - Eric T Choi
- Centers for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA.,Department of Surgery, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA
| | - Hong Wang
- Centers for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA.,Department of Pharmacology, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA
| | - Xiaofeng Yang
- Centers for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA. .,Cardiovascular Research and Thrombosis Research, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA. .,Department of Pharmacology, Lewis Katz School of Medicine at Temple University, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA. .,Department of Physiology, 3500 North Broad Street, MERB-1059, Philadelphia, PA, 19140, USA.
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44
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Li L, Faucher SP. The Membrane Protein LasM Promotes the Culturability of Legionella pneumophila in Water. Front Cell Infect Microbiol 2016; 6:113. [PMID: 27734007 PMCID: PMC5039212 DOI: 10.3389/fcimb.2016.00113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/12/2016] [Indexed: 11/13/2022] Open
Abstract
The water-borne pathogen Legionella pneumophila (Lp) strongly expresses the lpg1659 gene in water. This gene encodes a hypothetical protein predicted to be a membrane protein using in silico analysis. While no conserved domains were identified in Lpg1659, similar proteins are found in many Legionella species and other aquatic bacteria. RT-qPCR showed that lpg1659 is positively regulated by the alternative sigma factor RpoS, which is essential for Lp to survive in water. These observations suggest an important role of this novel protein in the survival of Lp in water. Deletion of lpg1659 did not affect cell morphology, membrane integrity or tolerance to high temperature. Moreover, lpg1659 was dispensable for growth of Lp in rich medium, and during infection of the amoeba Acanthamoeba castellanii and of THP-1 human macrophages. However, deletion of lpg1659 resulted in an early loss of culturability in water, while over-expression of this gene promoted the culturability of Lp. Therefore, these results suggest that lpg1659 is required for Lp to maintain culturability, and possibly long-term survival, in water. Since the loss of culturability observed in the absence of Lpg1659 was complemented by the addition of trace metals into water, this membrane protein is likely a transporter for acquiring essential trace metal for maintaining culturability in water and potentially in other metal-deprived conditions. Given its role in the survival of Lp in water, Lpg1659 was named LasM for Legionella aquatic survival membrane protein.
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Affiliation(s)
- Laam Li
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University Montreal, QC, Canada
| | - Sébastien P Faucher
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University Montreal, QC, Canada
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45
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Aoki JI, Coelho AC, Muxel SM, Zampieri RA, Sanchez EMR, Nerland AH, Floeter-Winter LM, Cotrim PC. Characterization of a Novel Endoplasmic Reticulum Protein Involved in Tubercidin Resistance in Leishmania major. PLoS Negl Trop Dis 2016; 10:e0004972. [PMID: 27606425 PMCID: PMC5015992 DOI: 10.1371/journal.pntd.0004972] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 08/11/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Tubercidin (TUB) is a toxic adenosine analog with potential antiparasitic activity against Leishmania, with mechanism of action and resistance that are not completely understood. For understanding the mechanisms of action and identifying the potential metabolic pathways affected by this drug, we employed in this study an overexpression/selection approach using TUB for the identification of potential targets, as well as, drug resistance genes in L. major. Although, TUB is toxic to the mammalian host, these findings can provide evidences for a rational drug design based on purine pathway against leishmaniasis. METHODOLOGY/PRINCIPAL FINDINGS After transfection of a cosmid genomic library into L. major Friedlin (LmjF) parasites and application of the overexpression/selection method, we identified two cosmids (cosTUB1 and cosTU2) containing two different loci capable of conferring significant levels of TUB resistance. In the cosTUB1 contained a gene encoding NUPM1-like protein, which has been previously described as associated with TUB resistance in L. amazonensis. In the cosTUB2 we identified and characterized a gene encoding a 63 kDa protein that we denoted as tubercidin-resistance protein (TRP). Functional analysis revealed that the transfectants were less susceptible to TUB than LmjF parasites or those transfected with the control vector. In addition, the trp mRNA and protein levels in cosTUB2 transfectants were higher than LmjF. TRP immunolocalization revealed that it was co-localized to the endoplasmic reticulum (ER), a cellular compartment with many functions. In silico predictions indicated that TRP contains only a hypothetical transmembrane domain. Thus, it is likely that TRP is a lumen protein involved in multidrug efflux transport that may be involved in the purine metabolic pathway. CONCLUSIONS/SIGNIFICANCE This study demonstrated for the first time that TRP is associated with TUB resistance in Leishmania. The next challenge is to determine how TRP mediates TUB resistance and whether purine metabolism is affected by this protein in the parasite. Finally, these findings may be helpful for the development of alternative anti-leishmanial drugs that target purine pathway.
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Affiliation(s)
- Juliana Ide Aoki
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Adriano Cappellazzo Coelho
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Sandra Marcia Muxel
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Ricardo Andrade Zampieri
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | - Paulo Cesar Cotrim
- Instituto de Medicina Tropical, Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
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Cozzetto D, Minneci F, Currant H, Jones DT. FFPred 3: feature-based function prediction for all Gene Ontology domains. Sci Rep 2016; 6:31865. [PMID: 27561554 PMCID: PMC4999993 DOI: 10.1038/srep31865] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/25/2016] [Indexed: 11/09/2022] Open
Abstract
Predicting protein function has been a major goal of bioinformatics for several decades, and it has gained fresh momentum thanks to recent community-wide blind tests aimed at benchmarking available tools on a genomic scale. Sequence-based predictors, especially those performing homology-based transfers, remain the most popular but increasing understanding of their limitations has stimulated the development of complementary approaches, which mostly exploit machine learning. Here we present FFPred 3, which is intended for assigning Gene Ontology terms to human protein chains, when homology with characterized proteins can provide little aid. Predictions are made by scanning the input sequences against an array of Support Vector Machines (SVMs), each examining the relationship between protein function and biophysical attributes describing secondary structure, transmembrane helices, intrinsically disordered regions, signal peptides and other motifs. This update features a larger SVM library that extends its coverage to the cellular component sub-ontology for the first time, prompted by the establishment of a dedicated evaluation category within the Critical Assessment of Functional Annotation. The effectiveness of this approach is demonstrated through benchmarking experiments, and its usefulness is illustrated by analysing the potential functional consequences of alternative splicing in human and their relationship to patterns of biological features.
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Affiliation(s)
- Domenico Cozzetto
- Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK
| | - Federico Minneci
- Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK
| | - Hannah Currant
- Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK
| | - David T Jones
- Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK
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Dashti ZJS, Gamieldien J, Christoffels A. Computational characterization of Iron metabolism in the Tsetse disease vector, Glossina morsitans: IRE stem-loops. BMC Genomics 2016; 17:561. [PMID: 27503259 PMCID: PMC4977773 DOI: 10.1186/s12864-016-2932-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 07/12/2016] [Indexed: 11/29/2022] Open
Abstract
Background Iron metabolism and regulation is an indispensable part of species survival, most importantly for blood feeding insects. Iron regulatory proteins are central regulators of iron homeostasis, whose binding to iron response element (IRE) stem-loop structures within the UTRs of genes regulate expression at the post-transcriptional level. Despite the extensive literature on the mechanism of iron regulation in human, less attention has been given to insect and more specifically the blood feeding insects, where research has mainly focused on the characterization of ferritin and transferrin. We thus, examined the mechanism of iron homeostasis through a genome-wide computational identification of IREs and other enriched motifs in the UTRs of Glossina morsitans with the view to identify new IRE-regulated genes. Results We identified 150 genes, of which two are known to contain IREs, namely the ferritin heavy chain and the MRCK-alpha. The remainder of the identified genes is considered novel including 20 hypothetical proteins, for which an iron-regulatory mechanism of action was inferred. Forty-three genes were found with IRE-signatures of regulation in two or more insects, while 46 were only found to be IRE-regulated in two species. Notably 39 % of the identified genes exclusively shared IRE-signatures in other Glossina species, which are potentially Glossina-specific adaptive measures in addressing its unique reproductive biology and blood meal-induced iron overload. In line with previous findings, we found no evidence pertaining to an IRE regulation of Transferrin, which highlight the importance of ferritin heavy chain and the other proposed transporters in the tsetse fly. In the context of iron-sequestration, key players of tsetse immune defence against trypanosomes have been introduced namely 14 stress and immune response genes, while 28 cell-envelop, transport, and binding genes were assigned a putative role in iron trafficking. Additionally, we identified and annotated enriched motifs in the UTRs of the putative IRE-regulated genes to derive at a co-regulatory network that maintains iron homeostasis in tsetse flies. Three putative microRNA-binding sites namely Gy-box, Brd-box and K-box motifs were identified among the regulatory motifs, enriched in the UTRs of the putative IRE-regulated genes. Conclusion Beyond our current view of iron metabolism in insects, with ferritin and transferrin as its key players, this study provides a comprehensive catalogue of genes with possible roles in the acquisition; transport and storage of iron hence iron homeostasis in the tsetse fly. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2932-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zahra Jalali Sefid Dashti
- South African Medical Research Council Bioinformatics Unit, The South African National Bioinformatics Institute (SANBI), University of the Western Cape, Robert Sobukwe Street, Bellville, South Africa
| | - Junaid Gamieldien
- South African Medical Research Council Bioinformatics Unit, The South African National Bioinformatics Institute (SANBI), University of the Western Cape, Robert Sobukwe Street, Bellville, South Africa
| | - Alan Christoffels
- South African Medical Research Council Bioinformatics Unit, The South African National Bioinformatics Institute (SANBI), University of the Western Cape, Robert Sobukwe Street, Bellville, South Africa.
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48
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Li N, Pu Y, Gong Y, Yu Y, Ding H. Genomic location and expression analysis of expansin gene family reveals the evolutionary and functional significance in Triticum aestivum. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0446-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Discovery of Azurin-Like Anticancer Bacteriocins from Human Gut Microbiome through Homology Modeling and Molecular Docking against the Tumor Suppressor p53. BIOMED RESEARCH INTERNATIONAL 2016; 2016:8490482. [PMID: 27239476 PMCID: PMC4867070 DOI: 10.1155/2016/8490482] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 03/31/2016] [Accepted: 04/12/2016] [Indexed: 01/01/2023]
Abstract
Azurin from Pseudomonas aeruginosa is known anticancer bacteriocin, which can specifically penetrate human cancer cells and induce apoptosis. We hypothesized that pathogenic and commensal bacteria with long term residence in human body can produce azurin-like bacteriocins as a weapon against the invasion of cancers. In our previous work, putative bacteriocins have been screened from complete genomes of 66 dominant bacteria species in human gut microbiota and subsequently characterized by subjecting them as functional annotation algorithms with azurin as control. We have qualitatively predicted 14 putative bacteriocins that possessed functional properties very similar to those of azurin. In this work, we perform a number of quantitative and structure-based analyses including hydrophobic percentage calculation, structural modeling, and molecular docking study of bacteriocins of interest against protein p53, a cancer target. Finally, we have identified 8 putative bacteriocins that bind p53 in a same manner as p28-azurin and azurin, in which 3 peptides (p1seq16, p2seq20, and p3seq24) shared with our previous study and 5 novel ones (p1seq09, p2seq05, p2seq08, p3seq02, and p3seq17) discovered in the first time. These bacteriocins are suggested for further in vitro tests in different neoplastic line cells.
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Nuruzzaman M, Cao H, Xiu H, Luo T, Li J, Chen X, Luo J, Luo Z. Transcriptomics-based identification of WRKY genes and characterization of a salt and hormone-responsive PgWRKY1 gene in Panax ginseng. Acta Biochim Biophys Sin (Shanghai) 2016; 48:117-31. [PMID: 26685304 DOI: 10.1093/abbs/gmv122] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 08/30/2015] [Indexed: 12/23/2022] Open
Abstract
WRKY proteins belong to a transcription factor (TF) family and play dynamic roles in many plant processes, including plant responses to abiotic and biotic stresses, as well as secondary metabolism. However, no WRKY gene in Panax ginseng C.A. Meyer has been reported to date. In this study, a number of WRKY unigenes from methyl jasmonate (MeJA)-treated adventitious root transcriptome of this species were identified using next-generation sequencing technology. A total of 48 promising WRKY unigenes encoding WRKY proteins were obtained by eliminating wrong and incomplete open reading frame (ORF). Phylogenetic analysis reveals 48 WRKY TFs, including 11 Group I, 36 Group II, and 1 Group III. Moreover, one MeJA-responsive unigene designated as PgWRKY1 was cloned and characterized. It contains an entire ORF of 1077 bp and encodes a polypeptide of 358 amino acid residues. The PgWRKY1 protein contains a single WRKY domain consisting of a conserved amino acid sequence motif WRKYGQK and a C2H2-type zinc-finger motif belonging to WRKY subgroup II-d. Subcellular localization of PgWRKY1-GFP fusion protein in onion and tobacco epidermis cells revealed that PgWRKY1 was exclusively present in the nucleus. Quantitative real-time polymerase chain reaction analysis demonstrated that the expression of PgWRKY1 was relatively higher in roots and lateral roots compared with leaves, stems, and seeds. Importantly, PgWRKY1 expression was significantly induced by salicylic acid, abscisic acid, and NaCl, but downregulated by MeJA treatment. These results suggested that PgWRKY1 might be a multiple stress-inducible gene responding to hormones and salt stresses.
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Affiliation(s)
- Mohammed Nuruzzaman
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Hongzhe Cao
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Hao Xiu
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Tiao Luo
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Jijia Li
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Xianghui Chen
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Junli Luo
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Zhiyong Luo
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
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