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Gate T, Hill L, Miller AJ, Sanders D. AtIAR1 is a Zn transporter that regulates auxin metabolism in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1437-1450. [PMID: 37988591 PMCID: PMC10901206 DOI: 10.1093/jxb/erad468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 11/20/2023] [Indexed: 11/23/2023]
Abstract
Root growth in Arabidopsis is inhibited by exogenous auxin-amino acid conjugates, and mutants resistant to one such conjugate [indole-3-acetic acid (IAA)-Ala] map to a gene (AtIAR1) that is a member of a metal transporter family. Here, we test the hypothesis that AtIAR1 controls the hydrolysis of stored conjugated auxin to free auxin through zinc transport. AtIAR1 complements a yeast mutant sensitive to zinc, but not manganese- or iron-sensitive mutants, and the transporter is predicted to be localized to the endoplasmic reticulum/Golgi in plants. A previously identified Atiar1 mutant and a non-expressed T-DNA mutant both exhibit altered auxin metabolism, including decreased IAA-glucose conjugate levels in zinc-deficient conditions and insensitivity to the growth effect of exogenous IAA-Ala conjugates. At a high concentration of zinc, wild-type plants show a novel enhanced response to root growth inhibition by exogenous IAA-Ala which is disrupted in both Atiar1 mutants. Furthermore, both Atiar1 mutants show changes in auxin-related phenotypes, including lateral root density and hypocotyl length. The findings therefore suggest a role for AtIAR1 in controlling zinc release from the secretory system, where zinc homeostasis plays a key role in regulation of auxin metabolism and plant growth regulation.
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Affiliation(s)
- Thomas Gate
- Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, UK
| | - Lionel Hill
- Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, UK
| | - Anthony J Miller
- Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, UK
| | - Dale Sanders
- Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, UK
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2
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Puccio G, Ingraffia R, Giambalvo D, Frenda AS, Harkess A, Sunseri F, Mercati F. Exploring the genetic landscape of nitrogen uptake in durum wheat: genome-wide characterization and expression profiling of NPF and NRT2 gene families. FRONTIERS IN PLANT SCIENCE 2023; 14:1302337. [PMID: 38023895 PMCID: PMC10665861 DOI: 10.3389/fpls.2023.1302337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023]
Abstract
Nitrate uptake by plants primarily relies on two gene families: Nitrate transporter 1/peptide transporter (NPF) and Nitrate transporter 2 (NRT2). Here, we extensively characterized the NPF and NRT2 families in the durum wheat genome, revealing 211 NPF and 20 NRT2 genes. The two families share many Cis Regulatory Elements (CREs) and Transcription Factor binding sites, highlighting a partially overlapping regulatory system and suggesting a coordinated response for nitrate transport and utilization. Analyzing RNA-seq data from 9 tissues and 20 cultivars, we explored expression profiles and co-expression relationships of both gene families. We observed a strong correlation between nucleotide variation and gene expression within the NRT2 gene family, implicating a shared selection mechanism operating on both coding and regulatory regions. Furthermore, NPF genes showed highly tissue-specific expression profiles, while NRT2s were mainly divided in two co-expression modules, one expressed in roots (NAR2/NRT3 dependent) and the other induced in anthers and/ovaries during maturation. Our evidences confirmed that the majority of these genes were retained after small-scale duplication events, suggesting a neo- or sub-functionalization of many NPFs and NRT2s. Altogether, these findings indicate that the expansion of these gene families in durum wheat could provide valuable genetic variability useful to identify NUE-related and candidate genes for future breeding programs in the context of low-impact and sustainable agriculture.
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Affiliation(s)
- Guglielmo Puccio
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
- Institute of Biosciences and BioResources (IBBR), National Research Council, Palermo, Italy
| | - Rosolino Ingraffia
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
| | - Dario Giambalvo
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
| | - Alfonso S. Frenda
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Francesco Sunseri
- Institute of Biosciences and BioResources (IBBR), National Research Council, Palermo, Italy
- Department Agraria , University Mediterranea of Reggio Calabria, Reggio Calabria, Italy
| | - Francesco Mercati
- Institute of Biosciences and BioResources (IBBR), National Research Council, Palermo, Italy
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3
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Yue T, Wang Y, Zhang L, Gu C, Xue H, Wang W, Lyu Q, Dun Y. Deep Learning for Genomics: From Early Neural Nets to Modern Large Language Models. Int J Mol Sci 2023; 24:15858. [PMID: 37958843 PMCID: PMC10649223 DOI: 10.3390/ijms242115858] [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: 09/30/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
The data explosion driven by advancements in genomic research, such as high-throughput sequencing techniques, is constantly challenging conventional methods used in genomics. In parallel with the urgent demand for robust algorithms, deep learning has succeeded in various fields such as vision, speech, and text processing. Yet genomics entails unique challenges to deep learning, since we expect a superhuman intelligence that explores beyond our knowledge to interpret the genome from deep learning. A powerful deep learning model should rely on the insightful utilization of task-specific knowledge. In this paper, we briefly discuss the strengths of different deep learning models from a genomic perspective so as to fit each particular task with proper deep learning-based architecture, and we remark on practical considerations of developing deep learning architectures for genomics. We also provide a concise review of deep learning applications in various aspects of genomic research and point out current challenges and potential research directions for future genomics applications. We believe the collaborative use of ever-growing diverse data and the fast iteration of deep learning models will continue to contribute to the future of genomics.
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Affiliation(s)
- Tianwei Yue
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA; (Y.W.); (L.Z.); (W.W.)
| | - Yuanxin Wang
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA; (Y.W.); (L.Z.); (W.W.)
| | - Longxiang Zhang
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA; (Y.W.); (L.Z.); (W.W.)
| | - Chunming Gu
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21218, USA;
| | - Haoru Xue
- The Robotics Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA;
| | - Wenping Wang
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA; (Y.W.); (L.Z.); (W.W.)
| | - Qi Lyu
- Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI 48824, USA;
| | - Yujie Dun
- School of Information and Communications Engineering, Xi’an Jiaotong University, Xi’an 710049, China;
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4
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Záhonová K, Füssy Z, Stairs CW, Leger MM, Tachezy J, Čepička I, Roger AJ, Hampl V. Comparative analysis of mitochondrion-related organelles in anaerobic amoebozoans. Microb Genom 2023; 9. [PMID: 37994879 DOI: 10.1099/mgen.0.001143] [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] [Indexed: 11/24/2023] Open
Abstract
Archamoebae comprises free-living or endobiotic amoebiform protists that inhabit anaerobic or microaerophilic environments and possess mitochondrion-related organelles (MROs) adapted to function anaerobically. We compared in silico reconstructed MRO proteomes of eight species (six genera) and found that the common ancestor of Archamoebae possessed very few typical components of the protein translocation machinery, electron transport chain and tricarboxylic acid cycle. On the other hand, it contained a sulphate activation pathway and bacterial iron-sulphur (Fe-S) assembly system of MIS-type. The metabolic capacity of the MROs, however, varies markedly within this clade. The glycine cleavage system is widely conserved among Archamoebae, except in Entamoeba, probably owing to its role in catabolic function or one-carbon metabolism. MRO-based pyruvate metabolism was dispensed within subgroups Entamoebidae and Rhizomastixidae, whereas sulphate activation could have been lost in isolated cases of Rhizomastix libera, Mastigamoeba abducta and Endolimax sp. The MIS (Fe-S) assembly system was duplicated in the common ancestor of Mastigamoebidae and Pelomyxidae, and one of the copies took over Fe-S assembly in their MRO. In Entamoebidae and Rhizomastixidae, we hypothesize that Fe-S cluster assembly in both compartments may be facilitated by dual localization of the single system. We could not find evidence for changes in metabolic functions of the MRO in response to changes in habitat; it appears that such environmental drivers do not strongly affect MRO reduction in this group of eukaryotes.
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Affiliation(s)
- Kristína Záhonová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia
- Life Science Research Centre, Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Zoltán Füssy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Courtney W Stairs
- Centre for Comparative Genomics and Evolutionary Bioinformatics, and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Present address: Microbiology Research Group, Department of Biology, Lund University, Lund, Sweden
| | - Michelle M Leger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Present address: Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
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Guo B, Zhang J, Yang C, Dong L, Ye H, Valliyodan B, Nguyen HT, Song L. The Late Embryogenesis Abundant Proteins in Soybean: Identification, Expression Analysis, and the Roles of GmLEA4_19 in Drought Stress. Int J Mol Sci 2023; 24:14834. [PMID: 37834282 PMCID: PMC10573439 DOI: 10.3390/ijms241914834] [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: 09/07/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Late embryogenesis abundant (LEA) proteins play important roles in regulating plant growth and responses to various abiotic stresses. In this research, a genome-wide survey was conducted to recognize the LEA genes in Glycine max. A total of 74 GmLEA was identified and classified into nine subfamilies based on their conserved domains and the phylogenetic analysis. Subcellular localization, the duplication of genes, gene structure, the conserved motif, and the prediction of cis-regulatory elements and tissue expression pattern were then conducted to characterize GmLEAs. The expression profile analysis indicated that the expression of several GmLEAs was a response to drought and salt stress. The co-expression-based gene network analysis suggested that soybean LEA proteins may exert regulatory effects through the metabolic pathways. We further explored GnLEA4_19 function in Arabidopsis and the results suggests that overexpressed GmLEA4_19 in Arabidopsis increased plant height under mild or serious drought stress. Moreover, the overexpressed GmLEA4_19 soybean also showed a drought tolerance phenotype. These results indicated that GmLEA4_19 plays an important role in the tolerance to drought and will contribute to the development of the soybean transgenic with enhanced drought tolerance and better yield. Taken together, this study provided insight for better understanding the biological roles of LEA genes in soybean.
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Affiliation(s)
- Binhui Guo
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (B.G.); (J.Z.); (C.Y.); (L.D.)
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing 210014, China
| | - Jianhua Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (B.G.); (J.Z.); (C.Y.); (L.D.)
| | - Chunhong Yang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (B.G.); (J.Z.); (C.Y.); (L.D.)
| | - Lu Dong
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (B.G.); (J.Z.); (C.Y.); (L.D.)
| | - Heng Ye
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (H.Y.); (H.T.N.)
| | - Babu Valliyodan
- Department of Agriculture and Environmental Sciences, Lincoln University, Jefferson City, MO 65101, USA;
| | - Henry T. Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (H.Y.); (H.T.N.)
| | - Li Song
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (B.G.); (J.Z.); (C.Y.); (L.D.)
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing 210014, China
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6
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Sanyal SK, Awasthi M, Ranjan P, Sharma S, Pandey GK, Kateriya S. Characterization of Chlamydomonas voltage-gated calcium channel and its interaction with photoreceptor support VGCC modulated photobehavioral response in the green alga. Int J Biol Macromol 2023; 245:125492. [PMID: 37343610 DOI: 10.1016/j.ijbiomac.2023.125492] [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: 04/22/2023] [Revised: 06/09/2023] [Accepted: 06/18/2023] [Indexed: 06/23/2023]
Abstract
Calcium (Ca2+) signaling plays a major role in regulating multiple processes in living cells. The photoreceptor potential in Chlamydomonas triggers the generation of all or no flagellar Ca2+ currents that cause membrane depolarization across the eyespot and flagella. Modulation in membrane potential causes changes in the flagellar waveform, and hence, alters the beating patterns of Chlamydomonas flagella. The rhodopsin-mediated eyespot membrane potential is generated by the photoreceptor Ca2+ current or P-current however, the flagellar Ca2+ currents are mediated by unidentified voltage-gated calcium (VGCC or CaV) and potassium channels (VGKC). The voltage-gated ion channel that associates with ChRs to generate Ca2+ influx across the flagella and its cellular distribution has not yet been identified. Here, we identified putative VGCCs from algae and predicted their novel properties through insilico analysis. We further present experimental evidence on Chlamydomonas reinhardtii VGCCs to predict their novel physiological roles. Our experimental evidences showed that CrVGCC4 localizes to the eyespot and flagella of Chlamydomonas and associates with channelrhodopsins (ChRs). Further in silico interactome analysis of CrVGCCs suggested that they putatively interact with photoreceptor proteins, calcium signaling, and intraflagellar transport components. Expression analysis indicated that these VGCCs and their putative interactors can be perturbed by light stimuli. Collectively, our data suggest that VGCCs in general, and VGCC4 in particular, might be involved in the regulation of the photobehavioral response of Chlamydomonas.
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Affiliation(s)
- Sibaji K Sanyal
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Mayanka Awasthi
- Department of Biochemistry, the University of Delhi South Campus, New Delhi 110021, India
| | - Peeyush Ranjan
- Department of Biochemistry, the University of Delhi South Campus, New Delhi 110021, India
| | - Sunita Sharma
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Girdhar K Pandey
- Department of Plant Molecular Biology, the University of Delhi South Campus, New Delhi 110021, India.
| | - Suneel Kateriya
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; Department of Biochemistry, the University of Delhi South Campus, New Delhi 110021, India.
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7
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Reduced mitochondria provide an essential function for the cytosolic methionine cycle. Curr Biol 2022; 32:5057-5068.e5. [PMID: 36347252 PMCID: PMC9746703 DOI: 10.1016/j.cub.2022.10.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/15/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022]
Abstract
The loss of mitochondria in oxymonad protists has been associated with the redirection of the essential Fe-S cluster assembly to the cytosol. Yet as our knowledge of diverse free-living protists broadens, the list of functions of their mitochondrial-related organelles (MROs) expands. We revealed another such function in the closest oxymonad relative, Paratrimastix pyriformis, after we solved the proteome of its MRO with high accuracy, using localization of organelle proteins by isotope tagging (LOPIT). The newly assigned enzymes connect to the glycine cleavage system (GCS) and produce folate derivatives with one-carbon units and formate. These are likely to be used by the cytosolic methionine cycle involved in S-adenosyl methionine recycling. The data provide consistency with the presence of the GCS in MROs of free-living species and its absence in most endobionts, which typically lose the methionine cycle and, in the case of oxymonads, the mitochondria.
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8
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Hooper CM, Castleden IR, Tanz SK, Grasso SV, Millar AH. Subcellular Proteomics as a Unified Approach of Experimental Localizations and Computed Prediction Data for Arabidopsis and Crop Plants. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1346:67-89. [PMID: 35113396 DOI: 10.1007/978-3-030-80352-0_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In eukaryotic organisms, subcellular protein location is critical in defining protein function and understanding sub-functionalization of gene families. Some proteins have defined locations, whereas others have low specificity targeting and complex accumulation patterns. There is no single approach that can be considered entirely adequate for defining the in vivo location of all proteins. By combining evidence from different approaches, the strengths and weaknesses of different technologies can be estimated, and a location consensus can be built. The Subcellular Location of Proteins in Arabidopsis database ( http://suba.live/ ) combines experimental data sets that have been reported in the literature and is analyzing these data to provide useful tools for biologists to interpret their own data. Foremost among these tools is a consensus classifier (SUBAcon) that computes a proposed location for all proteins based on balancing the experimental evidence and predictions. Further tools analyze sets of proteins to define the abundance of cellular structures. Extending these types of resources to plant crop species has been complex due to polyploidy, gene family expansion and contraction, and the movement of pathways and processes within cells across the plant kingdom. The Crop Proteins of Annotated Location database ( http://crop-pal.org/ ) has developed a range of subcellular location resources including a species-specific voting consensus for 12 plant crop species that offers collated evidence and filters for current crop proteomes akin to SUBA. Comprehensive cross-species comparison of these data shows that the sub-cellular proteomes (subcellulomes) depend only to some degree on phylogenetic relationship and are more conserved in major biosynthesis than in metabolic pathways. Together SUBA and cropPAL created reference subcellulomes for plants as well as species-specific subcellulomes for cross-species data mining. These data collections are increasingly used by the research community to provide a subcellular protein location layer, inform models of compartmented cell function and protein-protein interaction network, guide future molecular crop breeding strategies, or simply answer a specific question-where is my protein of interest inside the cell?
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Affiliation(s)
- Cornelia M Hooper
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Ian R Castleden
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Sandra K Tanz
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Sally V Grasso
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - A Harvey Millar
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia.
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9
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González-Robles A, González-Lázaro M, Lagunes-Guillén AE, Omaña-Molina M, Lares-Jiménez LF, Lares-Villa F, Martínez-Palomo A. Ultrastructural, Cytochemical, and Comparative Genomic Evidence of Peroxisomes in Three Genera of Pathogenic Free-Living Amoebae, Including the First Morphological Data for the Presence of This Organelle in Heteroloboseans. Genome Biol Evol 2020; 12:1734-1750. [PMID: 32602891 PMCID: PMC7549135 DOI: 10.1093/gbe/evaa129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2020] [Indexed: 12/13/2022] Open
Abstract
Peroxisomes perform various metabolic processes that are primarily related to the elimination of reactive oxygen species and oxidative lipid metabolism. These organelles are present in all major eukaryotic lineages, nevertheless, information regarding the presence of peroxisomes in opportunistic parasitic protozoa is scarce and in many cases it is still unknown whether these organisms have peroxisomes at all. Here, we performed ultrastructural, cytochemical, and bioinformatic studies to investigate the presence of peroxisomes in three genera of free-living amoebae from two different taxonomic groups that are known to cause fatal infections in humans. By transmission electron microscopy, round structures with a granular content limited by a single membrane were observed in Acanthamoeba castellanii, Acanthamoeba griffini, Acanthamoeba polyphaga, Acanthamoeba royreba, Balamuthia mandrillaris (Amoebozoa), and Naegleria fowleri (Heterolobosea). Further confirmation for the presence of peroxisomes was obtained by treating trophozoites in situ with diaminobenzidine and hydrogen peroxide, which showed positive reaction products for the presence of catalase. We then performed comparative genomic analyses to identify predicted peroxin homologues in these organisms. Our results demonstrate that a complete set of peroxins-which are essential for peroxisome biogenesis, proliferation, and protein import-are present in all of these amoebae. Likewise, our in silico analyses allowed us to identify a complete set of peroxins in Naegleria lovaniensis and three novel peroxin homologues in Naegleria gruberi. Thus, our results indicate that peroxisomes are present in these three genera of free-living amoebae and that they have a similar peroxin complement despite belonging to different evolutionary lineages.
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Affiliation(s)
- Arturo González-Robles
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Mónica González-Lázaro
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Anel Edith Lagunes-Guillén
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Maritza Omaña-Molina
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlanepantla, Estado de México, Mexico
| | - Luis Fernando Lares-Jiménez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, Mexico
| | - Fernando Lares-Villa
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, Mexico
| | - Adolfo Martínez-Palomo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
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10
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Yadav AK, Singla D. VacPred: Sequence-based prediction of plant vacuole proteins using machine-learning techniques. J Biosci 2020. [DOI: 10.1007/s12038-020-00076-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Sudianto E, Chaw SM. Two Independent Plastid accD Transfers to the Nuclear Genome of Gnetum and Other Insights on Acetyl-CoA Carboxylase Evolution in Gymnosperms. Genome Biol Evol 2019; 11:1691-1705. [PMID: 30924880 PMCID: PMC6595918 DOI: 10.1093/gbe/evz059] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2019] [Indexed: 12/26/2022] Open
Abstract
Acetyl-CoA carboxylase (ACCase) is the key regulator of fatty acid biosynthesis. In most plants, ACCase exists in two locations (cytosol and plastids) and in two forms (homomeric and heteromeric). Heteromeric ACCase comprises four subunits, three of them (ACCA-C) are nuclear encoded (nr) and the fourth (ACCD) is usually plastid encoded. Homomeric ACCase is encoded by a single nr-gene (ACC). We investigated the ACCase gene evolution in gymnosperms by examining the transcriptomes of newly sequenced Gnetum ula, combined with 75 transcriptomes and 110 plastomes of other gymnosperms. AccD-coding sequences are elongated through the insertion of repetitive DNA in four out of five cupressophyte families (except Sciadopityaceae) and were functionally transferred to the nucleus of gnetophytes and Sciadopitys. We discovered that, among the three genera of gnetophytes, only Gnetum has two copies of nr-accD. Furthermore, using protoplast transient expression assays, we experimentally verified that the nr-accD precursor proteins in Gnetum and Sciadopitys can be delivered to the plastids. Of the two nr-accD copies of Gnetum, one dually targets plastids and mitochondria, whereas the other potentially targets plastoglobuli. The distinct transit peptides, gene architectures, and flanking sequences between the two Gnetum accDs suggest that they have independent origins. Our findings are the first account of two distinctly targeted nr-accDs of any green plants and the most comprehensive analyses of ACCase evolution in gymnosperms to date.
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Affiliation(s)
- Edi Sudianto
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Battaglia ME, Martin MV, Lechner L, Martínez-Noël GMA, Salerno GL. The riddle of mitochondrial alkaline/neutral invertases: A novel Arabidopsis isoform mainly present in reproductive tissues and involved in root ROS production. PLoS One 2017; 12:e0185286. [PMID: 28945799 PMCID: PMC5612693 DOI: 10.1371/journal.pone.0185286] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/08/2017] [Indexed: 01/18/2023] Open
Abstract
Alkaline/neutral invertases (A/N-Inv), glucosidases that irreversibly hydrolyze sucrose into glucose and fructose, play significant roles in plant growth, development, and stress adaptation. They occur as multiple isoforms located in the cytosol or organelles. In Arabidopsis thaliana, two mitochondrial A/N-Inv genes (A/N-InvA and A/N-InvC) have already been investigated. In this study, we functionally characterized A/N-InvH, a third Arabidopsis gene coding for a mitochondrial-targeted protein. The phenotypic analysis of knockout mutant plants (invh) showed a severely reduced shoot growth, while root development was not affected. The emergence of the first floral bud and the opening of the first flower were the most affected stages, presenting a significant delay. A/N-InvH transcription is markedly active in reproductive tissues. It is also expressed in the elongation and apical meristem root zones. Our results show that A/N-InvH expression is not evident in photosynthetic tissues, despite being of relevance in developmental processes and mitochondrial functional status. NaCl and mannitol treatments increased A/N-InvH expression twofold in the columella root cap. Moreover, the absence of A/N-InvH prevented ROS formation, not only in invh roots of salt- and ABA-treated seedlings but also in invh control roots. We hypothesize that this isoform may take part in the ROS/sugar (sucrose or its hydrolysis products) signaling pathway network, involved in reproductive tissue development, cell elongation, and abiotic stress responses.
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Affiliation(s)
- Marina E. Battaglia
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Mar del Plata, Argentina
| | - María Victoria Martin
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Mar del Plata, Argentina
| | - Leandra Lechner
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Mar del Plata, Argentina
| | - Giselle M. A. Martínez-Noël
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Mar del Plata, Argentina
| | - Graciela L. Salerno
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Mar del Plata, Argentina
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Caló G, Scheidegger D, Martínez-Noël GMA, Salerno GL. Ancient signal for nitrogen status sensing in the green lineage: Functional evidence of CDPK repertoire in Ostreococcus tauri. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 118:377-384. [PMID: 28710945 DOI: 10.1016/j.plaphy.2017.07.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 07/07/2017] [Accepted: 07/07/2017] [Indexed: 05/08/2023]
Abstract
Calcium-dependent protein kinases (CDPKs) regulate plant development and many stress signalling pathways through the complex cytosolic [Ca2+] signalling. The genome of Ostreococcus tauri (Ot), a model prasinophyte organism that is on the base of the green lineage, harbours three sequences homologous to those encoding plant CDPKs with the three characteristic conserved domains (protein kinase, autoregulatory/autoinhibitory, and regulatory domain). Phylogenetic and structural analyses revealed that putative OtCDPK proteins are closely related to CDPKs from other Chlorophytes. We functionally characterised the first marine picophytoeukaryote CDPK gene (OtCDPK1) and showed that the expression of the three OtCDPK genes is up-regulated by nitrogen depletion. We conclude that CDPK signalling pathway might have originated early in the green lineage and may play a key role in prasinophytes by sensing macronutrient changes in the marine environment.
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Affiliation(s)
- Gonzalo Caló
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Centro de Investigaciones Biológicas, FIBA, 7600 Mar Del Plata, Argentina
| | - Dana Scheidegger
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Centro de Investigaciones Biológicas, FIBA, 7600 Mar Del Plata, Argentina
| | - Giselle M A Martínez-Noël
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Centro de Investigaciones Biológicas, FIBA, 7600 Mar Del Plata, Argentina
| | - Graciela L Salerno
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Centro de Investigaciones Biológicas, FIBA, 7600 Mar Del Plata, Argentina.
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14
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Liu TJ, Zhang CY, Yan HF, Zhang L, Ge XJ, Hao G. Complete plastid genome sequence of Primula sinensis (Primulaceae): structure comparison, sequence variation and evidence for accD transfer to nucleus. PeerJ 2016; 4:e2101. [PMID: 27375965 PMCID: PMC4928469 DOI: 10.7717/peerj.2101] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/10/2016] [Indexed: 11/22/2022] Open
Abstract
Species-rich genus Primula L. is a typical plant group with which to understand genetic variance between species in different levels of relationships. Chloroplast genome sequences are used to be the information resource for quantifying this difference and reconstructing evolutionary history. In this study, we reported the complete chloroplast genome sequence of Primula sinensis and compared it with other related species. This genome of chloroplast showed a typical circular quadripartite structure with 150,859 bp in sequence length consisting of 37.2% GC base. Two inverted repeated regions (25,535 bp) were separated by a large single-copy region (82,064 bp) and a small single-copy region (17,725 bp). The genome consists of 112 genes, including 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Among them, seven coding genes, seven tRNA genes and four rRNA genes have two copies due to their locations in the IR regions. The accD and infA genes lacking intact open reading frames (ORF) were identified as pseudogenes. SSR and sequence variation analyses were also performed on the plastome of Primula sinensis, comparing with another available plastome of P. poissonii. The four most variable regions, rpl36–rps8, rps16–trnQ, trnH–psbA and ndhC–trnV, were identified. Phylogenetic relationship estimates using three sub-datasets extracted from a matrix of 57 protein-coding gene sequences showed the identical result that was consistent with previous studies. A transcript found from P. sinensis transcriptome showed a high similarity to plastid accD functional region and was identified as a putative plastid transit peptide at the N-terminal region. The result strongly suggested that plastid accD has been functionally transferred to the nucleus in P. sinensis.
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Affiliation(s)
- Tong-Jian Liu
- College of Life Sciences, South China Agricultural University , Guangzhou , China
| | - Cai-Yun Zhang
- College of Life Sciences, South China Agricultural University , Guangzhou , China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou , China
| | - Lu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou , China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou , China
| | - Gang Hao
- College of Life Sciences, South China Agricultural University , Guangzhou , China
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15
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Jacoby RP, Millar AH, Taylor NL. Opportunities for wheat proteomics to discover the biomarkers for respiration-dependent biomass production, stress tolerance and cytoplasmic male sterility. J Proteomics 2016; 143:36-44. [DOI: 10.1016/j.jprot.2016.02.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 02/10/2016] [Accepted: 02/17/2016] [Indexed: 01/23/2023]
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16
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Lebrigand K, He LD, Thakur N, Arguel MJ, Polanowska J, Henrissat B, Record E, Magdelenat G, Barbe V, Raffaele S, Barbry P, Ewbank JJ. Comparative Genomic Analysis of Drechmeria coniospora Reveals Core and Specific Genetic Requirements for Fungal Endoparasitism of Nematodes. PLoS Genet 2016; 12:e1006017. [PMID: 27153332 PMCID: PMC4859500 DOI: 10.1371/journal.pgen.1006017] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 04/08/2016] [Indexed: 11/18/2022] Open
Abstract
Drechmeria coniospora is an obligate fungal pathogen that infects nematodes via the adhesion of specialized spores to the host cuticle. D. coniospora is frequently found associated with Caenorhabditis elegans in environmental samples. It is used in the study of the nematode's response to fungal infection. Full understanding of this bi-partite interaction requires knowledge of the pathogen's genome, analysis of its gene expression program and a capacity for genetic engineering. The acquisition of all three is reported here. A phylogenetic analysis placed D. coniospora close to the truffle parasite Tolypocladium ophioglossoides, and Hirsutella minnesotensis, another nematophagous fungus. Ascomycete nematopathogenicity is polyphyletic; D. coniospora represents a branch that has not been molecularly characterized. A detailed in silico functional analysis, comparing D. coniospora to 11 fungal species, revealed genes and gene families potentially involved in virulence and showed it to be a highly specialized pathogen. A targeted comparison with nematophagous fungi highlighted D. coniospora-specific genes and a core set of genes associated with nematode parasitism. A comparative gene expression analysis of samples from fungal spores and mycelia, and infected C. elegans, gave a molecular view of the different stages of the D. coniospora lifecycle. Transformation of D. coniospora allowed targeted gene knock-out and the production of fungus that expresses fluorescent reporter genes. It also permitted the initial characterisation of a potential fungal counter-defensive strategy, involving interference with a host antimicrobial mechanism. This high-quality annotated genome for D. coniospora gives insights into the evolution and virulence of nematode-destroying fungi. Coupled with genetic transformation, it opens the way for molecular dissection of D. coniospora physiology, and will allow both sides of the interaction between D. coniospora and C. elegans, as well as the evolutionary arms race that exists between pathogen and host, to be studied.
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Affiliation(s)
- Kevin Lebrigand
- CNRS and University Nice Sophia Antipolis, Institute of Molecular and Cellular Pharmacology, Sophia Antipolis, France
| | - Le D. He
- Centre d’Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280, Marseille, France
| | - Nishant Thakur
- Centre d’Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280, Marseille, France
| | - Marie-Jeanne Arguel
- CNRS and University Nice Sophia Antipolis, Institute of Molecular and Cellular Pharmacology, Sophia Antipolis, France
| | - Jolanta Polanowska
- Centre d’Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280, Marseille, France
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Eric Record
- INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, Polytech Marseille, CP 925, Marseille, France
- Aix-Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy-Polytech, CP 925, Marseille, France
| | - Ghislaine Magdelenat
- Commissariat à l'Energie Atomique, Institut de Génomique, Génoscope, Laboratoire de Biologie Moleculaire pour l'Etude des Génomes (LBioMEG), Evry, France
| | - Valérie Barbe
- Commissariat à l'Energie Atomique, Institut de Génomique, Génoscope, Laboratoire de Biologie Moleculaire pour l'Etude des Génomes (LBioMEG), Evry, France
| | - Sylvain Raffaele
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet Tolosan, France
| | - Pascal Barbry
- CNRS and University Nice Sophia Antipolis, Institute of Molecular and Cellular Pharmacology, Sophia Antipolis, France
- * E-mail: (PB); (JJE)
| | - Jonathan J. Ewbank
- Centre d’Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280, Marseille, France
- * E-mail: (PB); (JJE)
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17
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Zámbó V, Tóth M, Schlachter K, Szelényi P, Sarnyai F, Lotz G, Csala M, Kereszturi É. Cytosolic localization of NADH cytochrome b₅ oxidoreductase (Ncb5or). FEBS Lett 2016; 590:661-71. [PMID: 26878259 DOI: 10.1002/1873-3468.12097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 01/29/2016] [Accepted: 02/04/2016] [Indexed: 11/10/2022]
Abstract
Acyl-CoA desaturation in the endoplasmic reticulum (ER) membrane depends on cytosolic NADH or NADPH, whereas NADPH in the ER lumen is utilized by prereceptor glucocorticoid production. It was assumed that NADH cytochrome b5 oxidoreductase (Ncb5or) might connect Acyl-CoA desaturation to ER luminal redox. We aimed to clarify the ambiguous compartmentalization of Ncb5or and test the possible effect of stearoyl-CoA on microsomal NADPH level. Amino acid sequence analysis, fluorescence microscopy of GFP-tagged protein, immunocytochemistry, and western blot analysis of subcellular fractions unequivocally demonstrated that Ncb5or, either endogenous or exogenous, is localized in the cytoplasm and not in the ER lumen in cultured cells and liver tissue. Moreover, the involvement of ER-luminal reducing equivalents in stearoyl-CoA desaturation was excluded.
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Affiliation(s)
- Veronika Zámbó
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Mónika Tóth
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | | | - Péter Szelényi
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Farkas Sarnyai
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Gábor Lotz
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Miklós Csala
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Éva Kereszturi
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
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18
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Evolution of short inverted repeat in cupressophytes, transfer of accD to nucleus in Sciadopitys verticillata and phylogenetic position of Sciadopityaceae. Sci Rep 2016; 6:20934. [PMID: 26865528 PMCID: PMC4750060 DOI: 10.1038/srep20934] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/13/2016] [Indexed: 12/31/2022] Open
Abstract
Sciadopitys verticillata is an evergreen conifer and an economically valuable tree used in construction, which is the only member of the family Sciadopityaceae. Acquisition of the S. verticillata chloroplast (cp) genome will be useful for understanding the evolutionary mechanism of conifers and phylogenetic relationships among gymnosperm. In this study, we have first reported the complete chloroplast genome of S. verticillata. The total genome is 138,284 bp in length, consisting of 118 unique genes. The S. verticillata cp genome has lost one copy of the canonical inverted repeats and shown distinctive genomic structure comparing with other cupressophytes. Fifty-three simple sequence repeat loci and 18 forward tandem repeats were identified in the S. verticillata cp genome. According to the rearrangement of cupressophyte cp genome, we proposed one mechanism for the formation of inverted repeat: tandem repeat occured first, then rearrangement divided the tandem repeat into inverted repeats located at different regions. Phylogenetic estimates inferred from 59-gene sequences and cpDNA organizations have both shown that S. verticillata was sister to the clade consisting of Cupressaceae, Taxaceae, and Cephalotaxaceae. Moreover, accD gene was found to be lost in the S. verticillata cp genome, and a nucleus copy was identified from two transcriptome data.
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Hooper CM, Castleden IR, Aryamanesh N, Jacoby RP, Millar AH. Finding the Subcellular Location of Barley, Wheat, Rice and Maize Proteins: The Compendium of Crop Proteins with Annotated Locations (cropPAL). PLANT & CELL PHYSIOLOGY 2016; 57:e9. [PMID: 26556651 DOI: 10.1093/pcp/pcv170] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/27/2015] [Indexed: 05/10/2023]
Abstract
Barley, wheat, rice and maize provide the bulk of human nutrition and have extensive industrial use as agricultural products. The genomes of these crops each contains >40,000 genes encoding proteins; however, the major genome databases for these species lack annotation information of protein subcellular location for >80% of these gene products. We address this gap, by constructing the compendium of crop protein subcellular locations called crop Proteins with Annotated Locations (cropPAL). Subcellular location is most commonly determined by fluorescent protein tagging of live cells or mass spectrometry detection in subcellular purifications, but can also be predicted from amino acid sequence or protein expression patterns. The cropPAL database collates 556 published studies, from >300 research institutes in >30 countries that have been previously published, as well as compiling eight pre-computed subcellular predictions for all Hordeum vulgare, Triticum aestivum, Oryza sativa and Zea mays protein sequences. The data collection including metadata for proteins and published studies can be accessed through a search portal http://crop-PAL.org. The subcellular localization information housed in cropPAL helps to depict plant cells as compartmentalized protein networks that can be investigated for improving crop yield and quality, and developing new biotechnological solutions to agricultural challenges.
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Affiliation(s)
- Cornelia M Hooper
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009, Australia
| | - Ian R Castleden
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009, Australia
| | - Nader Aryamanesh
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009, Australia
| | - Richard P Jacoby
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009, Australia
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20
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Siehl DL, Tao Y, Albert H, Dong Y, Heckert M, Madrigal A, Lincoln-Cabatu B, Lu J, Fenwick T, Bermudez E, Sandoval M, Horn C, Green JM, Hale T, Pagano P, Clark J, Udranszky IA, Rizzo N, Bourett T, Howard RJ, Johnson DH, Vogt M, Akinsola G, Castle LA. Broad 4-hydroxyphenylpyruvate dioxygenase inhibitor herbicide tolerance in soybean with an optimized enzyme and expression cassette. PLANT PHYSIOLOGY 2014; 166:1162-76. [PMID: 25192697 PMCID: PMC4226376 DOI: 10.1104/pp.114.247205] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 08/23/2014] [Indexed: 05/04/2023]
Abstract
With an optimized expression cassette consisting of the soybean (Glycine max) native promoter modified for enhanced expression driving a chimeric gene coding for the soybean native amino-terminal 86 amino acids fused to an insensitive shuffled variant of maize (Zea mays) 4-hydroxyphenylpyruvate dioxygenase (HPPD), we achieved field tolerance in transgenic soybean plants to the HPPD-inhibiting herbicides mesotrione, isoxaflutole, and tembotrione. Directed evolution of maize HPPD was accomplished by progressively incorporating amino acids from naturally occurring diversity and novel substitutions identified by saturation mutagenesis, combined at random through shuffling. Localization of heterologously expressed HPPD mimicked that of the native enzyme, which was shown to be dually targeted to chloroplasts and the cytosol. Analysis of the native soybean HPPD gene revealed two transcription start sites, leading to transcripts encoding two HPPD polypeptides. The N-terminal region of the longer encoded peptide directs proteins to the chloroplast, while the short form remains in the cytosol. In contrast, maize HPPD was found almost exclusively in chloroplasts. Evolved HPPD enzymes showed insensitivity to five inhibitor herbicides. In 2013 field trials, transgenic soybean events made with optimized promoter and HPPD variant expression cassettes were tested with three herbicides and showed tolerance to four times the labeled rates of mesotrione and isoxaflutole and two times the labeled rates of tembotrione.
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Affiliation(s)
- Daniel L Siehl
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Yumin Tao
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Henrik Albert
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Yuxia Dong
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Matthew Heckert
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Alfredo Madrigal
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Brishette Lincoln-Cabatu
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Jian Lu
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Tamara Fenwick
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Ericka Bermudez
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Marian Sandoval
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Caroline Horn
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Jerry M Green
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Theresa Hale
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Peggy Pagano
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Jenna Clark
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Ingrid A Udranszky
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Nancy Rizzo
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Timothy Bourett
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Richard J Howard
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - David H Johnson
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Mark Vogt
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Goke Akinsola
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
| | - Linda A Castle
- DuPont Pioneer, Hayward, California 94545 (D.L.S., Y.T., H.A., Y.D., M.H., A.M., B.L.-C., J.L., T.F., E.B., M.S., C.H., I.A.U., L.A.C.);DuPont Stein-Haskell Research Center, Newark, Delaware 19711 (J.M.G., T.H., P.P., J.C.);DuPont Experimental Station, Wilmington, Delaware 19803 (N.R., T.B., R.J.H.); andDuPont Pioneer, Johnston, Iowa 50131 (D.H.J., M.V., G.A.)
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21
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Cristancho MA, Botero-Rozo DO, Giraldo W, Tabima J, Riaño-Pachón DM, Escobar C, Rozo Y, Rivera LF, Durán A, Restrepo S, Eilam T, Anikster Y, Gaitán AL. Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales. FRONTIERS IN PLANT SCIENCE 2014; 5:594. [PMID: 25400655 PMCID: PMC4215621 DOI: 10.3389/fpls.2014.00594] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 10/11/2014] [Indexed: 05/20/2023]
Abstract
Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333 Mb was built based on the 8 isolates; this assembly was used for subsequent analyses. Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3921 families were uncovered; a considerable proportion of the predicted proteins (73.8%) were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish races/isolates.
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Affiliation(s)
- Marco A. Cristancho
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
- *Correspondence: Marco A. Cristancho, Department of Plant Pathology, National Center for Coffee Research – CENICAFÉ, Km 4 vía a Manizales, Chinchiná 2427, Colombia e-mail:
| | - David Octavio Botero-Rozo
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
- Departamento de Ciencias Biológicas, Universidad de los AndesBogotá, Colombia
| | - William Giraldo
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Javier Tabima
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
- Departamento de Ciencias Biológicas, Universidad de los AndesBogotá, Colombia
| | | | - Carolina Escobar
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Yomara Rozo
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Luis F. Rivera
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Andrés Durán
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Silvia Restrepo
- Departamento de Ciencias Biológicas, Universidad de los AndesBogotá, Colombia
| | - Tamar Eilam
- Institute for Cereal Crops Improvement, Tel Aviv UniversityTel Aviv, Israel
| | - Yehoshua Anikster
- Institute for Cereal Crops Improvement, Tel Aviv UniversityTel Aviv, Israel
| | - Alvaro L. Gaitán
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
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22
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Narsai R, Devenish J, Castleden I, Narsai K, Xu L, Shou H, Whelan J. Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:1057-73. [PMID: 24147765 PMCID: PMC4253041 DOI: 10.1111/tpj.12357] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 09/30/2013] [Accepted: 10/04/2013] [Indexed: 05/04/2023]
Abstract
Omics research in Oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. We present Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. Rice DB has been designed to integrate the direct comparison of rice with Arabidopsis (Arabidopsis thaliana), based on orthology or 'expressology', thus using and combining available information from two pre-eminent plant models. To establish Rice DB, gene identifiers (more than 40 types) and annotations from a variety of sources were compiled, functional information based on large-scale and individual studies was manually collated, hundreds of microarrays were analysed to generate expression annotations, and the occurrences of potential functional regulatory motifs in promoter regions were calculated. A range of computational subcellular localization predictions were also run for all putative proteins encoded in the rice genome, and experimentally confirmed protein localizations have been collated, curated and linked to functional studies in rice. A single search box allows anything from gene identifiers (for rice and/or Arabidopsis), motif sequences, subcellular location, to keyword searches to be entered, with the capability of Boolean searches (such as AND/OR). To demonstrate the utility of Rice DB, several examples are presented including a rice mitochondrial proteome, which draws on a variety of sources for subcellular location data within Rice DB. Comparisons of subcellular location, functional annotations, as well as transcript expression in parallel with Arabidopsis reveals examples of conservation between rice and Arabidopsis, using Rice DB (http://ricedb.plantenergy.uwa.edu.au).
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Affiliation(s)
- Reena Narsai
- ARC Centre of Excellence in Plant Energy Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
- Centre for Computational Systems Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - James Devenish
- ARC Centre of Excellence in Plant Energy Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - Ian Castleden
- Centre for Computational Systems Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - Kabir Narsai
- ARC Centre of Excellence in Plant Energy Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - Lin Xu
- ARC Centre of Excellence in Plant Energy Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang UniversityHangzhou, 310058, China
| | - James Whelan
- ARC Centre of Excellence in Plant Energy Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
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23
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Li CR, Liang DD, Li J, Duan YB, Li H, Yang YC, Qin RY, Li L, Wei PC, Yang JB. Unravelling mitochondrial retrograde regulation in the abiotic stress induction of rice ALTERNATIVE OXIDASE 1 genes. PLANT, CELL & ENVIRONMENT 2013; 36:775-88. [PMID: 22994594 DOI: 10.1111/pce.12013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Mitochondrial retrograde regulation (MRR) is the transduction of mitochondrial signals to mediate nuclear gene expression. It is not clear whether MRR is a common regulation mechanism in plant abiotic stress response. In this study, we analysed the early abiotic stress response of the rice OsAOX1 genes, and the induction of OsAOX1a and OsAOX1b (OsAOX1a/b) was selected as a working model for the stress-induced MRR studies. We found that the induction mediated by the superoxide ion (O2·(-) )-generating chemical methyl viologen was stronger than that of hydrogen peroxide (H2 O2 ). The addition of reactive oxygen species (ROS) scavengers demonstrated that the stress induction was reduced by eliminating O2·(-) . Furthermore, the stress induction did not rely on chloroplast- or cytosol-derived O2·(-) . Next, we generated transgenic plants overexpressing the superoxide dismutase (SOD) gene at different subcellular locations. The results suggest that only the mitochondrial SOD, OsMSD, attenuated the stress induction of OsAOX1a/b specifically. Therefore, our findings demonstrate that abiotic stress initiates the MRR on OsAOX1a/b and that mitochondrial O2·(-) is involved in the process.
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Affiliation(s)
- Chun-Rong Li
- Institute of Rice Research, Anhui Academy of Agricultural Science, Hefei 230031, China
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24
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Rousseau-Gueutin M, Huang X, Higginson E, Ayliffe M, Day A, Timmis JN. Potential functional replacement of the plastidic acetyl-CoA carboxylase subunit (accD) gene by recent transfers to the nucleus in some angiosperm lineages. PLANT PHYSIOLOGY 2013; 161:1918-29. [PMID: 23435694 PMCID: PMC3613465 DOI: 10.1104/pp.113.214528] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Eukaryotic cells originated when an ancestor of the nucleated cell engulfed bacterial endosymbionts that gradually evolved into the mitochondrion and the chloroplast. Soon after these endosymbiotic events, thousands of ancestral prokaryotic genes were functionally transferred from the endosymbionts to the nucleus. This process of functional gene relocation, now rare in eukaryotes, continues in angiosperms. In this article, we show that the chloroplastic acetyl-CoA carboxylase subunit (accD) gene that is present in the plastome of most angiosperms has been functionally relocated to the nucleus in the Campanulaceae. Surprisingly, the nucleus-encoded accD transcript is considerably smaller than the plastidic version, consisting of little more than the carboxylase domain of the plastidic accD gene fused to a coding region encoding a plastid targeting peptide. We verified experimentally the presence of a chloroplastic transit peptide by showing that the product of the nuclear accD fused to green fluorescent protein was imported in the chloroplasts. The nuclear gene regulatory elements that enabled the erstwhile plastidic gene to become functional in the nuclear genome were identified, and the evolution of the intronic and exonic sequences in the nucleus is described. Relocation and truncation of the accD gene is a remarkable example of the processes underpinning endosymbiotic evolution.
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Affiliation(s)
- Mathieu Rousseau-Gueutin
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, South Australia 5005, Australia.
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25
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Tanz SK, Castleden I, Hooper CM, Vacher M, Small I, Millar HA. SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis. Nucleic Acids Res 2013; 41:D1185-91. [PMID: 23180787 PMCID: PMC3531127 DOI: 10.1093/nar/gks1151] [Citation(s) in RCA: 231] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 10/24/2012] [Accepted: 10/25/2012] [Indexed: 12/27/2022] Open
Abstract
The subcellular location database for Arabidopsis proteins (SUBA3, http://suba.plantenergy.uwa.edu.au) combines manual literature curation of large-scale subcellular proteomics, fluorescent protein visualization and protein-protein interaction (PPI) datasets with subcellular targeting calls from 22 prediction programs. More than 14 500 new experimental locations have been added since its first release in 2007. Overall, nearly 650 000 new calls of subcellular location for 35 388 non-redundant Arabidopsis proteins are included (almost six times the information in the previous SUBA version). A re-designed interface makes the SUBA3 site more intuitive and easier to use than earlier versions and provides powerful options to search for PPIs within the context of cell compartmentation. SUBA3 also includes detailed localization information for reference organelle datasets and incorporates green fluorescent protein (GFP) images for many proteins. To determine as objectively as possible where a particular protein is located, we have developed SUBAcon, a Bayesian approach that incorporates experimental localization and targeting prediction data to best estimate a protein's location in the cell. The probabilities of subcellular location for each protein are provided and displayed as a pictographic heat map of a plant cell in SUBA3.
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Affiliation(s)
- Sandra K. Tanz
- Centre of Excellence in Computational Systems Biology, ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis on Biomolecular Networks (CABiN), The University of Western Australia, Perth, WA 6009, Australia
| | - Ian Castleden
- Centre of Excellence in Computational Systems Biology, ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis on Biomolecular Networks (CABiN), The University of Western Australia, Perth, WA 6009, Australia
| | - Cornelia M. Hooper
- Centre of Excellence in Computational Systems Biology, ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis on Biomolecular Networks (CABiN), The University of Western Australia, Perth, WA 6009, Australia
| | - Michael Vacher
- Centre of Excellence in Computational Systems Biology, ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis on Biomolecular Networks (CABiN), The University of Western Australia, Perth, WA 6009, Australia
| | - Ian Small
- Centre of Excellence in Computational Systems Biology, ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis on Biomolecular Networks (CABiN), The University of Western Australia, Perth, WA 6009, Australia
| | - Harvey A. Millar
- Centre of Excellence in Computational Systems Biology, ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis on Biomolecular Networks (CABiN), The University of Western Australia, Perth, WA 6009, Australia
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26
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Artificial neural network for the prediction of tyrosine-based sorting signal recognition by adaptor complexes. J Biomed Biotechnol 2012; 2012:498031. [PMID: 22505811 PMCID: PMC3312419 DOI: 10.1155/2012/498031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 11/03/2011] [Indexed: 01/09/2023] Open
Abstract
Sorting of transmembrane proteins to various intracellular compartments depends on specific signals present within their cytosolic domains. Among these sorting signals, the tyrosine-based motif (YXXØ) is one of the best characterized and is recognized by μ-subunits of the four clathrin-associated adaptor complexes (AP-1 to AP-4). Despite their overlap in specificity, each μ-subunit has a distinct sequence preference dependent on the nature of the X-residues. Moreover, combinations of these residues exert cooperative or inhibitory effects towards interaction with the various APs. This complexity makes it impossible to predict a priori, the specificity of a given tyrosine-signal for a particular μ-subunit. Here, we describe the results obtained with a computational approach based on the Artificial Neural Network (ANN) paradigm that addresses the issue of tyrosine-signal specificity, enabling the prediction of YXXØ-μ interactions with accuracies over 90%. Therefore, this approach constitutes a powerful tool to help predict mechanisms of intracellular protein sorting.
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27
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Martínez-Turiño S, Hernández C. Analysis of the subcellular targeting of the smaller replicase protein of Pelargonium flower break virus. Virus Res 2012; 163:580-91. [PMID: 22222362 DOI: 10.1016/j.virusres.2011.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 12/13/2011] [Accepted: 12/16/2011] [Indexed: 12/30/2022]
Abstract
Replication of all positive RNA viruses occurs in association with intracellular membranes. In many cases, the mechanism of membrane targeting is unknown and there appears to be no correlation between virus phylogeny and the membrane systems recruited for replication. Pelargonium flower break virus (PFBV, genus Carmovirus, family Tombusviridae) encodes two proteins, p27 and its read-through product p86 (the viral RNA dependent-RNA polymerase), that are essential for replication. Recent reports with other members of the family Tombusviridae have shown that the smaller replicase protein is targeted to specific intracellular membranes and it is assumed to determine the subcellular localization of the replication complex. Using in vivo expression of green fluorescent protein (GFP) fusions in plant and yeast cells, we show here that PFBV p27 localizes in mitochondria. The same localization pattern was found for p86 that contains the p27 sequence at its N-terminus. Cellular fractionation of p27GFP-expressing cells confirmed the confocal microscopy observations and biochemical treatments suggested a tight association of the protein to membranes. Analysis of deletion mutants allowed identification of two regions required for targeting of p27 to mitochondria. These regions mapped toward the N- and C-terminus of the protein, respectively, and could function independently though with distinct efficiency. In an attempt to search for putative cellular factors involved in p27 localization, the subcellular distribution of the protein was checked in a selected series of knockout yeast strains and the outcome of this approach is discussed.
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Affiliation(s)
- Sandra Martínez-Turiño
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), Ciudad Politécnica de Innovación, Ed. 8E, Camino de Vera s/n, 46022 Valencia, Spain
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28
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Abstract
Many characterized fungal effector proteins are small secreted proteins. Effectors are defined as those proteins that alter host cell structure and/or function by facilitating pathogen infection. The identification of effectors by molecular and cell biology techniques is a difficult task. However, with the availability of whole-genome sequences, these proteins can now be predicted in silico. Here, we describe in detail how to identify and characterize effectors from a defined fungal proteome using in silico techniques.
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Affiliation(s)
- Ronnie de Jonge
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands.
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29
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Pervouchine DD, Khrameeva EE, Pichugina MY, Nikolaienko OV, Gelfand MS, Rubtsov PM, Mironov AA. Evidence for widespread association of mammalian splicing and conserved long-range RNA structures. RNA (NEW YORK, N.Y.) 2012; 18:1-15. [PMID: 22128342 PMCID: PMC3261731 DOI: 10.1261/rna.029249.111] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Pre-mRNA structure impacts many cellular processes, including splicing in genes associated with disease. The contemporary paradigm of RNA structure prediction is biased toward secondary structures that occur within short ranges of pre-mRNA, although long-range base-pairings are known to be at least as important. Recently, we developed an efficient method for detecting conserved RNA structures on the genome-wide scale, one that does not require multiple sequence alignments and works equally well for the detection of local and long-range base-pairings. Using an enhanced method that detects base-pairings at all possible combinations of splice sites within each gene, we now report RNA structures that could be involved in the regulation of splicing in mammals. Statistically, we demonstrate strong association between the occurrence of conserved RNA structures and alternative splicing, where local RNA structures are generally more frequent at alternative donor splice sites, while long-range structures are more associated with weak alternative acceptor splice sites. As an example, we validated the RNA structure in the human SF1 gene using minigenes in the HEK293 cell line. Point mutations that disrupted the base-pairing of two complementary boxes between exons 9 and 10 of this gene altered the splicing pattern, while the compensatory mutations that reestablished the base-pairing reverted splicing to that of the wild-type. There is statistical evidence for a Dscam-like class of mammalian genes, in which mutually exclusive RNA structures control mutually exclusive alternative splicing. In sum, we propose that long-range base-pairings carry an important, yet unconsidered part of the splicing code, and that, even by modest estimates, there must be thousands of such potentially regulatory structures conserved throughout the evolutionary history of mammals.
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Affiliation(s)
- Dmitri D Pervouchine
- Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, 119992, GSP-2 Russia.
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Mooney C, Wang YH, Pollastri G. SCLpred: protein subcellular localization prediction by N-to-1 neural networks. Bioinformatics 2011; 27:2812-9. [PMID: 21873639 DOI: 10.1093/bioinformatics/btr494] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
SUMMARY Knowledge of the subcellular location of a protein provides valuable information about its function and possible interaction with other proteins. In the post-genomic era, fast and accurate predictors of subcellular location are required if this abundance of sequence data is to be fully exploited. We have developed a subcellular localization predictor (SCLpred), which predicts the location of a protein into four classes for animals and fungi and five classes for plants (secreted, cytoplasm, nucleus, mitochondrion and chloroplast) using machine learning models trained on large non-redundant sets of protein sequences. The algorithm powering SCLpred is a novel Neural Network (N-to-1 Neural Network, or N1-NN) we have developed, which is capable of mapping whole sequences into single properties (a functional class, in this work) without resorting to predefined transformations, but rather by adaptively compressing the sequence into a hidden feature vector. We benchmark SCLpred against other publicly available predictors using two benchmarks including a new subset of Swiss-Prot Release 2010_06. We show that SCLpred surpasses the state of the art. The N1-NN algorithm is fully general and may be applied to a host of problems of similar shape, that is, in which a whole sequence needs to be mapped into a fixed-size array of properties, and the adaptive compression it operates may shed light on the space of protein sequences. AVAILABILITY The predictive systems described in this article are publicly available as a web server at http://distill.ucd.ie/distill/. CONTACT gianluca.pollastri@ucd.ie.
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Affiliation(s)
- Catherine Mooney
- School of Computer Science and Informatics, University College Dublin, Belfield, Ireland
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Delage L, Leblanc C, Nyvall Collén P, Gschloessl B, Oudot MP, Sterck L, Poulain J, Aury JM, Cock JM. In silico survey of the mitochondrial protein uptake and maturation systems in the brown alga Ectocarpus siliculosus. PLoS One 2011; 6:e19540. [PMID: 21611166 PMCID: PMC3097184 DOI: 10.1371/journal.pone.0019540] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 03/31/2011] [Indexed: 01/24/2023] Open
Abstract
The acquisition of mitochondria was a key event in eukaryote evolution. The aim of this study was to identify homologues of the components of the mitochondrial protein import machinery in the brown alga Ectocarpus and to use this information to investigate the evolutionary history of this fundamental cellular process. Detailed searches were carried out both for components of the protein import system and for related peptidases. Comparative and phylogenetic analyses were used to investigate the evolution of mitochondrial proteins during eukaryote diversification. Key observations include phylogenetic evidence for very ancient origins for many protein import components (Tim21, Tim50, for example) and indications of differences between the outer membrane receptors that recognize the mitochondrial targeting signals, suggesting replacement, rearrangement and/or emergence of new components across the major eukaryotic lineages. Overall, the mitochondrial protein import components analysed in this study confirmed a high level of conservation during evolution, indicating that most are derived from very ancient, ancestral proteins. Several of the protein import components identified in Ectocarpus, such as Tim21, Tim50 and metaxin, have also been found in other stramenopiles and this study suggests an early origin during the evolution of the eukaryotes.
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Affiliation(s)
- Ludovic Delage
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
| | - Catherine Leblanc
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
| | - Pi Nyvall Collén
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
| | - Bernhard Gschloessl
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
| | - Marie-Pierre Oudot
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lieven Sterck
- VIB Department of Plant Systems Biology, Ghent University, Ghent, Belgium
| | - Julie Poulain
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, Evry, France
- Centre National de la Recherche Scientifique, UMR 8030, Evry, France
- Université d'Evry, Evry, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, Evry, France
- Centre National de la Recherche Scientifique, UMR 8030, Evry, France
- Université d'Evry, Evry, France
| | - J. Mark Cock
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
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Bioinformatic identification of novel protein phosphatases in the dog genome. Mol Cell Biochem 2011; 351:149-56. [DOI: 10.1007/s11010-011-0722-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 01/05/2011] [Indexed: 12/17/2022]
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Mooney C, Wang YH, Pollastri G. De Novo Protein Subcellular Localization Prediction by N-to-1 Neural Networks. COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS 2011. [DOI: 10.1007/978-3-642-21946-7_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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In silico methods for identifying organellar and suborganellar targeting peptides in Arabidopsis chloroplast proteins and for predicting the topology of membrane proteins. Methods Mol Biol 2011; 774:243-80. [PMID: 21822844 DOI: 10.1007/978-1-61779-234-2_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Numerous experimental and in silico approaches have been developed for attempting to identify the -subcellular localisation of proteins. Approximately 2,000-4,000 proteins are thought to be targeted to plastids in plants, but a complete and unambiguous catalogue has yet to be drawn up. This article reviews the various prediction methods that identify plastid targeting sequences, and those that can help estimate location and topology within the plastid or plastid membranes. The most successful approaches are described in detail, with detailed notes to help avoid common pitfalls and advice on interpreting conflicting or ambiguous results. In most cases, it is best to try multiple approaches, and we also cover the powerful new integrated databases that provide a selected blend of experimental data and predictions.
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Choo KH, Tan TW, Ranganathan S. A comprehensive assessment of N-terminal signal peptides prediction methods. BMC Bioinformatics 2009; 10 Suppl 15:S2. [PMID: 19958512 PMCID: PMC2788353 DOI: 10.1186/1471-2105-10-s15-s2] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background Amino-terminal signal peptides (SPs) are short regions that guide the targeting of secretory proteins to the correct subcellular compartments in the cell. They are cleaved off upon the passenger protein reaching its destination. The explosive growth in sequencing technologies has led to the deposition of vast numbers of protein sequences necessitating rapid functional annotation techniques, with subcellular localization being a key feature. Of the myriad software prediction tools developed to automate the task of assigning the SP cleavage site of these new sequences, we review here, the performance and reliability of commonly used SP prediction tools. Results The available signal peptide data has been manually curated and organized into three datasets representing eukaryotes, Gram-positive and Gram-negative bacteria. These datasets are used to evaluate thirteen prediction tools that are publicly available. SignalP (both the HMM and ANN versions) maintains consistency and achieves the best overall accuracy in all three benchmarking experiments, ranging from 0.872 to 0.914 although other prediction tools are narrowing the performance gap. Conclusion The majority of the tools evaluated in this study encounter no difficulty in discriminating between secretory and non-secretory proteins. The challenge clearly remains with pinpointing the correct SP cleavage site. The composite scoring schemes employed by SignalP may help to explain its accuracy. Prediction task is divided into a number of separate steps, thus allowing each score to tackle a particular aspect of the prediction.
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Affiliation(s)
- Khar Heng Choo
- Institute for Infocomm Research, 1 Fusionopolis Way, #21-01 Connexis, Singapore.
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Armbruster U, Hertle A, Makarenko E, Zühlke J, Pribil M, Dietzmann A, Schliebner I, Aseeva E, Fenino E, Scharfenberg M, Voigt C, Leister D. Chloroplast proteins without cleavable transit peptides: rare exceptions or a major constituent of the chloroplast proteome? MOLECULAR PLANT 2009; 2:1325-35. [PMID: 19995733 DOI: 10.1093/mp/ssp082] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Most chloroplast proteins (cp proteins) are nucleus-encoded, synthesized on cytosolic ribosomes as precursor proteins containing a presequence (cTP), and post-translationally imported via the Tic/Toc complex into the organelle, where the cTP is removed. Only a few unambiguous instances of cp proteins that do not require cTPs (non-canonical cp proteins) have been reported so far. However, the survey of data from large-scale proteomic studies presented here suggests that the fraction of such proteins in the total cp proteome might be as large as approximately 30%. To explore this discrepancy, we chose a representative set of 28 putative non-canonical cp proteins, and used in vitro import and Red Fluorescent Protein (RFP)-fusion assays to determine their sub-cellular destinations. Four proteins, including embryo defective 1211, glycolate oxidase 2, protein disulfide isomerase-like protein (PDII), and a putative glutathione S-transferase, could be unambiguously assigned to the chloroplast. Several others ('potential cp proteins') were found to be imported into chloroplasts in vitro, but failed to localize to the organelle when RFP was fused to their C-terminal ends. Extrapolations suggest that the fraction of cp proteins that enter the inner compartments of the organelle, although they lack a cTP, might be as large as 11.4% of the total cp proteome. Our data also support the idea that cytosolic proteins that associate with the cp outer membrane might account for false positive cp proteins obtained in earlier studies.
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Affiliation(s)
- Ute Armbruster
- Lehrstuhl für Botanik, Department Biologie I, Ludwig-Maximilians-Universität München, Menzinger Str. 67, D-80638 München, Germany
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Keene SD, Greco TM, Parastatidis I, Lee SH, Hughes EG, Balice-Gordon RJ, Speicher DW, Ischiropoulos H. Mass spectrometric and computational analysis of cytokine-induced alterations in the astrocyte secretome. Proteomics 2009; 9:768-82. [PMID: 19132682 DOI: 10.1002/pmic.200800385] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The roles of astrocytes in the CNS have been expanding beyond the long held view of providing passive, supportive functions. Recent evidence has identified roles in neuronal development, extracellular matrix maintenance, and response to inflammatory challenges. Therefore, insights into astrocyte secretion are critically important for understanding physiological responses and pathological mechanisms in CNS diseases. Primary astrocyte cultures were treated with inflammatory cytokines for either a short (1 day) or sustained (7 days) exposure. Increased interleukin-6 secretion, nitric oxide production, cyclooxygenase-2 activation, and nerve growth factor (NGF) secretion confirmed the astrocytic response to cytokine treatment. MS/MS analysis, computational prediction algorithms, and functional classification were used to compare the astrocyte protein secretome from control and cytokine-exposed cultures. In total, 169 secreted proteins were identified, including both classically and nonconventionally secreted proteins that comprised components of the extracellular matrix and enzymes involved in processing of glycoproteins and glycosaminoglycans. Twelve proteins were detected exclusively in the secretome from cytokine-treated astrocytes, including matrix metalloproteinase-3 (MMP-3) and members of the chemokine ligand family. This compilation of secreted proteins provides a framework for identifying factors that influence the biochemical environment of the nervous system, regulate development, construct extracellular matrices, and coordinate the nervous system response to inflammation.
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Affiliation(s)
- Sarah Dunn Keene
- Stokes Research Institute and Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104-4318, USA
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Howell KA, Narsai R, Carroll A, Ivanova A, Lohse M, Usadel B, Millar AH, Whelan J. Mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of RNA instability in the germination process. PLANT PHYSIOLOGY 2009; 149:961-80. [PMID: 19074628 PMCID: PMC2633829 DOI: 10.1104/pp.108.129874] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 12/03/2008] [Indexed: 05/20/2023]
Abstract
Transcriptome and metabolite profiling of rice (Oryza sativa) embryo tissue during a detailed time course formed a foundation for examining transcriptional and posttranscriptional processes during germination. One hour after imbibition (HAI), independent of changes in transcript levels, rapid changes in metabolism occurred, including increases in hexose phosphates, tricarboxylic acid cycle intermediates, and gamma-aminobutyric acid. Later changes in the metabolome, including those involved in carbohydrate, amino acid, and cell wall metabolism, appeared to be driven by increases in transcript levels, given that the large group (over 6,000 transcripts) observed to increase from 12 HAI were enriched in metabolic functional categories. Analysis of transcripts encoding proteins located in the organelles of primary metabolism revealed that for the mitochondrial gene set, a greater proportion of transcripts peaked early, at 1 or 3 HAI, compared with the plastid set, and notably, many of these transcripts encoded proteins involved in transport functions. One group of over 2,000 transcripts displayed a unique expression pattern beginning with low levels in dry seeds, followed by a peak in expression levels at 1 or 3 HAI, before markedly declining at later time points. This group was enriched in transcription factors and signal transduction components. A subset of these transiently expressed transcription factors were further interrogated across publicly available rice array data, indicating that some were only expressed during the germination process. Analysis of the 1-kb upstream regions of transcripts displaying similar changes in abundance identified a variety of common sequence motifs, potential binding sites for transcription factors. Additionally, newly synthesized transcripts peaking at 3 HAI displayed a significant enrichment of sequence elements in the 3' untranslated region that have been previously associated with RNA instability. Overall, these analyses reveal that during rice germination, an immediate change in some metabolite levels is followed by a two-step, large-scale rearrangement of the transcriptome that is mediated by RNA synthesis and degradation and is accompanied by later changes in metabolite levels.
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Affiliation(s)
- Katharine A Howell
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
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Gaston D, Tsaousis AD, Roger AJ. Predicting proteomes of mitochondria and related organelles from genomic and expressed sequence tag data. Methods Enzymol 2009; 457:21-47. [PMID: 19426860 DOI: 10.1016/s0076-6879(09)05002-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In eukaryotes, determination of the subcellular location of a novel protein encoded in genomic or transcriptomic data provides useful clues as to its possible function. However, experimental localization studies are expensive and time-consuming. As a result, accurate in silico prediction of subcellular localization from sequence data alone is an extremely important field of study in bioinformatics. This is especially so as genomic studies expand beyond model system organisms to encompass the full diversity of eukaryotes. Here we review some of the more commonly used programs for prediction of proteins that function in mitochondria, or mitochondrion-related organelles in diverse eukaryotic lineages and provide recommendations on how to apply these methods. Furthermore, we compare the predictive performance of these programs on a mixed set of mitochondrial and non-mitochondrial proteins. Although N-terminal targeting peptide prediction programs tend to have the highest accuracy, they cannot be effectively used for partial coding sequences derived from high-throughput expressed sequence tag surveys where data for the N-terminus of the encoded protein is often missing. Therefore methods that do not rely on the presence of an N-terminal targeting sequence alone are extremely useful, especially for expressed sequence tag data. The best strategy for classification of unknown proteins is to use multiple programs, incorporating a variety of prediction strategies, and closely examine the predictions with an understanding of how each of those programs will likely handle the data.
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Affiliation(s)
- Daniel Gaston
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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Yoshihara C, Inoue K, Schichnes D, Ruzin S, Inwood W, Kustu S. An Rh1-GFP fusion protein is in the cytoplasmic membrane of a white mutant strain of Chlamydomonas reinhardtii. MOLECULAR PLANT 2008; 1:1007-20. [PMID: 19825599 PMCID: PMC2902906 DOI: 10.1093/mp/ssn074] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Accepted: 10/14/2008] [Indexed: 05/21/2023]
Abstract
The major Rhesus (Rh) protein of the green alga Chlamydomonas reinhardtii, Rh1, is homologous to Rh proteins of humans. It is an integral membrane protein involved in transport of carbon dioxide. To localize a fusion of intact Rh1 to the green fluorescent protein (GFP), we used as host a white (lts1) mutant strain of C. reinhardtii, which is blocked at the first step of carotenoid biosynthesis. The lts1 mutant strain accumulated normal amounts of Rh1 heterotrophically in the dark and Rh1-GFP was at the periphery of the cell co-localized with the cytoplasmic membrane dye FM4-64. Although Rh1 carries a potential chloroplast targeting sequence at its N-terminus, Rh1-GFP was clearly not associated with the chloroplast envelope membrane. Moreover, the N-terminal half of the protein was not imported into chloroplasts in vitro and N-terminal regions of Rh1 did not direct import of the small subunit of ribulose bisphosphate carboxylase (SSU). Despite caveats to this interpretation, which we discuss, current evidence indicates that Rh1 is a cytoplasmic membrane protein and that Rh1-GFP is among the first cytoplasmic membrane protein fusions to be obtained in C. reinhardtii. Although lts1 (white) mutant strains cannot be used to localize proteins within sub-compartments of the chloroplast because they lack thylakoid membranes, they should nonetheless be valuable for localizing many GFP fusions in Chlamydomonas.
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Affiliation(s)
- Corinne Yoshihara
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA
| | - Kentaro Inoue
- Department of Plant Sciences, 131 Asmundson Hall, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Denise Schichnes
- CNR Biological Imaging Facility, 381 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA
| | - Steven Ruzin
- CNR Biological Imaging Facility, 381 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA
| | - William Inwood
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA
| | - Sydney Kustu
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA
- To whom correspondence should be addressed. E-mail , fax (510) 642-4995, tel. (510) 643-9308
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Punta M, Ofran Y. The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function. PLoS Comput Biol 2008; 4:e1000160. [PMID: 18974821 PMCID: PMC2518264 DOI: 10.1371/journal.pcbi.1000160] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Marco Punta
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
- Columbia University Center for Computational Biology and Bioinformatics (C2B2), New York, New York, United States of America
- Northeast Structural Genomics Consortium (NESG), Columbia University, New York, New York, United States of America
| | - Yanay Ofran
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
- * E-mail:
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Abstract
Most chloroplast proteins are encoded in the nucleus and synthesized on free, cytosolic ribosomes in precursor form. Each precursor has an amino-terminal extension called a transit peptide, which directs the protein through a post-translational targeting pathway and is removed upon arrival inside the organelle. This 'protein import' process is mediated by the coordinate action of two multiprotein complexes, one in each of the envelope membranes: the TOC and TIC (Translocon at the Outer/ Inner envelope membrane of Chloroplasts) machines. Many components of these complexes have been identified biochemically in pea; these include transit peptide receptors, channel proteins, and molecular chaperones. Intriguingly, the Arabidopsis genome encodes multiple, homologous genes for receptor components of the TOC complex. Careful analysis indicated that the different receptor isoforms operate in different import pathways with distinct precursor recognition specificities. These 'substrate-specific' import pathways might play a role in the differentiation of different plastid types, and/or act to prevent deleterious competition effects between abundant and nonabundant precursors. Until recently, all proteins destined for internal chloroplast compartments were thought to possess a cleavable transit peptide, and to engage the TOC/TIC machinery. New studies using proteomics and other approaches have revealed that this is far from true. Remarkably, a significant number of chloroplast proteins are transported via a pathway that involves the endoplasmic reticulum and Golgi apparatus. Other recent reports have elucidated an intriguing array of protein targeting routes leading to the envelope membranes themselves.
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Affiliation(s)
- Paul Jarvis
- Department of Biology, University of Leicester, Leicester LE1 7RH, UK
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Zhou M, Boekhorst J, Francke C, Siezen RJ. LocateP: genome-scale subcellular-location predictor for bacterial proteins. BMC Bioinformatics 2008; 9:173. [PMID: 18371216 PMCID: PMC2375117 DOI: 10.1186/1471-2105-9-173] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 03/27/2008] [Indexed: 11/10/2022] Open
Abstract
Background In the past decades, various protein subcellular-location (SCL) predictors have been developed. Most of these predictors, like TMHMM 2.0, SignalP 3.0, PrediSi and Phobius, aim at the identification of one or a few SCLs, whereas others such as CELLO and Psortb.v.2.0 aim at a broader classification. Although these tools and pipelines can achieve a high precision in the accurate prediction of signal peptides and transmembrane helices, they have a much lower accuracy when other sequence characteristics are concerned. For instance, it proved notoriously difficult to identify the fate of proteins carrying a putative type I signal peptidase (SPIase) cleavage site, as many of those proteins are retained in the cell membrane as N-terminally anchored membrane proteins. Moreover, most of the SCL classifiers are based on the classification of the Swiss-Prot database and consequently inherited the inconsistency of that SCL classification. As accurate and detailed SCL prediction on a genome scale is highly desired by experimental researchers, we decided to construct a new SCL prediction pipeline: LocateP. Results LocateP combines many of the existing high-precision SCL identifiers with our own newly developed identifiers for specific SCLs. The LocateP pipeline was designed such that it mimics protein targeting and secretion processes. It distinguishes 7 different SCLs within Gram-positive bacteria: intracellular, multi-transmembrane, N-terminally membrane anchored, C-terminally membrane anchored, lipid-anchored, LPxTG-type cell-wall anchored, and secreted/released proteins. Moreover, it distinguishes pathways for Sec- or Tat-dependent secretion and alternative secretion of bacteriocin-like proteins. The pipeline was tested on data sets extracted from literature, including experimental proteomics studies. The tests showed that LocateP performs as well as, or even slightly better than other SCL predictors for some locations and outperforms current tools especially where the N-terminally anchored and the SPIase-cleaved secreted proteins are concerned. Overall, the accuracy of LocateP was always higher than 90%. LocateP was then used to predict the SCLs of all proteins encoded by completed Gram-positive bacterial genomes. The results are stored in the database LocateP-DB [1]. Conclusion LocateP is by far the most accurate and detailed protein SCL predictor for Gram-positive bacteria currently available.
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Affiliation(s)
- Miaomiao Zhou
- Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
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Hu XV, Chen X, Han KC, Mildvan AS, Liu JO. Kinetic and Mutational Studies of the Number of Interacting Divalent Cations Required by Bacterial and Human Methionine Aminopeptidases. Biochemistry 2007; 46:12833-43. [DOI: 10.1021/bi701127x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaoyi V. Hu
- Departments of Pharmacology and Molecular Sciences and Biological Chemistry and Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205
| | - Xiaochun Chen
- Departments of Pharmacology and Molecular Sciences and Biological Chemistry and Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205
| | - Kee Chung Han
- Departments of Pharmacology and Molecular Sciences and Biological Chemistry and Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205
| | - Albert S. Mildvan
- Departments of Pharmacology and Molecular Sciences and Biological Chemistry and Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205
| | - Jun O. Liu
- Departments of Pharmacology and Molecular Sciences and Biological Chemistry and Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205
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45
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Reumann S, Babujee L, Ma C, Wienkoop S, Siemsen T, Antonicelli GE, Rasche N, Lüder F, Weckwerth W, Jahn O. Proteome analysis of Arabidopsis leaf peroxisomes reveals novel targeting peptides, metabolic pathways, and defense mechanisms. THE PLANT CELL 2007; 19:3170-93. [PMID: 17951448 PMCID: PMC2174697 DOI: 10.1105/tpc.107.050989] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Revised: 09/12/2007] [Accepted: 09/24/2007] [Indexed: 05/18/2023]
Abstract
We have established a protocol for the isolation of highly purified peroxisomes from mature Arabidopsis thaliana leaves and analyzed the proteome by complementary gel-based and gel-free approaches. Seventy-eight nonredundant proteins were identified, of which 42 novel proteins had previously not been associated with plant peroxisomes. Seventeen novel proteins carried predicted peroxisomal targeting signals (PTS) type 1 or type 2; 11 proteins contained PTS-related peptides. Peroxisome targeting was supported for many novel proteins by in silico analyses and confirmed for 11 representative full-length fusion proteins by fluorescence microscopy. The targeting function of predicted and unpredicted signals was investigated and SSL>, SSI>, and ASL> were established as novel functional PTS1 peptides. In contrast with the generally accepted confinement of PTS2 peptides to the N-terminal domain, the bifunctional transthyretin-like protein was demonstrated to carry internally a functional PTS2. The novel enzymes include numerous enoyl-CoA hydratases, short-chain dehydrogenases, and several enzymes involved in NADP and glutathione metabolism. Seven proteins, including beta-glucosidases and myrosinases, support the currently emerging evidence for an important role of leaf peroxisomes in defense against pathogens and herbivores. The data provide new insights into the biology of plant peroxisomes and improve the prediction accuracy of peroxisome-targeted proteins from genome sequences.
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Affiliation(s)
- Sigrun Reumann
- Department of Plant Biochemistry, Georg-August-University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, D-37077 Goettingen, Germany.
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46
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Emanuelsson O, Brunak S, von Heijne G, Nielsen H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2007; 2:953-71. [PMID: 17446895 DOI: 10.1038/nprot.2007.131] [Citation(s) in RCA: 2450] [Impact Index Per Article: 144.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Determining the subcellular localization of a protein is an important first step toward understanding its function. Here, we describe the properties of three well-known N-terminal sequence motifs directing proteins to the secretory pathway, mitochondria and chloroplasts, and sketch a brief history of methods to predict subcellular localization based on these sorting signals and other sequence properties. We then outline how to use a number of internet-accessible tools to arrive at a reliable subcellular localization prediction for eukaryotic and prokaryotic proteins. In particular, we provide detailed step-by-step instructions for the coupled use of the amino-acid sequence-based predictors TargetP, SignalP, ChloroP and TMHMM, which are all hosted at the Center for Biological Sequence Analysis, Technical University of Denmark. In addition, we describe and provide web references to other useful subcellular localization predictors. Finally, we discuss predictive performance measures in general and the performance of TargetP and SignalP in particular.
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Affiliation(s)
- Olof Emanuelsson
- Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-10691 Stockholm, Sweden
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47
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Klee EW, Sosa CP. Computational classification of classically secreted proteins. Drug Discov Today 2007; 12:234-40. [PMID: 17331888 DOI: 10.1016/j.drudis.2007.01.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 01/05/2007] [Accepted: 01/23/2007] [Indexed: 11/21/2022]
Abstract
The ability to identify classically secreted proteins is an important component of targeted therapeutic studies and the discovery of circulating biomarkers. Here, we review some of the most recent programs available for the in silico prediction of secretory proteins, the performance of which is benchmarked with an independent set of annotated human proteins. The description of these programs and the results of this benchmarking provide insights into the most recently developed prediction programs, which will enable investigators to make more informed decisions about which program best addresses their research needs.
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Affiliation(s)
- Eric W Klee
- Stabile 3-15, Department of Laboratory Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
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