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Kumar V, Anand P, Srivastava A, Akhter Y, Verma D. The structural insights of L-asparaginase from Pseudomonas aeruginosa CSPS4 at elevated temperatures highlight its thermophilic nature. 3 Biotech 2024; 14:230. [PMID: 39280800 PMCID: PMC11391003 DOI: 10.1007/s13205-024-04072-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 08/28/2024] [Indexed: 09/18/2024] Open
Abstract
In the present investigation, a novel thermophilic L-asparaginase (Asn_PA) from Pseudomonas aeruginosa CSPS4 was investigated to explore its structural insights at elevated temperatures. Sequence analysis of Asn_PA depicted three conserved motifs (VVILATGGTIAG, DGIVITHGTDTLEETAYFL, and, LRKQGVQIIRSSHVNAGGF), of them, two motifs exhibit catalytically-important residues i.e., T45 and T125. A homology modelling-based structure model for Asn_PA was generated with 4PGA as the top-matched template. The predicted structure was validated and energy was minimized. Molecular docking was carried out cantered at the active site for asparagine and glutamine as its substrate ligands. The enzyme-substrate interaction analysis showed binding affinities of - 4.8 and - 4.1 kcal/mol for asparagine and glutamine respectively. Molecular dynamics (MD) simulation studies showed a better stability of Asn_PA at temperatures of 60 °C, over 40, 50 and, 80 °C, making this enzyme a novel L-asparaginase from other mesophilic P. aeruginosa strain. The trajectory analysis showed that RMSD, Rg, and, SASA values correlate well with each other in the different tested temperatures during the MD analysis. Thus, the present findings encourage extensive characterization of the Asn_PA using laboratory experiments to understand the structural behavior of the active site loop in an open or closed state with and without the substrate molecules. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04072-w.
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Affiliation(s)
- Vinay Kumar
- Department of Environmental Microbiology, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025 India
| | - Pragya Anand
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025 India
| | - Ankita Srivastava
- Department of Environmental Microbiology, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025 India
| | - Yusuf Akhter
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025 India
| | - Digvijay Verma
- Department of Environmental Microbiology, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025 India
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Xiao L, Liu Q, Cao X, Chen M, Zhang L, Yao Z, Zhao S. Detection of Secreted Effector Proteins from Phelipanche aegyptiaca During Invasion of Melon Roots. PHYTOPATHOLOGY 2023; 113:1548-1559. [PMID: 37454086 DOI: 10.1094/phyto-11-22-0441-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Parasites can interact with their host plants through the induction and delivery of secreted effector proteins that facilitate plant colonization by decomposing plant cell walls and inhibiting plant immune response to weaken the defense ability of the host. Yet effectors mediating parasitic plant-host interactions are poorly understood. Phelipanche aegyptiaca is an obligate root parasite plant causing severe yield and economic losses in agricultural fields worldwide. Host resistance against P. aegyptiaca occurred during the attachment period of parasitism. Comparative transcriptomics was used to assess resistant and susceptible interactions simultaneously between P. aegyptiaca and two contrasting melon cultivars. In total, 2,740 secreted proteins from P. aegyptiaca were identified here. Combined with transcriptome profiling, 209 candidate secreted effector proteins (CSEPs) were predicted, with functional annotations such as cell wall degrading enzymes, protease inhibitors, transferases, kinases, and elicitor proteins. A heterogeneous expression system in Nicotiana benthamiana was used to investigate the functions of 20 putatively effector genes among the CSEPs. Cluster 15140.0 can suppress BAX-triggered programmed cell death in N. benthamiana. These findings showed that the prediction of P. aegyptiaca effector proteins based on transcriptomic analysis and multiple bioinformatics software is effective and more accurate, providing insights into understanding the essential molecular nature of effectors and laying the foundation of revealing the parasite mechanism of P. aegyptiaca, which is helpful in understanding parasite-host plant interaction.
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Affiliation(s)
- Lifeng Xiao
- Xinjiang Production and Construction Corps, Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi University, Shihezi, Xinjiang 832003, China
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Qianqian Liu
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Xiaolei Cao
- Xinjiang Production and Construction Corps, Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Meixiu Chen
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Lu Zhang
- Xinjiang Production and Construction Corps, Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Zhaoqun Yao
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Sifeng Zhao
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang 832003, China
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Protein Myristoylation Plays a Role in the Nuclear Entry of the Parvovirus Minute Virus of Mice. J Virol 2022; 96:e0111822. [PMID: 35950857 PMCID: PMC9472656 DOI: 10.1128/jvi.01118-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Being nonpathogenic to humans, rodent parvoviruses (PVs) are naturally oncolytic viruses with great potential as anti-cancer agents. As these viruses replicate in the host cell nucleus, they must gain access to the nucleus during infection. The PV minute virus of mice (MVM) and several other PVs transiently disrupt the nuclear envelope (NE) and enter the nucleus through the resulting breaks. However, the molecular basis of this unique nuclear entry pathway remains uncharacterized. In this study, we used MVM as a model to investigate the molecular mechanism by which PVs induce NE disruption during viral nuclear entry. By combining bioinformatics analyses, metabolic labeling assays, mutagenesis, and pharmacological inhibition, we identified a functional myristoylation site at the sequence 78GGKVGH83 of the unique portion of the capsid protein VP1 (VP1u) of MVM. Performing proteolytic cleavage studies with a peptide containing this myristoylation site or with purified virions, we found tryptophan at position 77 of MVM VP1u is susceptible to chymotrypsin cleavage, implying this cleavage exposes G (glycine) 78 at the N-terminus of VP1u for myristoylation. Subsequent experiments using inhibitors of myristoylation and cellular proteases with MVM-infected cells, or an imaging-based quantitative NE permeabilization assay, further indicate protein myristoylation and a chymotrypsin-like activity are essential for MVM to locally disrupt the NE during viral nuclear entry. We thus propose a model for the nuclear entry of MVM in which NE disruption is mediated by VP1u myristoylation after the intact capsid undergoes proteolytic processing to expose the required N-terminal G for myristoylation. IMPORTANCE Rodent parvoviruses (PVs), including minute virus of mice (MVM), have the ability to infect and kill cancer cells and thereby possess great potential in anti-cancer therapy. In fact, some of these viruses are currently being investigated in both preclinical studies and clinical trials to treat a wide variety of cancers. However, the detailed mechanism of how PVs enter the cell nucleus remains unknown. In this study, we for the first time demonstrated a chemical modification called "myristoylation" of a MVM protein plays an essential role in the nuclear entry of the virus. We also showed, in addition to protein myristoylation, a chymotrypsin-like activity, which may come from cellular proteasomes, is required for MVM to get myristoylated and enter the nucleus. These findings deepen our understanding on how MVM and other related PVs infect host cells and provide new insights for the development of PV-based anti-cancer therapies.
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Izadpanah Qeshmi F, Homaei A, Khajeh K, Kamrani E, Fernandes P. Production of a Novel Marine Pseudomonas aeruginosa Recombinant L-Asparaginase: Insight on the Structure and Biochemical Characterization. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:599-613. [PMID: 35507234 DOI: 10.1007/s10126-022-10129-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
The present study focused on the cloning, expression, and characterization of L-asparaginase of marine Pseudomonas aeruginosa HR03 isolated from fish intestine. Thus, a gene fragment containing the L-asparaginase sequence of Pseudomonas aeruginosa HR03 isolated from the fish intestine was cloned in the pET21a vector and then expressed in Escherichia coli BL21 (DE3) cells. Thereafter, the recombinant L-asparaginase (HR03Asnase) was purified by nickel affinity chromatography, and the enzymatic properties of HR03Asnase, including the effects of pH and temperature on HR03Asnase activity and its kinetic parameters, were determined. The recombinant enzyme HR03Asnase showed the highest similarity to type I L-asparaginase from Pseudomonas aeruginosa. The three-dimensional (3D) modeling results indicate that HR03Asnase exists as a homotetramer. Its molecular weight was 35 kDa, and the maximum activity of the purified enzyme was observed at pH8 and at 40 °C. The km and Vmax of the enzyme obtained with L-asparagine as substrate were 10.904 mM and 3.44 × 10-2 mM/min, respectively. The maximum activity of HR03Asnase was reduced by 50% at 90 °C after 10-min incubation; however, the enzyme maintained more than 20% of its activity after 30-min incubation. This enzyme also maintained almost 50% of its activity at pH 12 after 40-min incubation. The evaluation of pH and temperature stability of HR03Asnase showed that the enzyme has a wide range of activity, which is a suitable characteristic for its application in different industries. Overall, the results of the present study indicate that marine sources are promising biological reservoirs for enzymes to be used for biotechnological purposes, and marine thermostable HR03Asnase is likely a potential candidate for its future usage in the pharmaceutical and food industries.
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Affiliation(s)
- Fatemeh Izadpanah Qeshmi
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, P.O. Box 3995, Bandar Abbas, Iran
| | - Ahmad Homaei
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, P.O. Box 3995, Bandar Abbas, Iran.
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ehsan Kamrani
- Fisheries Department, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Pedro Fernandes
- Department of Bioengineering and IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
- DREAMS and Faculty of Engineering, Universidade Lusófona de Humanidades E Tecnologias, Av. Campo Grande 376, 1749-024, Lisbon, Portugal
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High Molecular Weight Kininogen: A Review of the Structural Literature. Int J Mol Sci 2021; 22:ijms222413370. [PMID: 34948166 PMCID: PMC8706920 DOI: 10.3390/ijms222413370] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/02/2021] [Accepted: 12/11/2021] [Indexed: 12/23/2022] Open
Abstract
Kininogens are multidomain glycoproteins found in the blood of most vertebrates. High molecular weight kininogen demonstrate both carrier and co-factor activity as part of the intrinsic pathway of coagulation, leading to thrombin generation. Kininogens are the source of the vasoactive nonapeptide bradykinin. To date, attempts to crystallize kininogen have failed, and very little is known about the shape of kininogen at an atomic level. New advancements in the field of cryo-electron microscopy (cryoEM) have enabled researchers to crack the structure of proteins that has been refractory to traditional crystallography techniques. High molecular weight kininogen is a good candidate for structural investigation by cryoEM. The goal of this review is to summarize the findings of kininogen structural studies.
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Sahebi M, Tarighi S, Taheri P. The Arac-like transcriptional regulator YqhC is involved in pathogenicity of Erwinia amylovora. J Appl Microbiol 2021; 132:1319-1329. [PMID: 34480830 DOI: 10.1111/jam.15286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022]
Abstract
AIMS This study aimed to identify virulence-associated genes and functions that affect disease development on pear caused by Erwinia amylovora EaUMG3 isolated from Iran. METHODS AND RESULTS A mini-Tn5 transposon library was generated in EaUMG3. An E. amylovora mutant that had lost its ability to cause lesions on immature pear fruits, was selected for further analysis. This mutant was shown to have a transposon insertion in yqhC, a gene belongs to the AraC family of transcriptional regulators. A mutant of the wild-type EaUMG3 carrying an unmarked deletion of the yqhC gene was created using pDMS197. The Ea∆yqhC mutant showed reduced disease progression on immature pear fruits and pear plants, reduced motility and significantly lower levels of the virulence factors siderophore and amylovoran. Complementation with yqhC cloned in pBBR1MCS restored disease progression and the level of virulence factors to near wild type. CONCLUSION YqhC transcriptional regulator is necessary for full virulence of E. amylovora. In addition, this regulator affects virulence factors such as siderophore production, amylovoran production, and motility. SIGNIFICANCE AND IMPACT OF STUDY The identification of a novel transcriptional regulator with strong impact in the pathogenesis of E. amylovora, an organism causing significant economic losses in fruit production.
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Affiliation(s)
- Masood Sahebi
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Saeed Tarighi
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Parissa Taheri
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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Su C, Liu H, Wafula EK, Honaas L, de Pamphilis CW, Timko MP. SHR4z, a novel decoy effector from the haustorium of the parasitic weed Striga gesnerioides, suppresses host plant immunity. THE NEW PHYTOLOGIST 2020; 226:891-908. [PMID: 31788811 PMCID: PMC7187149 DOI: 10.1111/nph.16351] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/22/2019] [Indexed: 05/18/2023]
Abstract
Cowpea (Vigna unguiculata) cultivar B301 is resistant to races SG4 and SG3 of the root parasitic weed Striga gesnerioides, developing a hypersensitive response (HR) at the site of parasite attachment. By contrast, race SG4z overcomes B301 resistance and successfully parasitises the plant. Comparative transcriptomics and in silico analysis identified a small secreted effector protein dubbed Suppressor of Host Resistance 4z (SHR4z) in the SG4z haustorium that upon transfer to the host roots causes a loss of host immunity (i.e. decreased HR and increased parasite growth). SHR4z has significant homology to the short leucine-rich repeat (LRR) domain of SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK) family proteins and functions by binding to VuPOB1, a host BTB-BACK domain-containing ubiquitin E3 ligase homologue, leading to its rapid turnover. VuPOB1 is shown to be a positive regulator of HR since silencing of VuPOB1 expression in transgenic B301 roots lowers the frequency of HR and increases the levels of successful SG4 parasitism and overexpression decreases parasitism by SG4z. These findings provide new insights into how parasitic weeds overcome host defences and could potentially contribute to the development of novel strategies for controlling Striga and other parasitic weeds thereby enhancing crop productivity and food security globally.
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Affiliation(s)
- Chun Su
- Department of BiologyUniversity of VirginiaCharlottesvilleVA22904USA
| | - Hai Liu
- Department of BiologyUniversity of VirginiaCharlottesvilleVA22904USA
| | - Eric K. Wafula
- Department of BiologyThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Loren Honaas
- Department of BiologyThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | | | - Michael P. Timko
- Department of BiologyUniversity of VirginiaCharlottesvilleVA22904USA
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Tirnaz S, Zhang Y, Batley J. Genome-Wide Mining of Disease Resistance Gene Analogs Using Conserved Domains. Methods Mol Biol 2020; 2107:365-375. [PMID: 31893459 DOI: 10.1007/978-1-0716-0235-5_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The production of legume crop species is severely affected by disease, imposing a significant yield loss annually worldwide. Plant resistance gene analogs (RGAs) play specific roles in plant resistance responses, and their identification and subsequent application in breeding programs help to reduce this yield loss. RGAs contain conserved domains and motifs, which can be used for their identification and classification. Nucleotide-binding site-leucine-rich repeat (NLR), receptor like kinase (RLK), and receptor like protein (RLP) genes are the main types of RGAs. Computational identification and characterization of RGAs has been performed successfully among different plant species. Here, we explain the computational workflow for genome-wide RGA identification in legumes.
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Affiliation(s)
- Soodeh Tirnaz
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Yueqi Zhang
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia.
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Blanco JD, Radusky L, Climente-González H, Serrano L. FoldX accurate structural protein-DNA binding prediction using PADA1 (Protein Assisted DNA Assembly 1). Nucleic Acids Res 2019; 46:3852-3863. [PMID: 29608705 PMCID: PMC5934639 DOI: 10.1093/nar/gky228] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/20/2018] [Indexed: 12/20/2022] Open
Abstract
The speed at which new genomes are being sequenced highlights the need for genome-wide methods capable of predicting protein–DNA interactions. Here, we present PADA1, a generic algorithm that accurately models structural complexes and predicts the DNA-binding regions of resolved protein structures. PADA1 relies on a library of protein and double-stranded DNA fragment pairs obtained from a training set of 2103 DNA–protein complexes. It includes a fast statistical force field computed from atom-atom distances, to evaluate and filter the 3D docking models. Using published benchmark validation sets and 212 DNA–protein structures published after 2016 we predicted the DNA-binding regions with an RMSD of <1.8 Å per residue in >95% of the cases. We show that the quality of the docked templates is compatible with FoldX protein design tool suite to identify the crystallized DNA molecule sequence as the most energetically favorable in 80% of the cases. We highlighted the biological potential of PADA1 by reconstituting DNA and protein conformational changes upon protein mutagenesis of a meganuclease and its variants, and by predicting DNA-binding regions and nucleotide sequences in proteins crystallized without DNA. These results opens up new perspectives for the engineering of DNA–protein interfaces.
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Affiliation(s)
- Javier Delgado Blanco
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Leandro Radusky
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Héctor Climente-González
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, 08010 Barcelona, Spain
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Jiang YR, Wang TT, Chen DB, Xia RX, Li Q, Wang H, Liu YQ. Characterization of a highly conserved Antheraea pernyi spermidine synthase gene. 3 Biotech 2019; 9:224. [PMID: 31139539 DOI: 10.1007/s13205-019-1762-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/14/2019] [Indexed: 10/26/2022] Open
Abstract
In the present study, we isolated a spermidine synthase gene from Antheraea pernyi (ApSpds) using expressed sequence tag method. The obtained cDNA sequence of 1483 bp contains an open-reading frame of 864 bp encoding a polypeptide of 287 amino acids. Sequence analysis revealed that ApSpds belonged to class I of AdoMet-MTase family, and exhibited 30% identity to those from bacteria, 45-48% identity to fungi, 36-47% identity to plants, 52-54% identity to vertebrates and 53-80% identity to invertebrates. Phylogenetic analysis found that the used Spds protein sequences were well divided into five groups corresponding to bacteria, fungi, plants, invertebrates and vertebrates, respectively. These results further confirmed that Spds is highly conserved through evolution of life organisms. The ApSpds mRNA is expressed during all four developmental stages and is present in all examined tissues with the highest abundance in the muscle, in which the relative mRNA expression level was 1.6 times higher than in the fat body. Although not significant, the mRNA level decreased after high-temperature exposure suggesting that the Spds gene may not be involved in temperature stress tolerance in A. pernyi. Taken together, our results suggested that ApSpds play an important role in development of silkworm.
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Affiliation(s)
- Yi-Ren Jiang
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China
| | - Ting-Ting Wang
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China
| | - Dong-Bin Chen
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China
| | - Run-Xi Xia
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China
| | - Qun Li
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China
| | - Huan Wang
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China
| | - Yan-Qun Liu
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China
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Padalino G, Ferla S, Brancale A, Chalmers IW, Hoffmann KF. Combining bioinformatics, cheminformatics, functional genomics and whole organism approaches for identifying epigenetic drug targets in Schistosoma mansoni. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2018; 8:559-570. [PMID: 30455056 PMCID: PMC6288008 DOI: 10.1016/j.ijpddr.2018.10.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/22/2018] [Accepted: 10/22/2018] [Indexed: 02/07/2023]
Abstract
Schistosomiasis endangers the lives of greater than 200 million people every year and is predominantly controlled by a single class chemotherapy, praziquantel (PZQ). Development of PZQ replacement (to combat the threat of PZQ insensitivity/resistance arising) or combinatorial (to facilitate the killing of PZQ-insensitive juvenile schistosomes) chemotherapies would help sustain this control strategy into the future. Here, we re-categorise two families of druggable epigenetic targets in Schistosoma mansoni, the histone methyltransferases (HMTs) and the histone demethylases (HDMs). Amongst these, a S. mansoni Lysine Specific Demethylase 1 (SmLSD1, Smp_150560) homolog was selected for further analyses. Homology modelling of SmLSD1 and in silico docking of greater than four thousand putative inhibitors identified seven (L1 – L7) showing more favourable binding to the target pocket of SmLSD1 vs Homo sapiens HsLSD1; six of these seven (L1 – L6) plus three structural analogues of L7 (L8 – L10) were subsequently screened against schistosomula using the Roboworm anthelmintic discovery platform. The most active compounds (L10 - pirarubicin > L8 – danunorubicin hydrochloride) were subsequently tested against juvenile (3 wk old) and mature (7 wk old) schistosome stages and found to impede motility, suppress egg production and affect tegumental surfaces. When compared to a surrogate human cell line (HepG2), a moderate window of selectivity was observed for the most active compound L10 (selectivity indices - 11 for schistosomula, 9 for juveniles, 1.5 for adults). Finally, RNA interference of SmLSD1 recapitulated the egg-laying defect of schistosomes co-cultivated in the presence of L10 and L8. These preliminary results suggest that SmLSD1 represents an attractive new target for schistosomiasis; identification of more potent and selective SmLSD1 compounds, however, is essential. Nevertheless, the approaches described herein highlight an interdisciplinary strategy for selecting and screening novel/repositioned anti-schistosomals, which can be applied to any druggable (epigenetic) target encoded by the parasite's genome. Schistosoma mansoni contains 27 histone methyltransferases (HMTs) and 14 histone demethylases (HDMs). S. mansoni lysine specific demethylase 1 (SmLSD1) is a druggable target. Schistosomes treated with the putative SmLSD1 inhibitor pirarubicin or siRNAs targeting SmLSD1 are less fecund.
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Affiliation(s)
- Gilda Padalino
- The Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, SY23 3DA, Wales, UK.
| | - Salvatore Ferla
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, United Kingdom.
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, United Kingdom.
| | - Iain W Chalmers
- The Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, SY23 3DA, Wales, UK.
| | - Karl F Hoffmann
- The Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, SY23 3DA, Wales, UK.
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Cai G, Myers K, Fry WE, Hillman BI. Phytophthora infestans RNA virus 2, a novel RNA virus from Phytophthora infestans, does not belong to any known virus group. Arch Virol 2018; 164:567-572. [DOI: 10.1007/s00705-018-4050-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 09/23/2018] [Indexed: 12/12/2022]
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15
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Dudek CA, Dannheim H, Schomburg D. BrEPS 2.0: Optimization of sequence pattern prediction for enzyme annotation. PLoS One 2017; 12:e0182216. [PMID: 28750104 PMCID: PMC5531587 DOI: 10.1371/journal.pone.0182216] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 07/15/2017] [Indexed: 11/19/2022] Open
Abstract
The prediction of gene functions is crucial for a large number of different life science areas. Faster high throughput sequencing techniques generate more and larger datasets. The manual annotation by classical wet-lab experiments is not suitable for these large amounts of data. We showed earlier that the automatic sequence pattern-based BrEPS protocol, based on manually curated sequences, can be used for the prediction of enzymatic functions of genes. The growing sequence databases provide the opportunity for more reliable patterns, but are also a challenge for the implementation of automatic protocols. We reimplemented and optimized the BrEPS pattern generation to be applicable for larger datasets in an acceptable timescale. Primary improvement of the new BrEPS protocol is the enhanced data selection step. Manually curated annotations from Swiss-Prot are used as reliable source for function prediction of enzymes observed on protein level. The pool of sequences is extended by highly similar sequences from TrEMBL and SwissProt. This allows us to restrict the selection of Swiss-Prot entries, without losing the diversity of sequences needed to generate significant patterns. Additionally, a supporting pattern type was introduced by extending the patterns at semi-conserved positions with highly similar amino acids. Extended patterns have an increased complexity, increasing the chance to match more sequences, without losing the essential structural information of the pattern. To enhance the usability of the database, we introduced enzyme function prediction based on consensus EC numbers and IUBMB enzyme nomenclature. BrEPS is part of the Braunschweig Enzyme Database (BRENDA) and is available on a completely redesigned website and as download. The database can be downloaded and used with the BrEPScmd command line tool for large scale sequence analysis. The BrEPS website and downloads for the database creation tool, command line tool and database are freely accessible at http://breps.tu-bs.de.
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Affiliation(s)
- Christian-Alexander Dudek
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Henning Dannheim
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
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16
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Lee SH, Kim MS, Kim YJ, Kim TW, Kang SG, Lee HS. Transcriptomic profiling and its implications for the H 2 production of a non-methanogen deficient in the frhAGB-encoding hydrogenase. Appl Microbiol Biotechnol 2017; 101:5081-5088. [PMID: 28341885 DOI: 10.1007/s00253-017-8234-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 03/02/2017] [Accepted: 03/07/2017] [Indexed: 10/19/2022]
Abstract
The F420-reducing hydrogenase of methanogens functions in methanogenesis by providing reduced coenzyme F420 (F420H2) as an electron donor. In non-methanogens, however, their physiological function has not been identified yet. In this study, we constructed an ΔfrhA mutant, whose frhA gene encoding the hydrogenase α subunit was deleted, in the non-methanogenic Thermococcus onnurineus NA1 as a model organism. There was no significant difference in the formate-dependent growth between the mutant and the wild-type strains. Interestingly, the mutation in the frhA gene affected the expression of genes involved in various cellular functions such as H2 oxidation, chemotactic signal transduction, and carbon monoxide (CO) metabolism. Among these genes, the CO oxidation gene cluster, enabling CO-dependent growth and H2 production, showed a 2.8- to 7.0-fold upregulation by microarray-based whole transcriptome expression profiling. The levels of proteins produced by this gene cluster were also significantly increased not only under the formate condition but also under the CO condition. In a controlled bioreactor, where 100% CO was continuously fed, the ΔfrhA mutant exhibited significant increases in cell growth (2.8-fold) and H2 production (3.4-fold). These findings strongly imply that this hydrogenase is functional in non-methanogens and is related to various cellular metabolic processes through an unidentified mechanism. An understanding of the mechanism by which the frhA gene deletion affected the expression of other genes will provide insights that can be applied to the development of strategies for the enhancement of H2 production using CO as a substrate.
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Affiliation(s)
- Seong Hyuk Lee
- Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea
| | - Min-Sik Kim
- Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea.,Biomass and Waste Energy Laboratory, Korea Institute of Energy Research, Daejeon, 34129, Republic of Korea
| | - Yun Jae Kim
- Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea.,Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Tae Wan Kim
- Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea.,Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Sung Gyun Kang
- Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea. .,Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.
| | - Hyun Sook Lee
- Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea. .,Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.
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17
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Zhuo K, Chen J, Lin B, Wang J, Sun F, Hu L, Liao J. A novel Meloidogyne enterolobii effector MeTCTP promotes parasitism by suppressing programmed cell death in host plants. MOLECULAR PLANT PATHOLOGY 2017; 18:45-54. [PMID: 26808010 PMCID: PMC6638250 DOI: 10.1111/mpp.12374] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 05/20/2023]
Abstract
Meloidogyne enterolobii is one of the most important plant-parasitic nematodes that can overcome the Mi-1 resistance gene and damage many economically important crops. Translationally controlled tumour protein (TCTP) is a multifunctional protein that exists in various eukaryotes and plays an important role in parasitism. In this study, a novel M. enterolobii TCTP effector, named MeTCTP, was identified and functionally characterized. MeTCTP was specifically expressed within the dorsal gland and was up-regulated during M. enterolobii parasitism. Transient expression of MeTCTP in protoplasts from tomato roots showed that MeTCTP was localized in the cytoplasm of the host cells. Transgenic Arabidopsis thaliana plants overexpressing MeTCTP were more susceptible to M. enterolobii infection than wild-type plants in a dose-dependent manner. By contrast, in planta RNA interference (RNAi) targeting MeTCTP suppressed the expression of MeTCTP in infecting nematodes and attenuated their parasitism. Furthermore, MeTCTP could suppress programmed cell death triggered by the pro-apoptotic protein BAX. These results demonstrate that MeTCTP is a novel plant-parasitic nematode effector that promotes parasitism, probably by suppressing programmed cell death in host plants.
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Affiliation(s)
- Kan Zhuo
- Laboratory of Plant NematologySouth China Agricultural UniversityGuangzhou510642China
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhou510642China
| | - Jiansong Chen
- Laboratory of Plant NematologySouth China Agricultural UniversityGuangzhou510642China
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhou510642China
| | - Borong Lin
- Laboratory of Plant NematologySouth China Agricultural UniversityGuangzhou510642China
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhou510642China
| | - Jing Wang
- Laboratory of Plant NematologySouth China Agricultural UniversityGuangzhou510642China
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhou510642China
| | - Fengxia Sun
- Laboratory of Plant NematologySouth China Agricultural UniversityGuangzhou510642China
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhou510642China
| | - Lili Hu
- Laboratory of Plant NematologySouth China Agricultural UniversityGuangzhou510642China
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhou510642China
| | - Jinling Liao
- Laboratory of Plant NematologySouth China Agricultural UniversityGuangzhou510642China
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhou510642China
- Guangdong Vocational College of Ecological EngineeringGuangzhou510520China
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18
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Nagdas SK, Winfrey VP, Olson GE. Two fibrinogen-like proteins, FGL1 and FGL2 are disulfide-linked subunits of oligomers that specifically bind nonviable spermatozoa. Int J Biochem Cell Biol 2016; 80:163-172. [PMID: 27732889 DOI: 10.1016/j.biocel.2016.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 10/08/2016] [Indexed: 11/16/2022]
Abstract
Nevertheless, a nonviable sperm population is present in the cauda epididymidis of many species. Degenerating spermatozoa release enzymes that could have detrimental effects on the viability of neighboring cells, and they are source of autoantigens that induce an autoimmune response if they escape the blood-epididymis barrier. Does the epididymis have specialized protective mechanism(s) to segregate the viable sperm population from defective spermatozoa? Previously, we identified a fibrinogen-like protein-2 (fgl2) that specifically binds to and polymerizes into a cocoon-like complex coating defective spermatozoa and sperm fragments. The objective of the present study is to identify the subunit composition of the fgl2-containing oligomers both in the soluble and cocoon-like complex. Our proteomic studies indicate that the 260/280kDa oligomers (termed eFGL) contain two distinct disulfide-linked subunits; 64kDa fgl2 and 33kDa fgl1. Utilizing a PCR-based cloning strategy, the 33kDa polypeptide has been identified as fibrinogen-like protein-1 (fgl1). Immunocytochemical studies revealed that fgl1 selectively binds to defective spermatozoa in the cauda epididymidis. Northern blot analysis and in situ hybridization demonstrated the high expression of fgl1 in the principal cells of the proximal cauda epididymidis. Co-immunoprecipitation analyses of cauda epididymal fluid, using anti-fgl2, demonstrate that both fgl1 and fgl2 are present in the soluble eFGL. Our study is the first to show an association of fgl1 and fgl2 both in the soluble and in the sperm-associated eFGL. We conclude that our results provide new insights into the mechanisms by which the potentially unique epididymal protein functions in the recognition and elimination of defective spermatozoa.
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Affiliation(s)
- Subir K Nagdas
- Department of Chemistry and Physics, Fayetteville State University, Fayetteville, NC, 28301, United States; Department of Cell Biology, Vanderbilt University, Nashville, TN, United States.
| | - Virginia P Winfrey
- Department of Cell Biology, Vanderbilt University, Nashville, TN, United States
| | - Gary E Olson
- Department of Cell Biology, Vanderbilt University, Nashville, TN, United States
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19
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McLellan AS, Langlands K, Kealey T. Exhaustive identification of human class II basic helix-loop-helix proteins by virtual library screening. Mech Dev 2016; 119 Suppl 1:S285-91. [PMID: 14516699 DOI: 10.1016/s0925-4773(03)00130-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cellular proliferation, specification and differentiation in developing tissues are tightly coordinated by groups of transcription factors in response to extrinsic and intrinsic signals. Furthermore, renewable pools of stem cells in adult tissues are subject to similar regulation. Basic helix-loop-helix (bHLH) proteins are a group of transcription factors that exert such a determinative influence on a variety of developmental pathways from C. elegans to humans, and we wished to exclusively identify novel members from within the whole human bHLH family. We have, therefore, developed an 'empirical custom fingerprint', to define the class II bHLH domain and exclusively identify these proteins in silico. We have identified nine previously uncharacterised human class II proteins, four of which were novel, by interrogating conceptual translations of the GenBank HTGS database. RT-PCR and mammalian 2-hybrid analysis of a subset of the factors demonstrated that they were indeed expressed, and were able to interact with an appropriate binding partner in vitro. Thus, we are now approaching an almost complete listing of human class II bHLH factors.
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Affiliation(s)
- Andrew S McLellan
- Department of Clinical Biochemistry, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QR, UK.
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20
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Reaching optimized parameter set: protein secondary structure prediction using neural network. Neural Comput Appl 2016. [DOI: 10.1007/s00521-015-2150-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Yin W, Naini SM, Chen G, Hentschel DM, Humphreys BD, Bonventre JV. Mammalian Target of Rapamycin Mediates Kidney Injury Molecule 1-Dependent Tubule Injury in a Surrogate Model. J Am Soc Nephrol 2015; 27:1943-57. [PMID: 26538632 DOI: 10.1681/asn.2015050500] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/08/2015] [Indexed: 12/14/2022] Open
Abstract
Kidney injury molecule 1 (KIM-1), an epithelial phagocytic receptor, is markedly upregulated in the proximal tubule in various forms of acute and chronic kidney injury in humans and many other species. Whereas acute expression of KIM-1 has adaptive anti-inflammatory effects, chronic expression may be maladaptive in mice. Here, we characterized the zebrafish Kim family, consisting of Kim-1, Kim-3, and Kim-4. Kim-1 was markedly upregulated in kidney after gentamicin-induced injury and had conserved phagocytic activity in zebrafish. Both constitutive and tamoxifen-induced expression of Kim-1 in zebrafish kidney tubules resulted in loss of the tubule brush border, reduced GFR, pericardial edema, and increased mortality. Kim-1-induced kidney injury was associated with reduction of growth of adult fish. Kim-1 expression led to activation of the mammalian target of rapamycin (mTOR) pathway, and inhibition of this pathway with rapamycin increased survival. mTOR pathway inhibition in KIM-1-overexpressing transgenic mice also significantly ameliorated serum creatinine level, proteinuria, tubular injury, and kidney inflammation. In conclusion, persistent Kim-1 expression results in chronic kidney damage in zebrafish through a mechanism involving mTOR. This observation predicted the role of the mTOR pathway and the therapeutic efficacy of mTOR-targeted agents in KIM-1-mediated kidney injury and fibrosis in mice, demonstrating the utility of the Kim-1 renal tubule zebrafish models.
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Affiliation(s)
- Wenqing Yin
- Renal Division, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Said Movahedi Naini
- Renal Division, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Guochun Chen
- Renal Division, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Dirk M Hentschel
- Renal Division, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Benjamin D Humphreys
- Renal Division, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, Massachusetts; Harvard Stem Cell Institute, Cambridge, Massachusetts; and
| | - Joseph V Bonventre
- Renal Division, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, Massachusetts; Harvard Stem Cell Institute, Cambridge, Massachusetts; and Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology, Cambridge, Massachusetts
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22
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Mehr S, Verdes A, DeSalle R, Sparks J, Pieribone V, Gruber DF. Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae). BMC Genomics 2015; 16:445. [PMID: 26059236 PMCID: PMC4462082 DOI: 10.1186/s12864-015-1565-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background The amphinomid polychaete Hermodice carunculata is a cosmopolitan and ecologically important omnivore in coral reef ecosystems, preying on a diverse suite of reef organisms and potentially acting as a vector for coral disease. While amphinomids are a key group for determining the root of the Annelida, their phylogenetic position has been difficult to resolve, and their publically available genomic data was scarce. Results We performed deep transcriptome sequencing (Illumina HiSeq) and profiling on Hermodice carunculata collected in the Western Atlantic Ocean. We focused this study on 58,454 predicted Open Reading Frames (ORFs) of genes longer than 200 amino acids for our homology search, and Gene Ontology (GO) terms and InterPro IDs were assigned to 32,500 of these ORFs. We used this de novo assembled transcriptome to recover major signaling pathways and housekeeping genes. We also identify a suite of H. carunculata genes related to reproduction and immune response. Conclusions We provide a comprehensive catalogue of annotated genes for Hermodice carunculata and expand the knowledge of reproduction and immune response genes in annelids, in general. Overall, this study vastly expands the available genomic data for H. carunculata, of which previously consisted of only 279 nucleotide sequences in NCBI. This underscores the utility of Illumina sequencing for de novo transcriptome assembly in non-model organisms as a cost-effective and efficient tool for gene discovery and downstream applications, such as phylogenetic analysis and gene expression profiling. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1565-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shaadi Mehr
- Biological Science Department, State University of New York, College at Old Westbury, Old Westbury, NY, 11568, USA. .,American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA.
| | - Aida Verdes
- Baruch College and The Graduate Center, Department of Natural Sciences, City University of New York, New York, NY, 10010, USA.
| | - Rob DeSalle
- American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA.
| | - John Sparks
- American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA. .,American Museum of Natural History, Department of Ichthyology, American Museum of Natural History, Division of Vertebrate Zoology, New York, NY, 10024, USA.
| | - Vincent Pieribone
- John B. Pierce Laboratory, Cellular and Molecular Physiology, Yale University, New Haven, CT 06519, USA.
| | - David F Gruber
- American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA. .,Baruch College and The Graduate Center, Department of Natural Sciences, City University of New York, New York, NY, 10010, USA.
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23
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McDermott JE, Bruillard P, Overall CC, Gosink L, Lindemann SR. Prediction of multi-drug resistance transporters using a novel sequence analysis method. F1000Res 2015; 4:60. [PMID: 26913187 PMCID: PMC4743146 DOI: 10.12688/f1000research.6200.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/18/2015] [Indexed: 11/20/2022] Open
Abstract
There are many examples of groups of proteins that have similar function, but the determinants of functional specificity may be hidden by lack of sequence similarity, or by large groups of similar sequences with different functions. Transporters are one such protein group in that the general function, transport, can be easily inferred from the sequence, but the substrate specificity can be impossible to predict from sequence with current methods. In this paper we describe a linguistic-based approach to identify functional patterns from groups of unaligned protein sequences and its application to predict multi-drug resistance transporters (MDRs) from bacteria. We first show that our method can recreate known patterns from PROSITE for several motifs from unaligned sequences. We then show that the method, MDRpred, can predict MDRs with greater accuracy and positive predictive value than a collection of currently available family-based models from the Pfam database. Finally, we apply MDRpred to a large collection of protein sequences from an environmental microbiome study to make novel predictions about drug resistance in a potential environmental reservoir.
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Affiliation(s)
- Jason E. McDermott
- Biological Sciences, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Paul Bruillard
- National Security Divisions, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
| | | | - Luke Gosink
- National Security Divisions, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
| | - Stephen R. Lindemann
- Biological Sciences, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
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24
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McDermott JE, Bruillard P, Overall CC, Gosink L, Lindemann SR. Prediction of multi-drug resistance transporters using a novel sequence analysis method. F1000Res 2015; 4:60. [PMID: 26913187 PMCID: PMC4743146 DOI: 10.12688/f1000research.6200.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/05/2015] [Indexed: 03/26/2024] Open
Abstract
There are many examples of groups of proteins that have similar function, but the determinants of functional specificity may be hidden by lack of sequence similarity, or by large groups of similar sequences with different functions. Transporters are one such protein group in that the general function, transport, can be easily inferred from the sequence, but the substrate specificity can be impossible to predict from sequence with current methods. In this paper we describe a linguistic-based approach to identify functional patterns from groups of unaligned protein sequences and its application to predict multi-drug resistance transporters (MDRs) from bacteria. We first show that our method can recreate known patterns from PROSITE for several motifs from unaligned sequences. We then show that the method, MDRpred, can predict MDRs with greater accuracy and positive predictive value than a collection of currently available family-based models from the Pfam database. Finally, we apply MDRpred to a large collection of protein sequences from an environmental microbiome study to make novel predictions about drug resistance in a potential environmental reservoir.
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Affiliation(s)
- Jason E. McDermott
- Biological Sciences, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Paul Bruillard
- National Security Divisions, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
| | | | - Luke Gosink
- National Security Divisions, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
| | - Stephen R. Lindemann
- Biological Sciences, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
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25
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Cantacessi C, Hofmann A, Campbell BE, Gasser RB. Impact of next-generation technologies on exploring socioeconomically important parasites and developing new interventions. Methods Mol Biol 2015; 1247:437-474. [PMID: 25399114 DOI: 10.1007/978-1-4939-2004-4_31] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
High-throughput molecular and computer technologies have become instrumental for systems biological explorations of pathogens, including parasites. For instance, investigations of the transcriptomes of different developmental stages of parasitic nematodes give insights into gene expression, regulation and function in a parasite, which is a significant step to understanding their biology, as well as interactions with their host(s) and disease. This chapter (1) gives a background on some key parasitic nematodes of socioeconomic importance, (2) describes sequencing and bioinformatic technologies for large-scale studies of the transcriptomes and genomes of these parasites, (3) provides some recent examples of applications and (4) emphasizes the prospects of fundamental biological explorations of parasites using these technologies for the development of new interventions to combat parasitic diseases.
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Affiliation(s)
- Cinzia Cantacessi
- Department of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
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26
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Singh A, Meena M, Kumar D, Dubey AK, Hassan MI. Structural and functional analysis of various globulin proteins from soy seed. Crit Rev Food Sci Nutr 2015; 55:1491-502. [PMID: 24915310 DOI: 10.1080/10408398.2012.700340] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Storage proteins of soybean mostly consist of globulins, which are classified according to their sedimentation coefficient. Among 4 major types: 2S, 7S, 11S, and 15S of globulins, 7S and 11S constitute major fraction. The 11S fraction consists only of glycinin and 7S fraction majorly consists of β-conglycinin, small amounts of γ-conglycinin and basic 7S globulin (Bg7S). Glycinin exist as a hexamer while β-conglycinin as a trimer and Bg7S as a tetramer. Glycinin subunits are coded by 5 genes of a family, whereas about 15 genes are present for β-conglycinin subunits. Bg7S gene is present in four copies in soybean genome. Synthesis of all proteins takes place as a single polypeptide chain, which is cleaved after folding to yield different chains or subunits. Glycinin and β-Conglycinin are made for storage purpose. However, Bg7S has potential xylanase inhibition activity and protein kinase activity. Primary structure of Bg7S reveals 12 conserved cysteine residues involved in forming 6 disulfide bonds, which provides appreciable stability to protein. Secondary structure is predominately rich in β-sheets with few alpha helices. Bg7S shares structural similarity with various aspartic-proteases. In this review, our aim is to discuss sequence, structure, and function of various globulins present in Glycine max.
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Affiliation(s)
- Amandeep Singh
- a Division of Biotechnology, Netaji Subhas Institute of Technology , Azad Hind Fauz Marg, Sector-3, Dwarka, New Delhi , India
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27
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Haga SW, Wu HF. Overview of software options for processing, analysis and interpretation of mass spectrometric proteomic data. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:959-969. [PMID: 25303385 DOI: 10.1002/jms.3414] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 05/23/2014] [Accepted: 06/13/2014] [Indexed: 06/04/2023]
Abstract
Recently, the interests in proteomics have been intensively increased, and the proteomic methods have been widely applied to many problems in cell biology. If the age of 1990s is considered to be a decade of genomics, we can claim that the following years of the new century is a decade of proteomics. The rapid evolution of proteomics has continued through these years, with a series of innovations in separation techniques and the core technologies of two-dimensional gel electrophoresis and MS. Both technologies are fueled by automation and high throughput computation for profiling of proteins from biological systems. As Patterson ever mentioned, 'data analysis is the Achilles heel of proteomics and our ability to generate data now outstrips our ability to analyze it'. The development of automatic and high throughput technologies for rapid identification of proteins is essential for large-scale proteome projects and automatic protein identification and characterization is essential for high throughput proteomics. This review provides a snap shot of the tools and applications that are available for mass spectrometric high throughput biocomputation. The review starts with a brief introduction of proteomics and MS. Computational tools that can be employed at various stages of analysis are presented, including that for data processing, identification, quantification, and the understanding of the biological functions of individual proteins and their dynamic interactions. The challenges of computation software development and its future trends in MS-based proteomics have also been speculated.
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Affiliation(s)
- Steve W Haga
- Department of Computer Science and Engineering, National Sun Yat Sen University, Kaohsiung, 804, Taiwan
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28
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Structure modeling and hybrid virtual screening study of Alzheimer’s associated protease kallikrein 8 for the identification of novel inhibitors. Med Chem Res 2014. [DOI: 10.1007/s00044-014-0932-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Li J, Lu L, Jia Y, Li C. Effectiveness and durability of the rice pi-ta gene in Yunnan province of China. PHYTOPATHOLOGY 2014; 104:762-8. [PMID: 24450460 DOI: 10.1094/phyto-11-13-0302-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Rice blast is one of the most damaging diseases of rice worldwide. In the present study, we analyzed DNA sequence variation of avirulence (AVR) genes of AVR-Pita1 in field isolates of Magnaporthe oryzae in order to understand the effectiveness of the resistance gene Pi-ta in China. Genomic DNA of 366 isolates of M. oryzae collected from Yunnan province of China were used for polymerase chain reaction (PCR) amplification to examine the existence of AVR-Pita1 using gene-specific PCR markers. Results of PCR products revealed that 218 isolates of M. oryzae carry AVR-Pita1. Among of them, 62.5, 56.3, 58.5, 46.7, 72.4, and 57.4% of M. oryzae carry AVR-Pita1 from northeastern, southeast, western, northwest, southwestern, and central Yunnan province, respectively. The detection rate of AVR-Pita1 was, in order: southwestern > northeastern > western > central > southeastern > northwestern Yunnan province. Moreover, in total, 18 AVR-Pita1 haplotypes encoding 13 novel AVR-Pita1 variants were identified among 60 isolates. Most DNA sequence variation was found to occur in the exon region, resulting in amino acid substitution. Six virulent haplotypes of AVR-Pita1 to Pita were identified among 60 field isolates. The AVR-Pita1 has evolved to virulence from avirulent origins via base substitution. These findings demonstrate that AVR-Pita1 is under positive selection and mutations of AVR-Pita1 are responsible for defeating race-specific resistance in nature.
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Abstract
Phytophthora sp. is a genus in the oomycetes, which are similar to filamentous fungi in morphology and habitat, but phylogenetically more closely related to brown algae and diatoms and fall in the kingdom Stramenopila. In the past few years, several viruses have been characterized in Phytophthora species, including four viruses from Phytophthora infestans, the late blight pathogen, and an endornavirus from an unnamed Phytophthora species from Douglas fir. Studies on Phytophthora viruses have revealed several interesting systems. Phytophthora infestans RNA virus 1 (PiRV-1) and PiRV-2 are likely the first members of two new virus families; studies on PiRV-3 support the establishment of a new virus genus that is not affiliated with established virus families; PiRV-4 is a member of Narnaviridae, most likely in the genus Narnavirus; and Phytophthora endornavirus 1 (PEV1) was the first nonplant endornavirus at the time of reporting. Viral capsids have not been found in any of the above-mentioned viruses. PiRV-1 demonstrated a unique genome organization that requires further examination, and PiRV-2 may have played a role in late blight resurgence in 1980s-1990s.
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Affiliation(s)
- Guohong Cai
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, USA.
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Guo D, Hu X, Xie F, Wu X. Pattern matching with wildcards and gap-length constraints based on a centrality-degree graph. APPL INTELL 2012. [DOI: 10.1007/s10489-012-0394-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Xu D. Protein databases on the internet. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2012; Chapter 2:2.6.1-2.6.17. [PMID: 23151744 DOI: 10.1002/0471140864.ps0206s70] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein databases have become a crucial part of modern biology. Huge amounts of data for protein structures, functions, and particularly sequences are being generated. Searching databases is often the first step in the study of a new protein. Comparison between proteins or between protein families provides information about the relationship between proteins within a genome or across different species, and hence offers much more information than can be obtained by studying only an isolated protein. In addition, secondary databases derived from experimental databases are also widely available. These databases reorganize and annotate the data or provide predictions. The use of multiple databases often helps researchers understand the structure and function of a protein. Although some protein databases are widely known, they are far from being fully utilized in the protein science community. This unit provides a starting point for readers to explore the potential of protein databases on the Internet.
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Affiliation(s)
- Dong Xu
- Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri
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Freschi V, Bogliolo A, Liso A. Genome-wide computational approach for the prediction of duplications generating protein localization signals. Comput Biol Med 2012; 42:1091-7. [PMID: 23017829 DOI: 10.1016/j.compbiomed.2012.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 08/31/2012] [Accepted: 09/04/2012] [Indexed: 10/27/2022]
Abstract
Investigating the possible generation of motifs accountable for aberrant protein dislocation subsequent to the rise of short tandem duplications is interesting, given the pathogenic potential of this mechanism, as demonstrated in diseases such adult myeloid leukemia (AML). In this paper we introduce a new computational method for predicting genomic points which, after hypothetical mutation events such as micro-duplications, might encode molecular patterns such as localization or export signals. The proposed framework allows to study motifs of unconstrained length defined as regular expressions at a genome-wide level, providing an in silico platform capable of analyzing the potential effect of duplications on abnormal cellular localization.
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Affiliation(s)
- Valerio Freschi
- DiSBeF, Department of Base Sciences and Fundamentals, University of Urbino, Urbino, Italy.
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Characterization and crystal structure of the thermophilic ROK hexokinase from Thermus thermophilus. J Biosci Bioeng 2012; 114:150-4. [DOI: 10.1016/j.jbiosc.2012.03.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 03/22/2012] [Accepted: 03/26/2012] [Indexed: 11/22/2022]
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Cueva A, Concia L, Cella R. Molecular characterization of a Cyrtochilum loxense Somatic Embryogenesis Receptor-like Kinase (SERK) gene expressed during somatic embryogenesis. PLANT CELL REPORTS 2012; 31:1129-1139. [PMID: 22350407 DOI: 10.1007/s00299-012-1236-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Revised: 01/22/2012] [Accepted: 02/03/2012] [Indexed: 05/28/2023]
Abstract
Somatic embryogenesis is crucial for the propagation of endangered Ecuadorian orchid species, among them Cyrtochilum loxense, in view of the fact that their number in nature or in collections is quite reduced. One of the genes expressed during somatic and zygotic embryogenesis is Somatic Embryogenesis Receptor-like Kinase (SERK). Despite the development of somatic embryogenesis protocols for orchids, no SERK genes have been isolated from this family. This is the first report on the isolation of a full-length orchid SERK sequence, namely that of Cyrtochilum loxense (ClSERK). The identity of ClSERK was inferred by the presence of all domains typical of SERK proteins: a signal peptide, a leucine zipper domain, five LRRs, a serine proline-rich domain, a transmembrane domain, a kinase domain, and the C-terminal region. We have observed that the ClSERK gene is highly expressed in embryogenic calluses generated from protocorms at the time of appearance of embryonic morphological features. At later stages when embryos become well visible on calluses, ClSERK gene expression decreases. Compared to early stages of embryo formation on calluses, the expression detected in leaf tissue is far lower, thus suggesting a role of this gene during development.
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Affiliation(s)
- Augusta Cueva
- Ecology Institute, Universidad Técnica Particular de Loja, Loja, Ecuador.
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Cantacessi C, Campbell BE, Gasser RB. Key strongylid nematodes of animals — Impact of next-generation transcriptomics on systems biology and biotechnology. Biotechnol Adv 2012; 30:469-88. [DOI: 10.1016/j.biotechadv.2011.08.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 08/09/2011] [Accepted: 08/19/2011] [Indexed: 10/17/2022]
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SIMPSON GREGORYIC, SHARKEY LESLIEC, FRAY JOHN. ALTERED ABUNDANCE OF MESSENGER RNA TRANSCRIPTS WHOSE PRODUCTS HAVE MEMBRANE ATTACHMENT SITES IN PREGNANCY-INDUCED HYPERTENSION. J BIOL SYST 2012. [DOI: 10.1142/s021833900200069x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pregnancy-induced hypertensive disorders (PIH) are leading causes of maternal mortality. Although the mechanism responsible for initiating and maintaining the disorder is unproven, physiologic molecular attachments in kidney and placenta play a role. The SHHF/Mcc-facp (SHHF) rat has features of the disorder, including abnormal placenta gene expression. To gain a molecular understanding of the gene expression profile associated with PIH, kidneys and placentas of SHHF rats at gestation day 20 were compared to WKY controls using microarray technology. We report that SHHF rats have spontaneous PIH, elevated total placenta weights, and reduced total pup weights than WKY controls and that they also have greater total number of mRNA transcripts expressed in placenta. Kidneys of SHHF rats, on the other hand, not only expressed disproportionately more predicted gene products with attachment sites such as RGD motifs, N-glycosylation sites, and N-myristoylation sites they also responded more profoundly to oral administration of L-arginine. We conclude that the increased abundance of transcripts whose products engage in posttranslational attachments using RGD motifs, N-glycosylation sites, and N-myristoylation sites and the reversal of these increases by oral administration of L-arginine suggests that NO may be of importance in PIH at the level of molecular attachments.
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Affiliation(s)
- GREGORY I. C. SIMPSON
- Genomic Physiology Group, Cellular and Molecular Physiology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Veterinary Services Division, Ministry of Agriculture, Kingston, Jamaica
| | - LESLIE C. SHARKEY
- Department of Biomedical Sciences, Tufts University School of Veterinary Medicine, Grafton, Massachusetts, USA
| | - JOHN FRAY
- Genomic Physiology Group, Cellular and Molecular Physiology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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CANTACESSI C, CAMPBELL BE, JEX AR, YOUNG ND, HALL RS, RANGANATHAN S, GASSER RB. Bioinformatics meets parasitology. Parasite Immunol 2012; 34:265-75. [DOI: 10.1111/j.1365-3024.2011.01304.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Zha HG, Flowers VL, Yang M, Chen LY, Sun H. Acidic α-galactosidase is the most abundant nectarin in floral nectar of common tobacco (Nicotiana tabacum). ANNALS OF BOTANY 2012; 109:735-45. [PMID: 22271925 PMCID: PMC3286286 DOI: 10.1093/aob/mcr321] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 12/01/2011] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS To date, most floral nectarins (nectar proteins) are reported to function in nectar defence, particularly for insect-pollinated outcrossing species. We compared nectarin composition and abundance in selfing common tobacco (Nicotiana tobaccum) with outcrossing ornamental tobacco plants to elucidate the functional difference of nectarins in different reproductive systems. METHODS Common tobacco (CT) nectarins were separated by SDS-PAGE and the N terminus of the most abundant nectarin was sequenced via Edman degradation. The full-length nectarin gene was amplified and cloned from genomic DNA and mRNA with hiTail-PCR and RACE (rapid amplification of cDNA ends), and expression patterns were then investigated in different tissues using semi-quantitative reverse transcriptase PCR. Additionally, high-performance liquid chromatography and enzymatic analyses of nectar sugar composition, and other biochemical traits and functions of the novel nectarin were studied. KEY RESULTS The most abundant nectarin in CT nectar is an acidic α-galactosidase, here designated NTα-Gal. This compound has a molecular mass of 40 013 Da and a theoretical pI of 5·33. NTα-Gal has a conserved α-Gal characteristic signature, encodes a mature protein of 364 amino acids and is expressed in different organs. Compared with 27 other melliferous plant species from different families, CT floral nectar demonstrated the highest α-Gal activity, which is inhibited by d-galactose. Raffinose family oligosaccharides were not detected in CT nectar, indicating that NTα-Gal does not function in post-secretory hydrolysis. Moreover, tobacco plant fruits did not develop intact skin with galactose inhibition of NTα-Gal activity in nectar, suggesting that NTα-Gal induces cell-wall surface restructuring during the initial stages of fruit development. CONCLUSIONS α-Gal was the most abundant nectarin in selfing CT plants, but was not detected in the nectar of strictly outcrossing sister tobacco species. No function was demonstrated in antimicrobial defence. Therefore, floral nectarins in selfing species maintain their functional significance in reproductive organ development.
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Affiliation(s)
- Hong-Guang Zha
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - V. Lynn Flowers
- Department of Science, Tulane University, New Orleans, LA 70118, USA
| | - Min Yang
- Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ling-Yang Chen
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Hang Sun
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650204, China
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40
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Gasser RB, Cantacessi C. Heartworm genomics: unprecedented opportunities for fundamental molecular insights and new intervention strategies. Top Companion Anim Med 2012; 26:193-9. [PMID: 22152607 DOI: 10.1053/j.tcam.2011.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Vector-borne diseases, including canine heartworm disease (CHWD), are of major socioeconomic and canine health importance worldwide. Although many studies have provided insights into CHWD, to date there has been limited study of fundamental molecular aspects of Dirofilaria immitis itself, its relationship with the canine host, its vectors, as well as the potential of drug resistance to emerge, using advanced -omic technologies. This article takes a prospective view of the benefits that advanced -omics technologies will have toward understanding D. immitis and CHWD. Tackling key biological questions using these technologies will provide a "systems biology" context and could lead to radically new intervention and management strategies against heartworm.
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Affiliation(s)
- Robin B Gasser
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Abstract
Lipases are ubiquitous enzymes, widespread in nature. They were first isolated from bacteria in the early nineteenth century and the associated research continuously increased due to the particular characteristics of these enzymes. This chapter reviews the main sources, structural properties, and industrial applications of these highly studied enzymes.
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Affiliation(s)
- Leticia Casas-Godoy
- Equipe de Catalyse et Ingénierie Moléculaire Enzymatique, Laboratoire d'Ingénierie des Systèmes Biologiques et Procédés, Université de Toulouse, INSA, UPS, INP, LISBP, Toulouse, France
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42
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Schadich E, Mason D, Sin F. Co-expressed peJK genes of lobster (Jasus edwardsii). AUST J ZOOL 2012. [DOI: 10.1071/zo11105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Previous studies have shown that the two novel genes of southern rock lobster (Jasus edwardsii) named peJK2 and peJK3 are implicated in eyestalk hormonal regulation of the lobster moult cycle. Northern blot, in situ hybridisation studies and sequence analyses showed that their putative products might be transmembrane proteins associated with cell signal transduction of hormonal signals in the eyestalk during the intermoult phase of the moult cycle. The aim of this study was to analyse coexpression of peJK genes in different J. edwardsii tissues. Using reverse transcriptase–polymerase chain reaction (RT-PCR), the expression of peJK genes was analysed in seven different tissues (eyestalk, brain, epidermis, hepatopancreas, gill, muscle and heart) of an intermoult lobster. During RT-PCR analysis, a novel sequence was isolated, and was named peJK4. It shares 88% and 86% sequence identity with peJK2 and peJK3 respectively. The peJK2 and peJK4 genes are expressed in all tested tissues. Sequence analyses of the predicted peJK2 and peJK4 proteins revealed two common signal transduction motifs, transmembrane helices and protein kinase C. These results showed that the peJK genes of J. edwardsii are a complex group of genes and possibly involved in different signal transduction pathways.
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Affiliation(s)
- Dong Xu
- Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri Columbia Missouri
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44
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Nakamura T, Kashima Y, Mine S, Oku T, Uegaki K. Crystallization and preliminary crystallographic analysis of a putative glucokinase/hexokinase from Thermus thermophilus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1559-62. [PMID: 22139166 PMCID: PMC3232139 DOI: 10.1107/s1744309111041145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 10/06/2011] [Indexed: 11/10/2022]
Abstract
Glucokinase/hexokinase catalyzes the phosphorylation of glucose to glucose 6-phosphate, which is the first step of glycolysis. The open reading frame TTHA0299 of the extreme thermophile Thermus thermophilus encodes a putative glucokinase/hexokinase which contains the consensus sequence for proteins from the repressors, open reading frames and sugar kinases family. In this study, the glucokinase/hexokinase from T. thermophilus was purified and crystallized using polyethylene glycol 8000 as a precipitant. Diffraction data were collected and processed to 2.02 Å resolution. The crystal belonged to space group P2(1), with unit-cell parameters a = 70.93, b = 138.14, c = 75.16 Å, β = 95.41°.
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Affiliation(s)
- Tsutomu Nakamura
- National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577, Japan
| | - Yasuhiro Kashima
- Thermostable Enzyme Laboratory Co. Ltd, Kobe, Hyogo 650-0047, Japan
| | - Shouhei Mine
- National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577, Japan
| | - Takashi Oku
- Thermostable Enzyme Laboratory Co. Ltd, Kobe, Hyogo 650-0047, Japan
| | - Koichi Uegaki
- National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577, Japan
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45
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Yu GX. RULEMINER: A KNOWLEDGE SYSTEM FOR SUPPORTING HIGH-THROUGHPUT PROTEIN FUNCTION ANNOTATIONS. J Bioinform Comput Biol 2011; 2:615-37. [PMID: 15617156 DOI: 10.1142/s0219720004000752] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2003] [Revised: 03/23/2004] [Accepted: 03/24/2004] [Indexed: 11/18/2022]
Abstract
In this paper, we present RuleMiner, a knowledge system to facilitate a seamless integration of multi-sequence analysis tools and define profile-based rules for supporting high-throughput protein function annotations. This system consists of three essential components, Protein Function Groups (PFGs), PFG profiles and rules. The PFGs, established from an integrated analysis of current knowledge of protein functions from Swiss-Prot database and protein family-based sequence classifications, cover all possible cellular functions available in the database. The PFG profiles illustrate detailed protein features in the PFGs as in sequence conservations, the occurrences of sequence-based motifs, domains and species distributions. The rules, extracted from the PFG profiles, describe the clear relationships between these PFGs and all possible features. As a result, the RuleMiner is able to provide an enhanced capability for protein function analysis, such as results from the integrated sequence analysis tools for given proteins can be comparatively analyzed due to the clear feature-PFG relationships. Also, much needed guidance is readily available for such analysis. If the rules describe one-to-one (unique) relationships between the protein features and the PFGs, then these features can be utilized as unique functional identifiers and cellular functions of unknown proteins can be reliably determined. Otherwise, additional information has to be provided.
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Affiliation(s)
- Gong-Xin Yu
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA.
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46
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Kajava AV. Tandem repeats in proteins: from sequence to structure. J Struct Biol 2011; 179:279-88. [PMID: 21884799 DOI: 10.1016/j.jsb.2011.08.009] [Citation(s) in RCA: 169] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 08/15/2011] [Accepted: 08/17/2011] [Indexed: 10/17/2022]
Abstract
The bioinformatics analysis of proteins containing tandem repeats requires special computer programs and databases, since the conventional approaches predominantly developed for globular domains have limited success. Here, I survey bioinformatics tools which have been developed recently for identification and proteome-wide analysis of protein repeats. The last few years have also been marked by an emergence of new 3D structures of these proteins. Appraisal of the known structures and their classification uncovers a straightforward relationship between their architecture and the length of the repetitive units. This relationship and the repetitive character of structural folds suggest rules for better prediction of the 3D structures of such proteins. Furthermore, bioinformatics approaches combined with low resolution structural data, from biophysical techniques, especially, the recently emerged cryo-electron microscopy, lead to reliable prediction of the protein repeat structures and their mode of binding with partners within molecular complexes. This hybrid approach can actively be used for structural and functional annotations of proteomes.
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Affiliation(s)
- Andrey V Kajava
- Centre de Recherches de Biochimie Macromoléculaire, CNRS, Université Montpellier 1 et 2, 1919 Route de Mende, 34293 Montpellier, Cedex 5, France.
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Zhou S, Wan Q, Huang Y, Huang X, Cao J, Ye L, Lim TK, Lin Q, Qin Q. Proteomic analysis of Singapore grouper iridovirus envelope proteins and characterization of a novel envelope protein VP088. Proteomics 2011; 11:2236-48. [DOI: 10.1002/pmic.200900820] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2009] [Revised: 02/23/2011] [Accepted: 02/28/2011] [Indexed: 11/09/2022]
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Distinct properties of human HMGN5 reveal a rapidly evolving but functionally conserved nucleosome binding protein. Mol Cell Biol 2011; 31:2742-55. [PMID: 21518955 DOI: 10.1128/mcb.05216-11] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The HMGN family is a family of nucleosome-binding architectural proteins that affect the structure and function of chromatin in vertebrates. We report that the HMGN5 variant, encoded by a gene located on chromosome X, is a rapidly evolving protein with an acidic C-terminal domain that differs among vertebrate species. We found that the intranuclear organization and nucleosome interactions of human HMGN5 are distinct from those of mouse HMGN5 and that the C-terminal region of the protein is the main determinant of the chromatin interaction properties. Despite their apparent differences, both mouse and human HMGN5 proteins interact with histone H1, reduce its chromatin residence time, and can induce large-scale chromatin decompaction in living cells. Analysis of HMGN5 mutants suggests that distinct domains in HMGN5 affect specific steps in the interaction of H1 with chromatin. Elevated levels of either human or mouse HMGN5 affect the transcription of numerous genes, most in a variant-specific manner. Our study identifies HMGN5 as a rapidly evolving vertebrate nuclear protein with species-specific properties. HMGN5 has a highly disordered structure, binds dynamically to nucleosome core particles, modulates the binding of H1 to chromatin, reduces the compaction of the chromatin fiber, and affects transcription.
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Gasser RB, Cantacessi C, Campbell BE, Hofmann A, Otranto D. Major prospects for exploring canine vector borne diseases and novel intervention methods using 'omic technologies. Parasit Vectors 2011; 4:53. [PMID: 21489242 PMCID: PMC3095997 DOI: 10.1186/1756-3305-4-53] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 04/13/2011] [Indexed: 11/26/2022] Open
Abstract
Canine vector-borne diseases (CVBDs) are of major socioeconomic importance worldwide. Although many studies have provided insights into CVBDs, there has been limited exploration of fundamental molecular aspects of most pathogens, their vectors, pathogen-host relationships and disease and drug resistance using advanced, 'omic technologies. The aim of the present article is to take a prospective view of the impact that next-generation, 'omics technologies could have, with an emphasis on describing the principles of transcriptomic/genomic sequencing as well as bioinformatic technologies and their implications in both fundamental and applied areas of CVBD research. Tackling key biological questions employing these technologies will provide a 'systems biology' context and could lead to radically new intervention and management strategies against CVBDs.
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Affiliation(s)
- Robin B Gasser
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia
| | - Cinzia Cantacessi
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia
| | - Bronwyn E Campbell
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia
| | - Andreas Hofmann
- Structural Chemistry Program, Eskitis Institute for Cell & Molecular Therapies, Griffith University, Brisbane, Queensland, Australia
| | - Domenico Otranto
- Dipartimento di Sanità Pubblica e Zootecnia, Facoltà di Medicina Veterinaria, Università di Bari, Str. prov. le per Casamassima Km 3, 70010, Valenzano, Bari, Italy
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50
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Li X, Zhuo K, Luo M, Sun L, Liao J. Molecular cloning and characterization of a calreticulin cDNA from the pinewood nematode Bursaphelenchus xylophilus. Exp Parasitol 2011; 128:121-6. [PMID: 21371475 DOI: 10.1016/j.exppara.2011.02.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 02/18/2011] [Accepted: 02/21/2011] [Indexed: 10/18/2022]
Abstract
The cloning and characterization of a cDNA encoding a calreticulin from the pinewood nematode Bursaphelenchus xylophilus is described herein. The full-length cDNA (Bx-crt-1) contained a 1200 bp open reading frame that could be translated to a 399 amino acid polypeptide. The deduced protein contained highly conserved regions of a calreticulin gene and had 66.2-70.1% amino acid sequence identity to other calreticulin sequences from nematodes. RNAi, RT-PCR amplification, and southern blot suggest that Bx-crt-1 may be important for the development of B. xylophilus.
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Affiliation(s)
- Xundong Li
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou 510642, China
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