751
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A proposed integrated approach for the preclinical evaluation of phage therapy in Pseudomonas infections. Sci Rep 2016; 6:28115. [PMID: 27301427 PMCID: PMC4908380 DOI: 10.1038/srep28115] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/27/2016] [Indexed: 12/29/2022] Open
Abstract
Bacteriophage therapy is currently resurging as a potential complement/alternative to antibiotic treatment. However, preclinical evaluation lacks streamlined approaches. We here focus on preclinical approaches which have been implemented to assess bacteriophage efficacy against Pseudomonas biofilms and infections. Laser interferometry and profilometry were applied to measure biofilm matrix permeability and surface geometry changes, respectively. These biophysical approaches were combined with an advanced Airway Surface Liquid infection model, which mimics in vitro the normal and CF lung environments, and an in vivo Galleria larvae model. These assays have been implemented to analyze KTN4 (279,593 bp dsDNA genome), a type-IV pili dependent, giant phage resembling phiKZ. Upon contact, KTN4 immediately disrupts the P. aeruginosa PAO1 biofilm and reduces pyocyanin and siderophore production. The gentamicin exclusion assay on NuLi-1 and CuFi-1 cell lines revealed the decrease of extracellular bacterial load between 4 and 7 logs and successfully prevents wild-type Pseudomonas internalization into CF epithelial cells. These properties and the significant rescue of Galleria larvae indicate that giant KTN4 phage is a suitable candidate for in vivo phage therapy evaluation for lung infection applications.
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752
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Samaranayake N, Fernando SD, Neththikumara NF, Rodrigo C, Karunaweera ND, Dissanayake VHW. Association of HLA class I and II genes with cutaneous leishmaniasis: a case control study from Sri Lanka and a systematic review. BMC Infect Dis 2016; 16:292. [PMID: 27301744 PMCID: PMC4908677 DOI: 10.1186/s12879-016-1626-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 06/07/2016] [Indexed: 12/21/2022] Open
Abstract
Background The outcome of leishmaniasis is an interplay between Leishamania and the host. Identifying contributory host genetic factors is complicated by the variability in phenotype, ethnicity and parasite species. Leishmaniasis is caused exclusively by L. donovani in Sri Lanka with localized cutaneous leishmaniasis (LCL) being the predominant form. We report here an association study of human leucocyte antigen (HLA) class I and II genes with LCL in Sri Lanka, the first on HLA associations in cutaneous leishmaniasis in a South Asian population. Methods An existing DNA repository of 200 each of patients and controls was typed for HLA-DQ by PCR-SSP. Next generation sequencing-based typing for HLA-A, HLA-B and HLA-DRB1 alleles was done in a subset of 280 samples. Association tests were performed on 28,489 genotyped and imputed SNPs spanning a region of 1.4 Mb across the HLA genes. To compare our results with similar studies, we carried out a systematic review to document all HLA associations reported to-date for cutaneous and muco-cutaneous leishmaniasis. Results DRB1*04 DQB1*02 (P = 0.03; Pc = 0.09), DRB1*07 DQB1*02 (P = 0.03; Pc = 0.09) haplotypes were absent in patients. B*07 (P = 0.007; Pc = 0.13; OR = 0.36; 95 % CI = 0.17–0.77) allele and DRB1*15 DQB1*06 (P = 0.00; Pc < 0.01; OR = 0.3; 95 % CI = 0.2–.0.6) haplotype were over represented in controls and DRB1*15 (P = 0.002; Pc = 0.01) allele was over represented in patients. Two SNPs (rs281864595/rs1050517) in the antigen recognition region of HLA-B, comprised a haplotype more frequent in controls (P = 0.04). The alleles identified by the systematic review to predispose or to protect from cutaneous/mucocutaneous leishmaniasis remained highly heterogeneous in different populations studied. Conclusions Our preliminary findings suggest a role for some class I and class II HLA genes in determining predisposition to LCL in this population which should be corroborated with further studies. The systematic review reiterates this need, as the purported susceptibility or protection gained by certain HLA alleles or haplotypes has rarely been independently verified. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1626-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nilakshi Samaranayake
- Department of Parasitology, Faculty of Medicine, University of Colombo, 271, Kynsey Road, Colombo, 008, Sri Lanka
| | - Sumadhya D Fernando
- Department of Parasitology, Faculty of Medicine, University of Colombo, 271, Kynsey Road, Colombo, 008, Sri Lanka.
| | | | - Chaturaka Rodrigo
- Department of Clinical Medicine, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Nadira D Karunaweera
- Department of Parasitology, Faculty of Medicine, University of Colombo, 271, Kynsey Road, Colombo, 008, Sri Lanka
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753
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Heinz E, Stubenrauch CJ, Grinter R, Croft NP, Purcell AW, Strugnell RA, Dougan G, Lithgow T. Conserved Features in the Structure, Mechanism, and Biogenesis of the Inverse Autotransporter Protein Family. Genome Biol Evol 2016; 8:1690-705. [PMID: 27190006 PMCID: PMC4943183 DOI: 10.1093/gbe/evw112] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The bacterial cell surface proteins intimin and invasin are virulence factors that share a common domain structure and bind selectively to host cell receptors in the course of bacterial pathogenesis. The β-barrel domains of intimin and invasin show significant sequence and structural similarities. Conversely, a variety of proteins with sometimes limited sequence similarity have also been annotated as “intimin-like” and “invasin” in genome datasets, while other recent work on apparently unrelated virulence-associated proteins ultimately revealed similarities to intimin and invasin. Here we characterize the sequence and structural relationships across this complex protein family. Surprisingly, intimins and invasins represent a very small minority of the sequence diversity in what has been previously the “intimin/invasin protein family”. Analysis of the assembly pathway for expression of the classic intimin, EaeA, and a characteristic example of the most prevalent members of the group, FdeC, revealed a dependence on the translocation and assembly module as a common feature for both these proteins. While the majority of the sequences in the grouping are most similar to FdeC, a further and widespread group is two-partner secretion systems that use the β-barrel domain as the delivery device for secretion of a variety of virulence factors. This comprehensive analysis supports the adoption of the “inverse autotransporter protein family” as the most accurate nomenclature for the family and, in turn, has important consequences for our overall understanding of the Type V secretion systems of bacterial pathogens.
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Affiliation(s)
- Eva Heinz
- Department of Microbiology, Infection & Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Christopher J Stubenrauch
- Department of Microbiology, Infection & Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Rhys Grinter
- Department of Microbiology, Infection & Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia Institute of Microbiology and Infection, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Nathan P Croft
- Department of Biochemistry and Molecular Biology, Infection & Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Infection & Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Richard A Strugnell
- Department of Microbiology & Immunology, University of Melbourne, Parkville, Australia
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Trevor Lithgow
- Department of Microbiology, Infection & Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
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754
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Cheung JK, Wisniewski JA, Adams VM, Quinsey NS, Rood JI. Analysis of the virulence-associated RevSR two-component signal transduction system of Clostridium perfringens. Int J Med Microbiol 2016; 306:429-42. [PMID: 27267179 DOI: 10.1016/j.ijmm.2016.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/09/2016] [Accepted: 05/18/2016] [Indexed: 11/15/2022] Open
Abstract
Clostridium perfringens is a Gram-positive, anaerobic, spore-forming bacterium that causes human gas gangrene (clostridial myonecrosis) and food poisoning. Early studies showed that virulence was regulated by the VirSR two-component signal transduction system. However, our identification of the RevR orphan response regulator indicated that more than one system was involved in controlling virulence. To further characterize this virulence-associated regulator, gel mobility shift experiments, coupled with DNase I footprinting, were used to identify the RevR DNA binding sequence. Bioinformatics analysis suggested that an orphan sensor histidine kinase, CPE1757 (renamed RevS), was the cognate sensor of RevR. Interaction between RevS and RevR was demonstrated by use of a bacterial two-hybrid system and validated by protein-protein interaction studies using biolayer interferometry. To assess the involvement of RevS in virulence regulation, the revS gene was inactivated by Targetron insertion. When isogenic wild-type, revS and complemented revS strains were tested in a mouse myonecrosis model, the revS mutant was found to be attenuated in virulence, which was similar to the attenuation observed previously with the revR mutant. However, transcriptional analysis of selected RevR-regulated genes in the revS mutant revealed a different pattern of expression to a revR mutant, suggesting that the RevSR system is more complex than originally thought. Taken together, the results have led to the identification and characterization of the two essential parts of a new regulatory network that is involved in the regulation of virulence in C. perfringens.
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Affiliation(s)
- Jackie K Cheung
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Jessica A Wisniewski
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Vicki M Adams
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Noelene S Quinsey
- Protein Production Unit, Monash University, Clayton, Victoria 3800, Australia
| | - Julian I Rood
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia.
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755
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Warda AK, Siezen RJ, Boekhorst J, Wells-Bennik MHJ, de Jong A, Kuipers OP, Nierop Groot MN, Abee T. Linking Bacillus cereus Genotypes and Carbohydrate Utilization Capacity. PLoS One 2016; 11:e0156796. [PMID: 27272929 PMCID: PMC4896439 DOI: 10.1371/journal.pone.0156796] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/19/2016] [Indexed: 11/19/2022] Open
Abstract
We characterised carbohydrate utilisation of 20 newly sequenced Bacillus cereus strains isolated from food products and food processing environments and two laboratory strains, B. cereus ATCC 10987 and B. cereus ATCC 14579. Subsequently, genome sequences of these strains were analysed together with 11 additional B. cereus reference genomes to provide an overview of the different types of carbohydrate transporters and utilization systems found in B. cereus strains. The combined application of API tests, defined growth media experiments and comparative genomics enabled us to link the carbohydrate utilisation capacity of 22 B. cereus strains with their genome content and in some cases to the panC phylogenetic grouping. A core set of carbohydrates including glucose, fructose, maltose, trehalose, N-acetyl-glucosamine, and ribose could be used by all strains, whereas utilisation of other carbohydrates like xylose, galactose, and lactose, and typical host-derived carbohydrates such as fucose, mannose, N-acetyl-galactosamine and inositol is limited to a subset of strains. Finally, the roles of selected carbohydrate transporters and utilisation systems in specific niches such as soil, foods and the human host are discussed.
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Affiliation(s)
- Alicja K. Warda
- TI Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University, Wageningen, The Netherlands
- Wageningen UR Food & Biobased Research, Wageningen, The Netherlands
| | - Roland J. Siezen
- TI Food and Nutrition, Wageningen, The Netherlands
- Center for Molecular and Biomolecular Informatics, RadboudUMC, Nijmegen, The Netherlands
- Microbial Bioinformatics, Ede, The Netherlands
| | - Jos Boekhorst
- TI Food and Nutrition, Wageningen, The Netherlands
- Center for Molecular and Biomolecular Informatics, RadboudUMC, Nijmegen, The Netherlands
- NIZO Food Research B.V., Ede, The Netherlands
| | | | - Anne de Jong
- TI Food and Nutrition, Wageningen, The Netherlands
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Oscar P. Kuipers
- TI Food and Nutrition, Wageningen, The Netherlands
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Masja N. Nierop Groot
- TI Food and Nutrition, Wageningen, The Netherlands
- Wageningen UR Food & Biobased Research, Wageningen, The Netherlands
| | - Tjakko Abee
- TI Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University, Wageningen, The Netherlands
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756
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Meier D, Kruse J, Buttlar J, Friedrich M, Zenk F, Boesler B, Förstner KU, Hammann C, Nellen W. Analysis of the Microprocessor in Dictyostelium: The Role of RbdB, a dsRNA Binding Protein. PLoS Genet 2016; 12:e1006057. [PMID: 27272207 PMCID: PMC4894637 DOI: 10.1371/journal.pgen.1006057] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/26/2016] [Indexed: 11/28/2022] Open
Abstract
We identified the dsRNA binding protein RbdB as an essential component in miRNA processing in Dictyostelium discoideum. RbdB is a nuclear protein that accumulates, together with Dicer B, in nucleolar foci reminiscent of plant dicing bodies. Disruption of rbdB results in loss of miRNAs and accumulation of primary miRNAs. The phenotype can be rescued by ectopic expression of RbdB thus allowing for a detailed analysis of domain function. The lack of cytoplasmic dsRBD proteins involved in miRNA processing, suggests that both processing steps take place in the nucleus thus resembling the plant pathway. However, we also find features e.g. in the domain structure of Dicer which suggest similarities to animals. Reduction of miRNAs in the rbdB- strain and their increase in the Argonaute A knock out allowed the definition of new miRNAs one of which appears to belong to a new non-canonical class. miRNAs are essential regulators in eukaryotic cells and serve to control translation and stability of mRNAs. Processing of primary miRNA transcripts is carried out in two steps by evolutionary conserved machineries consisting mainly of double-strand specific RNases of the Dicer family and accessory double-strand RNA binding proteins (dsRBPs). Regulation occurs by effector proteins of the Argonaute family. While processing in plants is confined to the nucleus, the mechanisms is split into a nuclear and a cytoplasmic step in animals. By knock-out and complementation experiments, we identify RbdB in the amoebozoa Dictyostelium as the accessory dsRBP processing component for both steps. Fluorescence microscopy shows that RbdB co-localizes with the RNaseIII Dicer B in nucleolar foci suggesting mechanistic similarities to plants. Functional domain analysis of RbdB and the structure of Dicers, however, indicate similarities to animals. This places Dictyostelium at an evolutionary branch point between plants and animals. Deep sequencing reveals that the rbdB knock-out strain shows reduced accumulation of microRNAs. Comparison with the wild type and the miRNA overexpressing agnA knock-out strain, allowed for the identification of new miRNAs in Dictyostelium which may have escaped detection by other methods.
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Affiliation(s)
- Doreen Meier
- Department of Genetics, FB10, Kassel University, Kassel, Germany
| | - Janis Kruse
- Ribogenetics Biochemistry Laboratory, Department of Life Science and Chemistry, Molecular Life Sciences Research Center, Jacobs University, Bremen, Germany
| | - Jann Buttlar
- Department of Genetics, FB10, Kassel University, Kassel, Germany
| | | | - Fides Zenk
- Department of Genetics, FB10, Kassel University, Kassel, Germany
| | - Benjamin Boesler
- Department of Genetics, FB10, Kassel University, Kassel, Germany
| | | | - Christian Hammann
- Ribogenetics Biochemistry Laboratory, Department of Life Science and Chemistry, Molecular Life Sciences Research Center, Jacobs University, Bremen, Germany
| | - Wolfgang Nellen
- Department of Genetics, FB10, Kassel University, Kassel, Germany
- * E-mail:
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757
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Ricci L, Chaurasia A, Lapébie P, Dru P, Helm RR, Copley RR, Tiozzo S. Identification of differentially expressed genes from multipotent epithelia at the onset of an asexual development. Sci Rep 2016; 6:27357. [PMID: 27264734 PMCID: PMC4893630 DOI: 10.1038/srep27357] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/17/2016] [Indexed: 11/19/2022] Open
Abstract
Organisms that have evolved alternative modes of reproduction, complementary to the sexual mode, are found across metazoans. The chordate Botryllus schlosseri is an emerging model for asexual development studies. Botryllus can rebuild its entire body from a portion of adult epithelia in a continuous and stereotyped process called blastogenesis. Anatomy and ontogenies of blastogenesis are well described, however molecular signatures triggering this developmental process are entirely unknown. We isolated tissues at the site of blastogenesis onset and from the same epithelia where this process is never triggered. We linearly amplified an ultra-low amount of mRNA (<10ng) and generated three transcriptome datasets. To provide a conservative landscape of transcripts differentially expressed between blastogenic vs. non-blastogenic epithelia we compared three different mapping and analysis strategies with a de novo assembled transcriptome and partially assembled genome as references, additionally a self-mapping strategy on the dataset. A subset of differentially expressed genes were analyzed and validated by in situ hybridization. The comparison of different analyses allowed us to isolate stringent sets of target genes, including transcripts with potential involvement in the onset of a non-embryonic developmental pathway. The results provide a good entry point to approach regenerative event in a basal chordate.
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Affiliation(s)
- Lorenzo Ricci
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, 06230, Villefranche-sur-mer, France
| | - Ankita Chaurasia
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, 06230, Villefranche-sur-mer, France
| | - Pascal Lapébie
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, 06230, Villefranche-sur-mer, France
| | - Philippe Dru
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, 06230, Villefranche-sur-mer, France
| | - Rebecca R Helm
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Richard R Copley
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, 06230, Villefranche-sur-mer, France
| | - Stefano Tiozzo
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, 06230, Villefranche-sur-mer, France
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758
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Chaves AFA, Navarro MV, Castilho DG, Calado JCP, Conceição PM, Batista WL. A conserved dimorphism-regulating histidine kinase controls the dimorphic switching in Paracoccidioides brasiliensis. FEMS Yeast Res 2016; 16:fow047. [PMID: 27268997 DOI: 10.1093/femsyr/fow047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2016] [Indexed: 02/05/2023] Open
Abstract
Paracoccidioides brasiliensis and P. lutzii, thermally dimorphic fungi, are the causative agents of paracoccidioidomycosis (PCM). Paracoccidioides infection occurs when conidia or mycelium fragments are inhaled by the host, which causes the Paracoccidioides cells to transition to the yeast form. The development of disease requires conidia inside the host alveoli to differentiate into yeast cells in a temperature-dependent manner. We describe the presence of a two-component signal transduction system in P. brasiliensis, which we investigated by expression analysis of a hypothetical protein gene (PADG_07579) that showed high similarity with the dimorphism-regulating histidine kinase (DRK1) gene of Blastomyces dermatitidis and Histoplasma capsulatum This gene was sensitive to environmental redox changes, which was demonstrated by a dose-dependent decrease in transcript levels after peroxide stimulation and a subtler decrease in transcript levels after NO stimulation. Furthermore, the higher PbDRK1 levels after treatment with increasing NaCl concentrations suggest that this histidine kinase can play a role as osmosensing. In the mycelium-yeast (M→Y) transition, PbDRK1 mRNA expression increased 14-fold after 24 h incubation at 37°C, consistent with similar observations in other virulent fungi. These results demonstrate that the PbDRK1 gene is differentially expressed during the dimorphic M→Y transition. Finally, when P. brasiliensis mycelium cells were exposed to a histidine kinase inhibitor and incubated at 37°C, there was a delay in the dimorphic M→Y transition, suggesting that histidine kinases could be targets of interest for PCM therapy.
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Affiliation(s)
- Alison F A Chaves
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, Unidade José Alencar, Street São Nicolau, nº210, 4º floor, São Paulo 04023-900, Brazil
| | - Marina V Navarro
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, Unidade José Alencar, Street São Nicolau, nº210, 4º floor, São Paulo 04023-900, Brazil
| | - Daniele G Castilho
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, Unidade José Alencar, Street São Nicolau, nº210, 4º floor, São Paulo 04023-900, Brazil
| | - Juliana C P Calado
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, Unidade José Alencar, Street São Nicolau, nº210, 4º floor, São Paulo 04023-900, Brazil
| | - Palloma M Conceição
- Departamento de Ciências Farmacêuticas, Universidade Federal de São Paulo, Diadema 09913-030, São Paulo, Brazil
| | - Wagner L Batista
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, Unidade José Alencar, Street São Nicolau, nº210, 4º floor, São Paulo 04023-900, Brazil Departamento de Ciências Farmacêuticas, Universidade Federal de São Paulo, Diadema 09913-030, São Paulo, Brazil
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759
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Intact spore MALDI-TOF mass spectrometry and proteomic analysis of Puccinia pathogenic fungi. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1093-1103. [PMID: 27267623 DOI: 10.1016/j.bbapap.2016.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/27/2016] [Accepted: 06/02/2016] [Indexed: 11/20/2022]
Abstract
The aim of this work was to develop a method for the identification of pathogens causing rust diseases of crops using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of intact cells or spores (IC/IS). All optimizations were performed with Puccinia triticina, the causal agent of wheat leaf rust. Experiments included selection of washing solvents for spores, finding of an optimal concentration of spores in suspension and the most suitable matrix system as well as an evaluation of different sample preparation techniques. The best results were obtained when the spores were washed with acetonitrile/0.1% (v/v) trifluoroacetic acid, 7:3, v/v. A mixture of ferulic and sinapinic acids (5:15mgml(-1)) dissolved in acetonitrile/2.5% (v/v) trifluoroacetic acid, 7:3, v/v, was found optimal for the deposition of samples (50μg spores per μl) by two-layer volume technique. The optimized protocol was subsequently applied to other Puccinia species (Puccinia graminis, Puccinia striiformis and Puccinia coronata). Together with the use of the software BIOSPEAN, not only different species but also various pathotypes of the same species, which differ in their virulence, could be discriminated. There were 108 and 29 proteins identified from P. striiformis and P. graminis spores, respectively, after an acidic extraction in the matrix solvent mimicking the sample preparation for MALDI. Besides the presence of ribosomal proteins, histones, regulatory proteins and enzymes, also extracellular proteins participating in the pathogenesis were found. Finally, for both species, several proteins were assigned to signals in typical mass spectrometric profiles and suggested as diagnostic markers.
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760
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Haycocks JRJ, Grainger DC. Unusually Situated Binding Sites for Bacterial Transcription Factors Can Have Hidden Functionality. PLoS One 2016; 11:e0157016. [PMID: 27258043 PMCID: PMC4892627 DOI: 10.1371/journal.pone.0157016] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 05/23/2016] [Indexed: 01/13/2023] Open
Abstract
A commonly accepted paradigm of molecular biology is that transcription factors control gene expression by binding sites at the 5' end of a gene. However, there is growing evidence that transcription factor targets can occur within genes or between convergent genes. In this work, we have investigated one such target for the cyclic AMP receptor protein (CRP) of enterotoxigenic Escherichia coli. We show that CRP binds between two convergent genes. When bound, CRP regulates transcription of a small open reading frame, which we term aatS, embedded within one of the adjacent genes. Our work demonstrates that non-canonical sites of transcription factor binding can have hidden functionality.
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Affiliation(s)
- James R. J. Haycocks
- Institute of Microbiology and Infection, School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - David C. Grainger
- Institute of Microbiology and Infection, School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
- * E-mail:
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761
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Saripella GV, Sonnhammer ELL, Forslund K. Benchmarking the next generation of homology inference tools. Bioinformatics 2016; 32:2636-41. [PMID: 27256311 PMCID: PMC5013910 DOI: 10.1093/bioinformatics/btw305] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 05/05/2016] [Indexed: 12/21/2022] Open
Abstract
Motivation: Over the last decades, vast numbers of sequences were deposited in public databases. Bioinformatics tools allow homology and consequently functional inference for these sequences. New profile-based homology search tools have been introduced, allowing reliable detection of remote homologs, but have not been systematically benchmarked. To provide such a comparison, which can guide bioinformatics workflows, we extend and apply our previously developed benchmark approach to evaluate the ‘next generation’ of profile-based approaches, including CS-BLAST, HHSEARCH and PHMMER, in comparison with the non-profile based search tools NCBI-BLAST, USEARCH, UBLAST and FASTA. Method: We generated challenging benchmark datasets based on protein domain architectures within either the PFAM + Clan, SCOP/Superfamily or CATH/Gene3D domain definition schemes. From each dataset, homologous and non-homologous protein pairs were aligned using each tool, and standard performance metrics calculated. We further measured congruence of domain architecture assignments in the three domain databases. Results: CSBLAST and PHMMER had overall highest accuracy. FASTA, UBLAST and USEARCH showed large trade-offs of accuracy for speed optimization. Conclusion: Profile methods are superior at inferring remote homologs but the difference in accuracy between methods is relatively small. PHMMER and CSBLAST stand out with the highest accuracy, yet still at a reasonable computational cost. Additionally, we show that less than 0.1% of Swiss-Prot protein pairs considered homologous by one database are considered non-homologous by another, implying that these classifications represent equivalent underlying biological phenomena, differing mostly in coverage and granularity. Availability and Implementation: Benchmark datasets and all scripts are placed at (http://sonnhammer.org/download/Homology_benchmark). Contact:forslund@embl.de Supplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ganapathi Varma Saripella
- Science for Life Laboratory, Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-10691, Sweden
| | - Erik L L Sonnhammer
- Science for Life Laboratory, Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-10691, Sweden
| | - Kristoffer Forslund
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg 69117, Germany
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762
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Boari de Lima E, Meira W, de Melo-Minardi RC. Isofunctional Protein Subfamily Detection Using Data Integration and Spectral Clustering. PLoS Comput Biol 2016; 12:e1005001. [PMID: 27348631 PMCID: PMC4922564 DOI: 10.1371/journal.pcbi.1005001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 05/22/2016] [Indexed: 01/14/2023] Open
Abstract
As increasingly more genomes are sequenced, the vast majority of proteins may only be annotated computationally, given experimental investigation is extremely costly. This highlights the need for computational methods to determine protein functions quickly and reliably. We believe dividing a protein family into subtypes which share specific functions uncommon to the whole family reduces the function annotation problem's complexity. Hence, this work's purpose is to detect isofunctional subfamilies inside a family of unknown function, while identifying differentiating residues. Similarity between protein pairs according to various properties is interpreted as functional similarity evidence. Data are integrated using genetic programming and provided to a spectral clustering algorithm, which creates clusters of similar proteins. The proposed framework was applied to well-known protein families and to a family of unknown function, then compared to ASMC. Results showed our fully automated technique obtained better clusters than ASMC for two families, besides equivalent results for other two, including one whose clusters were manually defined. Clusters produced by our framework showed great correspondence with the known subfamilies, besides being more contrasting than those produced by ASMC. Additionally, for the families whose specificity determining positions are known, such residues were among those our technique considered most important to differentiate a given group. When run with the crotonase and enolase SFLD superfamilies, the results showed great agreement with this gold-standard. Best results consistently involved multiple data types, thus confirming our hypothesis that similarities according to different knowledge domains may be used as functional similarity evidence. Our main contributions are the proposed strategy for selecting and integrating data types, along with the ability to work with noisy and incomplete data; domain knowledge usage for detecting subfamilies in a family with different specificities, thus reducing the complexity of the experimental function characterization problem; and the identification of residues responsible for specificity.
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Affiliation(s)
- Elisa Boari de Lima
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Wagner Meira
- Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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763
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Lees JG, Dawson NL, Sillitoe I, Orengo CA. Functional innovation from changes in protein domains and their combinations. Curr Opin Struct Biol 2016; 38:44-52. [DOI: 10.1016/j.sbi.2016.05.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/17/2016] [Accepted: 05/24/2016] [Indexed: 10/21/2022]
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764
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Ramakrishnan G, Jain A, Chandra N, Srinivasan N. Computational recognition and analysis of hitherto uncharacterized nucleotide cyclase-like proteins in bacteria. Biol Direct 2016; 11:27. [PMID: 27246835 PMCID: PMC4886424 DOI: 10.1186/s13062-016-0130-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/24/2016] [Indexed: 11/10/2022] Open
Abstract
UNLABELLED Evolutionary relationship between class III nucleotide cyclases and an uncharacterized set of bacterial proteins from Actinobacteria, Bacteroidetes and Proteobacteria has been recognized and analyzed. Detailed analyses of sequence and structural features resulted in the recognition of potential cyclase function conferring residues and presence of signature topological motif (βααββαβ) in the uncharacterized set of bacterial proteins. Lack of transmembrane domains and signal peptide cleavage sites is suggestive of their cytosolic subcellular localization. Furthermore, analysis on evolutionarily conserved gene clusters of the predicted nucleotide cyclase-like proteins and their evolutionary relationship with nucleotide cyclases suggest their participation in cellular signalling events. Our analyses suggest expansion of class III nucleotide cyclases. REVIEWERS This article was reviewed by Eugene Koonin and Michael Gromiha.
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Affiliation(s)
- Gayatri Ramakrishnan
- Indian Institute of Science Mathematics Initiative, Indian Institute of Science, Bangalore, 560012, India.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Abha Jain
- Undergraduate studies, Indian Institute of Science, Bangalore, 560012, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
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765
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Tuveng TR, Arntzen MØ, Bengtsson O, Gardner JG, Vaaje-Kolstad G, Eijsink VG. Proteomic investigation of the secretome ofCellvibrio japonicusduring growth on chitin. Proteomics 2016; 16:1904-14. [DOI: 10.1002/pmic.201500419] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 04/05/2016] [Accepted: 05/09/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Tina Rise Tuveng
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
| | - Magnus Øverlie Arntzen
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
| | - Oskar Bengtsson
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
| | - Jeffrey G. Gardner
- Department of Biological Sciences; University of Maryland - Baltimore County; Baltimore MD USA
| | - Gustav Vaaje-Kolstad
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
| | - Vincent G.H. Eijsink
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences (NMBU); Aas Norway
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766
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Tóth Á, Barna T, Szabó E, Elek R, Hubert Á, Nagy I, Nagy I, Kriszt B, Táncsics A, Kukolya J. Cloning, Expression and Biochemical Characterization of Endomannanases from Thermobifida Species Isolated from Different Niches. PLoS One 2016; 11:e0155769. [PMID: 27223892 PMCID: PMC4880297 DOI: 10.1371/journal.pone.0155769] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/03/2016] [Indexed: 11/19/2022] Open
Abstract
Thermobifidas are thermotolerant, compost inhabiting actinomycetes which have complex polysaccharide hydrolyzing enzyme systems. The best characterized enzymes of these hydrolases are cellulases from T. fusca, while other important enzymes especially hemicellulases are not deeply explored. To fill this gap we cloned and investigated endomannanases from those reference strains of the Thermobifida genus, which have published data on other hydrolases (T. fusca TM51, T. alba CECT3323, T. cellulosilytica TB100T and T. halotolerans YIM90462T). Our phylogenetic analyses of 16S rDNA and endomannanase sequences revealed that T. alba CECT3323 is miss-classified; it belongs to the T. fusca species. The cloned and investigated endomannanases belong to the family of glycosyl hydrolases 5 (GH5), their size is around 50 kDa and they are modular enzymes. Their catalytic domains are extended by a C-terminal carbohydrate binding module (CBM) of type 2 with a 23–25 residues long interdomain linker region consisting of Pro, Thr and Glu/Asp rich repetitive tetrapeptide motifs. Their polypeptide chains exhibit high homology, interdomain sequence, which don’t show homology to each other, but all of them are built up from 3–6 times repeated tetrapeptide motifs) (PTDP-Tc, TEEP-Tf, DPGT-Th). All of the heterologously expressed Man5A enzymes exhibited activity only on mannan. The pH optima of Man5A enzymes from T. halotolerans, T. cellulosilytica and T. fusca are slightly different (7.0, 7.5 and 8.0, respectively) while their temperature optima span within the range of 70–75°C. The three endomannanases exhibited very similar kinetic performances on LBG-mannan substrate: 0.9–1.7mM of KM and 80–120 1/sec of turnover number. We detected great variability in heat stability at 70°C, which was influenced by the presence of Ca2+. The investigated endomannanases might be important subjects for studying the structure/function relation behind the heat stability and for industrial applications to hemicellulose degradation.
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Affiliation(s)
- Ákos Tóth
- Department of Applied and Environmental Microbiology, National Agricultural Research and Innovation Centre, Budapest, Hungary
| | - Terézia Barna
- Department of Genetics and Applied Microbiology, University of Debrecen, Hungary
| | - Erna Szabó
- Department of Genetics and Applied Microbiology, University of Debrecen, Hungary
| | - Rita Elek
- Department of Genetics and Applied Microbiology, University of Debrecen, Hungary
| | - Ágnes Hubert
- Department of Molecular Structural Biology, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - István Nagy
- Department of Molecular Structural Biology, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - István Nagy
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Balázs Kriszt
- Department of Environmental Protection and Environmental Safety, Szent István University, Gödöllő, Hungary
| | - András Táncsics
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary
| | - József Kukolya
- Department of Applied and Environmental Microbiology, National Agricultural Research and Innovation Centre, Budapest, Hungary
- * E-mail:
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767
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Qian L, Nie L, Chen M, Liu P, Zhu J, Zhai L, Tao SC, Cheng Z, Zhao Y, Tan M. Global Profiling of Protein Lysine Malonylation in Escherichia coli Reveals Its Role in Energy Metabolism. J Proteome Res 2016; 15:2060-71. [DOI: 10.1021/acs.jproteome.6b00264] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Lili Qian
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Litong Nie
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Ming Chen
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Ping Liu
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jun Zhu
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou 310018, PR China
| | - Linhui Zhai
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Sheng-ce Tao
- Shanghai
Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine
(Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Zhongyi Cheng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou 310018, PR China
| | - Yingming Zhao
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- Ben
May Department for Cancer Research, University of Chicago, Chicago, Illinois 60637, United States
| | - Minjia Tan
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
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768
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Kentache T, Jouenne T, Dé E, Hardouin J. Proteomic characterization of Nα- and Nε-acetylation in Acinetobacter baumannii. J Proteomics 2016; 144:148-58. [PMID: 27222042 DOI: 10.1016/j.jprot.2016.05.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/12/2016] [Accepted: 05/18/2016] [Indexed: 12/25/2022]
Abstract
Nα- and Nε-acetylation represent a pivotal post-translational modification used by both eukaryotes and prokaryotes to modulate diverse biological processes. Acinetobacter baumannii has been described as an important nosocomial pathogen for the past 30 years, frequently involved in ventilator-associated pneumonia, bloodstream and urinary tract infections. Many aspects of the biology of A. baumannii remain elusive, in particular the extent and function of N-acetylation. We investigated here N-acetylation in A. baumannii strain ATCC 17978 by proteomic analysis, and we showed the usefulness of using different analytical approaches. Overall, we identified 525 N-acetylated proteins in which, 145 were Nα-acetylated and 411 were Nε-acetylated. Among them, 41 proteins carried both types of N-acetylation. We found that N-acetylation may play a role in biofilm formation, bacterial virulence (e.g. in several iron acquisition pathways), as well as a number of phenotypes, such as, stress adaptation and drug resistance. BIOLOGICAL SIGNIFICANCE This study is the first to perform the N-acetylome of A. baumannii using different analytical approaches. Each analytical tool permitted to characterize distinctive modified peptides. The combination of all these methods allowed us to identify 145 and 411 Nα- and Nε-acetylated proteins. Besides the fact that acetylation was involved in central metabolism as previously described in other bacteria, some N-acetylated proteins showed interesting role in bacterial virulence (iron acquisition), biofilm formation, stress adaptation and drug resistance of A. baumannii.
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Affiliation(s)
- Takfarinas Kentache
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France
| | - Thierry Jouenne
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France
| | - Emmanuelle Dé
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France
| | - Julie Hardouin
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France.
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769
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Shim JE, Lee I. Weighted mutual information analysis substantially improves domain-based functional network models. Bioinformatics 2016; 32:2824-30. [PMID: 27207946 PMCID: PMC5018372 DOI: 10.1093/bioinformatics/btw320] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 05/16/2016] [Indexed: 11/30/2022] Open
Abstract
Motivation: Functional protein–protein interaction (PPI) networks elucidate molecular pathways underlying complex phenotypes, including those of human diseases. Extrapolation of domain–domain interactions (DDIs) from known PPIs is a major domain-based method for inferring functional PPI networks. However, the protein domain is a functional unit of the protein. Therefore, we should be able to effectively infer functional interactions between proteins based on the co-occurrence of domains. Results: Here, we present a method for inferring accurate functional PPIs based on the similarity of domain composition between proteins by weighted mutual information (MI) that assigned different weights to the domains based on their genome-wide frequencies. Weighted MI outperforms other domain-based network inference methods and is highly predictive for pathways as well as phenotypes. A genome-scale human functional network determined by our method reveals numerous communities that are significantly associated with known pathways and diseases. Domain-based functional networks may, therefore, have potential applications in mapping domain-to-pathway or domain-to-phenotype associations. Availability and Implementation: Source code for calculating weighted mutual information based on the domain profile matrix is available from www.netbiolab.org/w/WMI. Contact:Insuklee@yonsei.ac.kr Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jung Eun Shim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
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770
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Kawase R, Nishimura Y, Ashikawa Y, Sasagawa S, Murakami S, Yuge M, Okabe S, Kawaguchi K, Yamamoto H, Moriyuki K, Yamane S, Tsuruma K, Shimazawa M, Hara H, Tanaka T. EP300 Protects from Light-Induced Retinopathy in Zebrafish. Front Pharmacol 2016; 7:126. [PMID: 27242532 PMCID: PMC4871856 DOI: 10.3389/fphar.2016.00126] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/05/2016] [Indexed: 01/06/2023] Open
Abstract
Exposure of rhodopsin to bright white light can induce photoreceptor cell damage and degeneration. However, a comprehensive understanding of the mechanisms underlying light-induced retinopathy remains elusive. In this study, we performed comparative transcriptome analysis of three rodent models of light-induced retinopathy, and we identified 37 genes that are dysregulated in all three models. Gene ontology analysis revealed that this gene set is significantly associated with a cytokine signaling axis composed of signal transducer and activator of transcription 1 and 3 (STAT1/3), interleukin 6 signal transducer (IL6ST), and oncostatin M receptor (OSMR). Furthermore, the analysis suggested that the histone acetyltransferase EP300 may be a key upstream regulator of the STAT1/3–IL6ST/OSMR axis. To examine the role of EP300 directly, we developed a larval zebrafish model of light-induced retinopathy. Using this model, we demonstrated that pharmacological inhibition of EP300 significantly increased retinal cell apoptosis, decreased photoreceptor cell outer segments, and increased proliferation of putative Müller cells upon exposure to intense light. These results suggest that EP300 may protect photoreceptor cells from light-induced damage and that activation of EP300 may be a novel therapeutic approach for the treatment of retinal degenerative diseases.
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Affiliation(s)
- Reiko Kawase
- Department of Molecular and Cellular Pharmacology, Pharmacogenomics, and Pharmacoinformatics, Mie University Graduate School of Medicine Tsu, Japan
| | - Yuhei Nishimura
- Department of Molecular and Cellular Pharmacology, Pharmacogenomics, and Pharmacoinformatics, Mie University Graduate School of MedicineTsu, Japan; Mie University Medical Zebrafish Research CenterTsu, Japan; Department of Systems Pharmacology, Mie University Graduate School of MedicineTsu, Japan; Department of Omics Medicine, Mie University Industrial Technology Innovation InstituteTsu, Japan; Department of Bioinformatics, Mie University Life Science Research CenterTsu, Japan
| | - Yoshifumi Ashikawa
- Department of Molecular and Cellular Pharmacology, Pharmacogenomics, and Pharmacoinformatics, Mie University Graduate School of Medicine Tsu, Japan
| | - Shota Sasagawa
- Department of Molecular and Cellular Pharmacology, Pharmacogenomics, and Pharmacoinformatics, Mie University Graduate School of Medicine Tsu, Japan
| | - Soichiro Murakami
- Department of Molecular and Cellular Pharmacology, Pharmacogenomics, and Pharmacoinformatics, Mie University Graduate School of Medicine Tsu, Japan
| | - Mizuki Yuge
- Department of Molecular and Cellular Pharmacology, Pharmacogenomics, and Pharmacoinformatics, Mie University Graduate School of Medicine Tsu, Japan
| | - Shiko Okabe
- Department of Molecular and Cellular Pharmacology, Pharmacogenomics, and Pharmacoinformatics, Mie University Graduate School of Medicine Tsu, Japan
| | - Koki Kawaguchi
- Department of Molecular and Cellular Pharmacology, Pharmacogenomics, and Pharmacoinformatics, Mie University Graduate School of Medicine Tsu, Japan
| | | | | | | | - Kazuhiro Tsuruma
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University Gifu, Japan
| | - Masamitsu Shimazawa
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University Gifu, Japan
| | - Hideaki Hara
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University Gifu, Japan
| | - Toshio Tanaka
- Department of Molecular and Cellular Pharmacology, Pharmacogenomics, and Pharmacoinformatics, Mie University Graduate School of MedicineTsu, Japan; Mie University Medical Zebrafish Research CenterTsu, Japan; Department of Systems Pharmacology, Mie University Graduate School of MedicineTsu, Japan; Department of Omics Medicine, Mie University Industrial Technology Innovation InstituteTsu, Japan; Department of Bioinformatics, Mie University Life Science Research CenterTsu, Japan
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771
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Yan GX, Dang H, Tian M, Zhang J, Shodhan A, Ning YZ, Xiong J, Miao W. Cyc17, a meiosis-specific cyclin, is essential for anaphase initiation and chromosome segregation in Tetrahymena thermophila. Cell Cycle 2016; 15:1855-64. [PMID: 27192402 DOI: 10.1080/15384101.2016.1188238] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Although the role of cyclins in controlling nuclear division is well established, their function in ciliate meiosis remains unknown. In ciliates, the cyclin family has undergone massive expansion which suggests that diverse cell cycle systems exist, and this warrants further investigation. A screen for cyclins in the model ciliate Tetrahymena thermophila showed that there are 34 cyclins in this organism. Only 1 cyclin, Cyc17, contains the complete cyclin core and is specifically expressed during meiosis. Deletion of CYC17 led to meiotic arrest at the diakinesis-like metaphase I stage. Expression of genes involved in DNA metabolism and chromosome organization (chromatin remodeling and basic chromosomal structure) was repressed in cyc17 knockout matings. Further investigation suggested that Cyc17 is involved in regulating spindle pole attachment, and is thus essential for chromosome segregation at meiosis. These findings suggest a simple model in which chromosome segregation is influenced by Cyc17.
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Affiliation(s)
- Guan-Xiong Yan
- a Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , People's Republic of China.,b University of Chinese Academy of Sciences , Beijing , People's Republic of China
| | - Huai Dang
- c College of Life Sciences, Northwest Normal University , Lanzhou , People's Republic of China
| | - Miao Tian
- a Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , People's Republic of China.,d Department of Chromosome Biology and Max F. Perutz Laboratories , Center for Molecular Biology, University of Vienna , Vienna , Austria
| | - Jing Zhang
- a Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , People's Republic of China.,b University of Chinese Academy of Sciences , Beijing , People's Republic of China
| | - Anura Shodhan
- d Department of Chromosome Biology and Max F. Perutz Laboratories , Center for Molecular Biology, University of Vienna , Vienna , Austria
| | - Ying-Zhi Ning
- c College of Life Sciences, Northwest Normal University , Lanzhou , People's Republic of China
| | - Jie Xiong
- a Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Wei Miao
- a Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , People's Republic of China
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772
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Cenci U, Moog D, Curtis BA, Tanifuji G, Eme L, Lukeš J, Archibald JM. Heme pathway evolution in kinetoplastid protists. BMC Evol Biol 2016; 16:109. [PMID: 27193376 PMCID: PMC4870792 DOI: 10.1186/s12862-016-0664-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 04/21/2016] [Indexed: 01/09/2023] Open
Abstract
Background Kinetoplastea is a diverse protist lineage composed of several of the most successful parasites on Earth, organisms whose metabolisms have coevolved with those of the organisms they infect. Parasitic kinetoplastids have emerged from free-living, non-pathogenic ancestors on multiple occasions during the evolutionary history of the group. Interestingly, in both parasitic and free-living kinetoplastids, the heme pathway—a core metabolic pathway in a wide range of organisms—is incomplete or entirely absent. Indeed, Kinetoplastea investigated thus far seem to bypass the need for heme biosynthesis by acquiring heme or intermediate metabolites directly from their environment. Results Here we report the existence of a near-complete heme biosynthetic pathway in Perkinsela spp., kinetoplastids that live as obligate endosymbionts inside amoebozoans belonging to the genus Paramoeba/Neoparamoeba. We also use phylogenetic analysis to infer the evolution of the heme pathway in Kinetoplastea. Conclusion We show that Perkinsela spp. is a deep-branching kinetoplastid lineage, and that lateral gene transfer has played a role in the evolution of heme biosynthesis in Perkinsela spp. and other Kinetoplastea. We also discuss the significance of the presence of seven of eight heme pathway genes in the Perkinsela genome as it relates to its endosymbiotic relationship with Paramoeba. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0664-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ugo Cenci
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Halifax, Nova Scotia, Canada
| | - Daniel Moog
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Halifax, Nova Scotia, Canada
| | - Bruce A Curtis
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Halifax, Nova Scotia, Canada
| | - Goro Tanifuji
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Laura Eme
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Halifax, Nova Scotia, Canada
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, and Faculty of Sciences, University of South Bohemia, České Budӗjovice, Czech Republic.,Canadian Institute for Advanced Research, Toronto, Canada
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada. .,Centre for Comparative Genomics and Evolutionary Bioinformatics, Halifax, Nova Scotia, Canada. .,Canadian Institute for Advanced Research, Toronto, Canada.
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773
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Song A, Li P, Xin J, Chen S, Zhao K, Wu D, Fan Q, Gao T, Chen F, Guan Z. Transcriptome-Wide Survey and Expression Profile Analysis of Putative Chrysanthemum HD-Zip I and II Genes. Genes (Basel) 2016; 7:genes7050019. [PMID: 27196930 PMCID: PMC4880839 DOI: 10.3390/genes7050019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/05/2016] [Accepted: 05/03/2016] [Indexed: 12/30/2022] Open
Abstract
The homeodomain-leucine zipper (HD-Zip) transcription factor family is a key transcription factor family and unique to the plant kingdom. It consists of a homeodomain and a leucine zipper that serve in combination as a dimerization motif. The family can be classified into four subfamilies, and these subfamilies participate in the development of hormones and mediation of hormone action and are involved in plant responses to environmental conditions. However, limited information on this gene family is available for the important chrysanthemum ornamental species (Chrysanthemum morifolium). Here, we characterized 17 chrysanthemum HD-Zip genes based on transcriptome sequences. Phylogenetic analyses revealed that 17 CmHB genes were distributed in the HD-Zip subfamilies I and II and identified two pairs of putative orthologous proteins in Arabidopsis and chrysanthemum and four pairs of paralogous proteins in chrysanthemum. The software MEME was used to identify 7 putative motifs with E values less than 1e-3 in the chrysanthemum HD-Zip factors, and they can be clearly classified into two groups based on the composition of the motifs. A bioinformatics analysis predicted that 8 CmHB genes could be targeted by 10 miRNA families, and the expression of these 17 genes in response to phytohormone treatments and abiotic stresses was characterized. The results presented here will promote research on the various functions of the HD-Zip gene family members in plant hormones and stress responses.
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Affiliation(s)
- Aiping Song
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Peiling Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jingjing Xin
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Kunkun Zhao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Dan Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Qingqing Fan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Tianwei Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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774
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Sun C, Fu GY, Zhang CY, Hu J, Xu L, Wang RJ, Su Y, Han SB, Yu XY, Cheng H, Zhang XQ, Huo YY, Xu XW, Wu M. Isolation and Complete Genome Sequence of Algibacter alginolytica sp. nov., a Novel Seaweed-Degrading Bacteroidetes Bacterium with Diverse Putative Polysaccharide Utilization Loci. Appl Environ Microbiol 2016; 82:2975-2987. [PMID: 26969704 PMCID: PMC4959061 DOI: 10.1128/aem.00204-16] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 03/04/2016] [Indexed: 11/20/2022] Open
Abstract
The members of the phylum Bacteroidetes are recognized as some of the most important specialists for the degradation of polysaccharides. However, in contrast to research on Bacteroidetes in the human gut, research on polysaccharide degradation by marine Bacteroidetes is still rare. The genus Algibacter belongs to the Flavobacteriaceae family of the Bacteroidetes, and most species in this genus are isolated from or near the habitat of algae, indicating a preference for the complex polysaccharides of algae. In this work, a novel brown-seaweed-degrading strain designated HZ22 was isolated from the surface of a brown seaweed (Laminaria japonica). On the basis of its physiological, chemotaxonomic, and genotypic characteristics, it is proposed that strain HZ22 represents a novel species in the genus Algibacter with the proposed name Algibacter alginolytica sp. nov. The genome of strain HZ22, the type strain of this species, harbors 3,371 coding sequences (CDSs) and 255 carbohydrate-active enzymes (CAZymes), including 104 glycoside hydrolases (GHs) and 18 polysaccharide lyases (PLs); this appears to be the highest proportion of CAZymes (∼7.5%) among the reported strains in the class Flavobacteria Seventeen polysaccharide utilization loci (PUL) are predicted to be specific for marine polysaccharides, especially algal polysaccharides from red, green, and brown seaweeds. In particular, PUL N is predicted to be specific for alginate. Taking these findings together with the results of assays of crude alginate lyases, we prove that strain HZ22(T) can completely degrade alginate. This work reveals that strain HZ22(T) has good potential for the degradation of algal polysaccharides and that the structure and related mechanism of PUL in strain HZ22(T) are worth further research.
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Affiliation(s)
- Cong Sun
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Ge-Yi Fu
- Ocean College, Zhejiang University, Hangzhou, People's Republic of China
| | - Chong-Ya Zhang
- Ocean College, Zhejiang University, Hangzhou, People's Republic of China
| | - Jing Hu
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Lin Xu
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Rui-Jun Wang
- Ocean College, Zhejiang University, Hangzhou, People's Republic of China
| | - Yue Su
- Ocean College, Zhejiang University, Hangzhou, People's Republic of China
| | - Shuai-Bo Han
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Xiao-Yun Yu
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Hong Cheng
- Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou, People's Republic of China
- Second Institute of Oceanography, State Oceanic Administration, Hangzhou, People's Republic of China
| | - Xin-Qi Zhang
- School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Linan, People's Republic of China
| | - Ying-Yi Huo
- Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou, People's Republic of China
- Second Institute of Oceanography, State Oceanic Administration, Hangzhou, People's Republic of China
| | - Xue-Wei Xu
- Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou, People's Republic of China
- Second Institute of Oceanography, State Oceanic Administration, Hangzhou, People's Republic of China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- Ocean College, Zhejiang University, Hangzhou, People's Republic of China
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775
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Bruender NA, Bandarian V. The Radical S-Adenosyl-l-methionine Enzyme MftC Catalyzes an Oxidative Decarboxylation of the C-Terminus of the MftA Peptide. Biochemistry 2016; 55:2813-6. [PMID: 27158836 DOI: 10.1021/acs.biochem.6b00355] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ribosomally synthesized post-translationally modified peptides (RiPPs) are encoded in the genomes of a wide variety of microorganisms, in the proximity of open reading frames that encode enzymes that conduct extensive modifications, many of which are novel. Recently, members of the radical S-adenosyl-l-methionine (SAM) superfamily have been identified in these biosynthetic clusters. Herein, we demonstrate the putative radical SAM enzyme, MftC, oxidatively decarboxylates the C-terminus of the MftA peptide in the presence of the accessory protein MftB. The reaction catalyzed by MftC expands the repertoire of peptide-based radical SAM chemistry beyond the intramolecular cross-links.
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Affiliation(s)
- Nathan A Bruender
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
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776
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Botelho AMN, Costa MOC, Beltrame CO, Ferreira FA, Côrtes MF, Bandeira PT, Lima NCB, Souza RC, Almeida LGP, Vasconcelos ATR, Nicolás MF, Figueiredo AMS. Complete genome sequence of an agr-dysfunctional variant of the ST239 lineage of the methicillin-resistant Staphylococcus aureus strain GV69 from Brazil. Stand Genomic Sci 2016; 11:34. [PMID: 27152133 PMCID: PMC4857242 DOI: 10.1186/s40793-016-0154-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 04/25/2016] [Indexed: 11/29/2022] Open
Abstract
Staphylococcus aureus is a versatile Gram-positive coccus frequently found colonizing the skin and nasal membranes of humans. The acquisition of the staphylococcal cassette chromosome mec was a major milestone in the evolutionary path of methicillin-resistant S. aureus. This genetic element carries the mecA gene, the main determinant of methicillin resistance. MRSA is involved in a plethora of opportunistic infectious diseases. The accessory gene regulator is the major S. aureus quorum sensing system, playing an important role in staphylococcal virulence, including the development of biofilms. We report the complete genome sequence (NCBI BioProject ID: PRJNA264181) of the methicillin-resistant S. aureus strain GV69 (= CMVRS P4521), a variant of the ST239 lineage that presents with a natural attenuation of agr-RNAIII transcription and a moderate accumulation of biofilm.
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Affiliation(s)
- Ana M N Botelho
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902 RJ Brazil
| | - Maiana O C Costa
- Laboratório Nacional de Computação Científica, Petrópolis, 25651-075 RJ Brazil
| | - Cristiana O Beltrame
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902 RJ Brazil
| | - Fabienne A Ferreira
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902 RJ Brazil
| | - Marina F Côrtes
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902 RJ Brazil
| | - Paula T Bandeira
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902 RJ Brazil
| | - Nicholas C B Lima
- Laboratório Nacional de Computação Científica, Petrópolis, 25651-075 RJ Brazil
| | - Rangel C Souza
- Laboratório Nacional de Computação Científica, Petrópolis, 25651-075 RJ Brazil
| | - Luiz G P Almeida
- Laboratório Nacional de Computação Científica, Petrópolis, 25651-075 RJ Brazil
| | - Ana T R Vasconcelos
- Laboratório Nacional de Computação Científica, Petrópolis, 25651-075 RJ Brazil
| | - Marisa F Nicolás
- Laboratório Nacional de Computação Científica, Petrópolis, 25651-075 RJ Brazil
| | - Agnes M S Figueiredo
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902 RJ Brazil
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777
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Deforet M, van Ditmarsch D, Xavier JB. Cell-Size Homeostasis and the Incremental Rule in a Bacterial Pathogen. Biophys J 2016; 109:521-8. [PMID: 26244734 DOI: 10.1016/j.bpj.2015.07.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 07/01/2015] [Accepted: 07/02/2015] [Indexed: 01/04/2023] Open
Abstract
How populations of growing cells achieve cell-size homeostasis remains a major question in cell biology. Recent studies in rod-shaped bacteria support the "incremental rule" where each cell adds a constant length before dividing. Although this rule explains narrow cell-size distributions, its mechanism is still unknown. We show that the opportunistic pathogen Pseudomonas aeruginosa obeys the incremental rule to achieve cell-length homeostasis during exponential growth but shortens its cells when entering the stationary phase. We identify a mutant, called frik, which has increased antibiotic sensitivity, cells that are on average longer, and a fraction of filamentous cells longer than 10 μm. When growth slows due to entry in stationary phase, the distribution of frik cell sizes decreases and approaches wild-type length distribution. The rare filamentous cells have abnormally large nucleoids, suggesting that a deficiency in DNA segregation prevents cell division without slowing the exponential elongation rate.
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Affiliation(s)
- Maxime Deforet
- Program in Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Dave van Ditmarsch
- Program in Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - João B Xavier
- Program in Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, New York.
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778
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Dummer PD, Limou S, Rosenberg AZ, Heymann J, Nelson G, Winkler CA, Kopp JB. APOL1 Kidney Disease Risk Variants: An Evolving Landscape. Semin Nephrol 2016. [PMID: 26215860 DOI: 10.1016/j.semnephrol.2015.04.008] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Apolipoprotein L1 (APOL1) genetic variants account for much of the excess risk of chronic and end-stage kidney disease, which results in a significant global health disparity for persons of African ancestry. We estimate the lifetime risk of kidney disease in APOL1 dual-risk allele individuals to be at least 15%. Experimental evidence suggests a direct role of APOL1 in pore formation, cellular injury, and programmed cell death in renal injury. The APOL1 BH3 motif, often associated with cell death, is unlikely to play a role in APOL1-induced cytotoxicity because it is not conserved within the APOL family and is dispensable for cell death in vitro. We discuss two models for APOL1 trypanolytic activity: one involving lysosome permeabilization and another involving colloid-osmotic swelling of the cell body, as well as their relevance to human pathophysiology. Experimental evidence from human cell culture models suggests that both mechanisms may be operative. A systems biology approach whereby APOL1-associated perturbations in gene and protein expression in affected individuals are correlated with molecular pathways may be productive to elucidate APOL1 function in vivo.
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Affiliation(s)
- Patrick D Dummer
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Sophie Limou
- Molecular Epidemiology Genetics Section, Center for Cancer Research, National Cancer Institute, Frederick MD
| | - Avi Z Rosenberg
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD; Department of Pathology Johns Hopkins University, Baltimore, MD
| | - Jurgen Heymann
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - George Nelson
- Molecular Epidemiology Genetics Section, Center for Cancer Research, National Cancer Institute, Frederick MD
| | - Cheryl A Winkler
- Molecular Epidemiology Genetics Section, Center for Cancer Research, National Cancer Institute, Frederick MD
| | - Jeffrey B Kopp
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD.
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779
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Abstract
Radical S-adenosylmethionine (SAM) enzymes catalyze an astonishing array of complex and chemically challenging reactions across all domains of life. Of approximately 114,000 of these enzymes, 8 are known to be present in humans: MOCS1, molybdenum cofactor biosynthesis; LIAS, lipoic acid biosynthesis; CDK5RAP1, 2-methylthio-N(6)-isopentenyladenosine biosynthesis; CDKAL1, methylthio-N(6)-threonylcarbamoyladenosine biosynthesis; TYW1, wybutosine biosynthesis; ELP3, 5-methoxycarbonylmethyl uridine; and RSAD1 and viperin, both of unknown function. Aberrations in the genes encoding these proteins result in a variety of diseases. In this review, we summarize the biochemical characterization of these 8 radical S-adenosylmethionine enzymes and, in the context of human health, describe the deleterious effects that result from such genetic mutations.
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Affiliation(s)
- Bradley J Landgraf
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Erin L McCarthy
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Squire J Booker
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802.,The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, Pennsylvania 16802;
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780
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Bao Y, Song WM, Zhang HX. Role of Arabidopsis NHL family in ABA and stress response. PLANT SIGNALING & BEHAVIOR 2016; 11:e1180493. [PMID: 27110948 PMCID: PMC4977461 DOI: 10.1080/15592324.2016.1180493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Based on their sequence homology to Arabidopsis NDR1 and tobacco (Nicotiana tabacum) HIN1, 45 NHL (NDR1/HIN1-like) family genes are found in Arabidopsis genome. Recently, we reported that overexpression of NHL6, a member of NHL family, modulated seed germination under abiotic stresses through affecting ABA biosynthesis and signaling. We also carried out qPCR and investigated the expression of the other 8 member genes (NHL7a, 16, 17, 21, 25, 26, 41, 43) whose transcriptional data are publicly unavailable, and found that expression of NHL17 was induced more than 2 folds in ABA treated seedlings. Furthermore, in addition to the plasma membrane localization, YFP-NHL6 fusion protein was also observed in the cytosol (as dots) or on the membrane of small vacuoles or vesicles. As a member of the pathogen infection related genes, expression of NHL6 was significantly induced by salicylic acid and NHL6s are evolutionarily conserved among different plant species. A working model of NHL6 in ABA response was proposed.
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Affiliation(s)
- Yan Bao
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Plant Sciences Institute and the Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Wei-Meng Song
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Hong-Xia Zhang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- College of Agriculture, Ludong University, Yantai, China
- Hong-Xia Zhang ,
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781
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Farci D, Collu G, Kirkpatrick J, Esposito F, Piano D. RhVI1 is a membrane-anchored vacuolar invertase highly expressed in Rosa hybrida L. petals. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3303-12. [PMID: 27083698 PMCID: PMC4892724 DOI: 10.1093/jxb/erw148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Invertases are a widespread group of enzymes that catalyse the conversion of sucrose into fructose and glucose. Plants invertases and their substrates are essential factors that play an active role in primary metabolism and in cellular differentiation and by these activities they sustain development and growth. Being naturally present in multiple isoforms, invertases are known to be highly differentiated and tissue specific in such a way that every isoform is characteristic of a specific part of the plant. In this work, we report the identification of the invertase RhVI1 that was found to be highly expressed in rose petals. A characterization of this protein revealed that RhVI1 is a glycosylated membrane-anchored protein associated with the cytosolic side of the vacuolar membrane which occurs in vivo in a monomeric form. Purification yields have shown that the levels of expression decreased during the passage of petals from buds to mature and pre-senescent flowers. Moreover, the activity assay indicates RhVI1 to be an acidic vacuolar invertase. The physiological implications of these findings are discussed, suggesting a possible role of this protein during anthesis.
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Affiliation(s)
- Domenica Farci
- Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, University of Cagliari, Viale S. Ignazio da Laconi 13, 09123 Cagliari, Italy
| | - Gabriella Collu
- Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, University of Cagliari, Viale S. Ignazio da Laconi 13, 09123 Cagliari, Italy
| | - Joanna Kirkpatrick
- European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Francesca Esposito
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari,Cittadella Universitaria di Monserrato, SS554, 09042 Monserrato, Cagliari, Italy
| | - Dario Piano
- Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, University of Cagliari, Viale S. Ignazio da Laconi 13, 09123 Cagliari, Italy
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782
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Kloth KJ, Wiegers GL, Busscher-Lange J, van Haarst JC, Kruijer W, Bouwmeester HJ, Dicke M, Jongsma MA. AtWRKY22 promotes susceptibility to aphids and modulates salicylic acid and jasmonic acid signalling. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3383-96. [PMID: 27107291 PMCID: PMC4892728 DOI: 10.1093/jxb/erw159] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Aphids induce many transcriptional perturbations in their host plants, but the signalling cascades responsible and the effects on plant resistance are largely unknown. Through a genome-wide association (GWA) mapping study in Arabidopsis thaliana, we identified WRKY22 as a candidate gene associated with feeding behaviour of the green peach aphid, Myzus persicae The transcription factor WRKY22 is known to be involved in pathogen-triggered immunity, and WRKY22 gene expression has been shown to be induced by aphids. Assessment of aphid population development and feeding behaviour on knockout mutants and overexpression lines showed that WRKY22 increases susceptibility to M. persicae via a mesophyll-located mechanism. mRNA sequencing analysis of aphid-infested wrky22 knockout plants revealed the up-regulation of genes involved in salicylic acid (SA) signalling and down-regulation of genes involved in plant growth and cell-wall loosening. In addition, mechanostimulation of knockout plants by clip cages up-regulated jasmonic acid (JA)-responsive genes, resulting in substantial negative JA-SA crosstalk. Based on this and previous studies, WRKY22 is considered to modulate the interplay between the SA and JA pathways in response to a wide range of biotic and abiotic stimuli. Its induction by aphids and its role in suppressing SA and JA signalling make WRKY22 a potential target for aphids to manipulate host plant defences.
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Affiliation(s)
- Karen J Kloth
- Laboratory of Entomology, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands Laboratory of Plant Physiology, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands Plant Research International, Business Unit Bioscience, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Gerrie L Wiegers
- Laboratory of Entomology, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands Plant Research International, Business Unit Biointeractions & Plant Health, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Jacqueline Busscher-Lange
- Laboratory of Plant Physiology, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands Plant Research International, Business Unit Bioscience, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Jan C van Haarst
- Plant Research International, Business Unit Bioscience, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Willem Kruijer
- Biometris, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Harro J Bouwmeester
- Laboratory of Plant Physiology, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Maarten A Jongsma
- Plant Research International, Business Unit Bioscience, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands
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783
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Prediction of human protein–protein interaction by a domain-based approach. J Theor Biol 2016; 396:144-53. [DOI: 10.1016/j.jtbi.2016.02.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 01/29/2016] [Accepted: 02/20/2016] [Indexed: 02/04/2023]
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784
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Tranchevent LC, Ardeshirdavani A, ElShal S, Alcaide D, Aerts J, Auboeuf D, Moreau Y. Candidate gene prioritization with Endeavour. Nucleic Acids Res 2016; 44:W117-21. [PMID: 27131783 PMCID: PMC4987917 DOI: 10.1093/nar/gkw365] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/23/2016] [Indexed: 01/25/2023] Open
Abstract
Genomic studies and high-throughput experiments often produce large lists of candidate genes among which only a small fraction are truly relevant to the disease, phenotype or biological process of interest. Gene prioritization tackles this problem by ranking candidate genes by profiling candidates across multiple genomic data sources and integrating this heterogeneous information into a global ranking. We describe an extended version of our gene prioritization method, Endeavour, now available for six species and integrating 75 data sources. The performance (Area Under the Curve) of Endeavour on cross-validation benchmarks using ‘gold standard’ gene sets varies from 88% (for human phenotypes) to 95% (for worm gene function). In addition, we have also validated our approach using a time-stamped benchmark derived from the Human Phenotype Ontology, which provides a setting close to prospective validation. With this benchmark, using 3854 novel gene–phenotype associations, we observe a performance of 82%. Altogether, our results indicate that this extended version of Endeavour efficiently prioritizes candidate genes. The Endeavour web server is freely available at https://endeavour.esat.kuleuven.be/.
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Affiliation(s)
- Léon-Charles Tranchevent
- INSERM U1210, CNRS UMR5239, Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, Université de Lyon, 69364 Lyon, France
| | - Amin Ardeshirdavani
- Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, B-3001 Leuven, Belgium iMinds Future Health Department, KU Leuven, B-3001 Leuven, Belgium
| | - Sarah ElShal
- Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, B-3001 Leuven, Belgium iMinds Future Health Department, KU Leuven, B-3001 Leuven, Belgium
| | - Daniel Alcaide
- Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, B-3001 Leuven, Belgium iMinds Future Health Department, KU Leuven, B-3001 Leuven, Belgium
| | - Jan Aerts
- Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, B-3001 Leuven, Belgium iMinds Future Health Department, KU Leuven, B-3001 Leuven, Belgium
| | - Didier Auboeuf
- INSERM U1210, CNRS UMR5239, Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, Université de Lyon, 69364 Lyon, France
| | - Yves Moreau
- Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, B-3001 Leuven, Belgium iMinds Future Health Department, KU Leuven, B-3001 Leuven, Belgium
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785
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Alonso-López D, Gutiérrez MA, Lopes KP, Prieto C, Santamaría R, De Las Rivas J. APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. Nucleic Acids Res 2016; 44:W529-35. [PMID: 27131791 PMCID: PMC4987915 DOI: 10.1093/nar/gkw363] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 04/23/2016] [Indexed: 01/23/2023] Open
Abstract
APID (Agile Protein Interactomes DataServer) is an interactive web server that provides unified generation and delivery of protein interactomes mapped to their respective proteomes. This resource is a new, fully redesigned server that includes a comprehensive collection of protein interactomes for more than 400 organisms (25 of which include more than 500 interactions) produced by the integration of only experimentally validated protein–protein physical interactions. For each protein–protein interaction (PPI) the server includes currently reported information about its experimental validation to allow selection and filtering at different quality levels. As a whole, it provides easy access to the interactomes from specific species and includes a global uniform compendium of 90,379 distinct proteins and 678,441 singular interactions. APID integrates and unifies PPIs from major primary databases of molecular interactions, from other specific repositories and also from experimentally resolved 3D structures of protein complexes where more than two proteins were identified. For this purpose, a collection of 8,388 structures were analyzed to identify specific PPIs. APID also includes a new graph tool (based on Cytoscape.js) for visualization and interactive analyses of PPI networks. The server does not require registration and it is freely available for use at http://apid.dep.usal.es.
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Affiliation(s)
- Diego Alonso-López
- Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), 37007 Salamanca, Spain
| | - Miguel A Gutiérrez
- Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), 37007 Salamanca, Spain
| | - Katia P Lopes
- Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), 37007 Salamanca, Spain
| | - Carlos Prieto
- Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), 37007 Salamanca, Spain
| | - Rodrigo Santamaría
- Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), 37007 Salamanca, Spain
| | - Javier De Las Rivas
- Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), 37007 Salamanca, Spain
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786
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Marlow JJ, Skennerton CT, Li Z, Chourey K, Hettich RL, Pan C, Orphan VJ. Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities. Front Microbiol 2016; 7:563. [PMID: 27199908 PMCID: PMC4850331 DOI: 10.3389/fmicb.2016.00563] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 04/04/2016] [Indexed: 01/02/2023] Open
Abstract
Marine methane seep habitats represent an important control on the global flux of methane. Nucleotide-based meta-omics studies outline community-wide metabolic potential, but expression patterns of environmentally relevant proteins are poorly characterized. Proteomic stable isotope probing (proteomic SIP) provides additional information by characterizing phylogenetically specific, functionally relevant activity in mixed microbial communities, offering enhanced detection through system-wide product integration. Here we applied proteomic SIP to 15NH4+ and CH4 amended seep sediment microcosms in an attempt to track protein synthesis of slow-growing, low-energy microbial systems. Across all samples, 3495 unique proteins were identified, 11% of which were 15N-labeled. Consistent with the dominant anaerobic oxidation of methane (AOM) activity commonly observed in anoxic seep sediments, proteins associated with sulfate reduction and reverse methanogenesis—including the ANME-2 associated methylenetetrahydromethanopterin reductase (Mer)—were all observed to be actively synthesized (15N-enriched). Conversely, proteins affiliated with putative aerobic sulfur-oxidizing epsilon- and gammaproteobacteria showed a marked decrease over time in our anoxic sediment incubations. The abundance and phylogenetic range of 15N-enriched methyl-coenzyme M reductase (Mcr) orthologs, many of which exhibited novel post-translational modifications, suggests that seep sediments provide niches for multiple organisms performing analogous metabolisms. In addition, 26 proteins of unknown function were consistently detected and actively expressed under conditions supporting AOM, suggesting that they play important roles in methane seep ecosystems. Stable isotope probing in environmental proteomics experiments provides a mechanism to determine protein durability and evaluate lineage-specific responses in complex microbial communities placed under environmentally relevant conditions. Our work here demonstrates the active synthesis of a metabolically specific minority of enzymes, revealing the surprising longevity of most proteins over the course of an extended incubation experiment in an established, slow-growing, methane-impacted environmental system.
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Affiliation(s)
- Jeffrey J Marlow
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
| | - Connor T Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
| | - Zhou Li
- Chemical Sciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Karuna Chourey
- Chemical Sciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Chongle Pan
- Chemical Sciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
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787
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Swearingen KE, Lindner SE, Shi L, Shears MJ, Harupa A, Hopp CS, Vaughan AM, Springer TA, Moritz RL, Kappe SHI, Sinnis P. Interrogating the Plasmodium Sporozoite Surface: Identification of Surface-Exposed Proteins and Demonstration of Glycosylation on CSP and TRAP by Mass Spectrometry-Based Proteomics. PLoS Pathog 2016; 12:e1005606. [PMID: 27128092 PMCID: PMC4851412 DOI: 10.1371/journal.ppat.1005606] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 04/08/2016] [Indexed: 12/22/2022] Open
Abstract
Malaria parasite infection is initiated by the mosquito-transmitted sporozoite stage, a highly motile invasive cell that targets hepatocytes in the liver for infection. A promising approach to developing a malaria vaccine is the use of proteins located on the sporozoite surface as antigens to elicit humoral immune responses that prevent the establishment of infection. Very little of the P. falciparum genome has been considered as potential vaccine targets, and candidate vaccines have been almost exclusively based on single antigens, generating the need for novel target identification. The most advanced malaria vaccine to date, RTS,S, a subunit vaccine consisting of a portion of the major surface protein circumsporozoite protein (CSP), conferred limited protection in Phase III trials, falling short of community-established vaccine efficacy goals. In striking contrast to the limited protection seen in current vaccine trials, sterilizing immunity can be achieved by immunization with radiation-attenuated sporozoites, suggesting that more potent protection may be achievable with a multivalent protein vaccine. Here, we provide the most comprehensive analysis to date of proteins located on the surface of or secreted by Plasmodium falciparum salivary gland sporozoites. We used chemical labeling to isolate surface-exposed proteins on sporozoites and identified these proteins by mass spectrometry. We validated several of these targets and also provide evidence that components of the inner membrane complex are in fact surface-exposed and accessible to antibodies in live sporozoites. Finally, our mass spectrometry data provide the first direct evidence that the Plasmodium surface proteins CSP and TRAP are glycosylated in sporozoites, a finding that could impact the selection of vaccine antigens. Malaria remains one of the most important infectious diseases in the world, responsible for an estimated 500 million new cases and 600,000 deaths annually. The etiologic agents of the disease are protozoan parasites of the genus Plasmodium that have a complex cycle between mosquito and mammalian hosts. Though all clinical symptoms are attributable to the blood stages, it is only by attacking the transmission stages that we can make an impact on the economic and health burdens of malaria. Infection is initiated when mosquitoes inoculate sporozoites into the skin as they probe for blood. Sporozoites must locate blood vessels and enter the circulation to reach the liver where they invade and grow in hepatocytes. The inoculum is low and these early stages of infection are asymptomatic. Though the small amounts of material available for study has made large scale -omics studies difficult, killing the parasite at this stage would prevent infection and block downstream transmission to mosquitoes, thus preventing spread of disease. Here we use state-of-the-art biochemistry tools to identify the proteins on the sporozoite surface and find that two of the most studied proteins, CSP and TRAP, have post-translational modifications. These studies will aid investigations into the novel biology of sporozoites and importantly, significantly expand the pool of potential vaccine candidates.
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Affiliation(s)
| | - Scott E. Lindner
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Lirong Shi
- Johns Hopkins Malaria Research Institute and Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Melanie J. Shears
- Johns Hopkins Malaria Research Institute and Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Anke Harupa
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Christine S. Hopp
- Johns Hopkins Malaria Research Institute and Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Ashley M. Vaughan
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | | | - Robert L. Moritz
- Institute for Systems Biology, Seattle, Washington, United States of America
- * E-mail: (RLM); (SHIK); (PS)
| | - Stefan H. I. Kappe
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- * E-mail: (RLM); (SHIK); (PS)
| | - Photini Sinnis
- Johns Hopkins Malaria Research Institute and Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (RLM); (SHIK); (PS)
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788
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Belda E, van Heck RGA, José Lopez-Sanchez M, Cruveiller S, Barbe V, Fraser C, Klenk HP, Petersen J, Morgat A, Nikel PI, Vallenet D, Rouy Z, Sekowska A, Martins dos Santos VAP, de Lorenzo V, Danchin A, Médigue C. The revisited genome ofPseudomonas putidaKT2440 enlightens its value as a robust metabolicchassis. Environ Microbiol 2016; 18:3403-3424. [DOI: 10.1111/1462-2920.13230] [Citation(s) in RCA: 217] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/16/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Eugeni Belda
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
- Institut Pasteur, Unit of Insect Vector Genetics and Genomics, Department of Parasitology and Mycology; 28, rue du Dr. Roux, Paris, Cedex 15 75724 France
| | - Ruben G. A. van Heck
- Laboratory of Systems and Synthetic Biology, Wageningen University; Dreijenplein 10, Building number 316 6703 HB Wageningen The Netherlands
| | - Maria José Lopez-Sanchez
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière; Paris France
| | - Stéphane Cruveiller
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
| | - Valérie Barbe
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute, National Sequencing Center; 2 rue Gaston Crémieux 91057 Evry France
| | - Claire Fraser
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine; Baltimore MD USA
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
- School of Biology, Newcastle University; Newcastle upon Tyne NE1 7RU UK
| | - Jörn Petersen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Anne Morgat
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics; Geneva CH-1206 Switzerland
| | - Pablo I. Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC); C/Darwin 3 28049 Madrid Spain
| | - David Vallenet
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
| | - Zoé Rouy
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
| | - Agnieszka Sekowska
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière; Paris France
| | - Vitor A. P. Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University; Dreijenplein 10, Building number 316 6703 HB Wageningen The Netherlands
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC); C/Darwin 3 28049 Madrid Spain
| | - Antoine Danchin
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière; Paris France
| | - Claudine Médigue
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
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789
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Arai T, Obuchi S, Eguchi K, Seto Y. In vitro investigation of molecules involved in Lactobacillus gasseri SBT2055 adhesion to host intestinal tract components. J Appl Microbiol 2016; 120:1658-67. [PMID: 26999673 DOI: 10.1111/jam.13137] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 02/11/2016] [Accepted: 03/11/2016] [Indexed: 01/06/2023]
Abstract
AIMS The adhesion ability of Lactobacillus gasseri SBT2055 was investigated in vitro by searching for its adhesion molecules. METHODS AND RESULTS Lactobacillus gasseri SBT2055 showed adherence to host components, including two commercially available mucins, Caco-2 epithelial-like cells and the extracellular matrix molecule fibronectin (Fn). Its adhesion rates to host components were generally higher than those of other Lactobacillus strains. We examined sortase-dependent proteins (SDPs) anchored by a sortase enzyme encoded by srtA1. The adhesion rates of an srtA1 disruptant were lower than those of Lact. gasseri SBT2055, and the relative adherences were as follows: two mucins, 43 and 40%; Caco-2, 66% and Fn, 28%. Seven additional gene disruptants were generated to determine the precise SDPs that contribute to adhesion to each component. CONCLUSIONS The adhesion ability of Lact. gasseri SBT2055 was superior to those of other Lactobacillus strains. Additionally, four adhesion molecules were newly identified from candidate SDPs. SIGNIFICANCE AND IMPACT OF THE STUDY Although the contribution of SDPs to adhesion has been reported using sortase gene disruptants, this is the first report to identify the precise SDPs that act as adhesion molecules. Our results will contribute to achieving better understanding of probiotic bacterial adherence.
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Affiliation(s)
- T Arai
- Milk Science Research Institute, Megmilk Snow Brand Co., Ltd., Kawagoe-shi, Saitama, Japan
| | - S Obuchi
- Milk Science Research Institute, Megmilk Snow Brand Co., Ltd., Kawagoe-shi, Saitama, Japan
| | - K Eguchi
- Milk Science Research Institute, Megmilk Snow Brand Co., Ltd., Kawagoe-shi, Saitama, Japan
| | - Y Seto
- Milk Science Research Institute, Megmilk Snow Brand Co., Ltd., Kawagoe-shi, Saitama, Japan
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790
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Behrens CJ, Zelena K, Berger RG. Comparative Cold Shock Expression and Characterization of Fungal Dye-Decolorizing Peroxidases. Appl Biochem Biotechnol 2016; 179:1404-17. [PMID: 27106285 DOI: 10.1007/s12010-016-2073-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 04/03/2016] [Indexed: 11/29/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) from Auricularia auricula-judae, Bjerkandera adusta, Pleurotus ostreatus and Marasmius scorodonius (Basidiomycota) were expressed in Escherichia coli using the cold shock-inducible expression system pCOLD I DNA. Functional expression was achieved without the addition of hemin or the co-expression of any chaperones. The presence or absence of the native signal sequence had a strong impact on the success of the expression, but the effect was not consistent for the different DyPs. While BaDyP and AajDyP were stable at 50 °C, the more thermolabile MsP2 and PoDyp, upon catalytic intervention, lend themselves to more rapid thermal inactivation. The bleaching of norbixin (E 160b) using MsP2 was most efficient at pH 4.0, while BaDyP and AajDypP worked best in the weakly acidic to neutral range, indicating a choice of DyPs for a broad field of applications in different food matrices.
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Affiliation(s)
- Christoph J Behrens
- Gottfried Wilhelm Leibniz Universität Hannover, Institut für Lebensmittelchemie, Callinstraße 5, 30167, Hannover, Germany.
| | - Kateryna Zelena
- Gottfried Wilhelm Leibniz Universität Hannover, Institut für Lebensmittelchemie, Callinstraße 5, 30167, Hannover, Germany
| | - Ralf G Berger
- Gottfried Wilhelm Leibniz Universität Hannover, Institut für Lebensmittelchemie, Callinstraße 5, 30167, Hannover, Germany
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791
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Waghu FH, Barai RS, Idicula-Thomas S. Leveraging family-specific signatures for AMP discovery and high-throughput annotation. Sci Rep 2016; 6:24684. [PMID: 27089856 PMCID: PMC4836297 DOI: 10.1038/srep24684] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/04/2016] [Indexed: 01/30/2023] Open
Abstract
Antimicrobial peptides (AMPs) are diverse, biologically active, essential components of the innate immune system. As compared to conventional antibiotics, AMPs exhibit broad spectrum antimicrobial activity, reduced toxicity and reduced microbial resistance. They are widely researched for their therapeutic potential, especially against multi-drug resistant pathogens. AMPs are known to have family-specific sequence composition, which can be mined for their discovery and rational design. Here, we present a detailed family-based study on AMP families. The study involved the use of sequence signatures represented by patterns and hidden Markov models (HMMs) present in experimentally studied AMPs to identify novel AMPs. Along with AMPs, peptides hitherto lacking antimicrobial annotation were also retrieved and wet-lab studies on randomly selected sequences proved their antimicrobial activity against Escherichia coli. CAMPSign, a webserver has been created for researchers to effortlessly exploit the use of AMP family signatures for identification of AMPs. The webserver is available online at www.campsign.bicnirrh.res.in. In this work, we demonstrate an optimised and experimentally validated protocol along with a freely available webserver that uses family-based sequence signatures for accelerated discovery of novel AMPs.
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Affiliation(s)
- Faiza Hanif Waghu
- Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai-400012, India
| | - Ram Shankar Barai
- Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai-400012, India
| | - Susan Idicula-Thomas
- Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai-400012, India
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792
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Druce M, Hulo C, Masson P, Sommer P, Xenarios I, Le Mercier P, De Oliveira T. Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw045. [PMID: 27087306 PMCID: PMC4834208 DOI: 10.1093/database/baw045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 03/11/2016] [Indexed: 02/06/2023]
Abstract
The Human Immunodeficiency Virus (HIV) is one of the pathogens that cause the greatest global concern, with approximately 35 million people currently infected with HIV. Extensive HIV research has been performed, generating a large amount of HIV and host genomic data. However, no effective vaccine that protects the host from HIV infection is available and HIV is still spreading at an alarming rate, despite effective antiretroviral (ARV) treatment. In order to develop effective therapies, we need to expand our knowledge of the interaction between HIV and host proteins. In contrast to virus proteins, which often rapidly evolve drug resistance mutations, the host proteins are essentially invariant within all humans. Thus, if we can identify the host proteins needed for virus replication, such as those involved in transporting viral proteins to the cell surface, we have a chance of interrupting viral replication. There is no proteome resource that summarizes this interaction, making research on this subject a difficult enterprise. In order to fill this gap in knowledge, we curated a resource presents detailed annotation on the interaction between the HIV proteome and host proteins. Our resource was produced in collaboration with ViralZone and used manual curation techniques developed by UniProtKB/Swiss-Prot. Our new website also used previous annotations of the BioAfrica HIV-1 Proteome Resource, which has been accessed by approximately 10 000 unique users a year since its inception in 2005. The novel features include a dedicated new page for each HIV protein, a graphic display of its function and a section on its interaction with host proteins. Our new webpages also add information on the genomic location of each HIV protein and the position of ARV drug resistance mutations. Our improved BioAfrica HIV-1 Proteome Resource fills a gap in the current knowledge of biocuration. Database URL: http://www.bioafrica.net/proteomics/HIVproteome.html
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Affiliation(s)
- Megan Druce
- Africa Centre for Population Health, School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa Division of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Chantal Hulo
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Patrick Masson
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Paula Sommer
- Division of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ioannis Xenarios
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Philippe Le Mercier
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Tulio De Oliveira
- Africa Centre for Population Health, School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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793
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Yue Y, Meng Y, Ma H, Hou S, Cao G, Hong W, Shi Y, Guo P, Liu B, Shi F, Yang Y, Jin Y. A large family of Dscam genes with tandemly arrayed 5' cassettes in Chelicerata. Nat Commun 2016; 7:11252. [PMID: 27080167 PMCID: PMC4835542 DOI: 10.1038/ncomms11252] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/07/2016] [Indexed: 02/04/2023] Open
Abstract
Drosophila Dscam1 (Down Syndrome Cell Adhesion Molecules) and vertebrate clustered protocadherins (Pcdhs) are two classic examples of the extraordinary isoform diversity from a single genomic locus. Dscam1 encodes 38,016 distinct isoforms via mutually exclusive splicing in D. melanogaster, while the vertebrate clustered Pcdhs utilize alternative promoters to generate isoform diversity. Here we reveal a shortened Dscam gene family with tandemly arrayed 5' cassettes in Chelicerata. These cassette repeats generally comprise two or four exons, corresponding to variable Immunoglobulin 7 (Ig7) or Ig7-8 domains of Drosophila Dscam1. Furthermore, extraordinary isoform diversity has been generated through a combination of alternating promoter and alternative splicing. These sDscams have a high sequence similarity with Drosophila Dscam1, and share striking organizational resemblance to the 5' variable regions of vertebrate clustered Pcdhs. Hence, our findings have important implications for understanding the functional similarities between Drosophila Dscam1 and vertebrate Pcdhs, and may provide further mechanistic insights into the regulation of isoform diversity.
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Affiliation(s)
- Yuan Yue
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Yijun Meng
- College of Life and Environmental Sciences; Hangzhou Normal University, Hangzhou, Zhejiang ZJ310036, China
| | - Hongru Ma
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Shouqing Hou
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Guozheng Cao
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Weiling Hong
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Yang Shi
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Pengjuan Guo
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Baoping Liu
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Feng Shi
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Yun Yang
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Yongfeng Jin
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
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794
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Noon JB, Baum TJ. Horizontal gene transfer of acetyltransferases, invertases and chorismate mutases from different bacteria to diverse recipients. BMC Evol Biol 2016; 16:74. [PMID: 27068610 PMCID: PMC4828791 DOI: 10.1186/s12862-016-0651-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 04/05/2016] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Hoplolaimina plant-parasitic nematodes (PPN) are a lineage of animals with many documented cases of horizontal gene transfer (HGT). In a recent study, we reported on three likely HGT candidate genes in the soybean cyst nematode Heterodera glycines, all of which encode secreted candidate effectors with putative functions in the host plant. Hg-GLAND1 is a putative GCN5-related N-acetyltransferase (GNAT), Hg-GLAND13 is a putative invertase (INV), and Hg-GLAND16 is a putative chorismate mutase (CM), and blastp searches of the non-redundant database resulted in highest similarity to bacterial sequences. Here, we searched nematode and non-nematode sequence databases to identify all the nematodes possible that contain these three genes, and to formulate hypotheses about when they most likely appeared in the phylum Nematoda. We then performed phylogenetic analyses combined with model selection tests of alternative models of sequence evolution to determine whether these genes were horizontally acquired from bacteria. RESULTS Mining of nematode sequence databases determined that GNATs appeared in Hoplolaimina PPN late in evolution, while both INVs and CMs appeared before the radiation of the Hoplolaimina suborder. Also, Hoplolaimina GNATs, INVs and CMs formed well-supported clusters with different rhizosphere bacteria in the phylogenetic trees, and the model selection tests greatly supported models of HGT over descent via common ancestry. Surprisingly, the phylogenetic trees also revealed additional, well-supported clusters of bacterial GNATs, INVs and CMs with diverse eukaryotes and archaea. There were at least eleven and eight well-supported clusters of GNATs and INVs, respectively, from different bacteria with diverse eukaryotes and archaea. Though less frequent, CMs from different bacteria formed supported clusters with multiple different eukaryotes. Moreover, almost all individual clusters containing bacteria and eukaryotes or archaea contained species that inhabit very similar niches. CONCLUSIONS GNATs were horizontally acquired late in Hoplolaimina PPN evolution from bacteria most similar to the saprophytic and plant-pathogenic actinomycetes. INVs and CMs were horizontally acquired from bacteria most similar to rhizobacteria and Burkholderia soil bacteria, respectively, before the radiation of Hoplolaimina. Also, these three gene groups appear to have been frequent subjects of HGT from different bacteria to numerous, diverse lineages of eukaryotes and archaea, which suggests that these genes may confer important evolutionary advantages to many taxa. In the case of Hoplolaimina PPN, this advantage likely was an improved ability to parasitize plants.
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Affiliation(s)
- Jason B. Noon
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011 USA
| | - Thomas J. Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011 USA
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795
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Kirkegaard RH, Dueholm MS, McIlroy SJ, Nierychlo M, Karst SM, Albertsen M, Nielsen PH. Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters. ISME JOURNAL 2016; 10:2352-64. [PMID: 27058503 PMCID: PMC5030696 DOI: 10.1038/ismej.2016.43] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 02/15/2016] [Accepted: 02/22/2016] [Indexed: 12/13/2022]
Abstract
Members of the candidate phylum Hyd24-12 are globally distributed, but no genomic information or knowledge about their morphology, physiology or ecology is available. In this study, members of the Hyd24-12 lineage were shown to be present and abundant in full-scale mesophilic anaerobic digesters at Danish wastewater treatment facilities. In some samples, a member of the Hyd24-12 lineage was one of the most abundant genus-level bacterial taxa, accounting for up to 8% of the bacterial biomass. Three closely related and near-complete genomes were retrieved using metagenome sequencing of full-scale anaerobic digesters. Genome annotation and metabolic reconstruction showed that they are Gram-negative bacteria likely involved in acidogenesis, producing acetate and hydrogen from fermentation of sugars, and may play a role in the cycling of sulphur in the digesters. Fluorescence in situ hybridization revealed single rod-shaped cells dispersed within the flocs. The genomic information forms a foundation for a more detailed understanding of their role in anaerobic digestion and provides the first insight into a hitherto undescribed branch in the tree of life.
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Affiliation(s)
- Rasmus Hansen Kirkegaard
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Simonsen Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Simon Jon McIlroy
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Marta Nierychlo
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Søren Michael Karst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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796
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Giudice G, Sánchez-Cabo F, Torroja C, Lara-Pezzi E. ATtRACT-a database of RNA-binding proteins and associated motifs. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw035. [PMID: 27055826 PMCID: PMC4823821 DOI: 10.1093/database/baw035] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/01/2016] [Indexed: 12/21/2022]
Abstract
RNA-binding proteins (RBPs) play a crucial role in key cellular processes, including RNA transport, splicing, polyadenylation and stability. Understanding the interaction between RBPs and RNA is key to improve our knowledge of RNA processing, localization and regulation in a global manner. Despite advances in recent years, a unified non-redundant resource that includes information on experimentally validated motifs, RBPs and integrated tools to exploit this information is lacking. Here, we developed a database named ATtRACT (available athttp://attract.cnic.es) that compiles information on 370 RBPs and 1583 RBP consensus binding motifs, 192 of which are not present in any other database. To populate ATtRACT we (i) extracted and hand-curated experimentally validated data from CISBP-RNA, SpliceAid-F, RBPDB databases, (ii) integrated and updated the unavailable ASD database and (iii) extracted information from Protein-RNA complexes present in Protein Data Bank database through computational analyses. ATtRACT provides also efficient algorithms to search a specific motif and scan one or more RNA sequences at a time. It also allows discoveringde novomotifs enriched in a set of related sequences and compare them with the motifs included in the database.Database URL:http:// attract. cnic. es.
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Affiliation(s)
- Girolamo Giudice
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Melchor Fernández Almagro 3, Madrid 28029, Spain
| | | | - Carlos Torroja
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares, Melchor Fernández Almagro 3, Madrid 28029, Spain
| | - Enrique Lara-Pezzi
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Melchor Fernández Almagro 3, Madrid 28029, Spain National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
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797
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Tentacle Transcriptome and Venom Proteome of the Pacific Sea Nettle, Chrysaora fuscescens (Cnidaria: Scyphozoa). Toxins (Basel) 2016; 8:102. [PMID: 27058558 PMCID: PMC4848628 DOI: 10.3390/toxins8040102] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/07/2016] [Accepted: 03/22/2016] [Indexed: 12/26/2022] Open
Abstract
Jellyfish venoms are rich sources of toxins designed to capture prey or deter predators, but they can also elicit harmful effects in humans. In this study, an integrated transcriptomic and proteomic approach was used to identify putative toxins and their potential role in the venom of the scyphozoan jellyfish Chrysaora fuscescens. A de novo tentacle transcriptome, containing more than 23,000 contigs, was constructed and used in proteomic analysis of C. fuscescens venom to identify potential toxins. From a total of 163 proteins identified in the venom proteome, 27 were classified as putative toxins and grouped into six protein families: proteinases, venom allergens, C-type lectins, pore-forming toxins, glycoside hydrolases and enzyme inhibitors. Other putative toxins identified in the transcriptome, but not the proteome, included additional proteinases as well as lipases and deoxyribonucleases. Sequence analysis also revealed the presence of ShKT domains in two putative venom proteins from the proteome and an additional 15 from the transcriptome, suggesting potential ion channel blockade or modulatory activities. Comparison of these potential toxins to those from other cnidarians provided insight into their possible roles in C. fuscescens venom and an overview of the diversity of potential toxin families in cnidarian venoms.
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798
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Lehmann G, Udasin RG, Ciechanover A. On the linkage between the ubiquitin-proteasome system and the mitochondria. Biochem Biophys Res Commun 2016; 473:80-86. [DOI: 10.1016/j.bbrc.2016.03.055] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 03/14/2016] [Indexed: 12/20/2022]
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799
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Lovell JT, Schwartz S, Lowry DB, Shakirov EV, Bonnette JE, Weng X, Wang M, Johnson J, Sreedasyam A, Plott C, Jenkins J, Schmutz J, Juenger TE. Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C4 grass. Genome Res 2016; 26:510-8. [PMID: 26953271 PMCID: PMC4817774 DOI: 10.1101/gr.198135.115] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/26/2016] [Indexed: 01/18/2023]
Abstract
Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C4 grass,Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. While less well-represented, we observe 1294 genes (7.8%) with transeffects.Trans-by-environment interactions are weaker and much less common than cis G×E, occurring in only 0.7% oft rans-regulated genes. Finally, gene expression heterosis is highly enriched in expression phenotypes with significant G×E. As such, modes of inheritance that drive heterosis, such as dominance or overdominance, may be common among G×E genes. Interestingly, motifs specific to drought-responsive transcription factors are highly enriched in the promoters of genes exhibiting G×E and transregulation, indicating that expression G×E and heterosis may result from the evolution of transcription factors or their binding sites.P. hallii serves as the genomic model for its close relative and emerging biofuel crop, switchgrass (Panicum virgatum). Accordingly, the results here not only aid in the discovery of the genetic mechanisms that underlie local adaptation but also provide a foundation to improve switchgrass yield under water-limited conditions.
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Affiliation(s)
- John T Lovell
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Scott Schwartz
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - David B Lowry
- Department of Plant Sciences, Michigan State University, East Lansing, Michigan 48824, USA
| | - Eugene V Shakirov
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 42008, Republic of Tatarstan, Russia
| | - Jason E Bonnette
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Xiaoyu Weng
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Mei Wang
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jenifer Johnson
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | | | - Christopher Plott
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
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800
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Bruender NA, Wilcoxen J, Britt RD, Bandarian V. Biochemical and Spectroscopic Characterization of a Radical S-Adenosyl-L-methionine Enzyme Involved in the Formation of a Peptide Thioether Cross-Link. Biochemistry 2016; 55:2122-34. [PMID: 27007615 DOI: 10.1021/acs.biochem.6b00145] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide-derived natural products are a class of metabolites that afford the producing organism a selective advantage over other organisms in their biological niche. While the polypeptide antibiotics produced by the nonribosomal polypeptide synthetases (NRPS) are the most widely recognized, the ribosomally synthesized and post-translationally modified peptides (RiPPs) are an emerging group of natural products with diverse structures and biological functions. Both the NRPS derived peptides and the RiPPs undergo extensive post-translational modifications to produce structural diversity. Here we report the first characterization of the six cysteines in forty-five (SCIFF) [Haft, D. H. and Basu M. K. (2011) J. Bacteriol. 193, 2745-2755] peptide maturase Tte1186, which is a member of the radical S-adenosyl-l-methionine (SAM) superfamily. Tte1186 catalyzes the formation of a thioether cross-link in the peptide Tte1186a encoded by an orf located upstream of the maturase, under reducing conditions in the presence of SAM. Tte1186 contains three [4Fe-4S] clusters that are indispensable for thioether cross-link formation; however, only one cluster catalyzes the reductive cleavage of SAM. Mechanistic imperatives for the reaction catalyzed by the thioether forming radical SAM maturases will be discussed.
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Affiliation(s)
- Nathan A Bruender
- Chemistry Department, University of Utah , Salt Lake City, Utah 84112, United States
| | - Jarett Wilcoxen
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - R David Britt
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Vahe Bandarian
- Chemistry Department, University of Utah , Salt Lake City, Utah 84112, United States
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