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Levine TP. Structural bioinformatics predicts that the Retinitis Pigmentosa-28 protein of unknown function FAM161A is a homologue of the microtubule nucleation factor Tpx2. F1000Res 2020; 9:1052. [PMID: 33093951 PMCID: PMC7551519 DOI: 10.12688/f1000research.25870.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/13/2020] [Indexed: 11/20/2022] Open
Abstract
Background: FAM161A is a microtubule-associated protein conserved widely across eukaryotes, which is mutated in the inherited blinding disease Retinitis Pigmentosa-28. FAM161A is also a centrosomal protein, being a core component of a complex that forms an internal skeleton of centrioles. Despite these observations about the importance of FAM161A, current techniques used to examine its sequence reveal no homologies to other proteins. Methods: Sequence profiles derived from multiple sequence alignments of FAM161A homologues were constructed by PSI-BLAST and HHblits, and then used by the profile-profile search tool HHsearch, implemented online as HHpred, to identify homologues. These in turn were used to create profiles for reverse searches and pair-wise searches. Multiple sequence alignments were also used to identify amino acid usage in functional elements. Results: FAM161A has a single homologue: the targeting protein for
Xenopus kinesin-like protein-2 (Tpx2), which is a strong hit across more than 200 residues. Tpx2 is also a microtubule-associated protein, and it has been shown previously by a cryo-EM molecular structure to nucleate microtubules through two small elements: an extended loop and a short helix. The homology between FAM161A and Tpx2 includes these elements, as FAM161A has three copies of the loop, and one helix that has many, but not all, properties of the one in Tpx2. Conclusions: FAM161A and its homologues are predicted to be a previously unknown variant of Tpx2, and hence bind microtubules in the same way. This prediction allows precise, testable molecular models to be made of FAM161A-microtubule complexes.
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Affiliation(s)
- Timothy P Levine
- UCL Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
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David-Palma M, Libkind D, Brito PH, Silva M, Bellora N, Coelho MA, Heitman J, Gonçalves P, Sampaio JP. The Untapped Australasian Diversity of Astaxanthin-Producing Yeasts with Biotechnological Potential- Phaffia australis sp. nov. and Phaffia tasmanica sp. nov. Microorganisms 2020; 8:E1651. [PMID: 33114402 PMCID: PMC7692969 DOI: 10.3390/microorganisms8111651] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/18/2020] [Accepted: 10/21/2020] [Indexed: 01/28/2023] Open
Abstract
Phaffia is an orange-colored basidiomycetous yeast genus of the order Cystofilobasidiales that contains a single species, P. rhodozyma. This species is the only fungus known to produce the economically relevant carotenoid astaxanthin. Although Phaffia was originally found in the Northern hemisphere, its diversity in the southern part of the globe has been shown to be much greater. Here we analyze the genomes of two Australasian lineages that are markedly distinct from P. rhodozyma. The two divergent lineages were investigated within a comprehensive phylogenomic study of representatives of the Cystofilobasidiales that supported the recognition of two novel Phaffia species, for which we propose the names of P. australis sp. nov. and P. tasmanica sp. nov. Comparative genomics and other analyses confirmed that the two new species have the typical Phaffia hallmark-the six genes necessary for the biosynthesis of astaxanthin could be retrieved from the draft genome sequences, and this carotenoid was detected in culture extracts. In addition, the organization of the mating-type (MAT) loci is similar to that of P. rhodozyma, with synteny throughout most regions. Moreover, cases of trans-specific polymorphism involving pheromone receptor genes and pheromone precursor proteins in the three Phaffia species, together with their shared homothallism, provide additional support for their classification in a single genus.
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Affiliation(s)
- Márcia David-Palma
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (M.D.-P.); (P.H.B.); (M.S.); (M.A.C.); (P.G.)
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA;
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC)—CONICET/Universidad Nacional del Comahue, Bariloche, Rio Negro 8400, Argentina; (D.L.); (N.B.)
| | - Patrícia H. Brito
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (M.D.-P.); (P.H.B.); (M.S.); (M.A.C.); (P.G.)
| | - Margarida Silva
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (M.D.-P.); (P.H.B.); (M.S.); (M.A.C.); (P.G.)
| | - Nicolás Bellora
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC)—CONICET/Universidad Nacional del Comahue, Bariloche, Rio Negro 8400, Argentina; (D.L.); (N.B.)
| | - Marco A. Coelho
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (M.D.-P.); (P.H.B.); (M.S.); (M.A.C.); (P.G.)
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA;
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA;
| | - Paula Gonçalves
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (M.D.-P.); (P.H.B.); (M.S.); (M.A.C.); (P.G.)
| | - José Paulo Sampaio
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (M.D.-P.); (P.H.B.); (M.S.); (M.A.C.); (P.G.)
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53
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Arcas A, Wilkinson DG, Nieto MÁ. The Evolutionary History of Ephs and Ephrins: Toward Multicellular Organisms. Mol Biol Evol 2020; 37:379-394. [PMID: 31589243 PMCID: PMC6993872 DOI: 10.1093/molbev/msz222] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Eph receptor (Eph) and ephrin signaling regulate fundamental developmental processes through both forward and reverse signaling triggered upon cell–cell contact. In vertebrates, they are both classified into classes A and B, and some representatives have been identified in many metazoan groups, where their expression and functions have been well studied. We have extended previous phylogenetic analyses and examined the presence of Eph and ephrins in the tree of life to determine their origin and evolution. We have found that 1) premetazoan choanoflagellates may already have rudimental Eph/ephrin signaling as they have an Eph-/ephrin-like pair and homologs of downstream-signaling genes; 2) both forward- and reverse-downstream signaling might already occur in Porifera since sponges have most genes involved in these types of signaling; 3) the nonvertebrate metazoan Eph is a type-B receptor that can bind ephrins regardless of their membrane-anchoring structure, glycosylphosphatidylinositol, or transmembrane; 4) Eph/ephrin cross-class binding is specific to Gnathostomata; and 5) kinase-dead Eph receptors can be traced back to Gnathostomata. We conclude that Eph/ephrin signaling is of older origin than previously believed. We also examined the presence of protein domains associated with functional characteristics and the appearance and conservation of downstream-signaling pathways to understand the original and derived functions of Ephs and ephrins. We find that the evolutionary history of these gene families points to an ancestral function in cell–cell interactions that could contribute to the emergence of multicellularity and, in particular, to the required segregation of cell populations.
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Affiliation(s)
- Aida Arcas
- Instituto de Neurociencias (CSIC-UMH), Avda, San Juan de Alicante, Spain
| | - David G Wilkinson
- Neural Development Laboratory, The Francis Crick Institute, London, United Kingdom
| | - M Ángela Nieto
- Instituto de Neurociencias (CSIC-UMH), Avda, San Juan de Alicante, Spain
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54
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Mageeney CM, Mohammed HT, Dies M, Anbari S, Cudkevich N, Chen Y, Buceta J, Ware VC. Mycobacterium Phage Butters-Encoded Proteins Contribute to Host Defense against Viral Attack. mSystems 2020; 5:e00534-20. [PMID: 33024050 PMCID: PMC7542560 DOI: 10.1128/msystems.00534-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/15/2020] [Indexed: 01/21/2023] Open
Abstract
A diverse set of prophage-mediated mechanisms protecting bacterial hosts from infection has been recently uncovered within cluster N mycobacteriophages isolated on the host, Mycobacterium smegmatis mc2155. In that context, we unveil a novel defense mechanism in cluster N prophage Butters. By using bioinformatics analyses, phage plating efficiency experiments, microscopy, and immunoprecipitation assays, we show that Butters genes located in the central region of the genome play a key role in the defense against heterotypic viral attack. Our study suggests that a two-component system, articulated by interactions between protein products of genes 30 and 31, confers defense against heterotypic phage infection by PurpleHaze (cluster A/subcluster A3) or Alma (cluster A/subcluster A9) but is insufficient to confer defense against attack by the heterotypic phage Island3 (cluster I/subcluster I1). Therefore, based on heterotypic phage plating efficiencies on the Butters lysogen, additional prophage genes required for defense are implicated and further show specificity of prophage-encoded defense systems.IMPORTANCE Many sequenced bacterial genomes, including those of pathogenic bacteria, contain prophages. Some prophages encode defense systems that protect their bacterial host against heterotypic viral attack. Understanding the mechanisms undergirding these defense systems is crucial to appreciate the scope of bacterial immunity against viral infections and will be critical for better implementation of phage therapy that would require evasion of these defenses. Furthermore, such knowledge of prophage-encoded defense mechanisms may be useful for developing novel genetic tools for engineering phage-resistant bacteria of industrial importance.
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Affiliation(s)
- Catherine M Mageeney
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Hamidu T Mohammed
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Marta Dies
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Samira Anbari
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Netta Cudkevich
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Yanyan Chen
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Javier Buceta
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Vassie C Ware
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
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55
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Ruiz Echartea ME, Ritchie DW, Chauvot de Beauchêne I. Using restraints in
EROS‐DOCK
improves model quality in pairwise and multicomponent protein docking. Proteins 2020; 88:1121-1128. [DOI: 10.1002/prot.25959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 03/04/2020] [Accepted: 05/27/2020] [Indexed: 12/26/2022]
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56
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Dijkstra MJJ, van der Ploeg AJ, Feenstra KA, Fokkink WJ, Abeln S, Heringa J. Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit. Bioinformatics 2020; 35:5315-5317. [PMID: 31368486 PMCID: PMC6954659 DOI: 10.1093/bioinformatics/btz572] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 05/29/2019] [Accepted: 07/29/2019] [Indexed: 12/03/2022] Open
Abstract
Summary PRALINE 2 is a toolkit for custom multiple sequence alignment workflows. It can be used to incorporate sequence annotations, such as secondary structure or (DNA) motifs, into the alignment scoring, as well as to customize many other aspects of a progressive multiple alignment workflow. Availability and implementation PRALINE 2 is implemented in Python and available as open source software on GitHub: https://github.com/ibivu/PRALINE/.
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Affiliation(s)
- Maurits J J Dijkstra
- Department of Computer Science, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Atze J van der Ploeg
- Department of Computer Science, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - K Anton Feenstra
- Department of Computer Science, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Wan J Fokkink
- Department of Computer Science, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Sanne Abeln
- Department of Computer Science, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Jaap Heringa
- Department of Computer Science, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
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57
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Zheng XF, Liu XQ, Peng SY, Zhou Q, Xu B, Yuan H, Tang GL. Characterization of the Rifamycin-Degrading Monooxygenase From Rifamycin Producers Implicating Its Involvement in Saliniketal Biosynthesis. Front Microbiol 2020; 11:971. [PMID: 32582048 PMCID: PMC7283461 DOI: 10.3389/fmicb.2020.00971] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/22/2020] [Indexed: 01/18/2023] Open
Abstract
Rifamycin derivatives, such as rifampicin, have potent antibiotic activity and have long been used in the clinic as mainstay components for the treatment of tuberculosis, leprosy, and AIDS-associated mycobacterial infections. However, the extensive usage of these antibiotics has resulted in the rapid development of bacterial resistance. The resistance mechanisms mainly include mutations of the rifamycin target RNA polymerase of bacteria and enzymatic modifications of rifamycin antibiotics. One modification is the recently characterized rifamycin degradation catalyzed by Rox enzymes, which belong to the widely occurring flavin monooxygenases. Intriguingly, our recent sequence analysis revealed the rifamycin producers also encode Rox homologs that are not yet characterized. In this work, we expanded the study of the Rox-catalyzed rifamycin degradation. We first showed that the Rox proteins from rifamycin producers have the enzymatic rifamycin SV-degrading activity. Then we used the structurally diverse rifamycin compounds rifampicin and 16-demethylrifamycin W to probe the substrate scope and found that they each have a slightly different substrate scope. Finally, we demonstrated that Rox proteins can also catalyze the transformation of 16-demethylsalinisporamycin to 16-demethylsaliniketal A. Since 16-demethylsalinisporamycin and 16-demethylsaliniketal A are the counterpart analogs of salinisporamycin and saliniketal A, our biochemical findings not only uncover a previously uncharacterized self-resistance mechanism in the rifamycin producers, but also bridge the gap between the biosynthesis of the potential antitumor compound saliniketal A.
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Affiliation(s)
- Xiao-Fu Zheng
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China
| | - Xin-Qiang Liu
- CAS-Key Laboratory of Synthetic Biology, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shu-Ya Peng
- Institute of Microbial Pharmaceuticals, College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Qiang Zhou
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Bin Xu
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China
| | - Hua Yuan
- College of Life Sciences, Shanghai Normal University, Shanghai, China.,State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Gong-Li Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
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58
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Characterization of the primate TRIM gene family reveals the recent evolution in primates. Mol Genet Genomics 2020; 295:1281-1294. [PMID: 32564135 DOI: 10.1007/s00438-020-01698-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 06/09/2020] [Indexed: 10/24/2022]
Abstract
The tripartite motif (TRIM) gene family encodes diverse distinct proteins that play important roles in many biological processes. However, the molecular evolution and phylogenetic relationships of TRIM genes in primates are still elusive. We performed a genomic approach to identify and characterize TRIM genes in human and other six primate genomes. In total, 537 putative functional TRIM genes were identified and TRIM members varied among primates. A neighbor joining (NJ) tree based on the protein sequences of 82 human TRIM genes indicates seven TRIM groups, which is consistent with the results based on the architectural motifs. Many TRIM gene duplication events were identified, indicating a recent expansion of TRIM family in primate lineages. Interestingly, the chimpanzee genome shows the greatest TRIM gene expansion among the primates; however, its congeneric species, bonobo, has the least number of TRIM genes and no duplication event. Moreover, we identified a ~ 200 kb deletion on chromosome 11 of bonobos that results in a loss of cluster3 TRIM genes. The loss of TRIM genes might have occurred within the last 2 mys. Analysis of positive selection recovered 9 previously reported and 21 newly identified positively selected TRIM genes. In particular, most positive selected sites are located in the B30.2 domains. Our results have provided new insight into the evolution of primate TRIM genes and will broaden our understanding on the functions of the TRIM family.
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Complete genome analysis of Pantoea agglomerans-infecting bacteriophage vB_PagM_AAM22. Arch Virol 2020; 165:2111-2114. [PMID: 32556600 DOI: 10.1007/s00705-020-04705-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 05/18/2020] [Indexed: 12/27/2022]
Abstract
A novel myovirus, vB_PagM_AAM22 (AAM22), was isolated in Lithuania using Pantoea agglomerans as the host for phage propagation. The 49,744-bp genome of AAM22 has a G + C content of 48.4% and contains 96 probable protein-encoding genes and no genes for tRNA. In total, 34 ORFs were given a putative functional annotation, including genes associated with virion morphogenesis, DNA metabolism, and phage-host interactions. Based on comparative phylogenetic analysis, AAM22 cannot be assigned to any genus currently recognized by the ICTV and is a potential candidate to form a new genus within the family Myoviridae.
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Molecular Topology of RNA Polymerase I Upstream Activation Factor. Mol Cell Biol 2020; 40:MCB.00056-20. [PMID: 32253346 DOI: 10.1128/mcb.00056-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/27/2020] [Indexed: 11/20/2022] Open
Abstract
Upstream activation factor (UAF) is a multifunctional transcription factor in Saccharomyces cerevisiae that plays dual roles in activating RNA polymerase I (Pol I) transcription and repression of Pol II. For Pol I, UAF binds to a specific upstream element in the ribosomal DNA (rDNA) promoter and interacts with two other Pol I initiation factors, the TATA-binding protein (TBP) and core factor (CF). We used an integrated combination of chemical cross-linking mass spectrometry (CXMS), molecular genetics, protein biochemistry, and structural modeling to understand the topological framework responsible for UAF complex formation. Here, we report the molecular topology of the UAF complex, describe new structural and functional domains that play roles in UAF complex integrity, assembly, and biological function, and provide roles for previously identified UAF domains that include the Rrn5 SANT and histone fold domains. We highlight the role of new domains in Uaf30 that include an N-terminal winged helix domain and a disordered tethering domain as well as a BORCS6-like domain found in Rrn9. Together, our results reveal a unique network of topological features that coalesce around a histone tetramer-like core to form the dual-function UAF complex.
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Sharker MR, Sukhan ZP, Kim SC, Lee WK, Kho KH. Molecular Identification, Characterization, and Expression Analysis of a Gonadotropin-Releasing Hormone Receptor (GnRH-R) in Pacific Abalone, Haliotis discus hannai. Molecules 2020; 25:molecules25122733. [PMID: 32545589 PMCID: PMC7355911 DOI: 10.3390/molecules25122733] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/02/2020] [Accepted: 06/11/2020] [Indexed: 12/24/2022] Open
Abstract
A full-length cDNA sequence encoding a GnRH receptor was cloned from the pleuropedal ganglion of the Pacific abalone, Haliotis discus hannai. The cloned sequence is 1499-bp in length encoding a protein of 460 amino acid residues, with a molecular mass of 52.22 kDa and an isoelectric point (pI) of 9.57. The architecture of HdhGnRH-R gene exhibited key features of G protein-coupled receptors (GPCRs), including seven membrane spanning domains, putative N-linked glycosylation motifs, and phosphorylation sites of serine and threonine residues. It shared 63%, 52%, and 30% sequence identities with Octopus vulgaris, Limulus polyphemus, and Mizuhopecten yessoensis GnRH-R II sequences, respectively. Phylogenetic analysis indicated that HdhGnRH-R gene was clustered with GnRH-R II of O. vulgaris and O. bimaculoides. qPCR assay demonstrated that the mRNA expression level of this receptor was significantly higher in the pleuropedal ganglion than that in any other examined tissue. Transcriptional activities of this gene in gonadal tissues were significantly higher in the ripening stage. The mRNA expression of this gene was significantly higher in pleuropedal ganglion, testis, and ovary at higher effective accumulative temperature (1000 °C). In situ hybridization revealed that HdhGnRH-R mRNA was expressed in neurosecretory cells of pleuropedal ganglion. Our results suggest that HdhGnRH-R gene synthesized in the neural ganglia might be involved in the control of gonadal maturation and gametogenesis of H. discus hannai. This is the first report of GnRH-R in H. discus hannai and the results may contribute to further studies of GPCRs evolution or may useful for the development of aquaculture method of this abalone species.
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Affiliation(s)
| | | | | | | | - Kang Hee Kho
- Correspondence: ; Tel.: +82-616-597-168; Fax: +82-616-597-169
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Badawy S, Pajunen MI, Haiko J, Baka ZAM, Abou-Dobara MI, El-Sayed AKA, Skurnik M. Identification and Functional Analysis of Temperate Siphoviridae Bacteriophages of Acinetobacter baumannii. Viruses 2020; 12:v12060604. [PMID: 32486497 PMCID: PMC7354433 DOI: 10.3390/v12060604] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/25/2020] [Accepted: 05/29/2020] [Indexed: 02/07/2023] Open
Abstract
Acinetobacter baumannii is an opportunistic pathogen that presents a serious clinical challenge due to its increasing resistance to all available antibiotics. Phage therapy has been introduced recently to treat antibiotic-incurable A. baumannii infections. In search for new A. baumannii specific bacteriophages, 20 clinical A. baumannii strains were used in two pools in an attempt to enrich phages from sewage. The enrichment resulted in induction of resident prophage(s) and three temperate bacteriophages, named vB_AbaS_fEg-Aba01, vB_AbaS_fLi-Aba02 and vB_AbaS_fLi-Aba03, all able to infect only one strain (#6597) of the 20 clinical strains, were isolated. Morphological characteristics obtained by transmission electron microscopy together with the genomic information revealed that the phages belong to the family Siphoviridae. The ca. 35 kb genomic sequences of the phages were >99% identical to each other. The linear ds DNA genomes of the phages contained 10 nt cohesive end termini, 52–54 predicted genes, an attP site and one tRNA gene each. A database search revealed an >99% identical prophage in the genome of A. baumannii strain AbPK1 (acc. no. CP024576.1). Over 99% identical prophages were also identified from two of the original 20 clinical strains (#5707 and #5920) and both were shown to be spontaneously inducible, thus very likely being the origins of the isolated phages. The phage vB_AbaS_fEg-Aba01 was also able to lysogenize the susceptible strain #6597 demonstrating that it was fully functional. The phages showed a very narrow host range infecting only two A. baumannii strains. In conclusion, we have isolated and characterized three novel temperate Siphoviridae phages that infect A.baumannii.
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Affiliation(s)
- Shimaa Badawy
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 UH Helsinki, Finland; (S.B.); (M.I.P.)
- Department of Botany and Microbiology, Faculty of Science, Damietta University, 34511 New Damietta, Egypt; (Z.A.M.B.); (M.I.A.-D.); (A.K.A.E.-S.)
| | - Maria I. Pajunen
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 UH Helsinki, Finland; (S.B.); (M.I.P.)
| | - Johanna Haiko
- Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, 00290 Helsinki, Finland;
| | - Zakaria A. M. Baka
- Department of Botany and Microbiology, Faculty of Science, Damietta University, 34511 New Damietta, Egypt; (Z.A.M.B.); (M.I.A.-D.); (A.K.A.E.-S.)
| | - Mohamed I. Abou-Dobara
- Department of Botany and Microbiology, Faculty of Science, Damietta University, 34511 New Damietta, Egypt; (Z.A.M.B.); (M.I.A.-D.); (A.K.A.E.-S.)
| | - Ahmed K. A. El-Sayed
- Department of Botany and Microbiology, Faculty of Science, Damietta University, 34511 New Damietta, Egypt; (Z.A.M.B.); (M.I.A.-D.); (A.K.A.E.-S.)
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 UH Helsinki, Finland; (S.B.); (M.I.P.)
- Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, 00290 Helsinki, Finland;
- Correspondence: ; Tel.: +358-2941-26464
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Kim H, Kubori T, Yamazaki K, Kwak MJ, Park SY, Nagai H, Vogel JP, Oh BH. Structural basis for effector protein recognition by the Dot/Icm Type IVB coupling protein complex. Nat Commun 2020; 11:2623. [PMID: 32457311 PMCID: PMC7251119 DOI: 10.1038/s41467-020-16397-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 04/27/2020] [Indexed: 01/25/2023] Open
Abstract
The Legionella pneumophila Dot/Icm type IVB secretion system (T4BSS) is extremely versatile, translocating ~300 effector proteins into host cells. This specialized secretion system employs the Dot/Icm type IVB coupling protein (T4CP) complex, which includes IcmS, IcmW and LvgA, that are known to selectively assist the export of a subclass of effectors. Herein, the crystal structure of a four-subunit T4CP subcomplex bound to the effector protein VpdB reveals an interaction between LvgA and a linear motif in the C-terminus of VpdB. The same binding interface of LvgA also interacts with the C-terminal region of three additional effectors, SidH, SetA and PieA. Mutational analyses identified a FxxxLxxxK binding motif that is shared by VpdB and SidH, but not by SetA and PieA, showing that LvgA recognizes more than one type of binding motif. Together, this work provides a structural basis for how the Dot/Icm T4CP complex recognizes effectors, and highlights the multiple substrate-binding specificities of its adaptor subunit.
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Affiliation(s)
- Hyunmin Kim
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Tomoko Kubori
- Department of Microbiology, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu, 501-1194, Japan
| | - Kohei Yamazaki
- Department of Microbiology, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu, 501-1194, Japan.,Veterinary Public Health, Kitasato University, Higashi 23-35-1, Towada, Aomori, 034-8628, Japan
| | - Mi-Jeong Kwak
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,CKD Research Institute, Yongin, Gyeonggi, 16995, Republic of Korea
| | - Suk-Youl Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Hiroki Nagai
- Department of Microbiology, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu, 501-1194, Japan
| | - Joseph P Vogel
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Byung-Ha Oh
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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64
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Intrinsic Disorder in Tetratricopeptide Repeat Proteins. Int J Mol Sci 2020; 21:ijms21103709. [PMID: 32466138 PMCID: PMC7279152 DOI: 10.3390/ijms21103709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/12/2020] [Accepted: 05/22/2020] [Indexed: 12/27/2022] Open
Abstract
Among the realm of repeat containing proteins that commonly serve as “scaffolds” promoting protein-protein interactions, there is a family of proteins containing between 2 and 20 tetratricopeptide repeats (TPRs), which are functional motifs consisting of 34 amino acids. The most distinguishing feature of TPR domains is their ability to stack continuously one upon the other, with these stacked repeats being able to affect interaction with binding partners either sequentially or in combination. It is known that many repeat-containing proteins are characterized by high levels of intrinsic disorder, and that many protein tandem repeats can be intrinsically disordered. Furthermore, it seems that TPR-containing proteins share many characteristics with hybrid proteins containing ordered domains and intrinsically disordered protein regions. However, there has not been a systematic analysis of the intrinsic disorder status of TPR proteins. To fill this gap, we analyzed 166 human TPR proteins to determine the degree to which proteins containing TPR motifs are affected by intrinsic disorder. Our analysis revealed that these proteins are characterized by different levels of intrinsic disorder and contain functional disordered regions that are utilized for protein-protein interactions and often serve as targets of various posttranslational modifications.
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65
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Jin X, Liao Q, Liu B. PL-search: a profile-link-based search method for protein remote homology detection. Brief Bioinform 2020; 22:5840006. [PMID: 32427287 DOI: 10.1093/bib/bbaa051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 12/26/2022] Open
Abstract
Protein remote homology detection is a fundamental and important task for protein structure and function analysis. Several search methods have been proposed to improve the detection performance of the remote homologues and the accuracy of ranking lists. The position-specific scoring matrix (PSSM) profile and hidden Markov model (HMM) profile can contribute to improving the performance of the state-of-the-art search methods. In this paper, we improved the profile-link (PL) information for constructing PSSM or HMM profiles, and proposed a PL-based search method (PL-search). In PL-search, more robust PLs are constructed through the double-link and iterative extending strategies, and an accurate similarity score of sequence pairs is calculated from the two-level Jaccard distance for remote homologues. We tested our method on two widely used benchmark datasets. Our results show that whether HHblits, JackHMMER or position-specific iterated-BLAST is used, PL-search obviously improves the search performance in terms of ranking quality as well as the number of detected remote homologues. For ease of use of PL-search, both its stand-alone tool and the web server are constructed, which can be accessed at http://bliulab.net/PL-search/.
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66
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Buchan DWA, Jones DT. The PSIPRED Protein Analysis Workbench: 20 years on. Nucleic Acids Res 2020; 47:W402-W407. [PMID: 31251384 PMCID: PMC6602445 DOI: 10.1093/nar/gkz297] [Citation(s) in RCA: 818] [Impact Index Per Article: 204.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/02/2019] [Accepted: 04/15/2019] [Indexed: 02/07/2023] Open
Abstract
The PSIPRED Workbench is a web server offering a range of predictive methods to the bioscience community for 20 years. Here, we present the work we have completed to update the PSIPRED Protein Analysis Workbench and make it ready for the next 20 years. The main focus of our recent website upgrade work has been the acceleration of analyses in the face of increasing protein sequence database size. We additionally discuss any new software, the new hardware infrastructure, our webservices and web site. Lastly we survey updates to some of the key predictive algorithms available through our website.
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Affiliation(s)
- Daniel W A Buchan
- UCL Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK
| | - David T Jones
- UCL Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK
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67
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Šimoliūnienė M, Truncaitė L, Petrauskaitė E, Zajančkauskaitė A, Meškys R, Skapas M, Kaupinis A, Valius M, Šimoliūnas E. Pantoeaagglomerans-Infecting Bacteriophage vB_PagS_AAS21: A Cold-Adapted Virus Representing a Novel Genus within the Family Siphoviridae. Viruses 2020; 12:E479. [PMID: 32340233 PMCID: PMC7232348 DOI: 10.3390/v12040479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/31/2022] Open
Abstract
A novel cold-adapted siphovirus, vB_PagS_AAS21 (AAS21), was isolated in Lithuania using Pantoea agglomerans as the host for phage propagation. AAS21 has an isometric head (~85 nm in diameter) and a non-contractile flexible tail (~174 × 10 nm). With a genome size of 116,649 bp, bacteriophage AAS21 is the largest Pantoea-infecting siphovirus sequenced to date. The genome of AAS21 has a G+C content of 39.0% and contains 213 putative protein-encoding genes and 29 genes for tRNAs. A comparative sequence analysis revealed that 89 AAS21 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. In total, 63 AAS21 ORFs were functionally annotated, including those coding for the proteins responsible for virion morphogenesis, phage-host interactions, and DNA metabolism. Proteomic analysis led to the experimental identification of 19 virion proteins, including 11 that were predicted by bioinformatics approaches. Based on comparative phylogenetic analysis, AAS21 cannot be assigned to any genus currently recognized by ICTV and may represents a new branch of viruses within the family Siphoviridae.
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Affiliation(s)
- Monika Šimoliūnienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.P.); (A.Z.); (R.M.)
| | - Lidija Truncaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.P.); (A.Z.); (R.M.)
| | - Emilija Petrauskaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.P.); (A.Z.); (R.M.)
| | - Aurelija Zajančkauskaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.P.); (A.Z.); (R.M.)
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.P.); (A.Z.); (R.M.)
| | - Martynas Skapas
- Center for Physical Sciences and Technology, Saulėtekio av. 3, LT-10257 Vilnius, Lithuania;
| | - Algirdas Kaupinis
- Proteomics Centre, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Eugenijus Šimoliūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.P.); (A.Z.); (R.M.)
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68
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Medrano-Soto A, Ghazi F, Hendargo KJ, Moreno-Hagelsieb G, Myers S, Saier MH. Expansion of the Transporter-Opsin-G protein-coupled receptor superfamily with five new protein families. PLoS One 2020; 15:e0231085. [PMID: 32320418 PMCID: PMC7176098 DOI: 10.1371/journal.pone.0231085] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/17/2020] [Indexed: 02/06/2023] Open
Abstract
Here we provide bioinformatic evidence that the Organo-Arsenical Exporter (ArsP), Endoplasmic Reticulum Retention Receptor (KDELR), Mitochondrial Pyruvate Carrier (MPC), L-Alanine Exporter (AlaE), and the Lipid-linked Sugar Translocase (LST) protein families are members of the Transporter-Opsin-G Protein-coupled Receptor (TOG) Superfamily. These families share domains homologous to well-established TOG superfamily members, and their topologies of transmembranal segments (TMSs) are compatible with the basic 4-TMS repeat unit characteristic of this Superfamily. These repeat units tend to occur twice in proteins as a result of intragenic duplication events, often with subsequent gain/loss of TMSs in many superfamily members. Transporters within the ArsP family allow microbial pathogens to expel toxic arsenic compounds from the cell. Members of the KDELR family are involved in the selective retrieval of proteins that reside in the endoplasmic reticulum. Proteins of the MPC family are involved in the transport of pyruvate into mitochondria, providing the organelle with a major oxidative fuel. Members of family AlaE excrete L-alanine from the cell. Members of the LST family are involved in the translocation of lipid-linked glucose across the membrane. These five families substantially expand the range of substrates of transport carriers in the superfamily, although KDEL receptors have no known transport function. Clustering of protein sequences reveals the relationships among families, and the resulting tree correlates well with the degrees of sequence similarity documented between families. The analyses and programs developed to detect distant relatedness, provide insights into the structural, functional, and evolutionary relationships that exist between families of the TOG superfamily, and should be of value to many other investigators.
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Affiliation(s)
- Arturo Medrano-Soto
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Faezeh Ghazi
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Kevin J. Hendargo
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | | | - Scott Myers
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
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69
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Peng Q, Fang M, Liu X, Zhang C, Liu Y, Yuan Y. Isolation and Characterization of a Novel Phage for Controlling Multidrug-Resistant Klebsiella pneumoniae. Microorganisms 2020; 8:microorganisms8040542. [PMID: 32283667 PMCID: PMC7232175 DOI: 10.3390/microorganisms8040542] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 12/14/2022] Open
Abstract
The emergence of multidrug-resistant bacterial pathogens has severely threatened global health. A phage with the ability to efficiently and specifically lyse bacteria is considered an alternative for controlling multidrug-resistant bacterial pathogens. The discovery of novel agents for controlling the infections caused by K. pneumoniae is urgent due to the broad multidrug-resistance of K. pneumoniae. Only a few phage isolates have been reported to infect multidrug-resistant K. pneumoniae. In this study, by using the multidrug-resistant K. pneumoniae strain as an indicator, a novel phage called vB_KleS-HSE3, which maintains high antibacterial activity and high physical stability, was isolated from hospital sewage. This phage infected one of four tested multidrug-resistant K. pneumoniae strains. This phage belongs to the Siphoviridae family and a comparative genomic analysis showed that this phage is part of a novel phage lineage among the Siphoviridae family of phages that infect strains of Klebsiella. Based on its features, the vB_KleS-HSE3 phage has potential for controlling infections caused by multidrug-resistant K. pneumoniae.
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Affiliation(s)
- Qin Peng
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, China; (Q.P.); (M.F.); (X.L.); (C.Z.); (Y.L.)
| | - Meng Fang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, China; (Q.P.); (M.F.); (X.L.); (C.Z.); (Y.L.)
| | - Xushan Liu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, China; (Q.P.); (M.F.); (X.L.); (C.Z.); (Y.L.)
| | - Chunling Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, China; (Q.P.); (M.F.); (X.L.); (C.Z.); (Y.L.)
| | - Yue Liu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, China; (Q.P.); (M.F.); (X.L.); (C.Z.); (Y.L.)
| | - Yihui Yuan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
- Correspondence:
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70
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Sharker MR, Nou IS, Kho KH. Molecular characterization and spatiotemporal expression of prohormone convertase 2 in the Pacific abalone, Haliotis discus hannai. PLoS One 2020; 15:e0231353. [PMID: 32271824 PMCID: PMC7144994 DOI: 10.1371/journal.pone.0231353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/20/2020] [Indexed: 11/18/2022] Open
Abstract
Prohormone convertases (PCs) are subtilisin-like proteases responsible for the intracellular processing of prohormones and proneuropeptides in vertebrates and invertebrates. The full-length PC2 cDNA sequence was cloned from pleuropedal ganglion of Haliotis discus hannai, consisted of 2254-bp with an open reading frame of 1989-bp and encoded a protein of 662 amino acid residues. The architecture of Hdh PC2 displayed key features of PCs, including a signal peptide, a pro-segment domain with sites for autocatalytic activation, a catalytic domain, and a pro-protein domain (P-domain). It shares the highest homology of its amino acid sequence with the PC2 from H. asinina and to lesser extent with that of Homo sapiens and Rana catesbeiana PC2. Sequence alignment analysis indicated that Hdh PC2 was highly conserved in the catalytic domain, including a catalytic triad of serine proteinases of the subtilisin family at positions Asp-195, His-236, and Ser-412. The cloned sequence contained a canonical integrin binding sequence, and four cysteine residues involved in the formation of an intramolecular disulfide link. Phylogenetic analysis revealed that the Hdh PC2 is robustly clustered with the Has PC2. Quantitative PCR assay demonstrated that the Hdh PC2 was predominantly expressed in the pleuropedal ganglion rather than in other examined tissues. Although PC2 mRNA was expressed throughout the gametogenetic cycle of male and female abalone, the expression level was significantly higher in the ripening stage of female abalone. Also, a significantly higher expression was observed in the pleuropedal ganglion and gonadal tissues at a higher effective accumulative temperature (1000°C). In situ hybridization revealed that the PC2 mRNA expressing neurosecretory cells were distributed in the cortex region of the pleuropedal ganglion. According to the results, it can be concluded that pleuropedal ganglion is the highest site of PC2 activity, and this enzyme might be involved in the abalone reproduction process.
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Affiliation(s)
- Md Rajib Sharker
- Department of Fisheries Science, College of Fisheries and Ocean Sciences, Chonnam National University, Jeonnam, Republic of Korea
| | - Ill-Sup Nou
- Department of Horticulture, College of Life Science and Natural Resources, Sunchon National University, Jeollanam-do, Republic of Korea
| | - Kang Hee Kho
- Department of Fisheries Science, College of Fisheries and Ocean Sciences, Chonnam National University, Jeonnam, Republic of Korea
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71
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Chojnowski G, Choudhury K, Heuser P, Sobolev E, Pereira J, Oezugurel U, Lamzin VS. The use of local structural similarity of distant homologues for crystallographic model building from a molecular-replacement solution. Acta Crystallogr D Struct Biol 2020; 76:248-260. [PMID: 32133989 PMCID: PMC7057216 DOI: 10.1107/s2059798320000455] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 01/14/2020] [Indexed: 12/18/2022] Open
Abstract
The performance of automated protein model building usually decreases with resolution, mainly owing to the lower information content of the experimental data. This calls for a more elaborate use of the available structural information about macromolecules. Here, a new method is presented that uses structural homologues to improve the quality of protein models automatically constructed using ARP/wARP. The method uses local structural similarity between deposited models and the model being built, and results in longer main-chain fragments that in turn can be more reliably docked to the protein sequence. The application of the homology-based model extension method to the example of a CFA synthase at 2.7 Å resolution resulted in a more complete model with almost all of the residues correctly built and docked to the sequence. The method was also evaluated on 1493 molecular-replacement solutions at a resolution of 4.0 Å and better that were submitted to the ARP/wARP web service for model building. A significant improvement in the completeness and sequence coverage of the built models has been observed.
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Affiliation(s)
- Grzegorz Chojnowski
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Koushik Choudhury
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Philipp Heuser
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Egor Sobolev
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Joana Pereira
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Umut Oezugurel
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Victor S. Lamzin
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
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72
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Schäffer DE, Iyer LM, Burroughs AM, Aravind L. Functional Innovation in the Evolution of the Calcium-Dependent System of the Eukaryotic Endoplasmic Reticulum. Front Genet 2020; 11:34. [PMID: 32117448 PMCID: PMC7016017 DOI: 10.3389/fgene.2020.00034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/10/2020] [Indexed: 01/30/2023] Open
Abstract
The origin of eukaryotes was marked by the emergence of several novel subcellular systems. One such is the calcium (Ca2+)-stores system of the endoplasmic reticulum, which profoundly influences diverse aspects of cellular function including signal transduction, motility, division, and biomineralization. We use comparative genomics and sensitive sequence and structure analyses to investigate the evolution of this system. Our findings reconstruct the core form of the Ca2+-stores system in the last eukaryotic common ancestor as having at least 15 proteins that constituted a basic system for facilitating both Ca2+ flux across endomembranes and Ca2+-dependent signaling. We present evidence that the key EF-hand Ca2+-binding components had their origins in a likely bacterial symbiont other than the mitochondrial progenitor, whereas the protein phosphatase subunit of the ancestral calcineurin complex was likely inherited from the asgard archaeal progenitor of the stem eukaryote. This further points to the potential origin of the eukaryotes in a Ca2+-rich biomineralized environment such as stromatolites. We further show that throughout eukaryotic evolution there were several acquisitions from bacteria of key components of the Ca2+-stores system, even though no prokaryotic lineage possesses a comparable system. Further, using quantitative measures derived from comparative genomics we show that there were several rounds of lineage-specific gene expansions, innovations of novel gene families, and gene losses correlated with biological innovation such as the biomineralized molluscan shells, coccolithophores, and animal motility. The burst of innovation of new genes in animals included the wolframin protein associated with Wolfram syndrome in humans. We show for the first time that it contains previously unidentified Sel1, EF-hand, and OB-fold domains, which might have key roles in its biochemistry.
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Affiliation(s)
- Daniel E Schäffer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States.,Science, Mathematics, and Computer Science Magnet Program, Montgomery Blair High School, Silver Spring, MD, United States
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
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73
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Shin D, Mukherjee R, Liu Y, Gonzalez A, Bonn F, Liu Y, Rogov VV, Heinz M, Stolz A, Hummer G, Dötsch V, Luo ZQ, Bhogaraju S, Dikic I. Regulation of Phosphoribosyl-Linked Serine Ubiquitination by Deubiquitinases DupA and DupB. Mol Cell 2020; 77:164-179.e6. [PMID: 31732457 PMCID: PMC6941232 DOI: 10.1016/j.molcel.2019.10.019] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/07/2019] [Accepted: 10/11/2019] [Indexed: 12/21/2022]
Abstract
The family of bacterial SidE enzymes catalyzes non-canonical phosphoribosyl-linked (PR) serine ubiquitination and promotes infectivity of Legionella pneumophila. Here, we describe identification of two bacterial effectors that reverse PR ubiquitination and are thus named deubiquitinases for PR ubiquitination (DUPs; DupA and DupB). Structural analyses revealed that DupA and SidE ubiquitin ligases harbor a highly homologous catalytic phosphodiesterase (PDE) domain. However, unlike SidE ubiquitin ligases, DupA displays increased affinity to PR-ubiquitinated substrates, which allows DupA to cleave PR ubiquitin from substrates. Interfering with DupA-ubiquitin binding switches its activity toward SidE-type ligase. Given the high affinity of DupA to PR-ubiquitinated substrates, we exploited a catalytically inactive DupA mutant to trap and identify more than 180 PR-ubiquitinated host proteins in Legionella-infected cells. Proteins involved in endoplasmic reticulum (ER) fragmentation and membrane recruitment to Legionella-containing vacuoles (LCV) emerged as major SidE targets. The global map of PR-ubiquitinated substrates provides critical insights into host-pathogen interactions during Legionella infection.
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Affiliation(s)
- Donghyuk Shin
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Rukmini Mukherjee
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Yaobin Liu
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Alexis Gonzalez
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Florian Bonn
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Yan Liu
- Purdue Institute of Immunology, Inflammation, and Infectious Diseases and Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Vladimir V Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance and Cluster of Excellence Macromolecular Complexes (CEF), Goethe University, Frankfurt, Germany
| | - Marcel Heinz
- Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany; Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Alexandra Stolz
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany; Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance and Cluster of Excellence Macromolecular Complexes (CEF), Goethe University, Frankfurt, Germany
| | - Zhao-Qing Luo
- Purdue Institute of Immunology, Inflammation, and Infectious Diseases and Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Sagar Bhogaraju
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany.
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74
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Oki K, Lee FS, Mayo SL. Attempts to develop an enzyme converting DHIV to KIV. Protein Eng Des Sel 2019; 32:261-270. [PMID: 31872250 DOI: 10.1093/protein/gzz042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/01/2019] [Indexed: 11/13/2022] Open
Abstract
Dihydroxy-acid dehydratase (DHAD) catalyzes the dehydration of R-2,3-dihydroxyisovalerate (DHIV) to 2-ketoisovalerate (KIV) using an Fe-S cluster as a cofactor, which is sensitive to oxidation and expensive to synthesize. In contrast, sugar acid dehydratases catalyze the same chemical reactions using a magnesium ion. Here, we attempted to substitute the high-cost DHAD with a cost-efficient engineered sugar acid dehydratase using computational protein design (CPD). First, we tried without success to modify the binding pocket of a sugar acid dehydratase to accommodate the smaller, more hydrophobic DHIV. Then, we used a chemically activated substrate analog to react with sugar acid dehydratases or other enolase superfamily enzymes. Mandelate racemase from Pseudomonas putida (PpManR) and the putative sugar acid dehydratase from Salmonella typhimurium (StPutD) showed beta-elimination activity towards chlorolactate (CLD). CPD combined with medium-throughput selection improved the PpManR kcat/KM for CLD by four-fold. However, these enzyme variants did not show dehydration activity towards DHIV. Lastly, assuming phosphorylation could also be a good activation mechanism, we found that mevalonate-3-kinase (M3K) from Picrophilus torridus (PtM3K) exhibited adenosine triphosphate (ATP) hydrolysis activity when mixed with DHIV, indicating phosphorylation activity towards DHIV. Engineering PpManR or StPutD to accept 3-phospho-DHIV as a substrate was performed, but no variants with the desired activity were obtained.
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Affiliation(s)
- Kenji Oki
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., MC 114-96, Pasadena, CA 91125, USA.,Science & Innovation Center, Mitsubishi Chemical Corporation, Yokohama 227-8502, Japan
| | - Frederick S Lee
- Protabit LLC, 1010 Union St., Suite 110, Pasadena, CA 91101, USA
| | - Stephen L Mayo
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., MC 114-96, Pasadena, CA 91125, USA.,Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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75
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Guerra D, Lopes-Lima M, Froufe E, Gan HM, Ondina P, Amaro R, Klunzinger MW, Callil C, Prié V, Bogan AE, Stewart DT, Breton S. Variability of mitochondrial ORFans hints at possible differences in the system of doubly uniparental inheritance of mitochondria among families of freshwater mussels (Bivalvia: Unionida). BMC Evol Biol 2019; 19:229. [PMID: 31856711 PMCID: PMC6923999 DOI: 10.1186/s12862-019-1554-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 12/09/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Supernumerary ORFan genes (i.e., open reading frames without obvious homology to other genes) are present in the mitochondrial genomes of gonochoric freshwater mussels (Bivalvia: Unionida) showing doubly uniparental inheritance (DUI) of mitochondria. DUI is a system in which distinct female-transmitted and male-transmitted mitotypes coexist in a single species. In families Unionidae and Margaritiferidae, the transition from dioecy to hermaphroditism and the loss of DUI appear to be linked, and this event seems to affect the integrity of the ORFan genes. These observations led to the hypothesis that the ORFans have a role in DUI and/or sex determination. Complete mitochondrial genome sequences are however scarce for most families of freshwater mussels, therefore hindering a clear localization of DUI in the various lineages and a comprehensive understanding of the influence of the ORFans on DUI and sexual systems. Therefore, we sequenced and characterized eleven new mitogenomes from poorly sampled freshwater mussel families to gather information on the evolution and variability of the ORFan genes and their protein products. RESULTS We obtained ten complete plus one almost complete mitogenome sequence from ten representative species (gonochoric and hermaphroditic) of families Margaritiferidae, Hyriidae, Mulleriidae, and Iridinidae. ORFan genes are present only in DUI species from Margaritiferidae and Hyriidae, while non-DUI species from Hyriidae, Iridinidae, and Mulleriidae lack them completely, independently of their sexual system. Comparisons among the proteins translated from the newly characterized ORFans and already known ones provide evidence of conserved structures, as well as family-specific features. CONCLUSIONS The ORFan proteins show a comparable organization of secondary structures among different families of freshwater mussels, which supports a conserved physiological role, but also have distinctive family-specific features. Given this latter observation and the fact that the ORFans can be either highly mutated or completely absent in species that secondarily lost DUI depending on their respective family, we hypothesize that some aspects of the connection among ORFans, sexual systems, and DUI may differ in the various lineages of unionids.
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Affiliation(s)
- Davide Guerra
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC Canada
| | - Manuel Lopes-Lima
- CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, University of Porto, Campus Agrário de Vairão, Vairão, Portugal
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Elsa Froufe
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Han Ming Gan
- Deakin Genomics Centre, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria Australia
| | - Paz Ondina
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Facultade de Veterinaria, Universidade de Santiago de Compostela, Campus de Lugo, Lugo, Spain
| | - Rafaela Amaro
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Facultade de Veterinaria, Universidade de Santiago de Compostela, Campus de Lugo, Lugo, Spain
| | - Michael W. Klunzinger
- BWG Environmental, Brisbane, QLD Australia
- Mollusca, Department of Aquatic Zoology, Western Australian Museum, Welshpool, WA Australia
- School of Veterinary and Biological Sciences, Murdoch University, Perth, WA Australia
| | - Claudia Callil
- ECOBiv - Ecology and Conservation of Bivalves Research Group, Department of Biology and Zoology, Federal University of Mato Grosso, Cuiabá, MT Brazil
| | - Vincent Prié
- Institut Systématique Evolution Biodiversité ISYEB - Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | | | | | - Sophie Breton
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC Canada
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76
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Toledo-Patiño S, Chaubey M, Coles M, Höcker B. Reconstructing the Remote Origins of a Fold Singleton from a Flavodoxin-Like Ancestor. Biochemistry 2019; 58:4790-4793. [PMID: 31724394 PMCID: PMC6968885 DOI: 10.1021/acs.biochem.9b00900] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
![]()
Evolutionary processes that led to the emergence of structured
protein domains left footprints in the sequences of modern proteins.
We searched for such hints employing state-of-the-art sequence analysis
and found evidence that the HemD-like fold emerged from the flavodoxin-like
fold through segment swap and gene duplication. To verify this hypothesis,
we reverted these evolutionary steps experimentally, constructing
a HemD-half that resulted in a protein with the canonical flavodoxin-like
architecture. These results of fold reconstruction from the sequence
of a different fold strongly support our hypothesis of common ancestry.
It further illustrates the plasticity of modern proteins to form new
folded proteins.
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Affiliation(s)
- Saacnicteh Toledo-Patiño
- Department of Biochemistry , University of Bayreuth , 95447 Bayreuth , Germany.,Max Planck Institute for Developmental Biology , 72076 Tübingen , Germany
| | - Manish Chaubey
- Max Planck Institute for Developmental Biology , 72076 Tübingen , Germany
| | - Murray Coles
- Max Planck Institute for Developmental Biology , 72076 Tübingen , Germany
| | - Birte Höcker
- Department of Biochemistry , University of Bayreuth , 95447 Bayreuth , Germany.,Max Planck Institute for Developmental Biology , 72076 Tübingen , Germany
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77
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Brito GC, Schormann W, Gidda SK, Mullen RT, Andrews DW. Genome-wide analysis of Homo sapiens, Arabidopsis thaliana, and Saccharomyces cerevisiae reveals novel attributes of tail-anchored membrane proteins. BMC Genomics 2019; 20:835. [PMID: 31711414 PMCID: PMC6849228 DOI: 10.1186/s12864-019-6232-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/28/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Tail-anchored membrane proteins (TAMPs) differ from other integral membrane proteins, because they contain a single transmembrane domain at the extreme carboxyl-terminus and are therefore obliged to target to membranes post-translationally. Although 3-5% of all transmembrane proteins are predicted to be TAMPs only a small number are well characterized. RESULTS To identify novel putative TAMPs across different species, we used TAMPfinder software to identify 859, 657 and 119 putative TAMPs in human (Homo sapiens), plant (Arabidopsis thaliana), and yeast (Saccharomyces cerevisiae), respectively. Bioinformatics analyses of these putative TAMP sequences suggest that the list is highly enriched for authentic TAMPs. To experimentally validate the software predictions several human and plant proteins identified by TAMPfinder that were previously uncharacterized were expressed in cells and visualized at subcellular membranes by fluorescence microscopy and further analyzed by carbonate extraction or by bimolecular fluorescence complementation. With the exception of the pro-apoptotic protein harakiri, which is, peripherally bound to the membrane this subset of novel proteins behave like genuine TAMPs. Comprehensive bioinformatics analysis of the generated TAMP datasets revealed previously unappreciated common and species-specific features such as the unusual size distribution of and the propensity of TAMP proteins to be part of larger complexes. Additionally, novel features of the amino acid sequences that anchor TAMPs to membranes were also revealed. CONCLUSIONS The findings in this study more than double the number of predicted annotated TAMPs and provide new insights into the common and species-specific features of TAMPs. Furthermore, the list of TAMPs and annotations provide a resource for further investigation.
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Affiliation(s)
- Glauber Costa Brito
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, M4N 3M5, Canada
| | - Wiebke Schormann
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, M4N 3M5, Canada
| | - Satinder K Gidda
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - David W Andrews
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, M4N 3M5, Canada. .,Departments of Biochemistry and Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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78
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Identification, characterization, and expression analysis of a serotonin receptor involved in the reproductive process of the Pacific abalone, Haliotis discus hannai. Mol Biol Rep 2019; 47:555-567. [PMID: 31696430 DOI: 10.1007/s11033-019-05162-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/23/2019] [Indexed: 10/25/2022]
Abstract
Serotonin receptor (5-HT) is a biogenic amine acting as a neurotransmitter and neuromodulator that mediates various aspects of reproduction and gametogenesis. The full-length nucleotide sequence of Haliotis discus hannai encodes a protein of 417 amino acids with a predicted molecular mass of 46.54 kDa and isoelectric point of 8.94. The structural profile of 5-HTHdh displayed key features of G protein-coupled receptors, including seven hydrophobic transmembrane domains, putative N-linked glycosylation sites, and several phosphorylation consensus motifs. It shares the highest homology of its amino acid sequence with the 5-HT receptor from Haliotis asinina, and to lesser extent of human 5-HT receptor. The cloned sequence possesses two cysteine residues (Cys-115 and Cys-193), which are likely to form a disulfide bond. Phylogenetic comparison with other known 5-HT receptor genes revealed that the 5-HTHdh is most closely related to the 5-HTHa receptor. The three-dimensional structure of the 5-HTHdh showed multiple alpha helices which is separated by a helix-loop-helix (HLH) structure. Quantitative PCR demonstrated that the receptor mRNA was predominantly expressed in the pleuropedal ganglion. Significant differences in the transcriptional activity of the 5-HTHdh gene were observed in the ovary at the ripening stage. An exclusive expression was detected in pleuropedal ganglion, testis, and ovary at higher effective accumulative temperature (1000 °C). In situ hybridization showed that the 5-HTHdh expressing neurosecretory cells were distributed in the cortex of the pleuropedal ganglion. Our results suggest that 5-HTHdh synthesized in the neural ganglia may be involved in oocyte maturation and spawning of H. discus hannai.
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79
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Pereira J, Lupas AN. The ancestral KH peptide at the root of a domain family with three different folds. Bioinformatics 2019; 34:3961-3965. [PMID: 29912332 DOI: 10.1093/bioinformatics/bty480] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 06/12/2018] [Indexed: 11/13/2022] Open
Abstract
Motivation The direct ancestor of the DNA-protein world of today is considered to have been an RNA-peptide world, in which peptides were co-factors of RNA-mediated catalysis and replication. Evidence for these ancestral peptides, from which folded proteins evolved, can be derived even today from regions of local sequence similarity within globally dissimilar folds. One of these is the 45-residue motif common to both folds of the hnRNP K homology (KH) domain. Results In a survey of KH domains, we found a third fold that contains the KH motif at its core. This corresponds to the Small Domain of bacterial Ribonucleases G/E and, like type I and type II KH domains, it cannot be related to the others by a single genetic event, providing further support for the KH motif as an ancestral peptide predating folded proteins. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joana Pereira
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, Tübingen, Germany
| | - Andrei N Lupas
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, Tübingen, Germany
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80
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Ruetalo N, Anders S, Stollmaier C, Jäckl M, Schütz-Stoffregen MC, Stefan N, Wolf C, Wiesner S. The WW1 Domain Enhances Autoinhibition in Smurf Ubiquitin Ligases. J Mol Biol 2019; 431:4834-4847. [PMID: 31628949 DOI: 10.1016/j.jmb.2019.09.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/23/2019] [Accepted: 09/26/2019] [Indexed: 10/25/2022]
Abstract
Downregulation of ubiquitin (Ub) ligase activity prevents premature ubiquitination and is critical for cellular homeostasis. Nedd4 Ub ligases share a common domain architecture and yet are regulated in distinct ways through interactions of the catalytic HECT domain with the N-terminal C2 domain or the central WW domain region. Smurf1 and Smurf2 are two highly related Nedd4 ligases with ~70% overall sequence identity. Here, we show that the Smurf1 C2 domain interacts with the HECT domain and inhibits ligase activity in trans. However, in contrast to Smurf2, we find that full-length Smurf1 is a highly active Ub ligase, and we can attribute this striking difference in regulation to the lack of one WW domain (WW1) in Smurf1. Using NMR spectroscopy and biochemical assays, we identified the WW1 region as an additional inhibitory element in Smurf2 that cooperates with the C2 domain to enhance HECT domain binding and Smurf2 inhibition. Our work provides important insights into Smurf regulation and highlights that the activities of highly related proteins can be controlled in distinct ways.
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Affiliation(s)
- Natalia Ruetalo
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Samira Anders
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Carsten Stollmaier
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany; Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstr. 31, 93040 Regensburg, Germany
| | - Magnus Jäckl
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Mira C Schütz-Stoffregen
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany; Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstr. 31, 93040 Regensburg, Germany
| | - Nadine Stefan
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstr. 31, 93040 Regensburg, Germany
| | - Christine Wolf
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Silke Wiesner
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany; Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstr. 31, 93040 Regensburg, Germany.
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81
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Analysis of Heterodimeric "Mutual Synergistic Folding"-Complexes. Int J Mol Sci 2019; 20:ijms20205136. [PMID: 31623284 PMCID: PMC6829572 DOI: 10.3390/ijms20205136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/07/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022] Open
Abstract
Several intrinsically disordered proteins (IDPs) are capable to adopt stable structures without interacting with a folded partner. When the folding of all interacting partners happens at the same time, coupled with the interaction in a synergistic manner, the process is called Mutual Synergistic Folding (MSF). These complexes represent a discrete subset of IDPs. Recently, we collected information on their complexes and created the MFIB (Mutual Folding Induced by Binding) database. In a previous study, we compared homodimeric MSF complexes with homodimeric and monomeric globular proteins with similar amino acid sequence lengths. We concluded that MSF homodimers, compared to globular homodimeric proteins, have a greater solvent accessible main-chain surface area on the contact surface of the subunits, which becomes buried during dimerization. The main driving force of the folding is the mutual shielding of the water-accessible backbones, but the formation of further intermolecular interactions can also be relevant. In this paper, we will report analyses of heterodimeric MSF complexes. Our results indicate that the amino acid composition of the heterodimeric MSF monomer subunits slightly diverges from globular monomer proteins, while after dimerization, the amino acid composition of the overall MSF complexes becomes more similar to overall amino acid compositions of globular complexes. We found that inter-subunit interactions are strengthened, and additionally to the shielding of the solvent accessible backbone, other factors might play an important role in the stabilization of the heterodimeric structures, likewise energy gain resulting from the interaction of the two subunits with different amino acid compositions. We suggest that the shielding of the β-sheet backbones and the formation of a buried structural core along with the general strengthening of inter-subunit interactions together could be the driving forces of MSF protein structural ordering upon dimerization.
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82
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Bullock JMA, Thalassinos K, Topf M. Jwalk and MNXL web server: model validation using restraints from crosslinking mass spectrometry. Bioinformatics 2019; 34:3584-3585. [PMID: 29741581 PMCID: PMC6184817 DOI: 10.1093/bioinformatics/bty366] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 05/03/2018] [Indexed: 11/14/2022] Open
Abstract
Motivation Crosslinking Mass Spectrometry generates restraints that can be used to model proteins and protein complexes. Previously, we have developed two methods, to help users achieve better modelling performance from their crosslinking restraints: Jwalk, to estimate solvent accessible distances between crosslinked residues and MNXL, to assess the quality of the models based on these distances. Results Here, we present the Jwalk and MNXL webservers, which streamline the process of validating monomeric protein models using restraints from crosslinks. We demonstrate this by using the MNXL server to filter models made of varying quality, selecting the most native-like. Availability and implementation The webserver and source code are freely available from jwalk.ismb.lon.ac.uk and mnxl.ismb.lon.ac.uk. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joshua M A Bullock
- Institute for Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - Konstantinos Thalassinos
- Institute for Structural and Molecular Biology, Birkbeck College, University of London, London, UK.,Institute for Structural and Molecular Biology, UCL, University of London, London, UK
| | - Maya Topf
- Institute for Structural and Molecular Biology, Birkbeck College, University of London, London, UK
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83
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Pierce into the Native Structure of Ata, a Trimeric Autotransporter of Acinetobacter baumannii ATCC 17978. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09920-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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84
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Rehan S, Shahid S, Salminen TA, Jaakola VP, Paavilainen VO. Current Progress on Equilibrative Nucleoside Transporter Function and Inhibitor Design. SLAS DISCOVERY 2019; 24:953-968. [PMID: 31503511 DOI: 10.1177/2472555219870123] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Physiological nucleosides are used for the synthesis of DNA, RNA, and ATP in the cell and serve as universal mammalian signaling molecules that regulate physiological processes such as vasodilation and platelet aggregation by engaging with cell surface receptors. The same pathways that allow uptake of physiological nucleosides mediate the cellular import of synthetic nucleoside analogs used against cancer, HIV, and other viral diseases. Physiological nucleosides and nucleoside drugs are imported by two families of nucleoside transporters: the SLC28 concentrative nucleoside transporters (CNTs) and SLC29 equilibrative nucleoside transporters (ENTs). The four human ENT paralogs are expressed in distinct tissues, localize to different subcellular sites, and transport a variety of different molecules. Here we provide an overview of the known structure-function relationships of the ENT family with a focus on ligand binding and transport in the context of a new hENT1 homology model. We provide a generic residue numbering system for the different ENTs to facilitate the interpretation of mutational data produced using different ENT homologs. The discovery of paralog-selective small-molecule modulators is highly relevant for the design of new therapies and for uncovering the functions of poorly characterized ENT family members. Here, we discuss recent developments in the discovery of new paralog-selective small-molecule ENT inhibitors, including new natural product-inspired compounds. Recent progress in the ability to heterologously produce functional ENTs will allow us to gain insight into the structure and functions of different ENT family members as well as the rational discovery of highly selective inhibitors.
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Affiliation(s)
- Shahid Rehan
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,HiLIFE, University of Helsinki, Helsinki, Finland
| | - Saman Shahid
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Tiina A Salminen
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Veli-Pekka Jaakola
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Ville O Paavilainen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,HiLIFE, University of Helsinki, Helsinki, Finland
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85
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Aspromonte MC, Bellini M, Gasparini A, Carraro M, Bettella E, Polli R, Cesca F, Bigoni S, Boni S, Carlet O, Negrin S, Mammi I, Milani D, Peron A, Sartori S, Toldo I, Soli F, Turolla L, Stanzial F, Benedicenti F, Marino-Buslje C, Tosatto SCE, Murgia A, Leonardi E. Characterization of intellectual disability and autism comorbidity through gene panel sequencing. Hum Mutat 2019; 40:1346-1363. [PMID: 31209962 DOI: 10.1002/humu.23822] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/18/2019] [Accepted: 05/27/2019] [Indexed: 12/22/2022]
Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) are clinically and genetically heterogeneous diseases. Recent whole exome sequencing studies indicated that genes associated with different neurological diseases are shared across disorders and converge on common functional pathways. Using the Ion Torrent platform, we developed a low-cost next-generation sequencing gene panel that has been transferred into clinical practice, replacing single disease-gene analyses for the early diagnosis of individuals with ID/ASD. The gene panel was designed using an innovative in silico approach based on disease networks and mining data from public resources to score disease-gene associations. We analyzed 150 unrelated individuals with ID and/or ASD and a confident diagnosis has been reached in 26 cases (17%). Likely pathogenic mutations have been identified in another 15 patients, reaching a total diagnostic yield of 27%. Our data also support the pathogenic role of genes recently proposed to be involved in ASD. Although many of the identified variants need further investigation to be considered disease-causing, our results indicate the efficiency of the targeted gene panel on the identification of novel and rare variants in patients with ID and ASD.
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Affiliation(s)
- Maria C Aspromonte
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
| | - Mariagrazia Bellini
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
| | | | - Marco Carraro
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Elisa Bettella
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
| | - Roberta Polli
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
| | - Federica Cesca
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
| | - Stefania Bigoni
- Medical Genetics Unit, Ospedale Universitario S. Anna, Ferrara, Italy
| | - Stefania Boni
- Medical Genetics Unit, San Martino Hospital, Belluno, Italy
| | - Ombretta Carlet
- Epilepsy and Child Neurophysiology Unit, Scientific Institute IRCCS E. Medea, Treviso, Italy
| | - Susanna Negrin
- Epilepsy and Child Neurophysiology Unit, Scientific Institute IRCCS E. Medea, Treviso, Italy
| | - Isabella Mammi
- Medical Genetics Unit, Dolo General Hospital, Venezia, Italy
| | - Donatella Milani
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, University of Milano, Milan, Italy
| | - Angela Peron
- Child Neuropsychiatry Unit, Epilepsy Center, Department of Health Sciences, Santi Paolo-Carlo Hospital, University of Milano, Milano, Italy.,Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Stefano Sartori
- Paediatric Neurology Unit, Department of Woman and Child Health, University Hospital of Padova, Padova, Italy
| | - Irene Toldo
- Paediatric Neurology Unit, Department of Woman and Child Health, University Hospital of Padova, Padova, Italy
| | - Fiorenza Soli
- Medical Genetics Department, APSS Trento, Trento, Italy
| | - Licia Turolla
- Medical Genetics Unit, Local Health Authority, Treviso, Italy
| | - Franco Stanzial
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Francesco Benedicenti
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | | | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Institute of Neuroscience, National Research Council, Padova, Italy
| | - Alessandra Murgia
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
| | - Emanuela Leonardi
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
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86
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Brault ML, Petit JD, Immel F, Nicolas WJ, Glavier M, Brocard L, Gaston A, Fouché M, Hawkins TJ, Crowet J, Grison MS, Germain V, Rocher M, Kraner M, Alva V, Claverol S, Paterlini A, Helariutta Y, Deleu M, Lins L, Tilsner J, Bayer EM. Multiple C2 domains and transmembrane region proteins (MCTPs) tether membranes at plasmodesmata. EMBO Rep 2019; 20:e47182. [PMID: 31286648 PMCID: PMC6680132 DOI: 10.15252/embr.201847182] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 05/28/2019] [Accepted: 06/06/2019] [Indexed: 12/20/2022] Open
Abstract
In eukaryotes, membrane contact sites (MCS) allow direct communication between organelles. Plants have evolved a unique type of MCS, inside intercellular pores, the plasmodesmata, where endoplasmic reticulum (ER)-plasma membrane (PM) contacts coincide with regulation of cell-to-cell signalling. The molecular mechanism and function of membrane tethering within plasmodesmata remain unknown. Here, we show that the multiple C2 domains and transmembrane region protein (MCTP) family, key regulators of cell-to-cell signalling in plants, act as ER-PM tethers specifically at plasmodesmata. We report that MCTPs are plasmodesmata proteins that insert into the ER via their transmembrane region while their C2 domains dock to the PM through interaction with anionic phospholipids. A Atmctp3/Atmctp4 loss of function mutant induces plant developmental defects, impaired plasmodesmata function and composition, while MCTP4 expression in a yeast Δtether mutant partially restores ER-PM tethering. Our data suggest that MCTPs are unique membrane tethers controlling both ER-PM contacts and cell-to-cell signalling.
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Affiliation(s)
- Marie L Brault
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
| | - Jules D Petit
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
- Laboratoire de Biophysique Moléculaire aux InterfacesTERRA Research Centre, GX ABTUniversité de LiègeGemblouxBelgium
| | - Françoise Immel
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
| | - William J Nicolas
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
- Present address:
Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Marie Glavier
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
| | - Lysiane Brocard
- Bordeaux Imaging CentrePlant Imaging PlatformUMS 3420, INRA‐CNRS‐INSERM‐University of BordeauxVillenave‐d'OrnonFrance
| | - Amèlia Gaston
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
- Present address:
UMR 1332 BFPINRAUniversity of BordeauxBordeauxFrance
| | - Mathieu Fouché
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
- Present address:
UMR 1332 BFPINRAUniversity of BordeauxBordeauxFrance
| | | | - Jean‐Marc Crowet
- Laboratoire de Biophysique Moléculaire aux InterfacesTERRA Research Centre, GX ABTUniversité de LiègeGemblouxBelgium
- Present address:
Matrice Extracellulaire et Dynamique Cellulaire MEDyCUMR7369, CNRSUniversité de Reims‐Champagne‐ArdenneReimsFrance
| | - Magali S Grison
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
| | - Véronique Germain
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
| | - Marion Rocher
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
| | - Max Kraner
- Division of BiochemistryDepartment of BiologyFriedrich‐Alexander University Erlangen‐NurembergErlangenGermany
| | - Vikram Alva
- Department of Protein EvolutionMax Planck Institute for Developmental BiologyTübingenGermany
| | - Stéphane Claverol
- Proteome PlatformFunctional Genomic Center of BordeauxUniversity of BordeauxBordeaux CedexFrance
| | | | - Ykä Helariutta
- The Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
| | - Magali Deleu
- Laboratoire de Biophysique Moléculaire aux InterfacesTERRA Research Centre, GX ABTUniversité de LiègeGemblouxBelgium
| | - Laurence Lins
- Laboratoire de Biophysique Moléculaire aux InterfacesTERRA Research Centre, GX ABTUniversité de LiègeGemblouxBelgium
| | - Jens Tilsner
- Biomedical Sciences Research ComplexUniversity of St AndrewsFifeUK
- Cell and Molecular SciencesThe James Hutton InstituteDundeeUK
| | - Emmanuelle M Bayer
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
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87
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Shi Y, Wang X, He N, Xie Y, Hong B. Rescrutiny of the sansanmycin biosynthetic gene cluster leads to the discovery of a novel sansanmycin analogue with more potency against Mycobacterium tuberculosis. J Antibiot (Tokyo) 2019; 72:769-774. [PMID: 31341273 DOI: 10.1038/s41429-019-0210-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 06/24/2019] [Accepted: 06/28/2019] [Indexed: 01/21/2023]
Abstract
A novel sansanmycin analogue, sansanmycin Q (1), was identified by genome mining from the fermentation broth of Streptomyces sp. SS (CPCC 200442). In comparison with other sansanmycin compounds, sansanmycin Q has an extra glycine residue at the N-terminus of the pseudopeptide backbone. The additional glycine was proved to be assembled to sansanmycin A by SsaB, a tRNA-dependent aminoacyltransferase, based on the results of rescrutiny of sansanmycin biosynthetic gene cluster, and then overexpression and knockout of ssaB in the wild-type strain. The structure of sansanmycin Q was assigned by interpretation of NMR and mass spectral data. The results of the bioassay disclosed that sansanmycin Q exhibited more potency against Mycobacterium tuberculosis H37Rv and a rifampicin- and isoniazid-resistant strain than sansanmycin A.
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Affiliation(s)
- Yuanyuan Shi
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tiantanxili No.1, Beijing, China.,CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tiantanxili No.1, Beijing, China
| | - Xinwei Wang
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tiantanxili No.1, Beijing, China
| | - Ning He
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tiantanxili No.1, Beijing, China
| | - Yunying Xie
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tiantanxili No.1, Beijing, China.
| | - Bin Hong
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tiantanxili No.1, Beijing, China. .,CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tiantanxili No.1, Beijing, China.
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88
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Roux S, Krupovic M, Daly RA, Borges AL, Nayfach S, Schulz F, Sharrar A, Matheus Carnevali PB, Cheng JF, Ivanova NN, Bondy-Denomy J, Wrighton KC, Woyke T, Visel A, Kyrpides NC, Eloe-Fadrosh EA. Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes. Nat Microbiol 2019; 4:1895-1906. [PMID: 31332386 PMCID: PMC6813254 DOI: 10.1038/s41564-019-0510-x] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/05/2019] [Indexed: 01/02/2023]
Abstract
Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content and infection cycle. One of the most striking features of inoviruses is their ability to establish a chronic infection whereby the viral genome resides within the cell in either an exclusively episomal state or integrated into the host chromosome and virions are continuously released without killing the host. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications, such as phage display, or because of their effect on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here, we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly diverse group of inoviruses. Using a machine learning approach leveraging a combination of marker gene and genome features, we identified 10,295 inovirus-like sequences from microbial genomes and metagenomes. Collectively, our results call for reclassification of the current Inoviridae family into a viral order including six distinct proposed families associated with nearly all bacterial phyla across virtually every ecosystem. Putative inoviruses were also detected in several archaeal genomes, suggesting that, collectively, members of this supergroup infect hosts across the domains Bacteria and Archaea. Finally, we identified an expansive diversity of inovirus-encoded toxin–antitoxin and gene expression modulation systems, alongside evidence of both synergistic (CRISPR evasion) and antagonistic (superinfection exclusion) interactions with co-infecting viruses, which we experimentally validated in a Pseudomonas model. Capturing this previously obscured component of the global virosphere may spark new avenues for microbial manipulation approaches and innovative biotechnological applications. A machine learning approach was used to recover over 10,000 inovirus-like sequences from existing microbial genomes and metagenomes, consequently proposing the reclassification of the Inoviridae family to a viral order, and uncover the previously unrecognized diversity of these viruses across hosts and environments.
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Affiliation(s)
- Simon Roux
- DOE Joint Genome Institute, Walnut Creek, CA, USA.
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, Paris, France
| | - Rebecca A Daly
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Adair L Borges
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Allison Sharrar
- Department of Earth & Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA
| | | | | | | | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Axel Visel
- DOE Joint Genome Institute, Walnut Creek, CA, USA
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89
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Plattner M, Shneider MM, Arbatsky NP, Shashkov AS, Chizhov AO, Nazarov S, Prokhorov NS, Taylor NMI, Buth SA, Gambino M, Gencay YE, Brøndsted L, Kutter EM, Knirel YA, Leiman PG. Structure and Function of the Branched Receptor-Binding Complex of Bacteriophage CBA120. J Mol Biol 2019; 431:3718-3739. [PMID: 31325442 DOI: 10.1016/j.jmb.2019.07.022] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 01/21/2023]
Abstract
Bacteriophages recognize their host cells with the help of tail fiber and tailspike proteins that bind, cleave, or modify certain structures on the cell surface. The spectrum of ligands to which the tail fibers and tailspikes can bind is the primary determinant of the host range. Bacteriophages with multiple tailspike/tail fibers are thought to have a wider host range than their less endowed relatives but the function of these proteins remains poorly understood. Here, we describe the structure, function, and substrate specificity of three tailspike proteins of bacteriophage CBA120-TSP2, TSP3 and TSP4 (orf211 through orf213, respectively). We show that tailspikes TSP2, TSP3 and TSP4 are hydrolases that digest the O157, O77, and O78 Escherichia coli O-antigens, respectively. We demonstrate that recognition of the E. coli O157:H7 host by CBA120 involves binding to and digesting the O157 O-antigen by TSP2. We report the crystal structure of TSP2 in complex with a repeating unit of the O157 O-antigen. We demonstrate that according to the specificity of its tailspikes TSP2, TSP3, and TSP4, CBA120 can infect E. coli O157, O77, and O78, respectively. We also show that CBA120 infects Salmonella enterica serovar Minnesota, and this host range expansion is likely due to the function of TSP1. Finally, we describe the assembly pathway and the architecture of the TSP1-TSP2-TSP3-TSP4 branched complex in CBA120 and its related ViI-like phages.
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Affiliation(s)
- Michel Plattner
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555-0647, USA; École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Mikhail M Shneider
- Laboratory of Molecular Bioengineering, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
| | - Nikolay P Arbatsky
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander O Chizhov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Nazarov
- École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Nikolai S Prokhorov
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555-0647, USA
| | - Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Sergey A Buth
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555-0647, USA
| | - Michela Gambino
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Yilmaz Emre Gencay
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | | | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555-0647, USA.
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90
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Genomic differences within the phylum Marinimicrobia: From waters to sediments in the Mariana Trench. Mar Genomics 2019; 50:100699. [PMID: 31301991 DOI: 10.1016/j.margen.2019.100699] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 06/15/2019] [Accepted: 06/29/2019] [Indexed: 02/06/2023]
Abstract
Marinimicrobia are widespread from the marine surface to the hadal zone. Major clades of Marinimicrobia have evolved to different ecotypes along with energy gradients, but their genomes in deeper waters and sediments have rarely been studied. Here we obtained 11 Marinimicrobia draft genomes from the water column in the full-ocean depth and the hadal sediments in the Mariana Trench. All the predicted genomic capabilities of the metagenome-assembled genomes (MAGs) are indicative of heterotrophic lifestyle. The MAGs from the hadal depths are distinct from those from the mesopelagic and bathypelagic depths by enrichment of the genes involved in amino acids metabolism and mismatch repair. Compared with the MAGs from waters, those from the sediments were dramatically expanded by acquiring the genes responsible for chemotaxis, mobility and the two-component systems. Marinimicrobia were apparently differentiated in the environments with different depths, organic matters and electronic acceptors. Our results also posit a potential evolutionary relationship between the species inhabiting the waters and sediments, indicating the occurrence of allopatric speciation in Marinimicrobia.
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91
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Niekamp S, Coudray N, Zhang N, Vale RD, Bhabha G. Coupling of ATPase activity, microtubule binding, and mechanics in the dynein motor domain. EMBO J 2019; 38:e101414. [PMID: 31268607 PMCID: PMC6600642 DOI: 10.15252/embj.2018101414] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 04/24/2019] [Accepted: 04/30/2019] [Indexed: 01/10/2023] Open
Abstract
The movement of a molecular motor protein along a cytoskeletal track requires communication between enzymatic, polymer-binding, and mechanical elements. Such communication is particularly complex and not well understood in the dynein motor, an ATPase that is comprised of a ring of six AAA domains, a large mechanical element (linker) spanning over the ring, and a microtubule-binding domain (MTBD) that is separated from the AAA ring by a ~ 135 Å coiled-coil stalk. We identified mutations in the stalk that disrupt directional motion, have microtubule-independent hyperactive ATPase activity, and nucleotide-independent low affinity for microtubules. Cryo-electron microscopy structures of a mutant that uncouples ATPase activity from directional movement reveal that nucleotide-dependent conformational changes occur normally in one-half of the AAA ring, but are disrupted in the other half. The large-scale linker conformational change observed in the wild-type protein is also inhibited, revealing that this conformational change is not required for ATP hydrolysis. These results demonstrate an essential role of the stalk in regulating motor activity and coupling conformational changes across the two halves of the AAA ring.
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Affiliation(s)
- Stefan Niekamp
- Department of Cellular and Molecular PharmacologyHoward Hughes Medical InstituteUniversity of California San FranciscoSan FranciscoCAUSA
| | - Nicolas Coudray
- Department of Cell BiologySkirball Institute of Biomolecular MedicineNew York University School of MedicineNew YorkNYUSA
- Applied Bioinformatics LaboratoriesNew York University School of MedicineNew YorkNYUSA
| | - Nan Zhang
- Department of Cellular and Molecular PharmacologyHoward Hughes Medical InstituteUniversity of California San FranciscoSan FranciscoCAUSA
| | - Ronald D Vale
- Department of Cellular and Molecular PharmacologyHoward Hughes Medical InstituteUniversity of California San FranciscoSan FranciscoCAUSA
| | - Gira Bhabha
- Department of Cell BiologySkirball Institute of Biomolecular MedicineNew York University School of MedicineNew YorkNYUSA
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92
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Cai R, Wang Z, Wang G, Zhang H, Cheng M, Guo Z, Ji Y, Xi H, Wang X, Xue Y, Ur Rahman S, Sun C, Feng X, Lei L, Tong Y, Han W, Gu J. Biological properties and genomics analysis of vB_KpnS_GH-K3, a Klebsiella phage with a putative depolymerase-like protein. Virus Genes 2019; 55:696-706. [PMID: 31254238 DOI: 10.1007/s11262-019-01681-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 06/20/2019] [Indexed: 01/21/2023]
Abstract
Bacteriophages have been recently revisited as an alternative biocontrol tool due to the limitations of antibiotic treatment. In this study, we reported on the biological characteristics and genomic information of vB_KpnS_GH-K3 (abbreviated as GH-K3), a Klebsiella phage of the Siphoviridae family, which was previously isolated from a hospital sewage system. One-step growth curve analysis indicated that the burst size of GH-K3 was 291 PFU/cell. GH-K3 maintained a stable titer in a broad range of pH values (6-10) and temperature (up to 50 °C). Based on bioinformatics analysis, GH-K3 comprises of 49,427 bp containing a total of 77 open reading frames (ORFs), which share high degree of nucleotide similarity and close evolutionary relationships with at least 12 other Klebsiella phages. Of note, GH-K3 gp32 was identified as a unique ORF. The major segment of gp32 sequence at the C-terminus (residues 351-907) was found highly variable as determined by its mismatch with the nucleotide and protein sequences available at NCBI database. Furthermore, HHpred analysis indicated that GH-K3 gp32 contains three domains (PDB ID: 5W6S_A, 3GQ8_A and 1BHE_A) similar to depolymerase (depoKP36) of Klebsiella phage KP36 suggestive of a potential depolymerase activity during host receptor-binding in the processes of phage infection. Altogether, the current data revealed a novel putative depolymerase-like protein which is most likely to play an important role in phage-host interaction.
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Affiliation(s)
- Ruopeng Cai
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Zijing Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Gang Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Hao Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Mengjun Cheng
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Zhimin Guo
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, 130021, People's Republic of China
| | - Yalu Ji
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Hengyu Xi
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Xinwu Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Yibing Xue
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Sadeeq Ur Rahman
- College of Veterinary Sciences & Animal Husbandry, Abdul Wali Khan University, Mardan, 23200, Pakistan
| | - Changjiang Sun
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Xin Feng
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Liancheng Lei
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, People's Republic of China
| | - Wenyu Han
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Jingmin Gu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China.
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93
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Dafsari HS, Sprute R, Wunderlich G, Daimagüler HS, Karaca E, Contreras A, Becker K, Schulze-Rhonhof M, Kiening K, Karakulak T, Kloss M, Horn A, Pauls A, Nürnberg P, Altmüller J, Thiele H, Assmann B, Koy A, Cirak S. Novel mutations in KMT2B offer pathophysiological insights into childhood-onset progressive dystonia. J Hum Genet 2019; 64:803-813. [PMID: 31165786 DOI: 10.1038/s10038-019-0625-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/09/2019] [Accepted: 05/21/2019] [Indexed: 11/09/2022]
Abstract
Rapid progress has recently been made in the elucidation of the genetic basis of childhood-onset inherited generalized dystonia (IGD) due to the implementation of genomic sequencing methodologies. We identified four patients with childhood-onset IGD harboring novel disease-causing mutations in lysine-specific histone methyltransferase 2B gene (KMT2B) by whole-exome sequencing. The main focus of this paper is to gain novel pathophysiological insights through understanding the molecular consequences of these mutations. The disease course is mostly progressive, evolving from lower limbs into generalized dystonia, which could be associated with dysarthria, dysphonia, intellectual disability, orofacial dyskinesia, and sometimes distinct dysmorphic facial features. In two patients, motor performances improved after bilateral implantation of deep brain stimulation in the globus pallidus internus (GPi-DBS). Pharmacotherapy with trihexyphenidyl reduced dystonia in two patients. We discovered three novel KMT2B mutations. Our analyses revealed that the mutation in patient 1 (c.7463A > G, p.Y2488C) is localized in the highly conserved FYRC domain of KMT2B. This mutation holds the potential to alter the inter-domain FYR interactions, which could lead to KMT2B instability. The mutations in patients 2 and 3 (c.3596_3697insC, p.M1202Dfs*22; c.4229delA, p.Q1410Rfs*12) lead to predicted unstable transcripts, likely to be subject to degradation by non-sense-mediated decay. Childhood-onset progressive dystonia with orofacial involvement is one of the main clinical manifestations of KMT2B mutations. In all, 26% (18/69) of the reported cases have T2 signal alterations of the globus pallidus internus, mostly at a younger age. Anticholinergic medication and GPi-DBS are promising treatment options and shall be considered early.
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Affiliation(s)
- Hormos Salimi Dafsari
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Rosanne Sprute
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Gilbert Wunderlich
- Center for Rare Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Department of Neurology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Hülya-Sevcan Daimagüler
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Adriana Contreras
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Kerstin Becker
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Mira Schulze-Rhonhof
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Karl Kiening
- Department of Neurosurgery, University Hospital, Heidelberg, Germany
| | - Tülay Karakulak
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Manja Kloss
- Department of Neurology, University Hospital, Heidelberg, Germany
| | - Annette Horn
- Department of General Pediatrics and Neonatology, University Children's Hospital, Düsseldorf, Germany
| | - Amande Pauls
- Department of Neurology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Birgit Assmann
- Department of Neuropediatrics, University Children's Hospital, Heidelberg, Germany
| | - Anne Koy
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Center for Rare Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Sebahattin Cirak
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany. .,Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne, Germany. .,Center for Rare Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
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94
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Vallet S, Guéroult M, Belloy N, Dauchez M, Ricard-Blum S. A Three-Dimensional Model of Human Lysyl Oxidase, a Cross-Linking Enzyme. ACS OMEGA 2019; 4:8495-8505. [PMID: 31459939 PMCID: PMC6647939 DOI: 10.1021/acsomega.9b00317] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 05/03/2019] [Indexed: 06/10/2023]
Abstract
Lysyl oxidase (LOX) is a cross-linking enzyme identified 50 years ago, but its 3D structure is still unknown. We have thus built a 3D model of human LOX by homology modeling using the X-ray structure of human lysyl oxidase-like 2 as a template. This model is the first one to recapitulate all known biochemical features of LOX, namely, the coordination of the copper ion and the formation of the lysine tyrosylquinone cofactor and the disulfide bridges. Furthermore, this model is stable during a 1 μs molecular dynamics simulation. The catalytic site is located in a groove surrounded by two loops. The distance between these loops fluctuated during the simulations, which suggests that the groove forms a hinge with a variable opening, which is able to accommodate the various sizes of LOX substrates. This 3D model is a pre-requisite to perform docking experiments with LOX substrates and other partners to identify binding sites and to design new LOX inhibitors specific for therapeutic purpose.
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Affiliation(s)
- Sylvain
D. Vallet
- Univ
Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute
of Molecular and Supramolecular Chemistry and Biochemistry, UMR 5246, F-69622 Villeurbanne
Cedex, France
| | - Marc Guéroult
- UMR 7369 URCA/CNRS
Matrice Extracellulaire et Dynamique Cellulaire
(MEDyC) and Plateau de Modélisation Moléculaire Multi-échelle, Université de Reims Champagne-Ardenne, 51687 Reims Cedex
2, France
| | - Nicolas Belloy
- UMR 7369 URCA/CNRS
Matrice Extracellulaire et Dynamique Cellulaire
(MEDyC) and Plateau de Modélisation Moléculaire Multi-échelle, Université de Reims Champagne-Ardenne, 51687 Reims Cedex
2, France
| | - Manuel Dauchez
- UMR 7369 URCA/CNRS
Matrice Extracellulaire et Dynamique Cellulaire
(MEDyC) and Plateau de Modélisation Moléculaire Multi-échelle, Université de Reims Champagne-Ardenne, 51687 Reims Cedex
2, France
| | - Sylvie Ricard-Blum
- Univ
Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute
of Molecular and Supramolecular Chemistry and Biochemistry, UMR 5246, F-69622 Villeurbanne
Cedex, France
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95
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Blanco Capurro JI, Di Paola M, Gamarra MD, Martí MA, Modenutti CP. An efficient use of X-ray information, homology modeling, molecular dynamics and knowledge-based docking techniques to predict protein-monosaccharide complexes. Glycobiology 2019; 29:124-136. [PMID: 30407518 DOI: 10.1093/glycob/cwy102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 11/06/2018] [Indexed: 01/13/2023] Open
Abstract
Unraveling the structure of lectin-carbohydrate complexes is vital for understanding key biological recognition processes and development of glycomimetic drugs. Molecular Docking application to predict them is challenging due to their low affinity, hydrophilic nature and ligand conformational diversity. In the last decade several strategies, such as the inclusion of glycan conformation specific scoring functions or our developed solvent-site biased method, have improved carbohydrate docking performance but significant challenges remain, in particular, those related to receptor conformational diversity. In the present work we have analyzed conventional and solvent-site biased autodock4 performance concerning receptor conformational diversity as derived from different crystal structures (apo and holo), Molecular Dynamics snapshots and Homology-based models, for 14 different lectin-monosaccharide complexes. Our results show that both conventional and biased docking yield accurate lectin-monosaccharide complexes, starting from either apo or homology-based structures, even when only moderate (45%) sequence identity templates are available. An essential element for success is a proper combination of a middle-sized (10-100 structures) conformational ensemble, derived either from Molecular dynamics or multiple homology model building. Consistent with our previous works, results show that solvent-site biased methods improve overall performance, but that results are still highly system dependent. Finally, our results also show that docking can select the correct receptor structure within the ensemble, underscoring the relevance of joint evaluation of both ligand pose and receptor conformation.
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Affiliation(s)
- Juan I Blanco Capurro
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina
| | - Matias Di Paola
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcelo Daniel Gamarra
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina
| | - Carlos P Modenutti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina
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96
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Trentin LB, Santos ER, Oliveira Junior AG, Sosa-Gómez DR, Ribeiro BM, Ardisson-Araújo DMP. The complete genome of Rachiplusia nu nucleopolyhedrovirus (RanuNPV) and the identification of a baculoviral CPD-photolyase homolog. Virology 2019; 534:64-71. [PMID: 31200103 DOI: 10.1016/j.virol.2019.05.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 02/08/2023]
Abstract
We described a novel baculovirus isolated from the polyphagous insect pest Rachiplusia nu. The virus presented pyramidal-shaped occlusion bodies (OBs) with singly-embed nucleocapsids and a dose mortality response of 6.9 × 103 OBs/ml to third-instar larvae of R. nu. The virus genome is 128,587 bp long with a G + C content of 37.9% and 134 predicted ORFs. The virus is an alphabaculovirus closely related to Trichoplusia ni single nucleopolyhedrovirus, Chrysodeixis chalcites nucleopolyhedrovirus, and Chrysodeixis includens single nucleopolyhedrovirus and may constitute a new species. Surprisingly, we found co-evolution among the related viruses and their hosts at species level. Besides, auxiliary genes with homologs in other baculoviruses were found, e.g. a CPD-photolyase. The gene seemed to be result of a single event of horizontal transfer from lepidopterans to alphabaculovirus, followed by a transference from alpha to betabaculovirus. The predicted protein appears to be an active enzyme that ensures likely DNA protection from sunlight.
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Affiliation(s)
- Luana Beló Trentin
- Laboratory of Insect Virology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, 97105-900, Brazil.
| | - Ethiane R Santos
- Laboratory of Insect Virology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, 97105-900, Brazil.
| | | | | | - Bergmann Morais Ribeiro
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasilia, DF, 70910-900, Brazil.
| | - Daniel M P Ardisson-Araújo
- Laboratory of Insect Virology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, 97105-900, Brazil.
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97
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Fina Martin J, Palomino MM, Cutine AM, Modenutti CP, Fernández Do Porto DA, Allievi MC, Zanini SH, Mariño KV, Barquero AA, Ruzal SM. Exploring lectin-like activity of the S-layer protein of Lactobacillus acidophilus ATCC 4356. Appl Microbiol Biotechnol 2019; 103:4839-4857. [PMID: 31053916 DOI: 10.1007/s00253-019-09795-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 02/06/2023]
Abstract
The surface layer (S-layer) protein of Lactobacillus acidophilus is a crystalline array of self-assembling, proteinaceous subunits non-covalently bound to the outmost bacterial cell wall envelope and is involved in the adherence of bacteria to host cells. We have previously described that the S-layer protein of L. acidophilus possesses anti-viral and anti-bacterial properties. In this work, we extracted and purified S-layer proteins from L. acidophilus ATCC 4356 cells to study their interaction with cell wall components from prokaryotic (i.e., peptidoglycan and lipoteichoic acids) and eukaryotic origin (i.e., mucin and chitin), as well as with viruses, bacteria, yeast, and blood cells. Using chimeric S-layer fused to green fluorescent protein (GFP) from different parts of the protein, we analyzed their binding capacity. Our results show that the C-terminal part of the S-layer protein presents lectin-like activity, interacting with different glycoepitopes. We further demonstrate that lipoteichoic acid (LTA) serves as an anchor for the S-layer protein. Finally, a structure for the C-terminal part of S-layer and possible binding sites were predicted by a homology-based model.
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Affiliation(s)
- Joaquina Fina Martin
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Cdad. Universitaria, Pabellón II, 4 piso, Lab QB40, C1428EGA, CABA, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Maria Mercedes Palomino
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Cdad. Universitaria, Pabellón II, 4 piso, Lab QB40, C1428EGA, CABA, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Anabella M Cutine
- Laboratorio de Glicómica Funcional y Molecular, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428, Buenos Aires, Argentina
| | - Carlos P Modenutti
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Cdad. Universitaria, Pabellón II, 4 piso, Lab QB40, C1428EGA, CABA, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Dario A Fernández Do Porto
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Cdad. Universitaria, Pabellón II, 4 piso, Lab QB40, C1428EGA, CABA, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariana C Allievi
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Cdad. Universitaria, Pabellón II, 4 piso, Lab QB40, C1428EGA, CABA, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Sofia H Zanini
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Cdad. Universitaria, Pabellón II, 4 piso, Lab QB40, C1428EGA, CABA, Buenos Aires, Argentina
| | - Karina V Mariño
- Laboratorio de Glicómica Funcional y Molecular, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428, Buenos Aires, Argentina
| | - Andrea A Barquero
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Cdad. Universitaria, Pabellón II, 4 piso, Lab QB40, C1428EGA, CABA, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Sandra M Ruzal
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Cdad. Universitaria, Pabellón II, 4 piso, Lab QB40, C1428EGA, CABA, Buenos Aires, Argentina.
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina.
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98
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Wachter S, Jung J, Shafiq S, Basquin J, Fort C, Bastin P, Lorentzen E. Binding of IFT22 to the intraflagellar transport complex is essential for flagellum assembly. EMBO J 2019; 38:e101251. [PMID: 30940671 PMCID: PMC6484408 DOI: 10.15252/embj.2018101251] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/28/2019] [Accepted: 03/04/2019] [Indexed: 01/08/2023] Open
Abstract
Intraflagellar transport (IFT) relies on motor proteins and the IFT complex to construct cilia and flagella. The IFT complex subunit IFT22/RabL5 has sequence similarity with small GTPases although the nucleotide specificity is unclear because of non-conserved G4/G5 motifs. We show that IFT22 specifically associates with G-nucleotides and present crystal structures of IFT22 in complex with GDP, GTP, and with IFT74/81. Our structural analysis unravels an unusual GTP/GDP-binding mode of IFT22 bypassing the classical G4 motif. The GTPase switch regions of IFT22 become ordered upon complex formation with IFT74/81 and mediate most of the IFT22-74/81 interactions. Structure-based mutagenesis reveals that association of IFT22 with the IFT complex is essential for flagellum construction in Trypanosoma brucei although IFT22 GTP-loading is not strictly required.
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Affiliation(s)
- Stefanie Wachter
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jamin Jung
- Trypanosome Cell Biology Unit, Institut Pasteur & INSERM U1201, Paris, France
| | - Shahaan Shafiq
- Trypanosome Cell Biology Unit, Institut Pasteur & INSERM U1201, Paris, France
| | - Jerome Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Cécile Fort
- Trypanosome Cell Biology Unit, Institut Pasteur & INSERM U1201, Paris, France
| | - Philippe Bastin
- Trypanosome Cell Biology Unit, Institut Pasteur & INSERM U1201, Paris, France
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
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99
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Zhang J, Zhang K, Qi L, Hu Q, Shen Z, Liu B, Deng J, Zhang C, Zhang Y. DENN domain-containing protein FAM45A regulates the homeostasis of late/multivesicular endosomes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:916-929. [DOI: 10.1016/j.bbamcr.2019.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/25/2019] [Indexed: 11/27/2022]
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100
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Thoen E, Aas AB, Vik U, Brysting AK, Skrede I, Carlsen T, Kauserud H. A single ectomycorrhizal plant root system includes a diverse and spatially structured fungal community. MYCORRHIZA 2019; 29:167-180. [PMID: 30929039 DOI: 10.1007/s00572-019-00889-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 03/19/2019] [Indexed: 05/11/2023]
Abstract
Although only a relatively small proportion of plant species form ectomycorrhizae with fungi, it is crucial for growth and survival for a number of widespread woody plant species. Few studies have attempted to investigate the fine scale spatial structure of entire root systems of adult ectomycorrhizal (EcM) plants. Here, we use the herbaceous perennial Bistorta vivipara to map the entire root system of an adult EcM plant and investigate the spatial structure of its root-associated fungi. All EcM root tips were sampled, mapped and identified using a direct PCR approach and Sanger sequencing of the internal transcribed spacer region. A total of 32.1% of all sampled root tips (739 of 2302) were successfully sequenced and clustered into 41 operational taxonomic units (OTUs). We observed a clear spatial structuring of the root-associated fungi within the root system. Clusters of individual OTUs were observed in the younger parts of the root system, consistent with observations of priority effects in previous studies, but were absent from the older parts of the root system. This may suggest a succession and fragmentation of the root-associated fungi even at a very fine scale, where competition likely comes into play at different successional stages within the root system.
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Affiliation(s)
- Ella Thoen
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO box 1066, Blindern, 0316, Oslo, Norway.
| | - Anders B Aas
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO box 1066, Blindern, 0316, Oslo, Norway
- Bymiljøetaten Oslo Kommune, PO box 636, Løren, 0507, Oslo, Norway
| | - Unni Vik
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO box 1066, Blindern, 0316, Oslo, Norway
| | - Anne K Brysting
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO box 1066, Blindern, 0316, Oslo, Norway
| | - Inger Skrede
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO box 1066, Blindern, 0316, Oslo, Norway
| | - Tor Carlsen
- The Natural History museum, University of Oslo, PO box 1172, Blindern, 0318, Oslo, Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO box 1066, Blindern, 0316, Oslo, Norway
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