851
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Showmaker KC, Cobb MB, Johnson AC, Yang W, Garrett MR. Whole genome sequencing and novel candidate genes for CAKUT and altered nephrogenesis in the HSRA rat. Physiol Genomics 2020; 52:56-70. [PMID: 31841396 PMCID: PMC6985787 DOI: 10.1152/physiolgenomics.00112.2019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/09/2019] [Accepted: 12/09/2019] [Indexed: 12/30/2022] Open
Abstract
The HSRA rat is a model of congenital abnormalities of the kidney and urogenital tract (CAKUT). Our laboratory has used this model to investigate the role of nephron number (functional unit of the kidney) in susceptibility to develop kidney disease as 50-75% offspring are born with a single kidney (HSRA-S), while 25-50% are born with two kidneys (HSRA-C). HSRA-S rats develop increased kidney injury and hypertension with age compared with nephrectomized two-kidney animals (HSRA-UNX), suggesting that even slight differences in nephron number can be an important driver in decline in kidney function. The HSRA rat was selected and inbred from a family of outbred heterogeneous stock (NIH-HS) rats that exhibited a high incidence of CAKUT. The HS model was originally developed from eight inbred strains (ACI, BN, BUF, F344, M520, MR, WKY, and WN). The genetic make-up of the HSRA is therefore a mosaic of these eight inbred strains. Interestingly, the ACI progenitor of the HS model exhibits CAKUT in 10-15% of offspring with the genetic cause being attributed to the presence of a long-term repeat (LTR) within exon 1 of the c-Kit gene. Our hypothesis is that the HSRA and ACI share this common genetic cause, but other alleles in the HSRA genome contribute to the increased penetrance of CAKUT (75% HSRA vs. 15% in ACI). To facilitate genetic studies and better characterize the model, we sequenced the whole genome of the HSRA to a depth of ~50×. A genome-wide variant analysis of high-impact variants identified a number of novel genes that could be linked to CAKUT in the HSRA model. In summary, the identification of new genes/modifiers that lead to CAKUT/loss of one kidney in the HSRA model will provide greater insight into association between kidney development and susceptibility to develop cardiovascular disease later in life.
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Affiliation(s)
- Kurt C Showmaker
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, Mississippi
| | - Meredith B Cobb
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, Mississippi
| | - Ashley C Johnson
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, Mississippi
| | - Wenyu Yang
- College of Science, Huazhong Agricultural University, Wuhan, China
| | - Michael R Garrett
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, Mississippi
- Department of Medicine (Nephrology), University of Mississippi Medical Center, Jackson, Mississippi
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852
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Llabrés S, Tsenkov MI, MacGowan SA, Barton GJ, Zachariae U. Disease related single point mutations alter the global dynamics of a tetratricopeptide (TPR) α-solenoid domain. J Struct Biol 2020; 209:107405. [PMID: 31628985 PMCID: PMC6961204 DOI: 10.1016/j.jsb.2019.107405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 10/04/2019] [Accepted: 10/15/2019] [Indexed: 01/18/2023]
Abstract
Tetratricopeptide repeat (TPR) proteins belong to the class of α-solenoid proteins, in which repetitive units of α-helical hairpin motifs stack to form superhelical, often highly flexible structures. TPR domains occur in a wide variety of proteins, and perform key functional roles including protein folding, protein trafficking, cell cycle control and post-translational modification. Here, we look at the TPR domain of the enzyme O-linked GlcNAc-transferase (OGT), which catalyses O-GlcNAcylation of a broad range of substrate proteins. A number of single-point mutations in the TPR domain of human OGT have been associated with the disease Intellectual Disability (ID). By extended steered and equilibrium atomistic simulations, we show that the OGT-TPR domain acts as an elastic nanospring, and that each of the ID-related local mutations substantially affect the global dynamics of the TPR domain. Since the nanospring character of the OGT-TPR domain is key to its function in binding and releasing OGT substrates, these changes of its biomechanics likely lead to defective substrate interaction. We find that neutral mutations in the human population, selected by analysis of the gnomAD database, do not incur these changes. Our findings may not only help to explain the ID phenotype of the mutants, but also aid the design of TPR proteins with tailored biomechanical properties.
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Affiliation(s)
- Salomé Llabrés
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK.
| | - Maxim I Tsenkov
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Stuart A MacGowan
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Geoffrey J Barton
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK; Physics, School of Science and Engineering, University of Dundee, Dundee, UK.
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853
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Kallscheuer N, Wiegand S, Heuer A, Rensink S, Boersma AS, Jogler M, Boedeker C, Peeters SH, Rast P, Jetten MSM, Rohde M, Jogler C. Blastopirellula retiformator sp. nov. isolated from the shallow-sea hydrothermal vent system close to Panarea Island. Antonie van Leeuwenhoek 2020; 113:1811-1822. [PMID: 31894497 DOI: 10.1007/s10482-019-01377-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Aquatic bacteria belonging to the deep-branching phylum Planctomycetes play a major role in global carbon and nitrogen cycles. However, their uncommon morphology and physiology, and their roles and survival on biotic surfaces in marine environments, are only partially understood. Access to axenic cultures of different planctomycetal genera is key to study their complex lifestyles, uncommon cell biology and primary and secondary metabolism in more detail. Here, we describe the characterisation of strain Enr8T isolated from a marine biotic surface in the seawater close to the shallow-sea hydrothermal vent system off Panarea Island, an area with high temperature and pH gradients, and high availability of different sulphur and nitrogen sources resulting in a great microbial diversity. Strain Enr8T showed typical planctomycetal traits such as division by polar budding, aggregate formation and presence of fimbriae and crateriform structures. Growth was observed at ranges of 15-33 °C (optimum 30 °C), pH 6.0-8.0 (optimum 7.0) and at NaCl concentrations from 100 to 1200 mM (optimum 350-700 mM). Strain Enr8T forms white colonies on solid medium and white flakes in liquid culture. Its genome has a size of 6.20 Mb and a G + C content of 59.2%. Phylogenetically, the strain belongs to the genus Blastopirellula. We propose the name Blastopirellula retiformator sp. nov. for the novel species, represented by the type strain Enr8T (DSM 100415T = LMG 29081T).
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Affiliation(s)
| | - Sandra Wiegand
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | - Stephanie Rensink
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Alje S Boersma
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Mareike Jogler
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands.,Leibniz Institute DSMZ, Brunswick, Germany
| | | | - Stijn H Peeters
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Patrick Rast
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands.,Leibniz Institute DSMZ, Brunswick, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz-Centre for Infection Research (HZI), Brunswick, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands. .,Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
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854
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Shamimuzzaman M, Gardiner JM, Walsh AT, Triant DA, Le Tourneau JJ, Tayal A, Unni DR, Nguyen HN, Portwood JL, Cannon EKS, Andorf CM, Elsik CG. MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database. FRONTIERS IN PLANT SCIENCE 2020; 11:592730. [PMID: 33193550 PMCID: PMC7642280 DOI: 10.3389/fpls.2020.592730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/01/2020] [Indexed: 05/11/2023]
Abstract
MaizeMine is the data mining resource of the Maize Genetics and Genome Database (MaizeGDB; http://maizemine.maizegdb.org). It enables researchers to create and export customized annotation datasets that can be merged with their own research data for use in downstream analyses. MaizeMine uses the InterMine data warehousing system to integrate genomic sequences and gene annotations from the Zea mays B73 RefGen_v3 and B73 RefGen_v4 genome assemblies, Gene Ontology annotations, single nucleotide polymorphisms, protein annotations, homologs, pathways, and precomputed gene expression levels based on RNA-seq data from the Z. mays B73 Gene Expression Atlas. MaizeMine also provides database cross references between genes of alternative gene sets from Gramene and NCBI RefSeq. MaizeMine includes several search tools, including a keyword search, built-in template queries with intuitive search menus, and a QueryBuilder tool for creating custom queries. The Genomic Regions search tool executes queries based on lists of genome coordinates, and supports both the B73 RefGen_v3 and B73 RefGen_v4 assemblies. The List tool allows you to upload identifiers to create custom lists, perform set operations such as unions and intersections, and execute template queries with lists. When used with gene identifiers, the List tool automatically provides gene set enrichment for Gene Ontology (GO) and pathways, with a choice of statistical parameters and background gene sets. With the ability to save query outputs as lists that can be input to new queries, MaizeMine provides limitless possibilities for data integration and meta-analysis.
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Affiliation(s)
- Md Shamimuzzaman
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Jack M. Gardiner
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Amy T. Walsh
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Deborah A. Triant
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | | | - Aditi Tayal
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Deepak R. Unni
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Hung N. Nguyen
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - John L. Portwood
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA, United States
| | - Ethalinda K. S. Cannon
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA, United States
| | - Carson M. Andorf
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA, United States
| | - Christine G. Elsik
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, United States
- *Correspondence: Christine G. Elsik,
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855
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Peeters SH, Wiegand S, Kallscheuer N, Jogler M, Heuer A, Jetten MSM, Rast P, Boedeker C, Rohde M, Jogler C. Three marine strains constitute the novel genus and species Crateriforma conspicua in the phylum Planctomycetes. Antonie van Leeuwenhoek 2020; 113:1797-1809. [PMID: 31894495 DOI: 10.1007/s10482-019-01375-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/10/2019] [Indexed: 12/17/2022]
Abstract
Planctomycetes is a ubiquitous phylum of mostly aquatic bacteria that have a complex lifestyle and an unusual cell biology. Here, we describe three strains of the same novel genus and species isolated from three different environments; from a red biofilm at a hydrothermal vent in the Mediterranean Sea, from sediment in a salt-water fish tank, and from the surface of algae at the coast of the Balearic island Mallorca. The three strains Mal65T (DSM 100706T = LMG 29792T, Pan14r (DSM 29351 = LMG 29012), and V7 (DSM 29812 = CECT 9853 = VKM B-3427) show typical characteristics of the Planctomycetaceae family, such as cell division by budding, crateriform structures and growth in aggregates or rosettes. The strains are mesophilic, neutrophilic to alkaliphilic as well as chemoheterotrophic and exhibit doubling times between 12 and 35 h. Based on our phylogenetic analysis, the three strains represent a single novel species of a new genus, for which we propose the name Crateriforma conspicua gen. nov. sp. nov.
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Affiliation(s)
- Stijn H Peeters
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Sandra Wiegand
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | | | - Mareike Jogler
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands.,Department of Microbial Interactions, Institute of Microbiology, Friedrich-Schiller University, Jena, Germany
| | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | | | | | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands. .,Department of Microbial Interactions, Institute of Microbiology, Friedrich-Schiller University, Jena, Germany.
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856
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Maor‐Landaw K, van Oppen MJH, McFadden GI. Symbiotic lifestyle triggers drastic changes in the gene expression of the algal endosymbiont Breviolum minutum (Symbiodiniaceae). Ecol Evol 2020; 10:451-466. [PMID: 31993121 PMCID: PMC6972872 DOI: 10.1002/ece3.5910] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 10/25/2019] [Accepted: 11/18/2019] [Indexed: 01/13/2023] Open
Abstract
Coral-dinoflagellate symbiosis underpins the evolutionary success of corals reefs. Successful exchange of molecules between the cnidarian host and the Symbiodiniaceae algae enables the mutualistic partnership. The algae translocate photosynthate to their host in exchange for nutrients and shelter. The photosynthate must traverse multiple membranes, most likely facilitated by transporters. Here, we compared gene expression profiles of cultured, free-living Breviolum minutum with those of the homologous symbionts freshly isolated from the sea anemone Exaiptasia diaphana, a widely used model for coral hosts. Additionally, we assessed expression levels of a list of candidate host transporters of interest in anemones with and without symbionts. Our transcriptome analyses highlight the distinctive nature of the two algal life stages, with many gene expression level changes correlating to the different morphologies, cell cycles, and metabolisms adopted in hospite versus free-living. Morphogenesis-related genes that likely underpin the metamorphosis process observed when symbionts enter a host cell were up-regulated. Conversely, many down-regulated genes appear to be indicative of the protective and confined nature of the symbiosome. Our results emphasize the significance of transmembrane transport to the symbiosis, and in particular of ammonium and sugar transport. Further, we pinpoint and characterize candidate transporters-predicted to be localized variously to the algal plasma membrane, the host plasma membrane, and the symbiosome membrane-that likely serve pivotal roles in the interchange of material during symbiosis. Our study provides new insights that expand our understanding of the molecular exchanges that underpin the cnidarian-algal symbiotic relationship.
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Affiliation(s)
- Keren Maor‐Landaw
- School of BioSciencesThe University of MelbourneMelbourneVic.Australia
| | - Madeleine J. H. van Oppen
- School of BioSciencesThe University of MelbourneMelbourneVic.Australia
- Australian Institute of Marine ScienceTownsvilleQldAustralia
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857
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Bonnardel F, Perez S, Lisacek F, Imberty A. Structural Database for Lectins and the UniLectin Web Platform. Methods Mol Biol 2020; 2132:1-14. [PMID: 32306309 DOI: 10.1007/978-1-0716-0430-4_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The search for new biomolecules requires a clear understanding of biosynthesis and degradation pathways. This view applies to most metabolites as well as other molecule types such as glycans whose repertoire is still poorly characterized. Lectins are proteins that recognize specifically and interact noncovalently with glycans. This particular class of proteins is considered as playing a major role in biology. Glycan-binding is based on multivalence, which gives lectins a unique capacity to interact with surface glycans and significantly contribute to cell-cell recognition and interactions. Lectins have been studied for many years using multiple technologies and part of the resulting information is available online in databases. Unfortunately, the connectivity of these databases with the most popular omics databases (genomics, proteomics, and glycomics) remains limited. Moreover, lectin diversity is extended and requires setting out a flexible classification that remains compatible with new sequences and 3D structures that are continuously released. We have designed UniLectin as a new insight into the knowledge of lectins, their classification, and their biological role. This platform encompasses UniLectin3D, a curated database of lectin 3D structures that follows a periodically updated classification, a set of comparative and visualizing tools and gradually released modules dedicated to specific lectins predicted in sequence databases. The second module is PropLec, focused on β-propeller lectin prediction in all species based on five distinct family profiles. This chapter describes how UniLectin can be used to explore the diversity of lectins, their 3D structures, and associated functional information as well as to perform reliable predictions of β-propeller lectins.
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Affiliation(s)
- François Bonnardel
- Univ. Grenoble Alpes, CNRS, CERMAV, Grenoble, France.,Swiss Institute of Bioinformatics, Geneva, Switzerland.,Computer Science Department, UniGe, Geneva, Switzerland
| | - Serge Perez
- Univ. Grenoble Alpes, CNRS, CERMAV, Grenoble, France
| | - Frédérique Lisacek
- Swiss Institute of Bioinformatics, Geneva, Switzerland. .,Computer Science Department, UniGe, Geneva, Switzerland. .,Section of Biology, UniGe, Geneva, Switzerland.
| | - Anne Imberty
- Univ. Grenoble Alpes, CNRS, CERMAV, Grenoble, France.
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858
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Holliday GL, Brown SD, Mischel D, Polacco BJ, Babbitt PC. A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function. Database (Oxford) 2020; 2020:baaa034. [PMID: 32449511 PMCID: PMC7246345 DOI: 10.1093/database/baaa034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/18/2020] [Accepted: 04/27/2020] [Indexed: 12/12/2022]
Abstract
Determining the molecular function of enzymes discovered by genome sequencing represents a primary foundation for understanding many aspects of biology. Historically, classification of enzyme reactions has used the enzyme nomenclature system developed to describe the overall reactions performed by biochemically characterized enzymes, irrespective of their associated sequences. In contrast, functional classification and assignment for the millions of protein sequences of unknown function now available is largely done in two computational steps, first by similarity-based assignment of newly obtained sequences to homologous groups, followed by transferring to them the known functions of similar biochemically characterized homologs. Due to the fundamental differences in their etiologies and practice, `how' these chemistry- and evolution-centric functional classification systems relate to each other has been difficult to explore on a large scale. To investigate this issue in a new way, we integrated two published ontologies that had previously described each of these classification systems independently. The resulting infrastructure was then used to compare the functional assignments obtained from each classification system for the well-studied and functionally diverse enolase superfamily. Mapping these function assignments to protein structure and reaction similarity networks shows a profound and complex disconnect between the homology- and chemistry-based classification systems. This conclusion mirrors previous observations suggesting that except for closely related sequences, facile annotation transfer from small numbers of characterized enzymes to the huge number uncharacterized homologs to which they are related is problematic. Our extension of these comparisons to large enzyme superfamilies in a computationally intelligent manner provides a foundation for new directions in protein function prediction for the huge proportion of sequences of unknown function represented in major databases. Interactive sequence, reaction, substrate and product similarity networks computed for this work for the enolase and two other superfamilies are freely available for download from the Structure Function Linkage Database Archive (http://sfld.rbvi.ucsf.edu).
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Affiliation(s)
- Gemma L Holliday
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, 1700 4th Street, CA 94143, USA
- Present Address: Medicines Discovery Catapult, Mereside, Alderley Park, Alderley Edge SK10 4TG, UK
| | - Shoshana D Brown
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, 1700 4th Street, CA 94143, USA
| | - David Mischel
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, 1700 4th Street, CA 94143, USA
| | - Benjamin J Polacco
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, 1700 4th Street, CA 94143, USA
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, 1700 4th Street, CA 94143, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, 1700 4th Street, CA 94143, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, 1700 4th Street, CA 94143, USA
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859
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Waman VP, Blundell TL, Buchan DWA, Gough J, Jones D, Kelley L, Murzin A, Pandurangan AP, Sillitoe I, Sternberg M, Torres P, Orengo C. The Genome3D Consortium for Structural Annotations of Selected Model Organisms. Methods Mol Biol 2020; 2165:27-67. [PMID: 32621218 DOI: 10.1007/978-1-0716-0708-4_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Genome3D consortium is a collaborative project involving protein structure prediction and annotation resources developed by six world-leading structural bioinformatics groups, based in the United Kingdom (namely Blundell, Murzin, Gough, Sternberg, Orengo, and Jones). The main objective of Genome3D serves as a common portal to provide both predicted models and annotations of proteins in model organisms, using several resources developed by these labs such as CATH-Gene3D, DOMSERF, pDomTHREADER, PHYRE, SUPERFAMILY, FUGUE/TOCATTA, and VIVACE. These resources primarily use SCOP- and/or CATH-based protein domain assignments. Another objective of Genome3D is to compare structural classifications of protein domains in CATH and SCOP databases and to provide a consensus mapping of CATH and SCOP protein superfamilies. CATH/SCOP mapping analyses led to the identification of total of 1429 consensus superfamilies.Currently, Genome3D provides structural annotations for ten model organisms, including Homo sapiens, Arabidopsis thaliana, Mus musculus, Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Plasmodium falciparum, Staphylococcus aureus, and Schizosaccharomyces pombe. Thus, Genome3D serves as a common gateway to each structure prediction/annotation resource and allows users to perform comparative assessment of the predictions. It, thus, assists researchers to broaden their perspective on structure/function predictions of their query protein of interest in selected model organisms.
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Affiliation(s)
- Vaishali P Waman
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Daniel W A Buchan
- Department of Computer Science, University College London, London, UK
| | - Julian Gough
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - David Jones
- Department of Computer Science, University College London, London, UK
| | - Lawrence Kelley
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, UK
| | | | | | - Ian Sillitoe
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Michael Sternberg
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, UK
| | - Pedro Torres
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Christine Orengo
- Institute of Structural and Molecular Biology, University College London, London, UK.
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860
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Kumar M, Singh P, Murugesan S, Vetizou M, McCulloch J, Badger JH, Trinchieri G, Al Khodor S. Microbiome as an Immunological Modifier. Methods Mol Biol 2020; 2055:595-638. [PMID: 31502171 PMCID: PMC8276114 DOI: 10.1007/978-1-4939-9773-2_27] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Humans are living ecosystems composed of human cells and microbes. The microbiome is the collection of microbes (microbiota) and their genes. Recent breakthroughs in the high-throughput sequencing technologies have made it possible for us to understand the composition of the human microbiome. Launched by the National Institutes of Health in USA, the human microbiome project indicated that our bodies harbor a wide array of microbes, specific to each body site with interpersonal and intrapersonal variabilities. Numerous studies have indicated that several factors influence the development of the microbiome including genetics, diet, use of antibiotics, and lifestyle, among others. The microbiome and its mediators are in a continuous cross talk with the host immune system; hence, any imbalance on one side is reflected on the other. Dysbiosis (microbiota imbalance) was shown in many diseases and pathological conditions such as inflammatory bowel disease, celiac disease, multiple sclerosis, rheumatoid arthritis, asthma, diabetes, and cancer. The microbial composition mirrors inflammation variations in certain disease conditions, within various stages of the same disease; hence, it has the potential to be used as a biomarker.
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Affiliation(s)
- Manoj Kumar
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar
| | - Parul Singh
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar
| | - Selvasankar Murugesan
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar
| | - Marie Vetizou
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - John McCulloch
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Souhaila Al Khodor
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar.
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861
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Gouw M, Alvarado-Valverde J, Čalyševa J, Diella F, Kumar M, Michael S, Van Roey K, Dinkel H, Gibson TJ. How to Annotate and Submit a Short Linear Motif to the Eukaryotic Linear Motif Resource. Methods Mol Biol 2020; 2141:73-102. [PMID: 32696353 DOI: 10.1007/978-1-0716-0524-0_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over the past few years, it has become apparent that approximately 35% of the human proteome consists of intrinsically disordered regions. Many of these disordered regions are rich in short linear motifs (SLiMs) which mediate protein-protein interactions. Although these motifs are short and often partially conserved, they are involved in many important aspects of protein function, including cleavage, targeting, degradation, docking, phosphorylation, and other posttranslational modifications. The Eukaryotic Linear Motif resource (ELM) was established over 15 years ago as a repository to store and catalogue the scientific discoveries of motifs. Each motif in the database is annotated and curated manually, based on the experimental evidence gathered from publications. The entries themselves are submitted to ELM by filling in two annotation templates designed for motif class and motif instance annotation. In this protocol, we describe the steps involved in annotating new motifs and how to submit them to ELM.
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Affiliation(s)
- Marc Gouw
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jesús Alvarado-Valverde
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Jelena Čalyševa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Francesca Diella
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sushama Michael
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kim Van Roey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Holger Dinkel
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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862
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Lorenzo‐Orts L, Couto D, Hothorn M. Identity and functions of inorganic and inositol polyphosphates in plants. THE NEW PHYTOLOGIST 2020; 225:637-652. [PMID: 31423587 PMCID: PMC6973038 DOI: 10.1111/nph.16129] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/22/2019] [Indexed: 05/08/2023]
Abstract
Inorganic polyphosphates (polyPs) and inositol pyrophosphates (PP-InsPs) form important stores of inorganic phosphate and can act as energy metabolites and signaling molecules. Here we review our current understanding of polyP and inositol phosphate (InsP) metabolism and physiology in plants. We outline methods for polyP and InsP detection, discuss the known plant enzymes involved in their synthesis and breakdown, and summarize the potential physiological and signaling functions for these enigmatic molecules in plants.
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Affiliation(s)
- Laura Lorenzo‐Orts
- Structural Plant Biology LaboratoryDepartment of Botany and Plant BiologyUniversity of Geneva30 Quai E. AnsermetGeneva1211Switzerland
| | - Daniel Couto
- Structural Plant Biology LaboratoryDepartment of Botany and Plant BiologyUniversity of Geneva30 Quai E. AnsermetGeneva1211Switzerland
| | - Michael Hothorn
- Structural Plant Biology LaboratoryDepartment of Botany and Plant BiologyUniversity of Geneva30 Quai E. AnsermetGeneva1211Switzerland
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863
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Hraber P, O'Maille PE, Silberfarb A, Davis-Anderson K, Generous N, McMahon BH, Fair JM. Resources to Discover and Use Short Linear Motifs in Viral Proteins. Trends Biotechnol 2020; 38:113-127. [PMID: 31427097 PMCID: PMC7114124 DOI: 10.1016/j.tibtech.2019.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/11/2019] [Accepted: 07/15/2019] [Indexed: 12/23/2022]
Abstract
Viral proteins evade host immune function by molecular mimicry, often achieved by short linear motifs (SLiMs) of three to ten consecutive amino acids (AAs). Motif mimicry tolerates mutations, evolves quickly to modify interactions with the host, and enables modular interactions with protein complexes. Host cells cannot easily coordinate changes to conserved motif recognition and binding interfaces under selective pressure to maintain critical signaling pathways. SLiMs offer potential for use in synthetic biology, such as better immunogens and therapies, but may also present biosecurity challenges. We survey viral uses of SLiMs to mimic host proteins, and information resources available for motif discovery. As the number of examples continues to grow, knowledge management tools are essential to help organize and compare new findings.
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Affiliation(s)
- Peter Hraber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Paul E O'Maille
- Biosciences Division, SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
| | - Andrew Silberfarb
- Artificial Intelligence Center, SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
| | - Katie Davis-Anderson
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nicholas Generous
- Global Security Directorate, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Benjamin H McMahon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jeanne M Fair
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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864
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Decker Franco C, Wieser SN, Soria M, de Alba P, Florin-Christensen M, Schnittger L. In silico identification of immunotherapeutic and diagnostic targets in the glycosylphosphatidylinositol metabolism of the coccidian Sarcocystis aucheniae. Transbound Emerg Dis 2019; 67 Suppl 2:165-174. [PMID: 31880101 DOI: 10.1111/tbed.13438] [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] [Indexed: 12/13/2022]
Abstract
Meat of the South American camelids (SACs) llama and alpaca is an important source of animal protein and income for rural families in the Andes, and a product with significant growth potential for local and international markets. However, infestation with macroscopic cysts of the coccidian protozoon Sarcocystis aucheniae, a parasitosis known as SAC sarcocystosis, significantly hampers its commercialization. There are no validated methods to diagnose the presence of S. aucheniae cysts other than carcass examination. Moreover, there are no available drugs or vaccines to cure or prevent SAC sarcocystosis. Identification of relevant molecules that act at the host-pathogen interface can significantly contribute to the control of this disease. It has been shown for other pathogenic protozoa that glycosylphosphatidylinositol (GPI) is a critical molecule implicated in parasite survival and pathogenicity. This study focused on the identification of the enzymes that participate in the S. aucheniae GPI biosynthetic pathway and the repertoire of the parasite GPI-anchored proteins (GPI-APs). To this aim, RNA was extracted from parasite cysts and the transcriptome was sequenced and translated into amino acid sequences. The generated database was mined using sequences of well-characterized GPI biosynthetic enzymes of Saccharomyces cerevisiae and Toxoplasma gondii. Eleven enzymes predicted to participate in the S. aucheniae GPI biosynthetic pathway were identified. On the other hand, the database was searched for proteins carrying an N-terminal signal peptide and a single C-terminal transmembrane region containing a GPI anchor signal. Twenty-four GPI-anchored peptides were identified, of which nine are likely S. aucheniae-specific, and 15 are homologous to membrane proteins of other coccidians. Among the latter, 13 belong to the SRS domain superfamily, an extensive group of coccidian GPI-anchored proteins that mediate parasite interaction with their host. Phylogenetic analysis showed a great degree of intra- and inter-specific divergence among SRS family proteins. In vitro and in vivo experiments are needed to validate S. aucheniae GPI biosynthetic enzymes and GPI-APs as drug targets and/or as vaccine or diagnostic antigens.
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Affiliation(s)
- Cecilia Decker Franco
- Instituto de Patobiología Veterinaria, CICVyA, INTA-Castelar, Hurlingham, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Sarah N Wieser
- Instituto de Patobiología Veterinaria, CICVyA, INTA-Castelar, Hurlingham, Buenos Aires, Argentina
| | - Marcelo Soria
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Microbiología Agrícola, Facultad de Agronomía, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - Paloma de Alba
- Instituto de Patobiología Veterinaria, CICVyA, INTA-Castelar, Hurlingham, Buenos Aires, Argentina
| | - Mónica Florin-Christensen
- Instituto de Patobiología Veterinaria, CICVyA, INTA-Castelar, Hurlingham, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Leonhard Schnittger
- Instituto de Patobiología Veterinaria, CICVyA, INTA-Castelar, Hurlingham, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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865
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A systems biology approach reveals neuronal and muscle developmental defects after chronic exposure to ionising radiation in zebrafish. Sci Rep 2019; 9:20241. [PMID: 31882844 PMCID: PMC6934629 DOI: 10.1038/s41598-019-56590-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/13/2019] [Indexed: 11/11/2022] Open
Abstract
Contamination of the environment after the Chernobyl and Fukushima Daiichi nuclear power plant (NPP) disasters led to the exposure of a large number of humans and wild animals to radioactive substances. However, the sub-lethal consequences induced by these absorbed radiological doses remain understudied and the long-term biological impacts largely unknown. We assessed the biological effects of chronic exposure to ionizing radiation (IR) on embryonic development by exposing zebrafish embryo from fertilization and up to 120 hours post-fertilization (hpf) at dose rates of 0.5 mGy/h, 5 mGy/h and 50 mGy/h, thereby encompassing the field of low dose rates defined at 6 mGy/h. Chronic exposure to IR altered larval behaviour in a light-dark locomotor test and affected cardiac activity at a dose rate as low as 0.5 mGy/h. The multi-omics analysis of transcriptome, proteome and transcription factor binding sites in the promoters of the deregulated genes, collectively points towards perturbations of neurogenesis, muscle development, and retinoic acid (RA) signaling after chronic exposure to IR. Whole-mount RNA in situ hybridization confirmed the impaired expression of the transcription factors her4.4 in the central nervous system and myogenin in the developing muscles of exposed embryos. At the organ level, the assessment of muscle histology by transmission electron microscopy (TEM) demonstrated myofibers disruption and altered neuromuscular junctions in exposed larvae at 5 mGy/h and 50 mGy/h. The integration of these multi-level data demonstrates that chronic exposure to low dose rates of IR has an impact on neuronal and muscle progenitor cells, that could lead to motility defects in free swimming larvae at 120 hpf. The mechanistic understanding of these effects allows us to propose a model where deregulation of RA signaling by chronic exposure to IR has pleiotropic effects on neurogenesis and muscle development.
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866
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Description of three bacterial strains belonging to the new genus Novipirellula gen. nov., reclassificiation of Rhodopirellula rosea and Rhodopirellula caenicola and readjustment of the genus threshold of the phylogenetic marker rpoB for Planctomycetaceae. Antonie van Leeuwenhoek 2019; 113:1779-1795. [DOI: 10.1007/s10482-019-01374-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/07/2019] [Indexed: 02/07/2023]
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867
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Rose J, Visser F, Müller B, Senft M, Groscurth S, Sicking KF, Twyman RM, Prüfer D, Noll GA. Identification and molecular analysis of interaction sites in the MtSEO-F1 protein involved in forisome assembly. Int J Biol Macromol 2019; 144:603-614. [PMID: 31843608 DOI: 10.1016/j.ijbiomac.2019.12.092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 11/26/2022]
Abstract
Forisomes are large mechanoprotein complexes found solely in legumes such as Medicago truncatula. They comprise several "sieve element occlusion by forisome" (SEO-F) subunits, with MtSEO-F1 as the major structure-forming component. SEO-F proteins possess three conserved domains -an N-terminal domain (SEO-NTD), a potential thioredoxin fold, and a C-terminal domain (SEO-CTD)- but structural and biochemical data are scarce and little is known about the contribution of these domains to forisome assembly. To identify key amino acids involved in MtSEO-F1 dimerization and complex formation, we investigated protein-protein interactions by bimolecular fluorescence complementation and the analysis of yeast two-hybrid and random mutagenesis libraries. We identified a SEO-NTD core region as the major dimerization site, with abundant hydrophobic residues and rare charged residues suggesting dimerization is driven by the hydrophobic effect. We also found that ~45% of the full-length MtSEO-F1 sequence must be conserved for higher-order protein assembly, indicating that large interaction surfaces facilitate stable interactions, contributing to the high resilience of forisome bodies. Interestingly, the removal of 62 amino acids from the C-terminus did not disrupt forisome assembly. This is the first study unraveling interaction sites and mechanisms within the MtSEO-F1 protein at the level of dimerization and complex formation.
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Affiliation(s)
- Judith Rose
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany
| | - Franziska Visser
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany
| | - Boje Müller
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143 Münster, Germany
| | - Matthias Senft
- Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Sira Groscurth
- Stem Cell Network North Rhine-Westphalia, Merowingerplatz 1, 40225 Düsseldorf, Germany
| | - Kevin F Sicking
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany
| | | | - Dirk Prüfer
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143 Münster, Germany
| | - Gundula A Noll
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143 Münster, Germany.
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868
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Affiliation(s)
- Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International Centre for Clinical Research, St. Ann’s Hospital, 602 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International Centre for Clinical Research, St. Ann’s Hospital, 602 00 Brno, Czech Republic
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869
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Pan B, Chen X, Hou L, Zhang Q, Qu Z, Warren A, Miao M. Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within "Nassophorea-Synhymenia-Phyllopharyngea" Assemblage. Front Microbiol 2019; 10:2819. [PMID: 31921016 PMCID: PMC6920121 DOI: 10.3389/fmicb.2019.02819] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/20/2019] [Indexed: 11/13/2022] Open
Abstract
Ciliated protists (ciliates) are widely used for investigating evolution, mostly due to their successful radiation after their early evolutionary branching. In this study, we employed high-throughput sequencing technology to reveal the phylogenetic position of Synhymenia, as well as two classes Nassophorea and Phyllopharyngea, which have been a long-standing puzzle in the field of ciliate systematics and evolution. We obtained genomic and transcriptomic data from single cells of one synhymenian (Chilodontopsis depressa) and six other species of phyllopharyngeans (Chilodochona sp., Dysteria derouxi, Hartmannula sinica, Trithigmostoma cucullulus, Trochilia petrani, and Trochilia sp.). Phylogenomic analysis based on 157 orthologous genes comprising 173,835 amino acid residues revealed the affiliation of C. depressa within the class Phyllopharyngea, and the monophyly of Nassophorea, which strongly support the assignment of Synhymenia as a subclass within the class Phyllopharyngea. Comparative genomic analyses further revealed that C. depressa shares more orthologous genes with the class Nassophorea than with Phyllopharyngea, and the stop codon usage in C. depressa resembles that of Phyllopharyngea. Functional enrichment analysis demonstrated that biological pathways in C. depressa are more similar to Phyllopharyngea than Nassophorea. These results suggest that genomic and transcriptomic data can be used to provide insights into the evolutionary relationships within the "Nassophorea-Synhymenia-Phyllopharyngea" assemblage.
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Affiliation(s)
- Bo Pan
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, United States
| | - Lina Hou
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Qianqian Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Zhishuai Qu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.,Ecology Group, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Miao Miao
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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870
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Jiang P, Shao J, Nemchinov LG. Identification of emerging viral genomes in transcriptomic datasets of alfalfa (Medicago sativa L.). Virol J 2019; 16:153. [PMID: 31818304 PMCID: PMC6902351 DOI: 10.1186/s12985-019-1257-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/22/2019] [Indexed: 12/19/2022] Open
Abstract
Background Publicly available transcriptomic datasets have become a valuable tool for the discovery of new pathogens, particularly viruses. In this study, several coding-complete viral genomes previously not found or experimentally confirmed in alfalfa were identified in the plant datasets retrieved from the NCBI Sequence Read Archive. Methods Publicly available Medicago spp. transcriptomic datasets were retrieved from the NCBI SRA database. The raw reads were first mapped to the reference genomes of Medicago sativa and Medigago truncatula followed by the alignment of the unmapped reads to the NCBI viral genome database and de novo assembly using the SPAdes tool. When possible, assemblies were experimentally confirmed using 5′/3′ RACE and RT-PCRs. Results Twenty three different viruses were identified in the analyzed datasets, of which several represented emerging viruses not reported in alfalfa prior to this study. Among them were two strains of cnidium vein yellowing virus, lychnis mottle virus and Cactus virus X, for which coding-complete genomic sequences were obtained by a de novo assembly. Conclusions The results improve our knowledge of the diversity and host range of viruses infecting alfalfa, provide essential tools for their diagnostics and characterization and demonstrate the utility of transcriptomic datasets for the discovery of new pathogens.
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Affiliation(s)
- Peng Jiang
- USDA/ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705, USA
| | - Jonathan Shao
- USDA/ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705, USA
| | - Lev G Nemchinov
- USDA/ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705, USA.
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871
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Zeman M, Bárdy P, Vrbovská V, Roudnický P, Zdráhal Z, Růžičková V, Doškař J, Pantůček R. New Genus Fibralongavirus in Siphoviridae Phages of Staphylococcus pseudintermedius. Viruses 2019; 11:E1143. [PMID: 31835553 PMCID: PMC6950010 DOI: 10.3390/v11121143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/02/2019] [Accepted: 12/04/2019] [Indexed: 12/18/2022] Open
Abstract
Bacteriophages of the significant veterinary pathogen Staphylococcus pseudintermedius are rarely described morphologically and genomically in detail, and mostly include phages of the Siphoviridae family. There is currently no taxonomical classification for phages of this bacterial species. Here we describe a new phage designated vB_SpsS_QT1, which is related to phage 2638A originally described as a Staphylococcus aureus phage. Propagating strain S. aureus 2854 of the latter was reclassified by rpoB gene sequencing as S. pseudintermedius 2854 in this work. Both phages have a narrow but different host range determined on 54 strains. Morphologically, both of them belong to the family Siphoviridae, share the B1 morphotype, and differ from other staphylococcal phage genera by a single long fibre at the terminus of the tail. The complete genome of phage vB_SpsS_QT1 was sequenced with the IonTorrent platform and expertly annotated. Its linear genome with cohesive ends is 43,029 bp long and encodes 60 predicted genes with the typical modular structure of staphylococcal siphophages. A global alignment found the genomes of vB_SpsS_QT1 and 2638A to share 84% nucleotide identity, but they have no significant similarity of nucleotide sequences with other phage genomes available in public databases. Based on the morphological, phylogenetic, and genomic analyses, a novel genus Fibralongavirus in the family Siphoviridae is described with phage species vB_SpsS_QT1 and 2638A.
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Affiliation(s)
- Michal Zeman
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Pavol Bárdy
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Veronika Vrbovská
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Pavel Roudnický
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Vladislava Růžičková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Jiří Doškař
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Roman Pantůček
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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872
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Kim JH, Kim HK, Kim H, Chan BKK, Kang S, Kim W. Draft Genome Assembly of a Fouling Barnacle, Amphibalanus amphitrite (Darwin, 1854): The First Reference Genome for Thecostraca. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00465] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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873
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Wang J, Rousseau J, Kim E, Ehresmann S, Cheng YT, Duraine L, Zuo Z, Park YJ, Li-Kroeger D, Bi W, Wong LJ, Rosenfeld J, Gleeson J, Faqeih E, Alkuraya FS, Wierenga KJ, Chen J, Afenjar A, Nava C, Doummar D, Keren B, Juusola J, Grompe M, Bellen HJ, Campeau PM. Loss of Oxidation Resistance 1, OXR1, Is Associated with an Autosomal-Recessive Neurological Disease with Cerebellar Atrophy and Lysosomal Dysfunction. Am J Hum Genet 2019; 105:1237-1253. [PMID: 31785787 PMCID: PMC6904826 DOI: 10.1016/j.ajhg.2019.11.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 11/01/2019] [Indexed: 12/28/2022] Open
Abstract
We report an early-onset autosomal-recessive neurological disease with cerebellar atrophy and lysosomal dysfunction. We identified bi-allelic loss-of-function (LoF) variants in Oxidative Resistance 1 (OXR1) in five individuals from three families; these individuals presented with a history of severe global developmental delay, current intellectual disability, language delay, cerebellar atrophy, and seizures. While OXR1 is known to play a role in oxidative stress resistance, its molecular functions are not well established. OXR1 contains three conserved domains: LysM, GRAM, and TLDc. The gene encodes at least six transcripts, including some that only consist of the C-terminal TLDc domain. We utilized Drosophila to assess the phenotypes associated with loss of mustard (mtd), the fly homolog of OXR1. Strong LoF mutants exhibit late pupal lethality or pupal eclosion defects. Interestingly, although mtd encodes 26 transcripts, severe LoF and null mutations can be rescued by a single short human OXR1 cDNA that only contains the TLDc domain. Similar rescue is observed with the TLDc domain of NCOA7, another human homolog of mtd. Loss of mtd in neurons leads to massive cell loss, early death, and an accumulation of aberrant lysosomal structures, similar to what we observe in fibroblasts of affected individuals. Our data indicate that mtd and OXR1 are required for proper lysosomal function; this is consistent with observations that NCOA7 is required for lysosomal acidification.
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Affiliation(s)
- Julia Wang
- Program in Developmental Biology, Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Justine Rousseau
- Centre Hospitalier Universitaire Saint-Justine Research Center, CHU Sainte-Justine, Montreal, QC H3T 1J4, Canada
| | - Emily Kim
- Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA
| | - Sophie Ehresmann
- Centre Hospitalier Universitaire Saint-Justine Research Center, CHU Sainte-Justine, Montreal, QC H3T 1J4, Canada
| | - Yi-Ting Cheng
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lita Duraine
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhongyuan Zuo
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ye-Jin Park
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Li-Kroeger
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph Gleeson
- Rady Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Eissa Faqeih
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, 11525, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, 11525, Saudi Arabia
| | - Klaas J Wierenga
- Department of Pediatrics, Oklahoma University Health Sciences Center (OUHSC), Oklahoma City, OK 26901, USA; Department of Clinical Genomics, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Jiani Chen
- Department of Pediatrics, Oklahoma University Health Sciences Center (OUHSC), Oklahoma City, OK 26901, USA; Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexandra Afenjar
- Assistance Publique des Hôpitaux de Paris, Unité de Génétique Clinique, Hôpital Armand Trousseau, Groupe Hospitalier Universitaire Paris, 75012, France; Département de Génétique et Embryologie Médicale, CRMR des Malformations et Maladies Congénitales du Cervelet, GRC ConCer-LD, Sorbonne Universités, Hôpital Trousseau, Paris, 75012 France
| | - Caroline Nava
- Assistance Publique des Hôpitaux de Paris, Unité de Génétique Clinique, Hôpital Armand Trousseau, Groupe Hospitalier Universitaire Paris, 75012, France
| | - Diane Doummar
- Assistance Publique des Hôpitaux de Paris, Service de Neuropédiatrie, Hôpital Armand Trousseau, Groupe Hospitalier Universitaire Paris, 75012 France
| | - Boris Keren
- Assistance Publique des Hôpitaux de Paris, Unité de Génétique Clinique, Hôpital Armand Trousseau, Groupe Hospitalier Universitaire Paris, 75012, France
| | | | - Markus Grompe
- Department of Pediatrics, Oregon Health and Science University, Portland, Oregon 97201, USA; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97201, USA
| | - Hugo J Bellen
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute and Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Philippe M Campeau
- Centre Hospitalier Universitaire Saint-Justine Research Center, CHU Sainte-Justine, Montreal, QC H3T 1J4, Canada.
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874
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Chung HC, Nguyen VG, Huynh TML, Do HQ, Vo DC, Park YH, Park BK. Molecular-based investigation and genetic characterization of porcine stool-associated RNA virus (posavirus) lineages 1 to 3 in pigs in South Korea from 2017 to 2019. Res Vet Sci 2019; 128:286-292. [PMID: 31869594 DOI: 10.1016/j.rvsc.2019.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 11/07/2019] [Accepted: 11/19/2019] [Indexed: 12/25/2022]
Abstract
Recent results on the detection and genetic characterization of stool-associated RNA viruses from different species have increased the knowledge about the extreme genetic diversity of picornaviruses. This study aimed to investigate the presence of unclassified porcine stool-associated RNA viruses (posaviruses) in South Korea and to elucidate the molecular evolution of the viruses. By RT-PCR, posaviruses 1 and 3 were exclusively found in fecal samples and consistently detected in three consecutive years in six of eight provinces, with 148/697 (21.2%) and 33/84 (39.3%) positive samples and farms, respectively. Every age group but the older age groups (finisher, sow) had significantly higher positive rates of posavirus 1 than posavirus 3. An analysis of the RNA-dependent RNA polymerase sequences by likelihood mapping and maximum-likelihood-based phylogenetic analysis revealed that stool-associated RNA viruses formed four supergroups that were well separated from all recognized families of the order Picornavirales. Five genomes of Korean posaviruses generated in this study were phylogenetically grouped with posavirus 1 and posavirus 3 and were predicted to have the typical genome organization of picornaviruses.
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Affiliation(s)
- Hee-Chun Chung
- Department of Veterinary Medicine Virology Laboratory, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 151-742, Republic of Korea
| | - Van-Giap Nguyen
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Viet Nam
| | - Thi-My-Le Huynh
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Viet Nam
| | - Hai-Quynh Do
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
| | - Dinh-Chuong Vo
- Devision of Veterinary Epidemiology, Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Viet Nam
| | - Yong-Ho Park
- Department of Veterinary Microbiology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 151-742, Republic of Korea.
| | - Bong-Kyun Park
- Department of Veterinary Medicine Virology Laboratory, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 151-742, Republic of Korea.
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875
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Abstract
Vibrio cholerae, the causative agent of the diarrheal disease cholera, benefits from a sessile biofilm lifestyle that enhances survival outside the host but also contributes to host colonization and infectivity. The bacterial second messenger c-di-GMP has been identified as a central regulator of biofilm formation, including in V. cholerae; however, our understanding of the pathways that contribute to this process is incomplete. Here, we define a conserved signaling system that controls the stability of large adhesion proteins at the cell surface of V. cholerae, which are important for cell attachment and biofilm formation. Insight into the regulatory circuit underlying biofilm formation may inform targeted strategies to interfere with a process that renders this bacterium remarkably adaptable to changing environments. The dinucleotide second messenger c-di-GMP has emerged as a central regulator of reversible cell attachment during bacterial biofilm formation. A prominent cell adhesion mechanism first identified in pseudomonads combines two c-di-GMP-mediated processes: transcription of a large adhesin and its cell surface display via posttranslational proteolytic control. Here, we characterize an orthologous c-di-GMP effector system and show that it is operational in Vibrio cholerae, where it regulates two distinct classes of adhesins. Through structural analyses, we reveal a conserved autoinhibition mechanism of the c-di-GMP receptor that controls adhesin proteolysis and present a structure of a c-di-GMP-bound receptor module. We further establish functionality of the periplasmic protease controlled by the receptor against the two adhesins. Finally, transcription and functional assays identify physiological roles of both c-di-GMP-regulated adhesins in surface attachment and biofilm formation. Together, our studies highlight the conservation of a highly efficient signaling effector circuit for the control of cell surface adhesin expression and its versatility by revealing strain-specific variations.
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876
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Gordon L, Blechman J, Shimoni E, Gur D, Anand-Apte B, Levkowitz G. The fenestrae-associated protein Plvap regulates the rate of blood-borne protein passage into the hypophysis. Development 2019; 146:dev.177790. [PMID: 31740533 DOI: 10.1242/dev.177790] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 11/08/2019] [Indexed: 12/13/2022]
Abstract
To maintain body homeostasis, endocrine systems must detect and integrate blood-borne peripheral signals. This is mediated by fenestrae, specialized permeable pores in the endothelial membrane. Plasmalemma vesicle-associated protein (Plvap) is located in the fenestral diaphragm and is thought to play a role in the passage of proteins through the fenestrae. However, this suggested function has yet to be demonstrated directly. We studied the development of fenestrated capillaries in the hypophysis, a major neuroendocrine interface between the blood and brain. Using a transgenic biosensor to visualize the vascular excretion of the genetically tagged plasma protein DBP-EGFP, we show that the developmental acquisition of vascular permeability coincides with differential expression of zebrafish plvap orthologs in the hypophysis versus brain. Ultrastructural analysis revealed that plvapb mutants display deficiencies in fenestral diaphragms and increased density of hypophyseal fenestrae. Measurements of DBP-EGFP extravasation in plvapb mutants provided direct proof that Plvap limits the rate of blood-borne protein passage through fenestrated endothelia. We present the regulatory role of Plvap in the development of blood-borne protein detection machinery at a neuroendocrine interface through which hormones are released to the general circulation.
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Affiliation(s)
- Ludmila Gordon
- Department of Molecular Cell Biology, Weizmann Institute of Science, PO Box 26, Rehovot 7610001, Israel
| | - Janna Blechman
- Department of Molecular Cell Biology, Weizmann Institute of Science, PO Box 26, Rehovot 7610001, Israel
| | - Eyal Shimoni
- Chemical Research Support, Weizmann Institute of Science, PO Box 26, Rehovot 7610001, Israel
| | - Dvir Gur
- Department of Molecular Cell Biology, Weizmann Institute of Science, PO Box 26, Rehovot 7610001, Israel
| | - Bela Anand-Apte
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic Foundation, Cleveland OH 444195, USA
| | - Gil Levkowitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, PO Box 26, Rehovot 7610001, Israel
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877
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Lutz T, Flodman K, Copelas A, Czapinska H, Mabuchi M, Fomenkov A, He X, Bochtler M, Xu SY. A protein architecture guided screen for modification dependent restriction endonucleases. Nucleic Acids Res 2019; 47:9761-9776. [PMID: 31504772 PMCID: PMC6765204 DOI: 10.1093/nar/gkz755] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/18/2019] [Accepted: 08/31/2019] [Indexed: 11/15/2022] Open
Abstract
Modification dependent restriction endonucleases (MDREs) often have separate catalytic and modification dependent domains. We systematically looked for previously uncharacterized fusion proteins featuring a PUA or DUF3427 domain and HNH or PD-(D/E)XK catalytic domain. The enzymes were clustered by similarity of their putative modification sensing domains into several groups. The TspA15I (VcaM4I, CmeDI), ScoA3IV (MsiJI, VcaCI) and YenY4I groups, all featuring a PUA superfamily domain, preferentially cleaved DNA containing 5-methylcytosine or 5-hydroxymethylcytosine. ScoA3V, also featuring a PUA superfamily domain, but of a different clade, exhibited 6-methyladenine stimulated nicking activity. With few exceptions, ORFs for PUA-superfamily domain containing endonucleases were not close to DNA methyltransferase ORFs, strongly supporting modification dependent activity of the endonucleases. DUF3427 domain containing fusion proteins had very little or no endonuclease activity, despite the presence of a putative PD-(D/E)XK catalytic domain. However, their expression potently restricted phage T4gt in Escherichia coli cells. In contrast to the ORFs for PUA domain containing endonucleases, the ORFs for DUF3427 fusion proteins were frequently found in defense islands, often also featuring DNA methyltransferases.
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Affiliation(s)
- Thomas Lutz
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Kiersten Flodman
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Alyssa Copelas
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Honorata Czapinska
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Megumu Mabuchi
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Alexey Fomenkov
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.,Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Shuang-Yong Xu
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
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878
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Benz C, Urbaniak MD. Organising the cell cycle in the absence of transcriptional control: Dynamic phosphorylation co-ordinates the Trypanosoma brucei cell cycle post-transcriptionally. PLoS Pathog 2019; 15:e1008129. [PMID: 31830130 PMCID: PMC6907760 DOI: 10.1371/journal.ppat.1008129] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/07/2019] [Indexed: 11/18/2022] Open
Abstract
The cell division cycle of the unicellular eukaryote Trypanosome brucei is tightly regulated despite the paucity of transcriptional control that results from the arrangement of genes in polycistronic units and lack of dynamically regulated transcription factors. To identify the contribution of dynamic phosphorylation to T. brucei cell cycle control we have combined cell cycle synchronisation by centrifugal elutriation with quantitative phosphoproteomic analysis. Cell cycle regulated changes in phosphorylation site abundance (917 sites, average 5-fold change) were more widespread and of a larger magnitude than changes in protein abundance (443 proteins, average 2-fold change) and were mostly independent of each other. Hierarchical clustering of co-regulated phosphorylation sites according to their cell cycle profile revealed that a bulk increase in phosphorylation occurs across the cell cycle, with a significant enrichment of known cell cycle regulators and RNA binding proteins (RBPs) within the largest clusters. Cell cycle regulated changes in essential cell cycle kinases are temporally co-ordinated with differential phosphorylation of components of the kinetochore and eukaryotic initiation factors, along with many RBPs not previously linked to the cell cycle such as eight PSP1-C terminal domain containing proteins. The temporal profiles demonstrate the importance of dynamic phosphorylation in co-ordinating progression through the cell cycle, and provide evidence that RBPs play a central role in post-transcriptional regulation of the T. brucei cell cycle. Data are available via ProteomeXchange with identifier PXD013488.
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Affiliation(s)
- Corinna Benz
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
| | - Michael D. Urbaniak
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
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879
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Bergstrand LH, Neufeld JD, Doxey AC. Pygenprop: a Python library for programmatic exploration and comparison of organism genome properties. Bioinformatics 2019; 35:5063-5065. [PMID: 31240307 DOI: 10.1093/bioinformatics/btz522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/27/2019] [Accepted: 06/20/2019] [Indexed: 11/12/2022] Open
Abstract
SUMMARY A critical step in comparative genomics is the identification of differences in the presence/absence of encoded biochemical pathways among organisms. Our library, Pygenprop, facilitates these comparisons using data from the Genome Properties database. Pygenprop is written in Python and, unlike existing libraries, it is compatible with a variety of tools in the Python data science ecosystem, such as Jupyter Notebooks for interactive analyses and scikit-learn for machine learning. Pygenprop assigns YES, NO, or PARTIAL support for each property based on InterProScan annotations of open reading frames from an organism's genome. The library contains classes for representing the Genome Properties database as a whole and methods for detecting differences in property assignments between organisms. As the Genome Properties database grows, we anticipate widespread adoption of Pygenprop for routine genome analyses and integration within third-party bioinformatics software. AVAILABILITY AND IMPLEMENTATION Pygenprop is written in Python and is compatible with versions 3.6 or higher. Source code is available under Apache Licence Version 2 at https://github.com/Micromeda/pygenprop. The package can be installed from both PyPi (https://pypi.org/project/pygenprop) and Anaconda (https://anaconda.org/lbergstrand/pygenprop). Documentation is available on Read the Docs (http://pygenprop.rtfd.io/).
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Affiliation(s)
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, Waterloo, Canada
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880
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Simpkin AJ, Thomas JMH, Simkovic F, Keegan RM, Rigden DJ. Molecular replacement using structure predictions from databases. Acta Crystallogr D Struct Biol 2019; 75:1051-1062. [PMID: 31793899 PMCID: PMC6889911 DOI: 10.1107/s2059798319013962] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/12/2019] [Indexed: 01/19/2023] Open
Abstract
Molecular replacement (MR) is the predominant route to solution of the phase problem in macromolecular crystallography. Where the lack of a suitable homologue precludes conventional MR, one option is to predict the target structure using bioinformatics. Such modelling, in the absence of homologous templates, is called ab initio or de novo modelling. Recently, the accuracy of such models has improved significantly as a result of the availability, in many cases, of residue-contact predictions derived from evolutionary covariance analysis. Covariance-assisted ab initio models representing structurally uncharacterized Pfam families are now available on a large scale in databases, potentially representing a valuable and easily accessible supplement to the PDB as a source of search models. Here, the unconventional MR pipeline AMPLE is employed to explore the value of structure predictions in the GREMLIN and PconsFam databases. It was tested whether these deposited predictions, processed in various ways, could solve the structures of PDB entries that were subsequently deposited. The results were encouraging: nine of 27 GREMLIN cases were solved, covering target lengths of 109-355 residues and a resolution range of 1.4-2.9 Å, and with target-model shared sequence identity as low as 20%. The cluster-and-truncate approach in AMPLE proved to be essential for most successes. For the overall lower quality structure predictions in the PconsFam database, remodelling with Rosetta within the AMPLE pipeline proved to be the best approach, generating ensemble search models from single-structure deposits. Finally, it is shown that the AMPLE-obtained search models deriving from GREMLIN deposits are of sufficiently high quality to be selected by the sequence-independent MR pipeline SIMBAD. Overall, the results help to point the way towards the optimal use of the expanding databases of ab initio structure predictions.
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Affiliation(s)
- Adam J. Simpkin
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Jens M. H. Thomas
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Felix Simkovic
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Ronan M. Keegan
- STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, England
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
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881
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Zhang R, Li N, Liu Y, Han X, Tu T, Shen J, Xu S, Wu Q, Zhou J, Huang Z. Biochemical and structural properties of a low-temperature-active glycoside hydrolase family 43 β-xylosidase: Activity and instability at high neutral salt concentrations. Food Chem 2019; 301:125266. [DOI: 10.1016/j.foodchem.2019.125266] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 06/24/2019] [Accepted: 07/26/2019] [Indexed: 10/26/2022]
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882
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Dong MY, Fan XW, Pang XY, Li YZ. Decrypting tubby-like protein gene family of multiple functions in starch root crop cassava. AOB PLANTS 2019; 11:plz075. [PMID: 31871614 PMCID: PMC6920310 DOI: 10.1093/aobpla/plz075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 11/24/2019] [Indexed: 05/23/2023]
Abstract
Tubby-like proteins (TLPs) are ubiquitous in eukaryotes and function in abiotic stress tolerance of some plants. Cassava (Manihot esculenta Crantz) is a high-yield starch root crop and has a high tolerance to poor soil conditions and abiotic stress. However, little is known about TLP gene characteristics and their expression in cassava. We identified cassava TLP genes, MeTLPs, and further analysed structure, duplication, chromosome localization and collinearity, cis-acting elements in the promoter regions and expression patterns of MeTLPs, and three-dimensional structure of the encoded proteins MeTLPs. In conclusion, there is a MeTLP family containing 13 members, which are grouped into A and C subfamilies. There are 11 pairs of MeTLPs that show the duplication which took place between 10.11 and 126.69 million years ago. Two MeTLPs 6 and 9 likely originate from one gene in an ancestral species, may be common ancestors for other MeTLPs and would most likely not be eligible for ubiquitin-related protein degradation because their corresponding proteins (MeTLPs 6 and 9) have no the F-box domain in the N-terminus. MeTLPs feature differences in the number from TLPs in wheat, apple, Arabidopsis, poplar and maize, and are highlighted by segmental duplication but more importantly by the chromosomal collinearity with potato StTLPs. MeTLPs are at least related to abiotic stress tolerance in cassava. However, the subtle differences in function among MeTLPs are predictable partly because of their differential expression profiles, which are coupled with various cis‑acting elements existing in the promoter regions depending on genes.
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Affiliation(s)
- Ming-You Dong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Xian-Wei Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Xiang-Yu Pang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - You-Zhi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
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883
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Identification and Characterization of Aspergillus nidulans Mutants Impaired in Asexual Development under Phosphate Stress. Cells 2019; 8:cells8121520. [PMID: 31779253 PMCID: PMC6952808 DOI: 10.3390/cells8121520] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/22/2019] [Accepted: 11/22/2019] [Indexed: 01/04/2023] Open
Abstract
The transcription factor BrlA plays a central role in the production of asexual spores (conidia) in the fungus Aspergillus nidulans. BrlA levels are controlled by signal transducers known collectively as UDAs. Furthermore, it governs the expression of CDP regulators, which control most of the morphological transitions leading to the production of conidia. In response to the emergence of fungal cells in the air, the main stimulus triggering conidiation, UDA mutants such as the flbB deletant fail to induce brlA expression. Nevertheless, ΔflbB colonies conidiate profusely when they are cultured on a medium containing high H2PO4− concentrations, suggesting that the need for FlbB activity is bypassed. We used this phenotypic trait and an UV-mutagenesis procedure to isolate ΔflbB mutants unable to conidiate under these stress conditions. Transformation of mutant FLIP166 with a wild-type genomic library led to the identification of the putative transcription factor SocA as a multicopy suppressor of the FLIP (Fluffy, aconidial, In Phosphate) phenotype. Deregulation of socA altered both growth and developmental patterns. Sequencing of the FLIP166 genome enabled the identification and characterization of PmtCP282L as the recessive mutant form responsible for the FLIP phenotype. Overall, results validate this strategy for identifying genes/mutations related to the control of conidiation.
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884
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Strygina KV, Khlestkina EK. Structural and Functional Organization and Evolution of the WD40 Genes Involved in the Regulation of Flavonoid Biosynthesis in the Triticeae Tribe. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419110152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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885
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Zhang Z, Liu W, Ma Z, Zhu W, Jia L. Transcriptional characterization and response to defense elicitors of mevalonate pathway genes in cotton ( Gossypium arboreum L.). PeerJ 2019; 7:e8123. [PMID: 31768304 PMCID: PMC6874856 DOI: 10.7717/peerj.8123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/30/2019] [Indexed: 01/21/2023] Open
Abstract
The mevalonate (MVA) pathway is responsible for the biosynthesis of cytosolic terpenes including gossypol and its derivatives, which play an important role in the cotton plant’s defense against pathogens and herbivores. In this study, we identified and cloned 17 potentially functional genes encoding enzymes that catalyze the six steps of the MVA pathway in Gossypium arboreum. Expression pattern analysis by qRT-PCR demonstrated that these genes had tissue-specific expression profiles and were most prevalently expressed in roots. Moreover, these genes were up-regulated in response to several elicitors, including methyl jasmonate and salicylic acid, as well as Verticillium dahliae infection and Helicoverpa armigera infestation. This indicates that the MVA pathway genes are involved in the signaling pathway regulated by exogenous hormones and the resistance of cotton plants to pathogens and herbivores. Our results improve the understanding of cytosolic terpene biosynthesis in Gossypium species and lay the foundation for further research on gossypol biosynthesis.
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Affiliation(s)
- Zhiqiang Zhang
- Collaborative Innovation Center of Henan Grain Crops/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Wei Liu
- Collaborative Innovation Center of Henan Grain Crops/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Zongbin Ma
- Collaborative Innovation Center of Henan Grain Crops/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Wei Zhu
- Collaborative Innovation Center of Henan Grain Crops/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Lin Jia
- Collaborative Innovation Center of Henan Grain Crops/Agronomy College, Henan Agricultural University, Zhengzhou, China
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886
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The Resurgence of Dirigent Story: Time for a Bacterial Chapter. Curr Microbiol 2019; 77:517-521. [PMID: 31728698 DOI: 10.1007/s00284-019-01809-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/04/2019] [Indexed: 01/16/2023]
Abstract
For several decades, dirigent (DIR) domain-containing proteins have been assumed to be green lineage-specific, responsible for the defence response and lignan/lignin biosynthesis. Despite their high potential in terms of biotechnology and chemistry, to date there have been very few well-studied plant DIRs. However, recent achievements in sequencing technologies have allowed for discovery of DIR genes in bacteria. This prospective study suggests expansion of the focus of research to consider the existence of bacterial DIRs. It also considers the outlook for understanding DIR functioning with respect to the fields of green lineage evolution, organic synthesis, and biotechnology.
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887
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Vermassen A, Talon R, Andant C, Provot C, Desvaux M, Leroy S. Cell-Wall Hydrolases as Antimicrobials against Staphylococcus Species: Focus on Sle1. Microorganisms 2019; 7:microorganisms7110559. [PMID: 31726796 PMCID: PMC6921076 DOI: 10.3390/microorganisms7110559] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 12/29/2022] Open
Abstract
Some staphylococcal species are opportunistic pathogens of humans and/or animals with Staphylococcus epidermidis as one of the most important. It causes a broad spectrum of diseases in humans and animals. This species is able to form biofilms and has developed antibiotic resistance, which has motivated research on new antibacterial agents. Cell-wall hydrolases (CWHs) can constitute a potential alternative. Following a hijacking strategy, we inventoried the CWHs of S. epidermidis. The lytic potential of representative CWHs that could be turned against staphylococci was explored by turbidity assays which revealed that cell wall glycosidases were not efficient, while cell wall amidases and cell wall peptidases were able to lyse S. epidermidis. Sle1, which is encoded by chromosomal gene and composed of three anchoring LysM domains and a C-terminal CHAP (cysteine, histidine-dependent amidohydrolase/peptidase) domain, was one of the most active CWHs. The phylogeny of Sle1 revealed seven clusters mostly identified among staphylococci. Sle1 was able to lyse several staphylococcal species, including Staphylococcus aureus, both in planktonic and sessile forms, but not Micrococcus.
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Affiliation(s)
- Aurore Vermassen
- Université Clermont-Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France; (A.V.); (R.T.); (C.A.); (M.D.)
| | - Régine Talon
- Université Clermont-Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France; (A.V.); (R.T.); (C.A.); (M.D.)
| | - Carine Andant
- Université Clermont-Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France; (A.V.); (R.T.); (C.A.); (M.D.)
| | - Christian Provot
- BioFilm Control, Biopôle Clermont Limagne, F-63360 Saint-Beauzire, France;
| | - Mickaël Desvaux
- Université Clermont-Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France; (A.V.); (R.T.); (C.A.); (M.D.)
| | - Sabine Leroy
- Université Clermont-Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France; (A.V.); (R.T.); (C.A.); (M.D.)
- Correspondence:
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888
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Vasylkivska M, Jureckova K, Branska B, Sedlar K, Kolek J, Provaznik I, Patakova P. Transcriptional analysis of amino acid, metal ion, vitamin and carbohydrate uptake in butanol-producing Clostridium beijerinckii NRRL B-598. PLoS One 2019; 14:e0224560. [PMID: 31697692 PMCID: PMC6837493 DOI: 10.1371/journal.pone.0224560] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/16/2019] [Indexed: 11/19/2022] Open
Abstract
In-depth knowledge of cell metabolism and nutrient uptake mechanisms can lead to the development of a tool for improving acetone-butanol-ethanol (ABE) fermentation performance and help to overcome bottlenecks in the process, such as the high cost of substrates and low production rates. Over 300 genes potentially encoding transport of amino acids, metal ions, vitamins and carbohydrates were identified in the genome of the butanol-producing strain Clostridium beijerinckii NRRL B-598, based on similarity searches in protein function databases. Transcriptomic data of the genes were obtained during ABE fermentation by RNA-Seq experiments and covered acidogenesis, solventogenesis and sporulation. The physiological roles of the selected 81 actively expressed transport genes were established on the basis of their expression profiles at particular stages of ABE fermentation. This article describes how genes encoding the uptake of glucose, iron, riboflavin, glutamine, methionine and other nutrients take part in growth, production and stress responses of C. beijerinckii NRRL B-598. These data increase our knowledge of transport mechanisms in solventogenic Clostridium and may be used in the selection of individual genes for further research.
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Affiliation(s)
- Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
- * E-mail:
| | - Katerina Jureckova
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Karel Sedlar
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Jan Kolek
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Ivo Provaznik
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
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889
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Abildgaard AB, Stein A, Nielsen SV, Schultz-Knudsen K, Papaleo E, Shrikhande A, Hoffmann ER, Bernstein I, Gerdes AM, Takahashi M, Ishioka C, Lindorff-Larsen K, Hartmann-Petersen R. Computational and cellular studies reveal structural destabilization and degradation of MLH1 variants in Lynch syndrome. eLife 2019; 8:e49138. [PMID: 31697235 PMCID: PMC6837844 DOI: 10.7554/elife.49138] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022] Open
Abstract
Defective mismatch repair leads to increased mutation rates, and germline loss-of-function variants in the repair component MLH1 cause the hereditary cancer predisposition disorder known as Lynch syndrome. Early diagnosis is important, but complicated by many variants being of unknown significance. Here we show that a majority of the disease-linked MLH1 variants we studied are present at reduced cellular levels. We show that destabilized MLH1 variants are targeted for chaperone-assisted proteasomal degradation, resulting also in degradation of co-factors PMS1 and PMS2. In silico saturation mutagenesis and computational predictions of thermodynamic stability of MLH1 missense variants revealed a correlation between structural destabilization, reduced steady-state levels and loss-of-function. Thus, we suggest that loss of stability and cellular degradation is an important mechanism underlying many MLH1 variants in Lynch syndrome. Combined with analyses of conservation, the thermodynamic stability predictions separate disease-linked from benign MLH1 variants, and therefore hold potential for Lynch syndrome diagnostics.
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Affiliation(s)
- Amanda B Abildgaard
- Department of Biology, The Linderstrøm-Lang Centre for Protein ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Amelie Stein
- Department of Biology, The Linderstrøm-Lang Centre for Protein ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Sofie V Nielsen
- Department of Biology, The Linderstrøm-Lang Centre for Protein ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Katrine Schultz-Knudsen
- Department of Biology, The Linderstrøm-Lang Centre for Protein ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Elena Papaleo
- Department of Biology, The Linderstrøm-Lang Centre for Protein ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Amruta Shrikhande
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Eva R Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Inge Bernstein
- Department of Surgical GastroenterologyAalborg University HospitalAalborgDenmark
| | | | - Masanobu Takahashi
- Department of Medical OncologyTohoku University Hospital, Tohoku UniversitySendaiJapan
| | - Chikashi Ishioka
- Department of Medical OncologyTohoku University Hospital, Tohoku UniversitySendaiJapan
| | - Kresten Lindorff-Larsen
- Department of Biology, The Linderstrøm-Lang Centre for Protein ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Rasmus Hartmann-Petersen
- Department of Biology, The Linderstrøm-Lang Centre for Protein ScienceUniversity of CopenhagenCopenhagenDenmark
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890
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Öhlund P, Hayer J, Lundén H, Hesson JC, Blomström AL. Viromics Reveal a Number of Novel RNA Viruses in Swedish Mosquitoes. Viruses 2019; 11:v11111027. [PMID: 31694175 PMCID: PMC6893623 DOI: 10.3390/v11111027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 10/31/2019] [Accepted: 11/02/2019] [Indexed: 02/06/2023] Open
Abstract
Metagenomic studies of mosquitoes have revealed that their virome is far more diverse and includes many more viruses than just the pathogenic arboviruses vectored by mosquitoes. In this study, the virome of 953 female mosquitoes collected in the summer of 2017, representing six mosquito species from two geographic locations in Mid-Eastern Sweden, were characterized. In addition, the near-complete genome of nine RNA viruses were characterized and phylogenetically analysed. These viruses showed association to the viral orders Bunyavirales, Picornavirales, Articulavirales, and Tymovirales, and to the realm Ribovira. Hence, through this study, we expand the knowledge of the virome composition of different mosquito species in Sweden. In addition, by providing viral reference genomes from wider geographic regions and different mosquito species, future in silico recognition and assembly of viral genomes in metagenomic datasets will be facilitated.
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Affiliation(s)
- Pontus Öhlund
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07 Uppsala, Sweden; (H.L.); (A.-L.B.)
- Correspondence: ; Tel.: +46-18-672-409
| | - Juliette Hayer
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SLU-Global Bioinformatics Centre, Box 7023, 750 07 Uppsala, Sweden;
| | - Hanna Lundén
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07 Uppsala, Sweden; (H.L.); (A.-L.B.)
| | - Jenny C. Hesson
- Department of Medical Biochemistry and Microbiology/Zoonosis Science Center, Uppsala University, Box 582, 751 23 Uppsala, Sweden;
| | - Anne-Lie Blomström
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07 Uppsala, Sweden; (H.L.); (A.-L.B.)
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891
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Martelly W, Fellows B, Senior K, Marlowe T, Sharma S. Identification of a noncanonical RNA binding domain in the U2 snRNP protein SF3A1. RNA (NEW YORK, N.Y.) 2019; 25:1509-1521. [PMID: 31383795 PMCID: PMC6795144 DOI: 10.1261/rna.072256.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/31/2019] [Indexed: 06/10/2023]
Abstract
During splicing of pre-mRNA, 5' and 3' splice sites are brought within proximity by interactions between the pre-mRNA bound U1 and U2 snRNPs, followed by recruitment of the tri-snRNP for assembly of the mature spliceosome. Previously, we identified an interaction between the U2 snRNP-specific protein SF3A1 and the stem-loop 4 (SL4) of the U1 snRNA that occurs during the early steps of spliceosome assembly. Although harboring many annotated domains, SF3A1 lacks a canonical RNA binding domain. To identify the U1-SL4 binding region in SF3A1, we expressed amino- and carboxy-terminal deletion constructs using a HeLa cell-based cell free expression system. UV-crosslinking of the truncated proteins with 32P-U1-SL4 RNA identified the carboxy-terminal ubiquitin-like (UBL) domain of SF3A1 as the RNA binding region. Characterization of the interaction between SF3A1-UBL and U1-SL4 by electrophoretic mobility shift assay and surface plasmon resonance determined high binding affinity (KD = ∼97 nM), and revealed the double-stranded G-C rich stem of U1-SL4 as an important feature for binding to the UBL domain. Further, mutations of two conserved tyrosine residues, Y772 and Y773, were found to cause a two- and fivefold decrease in the binding affinity for U1-SL4, respectively. Finally, we found that SF3A1-UBL can specifically pull down the U1 snRNP from HeLa nuclear extract, demonstrating its capacity to bind U1-SL4 in the context of the intact snRNP. Thus, the data show that the UBL domain of SF3A1 can function as an RNA binding domain and that mutations in this region may interfere with U1-SL4 binding.
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Affiliation(s)
- William Martelly
- Department of Basic Medical Sciences, University of Arizona, College of Medicine-Phoenix, Phoenix, Arizona 85004, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Bernice Fellows
- Department of Basic Medical Sciences, University of Arizona, College of Medicine-Phoenix, Phoenix, Arizona 85004, USA
| | - Kristen Senior
- Department of Basic Medical Sciences, University of Arizona, College of Medicine-Phoenix, Phoenix, Arizona 85004, USA
| | - Tim Marlowe
- Molecular Analysis Core, University of Arizona, College of Medicine-Phoenix, Phoenix, Arizona 85004, USA
| | - Shalini Sharma
- Department of Basic Medical Sciences, University of Arizona, College of Medicine-Phoenix, Phoenix, Arizona 85004, USA
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892
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Dong MY, Fan XW, Li YZ. Cassava AGPase genes and their encoded proteins are different from those of other plants. PLANTA 2019; 250:1621-1635. [PMID: 31399791 DOI: 10.1007/s00425-019-03247-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/21/2019] [Indexed: 05/10/2023]
Abstract
Cassava AGPase and AGPase genes have some unique characteristics. ADP-glucose pyrophosphorylase (AGPase) is a rate-limiting enzyme for starch synthesis. In this study, cassava AGPase genes (MeAGP) were analyzed based on six cultivars and one wild species. A total of seven MeAGPs was identified, including four encoding AGPase large subunits (MeAGPLs 1, 2, 3 and 4) and three encoding AGPase small subunits (MeAGPSs 1, 2 and 3). The copy number of MeAGPs varied in cassava germplasm materials. There were 14 introns for MeAGPLs 1, 2 and 3, 13 introns for MeAGPL4, and 8 introns for other three MeAGPSs. Multiple conservative amino acid sequence motifs were found in the MeAGPs. There were differences in amino acids at binding sites of substrates and regulators among different MeAGP subunits and between MeAGPs and a potato AGPase small subunit (1YP2:B). MeAGPs were all located in chloroplasts. MeAGP expression was not only associated with gene copy number and types/combinations, regions and levels of the DNA methylation but was also affected by environmental factors with the involvement of various transcription factors in multiple regulation networks and in various cis-elements in the gene promoter regions. The MeAGP activity also changed with environmental conditions and had potential differences among the subunits. Taken together, MeAGPs differ in number from those of Arabidopsis, potato, maize, banana, sweet potato, and tomato.
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Affiliation(s)
- Ming-You Dong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, China
| | - Xian-Wei Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, China
| | - You-Zhi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, China.
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893
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Davis MN, Horne-Badovinac S, Naba A. In-silico definition of the Drosophila melanogaster matrisome. Matrix Biol Plus 2019; 4:100015. [PMID: 33543012 PMCID: PMC7852309 DOI: 10.1016/j.mbplus.2019.100015] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 01/02/2023] Open
Abstract
The extracellular matrix (ECM) is an assembly of hundreds of proteins that structurally supports the cells it surrounds and biochemically regulates their functions. Drosophila melanogaster has emerged as a powerful model organism to study fundamental mechanisms underlying ECM protein secretion, ECM assembly, and ECM roles in pathophysiological processes. However, as of today, we do not possess a well-defined list of the components forming the ECM of this organism. We previously reported the development of computational pipelines to define the matrisome - the ensemble of genes encoding ECM and ECM-associated proteins - of humans, mice, zebrafish and C. elegans. Using a similar approach, we report here that our pipeline has identified 641 genes constituting the Drosophila matrisome. We further classify these genes into different structural and functional categories, including an expanded way to classify genes encoding proteins forming apical ECMs. We illustrate how having a comprehensive list of Drosophila matrisome proteins can be used to annotate large proteomic datasets and identify unsuspected roles for the ECM in pathophysiological processes. Last, to aid the dissemination and usage of the proposed definition and categorization of the Drosophila matrisome by the scientific community, our list has been made available through three public portals: The Matrisome Project (http://matrisome.org), The FlyBase (https://flybase.org/), and GLAD (https://www.flyrnai.org/tools/glad/web/).
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Affiliation(s)
- Martin N. Davis
- Department of Physiology and Biophysics, University of Illinois at Chicago, 835 S. Wolcott Avenue, Chicago, IL 60612, USA
| | - Sally Horne-Badovinac
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, 835 S. Wolcott Avenue, Chicago, IL 60612, USA
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894
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Otamendi A, Perez-de-Nanclares-Arregi E, Oiartzabal-Arano E, Cortese MS, Espeso EA, Etxebeste O. Developmental regulators FlbE/D orchestrate the polarity site-to-nucleus dynamics of the fungal bZIP transcription factor FlbB. Cell Mol Life Sci 2019; 76:4369-4390. [PMID: 31065746 PMCID: PMC11105705 DOI: 10.1007/s00018-019-03121-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 04/17/2019] [Accepted: 04/29/2019] [Indexed: 12/19/2022]
Abstract
Permanently polarized cells have developed transduction mechanisms linking polarity sites with gene regulation in the nucleus. In neurons, one mechanism is based on long-distance retrograde migration of transcription factors (TFs). Aspergillus nidulans FlbB is the only known fungal TF shown to migrate retrogradely to nuclei from the polarized region of fungal cells known as hyphae. There, FlbB controls developmental transitions by triggering the production of asexual multicellular structures. FlbB dynamics in hyphae is orchestrated by regulators FlbE and FlbD. At least three FlbE domains are involved in the acropetal transport of FlbB, with a final MyoE/actin filament-dependent step from the subapex to the apex. Experiments employing a T2A viral peptide-containing chimera (FlbE::mRFP::T2A::FlbB::GFP) suggest that apical FlbB/FlbE interaction is inhibited to initiate a dynein-dependent FlbB transport to nuclei. FlbD controls the nuclear accumulation of FlbB through a cMyb domain and a C-terminal LxxLL motif. Overall, results elucidate a highly dynamic pattern of FlbB interactions, which enable timely developmental induction. Furthermore, this system establishes a reference for TF-based long-distance signaling in permanently polarized cells.
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Affiliation(s)
- Ainara Otamendi
- Biochemistry II Laboratory, Department of Applied Chemistry, Faculty of Chemistry, University of The Basque Country, Manuel de Lardizabal, 3, 20018, San Sebastian, Spain
| | - Elixabet Perez-de-Nanclares-Arregi
- Biochemistry II Laboratory, Department of Applied Chemistry, Faculty of Chemistry, University of The Basque Country, Manuel de Lardizabal, 3, 20018, San Sebastian, Spain
| | - Elixabet Oiartzabal-Arano
- Biochemistry II Laboratory, Department of Applied Chemistry, Faculty of Chemistry, University of The Basque Country, Manuel de Lardizabal, 3, 20018, San Sebastian, Spain
| | - Marc S Cortese
- Biochemistry II Laboratory, Department of Applied Chemistry, Faculty of Chemistry, University of The Basque Country, Manuel de Lardizabal, 3, 20018, San Sebastian, Spain
| | - Eduardo A Espeso
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Oier Etxebeste
- Biochemistry II Laboratory, Department of Applied Chemistry, Faculty of Chemistry, University of The Basque Country, Manuel de Lardizabal, 3, 20018, San Sebastian, Spain.
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895
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Busch JD, Cipullo M, Atanassov I, Bratic A, Silva Ramos E, Schöndorf T, Li X, Pearce SF, Milenkovic D, Rorbach J, Larsson NG. MitoRibo-Tag Mice Provide a Tool for In Vivo Studies of Mitoribosome Composition. Cell Rep 2019; 29:1728-1738.e9. [PMID: 31693908 PMCID: PMC6859486 DOI: 10.1016/j.celrep.2019.09.080] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/14/2019] [Accepted: 09/26/2019] [Indexed: 11/16/2022] Open
Abstract
Mitochondria harbor specialized ribosomes (mitoribosomes) necessary for the synthesis of key membrane proteins of the oxidative phosphorylation (OXPHOS) machinery located in the mitochondrial inner membrane. To date, no animal model exists to study mitoribosome composition and mitochondrial translation coordination in mammals in vivo. Here, we create MitoRibo-Tag mice as a tool enabling affinity purification and proteomics analyses of mitoribosomes and their interactome in different tissues. We also define the composition of an assembly intermediate formed in the absence of MTERF4, necessary for a late step in mitoribosomal biogenesis. We identify the orphan protein PUSL1, which interacts with a large subunit assembly intermediate, and demonstrate that it is an inner-membrane-associated mitochondrial matrix protein required for efficient mitochondrial translation. This work establishes MitoRibo-Tag mice as a powerful tool to study mitoribosomes in vivo, enabling future studies on the mitoribosome interactome under different physiological states, as well as in disease and aging. MitoRibo-Tag mice with a tag on mL62 were generated to study mitoribosomes in vivo The mitoribosome interactome of different mouse tissues was defined with proteomics PUSL1 was identified as a mitoribosome-interacting protein using MitoRibo-Tag mice MitoRibo-Tag mice allow mitoribosome analysis under different conditions and setups
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Affiliation(s)
- Jakob D Busch
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany; Faculty of Mathematics and Natural Sciences, University of Cologne, Albertus-Magnus-Platz, 50923 Cologne, Germany
| | - Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Research Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden; Max-Planck-Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Ilian Atanassov
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Ana Bratic
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Eduardo Silva Ramos
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Thomas Schöndorf
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany; Faculty of Mathematics and Natural Sciences, University of Cologne, Albertus-Magnus-Platz, 50923 Cologne, Germany
| | - Xinping Li
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Sarah F Pearce
- Department of Medical Biochemistry and Biophysics, Research Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden; Max-Planck-Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Dusanka Milenkovic
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Research Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden; Max-Planck-Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany; Department of Medical Biochemistry and Biophysics, Research Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden; Max-Planck-Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.
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896
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The subcellular localization of bHLH transcription factor TCF4 is mediated by multiple nuclear localization and nuclear export signals. Sci Rep 2019; 9:15629. [PMID: 31666615 PMCID: PMC6821749 DOI: 10.1038/s41598-019-52239-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/11/2019] [Indexed: 01/10/2023] Open
Abstract
Transcription factor 4 (TCF4) is a class I basic helix-loop-helix (bHLH) transcription factor which regulates the neurogenesis and specialization of cells. TCF4 also plays an important role in the development and functioning of the immune system. Additionally, TCF4 regulates the development of Sertoli cells and pontine nucleus neurons, myogenesis, melanogenesis and epithelial-mesenchymal transition. The ability of transcription factors to fulfil their function often depends on their intracellular trafficking between the nucleus and cytoplasm of the cell. The trafficking is regulated by specific sequences, i.e. the nuclear localization signal (NLS) and the nuclear export signal (NES). We performed research on the TCF4 trafficking regulating sequences by mapping and detailed characterization of motifs potentially acting as the NLS or NES. We demonstrate that the bHLH domain of TCF4 contains an NLS that overlaps two NESs. The results of in silico analyses show high conservation of the sequences, especially in the area of the NLS and NESs. This high conservation is not only between mouse and human TCF4, but also between TCF4 and other mammalian E proteins, indicating the importance of these sequences for the functioning of bHLH class I transcription factors.
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897
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Biological plasticity rescues target activity in CRISPR knock outs. Nat Methods 2019; 16:1087-1093. [PMID: 31659326 DOI: 10.1038/s41592-019-0614-5] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/11/2019] [Indexed: 12/26/2022]
Abstract
Gene knock outs (KOs) are efficiently engineered through CRISPR-Cas9-induced frameshift mutations. While the efficiency of DNA editing is readily verified by DNA sequencing, a systematic understanding of the efficiency of protein elimination has been lacking. Here we devised an experimental strategy combining RNA sequencing and triple-stage mass spectrometry to characterize 193 genetically verified deletions targeting 136 distinct genes generated by CRISPR-induced frameshifts in HAP1 cells. We observed residual protein expression for about one third of the quantified targets, at variable levels from low to original, and identified two causal mechanisms, translation reinitiation leading to N-terminally truncated target proteins or skipping of the edited exon leading to protein isoforms with internal sequence deletions. Detailed analysis of three truncated targets, BRD4, DNMT1 and NGLY1, revealed partial preservation of protein function. Our results imply that systematic characterization of residual protein expression or function in CRISPR-Cas9-generated KO lines is necessary for phenotype interpretation.
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898
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Crystal structure of the catalytic unit of GH 87-type α-1,3-glucanase Agl-KA from Bacillus circulans. Sci Rep 2019; 9:15295. [PMID: 31653959 PMCID: PMC6814745 DOI: 10.1038/s41598-019-51822-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/08/2019] [Indexed: 11/09/2022] Open
Abstract
Glycoside hydrolase (GH) 87-type α-1,3-glucanase hydrolyses the α-1,3-glucoside linkages of α-1,3-glucan, which is found in fungal cell walls and extracellular polysaccharides produced by oral Streptococci. In this study, we report on the molecular structure of the catalytic unit of GH 87-type α-1,3-glucanase, Agl-KA, from Bacillus circulans, as determined by x-ray crystallography at a resolution of 1.82 Å. The catalytic unit constitutes a complex structure of two tandemly connected domains-the N-terminal galactose-binding-like domain and the C-terminal right-handed β-helix domain. While the β-helix domain is widely found among polysaccharide-processing enzymes, complex formation with the galactose-binding-like domain was observed for the first time. Biochemical assays showed that Asp1067, Asp1090 and Asp1091 are important for catalysis, and these residues are indeed located at the putative substrate-binding cleft, which forms a closed end and explains the product specificity.
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899
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Bartholomew ES, Black K, Feng Z, Liu W, Shan N, Zhang X, Wu L, Bailey L, Zhu N, Qi C, Ren H, Liu X. Comprehensive Analysis of the Chitinase Gene Family in Cucumber ( Cucumis sativus L.): From Gene Identification and Evolution to Expression in Response to Fusarium oxysporum. Int J Mol Sci 2019; 20:E5309. [PMID: 31731414 PMCID: PMC6861899 DOI: 10.3390/ijms20215309] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/15/2019] [Accepted: 10/17/2019] [Indexed: 12/25/2022] Open
Abstract
Chitinases, a subgroup of pathogenesis-related proteins, are responsible for catalyzing the hydrolysis of chitin. Accumulating reports indicate that chitinases play a key role in plant defense against chitin-containing pathogens and are therefore good targets for defense response studies. Here, we undertook an integrated bioinformatic and expression analysis of the cucumber chitinases gene family to identify its role in defense against Fusarium oxysporum f. sp. cucumerinum. A total of 28 putative chitinase genes were identified in the cucumber genome and classified into five classes based on their conserved catalytic and binding domains. The expansion of the chitinase gene family was due mainly to tandem duplication events. The expression pattern of chitinase genes was organ-specific and 14 genes were differentially expressed in response to F. oxysporum challenge of fusarium wilt-susceptible and resistant lines. Furthermore, a class I chitinase, CsChi23, was constitutively expressed at high levels in the resistant line and may play a crucial role in building a basal defense and activating a rapid immune response against F. oxysporum. Whole-genome re-sequencing of both lines provided clues for the diverse expression patterns observed. Collectively, these results provide useful genetic resource and offer insights into the role of chitinases in cucumber-F. oxysporum interaction.
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Affiliation(s)
- Ezra S. Bartholomew
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Kezia Black
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Zhongxuan Feng
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Wan Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Nan Shan
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Xiao Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Licai Wu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Latoya Bailey
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Ning Zhu
- Changping Agricultural Technology Service Center, Beijing 102200, China; (N.Z.); (C.Q.)
| | - Changhong Qi
- Changping Agricultural Technology Service Center, Beijing 102200, China; (N.Z.); (C.Q.)
| | - Huazhong Ren
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Xingwang Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
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900
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Tóth T, Gyula P, Salamon P, Kis S, Sós-Hegedűs A, Szittya G. Molecular characterization and In Vitro synthesis of infectious RNA of a Turnip vein-clearing virus isolated from Alliaria petiolata in Hungary. PLoS One 2019; 14:e0224398. [PMID: 31648277 PMCID: PMC6812821 DOI: 10.1371/journal.pone.0224398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/11/2019] [Indexed: 11/18/2022] Open
Abstract
A tobamovirus was isolated from leaves of Alliaria petiolata plants, showing vein-clearing, interveinal chlorosis, and moderate deformation. Host range experiments revealed a high similarity of isolate ApH both to ribgrass mosaic viruses and turnip vein-clearing viruses. The complete nucleotide sequence of the viral genome was determined. The genomic RNA is composed of 6312 nucleotides and contains four open reading frames (ORF). ORF1 is 3324 nt-long and encodes a polypeptide of about 125.3 kDa. The ORF1 encoded putative replication protein contains an Alphavirus-like methyltransferase domain. ORF2 is 4806 nt-long and encodes a polypeptide of about 182 kDa. The ORF2 encoded putative replication protein contains an RNA-dependent RNA polymerase, catalytic domain. ORF3 encodes the putative cell-to-cell movement protein with a molecular weight of 30.1 kDa. ORF4 overlaps with ORF3 and encodes the coat protein with a size of 17.5 kDa. Sequence comparisons revealed that the ApH isolate has the highest similarity to turnip vein-clearing viruses and should be considered an isolate of Turnip vein-clearing virus (TVCV). This is the first report on the occurrence of TVCV in Hungary. In vitro transcripts prepared from the full-length cDNA clone of TVCV-ApH were highly infectious and induced typical symptoms characteristic to the original isolate of the virus. Since infectious clones of TVCV-ApH and crTMV (another isolate of TVCV) markedly differed in respect to recovery phenotype in Arabidopsis thaliana, it is feasible to carry out gene exchange or mutational studies to determine viral factors responsible for the symptom recovery phenotype.
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Affiliation(s)
- Tamás Tóth
- Department of Plant Biotechnology, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Gödöllő, Hungary
| | - Péter Gyula
- Department of Plant Biotechnology, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Gödöllő, Hungary
- * E-mail: (GS); (PG)
| | - Pál Salamon
- Department of Genetics, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Gödöllő, Hungary
| | - Szilvia Kis
- Department of Plant Biotechnology, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Gödöllő, Hungary
| | - Anita Sós-Hegedűs
- Department of Plant Biotechnology, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Gödöllő, Hungary
| | - György Szittya
- Department of Plant Biotechnology, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Gödöllő, Hungary
- * E-mail: (GS); (PG)
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