1
|
Araujo-Abad S, Rizzuti B, Vidal M, Abian O, Fárez-Vidal ME, Velazquez-Campoy A, de Juan Romero C, Neira JL. Unveiling the Binding between the Armadillo-Repeat Domain of Plakophilin 1 and the Intrinsically Disordered Transcriptional Repressor RYBP. Biomolecules 2024; 14:561. [PMID: 38785968 PMCID: PMC11117474 DOI: 10.3390/biom14050561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 04/29/2024] [Accepted: 05/04/2024] [Indexed: 05/25/2024] Open
Abstract
Plakophilin 1 (PKP1), a member of the p120ctn subfamily of the armadillo (ARM)-repeat-containing proteins, is an important structural component of cell-cell adhesion scaffolds although it can also be ubiquitously found in the cytoplasm and the nucleus. RYBP (RING 1A and YY1 binding protein) is a multifunctional intrinsically disordered protein (IDP) best described as a transcriptional regulator. Both proteins are involved in the development and metastasis of several types of tumors. We studied the binding of the armadillo domain of PKP1 (ARM-PKP1) with RYBP by using in cellulo methods, namely immunofluorescence (IF) and proximity ligation assay (PLA), and in vitro biophysical techniques, namely fluorescence, far-ultraviolet (far-UV) circular dichroism (CD), and isothermal titration calorimetry (ITC). We also characterized the binding of the two proteins by using in silico experiments. Our results showed that there was binding in tumor and non-tumoral cell lines. Binding in vitro between the two proteins was also monitored and found to occur with a dissociation constant in the low micromolar range (~10 μM). Finally, in silico experiments provided additional information on the possible structure of the binding complex, especially on the binding ARM-PKP1 hot-spot. Our findings suggest that RYBP might be a rescuer of the high expression of PKP1 in tumors, where it could decrease the epithelial-mesenchymal transition in some cancer cells.
Collapse
Affiliation(s)
- Salome Araujo-Abad
- Cancer Research Group, Faculty of Engineering and Applied Sciences, Universidad de Las Américas, 170124 Quito, Ecuador;
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Spain
| | - Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy;
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
| | - Miguel Vidal
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Calle Ramiro de Maeztu, 9, 28040 Madrid, Spain;
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - María Esther Fárez-Vidal
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Facultad de Medicina, Universidad de Granada, 18016 Granada, Spain;
- Instituto de Investigación Biomédica IBS, Granada, Complejo Hospitalario Universitario de Granada, Universidad de Granada, 18071 Granada, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Camino de Juan Romero
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Spain
- Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l’Almazara 11, 03203 Elche, Spain
| | - José L. Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
| |
Collapse
|
2
|
Wang S, Ma T, Xia X, Zhang L. Evolutionary insights and functional diversity of gasdermin family proteins and homologs in microorganisms. Front Immunol 2024; 15:1371611. [PMID: 38571940 PMCID: PMC10989679 DOI: 10.3389/fimmu.2024.1371611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024] Open
Abstract
The gasdermin protein family and its homologs in microorganisms have gained significant attention due to their roles in programmed cell death, immune defense, and microbial infection. This review summarizes the current research status of gasdermin proteins, their structural features, and functional roles in fungi, bacteria, and viruses. The review presents evolutionary parallels between mammalian and microbial defense systems, highlighting the conserved role of gasdermin proteins in regulating cell death processes and immunity. Additionally, the structural and functional characteristics of gasdermin homologs in microorganisms are summarized, shedding light on their potential as targets for therapeutic interventions. Future research directions in this field are also discussed to provide a roadmap for further investigation.
Collapse
Affiliation(s)
- Shule Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- School of Clinical Medicine, Shandong Second Medical University, Weifang, Shandong, China
| | - Tingbo Ma
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- School of Clinical Medicine, Shandong Second Medical University, Weifang, Shandong, China
| | - Xiaoyi Xia
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Leiliang Zhang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| |
Collapse
|
3
|
Penner TV, Lorente Cobo N, Patel DT, Patel DH, Savchenko A, Brassinga AKC, Prehna G. Structural characterization of the Sel1-like repeat protein LceB from Legionella pneumophila. Protein Sci 2024; 33:e4889. [PMID: 38160319 PMCID: PMC10868440 DOI: 10.1002/pro.4889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Legionella are freshwater Gram-negative bacteria that in their normal environment infect protozoa. However, this adaptation also allows Legionella to infect human alveolar macrophages and cause pneumonia. Central to Legionella pathogenesis are more than 330 secreted effectors, of which there are nine core effectors that are conserved in all pathogenic species. Despite their importance, the biochemical function of several core effectors remains unclear. To address this, we have taken a structural approach to characterize the core effector of unknown function LceB, or Lpg1356, from Legionella pneumophila. Here, we solve an X-ray crystal structure of LceB using an AlphaFold model for molecular replacement. The experimental structure shows that LceB adopts a Sel1-like repeat (SLR) fold as predicted. However, the crystal structure captured multiple conformations of LceB, all of which differed from the AlphaFold model. A comparison of the predicted model and the experimental models suggests that LceB is highly flexible in solution. Additionally, the molecular analysis of LceB using its close structural homologs reveals sequence and structural motifs of known biochemical function. Specifically, LceB harbors a repeated KAAEQG motif that both stabilizes the SLR fold and is known to participate in protein-protein interactions with eukaryotic host proteins. We also observe that LceB forms several higher-order oligomers in solution. Overall, our results have revealed that LceB has conformational flexibility, self-associates, and contains a molecular surface for binding a target host-cell protein. Additionally, our data provides structural insights into the SLR family of proteins that remain poorly studied.
Collapse
Affiliation(s)
- Tiffany V Penner
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Neil Lorente Cobo
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Deepak T Patel
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Dhruvin H Patel
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | | | - Gerd Prehna
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| |
Collapse
|
4
|
Doyle LA, Takushi B, Kibler RD, Milles LF, Orozco CT, Jones JD, Jackson SE, Stoddard BL, Bradley P. De novo design of knotted tandem repeat proteins. Nat Commun 2023; 14:6746. [PMID: 37875492 PMCID: PMC10598012 DOI: 10.1038/s41467-023-42388-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023] Open
Abstract
De novo protein design methods can create proteins with folds not yet seen in nature. These methods largely focus on optimizing the compatibility between the designed sequence and the intended conformation, without explicit consideration of protein folding pathways. Deeply knotted proteins, whose topologies may introduce substantial barriers to folding, thus represent an interesting test case for protein design. Here we report our attempts to design proteins with trefoil (31) and pentafoil (51) knotted topologies. We extended previously described algorithms for tandem repeat protein design in order to construct deeply knotted backbones and matching designed repeat sequences (N = 3 repeats for the trefoil and N = 5 for the pentafoil). We confirmed the intended conformation for the trefoil design by X ray crystallography, and we report here on this protein's structure, stability, and folding behaviour. The pentafoil design misfolded into an asymmetric structure (despite a 5-fold symmetric sequence); two of the four repeat-repeat units matched the designed backbone while the other two diverged to form local contacts, leading to a trefoil rather than pentafoil knotted topology. Our results also provide insights into the folding of knotted proteins.
Collapse
Affiliation(s)
- Lindsey A Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Brittany Takushi
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Ryan D Kibler
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Lukas F Milles
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Carolina T Orozco
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Jonathan D Jones
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Sophie E Jackson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA.
| | - Philip Bradley
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA.
- Division of Public Health Sciences and Program in Computational Biology, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N, Seattle, WA, 98009, USA.
| |
Collapse
|
5
|
Deryusheva EI, Machulin AV, Galzitskaya OV. Diversity and features of proteins with structural repeats. Biophys Rev 2023; 15:1159-1169. [PMID: 37974986 PMCID: PMC10643770 DOI: 10.1007/s12551-023-01130-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/28/2023] [Indexed: 11/19/2023] Open
Abstract
The review provides information on proteins with structural repeats, including their classification, characteristics, functions, and relevance in disease development. It explores methods for identifying structural repeats and specialized databases. The review also highlights the potential use of repeat proteins as drug design scaffolds and discusses their evolutionary mechanisms.
Collapse
Affiliation(s)
- Evgeniya I. Deryusheva
- Institute for Biological Instrumentation, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Russia
| | - Andrey V. Machulin
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Russia
| | - Oxana V. Galzitskaya
- Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Russia
- Institute of Theoretical and Experimental Biophysics of the Russian Academy of Sciences, Pushchino, Russia
| |
Collapse
|
6
|
Zheng Q, Daskalov A. Microbial gasdermins: More than a billion years of pyroptotic-like cell death. Semin Immunol 2023; 69:101813. [PMID: 37480832 DOI: 10.1016/j.smim.2023.101813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/16/2023] [Accepted: 07/17/2023] [Indexed: 07/24/2023]
Abstract
In the recent past, the concept of immunity has been extended to eukaryotic and prokaryotic microorganisms, like fungi and bacteria. The latest findings have drawn remarkable evolutionary parallels between metazoan and microbial defense-related genes, unveiling a growing number of shared transkingdom components of immune systems. One such component is the gasdermin family of pore-forming proteins - executioners of a highly inflammatory immune cell death program in mammals, termed pyroptosis. Pyroptotic cell death limits the spread of intracellular pathogens by eliminating infected cells and coordinates the broader inflammatory response to infection. The microbial gasdermins have similarly been implicated in defense-related cell death reactions in fungi, bacteria and archaea. Moreover, the discovery of the molecular regulators of gasdermin cytotoxicity in fungi and bacteria, has established additional evolutionary links to mammalian pyroptotic pathways. Here, we focus on the gasdermin proteins in microorganisms and their role in organismal defense and provide perspective on this remarkable case study in comparative immunology.
Collapse
Affiliation(s)
- Qi Zheng
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Asen Daskalov
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China; ImmunoConcEpT, CNRS UMR 5164, University of Bordeaux, Bordeaux, France.
| |
Collapse
|
7
|
Abstract
Investigation of fungal biology has been frequently motivated by the fact that many fungal species are important plant and animal pathogens. Such efforts have contributed significantly toward our understanding of fungal pathogenic lifestyles (virulence factors and strategies) and the interplay with host immune systems. In parallel, work on fungal allorecognition systems leading to the characterization of fungal regulated cell death determinants and pathways, has been instrumental for the emergent concept of fungal immunity. The uncovered evolutionary trans-kingdom parallels between fungal regulated cell death pathways and innate immune systems incite us to reflect further on the concept of a fungal immune system. Here, I briefly review key findings that have shaped the fungal immunity paradigm, providing a perspective on what I consider its most glaring knowledge gaps. Undertaking to fill such gaps would establish firmly the fungal immune system inside the broader field of comparative immunology.
Collapse
Affiliation(s)
- Asen Daskalov
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- ImmunoConcEpT, CNRS UMR 5164, University of Bordeaux, Bordeaux, France
- Corresponding author
| |
Collapse
|
8
|
Law CTY, Nivesvivat T, Xiong Q, Kulkeaw K, Shi L, Ruenchit P, Suwanpakdee D, Suwanpakdee P, Tongkrajang N, Sarasombath PT, Tsui SKW. Mitochondrial genome diversity of Balamuthia mandrillaris revealed by a fatal case of granulomatous amoebic encephalitis. Front Microbiol 2023; 14:1162963. [PMID: 37213512 PMCID: PMC10196457 DOI: 10.3389/fmicb.2023.1162963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/06/2023] [Indexed: 05/23/2023] Open
Abstract
Introduction Balamuthia (B.) mandrillaris is a free-living amoeba that can cause rare yet fatal granulomatous amoebic encephalitis (GAE). However, efficacious treatment for GAE is currently unavailable, especially when genomic studies on B. mandrillaris are limited. Methods In this study, B. mandrillaris strain KM-20 was isolated from the brain tissue of a GAE patient, and its mitochondrial genome was de novo assembled using high-coverage Nanopore long reads and Illumina short reads. Results and Discussion Phylogenetic and comparative analyses revealed a range of diversification in the mitochondrial genome of KM-20 and nine other B. mandrillaris strains. According to the mitochondrial genome alignment, one of the most variable regions was observed in the ribosomal protein S3 (rps3), which was caused by an array of novel protein tandem repeats. The repeating units in the rps3 protein tandem region present significant copy number variations (CNVs) among B. mandrillaris strains and suggest KM-20 as the most divergent strain for its highly variable sequence and highest copy number in rps3. Moreover, mitochondrial heteroplasmy was observed in strain V039, and two genotypes of rps3 are caused by the CNVs in the tandem repeats. Taken together, the copy number and sequence variations of the protein tandem repeats enable rps3 to be a perfect target for clinical genotyping assay for B. mandrillaris. The mitochondrial genome diversity of B. mandrillaris paves the way to investigate the phylogeny and diversification of pathogenic amoebae.
Collapse
Affiliation(s)
- Cherie Tsz-Yiu Law
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Thirapa Nivesvivat
- Infectious Disease Unit, Department of Pediatrics, Phramongkutklao Hospital, Bangkok, Thailand
| | - Qing Xiong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Kasem Kulkeaw
- Siriraj Integrative Center for Neglected Parasitic Diseases, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ling Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Pichet Ruenchit
- Siriraj Integrative Center for Neglected Parasitic Diseases, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Detchvijitr Suwanpakdee
- Infectious Disease Unit, Department of Pediatrics, Phramongkutklao Hospital, Bangkok, Thailand
| | - Piradee Suwanpakdee
- Neurology Division, Department of Pediatrics, Phramongkutklao Hospital, Bangkok, Thailand
| | - Nongnat Tongkrajang
- Siriraj Integrative Center for Neglected Parasitic Diseases, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Patsharaporn T. Sarasombath
- Siriraj Integrative Center for Neglected Parasitic Diseases, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Patsharaporn T. Sarasombath, ;
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- *Correspondence: Stephen Kwok-Wing Tsui,
| |
Collapse
|
9
|
Tandon K, Ricci F, Costa J, Medina M, Kühl M, Blackall LL, Verbruggen H. Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera. Gigascience 2022; 12:giac127. [PMID: 36683362 PMCID: PMC9868349 DOI: 10.1093/gigascience/giac127] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/17/2022] [Accepted: 12/22/2022] [Indexed: 01/24/2023] Open
Abstract
At present, our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed toward the millimeter-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals Porites lutea and Isopora palifera, through a compendium of ∼400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 classes. Skeletal microbiomes harbored a diverse array of stress response genes, including dimethylsulfoniopropionate synthesis (dsyB) and metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average of 22 ± 15 genes in P. lutea and 28 ± 23 in I. palifera with eukaryotic-like motifs thought to be involved in maintaining host association. We provide comprehensive insights into the putative functional role of the skeletal microbiome on key metabolic processes such as nitrogen fixation, dissimilatory and assimilatory nitrate, and sulfate reduction. Our study provides critical genomic resources for a better understanding of the coral skeletal microbiome and its role in holobiont functioning.
Collapse
Affiliation(s)
- Kshitij Tandon
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
| | - Francesco Ricci
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
- Biological, Earth and Environmental Sciences, The University of New South Wales, Kensington, NSW 2052, Australia
| | - Joana Costa
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, DK-3000 Helsingør, Denmark
| | - Linda L Blackall
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
| |
Collapse
|
10
|
Garcia L, Molina MC, Padgett-Pagliai KA, Torres PS, Bruna RE, García Véscovi E, González CF, Gadea J, Marano MR. A serralysin-like protein of Candidatus Liberibacter asiaticus modulates components of the bacterial extracellular matrix. Front Microbiol 2022; 13:1006962. [DOI: 10.3389/fmicb.2022.1006962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Huanglongbing (HLB), the current major threat for Citrus species, is caused by intracellular alphaproteobacteria of the genus Candidatus Liberibacter (CaL), with CaL asiaticus (CLas) being the most prevalent species. This bacterium inhabits phloem cells and is transmitted by the psyllid Diaphorina citri. A gene encoding a putative serralysin-like metalloprotease (CLIBASIA_01345) was identified in the CLas genome. The expression levels of this gene were found to be higher in citrus leaves than in psyllids, suggesting a function for this protease in adaptation to the plant environment. Here, we study the putative role of CLas-serralysin (Las1345) as virulence factor. We first assayed whether Las1345 could be secreted by two different surrogate bacteria, Rhizobium leguminosarum bv. viciae A34 (A34) and Serratia marcescens. The protein was detected only in the cellular fraction of A34 and S. marcescens expressing Las1345, and increased protease activity of those bacteria by 2.55 and 4.25-fold, respectively. In contrast, Las1345 expressed in Nicotiana benthamiana leaves did not show protease activity nor alterations in the cell membrane, suggesting that Las1345 do not function as a protease in the plant cell. Las1345 expression negatively regulated cell motility, exopolysaccharide production, and biofilm formation in Xanthomonas campestris pv. campestris (Xcc). This bacterial phenotype was correlated with reduced growth and survival on leaf surfaces as well as reduced disease symptoms in N. benthamiana and Arabidopsis. These results support a model where Las1345 could modify extracellular components to adapt bacterial shape and appendages to the phloem environment, thus contributing to virulence.
Collapse
|
11
|
Berger O, Battistella C, Chen Y, Oktawiec J, Siwicka ZE, Tullman-Ercek D, Wang M, Gianneschi NC. Mussel Adhesive-Inspired Proteomimetic Polymer. J Am Chem Soc 2022; 144:4383-4392. [PMID: 35238544 DOI: 10.1021/jacs.1c10936] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Herein, a synthetic polymer proteomimetic is described that reconstitutes the key structural elements and function of mussel adhesive protein. The proteomimetic was prepared via graft-through ring-opening metathesis polymerization of a norbornenyl-peptide monomer. The peptide was derived from the natural underwater glue produced by marine mussels that is composed of a highly repetitive 10 amino acid tandem repeat sequence. The hypothesis was that recapitulation of the repeating unit in this manner would provide a facile route to a nature-inspired adhesive. To this end, the material, in which the arrangement of peptide units was as side chains on a brush polymer rather than in a linear fashion as in the natural protein, was examined and compared to the native protein. Mechanical measurements of adhesion forces between solid surfaces revealed improved adhesion properties over the natural protein, making this strategy attractive for diverse applications. One such application is demonstrated, using the polymers as a surface adhesive for the immobilization of live cells.
Collapse
Affiliation(s)
- Or Berger
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Claudia Battistella
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Yusu Chen
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Julia Oktawiec
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Zofia E Siwicka
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Muzhou Wang
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Nathan C Gianneschi
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.,Department of Pharmacology, Northwestern University, Chicago, Illinois 60611, United States.,Department of Biomedical Engineering, Northwestern University, Chicago, Illinois 60611, United States.,Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States.,International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States.,Simpson-Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
12
|
Fungal gasdermin-like proteins are controlled by proteolytic cleavage. Proc Natl Acad Sci U S A 2022; 119:2109418119. [PMID: 35135876 PMCID: PMC8851545 DOI: 10.1073/pnas.2109418119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2022] [Indexed: 12/11/2022] Open
Abstract
Gasdermins are a family of pore-forming proteins controlling an inflammatory cell death reaction in the mammalian immune system. The pore-forming ability of the gasdermin proteins is released by proteolytic cleavage with the removal of their inhibitory C-terminal domain. Recently, gasdermin-like proteins have been discovered in fungi and characterized as cell death-inducing toxins in the context of conspecific non-self-discrimination (allorecognition). Although functional analogies have been established between mammalian and fungal gasdermins, the molecular pathways regulating gasdermin activity in fungi remain largely unknown. Here, we characterize a gasdermin-based cell death reaction controlled by the het-Q allorecognition genes in the filamentous fungus Podospora anserina We show that the cytotoxic activity of the HET-Q1 gasdermin is controlled by proteolysis. HET-Q1 loses a ∼5-kDa C-terminal fragment during the cell death reaction in the presence of a subtilisin-like serine protease termed HET-Q2. Mutational analyses and successful reconstitution of the cell death reaction in heterologous hosts (Saccharomyces cerevisiae and human 293T cells) suggest that HET-Q2 directly cleaves HET-Q1 to induce cell death. By analyzing the genomic landscape of het-Q1 homologs in fungi, we uncovered that the vast majority of the gasdermin genes are clustered with protease-encoding genes. These HET-Q2-like proteins carry either subtilisin-like or caspase-related proteases, which, in some cases, correspond to the N-terminal effector domain of nucleotide-binding and oligomerization-like receptor proteins. This study thus reveals the proteolytic regulation of gasdermins in fungi and establishes evolutionary parallels between fungal and mammalian gasdermin-dependent cell death pathways.
Collapse
|
13
|
Araiso Y, Imai K, Endo T. Role of the TOM Complex in Protein Import into Mitochondria: Structural Views. Annu Rev Biochem 2022; 91:679-703. [PMID: 35287471 DOI: 10.1146/annurev-biochem-032620-104527] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mitochondria are central to energy production, metabolism and signaling, and apoptosis. To make new mitochondria from preexisting mitochondria, the cell needs to import mitochondrial proteins from the cytosol into the mitochondria with the aid of translocators in the mitochondrial membranes. The translocase of the outer membrane (TOM) complex, an outer membrane translocator, functions as an entry gate for most mitochondrial proteins. Although high-resolution structures of the receptor subunits of the TOM complex were deposited in the early 2000s, those of entire TOM complexes became available only in 2019. The structural details of these TOM complexes, consisting of the dimer of the β-barrel import channel Tom40 and four α-helical membrane proteins, revealed the presence of several distinct paths and exits for the translocation of over 1,000 different mitochondrial precursor proteins. High-resolution structures of TOM complexes now open up a new era of studies on the structures, functions, and dynamics of the mitochondrial import system. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Yuhei Araiso
- Department of Clinical Laboratory Science, Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan; .,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
| |
Collapse
|
14
|
Decroës A, Li JM, Richardson L, Mutasa-Gottgens E, Lima-Mendez G, Mahillon M, Bragard C, Finn RD, Legrève A. Metagenomics approach for Polymyxa betae genome assembly enables comparative analysis towards deciphering the intracellular parasitic lifestyle of the plasmodiophorids. Genomics 2021; 114:9-22. [PMID: 34798282 DOI: 10.1016/j.ygeno.2021.11.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/24/2021] [Accepted: 11/10/2021] [Indexed: 12/28/2022]
Abstract
Genomic knowledge of the tree of life is biased to specific groups of organisms. For example, only six full genomes are currently available in the rhizaria clade. Here, we have applied metagenomic techniques enabling the assembly of the genome of Polymyxa betae (Rhizaria, Plasmodiophorida) RES F41 isolate from unpurified zoospore holobiont and comparison with the A26-41 isolate. Furthermore, the first P. betae mitochondrial genome was assembled. The two P. betae nuclear genomes were highly similar, each with just ~10.2 k predicted protein coding genes, ~3% of which were unique to each isolate. Extending genomic comparisons revealed a greater overlap with Spongospora subterranea than with Plasmodiophora brassicae, including orthologs of the mammalian cation channel sperm-associated proteins, raising some intriguing questions about zoospore physiology. This work validates our metagenomics pipeline for eukaryote genome assembly from unpurified samples and enriches plasmodiophorid genomics; providing the first full annotation of the P. betae genome.
Collapse
Affiliation(s)
- Alain Decroës
- Phytopathology-Applied Microbiology, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium.
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 315211 Ningbo, China
| | - Lorna Richardson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Euphemia Mutasa-Gottgens
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK; University of Hertfordshire, Hatfield, Herts AL10 9AB, UK
| | - Gipsi Lima-Mendez
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium
| | - Mathieu Mahillon
- Phytopathology-Applied Microbiology, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
| | - Claude Bragard
- Phytopathology-Applied Microbiology, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Anne Legrève
- Phytopathology-Applied Microbiology, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium.
| |
Collapse
|
15
|
Hallinan JP, Doyle LA, Shen BW, Gewe MM, Takushi B, Kennedy MA, Friend D, Roberts JM, Bradley P, Stoddard BL. Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces. Commun Biol 2021; 4:1240. [PMID: 34716407 PMCID: PMC8556268 DOI: 10.1038/s42003-021-02766-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 10/07/2021] [Indexed: 01/16/2023] Open
Abstract
Circular tandem repeat proteins (‘cTRPs’) are de novo designed protein scaffolds (in this and prior studies, based on antiparallel two-helix bundles) that contain repeated protein sequences and structural motifs and form closed circular structures. They can display significant stability and solubility, a wide range of sizes, and are useful as protein display particles for biotechnology applications. However, cTRPs also demonstrate inefficient self-assembly from smaller subunits. In this study, we describe a new generation of cTRPs, with longer repeats and increased interaction surfaces, which enhanced the self-assembly of two significantly different sizes of homotrimeric constructs. Finally, we demonstrated functionalization of these constructs with (1) a hexameric array of peptide-binding SH2 domains, and (2) a trimeric array of anti-SARS CoV-2 VHH domains. The latter proved capable of sub-nanomolar binding affinities towards the viral receptor binding domain and potent viral neutralization function. Jazmine Hallinan et al. report the development of a new generation of circular tandem repeat proteins with enhanced self-assembly. Functionalisation of these constructs with SARS CoV-2 VHH domains resulted in sub-nanomolar binding affinity to the viral receptor binding domain.
Collapse
Affiliation(s)
- Jazmine P Hallinan
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Lindsey A Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Betty W Shen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Mesfin M Gewe
- Lumen Bioscience Inc., 1441 North 34th Street, Seattle, WA, 98103, USA
| | - Brittany Takushi
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Madison A Kennedy
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Della Friend
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - James M Roberts
- Lumen Bioscience Inc., 1441 North 34th Street, Seattle, WA, 98103, USA
| | - Philip Bradley
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA. .,Division of Public Health Sciences and Program in Computational Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, 98009, USA.
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA.
| |
Collapse
|
16
|
Deryusheva EI, Machulin AV, Galzitskaya OV. Structural, Functional, and Evolutionary Characteristics of Proteins with Repeats. Mol Biol 2021. [DOI: 10.1134/s0026893321040038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
17
|
Daskalov A, Glass NL. Gasdermin and Gasdermin-Like Pore-Forming Proteins in Invertebrates, Fungi and Bacteria. J Mol Biol 2021; 434:167273. [PMID: 34599942 DOI: 10.1016/j.jmb.2021.167273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022]
Abstract
The gasdermin family of pore-forming proteins (PFPs) has recently emerged as key molecular players controlling immune-related cell death in mammals. Characterized mammalian gasdermins are activated through proteolytic cleavage by caspases or serine proteases, which remove an inhibitory carboxy-terminal domain, allowing the pore-formation process. Processed gasdermins form transmembrane pores permeabilizing the plasma membrane, which often results in lytic and inflammatory cell death. While the gasdermin-dependent cell death (pyroptosis) has been predominantly characterized in mammals, it now has become clear that gasdermins also control cell death in early vertebrates (teleost fish) and invertebrate animals such as corals (Cnidaria). Moreover, gasdermins and gasdermin-like proteins have been identified and characterized in taxa outside of animals, notably Fungi and Bacteria. Fungal and bacterial gasdermins share many features with mammalian gasdermins including their mode of activation through proteolysis. It has been shown that in some cases the proteolytic activation is executed by evolutionarily related proteases acting downstream of proteins resembling immune receptors controlling pyroptosis in mammals. Overall, these findings establish gasdermins and gasdermin-regulated cell death as an extremely ancient mechanism of cellular suicide and build towards an understanding of the evolution of regulated cell death in the context of immunology. Here, we review the broader gasdermin family, focusing on recent discoveries in invertebrates, fungi and bacteria.
Collapse
Affiliation(s)
- Asen Daskalov
- Institut de Biochimie et Génétique Cellulaires, University of Bordeaux, France.
| | - N Louise Glass
- The Plant and Microbial Biology Department, The University of California, Berkeley, CA 94720-3102, United States
| |
Collapse
|
18
|
Pereira J, Alva V. How do I get the most out of my protein sequence using bioinformatics tools? Acta Crystallogr D Struct Biol 2021; 77:1116-1126. [PMID: 34473083 PMCID: PMC8411974 DOI: 10.1107/s2059798321007907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/02/2021] [Indexed: 12/21/2022] Open
Abstract
Biochemical and biophysical experiments are essential for uncovering the three-dimensional structure and biological role of a protein of interest. However, meaningful predictions can frequently also be made using bioinformatics resources that transfer knowledge from a well studied protein to an uncharacterized protein based on their evolutionary relatedness. These predictions are helpful in developing specific hypotheses to guide wet-laboratory experiments. Commonly used bioinformatics resources include methods to identify and predict conserved sequence motifs, protein domains, transmembrane segments, signal sequences, and secondary as well as tertiary structure. Here, several such methods available through the MPI Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de) are described and how their combined use can provide meaningful information on a protein of unknown function is demonstrated. In particular, the identification of homologs of known structure using HHpred, internal repeats using HHrepID, coiled coils using PCOILS and DeepCoil, and transmembrane segments using Quick2D are focused on.
Collapse
Affiliation(s)
- Joana Pereira
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| |
Collapse
|
19
|
Izert MA, Szybowska PE, Górna MW, Merski M. The Effect of Mutations in the TPR and Ankyrin Families of Alpha Solenoid Repeat Proteins. FRONTIERS IN BIOINFORMATICS 2021; 1:696368. [PMID: 36303725 PMCID: PMC9581033 DOI: 10.3389/fbinf.2021.696368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/22/2021] [Indexed: 11/20/2022] Open
Abstract
Protein repeats are short, highly similar peptide motifs that occur several times within a single protein, for example the TPR and Ankyrin repeats. Understanding the role of mutation in these proteins is complicated by the competing facts that 1) the repeats are much more restricted to a set sequence than non-repeat proteins, so mutations should be harmful much more often because there are more residues that are heavily restricted due to the need of the sequence to repeat and 2) the symmetry of the repeats in allows the distribution of functional contributions over a number of residues so that sometimes no specific site is singularly responsible for function (unlike enzymatic active site catalytic residues). To address this issue, we review the effects of mutations in a number of natural repeat proteins from the tetratricopeptide and Ankyrin repeat families. We find that mutations are context dependent. Some mutations are indeed highly disruptive to the function of the protein repeats while mutations in identical positions in other repeats in the same protein have little to no effect on structure or function.
Collapse
Affiliation(s)
| | | | | | - Matthew Merski
- *Correspondence: Maria Wiktoria Górna, ; Matthew Merski,
| |
Collapse
|
20
|
Le LHM, Ying L, Ferrero RL. Nuclear trafficking of bacterial effector proteins. Cell Microbiol 2021; 23:e13320. [PMID: 33600054 DOI: 10.1111/cmi.13320] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023]
Abstract
Bacterial pathogens can subvert host responses by producing effector proteins that directly target the nucleus of eukaryotic cells in animals and plants. Nuclear-targeting proteins are categorised as either: "nucleomodulins," which have epigenetic-modulating activities; or "cyclomodulins," which specifically interfere with the host cell cycle. Bacteria can deliver these effector proteins to eukaryotic cells via a range of strategies. Despite an increasing number of reports describing the effects of bacterial effector proteins on nuclear processes in host cells, the intracellular pathways used by these proteins to traffic to the nucleus have yet to be fully elucidated. This review will describe current knowledge about how nucleomodulins and cyclomodulins enter eukaryotic cells, exploit endocytic pathways and translocate to the nucleus. We will also discuss the secretion of nuclear-targeting proteins or their release in bacterial membrane vesicles and the trafficking pathways employed by each of these forms. Besides their importance for bacterial pathogenesis, some nuclear-targeting proteins have been implicated in the development of chronic diseases and even cancer. A greater understanding of nuclear-targeting proteins and their actions will provide new insights into the pathogenesis of infectious diseases, as well as contribute to advances in the development of novel therapies against bacterial infections and possibly cancer.
Collapse
Affiliation(s)
- Lena Hoang My Le
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Le Ying
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Richard L Ferrero
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, Victoria, Australia.,Department of Molecular and Translational Science, Monash University, Melbourne, Victoria, Australia
| |
Collapse
|
21
|
Peixoto RS, Sweet M, Villela HDM, Cardoso P, Thomas T, Voolstra CR, Høj L, Bourne DG. Coral Probiotics: Premise, Promise, Prospects. Annu Rev Anim Biosci 2020; 9:265-288. [PMID: 33321044 DOI: 10.1146/annurev-animal-090120-115444] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The use of Beneficial Microorganisms for Corals (BMCs) has been proposed recently as a tool for the improvement of coral health, with knowledge in this research topic advancing rapidly. BMCs are defined as consortia of microorganisms that contribute to coral health through mechanisms that include (a) promoting coral nutrition and growth, (b) mitigating stress and impacts of toxic compounds, (c) deterring pathogens, and (d) benefiting early life-stage development. Here, we review the current proposed BMC approach and outline the studies that have proven its potential to increase coral resilience to stress. We revisit and expand the list of putative beneficial microorganisms associated with corals and their proposed mechanismsthat facilitate improved host performance. Further, we discuss the caveats and bottlenecks affecting the efficacy of BMCs and close by focusing on the next steps to facilitate application at larger scales that can improve outcomes for corals and reefs globally.
Collapse
Affiliation(s)
- Raquel S Peixoto
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil; .,IMAM-AquaRio, Rio de Janeiro Aquarium Research Center, Rio de Janeiro, 20220-360, Brazil.,Current affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby DE22 1GB, United Kingdom
| | - Helena D M Villela
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil;
| | - Pedro Cardoso
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil;
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Christian R Voolstra
- Department of Biology, University of Konstanz, Konstanz 78457, Germany.,Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Lone Høj
- Australian Institute of Marine Science, Townsville, Queensland 4810, Australia
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, Queensland 4810, Australia.,College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia
| |
Collapse
|
22
|
Kahraman A, Karakulak T, Szklarczyk D, von Mering C. Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network. Sci Rep 2020; 10:14453. [PMID: 32879328 PMCID: PMC7468103 DOI: 10.1038/s41598-020-71221-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/17/2020] [Indexed: 01/01/2023] Open
Abstract
Under normal conditions, cells of almost all tissue types express the same predominant canonical transcript isoform at each gene locus. In cancer, however, splicing regulation is often disturbed, leading to cancer-specific switches in the most dominant transcripts (MDT). To address the pathogenic impact of these switches, we have analyzed isoform-specific protein-protein interaction disruptions in 1,209 cancer samples covering 27 different cancer types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project of the International Cancer Genomics Consortium (ICGC). Our study revealed large variations in the number of cancer-specific MDT (cMDT) with the highest frequency in cancers of female reproductive organs. Interestingly, in contrast to the mutational load, cancers arising from the same primary tissue had a similar number of cMDT. Some cMDT were found in 100% of all samples in a cancer type, making them candidates for diagnostic biomarkers. cMDT tend to be located at densely populated network regions where they disrupted protein interactions in the proximity of pathogenic cancer genes. A gene ontology enrichment analysis showed that these disruptions occurred mostly in protein translation and RNA splicing pathways. Interestingly, samples with mutations in the spliceosomal complex tend to have higher number of cMDT, while other transcript expressions correlated with mutations in non-coding splice-site and promoter regions of their genes. This work demonstrates for the first time the large extent of cancer-specific alterations in alternative splicing for 27 different cancer types. It highlights distinct and common patterns of cMDT and suggests novel pathogenic transcripts and markers that induce large network disruptions in cancers.
Collapse
Affiliation(s)
- Abdullah Kahraman
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tülay Karakulak
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Damian Szklarczyk
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christian von Mering
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| |
Collapse
|
23
|
Timmers HTM. SAGA and TFIID: Friends of TBP drifting apart. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194604. [PMID: 32673655 DOI: 10.1016/j.bbagrm.2020.194604] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 01/24/2023]
Abstract
Transcription initiation constitutes a major checkpoint in gene regulation across all living organisms. Control of chromatin function is tightly linked to this checkpoint, which is best illustrated by the SAGA coactivator. This evolutionary conserved complex of 18-20 subunits was first discovered as a Gcn5p-containing histone acetyltransferase, but it also integrates a histone H2B deubiquitinase. The SAGA subunits are organized in a modular fashion around its central core. Strikingly, this central module of SAGA shares a number of proteins with the central core of the basal transcription factor TFIID. In this review I will compare the SAGA and TFIID complexes with respect to their shared subunits, structural organization, enzymatic activities and chromatin binding. I will place a special emphasis on the ancestry of SAGA and TFIID subunits, which suggests that these complexes evolved to control the activity of TBP (TATA-binding protein) in directing the assembly of transcription initiation complexes.
Collapse
Affiliation(s)
- H Th Marc Timmers
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK) partner site Freiburg, 79106 Freiburg, Germany; Department of Urology, Medical Center-University of Freiburg, Breisacher Straße 66, 79106 Freiburg, Germany.
| |
Collapse
|
24
|
Merski M, Młynarczyk K, Ludwiczak J, Skrzeczkowski J, Dunin-Horkawicz S, Górna MW. Self-analysis of repeat proteins reveals evolutionarily conserved patterns. BMC Bioinformatics 2020; 21:179. [PMID: 32381046 PMCID: PMC7204011 DOI: 10.1186/s12859-020-3493-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 04/15/2020] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Protein repeats can confound sequence analyses because the repetitiveness of their amino acid sequences lead to difficulties in identifying whether similar repeats are due to convergent or divergent evolution. We noted that the patterns derived from traditional "dot plot" protein sequence self-similarity analysis tended to be conserved in sets of related repeat proteins and this conservation could be quantitated using a Jaccard metric. RESULTS Comparison of these dot plots obviated the issues due to sequence similarity for analysis of repeat proteins. A high Jaccard similarity score was suggestive of a conserved relationship between closely related repeat proteins. The dot plot patterns decayed quickly in the absence of selective pressure with an expected loss of 50% of Jaccard similarity due to a loss of 8.2% sequence identity. To perform method testing, we assembled a standard set of 79 repeat proteins representing all the subgroups in RepeatsDB. Comparison of known repeat and non-repeat proteins from the PDB suggested that the information content in dot plots could be used to identify repeat proteins from pure sequence with no requirement for structural information. Analysis of the UniRef90 database suggested that 16.9% of all known proteins could be classified as repeat proteins. These 13.3 million putative repeat protein chains were clustered and a significant amount (82.9%) of clusters containing between 5 and 200 members were of a single functional type. CONCLUSIONS Dot plot analysis of repeat proteins attempts to obviate issues that arise due to the sequence degeneracy of repeat proteins. These results show that this kind of analysis can efficiently be applied to analyze repeat proteins on a large scale.
Collapse
Affiliation(s)
- Matthew Merski
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Krzysztof Młynarczyk
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Jan Ludwiczak
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Jakub Skrzeczkowski
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Stanisław Dunin-Horkawicz
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Maria W. Górna
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| |
Collapse
|
25
|
de Jonge PA, von Meijenfeldt FAB, van Rooijen LE, Brouns SJJ, Dutilh BE. Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages. Viruses 2019; 11:v11121085. [PMID: 31766550 PMCID: PMC6949934 DOI: 10.3390/v11121085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/17/2019] [Accepted: 11/19/2019] [Indexed: 12/12/2022] Open
Abstract
The human gut contains an expanse of largely unstudied bacteriophages. Among the most common are crAss-like phages, which were predicted to infect Bacteriodetes hosts. CrAssphage, the first crAss-like phage to be discovered, contains a protein encoding a Bacteroides-associated carbohydrate-binding often N-terminal (BACON) domain tandem repeat. Because protein domain tandem repeats are often hotspots of evolution, BACON domains may provide insight into the evolution of crAss-like phages. Here, we studied the biodiversity and evolution of BACON domains in bacteriophages by analysing over 2 million viral contigs. We found a high biodiversity of BACON in seven gut phage lineages, including five known crAss-like phage lineages and two novel gut phage lineages that are distantly related to crAss-like phages. In three BACON-containing phage lineages, we found that BACON domain tandem repeats were associated with phage tail proteins, suggestive of a possible role of these repeats in host binding. In contrast, individual BACON domains that did not occur in tandem were not found in the proximity of tail proteins. In two lineages, tail-associated BACON domain tandem repeats evolved largely through horizontal transfer of separate domains. In the third lineage that includes the prototypical crAssphage, the tandem repeats arose from several sequential domain duplications, resulting in a characteristic tandem array that is distinct from bacterial BACON domains. We conclude that phage tail-associated BACON domain tandem repeats have evolved in at least two independent cases in gut bacteriophages, including in the widespread gut phage crAssphage.
Collapse
Affiliation(s)
- Patrick A. de Jonge
- Theoretical Biology and Bioinformatics, Science4 Life, Utrecht University, 3584 CH Utrecht, The Netherlands; (P.A.d.J.); (F.A.B.v.M.); (L.E.v.R.)
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands;
| | - F. A. Bastiaan von Meijenfeldt
- Theoretical Biology and Bioinformatics, Science4 Life, Utrecht University, 3584 CH Utrecht, The Netherlands; (P.A.d.J.); (F.A.B.v.M.); (L.E.v.R.)
| | - Laura E. van Rooijen
- Theoretical Biology and Bioinformatics, Science4 Life, Utrecht University, 3584 CH Utrecht, The Netherlands; (P.A.d.J.); (F.A.B.v.M.); (L.E.v.R.)
| | - Stan J. J. Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands;
| | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science4 Life, Utrecht University, 3584 CH Utrecht, The Netherlands; (P.A.d.J.); (F.A.B.v.M.); (L.E.v.R.)
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
- Correspondence:
| |
Collapse
|
26
|
Liu X, Liu J, Wu Z, Chen L, Wang S, Wang P. Photo-cleavable purification/protection handle assisted synthesis of giant modified proteins with tandem repeats. Chem Sci 2019; 10:8694-8700. [PMID: 31803444 PMCID: PMC6849634 DOI: 10.1039/c9sc03693h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 08/04/2019] [Indexed: 12/15/2022] Open
Abstract
Proteins with tandem repeats have essential physical or biological roles in cells and have been widely investigated as biomaterials or vaccines. Chemically derived proteins with tandem repeats would be beneficial for research, owing to their accurate structures, possibly with precise modifications, produced by chemical synthesis. Traditional protein synthesis often leads to severe handling loss due to multiple ligations and HPLC purifications. To improve the protein synthesis efficiency, we developed a purification/protection handle consisting of a His6 tag and a photo-labile linker. This handle has great potential to facilitate purification with immobilized metal affinity chromatography techniques and also provides orthogonal protection for N-terminal Cys. The synthesis of the model proteins Muc1 and antifreeze glycoprotein mimics shows that the handle decreases the requirement for HPLC and enables both convergent and sequential assembly of peptide segments.
Collapse
Affiliation(s)
- Xueyi Liu
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs , School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , P. R. China .
| | - Jiazhi Liu
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs , School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , P. R. China .
| | - Zhichao Wu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources , Ministry of Education , College of Fisheries and Life Science , Shanghai Ocean University , Shanghai 201306 , China
| | - Liangbiao Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources , Ministry of Education , College of Fisheries and Life Science , Shanghai Ocean University , Shanghai 201306 , China
| | - Siyao Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs , School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , P. R. China .
| | - Ping Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs , School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , P. R. China .
| |
Collapse
|
27
|
Machulin A, Deryusheva E, Lobanov M, Galzitskaya O. Repeats in S1 Proteins: Flexibility and Tendency for Intrinsic Disorder. Int J Mol Sci 2019; 20:ijms20102377. [PMID: 31091666 PMCID: PMC6566611 DOI: 10.3390/ijms20102377] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/06/2019] [Accepted: 05/10/2019] [Indexed: 11/16/2022] Open
Abstract
An important feature of ribosomal S1 proteins is multiple copies of structural domains in bacteria, the number of which changes in a strictly limited range from one to six. For S1 proteins, little is known about the contribution of flexible regions to protein domain function. We exhaustively studied a tendency for intrinsic disorder and flexibility within and between structural domains for all available UniProt S1 sequences. Using charge–hydrophobicity plot cumulative distribution function (CH-CDF) analysis we classified 53% of S1 proteins as ordered proteins; the remaining proteins were related to molten globule state. S1 proteins are characterized by an equal ratio of regions connecting the secondary structure within and between structural domains, which indicates a similar organization of separate S1 domains and multi-domain S1 proteins. According to the FoldUnfold and IsUnstruct programs, in the multi-domain proteins, relatively short flexible or disordered regions are predominant. The lowest percentage of flexibility is in the central parts of multi-domain proteins. Our results suggest that the ratio of flexibility in the separate domains is related to their roles in the activity and functionality of S1: a more stable and compact central part in the multi-domain proteins is vital for RNA interaction, terminals domains are important for other functions.
Collapse
Affiliation(s)
- Andrey Machulin
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia.
| | - Evgenia Deryusheva
- Institute for Biological Instrumentation, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia.
| | - Mikhail Lobanov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia.
| | - Oxana Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia.
| |
Collapse
|
28
|
Thema N, Tshilwane S, Pretorius A, Son L, Smith R, Steyn H, Liebenberg J, van Kleef M. Identification and characterisation of conserved epitopes of E. ruminantium that activate Th1 CD4+ T cells: Towards the development of a multi-epitope vaccine. Mol Immunol 2019; 107:106-114. [DOI: 10.1016/j.molimm.2018.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/06/2018] [Accepted: 12/09/2018] [Indexed: 01/21/2023]
|
29
|
Evolution of plastid genomes of Holcoglossum (Orchidaceae) with recent radiation. BMC Evol Biol 2019; 19:63. [PMID: 30808310 PMCID: PMC6390633 DOI: 10.1186/s12862-019-1384-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 02/11/2019] [Indexed: 01/08/2023] Open
Abstract
Background The plastid is a semiautonomous organelle with its own genome. Plastid genomes have been widely used as models for studying phylogeny, speciation and adaptive evolution. However, most studies focus on comparisons of plastid genome evolution at high taxonomic levels, and comparative studies of the process of plastome evolution at the infrageneric or intraspecific level remain elusive. Holcoglossum is a small genus of Orchidaceae, consisting of approximately 20 species of recent radiation. This made it an ideal group to explore the plastome mutation mode at the infrageneric or intraspecific level. Results In this paper, we reported 15 complete plastid genomes from 12 species of Holcoglossum and 1 species of Vanda. The plastid genomes of Holcoglossum have a total length range between 145 kb and 148 kb, encoding a set of 102 genes. The whole set of ndh-gene families in Holcoglossum have been truncated or pseudogenized. Hairpin inversion in the coding region of the plastid gene ycf2 has been found. Conclusions Using a comprehensive comparative plastome analysis, we found that all the indels between different individuals of the same species resulted from the copy number variation of the short repeat sequence, which may be caused by replication slippage. Annotation of tandem repeats shows that the variation introduced by tandem repeats is widespread in plastid genomes. The hairpin inversion found in the plastid gene ycf2 occurred randomly in the Orchidaceae. Electronic supplementary material The online version of this article (10.1186/s12862-019-1384-5) contains supplementary material, which is available to authorized users.
Collapse
|
30
|
Li ZH, Ma X, Wang DY, Li YX, Wang CW, Jin XH. Evolution of plastid genomes of Holcoglossum (Orchidaceae) with recent radiation. BMC Evol Biol 2019. [PMID: 30808310 DOI: 10.1186/s12862-019-1384-1385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
BACKGROUND The plastid is a semiautonomous organelle with its own genome. Plastid genomes have been widely used as models for studying phylogeny, speciation and adaptive evolution. However, most studies focus on comparisons of plastid genome evolution at high taxonomic levels, and comparative studies of the process of plastome evolution at the infrageneric or intraspecific level remain elusive. Holcoglossum is a small genus of Orchidaceae, consisting of approximately 20 species of recent radiation. This made it an ideal group to explore the plastome mutation mode at the infrageneric or intraspecific level. RESULTS In this paper, we reported 15 complete plastid genomes from 12 species of Holcoglossum and 1 species of Vanda. The plastid genomes of Holcoglossum have a total length range between 145 kb and 148 kb, encoding a set of 102 genes. The whole set of ndh-gene families in Holcoglossum have been truncated or pseudogenized. Hairpin inversion in the coding region of the plastid gene ycf2 has been found. CONCLUSIONS Using a comprehensive comparative plastome analysis, we found that all the indels between different individuals of the same species resulted from the copy number variation of the short repeat sequence, which may be caused by replication slippage. Annotation of tandem repeats shows that the variation introduced by tandem repeats is widespread in plastid genomes. The hairpin inversion found in the plastid gene ycf2 occurred randomly in the Orchidaceae.
Collapse
Affiliation(s)
- Zhang-Hai Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Ma
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - De-Yi Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yun-Xia Li
- Fujian Agriculture and Forest University, Shanxiadian Road 15, Changshan District, Fuzhou, 350002, Fujian, China
| | - Cheng-Wang Wang
- Nanchang University, Xuefu Road 999, Honggutang District, Nanchang, Jiangxi, China
| | - Xiao-Hua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Science (CAS-SEABRI), Nay Pyi Taw, Myanmar.
| |
Collapse
|
31
|
Alex A, Antunes A. Whole-Genome Comparisons Among the Genus Shewanella Reveal the Enrichment of Genes Encoding Ankyrin-Repeats Containing Proteins in Sponge-Associated Bacteria. Front Microbiol 2019; 10:5. [PMID: 30787909 PMCID: PMC6372511 DOI: 10.3389/fmicb.2019.00005] [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: 03/20/2018] [Accepted: 01/07/2019] [Indexed: 11/13/2022] Open
Abstract
The bacterial members of the genus Shewanella are widely distributed and inhabit both freshwater and marine environments. Some members of Shewanella have gained considerable attention due to its ability to survive in redox-stratified environments. However, a gap of knowledge exists on the key genomic features of the sponge-associated Shewanella sp. involving the successful host-bacteria interaction, as sponge-symbiotic Shewanella are largely underrepresented in the public repositories. With the aim of identifying the genomic signatures of sponge-Shewanella association, we generated a high-quality genome data of a sponge-associated, Shewanella sp. OPT22, isolated from the intertidal marine sponge Ophlitaspongia papilla and performed comprehensive comparative analyses of 68 genome strains of the genus Shewanella including two previously reported genomes of sponge-associated bacteria, Shewanella spongiae KCTC 22492 and Shewanella sp. Alg231_23. The 16S rRNA-based phylogenetic reconstruction showed the well-supported affiliation of OPT22 and KCTC 22492 with previously reported sponge-associated bacteria, affirming the “sponge-specific” nature of these two bacterial strains isolated from different marine sponge species from the Atlantic and Pacific (East Sea) Oceans, respectively. The genome comparison of the 68 strains of Shewanella inhabiting different habitats revealed the unusual/previously unreported abundance of genes encoding for ankyrin-repeat containing proteins (ANKs) in the genomes of the two sponge-associated strains, OPT22 (ANKs; n = 45) and KCTC 22492 (ANKs; n = 52), which might be involved in sponge-Shewanella interactions. Focused analyses detected the syntenic organization of the gene cluster encoding major secretion system (type III/IV/VI) components and the presence of effector homologs in OPT22 and KCTC 22492 that seem to play a role in the virulence of the sponge bacteria. The genomic island (GI) of Shewanella sp. OPT22 was identified to localize a gene cluster encoding T4SS components and ANK (n = 1), whereas S. spongiae KCTC 22492 harbored a total of seven ANKs within multiple GIs. GIs may play a pivotal role in the dissemination of symbioses-related genes (ANKs) through the horizontal gene transfer, contributing to the diversification and adaptation of sponge-associated Shewanella. Overall, the genome analyses of Shewanella isolates from marine sponges revealed genomic repertoires that might be involved in establishing successful symbiotic relationships with the sponge hosts.
Collapse
Affiliation(s)
- Anoop Alex
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| |
Collapse
|
32
|
Podia V, Milioni D, Katsareli E, Valassakis C, Roussis A, Haralampidis K. Molecular and functional characterization of Arabidopsis thaliana VPNB1 gene involved in plant vascular development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:11-19. [PMID: 30466575 DOI: 10.1016/j.plantsci.2018.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/31/2018] [Accepted: 09/05/2018] [Indexed: 06/09/2023]
Abstract
Armadillo (ARM) repeat containing proteins constitute a large family in plants and are involved in diverse cellular functions, like signal transduction, proliferation and differentiation. In animals, ARM repeat proteins have been implicated in cancer development. In this study, we aimed in characterizing the VPNB1 gene from Arabidopsis thaliana and its role in plant development, by implementing a number of genetic and molecular approaches. AtVPNB1 encodes for an ARM repeat protein of unknown function, exclusively expressed in the cambium as well as in the differentiating xylem and phloem cells of the vascular system. Subcellular localization experiments showed that VPNB is confined in nucleoplasmic speckle-like structures unrelated to cajal bodies. Transgenic VPNB-impaired plants exhibit a slower growing phenotype and a non-canonical pattern of xylem tissue. On the contrary, VPNB overexpression lines display an inverted phenotype of increased growth, accompanied by an increased deposition of phloem and xylem cell layers. In line with the above data, qPCR analysis revealed a deregulation of several key master genes of secondary wall biosynthesis, underlining the involvement of VPNB1 in the regulation and differentiation of the root and shoot vascular tissue.
Collapse
Affiliation(s)
- Varvara Podia
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Dimitra Milioni
- Agricultural University of Athens, Department of Agricultural Biotechnology, Iera Odos 75, 11855 Athens, Greece.
| | - Efthimia Katsareli
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Chryssanthi Valassakis
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Andreas Roussis
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Kosmas Haralampidis
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| |
Collapse
|
33
|
Alex A, Antunes A. Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts. PLoS One 2018; 13:e0194368. [PMID: 29775460 PMCID: PMC5959193 DOI: 10.1371/journal.pone.0194368] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 03/01/2018] [Indexed: 11/18/2022] Open
Abstract
Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater. The analyses revealed a certain degree of commonality among the majority of sponge- and coral-associated bacteria. Isolates from other marine invertebrate host, tunicates, exhibited a genetic repertoire for cold adaptation and specific metabolic abilities including mucin degradation in the Antarctic tunicate-associated bacterium Pseudovibrio sp. Tun.PHSC04_5.I4. Reductive genome evolution was simultaneously detected in the flatworm-associated bacteria and the sponge-associated bacterium P. axinellae AD2, through the loss of major secretion systems (type III/VI) and virulence/symbioses factors such as proteins involved in adhesion and attachment to the host. Our study also unraveled the presence of a CRISPR-Cas system in P. stylochi UST20140214-052 a flatworm-associated bacterium possibly suggesting the role of CRISPR-based adaptive immune system against the invading virus particles. Detection of mobile elements and genomic islands (GIs) in all bacterial members highlighted the role of horizontal gene transfer for the acquisition of novel genetic features, likely enhancing the bacterial ecological fitness. These findings are insightful to understand the role of genome diversity in Pseudovibrio as an evolutionary strategy to increase their colonizing success across a wide range of marine eukaryotic hosts.
Collapse
Affiliation(s)
- Anoop Alex
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- * E-mail: (AA); (AA)
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- * E-mail: (AA); (AA)
| |
Collapse
|
34
|
Shapiro JA. Living Organisms Author Their Read-Write Genomes in Evolution. BIOLOGY 2017; 6:E42. [PMID: 29211049 PMCID: PMC5745447 DOI: 10.3390/biology6040042] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022]
Abstract
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
Collapse
Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
| |
Collapse
|
35
|
Islam Z, Nagampalli RSK, Fatima MT, Ashraf GM. New paradigm in ankyrin repeats: Beyond protein-protein interaction module. Int J Biol Macromol 2017; 109:1164-1173. [PMID: 29157912 DOI: 10.1016/j.ijbiomac.2017.11.101] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/13/2017] [Accepted: 11/16/2017] [Indexed: 01/06/2023]
Abstract
Classically, ankyrin repeat (ANK) proteins are built from tandems of two or more repeats and form curved solenoid structures that are associated with protein-protein interactions. These are short, widespread structural motif of around 33 amino acids repeats in tandem, having a canonical helix-loop-helix fold, found individually or in combination with other domains. The multiplicity of structural pattern enables it to form assemblies of diverse sizes, required for their abilities to confer multiple binding and structural roles of proteins. Three-dimensional structures of these repeats determined to date reveal a degree of structural variability that translates into the considerable functional versatility of this protein superfamily. Recent work on the ANK has proposed novel structural information, especially protein-lipid, protein-sugar and protein-protein interaction. Self-assembly of these repeats was also shown to prevent the associated protein in forming filaments. In this review, we summarize the latest findings and how the new structural information has increased our understanding of the structural determinants of ANK proteins. We discussed latest findings on how these proteins participate in various interactions to diversify the ANK roles in numerous biological processes, and explored the emerging and evolving field of designer ankyrins and its framework for protein engineering emphasizing on biotechnological applications.
Collapse
Affiliation(s)
- Zeyaul Islam
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, 13083-100, Brazil.
| | | | - Munazza Tamkeen Fatima
- Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, SP, 13083-862, Brazil
| | - Ghulam Md Ashraf
- King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah, 21589, Saudi Arabia.
| |
Collapse
|
36
|
Pugacheva V, Korotkov A, Korotkov E. Search of latent periodicity in amino acid sequences by means of genetic algorithm and dynamic programming. Stat Appl Genet Mol Biol 2017; 15:381-400. [PMID: 27337743 DOI: 10.1515/sagmb-2015-0079] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The aim of this study was to show that amino acid sequences have a latent periodicity with insertions and deletions of amino acids in unknown positions of the analyzed sequence. Genetic algorithm, dynamic programming and random weight matrices were used to develop a new mathematical algorithm for latent periodicity search. A multiple alignment of periods was calculated with help of the direct optimization of the position-weight matrix without using pairwise alignments. The developed algorithm was applied to analyze amino acid sequences of a small number of proteins. This study showed the presence of latent periodicity with insertions and deletions in the amino acid sequences of such proteins, for which the presence of latent periodicity was not previously known. The origin of latent periodicity with insertions and deletions is discussed.
Collapse
|
37
|
Perycz M, Krwawicz J, Bochtler M. A TALE-inspired computational screen for proteins that contain approximate tandem repeats. PLoS One 2017; 12:e0179173. [PMID: 28617832 PMCID: PMC5472282 DOI: 10.1371/journal.pone.0179173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/24/2017] [Indexed: 11/18/2022] Open
Abstract
TAL (transcription activator-like) effectors (TALEs) are bacterial proteins that are secreted from bacteria to plant cells to act as transcriptional activators. TALEs and related proteins (RipTALs, BurrH, MOrTL1 and MOrTL2) contain approximate tandem repeats that differ in conserved positions that define specificity. Using PERL, we screened ~47 million protein sequences for TALE-like architecture characterized by approximate tandem repeats (between 30 and 43 amino acids in length) and sequence variability in conserved positions, without requiring sequence similarity to TALEs. Candidate proteins were scored according to their propensity for nuclear localization, secondary structure, repeat sequence complexity, as well as covariation and predicted structural proximity of variable residues. Biological context was tentatively inferred from co-occurrence of other domains and interactome predictions. Approximate repeats with TALE-like features that merit experimental characterization were found in a protein of chestnut blight fungus, a eukaryotic plant pathogen.
Collapse
Affiliation(s)
- Malgorzata Perycz
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Poland
| | - Joanna Krwawicz
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Poland
| | - Matthias Bochtler
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Poland
- * E-mail:
| |
Collapse
|
38
|
Wang Y, Geng H, Dang X, Xiang H, Li T, Pan G, Zhou Z. Comparative Analysis of the Proteins with Tandem Repeats from 8 Microsporidia and Characterization of a Novel Endospore Wall Protein Colocalizing with Polar Tube from Nosema bombycis. J Eukaryot Microbiol 2017; 64:707-715. [PMID: 28321967 DOI: 10.1111/jeu.12412] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/09/2017] [Accepted: 03/09/2017] [Indexed: 11/27/2022]
Abstract
As a common feature of eukaryotic proteins, tandem amino acid repeat has been studied extensively in both animal and plant proteins. Here, a comparative analysis focusing on the proteins having tandem repeats was conducted in eight microsporidia, including four mammal-infecting microsporidia (Encephalitozoon cuniculi, Encephalitozoon intestinalis, Encephalitozoon hellem and Encephalitozoon bieneusi) and four insect-infecting microsporidia (Nosema apis, Nosema ceranae, Vavraia culicis and Nosema bombycis). We found that the proteins with tandem repeats were abundant in these species. The quantity of these proteins in insect-infecting microsporidia was larger than that of mammal-infecting microsporidia. Additionally, the hydrophilic residues were overrepresented in the tandem repeats of these eight microsporidian proteins and the amino acids residues in these tandem repeat sequences tend to be encoded by GC-rich codons. The tandem repeat position within proteins of insect-infecting microsporidia was randomly distributed, whereas the tandem repeats within proteins of mammal-infecting microsporidia rarely tend to be present in the N terminal regions, when compared with those present in the C terminal and middle regions. Finally, a hypothetical protein EOB14572 possessing four tandem repeats was successfully characterized as a novel endospore wall protein, which colocalized with polar tube of N. bombycis. Our study provided useful insight for the study of the proteins with tandem repeats in N. bombycis, but also further enriched the spore wall components of this obligate unicellular eukaryotic parasite.
Collapse
Affiliation(s)
- Ying Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Huixia Geng
- School of Mathematics and Finance, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Xiaoqun Dang
- Laboratory of Animal Biology, Chongqing Normal University, Chongqing, 400047, China
| | - Heng Xiang
- College of Animal Science and Technology, Southwest University, Chongqing, 400716, China
| | - Tian Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Guoqing Pan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Zeyang Zhou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China.,Laboratory of Animal Biology, Chongqing Normal University, Chongqing, 400047, China
| |
Collapse
|
39
|
Brumm PJ, Gowda K, Robb FT, Mead DA. The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor. Front Microbiol 2016; 7:1979. [PMID: 28066333 PMCID: PMC5167688 DOI: 10.3389/fmicb.2016.01979] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/25/2016] [Indexed: 11/13/2022] Open
Abstract
Here we report the complete genome sequence of the chemoorganotrophic, extremely thermophilic bacterium, Dictyoglomus turgidum, which is a Gram negative, strictly anaerobic bacterium. D. turgidum and D. thermophilum together form the Dictyoglomi phylum. The two Dictyoglomus genomes are highly syntenic, and both are distantly related to Caldicellulosiruptor spp. D. turgidum is able to grow on a wide variety of polysaccharide substrates due to significant genomic commitment to glycosyl hydrolases, 16 of which were cloned and expressed in our study. The GH5, GH10, and GH42 enzymes characterized in this study suggest that D. turgidum can utilize most plant-based polysaccharides except crystalline cellulose. The DNA polymerase I enzyme was also expressed and characterized. The pure enzyme showed improved amplification of long PCR targets compared to Taq polymerase. The genome contains a full complement of DNA modifying enzymes, and an unusually high copy number (4) of a new, ancestral family of polB type nucleotidyltransferases designated as MNT (minimal nucleotidyltransferases). Considering its optimal growth at 72°C, D. turgidum has an anomalously low G+C content of 39.9% that may account for the presence of reverse gyrase, usually associated with hyperthermophiles.
Collapse
Affiliation(s)
- Phillip J. Brumm
- C5-6 Technologies LLCFitchburg, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, USA
| | - Krishne Gowda
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, USA
- Lucigen CorporationMiddleton, WI, USA
| | - Frank T. Robb
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of MarylandBaltimore, MD, USA
| | - David A. Mead
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, USA
- Varigen Biosciences CorporationMadison, WI, USA
| |
Collapse
|
40
|
Zhou Y, He Q, Chen J, Liu Y, Mao Z, Lyu Z, Ni D, Long Y, Ju P, Liu J, Gu Y, Zhou Q. The expression patterns of Tetratricopeptide repeat domain 36 (Ttc36). Gene Expr Patterns 2016; 22:37-45. [PMID: 27826126 DOI: 10.1016/j.gep.2016.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/20/2016] [Accepted: 11/02/2016] [Indexed: 02/05/2023]
Abstract
Tetratricopeptide repeat domain 36 (Ttc36), whose coding protein belongs to tetratricopeptide repeat (TPR) motif family, has not been studied extensively. We for the first time showed that Ttc36 is evolutionarily conserved across mammals by bioinformatics. Rabbit anti-mouse Ttc36 polyclonal antibody was generated by injecting synthetic full-length peptides through "antigen intersection" strategy. Subsequently, we characterized Ttc36 expression profile in mouse, showing its expression in liver and kidney both from embryonic day 15.5 (E15.5) until adult, as well as in testis. Immunofluorescence staining showed that Ttc36 is diffusely expressed in liver, however, specifically in kidney cortex. Thus, we further compare Ttc36 with proximal tubules (PT) marker Lotus Tetragonolobus Lectin (LTL) and distal tubules (DT) marker Calbindin-D28k respectively by double immunofluorescence staining. Results showed the co-localization of Ttc36 with LTL rather than Calbindin-D28k. Collectively, on the basis of the expression pattern, Ttc36 is specifically expressed in proximal distal tubules.
Collapse
Affiliation(s)
- Yuru Zhou
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China; The Seventh Class of 2012 Year Entry, The Third Clinical College, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Qingling He
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Jihui Chen
- Department of Dermatology, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, 610041, PR China.
| | - Yunhong Liu
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Zhaomin Mao
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Zhongshi Lyu
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Dongsheng Ni
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Yaoshui Long
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Pan Ju
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Jianing Liu
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Yuping Gu
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Qin Zhou
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| |
Collapse
|
41
|
Abstract
Repeats are ubiquitous elements of proteins and they play important roles for cellular function and during evolution. Repeats are, however, also notoriously difficult to capture computationally and large scale studies so far had difficulties in linking genetic causes, structural properties and evolutionary trajectories of protein repeats. Here we apply recently developed methods for repeat detection and analysis to a large dataset comprising over hundred metazoan genomes. We find that repeats in larger protein families experience generally very few insertions or deletions (indels) of repeat units but there is also a significant fraction of noteworthy volatile outliers with very high indel rates. Analysis of structural data indicates that repeats with an open structure and independently folding units are more volatile and more likely to be intrinsically disordered. Such disordered repeats are also significantly enriched in sites with a high functional potential such as linear motifs. Furthermore, the most volatile repeats have a high sequence similarity between their units. Since many volatile repeats also show signs of recombination, we conclude they are often shaped by concerted evolution. Intriguingly, many of these conserved yet volatile repeats are involved in host-pathogen interactions where they might foster fast but subtle adaptation in biological arms races. KEY WORDS: protein evolution, domain rearrangements, protein repeats, concerted evolution.
Collapse
Affiliation(s)
- Andreas Schüler
- Institute for Evolution and Biodiversity, Westfalian Wilhelms University, Huefferstrasse 1, Muenster, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, Westfalian Wilhelms University, Huefferstrasse 1, Muenster, Germany
| |
Collapse
|
42
|
Comparison of protein repeat classifications based on structure and sequence families. Biochem Soc Trans 2016; 43:832-7. [PMID: 26517890 DOI: 10.1042/bst20150079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Tandem repeats (TR) in proteins are common in nature and have several unique functions. They come in various forms that are frequently difficult to recognize from a sequence. A previously proposed structural classification has been recently implemented in the RepeatsDB database. This defines five main classes, mainly based on repeat unit length, with subclasses representing specific folds. Sequence-based classifications, such as Pfam, provide an alternative classification based on evolutionarily conserved repeat families. Here, we discuss a detailed comparison between the structural classes in RepeatsDB and the corresponding Pfam repeat families and clans. Most instances are found to map one-to-one between structure and sequence. Some notable exceptions such as leucine-rich repeats (LRRs) and α-solenoids are discussed.
Collapse
|
43
|
Enzymes required for the biosynthesis of N-formylated sugars. Curr Opin Struct Biol 2016; 41:1-9. [PMID: 27209114 DOI: 10.1016/j.sbi.2016.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/12/2016] [Accepted: 04/13/2016] [Indexed: 12/25/2022]
Abstract
The N-formyltransferases, also known as transformylases, play key roles in de novo purine biosynthesis where they catalyze the transfer of formyl groups to primary amine acceptors. These enzymes require N10-formyltetrahydrofolate for activity. Due to their biological importance they have been extensively investigated for many years, and they are still serving as targets for antifolate drug design. Most of our understanding of the N-formyltransferases has been derived from these previous studies. It is now becoming increasingly apparent, however, that N-formylation also occurs on some amino sugars found on the O-antigens of pathogenic bacteria. This review focuses on recent developments in the biochemical and structural characterization of the sugar N-formyltransferases.
Collapse
|
44
|
Sun JX, Guo Y, Zhang X, Zhu WC, Chen YT, Hong XY. Effects of host interaction withWolbachiaon cytoplasmic incompatibility in the two-spotted spider miteTetranychus urticae. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12804] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jian-Xin Sun
- Department of Entomology; Nanjing Agricultural University; No.1, Weigang Nanjing Jiangsu 210095 China
| | - Yan Guo
- Department of Entomology; Nanjing Agricultural University; No.1, Weigang Nanjing Jiangsu 210095 China
| | - Xu Zhang
- Department of Entomology; Nanjing Agricultural University; No.1, Weigang Nanjing Jiangsu 210095 China
| | - Wen-Chao Zhu
- Department of Entomology; Nanjing Agricultural University; No.1, Weigang Nanjing Jiangsu 210095 China
| | - Ya-Ting Chen
- Department of Entomology; Nanjing Agricultural University; No.1, Weigang Nanjing Jiangsu 210095 China
| | - Xiao-Yue Hong
- Department of Entomology; Nanjing Agricultural University; No.1, Weigang Nanjing Jiangsu 210095 China
| |
Collapse
|
45
|
Schenkelaars Q, Fierro-Constain L, Renard E, Borchiellini C. Retracing the path of planar cell polarity. BMC Evol Biol 2016; 16:69. [PMID: 27039172 PMCID: PMC4818920 DOI: 10.1186/s12862-016-0641-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/22/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The Planar Cell Polarity pathway (PCP) has been described as the main feature involved in patterning cell orientation in bilaterian tissues. Recently, a similar phenomenon was revealed in cnidarians, in which the inhibition of this pathway results in the absence of cilia orientation in larvae, consequently proving the functional conservation of PCP signaling between Cnidaria and Bilateria. Nevertheless, despite the growing accumulation of databases concerning basal lineages of metazoans, very few information concerning the existence of PCP components have been gathered outside of Bilateria and Cnidaria. Thus, the origin of this module or its prevalence in early emerging metazoans has yet to be elucidated. RESULTS The present study addresses this question by investigating the genomes and transcriptomes from all poriferan lineages in addition to Trichoplax (Placozoa) and Mnemiopsis (Ctenophora) genomes for the presence of the core components of this pathway. Our results confirm that several PCP components are metazoan innovations. In addition, we show that all members of the PCP pathway, including a bona fide Strabismus ortholog (Van gogh), are retrieved only in one sponge lineage (Homoscleromorpha) out of four. This highly suggests that the full PCP pathway dates back at least to the emergence of homoscleromorph sponges. Consequently, several secondary gene losses would have occurred in the three other poriferan lineages including Amphimedon queenslandica (Demospongiae). Several proteins were not retrieved either in placozoans or ctenophores leading us to discuss the difficulties to predict orthologous proteins in basally branching animals. Finally, we reveal how the study of multigene families may be helpful to unravel the relationships at the base of the metazoan tree. CONCLUSION The PCP pathway antedates the radiation of Porifera and may have arisen in the last common ancestor of animals. Oscarella species now appear as key organisms to understand the ancestral function of PCP signaling and its potential links with Wnt pathways.
Collapse
Affiliation(s)
- Quentin Schenkelaars
- />Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE UMR 7263), Aix Marseille Université, CNRS, IRD, Avignon Université, Station marine d’Endoume, Batterie des Lions, 13007 Marseille, France
- />Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (IGe3), Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Laura Fierro-Constain
- />Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE UMR 7263), Aix Marseille Université, CNRS, IRD, Avignon Université, Station marine d’Endoume, Batterie des Lions, 13007 Marseille, France
| | - Emmanuelle Renard
- />Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE UMR 7263), Aix Marseille Université, CNRS, IRD, Avignon Université, Station marine d’Endoume, Batterie des Lions, 13007 Marseille, France
| | - Carole Borchiellini
- />Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE UMR 7263), Aix Marseille Université, CNRS, IRD, Avignon Université, Station marine d’Endoume, Batterie des Lions, 13007 Marseille, France
- />Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (IGe3), Faculty of Sciences, University of Geneva, Geneva, Switzerland
| |
Collapse
|
46
|
Korotkov EV, Korotkova MA. Developing a mathematical method to search for latent periodicity in protein amino-acid sequences with deletions and insertions. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915060159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|