1
|
Gupta T, Chahota R. Unique ankyrin repeat proteins in the genome of poxviruses-Boon or Wane, a critical review. Gene 2024; 927:148759. [PMID: 38992761 DOI: 10.1016/j.gene.2024.148759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/29/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024]
Abstract
Ankyrin repeat is a 33-amino acid motif commonly observed in eukaryotes and, to a lesser extent, in prokaryotes and archaea and rarely in viruses. This motif plays a crucial role in regulating various cellular processes like the cell cycle, transcription, cell signaling, and inflammatory responses through interactions between proteins. Poxviruses exhibit a distinctive feature of containing multiple ankyrin repeat proteins within their genomes. All the genera of poxviruses possess these proteins except molluscipox virus, crocodylidpox virus, and red squirrel poxvirus. An intriguing characteristic has generated notable interest in studying the functions of these proteins within poxvirus biology. Within poxviruses, ankyrin repeat proteins exhibit a distinct configuration, featuring ankyrin repeats in the N-terminal region and a cellular F-box homolog in the C-terminal region, which enables interactions with the cellular Skp, Cullin, F-box containing ubiquitin ligase complex. Through the examination of experimental evidences and discussions from current literature, this review elucidates the organization and role of ankyrin repeat proteins in poxviruses. Various research studies have highlighted the significant importance of these proteins in poxviral pathogenesis and, acting as factors that enhance virulence. Consequently, they represent viable targets for developing genetically altered viruses with decreased virulence, thus displaying potential as candidates for vaccines and antiviral therapeutic development contributing to safer and more effective strategies against poxviral infections.
Collapse
Affiliation(s)
- Tania Gupta
- Department of Veterinary Microbiology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana, Punjab, 141012 India; Department of Veterinary Microbiology, DGCN College of Veterinary and Animal Sciences, CSK Himachal Pradesh Agricultural University, Palampur, 176062 India
| | - Rajesh Chahota
- Department of Veterinary Microbiology, DGCN College of Veterinary and Animal Sciences, CSK Himachal Pradesh Agricultural University, Palampur, 176062 India.
| |
Collapse
|
2
|
R Parthiban AB, Palavesam A, Srinivasan S, Mohanan A, Ghosh S, Krishnaswamy Gopalan T. Molecular characterization of Ehrlichia canis from naturally infected dogs reveals a novel Asiatic-lineage and co-circulation of multiple lineages in India. Res Vet Sci 2024; 175:105311. [PMID: 38823355 DOI: 10.1016/j.rvsc.2024.105311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 06/03/2024]
Abstract
Canine monocytic ehrlichiosis caused by Ehrlichia canis is an important rickettsial pathogen of dogs transmitted by Rhipicephalus sanguineus sensu lato ticks in India. Globally, molecular characterization of E. canis is done using different E. canis gene targets. This study aimed to characterize genetic diversity of uncultured Ehrlichia species from dogs by 16S rRNA and partial gp200 gene (termed as p43 region) sequences data. Phylogeny based on 16S rRNA gene did not reveal any region-specific lineages. The phylogeny based on 5' region of E. canis gp200 gene (termed as p43 region) revealed four major clusters (A, B, C and D) and the Indian isolates fall under clusters A and B. Cluster A is characterized by an insertion of unique 141 bp tandem repeat sequence. Similar tandem repeat sequence was found in one of the E canis isolates from east-Asia, suggesting a possible divergence within this species. The study shows evidence for divergence of a new lineage within E. canis. The location of this insertion at the 'ankyrin repeat domains' containing region is suggestive of its possible role in modulation of host responses.
Collapse
Affiliation(s)
- Aravindh Babu R Parthiban
- Translational Research Platform for Veterinary Biologicals, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600051, India
| | - Azhahianambi Palavesam
- Translational Research Platform for Veterinary Biologicals, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600051, India.
| | - Sharmila Srinivasan
- Translational Research Platform for Veterinary Biologicals, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600051, India
| | - Arya Mohanan
- Translational Research Platform for Veterinary Biologicals, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600051, India
| | - Srikanta Ghosh
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
| | - Tirumurugaan Krishnaswamy Gopalan
- Translational Research Platform for Veterinary Biologicals, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600051, India
| |
Collapse
|
3
|
Srivastava P, Shukla A, Singh R, Kant R, Mishra N, Behera SP, Dwivedi GR, Yadav DK. Orientia tsutsugamushi: An Unusual Intracellular Bacteria-Adaptation Strategies, Available Antibiotics, and Alternatives for Treatment. Curr Microbiol 2024; 81:236. [PMID: 38907107 DOI: 10.1007/s00284-024-03754-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 05/28/2024] [Indexed: 06/23/2024]
Abstract
During evolution Orientia tsutsugamushi became a smarter obligate bacterium to establish as intracellular pathogens. O. tsutsugamushi is a human pathogenic bacterium responsible for 1 billion infections of scrub typhus. Several novel mechanisms make this bacterium unique (cell wall, genetic constitutions, secretion system, etc.). In 2007, O. tsutsugamushi Boryong was pioneer strain for whole-genome sequencing. But the fundamental biology of this bacterial cell is a mystery till date. The unusual biology makes this organism as model for host cell interaction. Only a few antibiotics are effective against this intracellular pathogen but emergence of less susceptibility toward antibiotics make the situation alarming. The review was captivated to highlight the unusual aspects of adaptation, antibiotics, and drugs beyond antibiotics.
Collapse
Affiliation(s)
- Prashansha Srivastava
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, 273013, India
| | - Aishwarya Shukla
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, 273013, India
| | - Rajeev Singh
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, 273013, India
| | - Rajni Kant
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, 273013, India
| | - Nalini Mishra
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, 273013, India
| | - Sthita P Behera
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, 273013, India
| | - Gaurav R Dwivedi
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, 273013, India.
| | - Dharmendra K Yadav
- College of Pharmacy, Gachon University of Medicine and Science, Hambakmoeiro 191, Yeonsu-Gu, Incheon, 21924, Korea
| |
Collapse
|
4
|
Das R, Arora R, Nadar K, Saroj S, Singh AK, Patil SA, Raman SK, Misra A, Bajpai U. Insights into the genomic features and lifestyle of B1 subcluster mycobacteriophages. J Basic Microbiol 2024; 64:e2400027. [PMID: 38548701 DOI: 10.1002/jobm.202400027] [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: 01/20/2024] [Accepted: 02/24/2024] [Indexed: 06/06/2024]
Abstract
Bacteriophages infecting Mycobacterium smegmatis mc2155 are numerous and, hence, are classified into clusters based on nucleotide sequence similarity. Analyzing phages belonging to clusters/subclusters can help gain deeper insights into their biological features and potential therapeutic applications. In this study, for genomic characterization of B1 subcluster mycobacteriophages, a framework of online tools was developed, which enabled functional annotation of about 55% of the previously deemed hypothetical proteins in B1 phages. We also studied the phenotype, lysogeny status, and antimycobacterial activity of 10 B1 phages against biofilm and an antibiotic-resistant M. smegmatis strain (4XR1). All 10 phages belonged to the Siphoviridae family, appeared temperate based on their spontaneous release from the putative lysogens and showed antibiofilm activity. The highest inhibitory and disruptive effects on biofilm were 64% and 46%, respectively. This systematic characterization using a combination of genomic and experimental tools is a promising approach to furthering our understanding of viral dark matter.
Collapse
Affiliation(s)
- Ritam Das
- Department of Life Science, Acharya Narendra Dev College, University of Delhi, Kalkaji, New Delhi, India
- Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Ritu Arora
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Kalkaji, New Delhi, India
| | - Kanika Nadar
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Kalkaji, New Delhi, India
| | - Saroj Saroj
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Kalkaji, New Delhi, India
| | - Amit K Singh
- Experimental Animal Facility, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Shripad A Patil
- Experimental Animal Facility, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Sunil K Raman
- Pharmaceutics and Pharmacokinetic Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Amit Misra
- Pharmaceutics and Pharmacokinetic Division, CSIR-Central Drug Research Institute, Lucknow, India
- Pharmaceutics and Pharmacokinetic Division, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Urmi Bajpai
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Kalkaji, New Delhi, India
| |
Collapse
|
5
|
Guo H, Zhao Q, Wang H, Zhu S, Dong H, Xie X, Wang L, Chen L, Han H. Molecular characterization and functional analysis of Eimeria tenella ankyrin repeat-containing protein. Eur J Protistol 2024; 94:126089. [PMID: 38749182 DOI: 10.1016/j.ejop.2024.126089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Chicken coccidiosis causes disastrous losses to the poultry industry all over the world. Eimeria tenella is the most prevalent of these disease-causing species. Our former RNA-seq indicated that E. tenella ankyrin repeat-containing protein (EtANK) was expressed differently between drug-sensitive (DS) and drug-resistant strains. In this study, we cloned EtANK and analyzed its translational and transcriptional levels using quantitative real-time PCR (qPCR) and western blotting. The data showed that EtANK was significantly upregulated in diclazuril-resistant (DZR) strain and maduramicin-resistant (MRR) strain compared with the drug-sensitive (DS) strain. In addition, the transcription levels in the DZR strains isolated from the field were higher than in the DS strain. The translation levels of EtANK were higher in unsporulated oocysts (UO) than in sporozoites (SZ), sporulated oocysts (SO), or second-generation merozoites (SM), and the protein levels in SM were significantly higher than in UO, SO, and SZ. The results of the indirect immunofluorescence localization showed that the protein was distributed mainly at the anterior region of SZ and on the surface and in the cytoplasm of SM. The fluorescence intensity increased further with its development in vitro. An anti-rEtANK polyclonal antibody inhibited the invasive ability of E. tenella in DF-1 cells. These results showed that EtANK may be related to host cell invasion, required for the parasite's growth in the host, and may be involved in the development of E. tenella resistance to some drugs.
Collapse
Affiliation(s)
- Huilin Guo
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture, Minhang, Shanghai 200241, PR China
| | - Qiping Zhao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture, Minhang, Shanghai 200241, PR China
| | - Haixia Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture, Minhang, Shanghai 200241, PR China
| | - Shunhai Zhu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture, Minhang, Shanghai 200241, PR China
| | - Hui Dong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture, Minhang, Shanghai 200241, PR China
| | - Xinrui Xie
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture, Minhang, Shanghai 200241, PR China
| | - Lihui Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture, Minhang, Shanghai 200241, PR China
| | - Lang Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture, Minhang, Shanghai 200241, PR China
| | - Hongyu Han
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture, Minhang, Shanghai 200241, PR China.
| |
Collapse
|
6
|
Nascimento Filho EG, Vieira ML, Dias M, Mendes MA, Sanchez FB, Setubal JC, Heinemann MB, Souza GO, Pimenta DC, Nascimento ALTO. Global proteome of the saprophytic strain Leptospira biflexa and comparative analysis with pathogenic strain Leptospira interrogans uncover new pathogenesis mechanisms. J Proteomics 2024; 297:105125. [PMID: 38364905 DOI: 10.1016/j.jprot.2024.105125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 01/08/2024] [Accepted: 02/05/2024] [Indexed: 02/18/2024]
Abstract
Leptospira is a genus of bacteria that includes free-living saprophytic species found in water or soil, and pathogenic species, which are the etiologic agents of leptospirosis. Besides all the efforts, there are only a few proteins described as virulence factors in the pathogenic strain L. interrogans. This work aims to perform L. biflexa serovar Patoc1 strain Paris global proteome and to compare with the proteome database of pathogenic L. interrogans serovar Copenhageni strain Fiocruz L1-130. We identified a total of 2327 expressed proteins of L. biflexa by mass spectrometry. Using the Get Homologues software with the global proteome of L. biflexa and L. interrogans, we found orthologous proteins classified into conserved, low conserved, and specific proteins. Comparative bioinformatic analyses were performed to understand the biological functions of the proteins, subcellular localization, the presence of signal peptide, structural domains, and motifs using public softwares. These results lead to the selection of 182 low conserved within the saprophyte, and 176 specific proteins of L. interrogans. It is anticipated that these findings will indicate further studies to uncover virulence factors in the pathogenic strain. This work presents for the first time the global proteome of saprophytic strain L. biflexa serovar Patoc, strain Patoc1. SIGNIFICANCE: The comparative analysis established an array of specific proteins in pathogenic strain that will narrow down the identification of immune protective proteins that will help fight leptospirosis.
Collapse
Affiliation(s)
- Edson G Nascimento Filho
- Laboratorio de Desenvolvimento de Vacinas, Instituto Butantan, SP, Brazil; Programa de Pos-Graduacao em Biotecnologia, USP-IBU-IPT, SP, Brazil
| | - Mônica L Vieira
- Departmento de Microbiologia, Instituto de Ciências Biológicas, UFMG, MG, Brazil
| | - Meriellen Dias
- Laboratorio Dempster, Departamento de Engenharia Química, Escola Politécnica, USP, SP, Brazil
| | - Maria A Mendes
- Laboratorio Dempster, Departamento de Engenharia Química, Escola Politécnica, USP, SP, Brazil
| | | | | | - Marcos B Heinemann
- Laboratório de Zoonoses Bacterianas do VPS, Faculdade de Medicina Veterinária e Zootecnia, USP, SP, Brazil
| | - Gisele O Souza
- Laboratório de Zoonoses Bacterianas do VPS, Faculdade de Medicina Veterinária e Zootecnia, USP, SP, Brazil
| | | | - Ana L T O Nascimento
- Laboratorio de Desenvolvimento de Vacinas, Instituto Butantan, SP, Brazil; Programa de Pos-Graduacao em Biotecnologia, USP-IBU-IPT, SP, Brazil.
| |
Collapse
|
7
|
Peng S, Ye L, Li Y, Wang F, Sun T, Wang L, Zhao J, Dong Z. Metagenomic insights into jellyfish-associated microbiome dynamics during strobilation. ISME COMMUNICATIONS 2024; 4:ycae036. [PMID: 38571744 PMCID: PMC10988111 DOI: 10.1093/ismeco/ycae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/05/2024]
Abstract
Host-associated microbiomes can play key roles in the metamorphosis of animals. Most scyphozoan jellyfish undergo strobilation in their life cycles, similar to metamorphosis in classic bilaterians. The exploration of jellyfish microbiomes may elucidate the ancestral mechanisms and evolutionary trajectories of metazoan-microbe associations and interactions during metamorphosis. However, current knowledge of the functional features of jellyfish microbiomes remains limited. Here, we performed a genome-centric analysis of associated microbiota across four successive life stages (polyp, early strobila, advanced strobila, and ephyra) during strobilation in the common jellyfish Aurelia coerulea. We observed shifts in taxonomic and functional diversity of microbiomes across distinct stages and proposed that the low microbial diversity in ephyra stage may be correlated with the high expression of the host-derived antimicrobial peptide aurelin. Furthermore, we recovered 43 high-quality metagenome-assembled genomes and determined the nutritional potential of the dominant Vibrio members. Interestingly, we observed increased abundances of genes related to the biosynthesis of amino acids, vitamins, and cofactors, as well as carbon fixation during the loss of host feeding ability, indicating the functional potential of Aurelia-associated microbiota to support the synthesis of essential nutrients. We also identified several potential mechanisms by which jellyfish-associated microbes establish stage-specific community structures and maintain stable colonization in dynamic host environments, including eukaryotic-like protein production, bacterial secretion systems, restriction-modification systems, and clustered regularly interspaced short palindromic repeats-Cas systems. Our study characterizes unique taxonomic and functional changes in jellyfish microbiomes during strobilation and provides foundations for uncovering the ancestral mechanism of host-microbe interactions during metamorphosis.
Collapse
Affiliation(s)
- Saijun Peng
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lijing Ye
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
| | - Yongxue Li
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanghan Wang
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingting Sun
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
| | - Lei Wang
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
| | - Jianmin Zhao
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijun Dong
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
8
|
Muro T, Hikida H, Fujii T, Kiuchi T, Katsuma S. Two Complete Genomes of Male-Killing Wolbachia Infecting Ostrinia Moth Species Illuminate Their Evolutionary Dynamics and Association with Hosts. MICROBIAL ECOLOGY 2023; 86:1740-1754. [PMID: 36810610 PMCID: PMC10497655 DOI: 10.1007/s00248-023-02198-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Wolbachia is an extremely widespread intracellular symbiont which causes reproductive manipulation on various arthropod hosts. Male progenies are killed in Wolbachia-infected lineages of the Japanese Ostrinia moth population. While the mechanism of male killing and the evolutionary interaction between host and symbiont are significant concerns for this system, the absence of Wolbachia genomic information has limited approaches to these issues. We determined the complete genome sequences of wFur and wSca, the male-killing Wolbachia of Ostrinia furnacalis and Ostrinia scapulalis. The two genomes shared an extremely high degree of homology, with over 95% of the predicted protein sequences being identical. A comparison of these two genomes revealed nearly minimal genome evolution, with a strong emphasis on the frequent genome rearrangements and the rapid evolution of ankyrin repeat-containing proteins. Additionally, we determined the mitochondrial genomes of both species' infected lineages and performed phylogenetic analyses to deduce the evolutionary dynamics of Wolbachia infection in the Ostrinia clade. According to the inferred phylogenetic relationship, two possible scenarios were proposed: (1) Wolbachia infection was established in the Ostrinia clade prior to the speciation of related species such as O. furnacalis and O. scapulalis, or (2) Wolbachia infection in these species was introgressively transferred from a currently unidentified relative. Simultaneously, the relatively high homology of mitochondrial genomes suggested recent Wolbachia introgression between infected Ostrinia species. The findings of this study collectively shed light on the host-symbiont interaction from an evolutionary standpoint.
Collapse
Affiliation(s)
- Tomohiro Muro
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Hiroyuki Hikida
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, 113-8657, Japan
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Takeshi Fujii
- Faculty of Agriculture, Setsunan University, Hirakata, Osaka, Japan
| | - Takashi Kiuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, 113-8657, Japan.
| |
Collapse
|
9
|
Harumoto T. Self-stabilization mechanism encoded by a bacterial toxin facilitates reproductive parasitism. Curr Biol 2023; 33:4021-4029.e6. [PMID: 37673069 DOI: 10.1016/j.cub.2023.08.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/30/2023] [Accepted: 08/10/2023] [Indexed: 09/08/2023]
Abstract
A wide variety of maternally transmitted endosymbionts in insects are associated with reproductive parasitism, whereby they interfere with host reproduction to increase the ratio of infected females and spread within populations.1,2 Recent successes in identifying bacterial factors responsible for reproductive parasitism3,4,5,6,7 as well as further omics approaches8,9,10,11,12 have highlighted the common appearance of deubiquitinase domains, although their biological roles-in particular, how they link to distinct manipulative phenotypes-remain poorly defined. Spiroplasma poulsonii is a helical and motile bacterial endosymbiont of Drosophila,13,14 which selectively kills male progeny with a male-killing toxin Spaid (S. poulsonii androcidin), which encodes an ovarian tumor (OTU) deubiquitinase domain.6 Artificial expression of Spaid in flies reproduces male-killing-associated pathologies that include abnormal apoptosis and neural defects during embryogenesis6,15,16,17,18,19; moreover, it highly accumulates on the dosage-compensated male X chromosome,20 congruent with cellular defects such as the DNA damage/chromatin bridge breakage specifically induced upon that chromosome.6,21,22,23 Here, I show that without the function of OTU, Spaid is polyubiquitinated and degraded through the host ubiquitin-proteasome pathway, leading to the attenuation of male-killing activity as shown previously.6 Furthermore, I find that Spaid utilizes its OTU domain to deubiquitinate itself in an intermolecular manner. Collectively, the deubiquitinase domain of Spaid serves as a self-stabilization mechanism to facilitate male killing in flies, optimizing a molecular strategy of endosymbionts that enables the efficient manipulation of the host at a low energetic cost.
Collapse
Affiliation(s)
- Toshiyuki Harumoto
- Hakubi Center for Advanced Research, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan; Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
| |
Collapse
|
10
|
González D, Morales-Olavarria M, Vidal-Veuthey B, Cárdenas JP. Insights into early evolutionary adaptations of the Akkermansia genus to the vertebrate gut. Front Microbiol 2023; 14:1238580. [PMID: 37779688 PMCID: PMC10540074 DOI: 10.3389/fmicb.2023.1238580] [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: 06/12/2023] [Accepted: 08/21/2023] [Indexed: 10/03/2023] Open
Abstract
Akkermansia, a relevant mucin degrader from the vertebrate gut microbiota, is a member of the deeply branched Verrucomicrobiota, as well as the only known member of this phylum to be described as inhabitants of the gut. Only a few Akkermansia species have been officially described so far, although there is genomic evidence addressing the existence of more species-level variants for this genus. This niche specialization makes Akkermansia an interesting model for studying the evolution of microorganisms to their adaptation to the gastrointestinal tract environment, including which kind of functions were gained when the Akkermansia genus originated or how the evolutionary pressure functions over those genes. In order to gain more insight into Akkermansia adaptations to the gastrointestinal tract niche, we performed a phylogenomic analysis of 367 high-quality Akkermansia isolates and metagenome-assembled genomes, in addition to other members of Verrucomicrobiota. This work was focused on three aspects: the definition of Akkermansia genomic species clusters and the calculation and functional characterization of the pangenome for the most represented species; the evolutionary relationship between Akkermansia and their closest relatives from Verrucomicrobiota, defining the gene families which were gained or lost during the emergence of the last Akkermansia common ancestor (LAkkCA) and; the evaluation of the evolutionary pressure metrics for each relevant gene family of main Akkermansia species. This analysis found 25 Akkermansia genomic species clusters distributed in two main clades, divergent from their non-Akkermansia relatives. Pangenome analyses suggest that Akkermansia species have open pangenomes, and the gene gain/loss model indicates that genes associated with mucin degradation (both glycoside hydrolases and peptidases), (micro)aerobic metabolism, surface interaction, and adhesion were part of LAkkCA. Specifically, mucin degradation is a very ancestral innovation involved in the origin of Akkermansia. Horizontal gene transfer detection suggests that Akkermansia could receive genes mostly from unknown sources or from other Gram-negative gut bacteria. Evolutionary metrics suggest that Akkemansia species evolved differently, and even some conserved genes suffered different evolutionary pressures among clades. These results suggest a complex evolutionary landscape of the genus and indicate that mucin degradation could be an essential feature in Akkermansia evolution as a symbiotic species.
Collapse
Affiliation(s)
- Dámariz González
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Mauricio Morales-Olavarria
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Boris Vidal-Veuthey
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Juan P. Cárdenas
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| |
Collapse
|
11
|
Shikov AE, Merkushova AV, Savina IA, Nizhnikov AA, Antonets KS. The man, the plant, and the insect: shooting host specificity determinants in Serratia marcescens pangenome. Front Microbiol 2023; 14:1211999. [PMID: 38029097 PMCID: PMC10656689 DOI: 10.3389/fmicb.2023.1211999] [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: 04/25/2023] [Accepted: 08/21/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Serratia marcescens is most commonly known as an opportunistic pathogen causing nosocomial infections. It, however, was shown to infect a wide range of hosts apart from vertebrates such as insects or plants as well, being either pathogenic or growth-promoting for the latter. Despite being extensively studied in terms of virulence mechanisms during human infections, there has been little evidence of which factors determine S. marcescens host specificity. On that account, we analyzed S. marcescens pangenome to reveal possible specificity factors. Methods We selected 73 high-quality genome assemblies of complete level and reconstructed the respective pangenome and reference phylogeny based on core genes alignment. To find an optimal pipeline, we tested current pangenomic tools and obtained several phylogenetic inferences. The pangenome was rich in its accessory component and was considered open according to the Heaps' law. We then applied the pangenome-wide associating method (pan-GWAS) and predicted positively associated gene clusters attributed to three host groups, namely, humans, insects, and plants. Results According to the results, significant factors relating to human infections included transcriptional regulators, lipoproteins, ABC transporters, and membrane proteins. Host preference toward insects, in its turn, was associated with diverse enzymes, such as hydrolases, isochorismatase, and N-acetyltransferase with the latter possibly exerting a neurotoxic effect. Finally, plant infection may be conducted through type VI secretion systems and modulation of plant cell wall synthesis. Interestingly, factors associated with plants also included putative growth-promoting proteins like enzymes performing xenobiotic degradation and releasing ammonium irons. We also identified overrepresented functional annotations within the sets of specificity factors and found that their functional characteristics fell into separate clusters, thus, implying that host adaptation is represented by diverse functional pathways. Finally, we found that mobile genetic elements bore specificity determinants. In particular, prophages were mainly associated with factors related to humans, while genetic islands-with insects and plants, respectively. Discussion In summary, functional enrichments coupled with pangenomic inferences allowed us to hypothesize that the respective host preference is carried out through distinct molecular mechanisms of virulence. To the best of our knowledge, the presented research is the first to identify specific genomic features of S. marcescens assemblies isolated from different hosts at the pangenomic level.
Collapse
Affiliation(s)
- Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Anastasiya V. Merkushova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Iuliia A. Savina
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| |
Collapse
|
12
|
Doering T, Tandon K, Topa SH, Pidot SJ, Blackall LL, van Oppen MJH. Genomic exploration of coral-associated bacteria: identifying probiotic candidates to increase coral bleaching resilience in Galaxea fascicularis. MICROBIOME 2023; 11:185. [PMID: 37596630 PMCID: PMC10439622 DOI: 10.1186/s40168-023-01622-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/14/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Reef-building corals are acutely threatened by ocean warming, calling for active interventions to reduce coral bleaching and mortality. Corals associate with a wide diversity of bacteria which can influence coral health, but knowledge of specific functions that may be beneficial for corals under thermal stress is scant. Under the oxidative stress theory of coral bleaching, bacteria that scavenge reactive oxygen (ROS) or nitrogen species (RNS) are expected to enhance coral thermal resilience. Further, bacterial carbon export might substitute the carbon supply from algal photosymbionts, enhance thermal resilience and facilitate bleaching recovery. To identify probiotic bacterial candidates, we sequenced the genomes of 82 pure-cultured bacteria that were isolated from the emerging coral model Galaxea fascicularis. RESULTS Genomic analyses showed bacterial isolates were affiliated with 37 genera. Isolates such as Ruegeria, Muricauda and Roseovarius were found to encode genes for the synthesis of the antioxidants mannitol, glutathione, dimethylsulfide, dimethylsulfoniopropionate, zeaxanthin and/or β-carotene. Genes involved in RNS-scavenging were found in many G. fascicularis-associated bacteria, which represents a novel finding for several genera (including Pseudophaeobacter). Transporters that are suggested to export carbon (semiSWEET) were detected in seven isolates, including Pseudovibrio and Roseibium. Further, a range of bacterial strains, including strains of Roseibium and Roseovarius, revealed genomic features that may enhance colonisation and association of bacteria with the coral host, such as secretion systems and eukaryote-like repeat proteins. CONCLUSIONS Our work provides an in-depth genomic analysis of the functional potential of G. fascicularis-associated bacteria and identifies novel combinations of traits that may enhance the coral's ability to withstand coral bleaching. Identifying and characterising bacteria that are beneficial for corals is critical for the development of effective probiotics that boost coral climate resilience. Video Abstract.
Collapse
Affiliation(s)
- Talisa Doering
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Kshitij Tandon
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Sanjida H. Topa
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC Australia
| | - Linda L. Blackall
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Madeleine J. H. van Oppen
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
- Australian Institute of Marine Science, Townsville, QLD Australia
| |
Collapse
|
13
|
Chen TT, Lin Y, Zhang S, Liu S, Song L, Zhong W, Luo ZQ, Han A. Atypical Legionella GTPase effector hijacks host vesicular transport factor p115 to regulate host lipid droplet. SCIENCE ADVANCES 2022; 8:eadd7945. [PMID: 36525490 PMCID: PMC9757750 DOI: 10.1126/sciadv.add7945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
The intracellular bacterial pathogen Legionella pneumophila uses hundreds of effector proteins to manipulate multiple processes of the host cells to establish a replicative niche known as Legionella-containing vacuole (LCV). Biogenesis of the LCV has been known to depend on host small guanosine triphosphatases (GTPases), but whether bacterial effector GTPases are also involved remains unknown. Here, we show that an ankyrin repeat containing effector LegA15 localizes directly in host lipid droplets (LDs), leading to Golgi apparatus fragmentation of the host cells by hijacking the host vesicular transport factor p115. LegA15 is a GTPase with a unique catalytic mechanism, unlike any eukaryotic small GTPases. Moreover, the effector LegA15 co-opts p115 to modulate homeostasis of the host LDs in its GTPase-dependent manner. Together, our data reveal that an atypical GTPase effector regulates the host LDs through impeding the vesicle secretion system of the host cells for intracellular life cycle of Legionella.
Collapse
Affiliation(s)
- Tao-Tao Chen
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences and Faculty of Medicine, Xiamen University, Xiamen, Fujian 361102, China
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Yanling Lin
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences and Faculty of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Shijun Zhang
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences and Faculty of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Shuxin Liu
- Department of Respiratory Medicine and Center of Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory of Zoonotic Diseases, The First Hospital, Jilin University, Changchun, China
| | - Lei Song
- Department of Respiratory Medicine and Center of Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory of Zoonotic Diseases, The First Hospital, Jilin University, Changchun, China
| | - Wenhong Zhong
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Zhao-Qing Luo
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Aidong Han
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences and Faculty of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| |
Collapse
|
14
|
A Wolbachia factor for male killing in lepidopteran insects. Nat Commun 2022; 13:6764. [PMID: 36376299 PMCID: PMC9663696 DOI: 10.1038/s41467-022-34488-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022] Open
Abstract
Bacterial symbionts, such as Wolbachia species, can manipulate the sexual development and reproduction of their insect hosts. For example, Wolbachia infection induces male-specific death in the Asian corn borer Ostrinia furnacalis by targeting the host factor Masculinizer (Masc), an essential protein for masculinization and dosage compensation in lepidopteran insects. Here we identify a Wolbachia protein, designated Oscar, which interacts with Masc via its ankyrin repeats. Embryonic expression of Oscar inhibits Masc-induced masculinization and leads to male killing in two lepidopteran insects, O. furnacalis and the silkworm Bombyx mori. Our study identifies a mechanism by which Wolbachia induce male killing of host progeny.
Collapse
|
15
|
Walser M, Mayor J, Rothenberger S. Designed Ankyrin Repeat Proteins: A New Class of Viral Entry Inhibitors. Viruses 2022; 14:2242. [PMID: 36298797 PMCID: PMC9611651 DOI: 10.3390/v14102242] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 08/08/2023] Open
Abstract
Designed ankyrin repeat proteins (DARPins) are engineered proteins comprising consensus designed ankyrin repeats as scaffold. Tightly packed repeats form a continuous hydrophobic core and a large groove-like solvent-accessible surface that creates a binding surface. DARPin domains recognizing a target of interest with high specificity and affinity can be generated using a synthetic combinatorial library and in vitro selection methods. They can be linked together in a single molecule to build multispecific and multifunctional proteins without affecting expression or function. The modular architecture of DARPins offers unprecedented possibilities of design and opens avenues for innovative antiviral strategies.
Collapse
Affiliation(s)
- Marcel Walser
- Molecular Partners AG, Wagistrasse 14, 8952 Zurich-Schlieren, Switzerland
| | - Jennifer Mayor
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700 Spiez, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Rue du Bugnon 48, 1011 Lausanne, Switzerland
| | - Sylvia Rothenberger
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700 Spiez, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Rue du Bugnon 48, 1011 Lausanne, Switzerland
| |
Collapse
|
16
|
Panda S, Swain SK, Sahu BP, Sarangi R. Gene expression and involvement of signaling pathways during host-pathogen interplay in Orientia tsutsugamushi infection. 3 Biotech 2022; 12:180. [PMID: 35860421 PMCID: PMC9295102 DOI: 10.1007/s13205-022-03239-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/18/2022] [Indexed: 11/22/2022] Open
Abstract
Scrub typhus is a neglected tropical disease that affects one-third of the world’s population. The disease is caused by Orientia tsutsugamushi (OT), an obligate intracellular Gram-negative bacterium. OT efficiently escapes from the endosomal pathway after entering the host cell and replicates inside cytosol. OT infection promotes cellular autophagy, the autonomous defense mechanism unlike other bacteria. This study has discussed the bacterial invasion process through the extracellular matrix and the immune response activated by the bacterium within the hosts. Furthermore, we have emphasized the importance of extracellular matrix and their cross-talk with the immune cells, such as, macrophages, neutrophils, and dendritic cells followed by their inflammatory response. We have also put an insight into the host factors associated with signaling pathways during scrub typhus disease with a special focus on the OT-induced stress response, autophagy, apoptosis, and innate immunity. Multiple cytokines and chemokines play a significant role in activating different immune-related signaling pathways. Due to the presence of high antigenic diversity among strains, the signaling pathways during the host–pathogen interplay of OT with its host is very complicated. Thus, it hinders to mitigate the severity of the pandemic occurred by the respective pathogen. Our investigation will provide a useful guide to better understand the virulence and physiology of this intracellular pathogen which will lead towards a better therapeutic diagnosis and vaccine development.
Collapse
Affiliation(s)
- Subhasmita Panda
- Department of Pediatrics, IMS and SUM Hospital, Siksha 'O' Anusandhan Deemed to be University, K8, Kalinga Nagar, Bhubaneswar, Odisha 751003 India
| | - Subrat Kumar Swain
- Centre for Genomics and Biomedical Informatics, IMS and SUM Hospital, Siksha 'O' Anusandhan Deemed to be University, K8, Kalinga Nagar, Bhubaneswar, Odisha 751003 India
| | - Basanta Pravas Sahu
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552 India
| | - Rachita Sarangi
- Department of Pediatrics, IMS and SUM Hospital, Siksha 'O' Anusandhan Deemed to be University, K8, Kalinga Nagar, Bhubaneswar, Odisha 751003 India
| |
Collapse
|
17
|
de Obeso Fernández Del Valle A, Gómez-Montalvo J, Maciver SK. Acanthamoeba castellanii exhibits intron retention during encystment. Parasitol Res 2022; 121:2615-2622. [PMID: 35776211 DOI: 10.1007/s00436-022-07578-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/14/2022] [Indexed: 11/24/2022]
Abstract
Intron retention (IR) refers to the mechanism of alternative splicing in which an intron is not excised from the mature transcript. IR in the cosmopolitan free-living amoeba Acanthamoeba castellanii has not been studied. We performed an analysis of RNA sequencing data during encystment to identify genes that presented differentially retained introns during this process. We show that IR increases during cyst formation, indicating a potential mechanism of gene regulation that could help downregulate metabolism. We identify 69 introns from 67 genes that are differentially retained comparing the trophozoite stage and encystment after 24 and 48 h. These genes include several hypothetical proteins. We show different patterns of IR during encystment taking as examples a lipase, a peroxin-3 protein, an Fbox domain containing protein, a proteasome subunit, a polynucleotide adenylyltransferase, and a tetratricopeptide domain containing protein. A better understanding of IR in Acanthamoeba, and even other protists, could help elucidate changes in life cycle and combat disease such as Acanthamoeba keratitis in which the cyst is key for its persistence.
Collapse
Affiliation(s)
- Alvaro de Obeso Fernández Del Valle
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Ave. Eugenio Garza Sada 2501, 64849, Monterrey, Mexico.
| | - Jesús Gómez-Montalvo
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Ave. Eugenio Garza Sada 2501, 64849, Monterrey, Mexico
| | - Sutherland K Maciver
- Centre for Discovery Brain Sciences, Edinburgh Medical School, Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, Scotland, UK
| |
Collapse
|
18
|
Poxviral ANKR/F-box Proteins: Substrate Adapters for Ubiquitylation and More. Pathogens 2022; 11:pathogens11080875. [PMID: 36014996 PMCID: PMC9414399 DOI: 10.3390/pathogens11080875] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 02/01/2023] Open
Abstract
Poxviruses are double-stranded DNA viruses that infect insects and a variety of vertebrate species. The large genomes of poxviruses contain numerous genes that allow these viruses to successfully establish infection, including those that help evade the host immune response and prevent cell death. Ankyrin-repeat (ANKR)/F-box proteins are almost exclusively found in poxviruses, and they function as substrate adapters for Skp1-Cullin-1-F-box protein (SCF) multi-subunit E3 ubiquitin (Ub)-ligases. In this regard, they use their C-terminal F-box domain to bind Skp1, Cullin-1, and Roc1 to recruit cellular E2 enzymes to facilitate the ubiquitylation, and subsequent proteasomal degradation, of proteins bound to their N-terminal ANKRs. However, these proteins do not just function as substrate adapters as they also have Ub-independent activities. In this review, we examine both Ub-dependent and -independent activities of ANKR/F-box proteins and discuss how poxviruses use these proteins to counteract the host innate immune response, uncoat their genome, replicate, block cell death, and influence transcription. Finally, we consider important outstanding questions that need to be answered in order to better understand the function of this versatile protein family.
Collapse
|
19
|
The PH Domain and C-Terminal polyD Motif of Phafin2 Exhibit a Unique Concurrence in Animals. MEMBRANES 2022; 12:membranes12070696. [PMID: 35877899 PMCID: PMC9324892 DOI: 10.3390/membranes12070696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 01/27/2023]
Abstract
Phafin2, a member of the Phafin family of proteins, contributes to a plethora of cellular activities including autophagy, endosomal cargo transportation, and macropinocytosis. The PH and FYVE domains of Phafin2 play key roles in membrane binding, whereas the C-terminal poly aspartic acid (polyD) motif specifically autoinhibits the PH domain binding to the membrane phosphatidylinositol 3-phosphate (PtdIns3P). Since the Phafin2 FYVE domain also binds PtdIns3P, the role of the polyD motif remains unclear. In this study, bioinformatics tools and resources were employed to determine the concurrence of the PH-FYVE module with the polyD motif among Phafin2 and PH-, FYVE-, or polyD-containing proteins from bacteria to humans. FYVE was found to be an ancient domain of Phafin2 and is related to proteins that are present in both prokaryotes and eukaryotes. Interestingly, the polyD motif only evolved in Phafin2 and PH- or both PH-FYVE-containing proteins in animals. PolyD motifs are absent in PH domain-free FYVE-containing proteins, which usually display cellular trafficking or autophagic functions. Moreover, the prediction of the Phafin2-interacting network indicates that Phafin2 primarily cross-talks with proteins involved in autophagy, protein trafficking, and neuronal function. Taken together, the concurrence of the polyD motif with the PH domain may be associated with complex cellular functions that evolved specifically in animals.
Collapse
|
20
|
Whole-Genome Sequencing and Comparative Genome Analysis of Fusarium solani-melongenae Causing Fusarium Root and Stem Rot in Sweetpotatoes. Microbiol Spectr 2022; 10:e0068322. [PMID: 35863027 PMCID: PMC9430127 DOI: 10.1128/spectrum.00683-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sweetpotato (Ipomoea batatas) is the eighth most important crop globally. However, the production and quality of sweetpotatoes are threatened by Fusarium diseases that are prevalent around the world. In this study, a Fusarium species that causes root and stem rot in sweetpotatoes was studied. The pathogenic fungus CRI 24-3 was isolated and sequenced using third- and next-generation sequencing techniques and a 49.6 Mb chromosome-level draft genome containing 15,374 putative coding genes were obtained. Molecular phylogenetic analysis showed that CRI 24-3 was an F. solani-melongenae strain within clade 3 of the F. solani species complex (FSSC). CRI 24-3 showed a relatively high number of virulence factors, such as carbohydrate-active enzymes (CAZymes), pathogen-host interaction (PHI) proteins, and terpene synthases (TSs), compared with the number of those identified in other sequenced FSSC members. Comparative genome analysis revealed considerable conservation and unique characteristics between CRI 24-3 and other FSSC species. In conclusion, the findings in the current study provide important genetic information about F. solani-melongenae and should be useful in the exploration of pathogenicity mechanisms and the development of Fusarium disease management strategies. IMPORTANCE Fusarium root and stem rot in sweetpotato are prevalent in the main sweetpotato-growing areas in China, and fungal isolation, morphological characteristics, and molecular phylogenetic analysis of the disease causal agent (F. solani-melongenae isolate CRI 24-3) were systematically studied. The genome sequence of F. solani-melongenae isolates CRI 24-3 was first reported, which should provide a basis for genome assembly of other closely related Fusarium species. Carbohydrate-active enzymes predicted in CRI 24-3 may be important to convert the substantial polysaccharides to sustainable and renewable energy. Moreover, other virulence factors facilitating Fusarium diseases, including effectors and toxic secondary metabolites, are ideal objects for pathogenicity mechanism research and molecular targets for fungicide development. The findings of comparative genome analysis of CRI 24-3 and 15 sequenced members of the F. solani species complex help promote an integral understanding of genomic features and evolutionary relationships in Fusarium.
Collapse
|
21
|
Wang P, Li M, Dong L, Zhang C, Xie W. Comparative Genomics of Thaumarchaeota From Deep-Sea Sponges Reveal Their Niche Adaptation. Front Microbiol 2022; 13:869834. [PMID: 35859738 PMCID: PMC9289680 DOI: 10.3389/fmicb.2022.869834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
Thaumarchaeota account for a large portion of microbial symbionts in deep-sea sponges and are even dominant in some cases. In this study, we investigated three new sponge-associated Thaumarchaeota from the deep West Pacific Ocean. Thaumarchaeota were found to be the most dominant phylum in this sponge by both prokaryotic 16S rRNA amplicons and metagenomic sequencing. Fifty-seven published Thaumarchaeota genomes from sponges and other habitats were included for genomic comparison. Similar to shallow sponge-associated Thaumarchaeota, those Thaumarchaeota in deep-sea sponges have extended genome sizes and lower coding density compared with their free-living lineages. Thaumarchaeota in deep-sea sponges were specifically enriched in genes related to stress adapting, symbiotic adhesion and stability, host–microbe interaction and protein transportation. The genes involved in defense mechanisms, such as the restriction-modification system, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system, and toxin-antitoxin system were commonly enriched in both shallow and deep sponge-associated Thaumarchaeota. Our study demonstrates the significant effects of both depth and symbiosis on forming genomic characteristics of Thaumarchaeota, and provides novel insights into their niche adaptation in deep-sea sponges.
Collapse
Affiliation(s)
- Peng Wang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Minchun Li
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Liang Dong
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Cheng Zhang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- *Correspondence: Wei Xie,
| |
Collapse
|
22
|
The Ankyrin Repeat Protein RARP-1 Is a Periplasmic Factor That Supports Rickettsia parkeri Growth and Host Cell Invasion. J Bacteriol 2022; 204:e0018222. [PMID: 35727033 DOI: 10.1128/jb.00182-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rickettsia spp. are obligate intracellular bacterial pathogens that have evolved a variety of strategies to exploit their host cell niche. However, the bacterial factors that contribute to this intracellular lifestyle are poorly understood. Here, we show that the conserved ankyrin repeat protein RARP-1 supports Rickettsia parkeri infection. Specifically, RARP-1 promotes efficient host cell entry and growth within the host cytoplasm, but it is not necessary for cell-to-cell spread or evasion of host autophagy. We further demonstrate that RARP-1 is not secreted into the host cytoplasm by R. parkeri. Instead, RARP-1 resides in the periplasm, and we identify several binding partners that are predicted to work in concert with RARP-1 during infection. Altogether, our data reveal that RARP-1 plays a critical role in the rickettsial life cycle. IMPORTANCE Rickettsia spp. are obligate intracellular bacterial pathogens that pose a growing threat to human health. Nevertheless, their strict reliance on a host cell niche has hindered investigation of the molecular mechanisms driving rickettsial infection. This study yields much-needed insight into the Rickettsia ankyrin repeat protein RARP-1, which is conserved across the genus but has not yet been functionally characterized. Earlier work had suggested that RARP-1 is secreted into the host cytoplasm. However, the results from this work demonstrate that R. parkeri RARP-1 resides in the periplasm and is important both for invasion of host cells and for growth in the host cell cytoplasm. These results reveal RARP-1 as a novel regulator of the rickettsial life cycle.
Collapse
|
23
|
Giddings LA, Kunstman K, Moumen B, Asiama L, Green S, Delafont V, Brockley M, Samba-Louaka A. Isolation and Genome Analysis of an Amoeba-Associated Bacterium Dyella terrae Strain Ely Copper Mine From Acid Rock Drainage in Vermont, United States. Front Microbiol 2022; 13:856908. [PMID: 35677904 PMCID: PMC9169046 DOI: 10.3389/fmicb.2022.856908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Protozoa play important roles in microbial communities, regulating populations via predation and contributing to nutrient cycling. While amoebae have been identified in acid rock drainage (ARD) systems, our understanding of their symbioses in these extreme environments is limited. Here, we report the first isolation of the amoeba Stemonitis from an ARD environment as well as the genome sequence and annotation of an associated bacterium, Dyella terrae strain Ely Copper Mine, from Ely Brook at the Ely Copper Mine Superfund site in Vershire, Vermont, United States. Fluorescent in situ hybridization analysis showed this bacterium colonizing cells of Stemonitis sp. in addition to being outside of amoebal cells. This amoeba-resistant bacterium is Gram-negative with a genome size of 5.36 Mbp and GC content of 62.5%. The genome of the D. terrae strain Ely Copper Mine encodes de novo biosynthetic pathways for amino acids, carbohydrates, nucleic acids, and lipids. Genes involved in nitrate (1) and sulfate (7) reduction, metal (229) and antibiotic resistance (37), and secondary metabolite production (6) were identified. Notably, 26 hydrolases were identified by RAST as well as other biomass degradation genes, suggesting roles in carbon and energy cycling within the microbial community. The genome also contains type IV secretion system genes involved in amoebae resistance, revealing how this bacterium likely survives predation from Stemonitis sp. This genome analysis and the association of D. terrae strain Ely Copper Mine with Stemonitis sp. provide insight into the functional roles of amoebae and bacteria within ARD environments.
Collapse
Affiliation(s)
- Lesley-Ann Giddings
- Department of Chemistry, Smith College, Northampton, MA, United States.,Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States
| | - Kevin Kunstman
- Research Resources Center, University of Illinois at Chicago, Chicago, IL, United States
| | - Bouziane Moumen
- Laboratoire Ecologie et Biologie des Interactions, Université de Poitiers, UMR7267, Poitiers, France
| | - Laurent Asiama
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States
| | - Stefan Green
- Research Resources Center, University of Illinois at Chicago, Chicago, IL, United States
| | - Vincent Delafont
- Laboratoire Ecologie et Biologie des Interactions, Université de Poitiers, UMR7267, Poitiers, France
| | - Matthew Brockley
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States
| | - Ascel Samba-Louaka
- Laboratoire Ecologie et Biologie des Interactions, Université de Poitiers, UMR7267, Poitiers, France
| |
Collapse
|
24
|
Kim Y, Wang J, Clemens EG, Grab DJ, Dumler JS. Anaplasma phagocytophilum Ankyrin A Protein (AnkA) Enters the Nucleus Using an Importin-β-, RanGTP-Dependent Mechanism. Front Cell Infect Microbiol 2022; 12:828605. [PMID: 35719343 PMCID: PMC9204287 DOI: 10.3389/fcimb.2022.828605] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/20/2022] [Indexed: 12/30/2022] Open
Abstract
Anaplasma phagocytophilum, a tick-borne obligately intracellular bacterium of neutrophils, causes human granulocytic anaplasmosis. Ankyrin A (AnkA), an effector protein with multiple ankyrin repeats (AR) is injected via type IV-secretion into the host neutrophil to gain access to the nucleus where it modifies the epigenome to promote microbial fitness and propagation. AR proteins transported into the host cell nucleus must use at least one of two known eukaryotic pathways, the classical importin β-dependent pathway, and/or the RanGDP- and AR (ankyrin-repeat)-dependent importin β-independent (RaDAR) pathway. Truncation of the first four AnkA N-terminal ARs (AR1-4), but not other regions, prevents AnkA nuclear accumulation. To investigate the mechanism of nuclear import, we created point mutations of AnkA N-terminal ARs, predicted to interfere with RaDAR protein import, and used importazole, a specific inhibitor of the importin α/β, RanGTP-dependent pathway. Nuclear colocalization analysis shows that nuclear localization of AnkA is unaffected by single AR1-4 mutations but is significantly reduced by single mutations in consecutive ARs suggesting RaDAR protein nuclear import. However, AnkA nuclear localization was also decreased with importazole, and with GTPγS. Furthermore, A. phagocytophilum growth in HL-60 cells was completely suppressed with importazole, indicating that A. phagocytophilum propagation requires a β-importin-dependent pathway. A typical classical NLS overlapping AR4 was subsequently identified suggesting the primacy of the importin-α/β system in AnkA nuclear localization. Whether the mutational studies of putative key residues support RaDAR NLS function or simply reflect structural changes that diminish engagement of an AR-NLS-importin pathway needs to be resolved through careful structure-function studies.
Collapse
Affiliation(s)
- Yuri Kim
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Jianyang Wang
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Emily G. Clemens
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Dennis J. Grab
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - J. Stephen Dumler
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States,*Correspondence: J. Stephen Dumler,
| |
Collapse
|
25
|
Sharma D, Kumar S, Sharma A, Kumar R, Kumar R, Kulharia M, Kumar M. Functional assignment to hypothetical proteins in Orientia tsutsugamushistrain Ikeda. Bioinformation 2022; 18:188-195. [PMID: 36518125 PMCID: PMC9722422 DOI: 10.6026/97320630018188] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/11/2022] [Accepted: 03/31/2022] [Indexed: 09/19/2023] Open
Abstract
Orientia tsutsugamushi(O. tsutsugamushi) is an intracellular bacterial pathogen which causes zoonosis scrub typhus in humans. Genome of O. tsutsugamushi strain Ikeda contains 214 hypothetical proteins (HPs) which is nearly 20% of the total proteins. Domain and family based functional analysis of HPs results in the annotation of 44 hypothetical proteins. The annotated HPs were classified in to five main classes namely, gene expression and regulation, transport, metabolism, cell signaling and proteolysis. Thus, computational analysis of HPs helps to understand their putative roles in various biological and cellular processes, including pathogenesis for further consideration as potential therapeutic targets.
Collapse
Affiliation(s)
- Dixit Sharma
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, India - 176206
| | - Sunil Kumar
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, India - 176206
| | - Ankita Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, India - 176206
| | - Rakesh Kumar
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, India - 176206
| | - Ranjit Kumar
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, India - 176206
| | - Mahesh Kulharia
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, India - 176206
| | - Manish Kumar
- Department of Chemistry and Chemical Sciences, School of Physical and Material Science, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, India - 176206
| |
Collapse
|
26
|
Maharajan AD, Hjerde E, Hansen H, Willassen NP. Quorum Sensing Controls the CRISPR and Type VI Secretion Systems in Aliivibrio wodanis 06/09/139. Front Vet Sci 2022; 9:799414. [PMID: 35211539 PMCID: PMC8861277 DOI: 10.3389/fvets.2022.799414] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/12/2022] [Indexed: 12/26/2022] Open
Abstract
For bacteria to thrive in an environment with competitors, phages and environmental cues, they use different strategies, including Type VI Secretion Systems (T6SSs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) to compete for space. Bacteria often use quorum sensing (QS), to coordinate their behavior as the cell density increases. Like other aliivibrios, Aliivibrio wodanis 06/09/139 harbors two QS systems, the main LuxS/LuxPQ system and an N-acyl homoserine lactone (AHL)-mediated AinS/AinR system and a master QS regulator, LitR. To explore the QS and survival strategies, we performed genome analysis and gene expression profiling on A. wodanis and two QS mutants (ΔainS and ΔlitR) at two cell densities (OD600 2.0 and 6.0) and temperatures (6 and 12°C). Genome analysis of A. wodanis revealed two CRISPR systems, one without a cas loci (CRISPR system 1) and a type I-F CRISPR system (CRISPR system 2). Our analysis also identified three main T6SS clusters (T6SS1, T6SS2, and T6SS3) and four auxiliary clusters, as well about 80 potential Type VI secretion effectors (T6SEs). When comparing the wildtype transcriptome data at different cell densities and temperatures, 13–18% of the genes were differentially expressed. The CRISPR system 2 was cell density and temperature-independent, whereas the CRISPR system 1 was temperature-dependent and cell density-independent. The primary and auxiliary clusters of T6SSs were both cell density and temperature-dependent. In the ΔlitR and ΔainS mutants, several CRISPR and T6SS related genes were differentially expressed. Deletion of litR resulted in decreased expression of CRISPR system 1 and increased expression of CRISPR system 2. The T6SS1 and T6SS2 gene clusters were less expressed while the T6SS3 cluster was highly expressed in ΔlitR. Moreover, in ΔlitR, the hcp1 gene was strongly activated at 6°C compared to 12°C. AinS positively affected the csy genes in the CRISPR system 2 but did not affect the CRISPR arrays. Although AinS did not significantly affect the expression of T6SSs, the hallmark genes of T6SS (hcp and vgrG) were AinS-dependent. The work demonstrates that T6SSs and CRISPR systems in A. wodanis are QS dependent and may play an essential role in survival in its natural environment.
Collapse
Affiliation(s)
- Amudha Deepalakshmi Maharajan
- Norwegian Structural Biology Center and Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
- *Correspondence: Amudha Deepalakshmi Maharajan
| | - Erik Hjerde
- Norwegian Structural Biology Center and Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
- Centre for Bioinformatics, Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Hilde Hansen
- Norwegian Structural Biology Center and Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Nils Peder Willassen
- Norwegian Structural Biology Center and Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
- Centre for Bioinformatics, Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
- Nils Peder Willassen
| |
Collapse
|
27
|
Massey JH, Newton ILG. Diversity and function of arthropod endosymbiont toxins. Trends Microbiol 2022; 30:185-198. [PMID: 34253453 PMCID: PMC8742837 DOI: 10.1016/j.tim.2021.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 02/03/2023]
Abstract
Bacterial endosymbionts induce dramatic phenotypes in their arthropod hosts, including cytoplasmic incompatibility, feminization, parthenogenesis, male killing, parasitoid defense, and pathogen blocking. The molecular mechanisms underlying these effects remain largely unknown but recent evidence suggests that protein toxins secreted by the endosymbionts play a role. Here, we describe the diversity and function of endosymbiont proteins with homology to known bacterial toxins. We focus on maternally transmitted endosymbionts belonging to the Wolbachia, Rickettsia, Arsenophonus, Hamiltonella, Spiroplasma, and Cardinium genera because of their ability to induce the above phenotypes. We identify at least 16 distinct toxin families with diverse enzymatic activities, including AMPylases, nucleases, proteases, and glycosyltransferases. Notably, several annotated toxins contain domains with homology to eukaryotic proteins, suggesting that arthropod endosymbionts mimic host biochemistry to manipulate host physiology, similar to bacterial pathogens.
Collapse
Affiliation(s)
| | - Irene L. G. Newton
- Department of Biology, Indiana University, Bloomington, Indiana, USA,Corresponding author,
| |
Collapse
|
28
|
Akkapeddi P, Teng KW, Koide S. Monobodies as tool biologics for accelerating target validation and druggable site discovery. RSC Med Chem 2021; 12:1839-1853. [PMID: 34820623 PMCID: PMC8597423 DOI: 10.1039/d1md00188d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/26/2021] [Indexed: 12/21/2022] Open
Abstract
Despite increased investment and technological advancement, new drug approvals have not proportionally increased. Low drug approval rates, particularly for new targets, are linked to insufficient target validation at early stages. Thus, there remains a strong need for effective target validation techniques. Here, we review the use of synthetic binding proteins as tools for drug target validation, with focus on the monobody platform among several advanced synthetic binding protein platforms. Monobodies with high affinity and high selectivity can be rapidly developed against challenging targets, such as KRAS mutants, using protein engineering technologies. They have strong tendency to bind to functional sites and thus serve as drug-like molecules, and they can serve as targeting ligands for constructing bio-PROTACs. Genetically encoded monobodies are effective "tool biologics" for validating intracellular targets. They promote crystallization and help reveal the atomic structures of the monobody-target interface, which can inform drug design. Using case studies, we illustrate the potential of the monobody technology in accelerating target validation and small-molecule drug discovery.
Collapse
Affiliation(s)
- Padma Akkapeddi
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
| | - Kai Wen Teng
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine New York NY USA
| |
Collapse
|
29
|
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
|
30
|
Waterworth SC, Parker-Nance S, Kwan JC, Dorrington RA. Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts. mBio 2021; 12:e0157721. [PMID: 34519538 PMCID: PMC8546597 DOI: 10.1128/mbio.01577-21] [Citation(s) in RCA: 3] [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: 06/07/2021] [Accepted: 08/13/2021] [Indexed: 11/20/2022] Open
Abstract
The fossil record indicates that the earliest evidence of extant marine sponges (phylum Porifera) existed during the Cambrian explosion and that their symbiosis with microbes may have begun in their extinct ancestors during the Precambrian period. Many symbionts have adapted to their sponge host, where they perform specific, specialized functions. There are also widely distributed bacterial taxa such as Poribacteria, SAUL, and Tethybacterales that are found in a broad range of invertebrate hosts. Here, we added 11 new genomes to the Tethybacterales order, identified a novel family, and show that functional potential differs between the three Tethybacterales families. We compare the Tethybacterales with the well-characterized Entoporibacteria and show that these symbionts appear to preferentially associate with low-microbial abundance (LMA) and high-microbial abundance (HMA) sponges, respectively. Within these sponges, we show that these symbionts likely perform distinct functions and may have undergone multiple association events, rather than a single association event followed by coevolution. IMPORTANCE Marine sponges often form symbiotic relationships with bacteria that fulfil a specific need within the sponge holobiont, and these symbionts are often conserved within a narrow range of related taxa. To date, there exist only three known bacterial taxa (Entoporibacteria, SAUL, and Tethybacterales) that are globally distributed and found in a broad range of sponge hosts, and little is known about the latter two. We show that the functional potential of broad-host range symbionts is conserved at a family level and that these symbionts have been acquired several times over evolutionary history. Finally, it appears that the Entoporibacteria are associated primarily with high-microbial abundance sponges, while the Tethybacterales associate with low-microbial abundance sponges.
Collapse
Affiliation(s)
- Samantha C. Waterworth
- Division of Pharmaceutical Sciences, University of Wisconsin, Madison, Wisconsin, USA
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Shirley Parker-Nance
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
- South African Environmental Observation Network, Elwandle Coastal Node, Gqeberha (Port Elizabeth), South Africa
| | - Jason C. Kwan
- Division of Pharmaceutical Sciences, University of Wisconsin, Madison, Wisconsin, USA
| | - Rosemary A. Dorrington
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
- South African Institute for Aquatic Biodiversity, Makhanda, South Africa
| |
Collapse
|
31
|
Tortorelli G, Oakley CA, Davy SK, van Oppen MJH, McFadden GI. Cell wall proteomic analysis of the cnidarian photosymbionts Breviolum minutum and Cladocopium goreaui. J Eukaryot Microbiol 2021; 69:e12870. [PMID: 34448326 PMCID: PMC9293036 DOI: 10.1111/jeu.12870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The algal cell wall is an important cellular component that functions in defense, nutrient utilization, signaling, adhesion, and cell–cell recognition—processes important in the cnidarian–dinoflagellate symbiosis. The cell wall of symbiodiniacean dinoflagellates is not well characterized. Here, we present a method to isolate cell walls of Symbiodiniaceae and prepare cell‐wall‐enriched samples for proteomic analysis. Label‐free liquid chromatography–electrospray ionization tandem mass spectrometry was used to explore the surface proteome of two Symbiodiniaceae species from the Great Barrier Reef: Breviolum minutum and Cladocopium goreaui. Transporters, hydrolases, translocases, and proteins involved in cell‐adhesion and protein–protein interactions were identified, but the majority of cell wall proteins had no homologues in public databases. We propose roles for some of these proteins in the cnidarian–dinoflagellate symbiosis. This work provides the first proteomics investigation of cell wall proteins in the Symbiodiniaceae and represents a basis for future explorations of the roles of cell wall proteins in Symbiodiniaceae and other dinoflagellates.
Collapse
Affiliation(s)
- Giada Tortorelli
- School of Biosciences, The University of Melbourne, Melbourne, Vic, Australia
| | - Clinton A Oakley
- School of Biological Sciences, Victoria University of Wellington, Kelburn, New Zealand
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Kelburn, New Zealand
| | - Madeleine J H van Oppen
- School of Biosciences, The University of Melbourne, Melbourne, Vic, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia
| | - Geoffrey I McFadden
- School of Biosciences, The University of Melbourne, Melbourne, Vic, Australia
| |
Collapse
|
32
|
Jensen S, Frank JA, Arntzen MØ, Duperron S, Vaaje-Kolstad G, Hovland M. Endozoicomonadaceae symbiont in gills of Acesta clam encodes genes for essential nutrients and polysaccharide degradation. FEMS Microbiol Ecol 2021; 97:6275716. [PMID: 33988698 PMCID: PMC8755941 DOI: 10.1093/femsec/fiab070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 05/12/2021] [Indexed: 01/29/2023] Open
Abstract
Gammaproteobacteria from the family Endozoicomonadaceae have emerged as widespread associates of dense marine animal communities. Their abundance in coral reefs involves symbiotic relationships and possibly host nutrition. We explored functions encoded in the genome of an uncultured Endozoicomonadaceae 'Candidatus Acestibacter aggregatus' that lives inside gill cells of large Acesta excavata clams in deep-water coral reefs off mid-Norway. The dominance and deep branching lineage of this symbiont was confirmed using 16S rRNA gene sequencing and phylogenomic analysis from shotgun sequencing data. The 4.5 Mb genome binned in this study has a low GC content of 35% and is enriched in transposon and chaperone gene annotations indicating ongoing adaptation. Genes encoding functions potentially involved with the symbiosis include ankyrins, repeat in toxins, secretion and nutritional systems. Complete pathways were identified for the synthesis of eleven amino acids and six B-vitamins. A minimal chitinolytic machinery was indicated from a glycosyl hydrolase GH18 and a lytic polysaccharide monooxygenase LPMO10. Expression of the latter was confirmed using proteomics. Signal peptides for secretion were identified for six polysaccharide degrading enzymes, ten proteases and three lipases. Our results suggest a nutritional symbiosis fuelled by enzymatic products from extracellular degradation processes.
Collapse
Affiliation(s)
- Sigmund Jensen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1432 Ås, Norway
| | - Jeremy A Frank
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1432 Ås, Norway
| | - Magnus Ø Arntzen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1432 Ås, Norway
| | - Sébastien Duperron
- UMR 7245 Muséum National d'Histoire Naturelle/CNRS Molécules de Communication et Adaptation des Micro-organismes and Institut Universitaire de France, CP39, 12 rue Buffon, F-75231 Paris Cedex 05, France
| | - Gustav Vaaje-Kolstad
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1432 Ås, Norway
| | - Martin Hovland
- Department of Biology, University of Bergen, PO Box 7803, 5020 Bergen, Norway.,Centre for Geobiology, University of Bergen, PO Box 7803, 5020 Bergen, Norway
| |
Collapse
|
33
|
Botwright NA, Mohamed AR, Slinger J, Lima PC, Wynne JW. Host-Parasite Interaction of Atlantic salmon ( Salmo salar) and the Ectoparasite Neoparamoeba perurans in Amoebic Gill Disease. Front Immunol 2021; 12:672700. [PMID: 34135900 PMCID: PMC8202022 DOI: 10.3389/fimmu.2021.672700] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/05/2021] [Indexed: 12/13/2022] Open
Abstract
Marine farmed Atlantic salmon (Salmo salar) are susceptible to recurrent amoebic gill disease (AGD) caused by the ectoparasite Neoparamoeba perurans over the growout production cycle. The parasite elicits a highly localized response within the gill epithelium resulting in multifocal mucoid patches at the site of parasite attachment. This host-parasite response drives a complex immune reaction, which remains poorly understood. To generate a model for host-parasite interaction during pathogenesis of AGD in Atlantic salmon the local (gill) and systemic transcriptomic response in the host, and the parasite during AGD pathogenesis was explored. A dual RNA-seq approach together with differential gene expression and system-wide statistical analyses of gene and transcription factor networks was employed. A multi-tissue transcriptomic data set was generated from the gill (including both lesioned and non-lesioned tissue), head kidney and spleen tissues naïve and AGD-affected Atlantic salmon sourced from an in vivo AGD challenge trial. Differential gene expression of the salmon host indicates local and systemic upregulation of defense and immune responses. Two transcription factors, znfOZF-like and znf70-like, and their associated gene networks significantly altered with disease state. The majority of genes in these networks are candidates for mediators of the immune response, cellular proliferation and invasion. These include Aurora kinase B-like, rho guanine nucleotide exchange factor 25-like and protein NDNF-like inhibited. Analysis of the N. perurans transcriptome during AGD pathology compared to in vitro cultured N. perurans trophozoites, as a proxy for wild type trophozoites, identified multiple gene candidates for virulence and indicates a potential master regulatory gene system analogous to the two-component PhoP/Q system. Candidate genes identified are associated with invasion of host tissue, evasion of host defense mechanisms and formation of the mucoid lesion. We generated a novel model for host-parasite interaction during AGD pathogenesis through integration of host and parasite functional profiles. Collectively, this dual transcriptomic study provides novel molecular insights into the pathology of AGD and provides alternative theories for future research in a step towards improved management of AGD.
Collapse
Affiliation(s)
- Natasha A Botwright
- Livestock and Aquaculture, CSIRO Agriculture and Food, St Lucia, QLD, Australia
| | - Amin R Mohamed
- Livestock and Aquaculture, CSIRO Agriculture and Food, St Lucia, QLD, Australia
| | - Joel Slinger
- Livestock and Aquaculture, CSIRO Agriculture and Food, Woorim, QLD, Australia
| | - Paula C Lima
- Livestock and Aquaculture, CSIRO Agriculture and Food, St Lucia, QLD, Australia
| | - James W Wynne
- Livestock and Aquaculture, CSIRO Agriculture and Food, Hobart, TAS, Australia
| |
Collapse
|
34
|
Vera-Ponce León A, Dominguez-Mirazo M, Bustamante-Brito R, Higareda-Alvear V, Rosenblueth M, Martínez-Romero E. Functional genomics of a Spiroplasma associated with the carmine cochineals Dactylopius coccus and Dactylopius opuntiae. BMC Genomics 2021; 22:240. [PMID: 33823812 PMCID: PMC8025503 DOI: 10.1186/s12864-021-07540-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 03/18/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Spiroplasma is a widely distributed endosymbiont of insects, arthropods, and plants. In insects, Spiroplasma colonizes the gut, hemolymph, and reproductive organs of the host. Previous metagenomic surveys of the domesticated carmine cochineal Dactylopius coccus and the wild cochineal D. opuntiae reported sequences of Spiroplasma associated with these insects. However, there is no analysis of the genomic capabilities and the interaction of this Spiroplasma with Dactylopius. RESULTS Here we present three Spiroplasma genomes independently recovered from metagenomes of adult males and females of D. coccus, from two different populations, as well as from adult females of D. opuntiae. Single-copy gene analysis showed that these genomes were > 92% complete. Phylogenomic analyses classified these genomes as new members of Spiroplasma ixodetis. Comparative genome analysis indicated that they exhibit fewer genes involved in amino acid and carbon catabolism compared to other spiroplasmas. Moreover, virulence factor-encoding genes (i.e., glpO, spaid and rip2) were found incomplete in these S. ixodetis genomes. We also detected an enrichment of genes encoding the type IV secretion system (T4SS) in S. ixodetis genomes of Dactylopius. A metratranscriptomic analysis of D. coccus showed that some of these T4SS genes (i.e., traG, virB4 and virD4) in addition to the superoxide dismutase sodA of S. ixodetis were overexpressed in the ovaries. CONCLUSION The symbiont S. ixodetis is a new member of the bacterial community of D. coccus and D. opuntiae. The recovery of incomplete virulence factor-encoding genes in S. ixodetis of Dactylopius suggests that this bacterium is a non-pathogenic symbiont. A high number of genes encoding the T4SS, in the S. ixodetis genomes and the overexpression of these genes in the ovary and hemolymph of the host suggest that S. ixodetis use the T4SS to interact with the Dactylopius cells. Moreover, the transcriptional differences of S. ixodetis among the gut, hemolymph and ovary tissues of D. coccus indicate that this bacterium can respond and adapt to the different conditions (e.g., oxidative stress) present within the host. All this evidence proposes that there is a strong interaction and molecular signaling in the symbiosis between S. ixodetis and the carmine cochineal Dactylopius.
Collapse
Affiliation(s)
- Arturo Vera-Ponce León
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico. .,Present Address: Faculty of Biotechnology, Chemistry and Food Science, Norwegian University of Life Sciences, 1433, Ås, Norway.
| | - Marian Dominguez-Mirazo
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Present Address: School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Rafael Bustamante-Brito
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Víctor Higareda-Alvear
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mónica Rosenblueth
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Esperanza Martínez-Romero
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| |
Collapse
|
35
|
Voss OH, Rahman MS. Rickettsia-host interaction: strategies of intracytosolic host colonization. Pathog Dis 2021; 79:ftab015. [PMID: 33705517 PMCID: PMC8023194 DOI: 10.1093/femspd/ftab015] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/09/2021] [Indexed: 12/29/2022] Open
Abstract
Bacterial infection is a highly complex biological process involving a dynamic interaction between the invading microorganism and the host. Specifically, intracellular pathogens seize control over the host cellular processes including membrane dynamics, actin cytoskeleton, phosphoinositide metabolism, intracellular trafficking and immune defense mechanisms to promote their host colonization. To accomplish such challenging tasks, virulent bacteria deploy unique species-specific secreted effectors to evade and/or subvert cellular defense surveillance mechanisms to establish a replication niche. However, despite superficially similar infection strategies, diverse Rickettsia species utilize different effector repertoires to promote host colonization. This review will discuss our current understandings on how different Rickettsia species deploy their effector arsenal to manipulate host cellular processes to promote their intracytosolic life within the mammalian host.
Collapse
Affiliation(s)
- Oliver H Voss
- Department of Microbiology and Immunology, University of Maryland School of Medicine, HSF2, room 416, 20 Penn St, Baltimore, MD 21201, USA
| | - M Sayeedur Rahman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, HSF2, room 416, 20 Penn St, Baltimore, MD 21201, USA
| |
Collapse
|
36
|
Questing functions and structures of hypothetical proteins from Campylobacter jejuni: a computer-aided approach. Biosci Rep 2021; 40:225019. [PMID: 32458979 PMCID: PMC7284324 DOI: 10.1042/bsr20193939] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 05/17/2020] [Accepted: 05/26/2020] [Indexed: 12/12/2022] Open
Abstract
Campylobacter jejuni (C. jejuni) is considered to be one of the most frequent causes of bacterial gastroenteritis globally, especially in young children. The genome of C. jejuni contains many proteins with unknown functions termed as hypothetical proteins (HPs). These proteins might have essential biological role to show the full spectrum of this bacterium. Hence, our study aimed to determine the functions of HPs, pertaining to the genome of C. jejuni. An in-silico work flow integrating various tools were performed for functional assignment, three-dimensional structure determination, domain architecture predictors, subcellular localization, physicochemical characterization, and protein-protein interactions (PPIs). Sequences of 267 HPs of C. jejuni were analyzed and successfully attributed the function of 49 HPs with higher confidence. Here, we found proteins with enzymatic activity, transporters, binding and regulatory proteins as well as proteins with biotechnological interest. Assessment of the performance of various tools used in this analysis revealed an accuracy of 95% using receiver operating characteristic (ROC) curve analysis. Functional and structural predictions and the results from ROC analyses provided the validity of in-silico tools used in the present study. The approach used for this analysis leads us to assign the function of unknown proteins and relate them with the functions that have already been described in previous literature.
Collapse
|
37
|
Schwelm A, Ludwig-Müller J. Molecular Pathotyping of Plasmodiophora brassicae-Genomes, Marker Genes, and Obstacles. Pathogens 2021; 10:pathogens10030259. [PMID: 33668372 PMCID: PMC7996130 DOI: 10.3390/pathogens10030259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/16/2021] [Accepted: 02/21/2021] [Indexed: 11/16/2022] Open
Abstract
Here we review the usefulness of the currently available genomic information for the molecular identification of pathotypes. We focused on effector candidates and genes implied to be pathotype specific and tried to connect reported marker genes to Plasmodiophora brassicae genome information. The potentials for practical applications, current obstacles and future perspectives are discussed.
Collapse
|
38
|
Clinical and immunological responses in sheep after inoculation with Himar1-transformed Anaplasma phagocytophilum and subsequent challenge with a virulent strain of the bacterium. Vet Immunol Immunopathol 2020; 231:110165. [PMID: 33316536 DOI: 10.1016/j.vetimm.2020.110165] [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: 06/04/2020] [Revised: 11/18/2020] [Accepted: 11/29/2020] [Indexed: 11/21/2022]
Abstract
In Norway, the tick-transmitted bacterium Anaplasma phagocytophilum is estimated to cause tick-borne fever (TBF) in 300 000 lambs on pastures each year, resulting in economic and animal welfare consequences. Today, prophylactic measures mainly involve the use of acaricides, but a vaccine has been requested by farmers and veterinarians for decades. Several attempts have been made to produce a vaccine against A. phagocytophilum including antigenic surface proteins, inactivated whole cell vaccines and challenge followed by treatment. In the current study, a virulent wild type strain of A. phagocytophilum named Ap.Norvar1 (16S rRNA sequence partial identical to sequence in GenBank acc.no M73220) was subject to genetic transformation with a Himar1-transposon, which resulted in three bacterial mutants, capable of propagation in a tick cell line (ISE6). In order to test the immunogenicity and pathogenicity of the live, mutated bacteria, these were clinically tested in an inoculation- and challenge study in sheep. One group was inoculated with the Ap.Norvar1 as an infection control. After inoculation, the sheep inoculated with mutated bacteria and the Ap.Norvar1 developed typical clinical signs of infection and humoral immune response. After challenge with Ap.Norvar1, 28 days later all groups inoculated with mutated bacteria showed clinical signs of tick-borne fever and bacteremia while the group initially inoculated with the Ap.Norvar1, showed protection against clinical disease. The current study shows a weak, but partial protection against infection in animals inoculated with mutated bacteria, while animals that received Ap.Norvar1 both for inoculation and challenge, responded with homologues protection.
Collapse
|
39
|
Gulyaeva AA, Gorbalenya AE. A nidovirus perspective on SARS-CoV-2. Biochem Biophys Res Commun 2020; 538:24-34. [PMID: 33413979 PMCID: PMC7664520 DOI: 10.1016/j.bbrc.2020.11.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023]
Abstract
Two pandemics of respiratory distress diseases associated with zoonotic introductions of the species Severe acute respiratory syndrome-related coronavirus in the human population during 21st century raised unprecedented interest in coronavirus research and assigned it unseen urgency. The two viruses responsible for the outbreaks, SARS-CoV and SARS-CoV-2, respectively, are in the spotlight, and SARS-CoV-2 is the focus of the current fast-paced research. Its foundation was laid down by studies of many corona- and related viruses that collectively form the vast order Nidovirales. Comparative genomics of nidoviruses played a key role in this advancement over more than 30 years. It facilitated the transfer of knowledge from characterized to newly identified viruses, including SARS-CoV and SARS-CoV-2, as well as contributed to the dissection of the nidovirus proteome and identification of patterns of variations between different taxonomic groups, from species to families. This review revisits selected cases of protein conservation and variation that define nidoviruses, illustrates the remarkable plasticity of the proteome during nidovirus adaptation, and asks questions at the interface of the proteome and processes that are vital for nidovirus reproduction and could inform the ongoing research of SARS-CoV-2.
Collapse
Affiliation(s)
- Anastasia A Gulyaeva
- Department of Medical Microbiology, Leiden University Medical Center, 2300 RC, Leiden, the Netherlands
| | - Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, 2300 RC, Leiden, the Netherlands; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119899, Moscow, Russia.
| |
Collapse
|
40
|
Comparative Transcriptome Analysis of Two Root-Feeding Grape Phylloxera ( D. vitifoliae) Lineages Feeding on a Rootstock and V. vinifera. INSECTS 2020; 11:insects11100691. [PMID: 33053741 PMCID: PMC7601026 DOI: 10.3390/insects11100691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022]
Abstract
Simple Summary Grape phylloxera is an American native insect pest that caused heavy damages to the vineyards worldwide since its spreading to wine regions since the 1850s. This insect, able to feed on leaves and roots, induces plant galls and manipulates the grapevine physiology leading to plant damage and may cause plant death. The most successful treatment was the use of mostly partially resistant rootstocks. The degree of resistance is affected by environment, grapevine management and the insect biotype. In this study, we analyse the interaction of insect biotypes feeding on particular host plants. Therefore we evaluated the gene expression of Phylloxera feeding on a susceptible host versus feeding on a rootstock in two different developmental stages. We discovered (mainly in advanced insect developmental stages) genes expressed in higher proportion in one insect compared to the other. These genes related to chemosensory; in plant physiology manipulation and root deformation and insect digestive traits may play a role in the plant-insect interaction determining plant resistance in response to the pest attack. Abstract Grape phylloxera is one of the most dangerous insect pests for worldwide viticulture. The leaf- and root-galling phylloxerid has been managed by grafting European grapevines onto American rootstock hybrids. Recent reports pinpoint the appearance of host-adapted biotypes, but information about the biomolecular characteristics underlying grape phylloxera biotypisation and its role in host performance is scarce. Using RNA-sequencing, we sequenced the transcriptome of two larval stages: L1 (probing) and L2-3 (feeding) larvae of two root-feeding grape phylloxera lineages feeding on the rootstock Teleki 5C (biotype C) and V. vinifera Riesling (biotype A). In total, 7501 differentially expressed genes (DEGs) were commonly modulated by the two biotypes. For the probing larvae, we found an increased number of DEGs functionally associated with insect chemoreception traits, such as odorant-binding proteins, chemosensory proteins, ionotropic, odorant, and gustatory receptors. The transcriptomic profile of feeding larvae was enriched with DEGs associated with the primary metabolism. Larvae feeding on the tolerant rootstock Teleki 5C exhibited higher numbers of plant defense suppression-associated DEGs than larvae feeding on the susceptible host. Based on the identified DEGs, we discuss their potential role for the compatible grape phylloxera–Vitis interaction belowground. This study was the first to compare the transcriptomes of two grape phylloxera lineages feeding on a tolerant and susceptible host, respectively, and to identify DEGs involved in the molecular interaction with these hosts. Our data provide a source for future studies on host adaptation mechanisms of grape phylloxera and help to elucidate grape phylloxera resistance further.
Collapse
|
41
|
Carneiro Dutra HL, Deehan MA, Frydman H. Wolbachia and Sirtuin-4 interaction is associated with alterations in host glucose metabolism and bacterial titer. PLoS Pathog 2020; 16:e1008996. [PMID: 33048997 PMCID: PMC7584242 DOI: 10.1371/journal.ppat.1008996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 10/23/2020] [Accepted: 09/18/2020] [Indexed: 12/30/2022] Open
Abstract
Wolbachia is an intracellular bacterial symbiont of arthropods notorious for inducing many reproductive manipulations that foster its dissemination. Wolbachia affects many aspects of host biology, including metabolism, longevity and physiology, being described as a nutrient provisioning or metabolic parasite, depending on the host-microbe association. Sirtuins (SIRTs) are a family of NAD+-dependent post-translational regulatory enzymes known to affect many of the same processes altered by Wolbachia, including aging and metabolism, among others. Despite a clear overlap in control of host-derived pathways and physiology, no work has demonstrated a link between these two regulators. We used genetically tractable Drosophila melanogaster to explore the role of sirtuins in shaping signaling pathways in the context of a host-symbiont model. By using transcriptional profiling and metabolic assays in the context of genetic knockouts/over-expressions, we examined the effect of several Wolbachia strains on host sirtuin expression across distinct tissues and timepoints. We also quantified the downstream effects of the sirtuin x Wolbachia interaction on host glucose metabolism, and in turn, how it impacted Wolbachia titer. Our results indicate that the presence of Wolbachia is associated with (1) reduced sirt-4 expression in a strain-specific manner, and (2) alterations in host glutamate dehydrogenase expression and ATP levels, key components of glucose metabolism. We detected high glucose levels in Wolbachia-infected flies, which further increased when sirt-4 was over-expressed. However, under sirt-4 knockout, flies displayed a hypoglycemic state not rescued to normal levels in the presence of Wolbachia. Finally, whole body sirt-4 over-expression resulted in reduced Wolbachia ovarian titer. Our results expand knowledge of Wolbachia-host associations in the context of a yet unexplored class of host post-translational regulatory enzymes with implications for conserved host signaling pathways and bacterial titer, factors known to impact host biology and the symbiont's ability to spread through populations.
Collapse
Affiliation(s)
| | - Mark Anthony Deehan
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Horacio Frydman
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- National Emerging Infectious Disease Laboratory, Boston University, Boston, Massachusetts, United States of America
| |
Collapse
|
42
|
Shropshire JD, Leigh B, Bordenstein SR. Symbiont-mediated cytoplasmic incompatibility: what have we learned in 50 years? eLife 2020; 9:61989. [PMID: 32975515 PMCID: PMC7518888 DOI: 10.7554/elife.61989] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/14/2020] [Indexed: 12/12/2022] Open
Abstract
Cytoplasmic incompatibility (CI) is the most common symbiont-induced reproductive manipulation. Specifically, symbiont-induced sperm modifications cause catastrophic mitotic defects in the fertilized embryo and ensuing lethality in crosses between symbiotic males and either aposymbiotic females or females harboring a different symbiont strain. However, if the female carries the same symbiont strain, then embryos develop properly, thereby imparting a relative fitness benefit to symbiont-transmitting mothers. Thus, CI drives maternally-transmitted bacteria to high frequencies in arthropods worldwide. In the past two decades, CI experienced a boom in interest due to its (i) deployment in worldwide efforts to curb mosquito-borne diseases, (ii) causation by bacteriophage genes, cifA and cifB, that modify sexual reproduction, and (iii) important impacts on arthropod speciation. This review serves as a gateway to experimental, conceptual, and quantitative themes of CI and outlines significant gaps in understanding CI’s mechanism that are ripe for investigation from diverse subdisciplines in the life sciences.
Collapse
Affiliation(s)
- J Dylan Shropshire
- Department of Biological Sciences, Vanderbilt University, Nashville, United States.,Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, United States
| | - Brittany Leigh
- Department of Biological Sciences, Vanderbilt University, Nashville, United States.,Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, United States
| | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, United States.,Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, United States.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, United States.,Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, United States
| |
Collapse
|
43
|
Abstract
The diversified NF-κB transcription factor family has been extensively characterized in organisms ranging from flies to humans. However, homologs of NF-κB and many upstream signaling components have recently been characterized in basal phyla, including Cnidaria (sea anemones, corals, hydras, and jellyfish), Porifera (sponges), and single-celled protists, including Capsaspora owczarzaki and some choanoflagellates. Herein, we review what is known about basal NF-κBs and how that knowledge informs on the evolution and conservation of key sequences and domains in NF-κB, as well as the regulation of NF-κB activity. The structures and DNA-binding activities of basal NF-κB proteins resemble those of mammalian NF-κB p100 proteins, and their posttranslational activation appears to have aspects of both canonical and noncanonical pathways in mammals. Several studies suggest that the single NF-κB proteins found in some basal organisms have dual roles in development and immunity. Further research on NF-κB in invertebrates will reveal information about the evolutionary roots of this major signaling pathway, will shed light on the origins of regulated innate immunity, and may have relevance to our understanding of the responses of ecologically important organisms to changing environmental conditions and emerging pathogen-based diseases.
Collapse
Affiliation(s)
- Leah M Williams
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Thomas D Gilmore
- Department of Biology, Boston University, Boston, Massachusetts, USA
| |
Collapse
|
44
|
Lin HC, Chu LJ, Huang PJ, Cheng WH, Zheng YH, Huang CY, Hong SW, Chen LC, Lin HA, Wang JY, Chen RM, Lin WN, Tang P, Huang KY. Proteomic signatures of metronidazole-resistant Trichomonas vaginalis reveal novel proteins associated with drug resistance. Parasit Vectors 2020; 13:274. [PMID: 32487244 PMCID: PMC7268490 DOI: 10.1186/s13071-020-04148-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/25/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Trichomoniasis is the most common non-viral sexually transmitted disease caused by the protozoan parasite Trichomonas vaginalis. Metronidazole (MTZ) is a widely used drug for the treatment of trichomoniasis; however, increased resistance of the parasite to MTZ has emerged as a highly problematic public health issue. METHODS We conducted iTRAQ-based analysis to profile the proteomes of MTZ-sensitive (MTZ-S) and MTZ-resistant (MTZ-R) parasites. STRING and gene set enrichment analysis (GESA) were utilized to explore the protein-protein interaction networks and enriched pathways of the differentially expressed proteins, respectively. Proteins potentially related to MTZ resistance were selected for functional validation. RESULTS A total of 3123 proteins were identified from the MTZ-S and MTZ-R proteomes in response to drug treatment. Among the identified proteins, 304 proteins were differentially expressed in the MTZ-R proteome, including 228 upregulated and 76 downregulated proteins. GSEA showed that the amino acid-related metabolism, including arginine, proline, alanine, aspartate, and glutamate are the most upregulated pathways in the MTZ-R proteome, whereas oxidative phosphorylation is the most downregulated pathway. Ten proteins categorized into the gene set of oxidative phosphorylation were ATP synthase subunit-related proteins. Drug resistance was further examined in MTZ-S parasites pretreated with the ATP synthase inhibitors oligomycin and bafilomycin A1, showing enhanced MTZ resistance and potential roles of ATP synthase in drug susceptibility. CONCLUSIONS We provide novel insights into previously unidentified proteins associated with MTZ resistance, paving the way for future development of new drugs against MTZ-refractory trichomoniasis.
Collapse
Affiliation(s)
- Hsin-Chung Lin
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei City, 114, Taiwan
| | - Lichieh Julie Chu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan City, 333, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan City, 333, Taiwan
| | - Po-Jung Huang
- Department of Biomedical Sciences, Chang Gung University, Taoyuan City, 333, Taiwan.,Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan City, 333, Taiwan
| | - Wei-Hung Cheng
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan City, 333, Taiwan
| | - Yu-Hsing Zheng
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei City, 114, Taiwan
| | - Ching-Yun Huang
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei City, 114, Taiwan
| | - Shu-Wen Hong
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei City, 114, Taiwan
| | - Lih-Chyang Chen
- Department of Medicine, Mackay Medical College, New Taipei City, 252, Taiwan
| | - Hsin-An Lin
- Division of Infection, Department of Medicine, Tri-Service General Hospital SongShan Branch, Taipei City, 105, Taiwan
| | - Jui-Yang Wang
- Division of Family Medicine, Tri-Service General Hospital Songshan Branch, Taipei City, 105, Taiwan
| | - Ruei-Min Chen
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei City, 114, Taiwan
| | - Wei-Ning Lin
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City, 242, Taiwan
| | - Petrus Tang
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan City, 333, Taiwan
| | - Kuo-Yang Huang
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei City, 114, Taiwan.
| |
Collapse
|
45
|
Engelberts JP, Robbins SJ, de Goeij JM, Aranda M, Bell SC, Webster NS. Characterization of a sponge microbiome using an integrative genome-centric approach. THE ISME JOURNAL 2020; 14:1100-1110. [PMID: 31992859 PMCID: PMC7174397 DOI: 10.1038/s41396-020-0591-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 01/08/2020] [Accepted: 01/16/2020] [Indexed: 11/09/2022]
Abstract
Marine sponges often host diverse and species-specific communities of microorganisms that are critical for host health. Previous functional genomic investigations of the sponge microbiome have focused primarily on specific symbiont lineages, which frequently make up only a small fraction of the overall community. Here, we undertook genome-centric analysis of the symbiont community in the model species Ircinia ramosa and analyzed 259 unique, high-quality metagenome-assembled genomes (MAGs) that comprised 74% of the I. ramosa microbiome. Addition of these MAGs to genome trees containing all publicly available microbial sponge symbionts increased phylogenetic diversity by 32% within the archaea and 41% within the bacteria. Metabolic reconstruction of the MAGs showed extensive redundancy across taxa for pathways involved in carbon fixation, B-vitamin synthesis, taurine metabolism, sulfite oxidation, and most steps of nitrogen metabolism. Through the acquisition of all major taxa present within the I. ramosa microbiome, we were able to analyze the functional potential of a sponge-associated microbial community in unprecedented detail. Critical functions, such as carbon fixation, which had previously only been assigned to a restricted set of sponge-associated organisms, were actually spread across diverse symbiont taxa, whereas other essential pathways, such as ammonia oxidation, were confined to specific keystone taxa.
Collapse
Affiliation(s)
- J Pamela Engelberts
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Steven J Robbins
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jasper M de Goeij
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Manuel Aranda
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sara C Bell
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Nicole S Webster
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
- Australian Institute of Marine Science, Townsville, QLD, Australia.
| |
Collapse
|
46
|
First Whole Genome Sequence of Anaplasma platys, an Obligate Intracellular Rickettsial Pathogen of Dogs. Pathogens 2020; 9:pathogens9040277. [PMID: 32290349 PMCID: PMC7238063 DOI: 10.3390/pathogens9040277] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/02/2020] [Accepted: 04/08/2020] [Indexed: 01/31/2023] Open
Abstract
We have assembled the first genome draft of Anaplasma platys, an obligate intracellular rickettsia, and the only known bacterial pathogen infecting canine platelets. A. platys is a not-yet-cultivated bacterium that causes infectious cyclic canine thrombocytopenia, a potentially fatal disease in dogs. Despite its global distribution and veterinary relevance, no genome sequence has been published so far for this pathogen. Here, we used a strategy based on metagenome assembly to generate a draft of the A. platys genome using the blood of an infected dog. The assembled draft is similar to other Anaplasma genomes in size, gene content, and synteny. Notable differences are the apparent absence of rbfA, a gene encoding a 30S ribosome-binding factor acting as a cold-shock protein, as well as two genes involved in biotin metabolism. We also observed differences associated with expanded gene families, including those encoding outer membrane proteins, a type IV secretion system, ankyrin repeat-containing proteins, and proteins with predicted intrinsically disordered regions. Several of these families have members highly divergent in sequence, likely to be associated with survival and interactions within the host and the vector. The sequence of the A. platys genome can benefit future studies regarding invasion, survival, and pathogenesis of Anaplasma species, while paving the way for the better design of treatment and prevention strategies against these neglected intracellular pathogens.
Collapse
|
47
|
Kitamata M, Hotta M, Hamada‐Nakahara S, Suetsugu S. The membrane binding and deformation property of vaccinia virus K1 ankyrin repeat domain protein. Genes Cells 2020; 25:187-196. [DOI: 10.1111/gtc.12749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/11/2020] [Accepted: 01/15/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Manabu Kitamata
- Graduate School of Science and Technology Nara Institute of Science and Technology Ikoma Japan
| | - Mitsukuni Hotta
- Graduate School of Science and Technology Nara Institute of Science and Technology Ikoma Japan
| | | | - Shiro Suetsugu
- Graduate School of Science and Technology Nara Institute of Science and Technology Ikoma Japan
| |
Collapse
|
48
|
Bing XL, Zhao DS, Sun JT, Zhang KJ, Hong XY. Genomic Analysis of Wolbachia from Laodelphax striatellus (Delphacidae, Hemiptera) Reveals Insights into Its "Jekyll and Hyde" Mode of Infection Pattern. Genome Biol Evol 2020; 12:3818-3831. [PMID: 31958110 PMCID: PMC7046167 DOI: 10.1093/gbe/evaa006] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2020] [Indexed: 12/26/2022] Open
Abstract
Wolbachia is a widely distributed intracellular bacterial endosymbiont among invertebrates. The wStriCN, the Wolbachia strain that naturally infects an agricultural pest Laodelphax striatellus, has a "Jekyll and Hyde" mode of infection pattern with positive and negative effects: It not only kills many offspring by inducing cytoplasmic incompatibility (CI) but also significantly increases host fecundity. In this study, we assembled the draft genome of wStriCN and compared it with other Wolbachia genomes to look for clues to its Jekyll and Hyde characteristics. The assembled wStriCN draft genome is 1.79 Mb in size, which is the largest Wolbachia genome in supergroup B. Phylogenomic analysis showed that wStriCN is closest to Wolbachia from Asian citrus psyllid Diaphorina citri. These strains formed a monophylogentic clade within supergroup B. Compared with other Wolbachia genomes, wStriCN contains the most diverse insertion sequence families, the largest amount of prophage sequences, and the most ankyrin domain protein coding genes. The wStriCN genome encodes components of multiple secretion systems, including Types I, II, IV, VI, Sec, and Tac. We detected three pairs of homologs for CI factors CifA and CifB. These proteins harbor the catalytic domains responsible for CI phenotypes but are phylogenetically and structurally distinct from all known Cif proteins. The genome retains pathways for synthesizing biotin and riboflavin, which may explain the beneficial roles of wStriCN in its host planthoppers, which feed on nutrient-poor plant sap. Altogether, the genomic sequencing of wStriCN provides insight into understanding the phylogeny and biology of Wolbachia.
Collapse
Affiliation(s)
- Xiao-Li Bing
- Department of Entomology, Nanjing Agricultural University, Jiangsu, China
| | - Dian-Shu Zhao
- Department of Entomology, Nanjing Agricultural University, Jiangsu, China
| | - Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Jiangsu, China
| | - Kai-Jun Zhang
- Department of Entomology, Nanjing Agricultural University, Jiangsu, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Jiangsu, China
| |
Collapse
|
49
|
Chagula DB, Rechciński T, Rudnicka K, Chmiela M. Ankyrins in human health and disease - an update of recent experimental findings. Arch Med Sci 2020; 16:715-726. [PMID: 32542072 PMCID: PMC7286341 DOI: 10.5114/aoms.2019.89836] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/25/2018] [Indexed: 12/17/2022] Open
Abstract
Ankyrins are adaptor molecules that in eukaryotic cells form complexes with ion channel proteins, cell adhesion and signalling molecules and components of the cytoskeleton. They play a pivotal role as scaffolding proteins, in the structural anchoring to the muscle membrane, in muscle development, neurogenesis and synapse formation. Dysfunction of ankyrins is implicated in numerous diseases such as hereditary spherocytosis, neurodegeneration of Purkinje cells, cardiac arrhythmia, Brugada syndrome, bipolar disorders and schizophrenia, congenital myopathies and congenital heart disease as well as cancers. Detecting either down- or over-expression of ankyrins and ergo their use as biomarkers can provide a new paradigm in the diagnosis of these diseases. This paper provides an outline of knowledge about the structure of ankyrins, and by making use of recent experimental research studies critically discusses their role in several health disorders. Moreover, therapeutic options utilizing engineered ankyrins, designed ankyrin repeat proteins (DARPins), are discussed.
Collapse
Affiliation(s)
- Damian B. Chagula
- Laboratory of Gastroimmunology, Department of Immunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Tomasz Rechciński
- Department of Cardiology, Bieganski Regional Speciality Hospital, Medical University of Lodz, Lodz, Poland
| | - Karolina Rudnicka
- Laboratory of Gastroimmunology, Department of Immunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Magdalena Chmiela
- Laboratory of Gastroimmunology, Department of Immunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
- Corresponding author: Prof. Magdalena Chmiela Laboratory of Gastroimmunology, Department of Immmunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha St, 90-237 Lodz, Poland, E-mail:
| |
Collapse
|
50
|
Yoon S, Parnell E, Kasherman M, Forrest MP, Myczek K, Premarathne S, Sanchez Vega MC, Piper M, Burne THJ, Jolly LA, Wood SA, Penzes P. Usp9X Controls Ankyrin-Repeat Domain Protein Homeostasis during Dendritic Spine Development. Neuron 2019; 105:506-521.e7. [PMID: 31813652 DOI: 10.1016/j.neuron.2019.11.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 09/26/2019] [Accepted: 11/01/2019] [Indexed: 12/19/2022]
Abstract
Variants in the ANK3 gene encoding ankyrin-G are associated with neurodevelopmental disorders, including intellectual disability, autism, schizophrenia, and bipolar disorder. However, no upstream regulators of ankyrin-G at synapses are known. Here, we show that ankyrin-G interacts with Usp9X, a neurodevelopmental-disorder-associated deubiquitinase (DUB). Usp9X phosphorylation enhances their interaction, decreases ankyrin-G polyubiquitination, and stabilizes ankyrin-G to maintain dendritic spine development. In forebrain-specific Usp9X knockout mice (Usp9X-/Y), ankyrin-G as well as multiple ankyrin-repeat domain (ANKRD)-containing proteins are transiently reduced at 2 but recovered at 12 weeks postnatally. However, reduced cortical spine density in knockouts persists into adulthood. Usp9X-/Y mice display increase of ankyrin-G ubiquitination and aggregation and hyperactivity. USP9X mutations in patients with intellectual disability and autism ablate its catalytic activity or ankyrin-G interaction. Our data reveal a DUB-dependent mechanism of ANKRD protein homeostasis, the impairment of which only transiently affects ANKRD protein levels but leads to persistent neuronal, behavioral, and clinical abnormalities.
Collapse
Affiliation(s)
- Sehyoun Yoon
- Department of Physiology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Euan Parnell
- Department of Physiology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Maria Kasherman
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia; The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Marc P Forrest
- Department of Physiology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kristoffer Myczek
- Department of Physiology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Susitha Premarathne
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | | | - Michael Piper
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072 Australia; Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas H J Burne
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia; Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, QLD 4076, Australia
| | - Lachlan A Jolly
- Robinson Research Institute, School of Medicine, University of Adelaide, Adelaide, SA 5005, Australia
| | - Stephen A Wood
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Peter Penzes
- Department of Physiology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| |
Collapse
|