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Alam K, Islam MM, Gong K, Abbasi MN, Li R, Zhang Y, Li A. In silico genome mining of potential novel biosynthetic gene clusters for drug discovery from Burkholderia bacteria. Comput Biol Med 2022; 140:105046. [PMID: 34864585 DOI: 10.1016/j.compbiomed.2021.105046] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/15/2021] [Accepted: 11/15/2021] [Indexed: 11/25/2022]
Abstract
As an emerging resource, Gram-negative Burkholderia bacteria were able to produce a wide range of bioactive secondary metabolites with potential therapeutic and biotechnological applications. Genome mining has emerged as an influential platform for screening and pinpointing natural product diversity with the increasing number of Burkholderia genome sequences. Here, for genome mining of potential biosynthetic gene clusters (BGCs) and prioritizing prolific producing Burkholderia strains, we investigated the relationship between species evolution and distribution of main BGC groups using computational analysis of complete genome sequences of 248 Burkholderia species publicly available. We uncovered significantly differential distribution patterns of BGCs in the Burkholderia phyla, even among strains that are genetically very similar. We found various types of BGCs in Burkholderia, including some representative and most common BGCs for biosynthesis of encrypted or known terpenes, non-ribosomal peptides (NRPs) and some hybrid BGCs for cryptic products. We also observed that Burkholderia contain a lot of unspecified BGCs, representing high potentials to produce novel compounds. Analysis of BGCs for RiPPs (Ribosomally synthesized and posttranslationally modified peptides) and a texobactin-like BGC as examples showed wide classification and diversity of RiPP BGCs in Burkholderia at species level and metabolite predication. In conclusion, as the biggest investigation in silico by far on BGCs of the particular genus Burkholderia, our data implied a great diversity of natural products in Burkholderia and BGC distributions closely related to phylogenetic variation, and suggested different or concurrent strategies used to identify new drug molecules from these microorganisms will be important for the selection of potential BGCs and prolific producing strains for drug discovery.
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Affiliation(s)
- Khorshed Alam
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
| | - Md Mahmudul Islam
- Department of Microbiology, Rajshahi Institute of Biosciences (RIB), Affi. University of Rajshahi, Rajshahi, 6212, Bangladesh.
| | - Kai Gong
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
| | - Muhammad Nazeer Abbasi
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
| | - Ruijuan Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
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Lin Y, Wang Q, Chen H, Yan N, Wu F, Wang Z, Li C, Liu Y. Genome-wide association mapping of Fusarium crown rot resistance in Aegilops tauschii. FRONTIERS IN PLANT SCIENCE 2022; 13:998622. [PMID: 36247594 PMCID: PMC9562832 DOI: 10.3389/fpls.2022.998622] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 08/29/2022] [Indexed: 05/13/2023]
Abstract
Fusarium crown rot (FCR), caused by various Fusarium species, is a primary fungal disease in most wheat-growing regions worldwide. A. tauschii, the diploid wild progenitor of the D-genome of common wheat, is a reservoir of genetic diversity for improving bread wheat biotic and abiotic resistance/tolerance. A worldwide collection of 286 A. tauschii accessions was used to evaluate FCR resistance. Population structure analysis revealed that 115 belonged to the A. tauschii ssp. strangulata subspecies, and 171 belonged to the A. tauschii ssp. tauschii subspecies. Five accessions with disease index values lower than 20 showed moderate resistance to FCR. These five originated from Afghanistan, China, Iran, Uzbekistan, and Turkey, all belonging to the tauschii subspecies. Genome-wide association mapping using 6,739 single nucleotide polymorphisms (SNPs) revealed that two SNPs on chromosome 2D and four SNPs on chromosome 7D were significantly associated with FCR resistance. Almost all FCR resistance alleles were presented in accessions from the tauschii subspecies, and only 4, 11, and 19 resistance alleles were presented in accessions from the strangulata subspecies. Combining phenotypic correlation analysis and genome-wide association mapping confirmed that FCR resistance loci were independent of flowering time, heading date, and plant height in this association panel. Six genes encoding disease resistance-related proteins were selected as candidates for further validation. The identified resistant A. tauschii accessions will provide robust resistance gene sources for breeding FCR-resistant cultivars. The associated loci/genes will accelerate and improve FCR in breeding programs by deploying marker-assisted selection.
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Affiliation(s)
- Yu Lin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Hao Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Ning Yan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Fangkun Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhiqiang Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Caixia Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Yaxi Liu, ;
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Seabra SG, Libin PJK, Theys K, Zhukova A, Potter BI, Nebenzahl-Guimaraes H, Gorbalenya AE, Sidorov IA, Pimentel V, Pingarilho M, de Vasconcelos ATR, Dellicour S, Khouri R, Gascuel O, Vandamme AM, Baele G, Cuypers L, Abecasis AB. OUP accepted manuscript. Virus Evol 2022; 8:veac029. [PMID: 35478717 PMCID: PMC9035895 DOI: 10.1093/ve/veac029] [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: 10/12/2021] [Revised: 01/24/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
The Zika virus (ZIKV) disease caused a public health emergency of international concern that started in February 2016. The overall number of ZIKV-related cases increased until November 2016, after which it declined sharply. While the evaluation of the potential risk and impact of future arbovirus epidemics remains challenging, intensified surveillance efforts along with a scale-up of ZIKV whole-genome sequencing provide an opportunity to understand the patterns of genetic diversity, evolution, and spread of ZIKV. However, a classification system that reflects the true extent of ZIKV genetic variation is lacking. Our objective was to characterize ZIKV genetic diversity and phylodynamics, identify genomic footprints of differentiation patterns, and propose a dynamic classification system that reflects its divergence levels. We analysed a curated dataset of 762 publicly available sequences spanning the full-length coding region of ZIKV from across its geographical span and collected between 1947 and 2021. The definition of genetic groups was based on comprehensive evolutionary dynamics analyses, which included recombination and phylogenetic analyses, within- and between-group pairwise genetic distances comparison, detection of selective pressure, and clustering analyses. Evidence for potential recombination events was detected in a few sequences. However, we argue that these events are likely due to sequencing errors as proposed in previous studies. There was evidence of strong purifying selection, widespread across the genome, as also detected for other arboviruses. A total of 50 sites showed evidence of positive selection, and for a few of these sites, there was amino acid (AA) differentiation between genetic clusters. Two main genetic clusters were defined, ZA and ZB, which correspond to the already characterized ‘African’ and ‘Asian’ genotypes, respectively. Within ZB, two subgroups, ZB.1 and ZB.2, represent the Asiatic and the American (and Oceania) lineages, respectively. ZB.1 is further subdivided into ZB.1.0 (a basal Malaysia sequence sampled in the 1960s and a recent Indian sequence), ZB.1.1 (South-Eastern Asia, Southern Asia, and Micronesia sequences), and ZB.1.2 (very similar sequences from the outbreak in Singapore). ZB.2 is subdivided into ZB.2.0 (basal American sequences and the sequences from French Polynesia, the putative origin of South America introduction), ZB.2.1 (Central America), and ZB.2.2 (Caribbean and North America). This classification system does not use geographical references and is flexible to accommodate potential future lineages. It will be a helpful tool for studies that involve analyses of ZIKV genomic variation and its association with pathogenicity and serve as a starting point for the public health surveillance and response to on-going and future epidemics and to outbreaks that lead to the emergence of new variants.
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Affiliation(s)
| | | | | | - Anna Zhukova
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, 25-28 rue du Dr Roux, Paris F-75015, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 25-28 rue du Dr Roux, Paris F-75015, France
| | | | - Hanna Nebenzahl-Guimaraes
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, Lisboa 1349-008, Portugal
| | | | | | - Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, Lisboa 1349-008, Portugal
| | - Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, Lisboa 1349-008, Portugal
| | | | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, KU Leuven, Herestraat 49 - box 1030, Leuven 3000, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP 264/3, 50 av. F.D. Roosevelt, Bruxelles B-1050, Belgium
| | | | | | | | | | - Lize Cuypers
- Department of Laboratory Medicine, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Ana B Abecasis
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, Lisboa 1349-008, Portugal
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4654
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Zhu Q, Mirarab S. Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies. Methods Mol Biol 2022; 2569:137-165. [PMID: 36083447 DOI: 10.1007/978-1-0716-2691-7_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Phylogenomics is the inference of phylogenetic trees based on multiple marker genes sampled in the genomes of interest. An important challenge in phylogenomics is the potential incongruence among the evolutionary histories of individual genes, which can be widespread in microorganisms due to the prevalence of horizontal gene transfer. This protocol introduces the procedures for building a phylogenetic tree of a large number of microbial genomes using a broad sampling of marker genes that are representative of whole-genome evolution. The protocol highlights the use of a gene tree summary method, which can effectively reconstruct the species tree while accounting for the topological conflicts among individual gene trees. The pipeline described in this protocol is scalable to tens of thousands of genomes while retaining high accuracy. We discussed multiple software tools, libraries, and scripts to enable convenient adoption of the protocol. The protocol is suitable for microbiology and microbiome studies based on public genomes and metagenomic data.
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Affiliation(s)
- Qiyun Zhu
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA.
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA, USA
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Riesco R, Ortúzar M, Fernández-Ábalos JM, Trujillo ME. Deciphering Genomes: Genetic Signatures of Plant-Associated Micromonospora. FRONTIERS IN PLANT SCIENCE 2022; 13:872356. [PMID: 35401599 PMCID: PMC8990736 DOI: 10.3389/fpls.2022.872356] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/28/2022] [Indexed: 05/13/2023]
Abstract
Understanding plant-microbe interactions with the possibility to modulate the plant's microbiome is essential to design new strategies for a more productive and sustainable agriculture and to maintain natural ecosystems. Therefore, a key question is how to design bacterial consortia that will yield the desired host phenotype. This work was designed to identify the potential genomic features involved in the interaction between Micromonospora and known host plants. Seventy-four Micromonospora genomes representing diverse environments were used to generate a database of all potentially plant-related genes using a novel bioinformatic pipeline that combined screening for microbial-plant related features and comparison with available plant host proteomes. The strains were recovered in three clusters, highly correlated with several environments: plant-associated, soil/rhizosphere, and marine/mangrove. Irrespective of their isolation source, most strains shared genes coding for commonly screened plant growth promotion features, while differences in plant colonization related traits were observed. When Arabidopsis thaliana plants were inoculated with representative Micromonospora strains selected from the three environments, significant differences were in found in the corresponding plant phenotypes. Our results indicate that the identified genomic signatures help select those strains with the highest probability to successfully colonize the plant and contribute to its wellbeing. These results also suggest that plant growth promotion markers alone are not good indicators for the selection of beneficial bacteria to improve crop production and the recovery of ecosystems.
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Li Z, Li Z, Peng Y, Lu X, Kan B. Trans-Regional and Cross-Host Spread of <i>mcr</i>-Carrying Plasmids Revealed by Complete Plasmid Sequences — 44 Countries, 1998−2020. China CDC Wkly 2022; 4:242-248. [PMID: 35433080 PMCID: PMC9005491 DOI: 10.46234/ccdcw2022.058] [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: 02/17/2022] [Accepted: 03/20/2022] [Indexed: 01/05/2023] Open
Abstract
Background The surveillance of antimicrobial resistance genes (ARGs) and bacteria is one critical approach to prevent and control antimicrobial resistance (AMR). Next-generation sequencing (NGS) is a powerful tool in monitoring the emergence and spread of ARGs and resistant bacteria. The horizontal transfer of ARGs across host bacteria mediated by plasmids is a challenge in NGS surveillance for resistance because short-read sequencing can hardly generate the complete plasmid genome sequence, and the correlation between ARGs and plasmids are difficult to determine. Methods The complete genome sequences of 455 mcr-carrying plasmids (pMCRs), and the data of their host bacteria and isolation regions were collected from the NCBI database. Genes of Inc types and ARGs were searched for each plasmid. The genome similarity of these plasmids was analyzed by pangenome clustering and genome alignment.
Results A total of 52 Inc types, including a variety of fusion plasmids containing 2 or more Inc types were identified in these pMCRs and carried by complex host bacteria. The cooccurrence of ARGs in pMCRs was generally observed, with an average of 3.9 ARGs per plasmid. Twenty-two clusters with consistent or highly similar sequences and gene compositions were identified by the pangenome clustering, which were characterized with distributions in different countries/regions, years or host bacteria in each cluster. Discussion Based on the complete plasmid sequences, distribution of mcr genes in different Inc type plasmids, their co-existence with other AMRs, and transmission of one pMCR across regions and host bacteria can be revealed definitively. Complete plasmid genomes and comparisons in the laboratory network are necessary for spread tracing of ARG-carrying plasmids and risk assessment in AMR surveillance.
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Affiliation(s)
- Zhe Li
- State Key Laboratory of Infectious Disease Prevention and Control; National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhenpeng Li
- State Key Laboratory of Infectious Disease Prevention and Control; National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yao Peng
- State Key Laboratory of Infectious Disease Prevention and Control; National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xin Lu
- State Key Laboratory of Infectious Disease Prevention and Control; National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Xin Lu,
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control; National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Biao Kan,
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Investigating the role of carbohydrate-binding module 34 in cyclomaltodextrinase from Geobacillus thermopakistaniensis: structural and functional analyses. 3 Biotech 2022; 12:25. [PMID: 35036273 PMCID: PMC8702598 DOI: 10.1007/s13205-021-03089-9] [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: 10/07/2021] [Accepted: 12/09/2021] [Indexed: 01/03/2023] Open
Abstract
Carbohydrate-binding modules (CBMs) are noncatalytic regions found in several enzymes of glycoside hydrolase family 13 and are proposed to orient substrates to the catalytic site. In this study, a substantial information on the conserved aromatic residues in CBM34 regions of characterized bacterial cyclolmaltodextrinases (CDases) has been presented. Molecular modeling of CDase from Geobacillus thermopakistaniensis (CDase Gt ) revealed a change in the active site geometry due to CBM34 truncation. The binding energies of full-length (CDase Gt ) and CBM34 truncated (CDase Gt -ΔN) models showed opposite trends. The least preferred substrate molecule by the full-length model was the most preferred by the CBM34 truncated one. These exciting in silico findings were experimentally verified by recombinant production and characterization of the full-length and the CBM34 truncated proteins. Both the enzymes showed similar optimum pH and temperature. However, substrate specificity was in the reverse order. These experimental verifications matched the homology modeling and docking predictions. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03089-9.
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Yi B, Dalpke AH. Revisiting the intrageneric structure of the genus Pseudomonas with complete whole genome sequence information: Insights into diversity and pathogen-related genetic determinants. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 97:105183. [PMID: 34920102 DOI: 10.1016/j.meegid.2021.105183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 08/09/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Pseudomonas spp. exhibit considerable differences in host specificity and virulence. Most Pseudomonas species were isolated exclusively from environmental sources, ranging from soil to plants, but some Pseudomonas species have been detected from versatile sources, including both human host and environmental sources. Understanding genome variations that generate the tremendous diversity in Pseudomonas biology is important in controlling the incidence of infections. With a data set of 704 Pseudomonas complete whole genome sequences representing 186 species, Pseudomonas intrageneric structure was investigated by hierarchical clustering based on average nucleotide identity, and by phylogeny analysis based on concatenated core-gene alignment. Further comparative functional analyses indicated that Pseudomonas species only living in natural habitats lack multiple functions that are important in the regulation of bacterial pathogenesis, indicating the possession of these functions might be characteristic of Pseudomonas human pathogens. Moreover, we have performed pan-genome based homogeneity analyses, and detected genes with conserved structures but diversified functions across the Pseudomonas genomes, suggesting these genes play a role in driving diversity. In summary, this study provided insights into the dynamics of genome diversity and pathogen-related genetic determinants in Pseudomonas, which might help the development of more targeted antibiotics for the treatment of Pseudomonas infections.
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Affiliation(s)
- Buqing Yi
- Institute of Medical Microbiology and Virology, Medical Faculty, Technische Universität Dresden, Dresden, Germany.
| | - Alexander H Dalpke
- Institute of Medical Microbiology and Virology, Medical Faculty, Technische Universität Dresden, Dresden, Germany.
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4659
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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4660
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Manoj RRS, Latrofa MS, Bezerra-Santos MA, Sgroi G, Samarelli R, Mendoza-Roldan JA, Otranto D. Molecular detection and characterization of the endosymbiont Wolbachia in the European hedgehog flea, Archaeopsylla erinacei. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 97:105161. [PMID: 34843992 DOI: 10.1016/j.meegid.2021.105161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 06/13/2023]
Abstract
Wolbachia, the endosymbiont of arthropods and onchocercid nematodes is present in many medically important insect species, being also considered for the indirect control of parasitic ones. Archaeopsylla erinacei is a flea species infesting hedgehogs acting as vector of Rickettsia felis, Bartonella henselae, and Rickettsia helvetica, thus having public health relevance. The Wolbachia surface protein (wsp) and 16S rRNA genes were used to determine the presence, prevalence and molecular typing of Wolbachia in this flea species collected in two regions of southern Italy. Of the 45 fleas tested (n = 16 males, 35.6%; n = 29 females, 64.4%), 43 (95.6%; 95% CI: 84.8-99.2) scored positive for Wolbachia, of which 15 (33.3%) and 28 (62.2%) were males and females, respectively. The sex-wise prevalence of this endosymbiont was almost equal in both sexes (males 93.8%; 95% CI: 69.5-99.7; females 96.7%; 95% CI: 83.1-99.8). Single locus sequence analysis (SLST) of Wolbachia revealed two sequence types for 16S rRNA gene, named as wAr_15227 and wAr_15234, which came from two different areas, equally distributed in male and female fleas, whilst only one sequence type was identified for wsp gene. The phylogenetic analysis placed the two 16S rRNA sequence types in paraphyletic clades belonging to the supergroup A and B, respectively. Whilst, the tree of wsp gene clustered the corresponding sequence in the same clade including those of Wolbachia supergroup A. In MLST analyses, both Wolbachia sequence types clustered in a monophyletic clade with Drosophila nikananu (wNik) and Drosophila sturtevanti (wStv) from supergroup A. ClonalFrame analysis revealed a recombination event in the wAr_15234 strain which came from Apulia region. Scientific knowledge of the presence/prevalence of Wolbachia among medically important fleas, may contribute to develop an alternative biological method for the vector control.
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Affiliation(s)
| | | | | | - Giovanni Sgroi
- Department of Veterinary Medicine, University of Bari, Valenzano, Italy
| | | | | | - Domenico Otranto
- Department of Veterinary Medicine, University of Bari, Valenzano, Italy; Faculty of Veterinary Sciences, Bu-Ali Sina University, Hamedan, Iran.
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KITA DANIELAM, GIOVANELLA PATRICIA, YOSHINAGA THAÍST, PELLIZZER ELISAP, SETTE LARAD. Antarctic fungi applied to textile dye bioremediation. AN ACAD BRAS CIENC 2022; 94:e20210234. [DOI: 10.1590/0001-3765202220210234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 07/13/2021] [Indexed: 11/21/2022] Open
Affiliation(s)
- DANIELA M. KITA
- Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Brazil
| | - PATRICIA GIOVANELLA
- Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Brazil; Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Brazil
| | | | | | - LARA D. SETTE
- Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Brazil; Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Brazil
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Lindquist P, Gasbjerg LS, Mokrosinski J, Holst JJ, Hauser AS, Rosenkilde MM. The Location of Missense Variants in the Human GIP Gene Is Indicative for Natural Selection. Front Endocrinol (Lausanne) 2022; 13:891586. [PMID: 35846282 PMCID: PMC9277503 DOI: 10.3389/fendo.2022.891586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022] Open
Abstract
The intestinal hormone, glucose-dependent insulinotropic polypeptide (GIP), is involved in important physiological functions, including postprandial blood glucose homeostasis, bone remodeling, and lipid metabolism. While mutations leading to physiological changes can be identified in large-scale sequencing, no systematic investigation of GIP missense variants has been performed. Here, we identified 168 naturally occurring missense variants in the human GIP genes from three independent cohorts comprising ~720,000 individuals. We examined amino acid changing variants scattered across the pre-pro-GIP peptide using in silico effect predictions, which revealed that the sequence of the fully processed GIP hormone is more protected against mutations than the rest of the precursor protein. Thus, we observed a highly species-orthologous and population-specific conservation of the GIP peptide sequence, suggestive of evolutionary constraints to preserve the GIP peptide sequence. Elucidating the mutational landscape of GIP variants and how they affect the structural and functional architecture of GIP can aid future biological characterization and clinical translation.
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Affiliation(s)
- Peter Lindquist
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lærke Smidt Gasbjerg
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jacek Mokrosinski
- Novo Nordisk Research Center Indianapolis, Indianapolis, IN, United States
| | - Jens Juul Holst
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alexander Sebastian Hauser
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Alexander Sebastian Hauser, ; Mette Marie Rosenkilde,
| | - Mette Marie Rosenkilde
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Alexander Sebastian Hauser, ; Mette Marie Rosenkilde,
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4663
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McNutt ZA, Gandhi MD, Shatoff EA, Roy B, Devaraj A, Bundschuh R, Fredrick K. Comparative Analysis of anti-Shine- Dalgarno Function in Flavobacterium johnsoniae and Escherichia coli. Front Mol Biosci 2021; 8:787388. [PMID: 34966783 PMCID: PMC8710568 DOI: 10.3389/fmolb.2021.787388] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/08/2021] [Indexed: 12/03/2022] Open
Abstract
The anti-Shine-Dalgarno (ASD) sequence of 16S rRNA is highly conserved across Bacteria, and yet usage of Shine-Dalgarno (SD) sequences in mRNA varies dramatically, depending on the lineage. Here, we compared the effects of ASD mutagenesis in Escherichia coli, a Gammaproteobacteria which commonly employs SD sequences, and Flavobacterium johnsoniae, a Bacteroidia which rarely does. In E. coli, 30S subunits carrying any single substitution at positions 1,535–1,539 confer dominant negative phenotypes, whereas subunits with mutations at positions 1,540–1,542 are sufficient to support cell growth. These data suggest that CCUCC (1,535–1,539) represents the functional core of the element in E. coli. In F. johnsoniae, deletion of three ribosomal RNA (rrn) operons slowed growth substantially, a phenotype largely rescued by a plasmid-borne copy of the rrn operon. Using this complementation system, we found that subunits with single mutations at positions 1,535–1,537 are as active as control subunits, in sharp contrast to the E. coli results. Moreover, subunits with quadruple substitution or complete replacement of the ASD retain substantial, albeit reduced, activity. Sedimentation analysis revealed that these mutant subunits are overrepresented in the subunit fractions and underrepresented in polysome fractions, suggesting some defect in 30S biogenesis and/or translation initiation. Nonetheless, our collective data indicate that the ASD plays a much smaller role in F. johnsoniae than in E. coli, consistent with SD usage in the two organisms.
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Affiliation(s)
- Zakkary A McNutt
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, United States.,Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Mai D Gandhi
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Elan A Shatoff
- Center for RNA Biology, The Ohio State University, Columbus, OH, United States.,Department of Physics, The Ohio State University, Columbus, OH, United States
| | - Bappaditya Roy
- Center for RNA Biology, The Ohio State University, Columbus, OH, United States.,Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Aishwarya Devaraj
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, United States.,Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Ralf Bundschuh
- Center for RNA Biology, The Ohio State University, Columbus, OH, United States.,Department of Physics, The Ohio State University, Columbus, OH, United States.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United, States.,Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Kurt Fredrick
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, United States.,Center for RNA Biology, The Ohio State University, Columbus, OH, United States.,Department of Microbiology, The Ohio State University, Columbus, OH, United States
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4664
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Majewski P, Gutowska A, Smith DGE, Hauschild T, Majewska P, Hryszko T, Gizycka D, Kedra B, Kochanowicz J, Glowiński J, Drewnowska J, Swiecicka I, Sacha PT, Wieczorek P, Iwaniuk D, Sulewska A, Charkiewicz R, Makarewicz K, Zebrowska A, Czaban S, Radziwon P, Niklinski J, Tryniszewska EA. Plasmid Mediated mcr-1.1 Colistin-Resistance in Clinical Extraintestinal Escherichia coli Strains Isolated in Poland. Front Microbiol 2021; 12:547020. [PMID: 34956105 PMCID: PMC8703133 DOI: 10.3389/fmicb.2021.547020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 11/02/2021] [Indexed: 01/27/2023] Open
Abstract
Objectives: The growing incidence of multidrug-resistant (MDR) bacteria is an inexorable and fatal challenge in modern medicine. Colistin is a cationic polypeptide considered a “last-resort” antimicrobial for treating infections caused by MDR Gram-negative bacterial pathogens. Plasmid-borne mcr colistin resistance emerged recently, and could potentially lead to essentially untreatable infections, particularly in hospital and veterinary (livestock farming) settings. In this study, we sought to establish the molecular basis of colistin-resistance in six extraintestinal Escherichia coli strains. Methods: Molecular investigation of colistin-resistance was performed in six extraintestinal E. coli strains isolated from patients hospitalized in Medical University Hospital, Bialystok, Poland. Complete structures of bacterial chromosomes and plasmids were recovered with use of both short- and long-read sequencing technologies and Unicycler hybrid assembly. Moreover, an electrotransformation assay was performed in order to confirm IncX4 plasmid influence on colistin-resistance phenotype in clinical E. coli strains. Results: Here we report on the emergence of six mcr-1.1-producing extraintestinal E. coli isolates with a number of virulence factors. Mobile pEtN transferase-encoding gene, mcr-1.1, has been proved to be encoded within a type IV secretion system (T4SS)-containing 33.3 kbp IncX4 plasmid pMUB-MCR, next to the PAP2-like membrane-associated lipid phosphatase gene. Conclusion: IncX4 mcr-containing plasmids are reported as increasingly disseminated among E. coli isolates, making it an “epidemic” plasmid, responsible for (i) dissemination of colistin-resistance determinants between different E. coli clones, and (ii) circulation between environmental, industrial, and clinical settings. Great effort needs to be taken to avoid further dissemination of plasmid-mediated colistin resistance among clinically relevant Gram-negative bacterial pathogens.
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Affiliation(s)
- Piotr Majewski
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Anna Gutowska
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - David G E Smith
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Tomasz Hauschild
- Department of Microbiology, Institute of Biology, University of Białystok, Białystok, Poland
| | | | - Tomasz Hryszko
- Second Department of Nephrology and Hypertension with Dialysis Unit, Medical University of Białystok, Białystok, Poland
| | - Dominika Gizycka
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Boguslaw Kedra
- Second Department of General and Gastroenterological Surgery, Medical University of Białystok, Białystok, Poland
| | - Jan Kochanowicz
- Department of Neurology, Medical University of Białystok, Białystok, Poland
| | - Jerzy Glowiński
- Department of Vascular Surgery and Transplantation, Medical University of Białystok, Białystok, Poland
| | - Justyna Drewnowska
- Department of Microbiology, Institute of Biology, University of Białystok, Białystok, Poland
| | - Izabela Swiecicka
- Department of Microbiology, Institute of Biology, University of Białystok, Białystok, Poland
| | - Pawel T Sacha
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Piotr Wieczorek
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Dominika Iwaniuk
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Anetta Sulewska
- Department of Clinical Molecular Biology, Medical University of Białystok, Białystok, Poland
| | - Radoslaw Charkiewicz
- Department of Clinical Molecular Biology, Medical University of Białystok, Białystok, Poland
| | | | | | - Slawomir Czaban
- Department of Anesthesiology and Intensive Care, Medical University of Białystok, Białystok, Poland
| | - Piotr Radziwon
- Regional Centre for Transfusion Medicine, Białystok, Poland.,Department of Hematology, Medical University of Białystok, Białystok, Poland
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Białystok, Białystok, Poland
| | - Elzbieta A Tryniszewska
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
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4665
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Luo J, Chen J, Guo W, Yang Z, Lim KJ, Wang Z. Reassessment of Annamocarya sinesis ( Carya sinensis) Taxonomy through Concatenation and Coalescence Phylogenetic Analysis. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010052. [PMID: 35009055 PMCID: PMC8747223 DOI: 10.3390/plants11010052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 05/20/2023]
Abstract
Due to its peculiar morphological characteristics, there is dispute as to whether the genus of Annamocarya sinensis, a species of Juglandaceae, is Annamocarya or Carya. Most morphologists believe it should be distinguished from the Carya genus while genomicists suggest that A. sinensis belongs to the Carya genus. To explore the taxonomic status of A. sinensis using chloroplast genes, we collected chloroplast genomes of 16 plant species and assembled chloroplast genomes of 10 unpublished Carya species. We analyzed all 26 species' chloroplast genomes through two analytical approaches (concatenation and coalescence), using the entire and unique chloroplast coding sequence (CDS) and entire and protein sequences. Our results indicate that the analysis of the CDS and protein sequences or unique CDS and unique protein sequence of chloroplast genomes shows that A. sinensis indeed belongs to the Carya genus. In addition, our analysis shows that, compared to single chloroplast genes, the phylogeny trees constructed using numerous genes showed higher consistency. Moreover, the phylogenetic analysis calculated with the coalescence method and unique gene sequences was more robust than that done with the concatenation method, particularly for analyzing phylogenetically controversial species. Through the analysis, our results concluded that A. sinensis should be called C. sinensis.
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Affiliation(s)
- Jie Luo
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (J.L.); (J.C.); (W.G.); (Z.Y.)
| | - Junhao Chen
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (J.L.); (J.C.); (W.G.); (Z.Y.)
- Department of Biology, Saint Louis University, St. Louis, MO 63104, USA
| | - Wenlei Guo
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (J.L.); (J.C.); (W.G.); (Z.Y.)
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhengfu Yang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (J.L.); (J.C.); (W.G.); (Z.Y.)
| | - Kean-Jin Lim
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (J.L.); (J.C.); (W.G.); (Z.Y.)
- Correspondence: (K.-J.L.); (Z.W.)
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (J.L.); (J.C.); (W.G.); (Z.Y.)
- Correspondence: (K.-J.L.); (Z.W.)
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4666
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Matsvay A, Dyachkova M, Mikhaylov I, Kiselev D, Say A, Burskaia V, Artyushin I, Khafizov K, Shipulin G. Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Novel Tern Atadenovirus. Microorganisms 2021; 10:31. [PMID: 35056480 PMCID: PMC8781740 DOI: 10.3390/microorganisms10010031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 01/03/2023] Open
Abstract
Discovery and study of viruses carried by migratory birds are tasks of high importance due to the host's ability to spread infectious diseases over significant distances. With this paper, we present and characterize the first complete genome sequence of atadenovirus from a tern bird (common tern, Sterna hirundo) preliminarily named tern atadenovirus 1 (TeAdV-1). TeAdV-1 genome is a linear double-stranded DNA molecule, 31,334 base pairs which contain 30 methionine-initiated open reading frames with gene structure typical for Atadenovirus genus, and the shortest known inverted terminal repeats (ITRs) within the Atadenovirus genus consisted of 25 bases. The nucleotide composition of the genome is characterized by a low G + C content (33.86%), which is the most AT-rich genome of known avian adenoviruses within Atadenovirus genus. The nucleotide sequence of the TeAdV-1 genome shows high divergence compared to known representatives of the Atadenovirus genus with the highest similarity to the duck atadenovirus 1 (53.7%). Phylogenetic analysis of the protein sequences of core genes confirms the taxonomic affiliation of the new representative to the genus Atadenovirus with the degree of divergence from the known representatives exceeding the interspecies distance within the genus. Thereby we proposed a novel TeAdV-1 to be considered as a separate species.
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Affiliation(s)
- Alina Matsvay
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, 115184 Moscow, Russia
| | - Marina Dyachkova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Ivan Mikhaylov
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Daniil Kiselev
- Institute for Neurosciences of Montpellier, University of Montpellier, INSERM, 34091 Montpellier, France
| | - Anna Say
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | | | - Ilya Artyushin
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Kamil Khafizov
- Moscow Institute of Physics and Technology, National Research University, 115184 Moscow, Russia
| | - German Shipulin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
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4667
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Krishna Deepak RNV, Verma RK, Hartono YD, Yew WS, Fan H. Recent Advances in Structure, Function, and Pharmacology of Class A Lipid GPCRs: Opportunities and Challenges for Drug Discovery. Pharmaceuticals (Basel) 2021; 15:12. [PMID: 35056070 PMCID: PMC8779880 DOI: 10.3390/ph15010012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/17/2021] [Accepted: 12/17/2021] [Indexed: 01/01/2023] Open
Abstract
Great progress has been made over the past decade in understanding the structural, functional, and pharmacological diversity of lipid GPCRs. From the first determination of the crystal structure of bovine rhodopsin in 2000, much progress has been made in the field of GPCR structural biology. The extraordinary progress in structural biology and pharmacology of GPCRs, coupled with rapid advances in computational approaches to study receptor dynamics and receptor-ligand interactions, has broadened our comprehension of the structural and functional facets of the receptor family members and has helped usher in a modern age of structure-based drug design and development. First, we provide a primer on lipid mediators and lipid GPCRs and their role in physiology and diseases as well as their value as drug targets. Second, we summarize the current advancements in the understanding of structural features of lipid GPCRs, such as the structural variation of their extracellular domains, diversity of their orthosteric and allosteric ligand binding sites, and molecular mechanisms of ligand binding. Third, we close by collating the emerging paradigms and opportunities in targeting lipid GPCRs, including a brief discussion on current strategies, challenges, and the future outlook.
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Affiliation(s)
- R. N. V. Krishna Deepak
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix #07-01, Singapore 138671, Singapore; (R.K.V.); (Y.D.H.)
| | - Ravi Kumar Verma
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix #07-01, Singapore 138671, Singapore; (R.K.V.); (Y.D.H.)
| | - Yossa Dwi Hartono
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix #07-01, Singapore 138671, Singapore; (R.K.V.); (Y.D.H.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore;
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Wen Shan Yew
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore;
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Hao Fan
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix #07-01, Singapore 138671, Singapore; (R.K.V.); (Y.D.H.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore;
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4668
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Abstract
In the beer brewing industry, microbial spoilage presents a consistent threat that must be monitored and controlled to ensure the palatability of a finished product. Many of the predominant beer spoilage microbes have been identified and characterized, but the mechanisms of contamination and persistence remain an open area of study. Postproduction, many beers are distributed as kegs that are attached to draft delivery systems in retail settings where ample opportunities for microbial spoilage are present. As such, restaurants and bars can experience substantial costs and downtime for cleaning when beer draft lines become heavily contaminated. Spoilage monitoring on the retail side of the beer industry is often overlooked, yet this arena may represent one of the largest threats to the profitability of a beer if its flavor profile becomes substantially distorted by contaminating microbes. In this study, we sampled and cultured microbial communities found in beers dispensed from a retail draft system to identify the contaminating bacteria and yeasts. We also evaluated their capability to establish new biofilms in a controlled setting. Among four tested beer types, we identified over a hundred different contaminant bacteria and nearly 20 wild yeasts. The culturing experiments demonstrated that most of these microbes were viable and capable of joining new biofilm communities. These data provide an important reference for monitoring specific beer spoilage microbes in draft systems and we provide suggestions for cleaning protocol improvements. IMPORTANCE Beer production, packaging, and service are each vulnerable to contamination by microbes that metabolize beer chemicals and impart undesirable flavors, which can result in the disposal of entire batches. Therefore, great effort is taken by brewmasters to reduce and monitor contamination during production and packaging. A commonly overlooked quality control stage of a beer supply chain is at the retail service end, where beer kegs supply draft lines in bars and restaurants under nonsterile conditions. We found that retail draft line contamination is rampant and that routine line cleaning methods are insufficient to efficiently suppress beer spoilage. Thus, many customers unknowingly consume spoiled versions of the beers they consume. This study identified the bacteria and yeast that were resident in retail draft beer samples and also investigated their abilities to colonize tubing material as members of biofilm communities.
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4669
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Cortés-Albayay C, Sangal V, Klenk HP, Nouioui I. Comparative Genomic Study of Vinyl Chloride Cluster and Description of Novel Species, Mycolicibacterium vinylchloridicum sp. nov. Front Microbiol 2021; 12:767895. [PMID: 35003006 PMCID: PMC8727900 DOI: 10.3389/fmicb.2021.767895] [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: 08/31/2021] [Accepted: 11/16/2021] [Indexed: 11/30/2022] Open
Abstract
Advanced physicochemical and chemical absorption methods for chlorinated ethenes are feasible but incur high costs and leave traces of pollutants on the site. Biodegradation of such pollutants by anaerobic or aerobic bacteria is emerging as a potential alternative. Several mycobacteria including Mycolicibacterium aurum L1, Mycolicibacterium chubuense NBB4, Mycolicibacterium rhodesiae JS60, Mycolicibacterium rhodesiae NBB3 and Mycolicibacterium smegmatis JS623 have previously been described as assimilators of vinyl chloride (VC). In this study, we compared nucleotide sequence of VC cluster and performed a taxogenomic evaluation of these mycobacterial species. The results showed that the complete VC cluster was acquired by horizontal gene transfer and not intrinsic to the genus Mycobacterium sensu lato. These results also revealed the presence of an additional xcbF1 gene that seems to be involved in Coenzyme M biosynthesis, which is ultimately used in the VC degradation pathway. Furthermore, we suggest for the first time that S/N-Oxide reductase encoding gene was involved in the dissociation of the SsuABC transporters from the organosulfur, which play a crucial role in the Coenzyme M biosynthesis. Based on genomic data, M. aurum L1, M. chubuense NBB4, M. rhodesiae JS60, M. rhodesiae NBB3 and M. smegmatis JS623 were misclassified and form a novel species within the genus Mycobacterium sensu lato. Mycolicibacterium aurum L1T (CECT 8761T = DSM 6695T) was the subject of polyphasic taxonomic studies and showed ANI and dDDH values of 84.7 and 28.5% with its close phylogenetic neighbour, M. sphagni ATCC 33027T. Phenotypic, chemotaxonomic and genomic data considering strain L1T (CECT 8761T = DSM 6695T) as a type strain of novel species with the proposed name, Mycolicibacterium vinylchloridicum sp. nov.
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Affiliation(s)
- Carlos Cortés-Albayay
- Faculty of Science, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Hans-Peter Klenk
- Faculty of Science, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Imen Nouioui
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- *Correspondence: Imen Nouioui,
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4670
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Castro-Jaimes S, Guerrero G, Bello-López E, Cevallos MA. Replication initiator proteins of Acinetobacter baumannii plasmids: An update note. Plasmid 2021; 119-120:102616. [PMID: 34953823 DOI: 10.1016/j.plasmid.2021.102616] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 11/26/2022]
Abstract
The bioinformatic analysis that we made of 492 Acinetobacter baumannii plasmid sequences identified 418 genes encoding Replication Initiator (Rep) proteins that fell into at least fourteen groups according to the protein domains that they contained. The most abundant group of Rep proteins contained a Rep_3 superfamily domain, followed by Rep proteins containing Replicase/PriCT_1 superfamily domains, and then by Reps possessing only an HTH_MerR-SF superfamily domain. The remaining eleven groups contain only a few members. To evaluate the diversity of these Rep proteins, we classify them using the current scheme of GR homology groups, which contains 34 groups. However, we needed to create 22 additional GR homology groups to capture all the Rep protein diversity of the plasmid collection. Finally, our bioinformatic analysis suggests that a large fraction of the plasmids seem to have a restricted host range limited to Acinetobacter species, except for those belonging to GR38 that have a very wide host range. To facilitate the future analysis of the Rep proteins, we included a list of the DNA and protein sequences, in fasta format, of the representatives of each one of the GR homology groups.
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Affiliation(s)
- Semiramis Castro-Jaimes
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca CP62210, Morelos, Mexico
| | - Gabriela Guerrero
- Unidad de Análisis Bioinformático, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca CP62210, Morelos, Mexico
| | - Elena Bello-López
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca CP62210, Morelos, Mexico
| | - Miguel A Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca CP62210, Morelos, Mexico.
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4671
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Beresford-Jones BS, Forster SC, Stares MD, Notley G, Viciani E, Browne HP, Boehmler DJ, Soderholm AT, Kumar N, Vervier K, Cross JR, Almeida A, Lawley TD, Pedicord VA. The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping. Cell Host Microbe 2021; 30:124-138.e8. [PMID: 34971560 PMCID: PMC8763404 DOI: 10.1016/j.chom.2021.12.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/05/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022]
Abstract
Human health and disease have increasingly been shown to be impacted by the gut microbiota, and mouse models are essential for investigating these effects. However, the compositions of human and mouse gut microbiotas are distinct, limiting translation of microbiota research between these hosts. To address this, we constructed the Mouse Gastrointestinal Bacteria Catalogue (MGBC), a repository of 26,640 high-quality mouse microbiota-derived bacterial genomes. This catalog enables species-level analyses for mapping functions of interest and identifying functionally equivalent taxa between the microbiotas of humans and mice. We have complemented this with a publicly deposited collection of 223 bacterial isolates, including 62 previously uncultured species, to facilitate experimental investigation of individual commensal bacteria functions in vitro and in vivo. Together, these resources provide the ability to identify and test functionally equivalent members of the host-specific gut microbiotas of humans and mice and support the informed use of mouse models in human microbiota research.
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Affiliation(s)
- Benjamin S Beresford-Jones
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Mark D Stares
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - George Notley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elisa Viciani
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Hilary P Browne
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Daniel J Boehmler
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amelia T Soderholm
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Nitin Kumar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kevin Vervier
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Justin R Cross
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandre Almeida
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Trevor D Lawley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Virginia A Pedicord
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.
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4672
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Cargo Genes of Tn 7-Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes. mBio 2021; 12:e0293821. [PMID: 34872347 PMCID: PMC8649781 DOI: 10.1128/mbio.02938-21] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Transposition is a major mechanism of horizontal gene mobility in prokaryotes. However, exploration of the genes mobilized by transposons (cargo) is hampered by the difficulty in delineating integrated transposons from their surrounding genetic context. Here, we present a computational approach that allowed us to identify the boundaries of 6,549 Tn7-like transposons. We found that 96% of these transposons carry at least one cargo gene. Delineation of distinct communities in a gene-sharing network demonstrates how transposons function as a conduit of genes between phylogenetically distant hosts. Comparative analysis of the cargo genes reveals significant enrichment of mobile genetic elements (MGEs) nested within Tn7-like transposons, such as insertion sequences and toxin-antitoxin modules, and of genes involved in recombination, anti-MGE defense, and antibiotic resistance. More unexpectedly, cargo also includes genes encoding central carbon metabolism enzymes. Twenty-two Tn7-like transposons carry both an anti-MGE defense system and antibiotic resistance genes, illustrating how bacteria can overcome these combined pressures upon acquisition of a single transposon. This work substantially expands the distribution of Tn7-like transposons, defines their evolutionary relationships, and provides a large-scale functional classification of prokaryotic genes mobilized by transposition.
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4673
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Taxon-Specific Shifts in Bacterial and Archaeal Transcription of Dissolved Organic Matter Cycling Genes in a Stratified Fjord. mSystems 2021; 6:e0057521. [PMID: 34904860 PMCID: PMC8670421 DOI: 10.1128/msystems.00575-21] [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] [Indexed: 11/20/2022] Open
Abstract
A considerable fraction of organic matter derived from photosynthesis in the euphotic zone settles into the ocean’s interior and, as it progresses, is degraded by diverse microbial consortia that utilize a suite of extracellular enzymes and membrane transporters. Still, the molecular details that regulate carbon cycling across depths remain little explored. As stratification in fjords has made them attractive models to explore patterns in biological oceanography, we here analyzed bacterial and archaeal transcription in samples from five depth layers in the Gullmar Fjord, Sweden. Transcriptional variation over depth correlated with gradients in chlorophyll a and nutrient concentrations. Differences in transcription between sampling dates (summer and early autumn) were strongly correlated with ammonium concentrations, which potentially was linked with a stronger influence of (micro-)zooplankton grazing in summer. Transcriptional investment in carbohydrate-active enzymes (CAZymes) decreased with depth and shifted toward peptidases, partly a result of elevated CAZyme transcription by Flavobacteriales, Cellvibrionales, and Synechococcales at 2 to 25 m and a dominance of peptidase transcription by Alteromonadales and Rhodobacterales from 50 m down. In particular, CAZymes for chitin, laminarin, and glycogen were important. High levels of transcription of ammonium transporter genes by Thaumarchaeota at depth (up to 18% of total transcription), along with the genes for ammonia oxidation and CO2 fixation, indicated that chemolithoautotrophy contributed to the carbon flux in the fjord. The taxon-specific expression of functional genes for processing of the marine pool of dissolved organic matter and inorganic nutrients across depths emphasizes the importance of different microbial foraging mechanisms over spatiotemporal scales for shaping biogeochemical cycles. IMPORTANCE It is generally recognized that stratification in the ocean strongly influences both the community composition and the distribution of ecological functions of microbial communities, which in turn are expected to shape the biogeochemical cycling of essential elements over depth. Here, we used metatranscriptomics analysis to infer molecular detail on the distribution of gene systems central to the utilization of organic matter in a stratified marine system. We thereby uncovered that pronounced shifts in the transcription of genes encoding CAZymes, peptidases, and membrane transporters occurred over depth among key prokaryotic orders. This implies that sequential utilization and transformation of organic matter through the water column is a key feature that ultimately influences the efficiency of the biological carbon pump.
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4674
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Kim JL, Ben-Dor S, Rosenfeld-Gur E, Futerman AH. A novel C-terminal DxRSDxE motif in ceramide synthases involved in dimer formation. J Biol Chem 2021; 298:101517. [PMID: 34942147 PMCID: PMC8789539 DOI: 10.1016/j.jbc.2021.101517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 01/21/2023] Open
Abstract
Ceramide is a lipid moiety synthesized via the enzymatic activity of ceramide synthases (CerSs), six of which have been identified in mammalian cells, and each of which uses a unique subset of acyl-CoAs for ceramide synthesis. The CerSs are part of a larger gene family, the Tram-Lag-CLN8 domain family. Here, we identify a unique, C-terminal motif, the DxRSDxE motif, which is only found in CerSs and not in other Tram-Lag-CLN8 family members. Deletion of this motif in either CerS2 or in CerS6 did not affect the ability of either enzyme to generate ceramide using both an in vitro assay and metabolic labeling, but deletion of this motif did affect the activity of CerS2 when coexpressed with CerS6. Surprisingly, transfection of cells with either CerS2 or CerS6 lacking the motif did not result in changes in cellular ceramide levels. We found that CerS2 and CerS6 interact with each other, as shown by immunoprecipitation, but deletion of the DxRSDxE motif impeded this interaction. Moreover, proteomics analysis of cells transfected with CerS6Δ338–344 indicated that deletion of the C-terminal motif impacted cellular protein expression, and in particular, the levels of ORMDL1, a negative regulator of sphingolipid synthesis. We suggest that this novel C-terminal motif regulates CerS dimer formation and thereby impacts ceramide synthesis.
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Affiliation(s)
- Jiyoon L Kim
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shifra Ben-Dor
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eden Rosenfeld-Gur
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel; The Joseph Meyerhoff Professor of Biochemistry at the Weizmann Institute of Science.
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4675
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Shani N, Oberhaensli S, Berthoud H, Schmidt RS, Bachmann HP. Antimicrobial Susceptibility of Lactobacillus delbrueckii subsp. lactis from Milk Products and Other Habitats. Foods 2021; 10:foods10123145. [PMID: 34945696 PMCID: PMC8701367 DOI: 10.3390/foods10123145] [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] [Received: 11/15/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
As components of many cheese starter cultures, strains of Lactobacillus delbrueckii subsp. lactis (LDL) must be tested for their antimicrobial susceptibility to avoid the potential horizontal transfer of antibiotic resistance (ABR) determinants in the human body or in the environment. To this end, a phenotypic test, as well as a screening for antibiotic resistance genes (ARGs) in genome sequences, is commonly performed. Historically, microbiological cutoffs (MCs), which are used to classify strains as either 'sensitive' or 'resistant' based on the minimal inhibitory concentrations (MICs) of a range of clinically-relevant antibiotics, have been defined for the whole group of the obligate homofermentative lactobacilli, which includes LDL among many other species. This often leads to inaccuracies in the appreciation of the ABR status of tested LDL strains and to false positive results. To define more accurate MCs for LDL, we analyzed the MIC profiles of strains originating from various habitats by using the broth microdilution method. These strains' genomes were sequenced and used to complement our analysis involving a search for ARGs, as well as to assess the phylogenetic proximity between strains. Of LDL strains, 52.1% displayed MICs that were higher than the defined MCs for kanamycin, 9.9% for chloramphenicol, and 5.6% for tetracycline, but no ARG was conclusively detected. On the other hand, all strains displayed MICs below the defined MCs for ampicillin, gentamycin, erythromycin, and clindamycin. Considering our results, we propose the adaptation of the MCs for six of the tested clinically-relevant antibiotics to improve the accuracy of phenotypic antibiotic testing.
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Affiliation(s)
- Noam Shani
- Competence Division Methods Development and Analytics, Agroscope, Schwarzenburgstrasse 161, 3003 Bern, Switzerland;
- Correspondence:
| | - Simone Oberhaensli
- Interfaculty Bioinformatics Unit and SIB Swiss Institute of Bioinformatics, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland;
| | - Hélène Berthoud
- Competence Division Methods Development and Analytics, Agroscope, Schwarzenburgstrasse 161, 3003 Bern, Switzerland;
| | - Remo S. Schmidt
- Research Division Food Microbial Systems, Agroscope, Schwarzenburgstrasse 161, 3003 Bern, Switzerland; (R.S.S.); (H.-P.B.)
| | - Hans-Peter Bachmann
- Research Division Food Microbial Systems, Agroscope, Schwarzenburgstrasse 161, 3003 Bern, Switzerland; (R.S.S.); (H.-P.B.)
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4676
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A novel gene order and remolded tRNAs revealed in the mitogenome of Asian gecarcinucid freshwater crabs (Brachyura, Gecarcinucidae). Gene 2021; 813:146102. [PMID: 34933078 DOI: 10.1016/j.gene.2021.146102] [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: 07/16/2021] [Revised: 10/13/2021] [Accepted: 11/16/2021] [Indexed: 11/21/2022]
Abstract
Here we report the first mitochondrial genomes (mitogenomes) of four species of gecarcinucid freshwater crabs (FWCs) in two genera, two from China (Somanniathelphusa hainanensis and S. yangshanensis), one from Laos (Esanthelphusa dugasti), and one from Myanmar (Esanthelphusa keyini). A novel gecarcinucid mitochondrial gene order (GMGO2) that was only found in E. dugasti that contains a total of 42 genes, including one pseudogene, two remolded tRNAs and two duplicated tRNAs. The GMGO2 of E. dugasti was compared with the brachyuran ground-pattern mitochondrial gene order (BMGO), revealing the rearrangements of the positions of 10 tRNAs, two PCGs, and one mNCR. The three other gecarcinucids in this study were all found to possess a previously reported gecarcinucid mitochondrial gene order (GMGO1). The phylogenetic tree reconstructed using the secondary structures of 22 tRNAs of the mitogenomes of 41 species of FWCs provides insights into the evolution of the mitogenome of E. dugasti (GMGO2) which includes remolded and duplicated tRNAs.
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4677
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Zeugner LE, Krüger K, Barrero-Canosa J, Amann RI, Fuchs BM. In situ visualization of glycoside hydrolase family 92 genes in marine flavobacteria. ISME COMMUNICATIONS 2021; 1:81. [PMID: 37938716 PMCID: PMC9723552 DOI: 10.1038/s43705-021-00082-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/24/2021] [Accepted: 12/02/2021] [Indexed: 11/09/2023]
Abstract
Gene clusters rich in carbohydrate-active enzymes within Flavobacteriia genera provide a competitiveness for their hosts to degrade diatom-derived polysaccharides. One such widely distributed polysaccharide is glucuronomannan, a main cell wall component of diatoms. A conserved gene cluster putatively degrading glucuronomannan was found previously among various flavobacterial taxa in marine metagenomes. Here, we aimed to visualize two glycoside hydrolase family 92 genes coding for α-mannosidases with fluorescently-labeled polynucleotide probes using direct-geneFISH. Reliable in situ localization of single-copy genes was achieved with an efficiency up to 74% not only in the flavobacterial strains Polaribacter Hel1_33_49 and Formosa Hel1_33_131 but also in planktonic samples from the North Sea. In combination with high-resolution microscopy, direct-geneFISH gave visual evidence of the contrasting lifestyles of closely related Polaribacter species in those samples and allowed for the determination of gene distribution among attached and free-living cells. We also detected highly similar GH92 genes in yet unidentified taxa by broadening probe specificities, enabling a visualization of the functional trait in subpopulations across the borders of species and genera. Such a quantitative insight into the niche separation of flavobacterial taxa complements our understanding of the ecology of polysaccharide-degrading bacteria beyond omics-based techniques on a single-cell level.
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Affiliation(s)
- Laura E Zeugner
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Karen Krüger
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jimena Barrero-Canosa
- Technical University of Berlin, Institute of Environmental Technology, Environmental Microbiology, Berlin, Germany
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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4678
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Biosca EG, Català-Senent JF, Figàs-Segura À, Bertolini E, López MM, Álvarez B. Genomic Analysis of the First European Bacteriophages with Depolymerase Activity and Biocontrol Efficacy against the Phytopathogen Ralstonia solanacearum. Viruses 2021; 13:v13122539. [PMID: 34960808 PMCID: PMC8703784 DOI: 10.3390/v13122539] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 12/28/2022] Open
Abstract
Ralstonia solanacearum is the causative agent of bacterial wilt, one of the most destructive plant diseases. While chemical control has an environmental impact, biological control strategies can allow sustainable agrosystems. Three lytic bacteriophages (phages) of R. solanacearum with biocontrol capacity in environmental water and plants were isolated from river water in Europe but not fully analysed, their genomic characterization being fundamental to understand their biology. In this work, the phage genomes were sequenced and subjected to bioinformatic analysis. The morphology was also observed by electron microscopy. Phylogenetic analyses were performed with a selection of phages able to infect R. solanacearum and the closely related phytopathogenic species R. pseudosolanacearum. The results indicated that the genomes of vRsoP-WF2, vRsoP-WM2 and vRsoP-WR2 range from 40,688 to 41,158 bp with almost 59% GC-contents, 52 ORFs in vRsoP-WF2 and vRsoP-WM2, and 53 in vRsoP-WR2 but, with only 22 or 23 predicted proteins with functional homologs in databases. Among them, two lysins and one exopolysaccharide (EPS) depolymerase, this type of depolymerase being identified in R. solanacearum phages for the first time. These three European phages belong to the same novel species within the Gyeongsanvirus, Autographiviridae family (formerly Podoviridae). These genomic data will contribute to a better understanding of the abilities of these phages to damage host cells and, consequently, to an improvement in the biological control of R. solanacearum.
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Affiliation(s)
- Elena G. Biosca
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain; (J.F.C.-S.); (À.F.-S.); (E.B.); (B.Á.)
- Correspondence:
| | - José Francisco Català-Senent
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain; (J.F.C.-S.); (À.F.-S.); (E.B.); (B.Á.)
- Centro de Investigación Príncipe Felipe, Unidad de Bioinformática y Bioestadística, 46012 Valencia, Spain
| | - Àngela Figàs-Segura
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain; (J.F.C.-S.); (À.F.-S.); (E.B.); (B.Á.)
| | - Edson Bertolini
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain; (J.F.C.-S.); (À.F.-S.); (E.B.); (B.Á.)
- Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91540-000, Brazil
| | - María M. López
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Valencia, Spain;
| | - Belén Álvarez
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain; (J.F.C.-S.); (À.F.-S.); (E.B.); (B.Á.)
- Departamento de Investigación Aplicada y Extensión Agraria, Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario (IMIDRA), 28800 Alcalá de Henares, Spain
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4679
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Gu C, Liang Y, Li J, Shao H, Jiang Y, Zhou X, Gao C, Li X, Zhang W, Guo C, He H, Wang H, Sung YY, Mok WJ, Wong LL, Suttle CA, McMinn A, Tian J, Wang M. Saline lakes on the Qinghai-Tibet Plateau harbor unique viral assemblages mediating microbial environmental adaption. iScience 2021; 24:103439. [PMID: 34988389 PMCID: PMC8710556 DOI: 10.1016/j.isci.2021.103439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/10/2021] [Accepted: 11/10/2021] [Indexed: 12/21/2022] Open
Abstract
The highest plateau on Earth, Qinghai-Tibet Plateau, contains thousands of lakes with broad salinity and diverse and unique microbial communities. However, little is known about their co-occurring viruses. Herein, we identify 4,560 viral Operational Taxonomic Units (vOTUs) from six viromes of three saline lakes on Qinghai-Tibet Plateau, with less than 1% that could be classified. Most of the predicted vOTUs were associated with the dominant bacterial and archaeal phyla. Virus-encoded auxiliary metabolic genes suggest that viruses influence microbial metabolisms of carbon, nitrogen, sulfur, and lipid; the antibiotic resistance mediation; and their salinity adaption. The six viromes clustered together with the ice core viromes and bathypelagic ocean viromes and might represent a new viral habitat. This study has revealed the unique characteristics and potential ecological roles of DNA viromes in the lakes of the highest plateau and established a foundation for the recognition of the viral roles in plateau lake ecosystems.
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Affiliation(s)
- Chengxiang Gu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Jiansen Li
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China
- Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Yong Jiang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Xinhao Zhou
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Chen Gao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Xianrong Li
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Wenjing Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Cui Guo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Hui He
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Hualong Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Yeong Yik Sung
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), 21030 Kuala Nerus, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), 21030 Kuala Nerus, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), 21030 Kuala Nerus, Malaysia
| | - Curtis A. Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology, and Botany and Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7001, Australia
| | - Jiwei Tian
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
- The affiliated hospital of Qingdao University, Qingdao 266000, China
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4680
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Wu R, Wang L, Xie J, Zhang Z. Diversity and Function of Wolf Spider Gut Microbiota Revealed by Shotgun Metagenomics. Front Microbiol 2021; 12:758794. [PMID: 34975785 PMCID: PMC8718803 DOI: 10.3389/fmicb.2021.758794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/23/2021] [Indexed: 11/29/2022] Open
Abstract
Wolf spiders (Lycosidae) are crucial component of integrated pest management programs and the characteristics of their gut microbiota are known to play important roles in improving fitness and survival of the host. However, there are only few studies of the gut microbiota among closely related species of wolf spider. Whether wolf spiders gut microbiota vary with habitats remains unknown. Here, we used shotgun metagenomic sequencing to compare the gut microbiota of two wolf spider species, Pardosa agraria and P. laura from farmland and woodland ecosystems, respectively. The results show that the gut microbiota of Pardosa spiders is similar in richness and abundance. Approximately 27.3% of the gut microbiota of P. agraria comprises Proteobacteria, and approximately 34.4% of the gut microbiota of P. laura comprises Firmicutes. We assembled microbial genomes and found that the gut microbiota of P. laura are enriched in genes for carbohydrate metabolism. In contrast, those of P. agraria showed a higher proportion of genes encoding acetyltransferase, an enzyme involved in resistance to antibiotics. We reconstructed three high-quality and species-level microbial genomes: Vulcaniibacterium thermophilum, Anoxybacillus flavithermus and an unknown bacterium belonging to the family Simkaniaceae. Our results contribute to an understanding of the diversity and function of gut microbiota in closely related spiders.
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Affiliation(s)
- Runbiao Wu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
| | - Luyu Wang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
| | - Jianping Xie
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
| | - Zhisheng Zhang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
- *Correspondence: Zhisheng Zhang, , orcid.org/0000-0002-9304-1789
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4681
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Maravilla AJ, Rosato M, Álvarez I, Nieto Feliner G, Rosselló JA. Interstitial Arabidopsis-Type Telomeric Repeats in Asteraceae. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122794. [PMID: 34961265 PMCID: PMC8705333 DOI: 10.3390/plants10122794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 05/13/2023]
Abstract
Tandem repeats of telomeric-like motifs at intra-chromosomal regions, known as interstitial telomeric repeats (ITR), have drawn attention as potential markers of structural changes, which might convey information about evolutionary relationships if preserved through time. Building on our previous work that reported outstanding ITR polymorphisms in the genus Anacyclus, we undertook a survey across 132 Asteraceae species, focusing on the six most speciose subfamilies and considering all the ITR data published to date. The goal was to assess whether the presence, site number, and chromosomal location of ITRs convey any phylogenetic signal. We conducted fluorescent in situ hybridization (FISH) using an Arabidopsis-type telomeric sequence as a probe on karyotypes obtained from mitotic chromosomes. FISH signals of ITR sites were detected in species of subfamilies Asteroideae, Carduoideae, Cichorioideae, Gymnarhenoideae, and Mutisioideae, but not in Barnadesioideae. Although six small subfamilies have not yet been sampled, altogether, our results suggest that the dynamics of ITR formation in Asteraceae cannot accurately trace the complex karyological evolution that occurred since the early diversification of this family. Thus, ITRs do not convey a reliable signal at deep or shallow phylogenetic levels and cannot help to delimitate taxonomic categories, a conclusion that might also hold for other important families such as Fabaceae.
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Affiliation(s)
- Alexis J. Maravilla
- Jardín Botánico, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, c/Quart 80, E-46008 Valencia, Spain; (A.J.M.); (M.R.)
| | - Marcela Rosato
- Jardín Botánico, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, c/Quart 80, E-46008 Valencia, Spain; (A.J.M.); (M.R.)
| | - Inés Álvarez
- Real Jardín Botánico (RJB), Consejo Superior de Investigaciones Científicas (CSIC), Plaza de Murillo 2, E-28014 Madrid, Spain; (I.Á.); (G.N.F.)
| | - Gonzalo Nieto Feliner
- Real Jardín Botánico (RJB), Consejo Superior de Investigaciones Científicas (CSIC), Plaza de Murillo 2, E-28014 Madrid, Spain; (I.Á.); (G.N.F.)
| | - Josep A. Rosselló
- Jardín Botánico, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, c/Quart 80, E-46008 Valencia, Spain; (A.J.M.); (M.R.)
- Correspondence: ; Tel.: +34-963-156-800
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4682
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Research and Innovation Supporting the European Sustainable and Smart Mobility Strategy: A Technology Perspective from Recent European Union Projects. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app112411981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Many concepts and innovations aim to improve transport and mobility, while helping to decrease the externalities that transport imposes on society. Research and innovation monitoring tools are important to assess the current state of development so that research funding and policy making efforts can be aligned optimally. This paper presents a comprehensive approach which links technological developments in the transport sector in Europe to the objectives of the most recent policy developments, in particular, the 2020 European Sustainable and Smart Mobility Strategy. It does so by identifying and evaluating technologies from European Union-funded projects between 2007 and 2020, by means of a technology taxonomy. Information is provided at an aggregated level on funding characteristics of both projects and the technologies, while at the same time, the level of maturity of researched technologies in the most recent projects is identified. This study can aid policy makers to support the future development of transport technologies as part of pertinent policy strategies and identify research gaps.
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4683
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Diverse Single-Stranded DNA Viruses Identified in Chicken Buccal Swabs. Microorganisms 2021; 9:microorganisms9122602. [PMID: 34946202 PMCID: PMC8703526 DOI: 10.3390/microorganisms9122602] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/11/2021] [Accepted: 12/13/2021] [Indexed: 11/18/2022] Open
Abstract
High-throughput sequencing approaches offer the possibility to better understand the complex microbial communities associated with animals. Viral metagenomics has facilitated the discovery and identification of many known and unknown viruses that inhabit mucosal surfaces of the body and has extended our knowledge related to virus diversity. We used metagenomics sequencing of chicken buccal swab samples and identified various small DNA viruses with circular genome organization. Out of 134 putative circular viral-like circular genome sequences, 70 are cressdnaviruses and 26 are microviruses, whilst the remaining 38 most probably represent sub-genomic molecules. The cressdnaviruses found in this study belong to the Circoviridae, Genomoviridae and Smacoviridae families as well as previously described CRESS1 and naryavirus groups. Among these, genomoviruses and smacoviruses were the most prevalent across the samples. Interestingly, we also identified 26 bacteriophages that belong to the Microviridae family, whose members are known to infect enterobacteria.
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4684
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Braglia L, Breviario D, Gianì S, Gavazzi F, De Gregori J, Morello L. New Insights into Interspecific Hybridization in Lemna L. Sect. Lemna (Lemnaceae Martinov). PLANTS 2021; 10:plants10122767. [PMID: 34961238 PMCID: PMC8703825 DOI: 10.3390/plants10122767] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/01/2021] [Accepted: 12/09/2021] [Indexed: 11/16/2022]
Abstract
Duckweeds have been increasingly studied in recent years, both as model plants and in view of their potential applications as a new crop in a circular bioeconomy perspective. In order to select species and clones with the desired attributes, the correct identification of the species is fundamental. Molecular methods have recently provided a more solid base for taxonomy and yielded a consensus phylogenetic tree, although some points remain to be elucidated. The duckweed genus Lemna L. comprises twelve species, grouped in four sections, which include very similar sister species. The least taxonomically resolved is sect. Lemna, presenting difficulties in species delimitation using morphological and even barcoding molecular markers. Ambiguous species boundaries between Lemna minor L. and Lemna japonica Landolt have been clarified by Tubulin Based Polymorphism (TBP), with the discovery of interspecific hybrids. In the present work, we extended TBP profiling to a larger number of clones in sect. Lemna, previously classified using only morphological features, in order to test that classification, and to investigate the possible existence of other hybrids in this section. The analysis revealed several misidentifications of clones, in particular among the species L. minor, L. japonica and Lemna gibba L., and identified six putative ‘L. gibba’ clones as interspecific hybrids between L. minor and L. gibba.
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4685
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Olo Ndela E, Enault F, Toussaint A. Transposable Prophages in Leptospira: An Ancient, Now Diverse, Group Predominant in Causative Agents of Weil's Disease. Int J Mol Sci 2021; 22:13434. [PMID: 34948244 PMCID: PMC8705779 DOI: 10.3390/ijms222413434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/06/2021] [Accepted: 12/11/2021] [Indexed: 12/24/2022] Open
Abstract
The virome associated with the corkscrew shaped bacterium Leptospira, responsible for Weil's disease, is scarcely known, and genetic tools available for these bacteria remain limited. To reduce these two issues, potential transposable prophages were searched in Leptospiraceae genomes. The 236 predicted transposable prophages were particularly abundant in the most pathogenic leptospiral clade, being potentially involved in the acquisition of virulent traits. According to genomic similarities and phylogenies, these prophages are distantly related to known transposable phages and are organized into six groups, one of them encompassing prophages with unusual TA-TA ends. Interestingly, structural and transposition proteins reconstruct different relationships between groups, suggesting ancestral recombinations. Based on the baseplate phylogeny, two large clades emerge, with specific gene-contents and high sequence divergence reflecting their ancient origin. Despite their high divergence, the size and overall genomic organization of all prophages are very conserved, a testimony to the highly constrained nature of their genomes. Finally, similarities between these prophages and the three known non-transposable phages infecting L. biflexa, suggest gene transfer between different Caudovirales inside their leptospiral host, and the possibility to use some of the transposable prophages in that model strain.
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Affiliation(s)
- Eric Olo Ndela
- Laboratoire Microorganismes: Genome Environment (LMGE), Université Clermont Auvergne, CNRS, F-63000 Clermont-Ferrand, France;
| | - François Enault
- Laboratoire Microorganismes: Genome Environment (LMGE), Université Clermont Auvergne, CNRS, F-63000 Clermont-Ferrand, France;
| | - Ariane Toussaint
- Microbiologie Cellulaire et Moléculaire, Université Libre de Bruxelles, IBMM-DBM, 12 Rue des Professeurs Jeneer et Brachet, B-6041 Gosselies, Belgium;
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4686
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Sharifi F, Ye Y. Identification and classification of reverse transcriptases in bacterial genomes and metagenomes. Nucleic Acids Res 2021; 50:e29. [PMID: 34904653 PMCID: PMC8934634 DOI: 10.1093/nar/gkab1207] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/17/2021] [Accepted: 11/22/2021] [Indexed: 02/07/2023] Open
Abstract
Reverse transcriptases (RTs) are found in different systems including group II introns, Diversity Generating Retroelements (DGRs), retrons, CRISPR-Cas systems, and Abortive Infection (Abi) systems in prokaryotes. Different classes of RTs can play different roles, such as template switching and mobility in group II introns, spacer acquisition in CRISPR-Cas systems, mutagenic retrohoming in DGRs, programmed cell suicide in Abi systems, and recently discovered phage defense in retrons. While some classes of RTs have been studied extensively, others remain to be characterized. There is a lack of computational tools for identifying and characterizing various classes of RTs. In this study, we built a tool (called myRT) for identification and classification of prokaryotic RTs. In addition, our tool provides information about the genomic neighborhood of each RT, providing potential functional clues. We applied our tool to predict RTs in all complete and draft bacterial genomes, and created a collection that can be used for exploration of putative RTs and their associated protein domains. Application of myRT to metagenomes showed that gut metagenomes encode proportionally more RTs related to DGRs, outnumbering retron-related RTs, as compared to the collection of reference genomes. MyRT is both available as a standalone software (https://github.com/mgtools/myRT) and also through a website (https://omics.informatics.indiana.edu/myRT/).
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Affiliation(s)
- Fatemeh Sharifi
- Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA
| | - Yuzhen Ye
- Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA
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4687
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Emser SV, Schaschl H, Millesi E, Steinborn R. Extension of Mitogenome Enrichment Based on Single Long-Range PCR: mtDNAs and Putative Mitochondrial-Derived Peptides of Five Rodent Hibernators. Front Genet 2021; 12:685806. [PMID: 35027919 PMCID: PMC8749263 DOI: 10.3389/fgene.2021.685806] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022] Open
Abstract
Enriching mitochondrial DNA (mtDNA) for sequencing entire mitochondrial genomes (mitogenomes) can be achieved by single long-range PCR. This avoids interference from the omnipresent nuclear mtDNA sequences (NUMTs). The approach is currently restricted to the use of samples collected from humans and ray-finned fishes. Here, we extended the use of single long-range PCR by introducing back-to-back oligonucleotides that target a sequence of extraordinary homology across vertebrates. The assay was applied to five hibernating rodents, namely alpine marmot, Arctic and European ground squirrels, and common and garden dormice, four of which have not been fully sequenced before. Analysis of the novel mitogenomes focussed on the prediction of mitochondrial-derived peptides (MDPs) providing another level of information encoded by mtDNA. The comparison of MOTS-c, SHLP4 and SHLP6 sequences across vertebrate species identified segments of high homology that argue for future experimentation. In addition, we evaluated four candidate polymorphisms replacing an amino acid in mitochondrially encoded subunits of the oxidative phosphorylation (OXPHOS) system that were reported in relation to cold-adaptation. No obvious pattern was found for the diverse sets of mammalian species that either apply daily or multiday torpor or otherwise cope with cold. In summary, our single long-range PCR assay applying a pair of back-to-back primers that target a consensus sequence motif of Vertebrata has potential to amplify (intact) mitochondrial rings present in templates from a taxonomically diverse range of vertebrates. It could be promising for studying novel mitogenomes, mitotypes of a population and mitochondrial heteroplasmy in a sensitive, straightforward and flexible manner.
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Affiliation(s)
- Sarah V. Emser
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Helmut Schaschl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Eva Millesi
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Ralf Steinborn
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
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4688
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Mikhaylova YV, Puzanskiy RK, Shishova MF. Evolution of 14-3-3 Proteins in Angiosperm Plants: Recurring Gene Duplication and Loss. PLANTS (BASEL, SWITZERLAND) 2021; 10:2724. [PMID: 34961196 PMCID: PMC8703263 DOI: 10.3390/plants10122724] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/30/2021] [Accepted: 12/08/2021] [Indexed: 11/18/2022]
Abstract
14-3-3 proteins are key regulatory factors in plants and are involved in a broad range of physiological processes. We addressed the evolutionary history of 14-3-3s from 46 angiosperm species, including basal angiosperm Amborella and major lineage of monocotyledons and eudicotyledons. Orthologs of Arabidopsis isoforms were detected. There were several rounds of duplication events in the evolutionary history of the 14-3-3 protein family in plants. At least four subfamilies (iota, epsilon, kappa, and psi) formed as a result of ancient duplication in a common ancestor of angiosperm plants. Recent duplication events followed by gene loss in plant lineage, among others Brassicaceae, Fabaceae, and Poaceae, further shaped the high diversity of 14-3-3 isoforms in plants. Coexpression data showed that 14-3-3 proteins formed different functional groups in different species. In some species, evolutionarily related groups of 14-3-3 proteins had coexpressed together under certain physiological conditions, whereas in other species, closely related isoforms expressed in the opposite manner. A possible explanation is that gene duplication and loss is accompanied by functional plasticity of 14-3-3 proteins.
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Affiliation(s)
- Yulia V. Mikhaylova
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, Professor Popov str., 2, 197376 St. Petersburg, Russia
| | - Roman K. Puzanskiy
- Laboratory of Analytical Phytochemistry, Komarov Botanical Institute of the Russian Academy of Sciences, Professor Popov str., 2, 197376 St. Petersburg, Russia;
- Department of Plant Physiology and Biochemistry, Saint-Petersburg State University, Universitetskaya em., 7/9, 199034 St. Petersburg, Russia
| | - Maria F. Shishova
- Department of Plant Physiology and Biochemistry, Saint-Petersburg State University, Universitetskaya em., 7/9, 199034 St. Petersburg, Russia
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4689
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Mao Z, Gräßle F, Frey J, Franchini P, Schleheck D, Müller N, Schink B. Phosphitispora fastidiosa gen. nov. sp. nov., a new dissimilatory phosphite-oxidizing anaerobic bacterium isolated from anaerobic sewage sludge. Int J Syst Evol Microbiol 2021; 71. [PMID: 34878375 DOI: 10.1099/ijsem.0.005142] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A new strictly anaerobic bacterium, strain DYL19T, was enriched and isolated with phosphite as the sole electron donor and CO2 as a single carbon source and electron acceptor from anaerobic sewage sludge sampled at a sewage treatment plant in Constance, Germany. It is a Gram-positive, spore-forming, slightly curved, rod-shaped bacterium which oxidizes phosphite to phosphate while reducing CO2 to biomass and small amounts of acetate. Optimal growth is observed at 30 °C, pH 7.2, with a doubling time of 3 days. Beyond phosphite, no further inorganic or organic electron donor can be used, and no other electron acceptor than CO2 is reduced. Sulphate inhibits growth with phosphite and CO2. The G+C content is 45.95 mol%, and dimethylmenaquinone-7 is the only quinone detectable in the cells. On the basis of 16S rRNA gene sequence analysis and other chemotaxonomic properties, strain DYL19T is described as the type strain of a new genus and species, Phosphitispora fastidiosa gen. nov., sp. nov.
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Affiliation(s)
- Zhuqing Mao
- Department of Biology, University of Konstanz, Constance, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
| | - Fabian Gräßle
- Department of Biology, University of Konstanz, Constance, Germany
| | - Jasmin Frey
- Department of Biology, University of Konstanz, Constance, Germany
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Constance, Germany
| | - David Schleheck
- Department of Biology, University of Konstanz, Constance, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
| | - Nicolai Müller
- Department of Biology, University of Konstanz, Constance, Germany
| | - Bernhard Schink
- Department of Biology, University of Konstanz, Constance, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
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4690
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The CbbQO-type rubisco activases encoded in carboxysome gene clusters can activate carboxysomal form IA rubiscos. J Biol Chem 2021; 298:101476. [PMID: 34890642 PMCID: PMC8718961 DOI: 10.1016/j.jbc.2021.101476] [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: 08/23/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 01/15/2023] Open
Abstract
The CO2-fixing enzyme rubisco is responsible for almost all carbon fixation. This process frequently requires rubisco activase (Rca) machinery, which couples ATP hydrolysis to the removal of inhibitory sugar phosphates, including the rubisco substrate ribulose 1,5-bisphosphate (RuBP). Rubisco is sometimes compartmentalized in carboxysomes, bacterial microcompartments that enable a carbon dioxide concentrating mechanism (CCM). Characterized carboxysomal rubiscos, however, are not prone to inhibition, and often no activase machinery is associated with these enzymes. Here, we characterize two carboxysomal rubiscos of the form IAC clade that are associated with CbbQO-type Rcas. These enzymes release RuBP at a much lower rate than the canonical carboxysomal rubisco from Synechococcus PCC6301. We found that CbbQO-type Rcas encoded in carboxysome gene clusters can remove RuBP and the tight-binding transition state analog carboxy-arabinitol 1,5-bisphosphate from cognate rubiscos. The Acidithiobacillus ferrooxidans genome encodes two form IA rubiscos associated with two sets of cbbQ and cbbO genes. We show that the two CbbQO activase systems display specificity for the rubisco enzyme encoded in the same gene cluster, and this property can be switched by substituting the C-terminal three residues of the large subunit. Our findings indicate that the kinetic and inhibitory properties of proteobacterial form IA rubiscos are diverse and predict that Rcas may be necessary for some α-carboxysomal CCMs. These findings will have implications for efforts aiming to introduce biophysical CCMs into plants and other hosts for improvement of carbon fixation of crops.
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4691
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Hatirnaz Ng O, Akyoney S, Sahin I, Soykam HO, Bayram Akcapinar G, Ozdemir O, Kancagi DD, Sir Karakus G, Yurtsever B, Kocagoz AS, Ovali E, Ozbek U. Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. PLoS One 2021; 16:e0260438. [PMID: 34871297 PMCID: PMC8648120 DOI: 10.1371/journal.pone.0260438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/10/2021] [Indexed: 12/11/2022] Open
Abstract
The Coronavirus Disease 2019 (COVID-19) was declared a pandemic in March 2020 by the World Health Organization (WHO). As of May 25th, 2021 there were 2.059.941 SARS-COV2 genome sequences that have been submitted to the GISAID database, with numerous variations. Here, we aim to analyze the SARS-CoV-2 genome data submitted to the GISAID database from Turkey and to determine the variant and clade distributions by the end of May 2021, in accordance with their appearance timeline. We compared these findings to USA, Europe, and Asia data as well. We have also evaluated the effects of spike protein variations, detected in a group of genome sequences of 13 patients who applied to our clinic, by using 3D modeling algorithms. For this purpose, we analyzed 4607 SARS-CoV-2 genome sequences submitted by different lab centers from Turkey to the GISAID database between March 2020 and May 2021. Described mutations were also introduced in silico to the spike protein structure to analyze their isolated impacts on the protein structure. The most abundant clade was GR followed by G, GH, and GRY and we did not detect any V clade. The most common variant was B.1, followed by B.1.1, and the UK variant, B.1.1.7. Our results clearly show a concordance between the variant distributions, the number of cases, and the timelines of different variant accumulations in Turkey. The 3D simulations indicate an increase in the surface hydrophilicity of the reference spike protein and the detected mutations. There was less surface hydrophilicity increase in the Asp614Gly mutation, which exhibits a more compact conformation around the ACE-2 receptor binding domain region, rendering the structure in a “down” conformation. Our genomic findings can help to model vaccination programs and protein modeling may lead to different approaches for COVID-19 treatment strategies.
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Affiliation(s)
- Ozden Hatirnaz Ng
- Department of Medical Biology, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
- Acibadem Mehmet Ali Aydinlar University Rare Diseases and Orphan Drugs Application and Research Center (ACURARE), Istanbul, Turkey
| | - Sezer Akyoney
- Department of Medical Biology, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
- Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ilayda Sahin
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Department of Medical Genetics, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
| | - Huseyin Okan Soykam
- Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Gunseli Bayram Akcapinar
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ozkan Ozdemir
- Acibadem Mehmet Ali Aydinlar University Rare Diseases and Orphan Drugs Application and Research Center (ACURARE), Istanbul, Turkey
- Department of Genome Studies, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | | | | | - Bulut Yurtsever
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
| | - Ayse Sesin Kocagoz
- Department of Infectious Diseases and Clinical Microbiology, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
| | - Ercument Ovali
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
| | - Ugur Ozbek
- Acibadem Mehmet Ali Aydinlar University Rare Diseases and Orphan Drugs Application and Research Center (ACURARE), Istanbul, Turkey
- Department of Medical Genetics, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
- * E-mail:
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4692
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Lin S, Sun B, Shi X, Xu Y, Gu Y, Gu X, Ma X, Wan T, Xu J, Su J, Lou Y, Zheng M. Comparative Genomic and Pan-Genomic Characterization of Staphylococcus epidermidis From Different Sources Unveils the Molecular Basis and Potential Biomarkers of Pathogenic Strains. Front Microbiol 2021; 12:770191. [PMID: 34867904 PMCID: PMC8634615 DOI: 10.3389/fmicb.2021.770191] [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: 09/03/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Coagulase-negative Staphylococcus (CoNS) is the most common pathogen causing traumatic endophthalmitis. Among which, Staphylococcus epidermidis is the most common species that colonizes human skin, eye surfaces, and nasal cavity. It is also the main cause of nosocomial infection, specially foreign body-related bloodstream infections (FBR-BSIs). Although some studies have reported the genome characteristics of S. epidermidis, the genome of ocular trauma-sourced S. epidermidis strain and a comprehensive understanding of its pathogenicity are still lacking. Our study sequenced, analyzed, and reported the whole genomes of 11 ocular trauma-sourced samples of S. epidermidis that caused traumatic endophthalmitis. By integrating publicly available genomes, we obtained a total of 187 S. epidermidis samples from healthy and diseased eyes, skin, respiratory tract, and blood. Combined with pan-genome, phylogenetic, and comparative genomic analyses, our study showed that S. epidermidis, regardless of niche source, exhibits two founder lineages with different pathogenicity. Moreover, we identified several potential biomarkers associated with the virulence of S. epidermidis, including essD, uhpt, sdrF, sdrG, fbe, and icaABCDR. EssD and uhpt have high homology with esaD and hpt in Staphylococcus aureus, showing that the genomes of S. epidermidis and S. aureus may have communicated during evolution. SdrF, sdrG, fbe, and icaABCDR are related to biofilm formation. Compared to S. epidermidis from blood sources, ocular-sourced strains causing intraocular infection had no direct relationship with biofilm formation. In conclusion, this study provided additional data resources for studies on S. epidermidis and improved our understanding of the evolution and pathogenicity among strains of different sources.
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Affiliation(s)
- Shudan Lin
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Bianjin Sun
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Xinrui Shi
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Yi Xu
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Yunfeng Gu
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Xiaobin Gu
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xueli Ma
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Tian Wan
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Jie Xu
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Jianzhong Su
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Yongliang Lou
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Meiqin Zheng
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
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4693
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Prevalence of Antifungal Resistance, Genetic Basis of Acquired Azole and Echinocandin Resistance, and Genotyping of Candida krusei recovered from an International Collection. Antimicrob Agents Chemother 2021; 66:e0185621. [PMID: 34871096 DOI: 10.1128/aac.01856-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study was designed to evaluate the prevalence of antifungal resistance, genetic mechanisms associated with in vitro induction of azole and echinocandin resistance and genotyping of Candida krusei, which is intrinsically resistant to fluconazole and is recovered from clinical and non-clinical sources from different countries. Our results indicated that all the isolates were susceptible or had the wild phenotype (WT) to azoles, amphotericin B, and only 1.27% showed non-WT for flucytosine. Although 70.88% of the isolates were resistant to caspofungin, none of them were categorized as echinocandin-resistant as all were susceptible to micafungin and no FKS1 hotspot 1 (HS1) or HS2 mutations were detected. In vitro induction of azole and echinocandin resistance confirmed the rapid development of resistance at low concentrations of fluconazole (4 μg/ml), voriconazole (0.06 μg/ml) and micafungin (0.03 μg/ml), with no difference between clinical and non-clinical isolates in the resistance development. Overexpression of ABC1 gene and FKS1 HS1 mutations were the major mechanisms responsible for azole and echinocandin resistance, respectively. Genotyping of our 79 isolates coupled with 217 other isolates from different sources and geography confirmed that the isolates belong to two main subpopulations, with isolates from human clinical material and Asia being more predominant in cluster 1, and environmental and animals isolates and those from Europe in cluster 2. Our results are of critical concern, since realizing that the C. krusei resistance mechanisms and their genotyping are crucial for guiding specific therapy and for exploring the potential infection source.
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4694
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Maixner F, Sarhan MS, Huang KD, Tett A, Schoenafinger A, Zingale S, Blanco-Míguez A, Manghi P, Cemper-Kiesslich J, Rosendahl W, Kusebauch U, Morrone SR, Hoopmann MR, Rota-Stabelli O, Rattei T, Moritz RL, Oeggl K, Segata N, Zink A, Reschreiter H, Kowarik K. Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period. Curr Biol 2021; 31:5149-5162.e6. [PMID: 34648730 PMCID: PMC8660109 DOI: 10.1016/j.cub.2021.09.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/16/2021] [Accepted: 09/14/2021] [Indexed: 02/06/2023]
Abstract
We subjected human paleofeces dating from the Bronze Age to the Baroque period (18th century AD) to in-depth microscopic, metagenomic, and proteomic analyses. The paleofeces were preserved in the underground salt mines of the UNESCO World Heritage site of Hallstatt in Austria. This allowed us to reconstruct the diet of the former population and gain insights into their ancient gut microbiome composition. Our dietary survey identified bran and glumes of different cereals as some of the most prevalent plant fragments. This highly fibrous, carbohydrate-rich diet was supplemented with proteins from broad beans and occasionally with fruits, nuts, or animal food products. Due to these traditional dietary habits, all ancient miners up to the Baroque period have gut microbiome structures akin to modern non-Westernized individuals whose diets are also mainly composed of unprocessed foods and fresh fruits and vegetables. This may indicate a shift in the gut community composition of modern Westernized populations due to quite recent dietary and lifestyle changes. When we extended our microbial survey to fungi present in the paleofeces, in one of the Iron Age samples, we observed a high abundance of Penicillium roqueforti and Saccharomyces cerevisiae DNA. Genome-wide analysis indicates that both fungi were involved in food fermentation and provides the first molecular evidence for blue cheese and beer consumption in Iron Age Europe.
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Affiliation(s)
- Frank Maixner
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy.
| | - Mohamed S Sarhan
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Kun D Huang
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy; Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, Via Edmund Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Adrian Tett
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy; CUBE (Division of Computational Systems Biology), Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Alexander Schoenafinger
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy; Institute of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Stefania Zingale
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Aitor Blanco-Míguez
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Paolo Manghi
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Jan Cemper-Kiesslich
- Interfaculty Department of Legal Medicine & Department of Classics, University of Salzburg, Ignaz-Harrer-Straße 79, 5020 Salzburg, Austria
| | - Wilfried Rosendahl
- Reiss-Engelhorn-Museen, Zeughaus C5, 68159 Mannheim, Germany; Curt-Egelhorn-Zentrum Archäomtrie, D6,3, 61859 Mannheim, Germany
| | - Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Seamus R Morrone
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Michael R Hoopmann
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Omar Rota-Stabelli
- Center Agriculture Food Environment (C3A), University of Trento, 38010 San Michele all'Adige (TN), Italy
| | - Thomas Rattei
- CUBE (Division of Computational Systems Biology), Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Klaus Oeggl
- Institute of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Nicola Segata
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Albert Zink
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Hans Reschreiter
- Prehistoric Department, Museum of Natural History Vienna, Burgring 7, 1010 Vienna, Austria
| | - Kerstin Kowarik
- Prehistoric Department, Museum of Natural History Vienna, Burgring 7, 1010 Vienna, Austria.
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4695
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Palacios-Gorba C, Moura A, Gomis J, Leclercq A, Gómez-Martín Á, Bracq-Dieye H, Mocé ML, Tessaud-Rita N, Jiménez-Trigos E, Vales G, García-Muñoz Á, Thouvenot P, García-Roselló E, Lecuit M, Quereda JJ. Ruminant-associated Listeria monocytogenes isolates belong preferentially to dairy-associated hypervirulent clones: a longitudinal study in 19 farms. Environ Microbiol 2021; 23:7617-7631. [PMID: 34863016 DOI: 10.1111/1462-2920.15860] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/24/2021] [Indexed: 01/18/2023]
Abstract
Studies have shown that ruminants constitute reservoirs of Listeria monocytogenes, but little is known about the epidemiology and genetic diversity of this pathogen within farms. Here we conducted a large-scale longitudinal study to monitor Listeria spp. in 19 dairy farms during three consecutive seasons (N = 3251 samples). L. innocua was the most prevalent species, followed by L. monocytogenes. Listeria monocytogenes was detected in 52.6% of farms and more frequently in cattle (4.1%) and sheep (4.5%) than in goat farms (0.2%). Lineage I accounted for 69% of L. monocytogenes isolates. Among animal samples, the most prevalent sublineages (SL) and clonal complexes (CC) were SL1/CC1, SL219/CC4, SL26/CC26 and SL87/CC87, whereas SL666/CC666 was most prevalent in environmental samples. Sixty-one different L. monocytogenes cgMLST types were found, 28% common to different animals and/or surfaces within the same farm and 21% previously reported elsewhere in the context of food and human surveillance. Listeria monocytogenes prevalence was not affected by farm hygiene but by season: higher prevalence was observed during winter in cattle, and during winter and spring in sheep farms. Cows in their second lactation had a higher probability of L. monocytogenes faecal shedding. This study highlights dairy farms as a reservoir for hypervirulent L. monocytogenes.
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Affiliation(s)
- Carla Palacios-Gorba
- Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Alexandra Moura
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France.,Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, 75015, France
| | - Jesús Gomis
- Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Alexandre Leclercq
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France.,Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, 75015, France
| | - Ángel Gómez-Martín
- Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Hélène Bracq-Dieye
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France.,Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, 75015, France
| | - María L Mocé
- Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Nathalie Tessaud-Rita
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France.,Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, 75015, France
| | - Estrella Jiménez-Trigos
- Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Guillaume Vales
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France.,Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, 75015, France
| | - Ángel García-Muñoz
- Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Pierre Thouvenot
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France.,Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, 75015, France
| | - Empar García-Roselló
- Departamento Medicina y Cirugía Animal, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Marc Lecuit
- Institut Pasteur, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France.,Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, 75015, France.,Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, Institut Imagine, APHP, Paris, France
| | - Juan J Quereda
- Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
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4696
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Yao Y, Falgenhauer L, Falgenhauer J, Hauri AM, Heinmüller P, Domann E, Chakraborty T, Imirzalioglu C. Carbapenem-Resistant Citrobacter spp. as an Emerging Concern in the Hospital-Setting: Results From a Genome-Based Regional Surveillance Study. Front Cell Infect Microbiol 2021; 11:744431. [PMID: 34858870 PMCID: PMC8632029 DOI: 10.3389/fcimb.2021.744431] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
The rise of Carbapenem-resistant Enterobacterales (CRE) represents an increasing threat to patient safety and healthcare systems worldwide. Citrobacter spp., long considered not to be a classical nosocomial pathogen, in contrast to Klebsiella pneumoniae and Escherichia coli, is fast gaining importance as a clinical multidrug-resistant pathogen. We analyzed the genomes of 512 isolates of 21 CRE species obtained from 61 hospitals within a three-year-period and found that Citrobacter spp. (C. freundii, C. portucalensis, C. europaeus, C. koseri and C. braakii) were increasingly detected (n=56) within the study period. The carbapenemase-groups detected in Citrobacter spp. were KPC, OXA-48/-like and MBL (VIM, NDM) accounting for 42%, 31% and 27% respectively, which is comparable to those of K. pneumoniae in the same study. They accounted for 10%, 17% and 14% of all carbapenemase-producing CRE detected in 2017, 2018 and 2019, respectively. The carbapenemase genes were almost exclusively located on plasmids. The high genomic diversity of C. freundii is represented by 22 ST-types. KPC-2 was the predominantly detected carbapenemase (n=19) and was located in 95% of cases on a highly-conserved multiple-drug-resistance-gene-carrying pMLST15 IncN plasmid. KPC-3 was rarely detected and was confined to a clonal outbreak of C. freundii ST18. OXA-48 carbapenemases were located on plasmids of the IncL/M (pOXA-48) type. About 50% of VIM-1 was located on different IncN plasmids (pMLST7, pMLST5). These results underline the increasing importance of the Citrobacter species as emerging carriers of carbapenemases and therefore as potential disseminators of Carbapenem- and multidrug-resistance in the hospital setting.
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Affiliation(s)
- Yancheng Yao
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Giessen, Germany
| | - Linda Falgenhauer
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Giessen, Germany.,Institute for Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Jane Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Giessen, Germany
| | - Anja M Hauri
- Department of Epimeiology, Hessisches Landesprüfungs- und Untersuchungsamt im Gesundheitswesen (HLPUG), Dillenburg, Germany.,Department of Epimeiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Petra Heinmüller
- Department of Epimeiology, Hessisches Landesprüfungs- und Untersuchungsamt im Gesundheitswesen (HLPUG), Dillenburg, Germany
| | - Eugen Domann
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Giessen, Germany.,Institute for Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Giessen, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Giessen, Germany
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4697
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van den Bent I, Makrodimitris S, Reinders M. The Power of Universal Contextualized Protein Embeddings in Cross-species Protein Function Prediction. Evol Bioinform Online 2021; 17:11769343211062608. [PMID: 34880594 PMCID: PMC8647222 DOI: 10.1177/11769343211062608] [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: 05/22/2021] [Accepted: 11/03/2021] [Indexed: 11/16/2022] Open
Abstract
Computationally annotating proteins with a molecular function is a difficult problem that is made even harder due to the limited amount of available labeled protein training data. Unsupervised protein embeddings partly circumvent this limitation by learning a universal protein representation from many unlabeled sequences. Such embeddings incorporate contextual information of amino acids, thereby modeling the underlying principles of protein sequences insensitive to the context of species. We used an existing pre-trained protein embedding method and subjected its molecular function prediction performance to detailed characterization, first to advance the understanding of protein language models, and second to determine areas of improvement. Then, we applied the model in a transfer learning task by training a function predictor based on the embeddings of annotated protein sequences of one training species and making predictions on the proteins of several test species with varying evolutionary distance. We show that this approach successfully generalizes knowledge about protein function from one eukaryotic species to various other species, outperforming both an alignment-based and a supervised-learning-based baseline. This implies that such a method could be effective for molecular function prediction in inadequately annotated species from understudied taxonomic kingdoms.
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Affiliation(s)
- Irene van den Bent
- Delft Bioinformatics Lab, Delft
University of Technology, Delft, the Netherlands
| | - Stavros Makrodimitris
- Delft Bioinformatics Lab, Delft
University of Technology, Delft, the Netherlands
- Keygene N.V., Wageningen, the
Netherlands
| | - Marcel Reinders
- Delft Bioinformatics Lab, Delft
University of Technology, Delft, the Netherlands
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4698
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Genome-Wide Analysis of WRKY Gene Family and the Dynamic Responses of Key WRKY Genes Involved in Ostrinia furnacalis Attack in Zea mays. Int J Mol Sci 2021; 22:ijms222313045. [PMID: 34884854 PMCID: PMC8657575 DOI: 10.3390/ijms222313045] [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: 11/06/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
WRKY transcription factors comprise one of the largest gene families and serve as key regulators of plant defenses against herbivore attack. However, studies related to the roles of WRKY genes in response to herbivory are limited in maize. In this study, a total of 128 putative maize WRKY genes (ZmWRKYs) were identified from the new maize genome (v4). These genes were divided into seven subgroups (groups I, IIa–e, and III) based on phylogenomic analysis, with distinct motif compositions in each subgroup. Syntenic analysis revealed that 72 (56.3%) of the genes were derived from either segmental or tandem duplication events (69 and 3, respectively), suggesting a pivotal role of segmental duplication in the expansion of the ZmWRKY family. Importantly, transcriptional regulation prediction showed that six key WRKY genes contribute to four major defense-related pathways: L-phenylalanine biosynthesis II and flavonoid, benzoxazinoid, and jasmonic acid (JA) biosynthesis. These key WRKY genes were strongly induced in commercial maize (Jingke968) infested with the Asian corn borer, Ostrinia furnacalis, for 0, 2, 4, 12 and 24 h in the field, and their expression levels were highly correlated with predicted target genes, suggesting that these genes have important functions in the response to O. furnacalis. Our results provide a comprehensive understanding of the WRKY gene family based on the new assembly of the maize genome and lay the foundation for further studies into functional characteristics of ZmWRKY genes in commercial maize defenses against O. furnacalis in the field.
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4699
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Wan Y, Mills E, Leung RC, Vieira A, Zhi X, Croucher NJ, Woodford N, Jauneikaite E, Ellington MJ, Sriskandan S. Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom. Microb Genom 2021; 7:000702. [PMID: 34860151 PMCID: PMC8767348 DOI: 10.1099/mgen.0.000702] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/01/2021] [Indexed: 01/18/2023] Open
Abstract
Antimicrobial resistance in enteric or urinary Escherichia coli is a risk factor for invasive E. coli infections. Due to widespread trimethoprim resistance amongst urinary E. coli and increased bacteraemia incidence, a national recommendation to prescribe nitrofurantoin for uncomplicated urinary tract infection was made in 2014. Nitrofurantoin resistance is reported in <6% urinary E. coli isolates in the UK, however, mechanisms underpinning nitrofurantoin resistance in these isolates remain unknown. This study aimed to identify the genetic basis of nitrofurantoin resistance in urinary E. coli isolates collected from north west London and then elucidate resistance-associated genetic alterations in available UK E. coli genomes. As a result, an algorithm was developed to predict nitrofurantoin susceptibility. Deleterious mutations and gene-inactivating insertion sequences in chromosomal nitroreductase genes nfsA and/or nfsB were identified in genomes of nine confirmed nitrofurantoin-resistant urinary E. coli isolates and additional 11 E. coli isolates that were highlighted by the prediction algorithm and subsequently validated to be nitrofurantoin-resistant. Eight categories of allelic changes in nfsA , nfsB , and the associated gene ribE were detected in 12412 E. coli genomes from the UK. Evolutionary analysis of these three genes revealed homoplasic mutations and explained the previously reported order of stepwise mutations. The mobile gene complex oqxAB , which is associated with reduced nitrofurantoin susceptibility, was identified in only one of the 12412 genomes. In conclusion, mutations and insertion sequences in nfsA and nfsB were leading causes of nitrofurantoin resistance in UK E. coli . As nitrofurantoin exposure increases in human populations, the prevalence of nitrofurantoin resistance in carriage E. coli isolates and those from urinary and bloodstream infections should be monitored.
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Affiliation(s)
- Yu Wan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ewurabena Mills
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Rhoda C.Y. Leung
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Present address: Department of Microbiology, Queen Mary Hospital, Hong Kong S.A.R., PR China
| | - Ana Vieira
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Xiangyun Zhi
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Nicholas J. Croucher
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, Colindale, London, United Kingdom
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Matthew J. Ellington
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, Colindale, London, United Kingdom
| | - Shiranee Sriskandan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
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4700
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Romero P, Gabrielli A, Sampedro R, Perea-García A, Puig S, Lafuente MT. Identification and molecular characterization of the high-affinity copper transporters family in Solanum lycopersicum. Int J Biol Macromol 2021; 192:600-610. [PMID: 34655579 DOI: 10.1016/j.ijbiomac.2021.10.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/27/2021] [Accepted: 10/03/2021] [Indexed: 11/17/2022]
Abstract
Copper (Cu) plays a key role as cofactor in the plant proteins participating in essential cellular processes, such as electron transport and free radical scavenging. Despite high-affinity Cu transporters (COPTs) being key participants in Cu homeostasis maintenance, very little is known about COPTs in tomato (Solanum lycopersicum) even though it is the most consumed fruit worldwide and this crop is susceptible to suboptimal Cu conditions. In this study, a six-member family of COPT (SlCOPT1-6) was identified and characterized. SlCOPTs have a conserved architecture consisting of three transmembrane domains and β-strains. However, the presence of essential methionine residues, a methionine-enriched amino-terminal region, an Mx3Mx12Gx3G Cu-binding motif and a cysteine rich carboxy-terminal region, all required for their functionality, is more variable among members. Accordingly, functional complementation assays in yeast indicate that SlCOPT1 and SlCOPT2 are able to transport Cu inside the cell, while SlCOPT3 and SlCOPT5 are only partially functional. In addition, protein interaction network analyses reveal the connection between SlCOPTs and Cu PIB-type ATPases, other metal transporters, and proteins related to the peroxisome. Gene expression analyses uncover organ-dependency, fruit vasculature tissue specialization and ripening-dependent gene expression profiles, as well as different response to Cu deficiency or toxicity in an organ-dependent manner.
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Affiliation(s)
- Paco Romero
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA-CSIC), Catedrático Agustín Escardino 7, 46980 Paterna, Valencia, Spain.
| | - Alessandro Gabrielli
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA-CSIC), Catedrático Agustín Escardino 7, 46980 Paterna, Valencia, Spain.
| | - Raúl Sampedro
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA-CSIC), Catedrático Agustín Escardino 7, 46980 Paterna, Valencia, Spain.
| | - Ana Perea-García
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA-CSIC), Catedrático Agustín Escardino 7, 46980 Paterna, Valencia, Spain.
| | - Sergi Puig
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA-CSIC), Catedrático Agustín Escardino 7, 46980 Paterna, Valencia, Spain.
| | - María Teresa Lafuente
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA-CSIC), Catedrático Agustín Escardino 7, 46980 Paterna, Valencia, Spain.
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