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Mutagenesis and structural modeling implicate RME-8 IWN domains as conformational control points. PLoS Genet 2022; 18:e1010296. [DOI: 10.1371/journal.pgen.1010296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/08/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022] Open
Abstract
After endocytosis, transmembrane cargo is differentially sorted into degradative or recycling pathways. This process is facilitated by recruitment into physically distinct degradative or recycling microdomains on the limiting membrane of individual endosomes. Endosomal sorting complexes required for transport (ESCRT) mark the degradative microdomain, while the recycling domain is marked by the retromer complex and associated proteins RME-8 and SNX-1. The separation of endosomal microdomains is also controlled by RME-8 and SNX-1, at least in part via removal of degradative component HRS/HGRS-1 from the recycling microdomain. This activity is likely due to recruitment and activation of chaperone Hsc70 on the endosome by the RME-8 DNAJ domain. To better understand the mechanism of RME-8 function we performed a new phylogenetic analysis of RME-8 and identified new conserved sequence features. In a complementary approach, we performed structure-function analysis that identified the C-terminus as important for microdomain localization and likely substrate binding, while N-terminal sequences beyond the known single N-terminal PH-like domain are important for endosome recruitment. Random mutagenesis identified IWN4, and by analogy IWN3, to be important for the autoinhibitory DNAJ domain binding, with IWN3 playing a critical role in HRS uncoating activity. Combining AlphaFold structural predictions with in vivo mutation analysis of RME-8, we propose a model whereby SNX-1 and the IWN domains control the conformation of RME-8 and hence the productive exposure of the DNAJ domain. Furthermore, we propose that the activation of RME-8 is cyclical, with SNX-1 acting as an activator and a target of RME-8 uncoating activity.
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Li Z, Zheng N, An Q, Li X, Sun S, Zhang W, Ji Y, Wang S, Li P. Impact of environmental factors and bacterial interactions on dust mite allergens in different indoor dust. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:157177. [PMID: 35803427 DOI: 10.1016/j.scitotenv.2022.157177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/11/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Indoor dust is the main carrier of indoor pollutants, especially dust mite allergens and bacteria, they can trigger asthma, rhinitis, eczema and other allergic diseases. However, the interactions between dust mite allergens and bacterial communities in different types of indoor dust are not clear. The study focused on particulate and flocculent fibrous dust, explored the concentrations of Der p 1 (Dermatophagoides pteronyssinus) and Der f 1 (D. farinae) in 46 households in Changchun and their environmental influences, characterized the bacterial communities by high-throughput sequencing, and the interactions between Der p 1, Der f 1 and bacterial communities were explored. The results showed that Der p 1 and Der f 1 tended to accumulate more in flocculent fibrous dust, and Der p 1 predominated in the indoor dust samples. The floor height, years of housing occupancy and the living areas all affected the concentrations of dust mite allergens. In bacterial community, Proteobacteria, Firmicutes and Actinobacteria were leading phyla in the two types of dust. Kocuria, Blastococcus and Massilia were dominating genera in particulate dust and Acinetobacter, Lactobacillus, Corynebacterium_1 were dominating genera in flocculent fibrous dust. The overall diversity and species richness of bacteria in particulate dust were significantly higher than those in flocculent dust (p < 0.001). The living area was an important environmental factor affecting the bacterial community in flocculent fibrous dust (p < 0.01). The interaction between the relative abundance of Proteobacteria, Firmicutes and Actinobacteria and dust mite allergen concentrations significantly differed between the two dust types, indicating that bacteria could be used both as food and to establish symbiotic relationships with household dust mites (HDMs) hosts and provide nutrition.
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Affiliation(s)
- Zimeng Li
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Na Zheng
- College of New Energy and Environment, Jilin University, Changchun, 130012, China; Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130012, China.
| | - Qirui An
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Xiaoqian Li
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Siyu Sun
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Wenhui Zhang
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Yining Ji
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Sujing Wang
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Pengyang Li
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
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Budimir I, Giampieri E, Saccenti E, Suarez-Diez M, Tarozzi M, Dall'Olio D, Merlotti A, Curti N, Remondini D, Castellani G, Sala C. Intraspecies characterization of bacteria via evolutionary modeling of protein domains. Sci Rep 2022; 12:16595. [PMID: 36198716 PMCID: PMC9534902 DOI: 10.1038/s41598-022-21036-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/22/2022] [Indexed: 12/04/2022] Open
Abstract
The ability to detect and characterize bacteria within a biological sample is crucial for the monitoring of infections and epidemics, as well as for the study of human health and its relationship with commensal microorganisms. To this aim, a commonly used technique is the 16S rRNA gene targeted sequencing. PCR-amplified 16S sequences derived from the sample of interest are usually clustered into the so-called Operational Taxonomic Units (OTUs) based on pairwise similarities. Then, representative OTU sequences are compared with reference (human-made) databases to derive their phylogeny and taxonomic classification. Here, we propose a new reference-free approach to define the phylogenetic distance between bacteria based on protein domains, which are the evolving units of proteins. We extract the protein domain profiles of 3368 bacterial genomes and we use an ecological approach to model their Relative Species Abundance distribution. Based on the model parameters, we then derive a new measurement of phylogenetic distance. Finally, we show that such model-based distance is capable of detecting differences between bacteria in cases in which the 16S rRNA-based method fails, providing a possibly complementary approach , which is particularly promising for the analysis of bacterial populations measured by shotgun sequencing.
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Affiliation(s)
- Iva Budimir
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Enrico Giampieri
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Martina Tarozzi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
| | - Daniele Dall'Olio
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Alessandra Merlotti
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Nico Curti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
| | - Daniel Remondini
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Gastone Castellani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy.
| | - Claudia Sala
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
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Nandeibam J, Singh YRB, Sharma KC, Devi KR, Mukherjee PK, Devi SI. Bacterial diversity of a floating vegetation (Phumdi) of Loktak Lake and its extracellular enzymes and bacterial antagonistic property. Arch Microbiol 2022; 204:657. [PMID: 36182972 DOI: 10.1007/s00203-022-03267-0] [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: 07/22/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/02/2022]
Abstract
134 bacterial strains were isolated from phumdis of Loktak Lake. Through 16S rRNA sequencing, Bacillus sp. (23, 17.1%), Staphylococcus sp. (14, 10.4%), Pseudomonas sp. (11, 8.2%) and Acinetobacter sp. (8, 5.9%) were identified as the predominant bacterial taxa of Loktak Lake. B. pumulis (12, 8.9%), S. arlettae (4, 2.9%), P. knackmussii (6, 4.4%) are the leading species of Bacillus, Staphylococcus and Pseudomonas, respectively. Similarly, A. seifertii (2, 1.4%) and A. calcoaceticus (2, 1.4%) are the common species of Acinetobacter. 75 (55.9%) bacterial strains showed the ability to hydrolyze one or more extracellular enzymes tested. Among the extracellular enzymes produced by the bacterial isolates, the presence of elastase activity cannot be underestimated, since the enzyme is involved in the process of bacterial lung infection. Phosphate solubilizing activity could be seen in 11.1% of the bacterial isolates. 27 (20.1%) of the strains shown to have antagonistic activity against one or more tested pathogens. An isolate, MRC 52 showed antagonistic activity against eleven different pathogens including carbapenem resistant E. coli which was further subjected to extraction and identification of the biomolecule exerting the antimicrobial property. Based on GC-MS analysis, the bioactive compound was identified as phenyl ethyl alcohol.
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Affiliation(s)
- Jusna Nandeibam
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat, Imphal, 795001, Manipur, India
| | - Y Randhir Babu Singh
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat, Imphal, 795001, Manipur, India
| | - K Chandradev Sharma
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat, Imphal, 795001, Manipur, India
| | - Kh Ranjana Devi
- Department of Microbiology, Regional Institute of Medical Sciences, Imphal, 795004, Manipur, India
| | - Pulok Kumar Mukherjee
- Phyto Pharmaceutical Laboratory, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat, Imphal, 795001, Manipur, India
| | - S Indira Devi
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat, Imphal, 795001, Manipur, India.
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Akinyemi MO, Finucan J, Grytsay A, Osaiyuwu OH, Adegbaju MS, Ogunade IM, Thomas BN, Peters SO, Morenikeji OB. Molecular Evolution and Inheritance Pattern of Sox Gene Family among Bovidae. Genes (Basel) 2022; 13:genes13101783. [PMID: 36292668 PMCID: PMC9602320 DOI: 10.3390/genes13101783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/21/2022] [Accepted: 09/28/2022] [Indexed: 11/04/2022] Open
Abstract
Sox genes are an evolutionarily conserved family of transcription factors that play important roles in cellular differentiation and numerous complex developmental processes. In vertebrates, Sox proteins are required for cell fate decisions, morphogenesis, and the control of self-renewal in embryonic and adult stem cells. The Sox gene family has been well-studied in multiple species including humans but there has been scanty or no research into Bovidae. In this study, we conducted a detailed evolutionary analysis of this gene family in Bovidae, including their physicochemical properties, biological functions, and patterns of inheritance. We performed a genome-wide cataloguing procedure to explore the Sox gene family using multiple bioinformatics tools. Our analysis revealed a significant inheritance pattern including conserved motifs that are critical to the ability of Sox proteins to interact with the regulatory regions of target genes and orchestrate multiple developmental and physiological processes. Importantly, we report an important conserved motif, EFDQYL/ELDQYL, found in the SoxE and SoxF groups but not in other Sox groups. Further analysis revealed that this motif sequence accounts for the binding and transactivation potential of Sox proteins. The degree of protein–protein interaction showed significant interactions among Sox genes and related genes implicated in embryonic development and the regulation of cell differentiation. We conclude that the Sox gene family uniquely evolved in Bovidae, with a few exhibiting important motifs that drive several developmental and physiological processes.
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Affiliation(s)
- Mabel O. Akinyemi
- Department of Biological Sciences, Fairleigh Dickinson University, Madison, NJ 07940, USA
| | - Jessica Finucan
- Department of Biological Sciences, Fairleigh Dickinson University, Madison, NJ 07940, USA
| | - Anastasia Grytsay
- Division of Biological and Health Sciences, University of Pittsburgh, Bradford, PA 16701, USA
| | - Osamede H. Osaiyuwu
- Department of Animal Science, Faculty of Agriculture, University of Ibadan, Ibadan 200005, Nigeria
| | - Muyiwa S. Adegbaju
- Institute for Plant Biotechnology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Ibukun M. Ogunade
- Division of Animal and Nutritional Science, West Virginia University, Morgantown, WV 26505, USA
| | - Bolaji N. Thomas
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Sunday O. Peters
- Department of Animal Science, Berry College, Mount Berry, GA 30149, USA
| | - Olanrewaju B. Morenikeji
- Division of Biological and Health Sciences, University of Pittsburgh, Bradford, PA 16701, USA
- Correspondence: ; Tel.: +1-(585)-490-7271
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Tian D, Xie Q, Deng Z, Xue J, Li W, Zhang Z, Dai Y, Zheng B, Lu T, De Smet I, Guo Y. Small secreted peptides encoded on the wheat ( triticum aestivum L.) genome and their potential roles in stress responses. FRONTIERS IN PLANT SCIENCE 2022; 13:1000297. [PMID: 36212358 PMCID: PMC9532867 DOI: 10.3389/fpls.2022.1000297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
Small secreted peptides (SSPs) are important signals for cell-to-cell communication in plant, involved in a variety of growth and developmental processes, as well as responses to stresses. While a large number of SSPs have been identified and characterized in various plant species, little is known about SSPs in wheat, one of the most important cereal crops. In this study, 4,981 putative SSPs were identified on the wheat genome, among which 1,790 TaSSPs were grouped into 38 known SSP families. The result also suggested that a large number of the putaitive wheat SSPs, Cys-rich peptides in particular, remained to be characterized. Several TaSSP genes were found to encode multiple SSP domains, including CLE, HEVEIN and HAIRPININ domains, and two potentially novel TaSSP family DYY and CRP8CI were identified manually among unpredicted TaSSPs. Analysis on the transcriptomic data showed that a great proportion of TaSSPs were expressed in response to abiotic stresses. Exogenous application of the TaCEPID peptide encoded by TraesCS1D02G130700 enhanced the tolerance of wheat plants to drought and salinity, suggesting porential roles of SSPs in regulating stress responses in wheat.
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Affiliation(s)
- Dongdong Tian
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Qi Xie
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Zhichao Deng
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Jin Xue
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Wei Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Zenglin Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yifei Dai
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Tiegang Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
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A revisit to universal single-copy genes in bacterial genomes. Sci Rep 2022; 12:14550. [PMID: 36008577 PMCID: PMC9411617 DOI: 10.1038/s41598-022-18762-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/18/2022] [Indexed: 11/08/2022] Open
Abstract
Universal single-copy genes (USCGs) are widely used for species classification and taxonomic profiling. Despite many studies on USCGs, our understanding of USCGs in bacterial genomes might be out of date, especially how different the USCGs are in different studies, how well a set of USCGs can distinguish two bacterial species, whether USCGs can separate different strains of a bacterial species, to name a few. To fill the void, we studied USCGs in the most updated complete bacterial genomes. We showed that different USCG sets are quite different while coming from highly similar functional categories. We also found that although USCGs occur once in almost all bacterial genomes, each USCG does occur multiple times in certain genomes. We demonstrated that USCGs are reliable markers to distinguish different species while they cannot distinguish different strains of most bacterial species. Our study sheds new light on the usage and limitations of USCGs, which will facilitate their applications in evolutionary, phylogenomic, and metagenomic studies.
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Ambroset C, Peticca A, Tricot A, Tardy F. Genomic features of Mycoplasma bovis subtypes currently circulating in France. BMC Genomics 2022; 23:603. [PMID: 35986252 PMCID: PMC9392320 DOI: 10.1186/s12864-022-08818-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/04/2022] [Indexed: 12/04/2022] Open
Abstract
Background Mycoplasma (M.) bovis is a major etiological agent of bovine respiratory disease, which is the most economically costly disease of cattle worldwide. Cattle disease surveillance on M. bovis is increasingly using gene-based techniques, such as multilocus sequence typing (MLST), or genome-based techniques such as core genome MLST that both require only partial genomic data. However, accurate up-to-date surveillance also demands complete, circular genomes that can be used as reference to track the evolution of the different lineages. Yet, in France, two of the main subtypes currently circulating still have no representing genome in public databases. Here, to address this gap, we provide and compare three new complete M. bovis genomes obtained from recent clinical isolates that represent major subtypes circulating in France and Europe. Results Genomes were obtained using a hybrid assembly strategy (Illumina and Nanopore) with fine-tuning of settings and inputs used in the Unicycler assembly pipeline, such as size selection of reads and quality trimming of the FASTQ files. The main characteristics and synteny of the genomes were compared. The three genomes mainly differed by their content in terms of mobile genetic elements, i.e. integrative conjugative elements (ICE) and insertion sequences (IS), a feature that impacts their structure. For instance, strain L15527, representing subtype3 (st3), harbours an exceptionally high number of ICEs, which results in a bigger-sized genome than all those previously described and could be associated with the propensity of st3 to gain and fix mutations through chromosomal transfer mechanisms. In contrast, strain F9160, of st1, is very close to the PG45 type strain isolated in 1961 in the USA, and harbours a huge number of IS. These features may be associated with an evolution towards a host-restricted state or in a “closed” host or environment reservoir until a recent re-emergence. Conclusions Whole-genome comparison of the three French M. bovis subtypes provides valuable resources for future studies combining epidemiology, phylogenetic data, and phylodynamic methods. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08818-9.
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Fabre A, Mancini J. When LUCA met gnomAD: genetic constraints on universal genes in humans. Intractable Rare Dis Res 2022; 11:149-152. [PMID: 36200033 PMCID: PMC9437994 DOI: 10.5582/irdr.2022.01063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/24/2022] [Accepted: 07/11/2022] [Indexed: 11/05/2022] Open
Abstract
LUCA, the last universal common ancestor, is the hypothetical most recent common ancestor of the three domains of life which share the universal genes (UG). It seems interesting to evaluate whether the UG phylogeny has had an impact on current Human gene constraints. A list of human homologs of UG was retrieved from the eggNOG database. We analyzed this LUCA gene (LG) group, and a random sample of 500 genes from the gnomAD database (RG group). Gene constraint metrics were retrieved from gnomAD and associations with Mendelian diseases and modes of inheritance were retrieved from OMIM. The LG group consisted of 277 genes and the RG group, 492 (8 genes were in LG group). 38.6% of the genes in the LG group and 25.2% of the genes in the RG group were associated with a Mendelian disease (p < 0.0001). The mode of inheritance was more often autosomal recessive (69.0 vs. 50.5%), and less often autosomal dominant (19.0 vs. 31.3%), or mixed (6.0 vs. 12.1%) for those associated with the LG group (p = 0.048). The LG group was significantly more constrained for missense variants (MOEUF, 0.919 vs. 0.997, p < 0.0001) and was borderline significantly more constrained for loss-of-function variants (LOEUF, 0.872 vs. 0.947, p = 0.051). These results suggest that the UG in humans differs from the rest of the genome in terms of constraints and associated Mendelian diseases. It suggests that phylogenic data can explain some of the characteristics of human genes and could help in interpreting variants.
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Affiliation(s)
- Alexandre Fabre
- Aix Marseille Univ, INSERM, MMG, Marseille, France
- APHM, Multidisciplinary Pediatrics Department, Timone Enfant Hospital, Marseille, France
- Address correspondence to:Alexandre Fabre, Pediatric Multidisciplinary Department, Timone Enfant Hospital, APHM, 264 Rue Saint Pierre 13005 Marseille, France. E-mail:
| | - Julien Mancini
- Aix-Marseille Univ, INSERM, IRD, ISSPAM, SESSTIM, Marseille, France
- APHM, BIOSTIC, Hop Timone, Marseille, France
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60
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Fan X, Wang C, Bunker DE. Population Structure of German Cockroaches (Blattodea: Ectobiidae) in an Urban Environment Based on Single Nucleotide Polymorphisms. JOURNAL OF MEDICAL ENTOMOLOGY 2022; 59:1319-1327. [PMID: 35462399 DOI: 10.1093/jme/tjac036] [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: 10/14/2021] [Indexed: 06/14/2023]
Abstract
German cockroaches (Blattella germanica L.) harbor and disperse medically important pathogens and are a source of allergens that impact human health and wellbeing. Management of this pest requires an understanding of their distribution and dispersal. In this study, we collected German cockroaches from three apartment buildings in New Jersey, USA. We identified single-nucleotide polymorphisms (SNPs) from DNA extractions using next generation sequencing. We analyzed the SNPs and characterized cockroach population genetic structure using Fst, principal component, phylogenetic, and STRUCTURE analyses. We found significant differences in German cockroach population structure among the buildings. Within buildings, we found variable population structure that may be evidence for multiple colonization events. This study shows that SNPs derived from next generation sequencing provide a powerful tool for analyzing the genetic population structure of these medically important pests.
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Affiliation(s)
- X Fan
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - C Wang
- Department of Entomology, Rutgers, The State University of New Jersey, 96 Lipman Drive, New Brunswick, NJ, 08901, USA
| | - D E Bunker
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA
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Chotiwan N, Brito-Sierra CA, Ramirez G, Lian E, Grabowski JM, Graham B, Hill CA, Perera R. Expression of fatty acid synthase genes and their role in development and arboviral infection of Aedes aegypti. Parasit Vectors 2022; 15:233. [PMID: 35761349 PMCID: PMC9235097 DOI: 10.1186/s13071-022-05336-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/24/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Fatty acids are the building blocks of complex lipids essential for living organisms. In mosquitoes, fatty acids are involved in cell membrane production, energy conservation and expenditure, innate immunity, development and reproduction. Fatty acids are synthesized by a multifunctional enzyme complex called fatty acid synthase (FAS). Several paralogues of FAS were found in the Aedes aegypti mosquito. However, the molecular characteristics and expression of some of these paralogues have not been investigated. METHODS Genome assemblies of Ae. aegypti were analyzed, and orthologues of human FAS was identified. Phylogenetic analysis and in silico molecular characterization were performed to identify the functional domains of the Ae. aegypti FAS (AaFAS). Quantitative analysis and loss-of-function experiments were performed to determine the significance of different AaFAS transcripts in various stages of development, expression following different diets and the impact of AaFAS on dengue virus, serotype 2 (DENV2) infection and transmission. RESULTS We identified seven putative FAS genes in the Ae. aegypti genome assembly, based on nucleotide similarity to the FAS proteins (tBLASTn) of humans, other mosquitoes and invertebrates. Bioinformatics and molecular analyses suggested that only five of the AaFAS genes produce mRNA and therefore represent complete gene models. Expression levels of AaFAS varied among developmental stages and between male and female Ae. aegypti. Quantitative analyses revealed that expression of AaFAS1, the putative orthologue of the human FAS, was highest in adult females. Transient knockdown (KD) of AaFAS1 did not induce a complete compensation by other AaFAS genes but limited DENV2 infection of Aag2 cells in culture and the midgut of the mosquito. CONCLUSION AaFAS1 is the predominant AaFAS in adult mosquitoes. It has the highest amino acid similarity to human FAS and contains all enzymatic domains typical of human FAS. AaFAS1 also facilitated DENV2 replication in both cell culture and in mosquito midguts. Our data suggest that AaFAS1 may play a role in transmission of dengue viruses and could represent a target for intervention strategies.
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Affiliation(s)
- Nunya Chotiwan
- grid.47894.360000 0004 1936 8083Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO USA ,grid.10223.320000 0004 1937 0490Present Address: Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakan, Thailand
| | - Carlos A. Brito-Sierra
- grid.169077.e0000 0004 1937 2197Department of Entomology, Purdue University, West Lafayette, IL USA ,grid.169077.e0000 0004 1937 2197Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN USA ,grid.417540.30000 0000 2220 2544Present Address: Lilly Research Laboratories, Eli Lilly and Company, IN Indianapolis, USA
| | - Gabriella Ramirez
- grid.47894.360000 0004 1936 8083Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO USA
| | - Elena Lian
- grid.47894.360000 0004 1936 8083Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO USA
| | - Jeffrey M. Grabowski
- grid.169077.e0000 0004 1937 2197Department of Entomology, Purdue University, West Lafayette, IL USA ,grid.417439.c0000 0004 4665 2602Present Address: Foundation for Advanced Education in the Sciences at the NIH, Bethesda, MD USA
| | - Babara Graham
- grid.47894.360000 0004 1936 8083Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO USA
| | - Catherine A. Hill
- grid.169077.e0000 0004 1937 2197Department of Entomology, Purdue University, West Lafayette, IL USA ,grid.169077.e0000 0004 1937 2197Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN USA
| | - Rushika Perera
- grid.47894.360000 0004 1936 8083Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO USA
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Wei X, Ling X, Yang L, Zhang J, Cui M, He Z, Zhao X, Sun M. Analysis of Microbial Community Structure and Diversity in Burial Soil of Yangguanzhai Cemetery. Front Microbiol 2022; 13:845870. [PMID: 35711760 PMCID: PMC9197465 DOI: 10.3389/fmicb.2022.845870] [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: 12/30/2021] [Accepted: 03/28/2022] [Indexed: 12/02/2022] Open
Abstract
As one of the common physical remains in archaeological discoveries, human bones are important bases for studying the history of human development, which is of great significance for exploring the evolution law of ancient human, reconstructing ancient human society, and tracking the development of human civilization. However, in the process of human bone burial, in addition to being affected by physical and chemical factors, it will also be affected by microorganisms in the buried soil, resulting in a variety of diseases. According to the determination and analysis of the microbial community structure and diversity in the burial soil of Yangguanzhai Site in Gaoling District in Xi’an city, Shaanxi Province, this paper attempts to explore the influence of microorganisms in the burial environment on human bones, in order to provide scientific proof for the microbial prevention and control of bone relics in the archaeological excavation site. For the first time, Illumina NovaSeq high-throughput sequencing technology was used to analyze the microbial community structure in the burial soil. At the phylum level, there were 8 dominant bacteria species in the soil samples of tombs, which were Firmicutes, Actinobacteriota, Actinobacteria, Proteobacteria, Acidobacteriota, Methylomirabilota, Chloroflexi, Bacteroidota. At the genus level, there were 12 dominant species in the soil samples of tombs, including MIZ17, MND1, Gaiella, oc32, Kroppenstedtia, Halomonas, Bacteroides, Dongia, Faecalibacterium, Nocardioides, Pseudomonas, Pseudonocardia. The overall microorganisms in the soil of Yangguanzhai Cemetery were relatively well-distributed, and the microbial community structure near human bones is the most abundant and diverse. Therefore, it is necessary to take some measures to control microorganisms and protect human bones.
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Affiliation(s)
- Xiaoyang Wei
- School of Cultural Heritage, Northwest University, Xi'an, China
| | - Xue Ling
- School of Cultural Heritage, Northwest University, Xi'an, China
| | - Liping Yang
- Shaanxi Academy of Archaeology, Xi'an, China
| | - Jun Zhang
- School of Life Sciences, Northwest University, Xi'an, China
| | - Menghe Cui
- Shaanxi Academy of Archaeology, Xi'an, China
| | - Zhang He
- Shaanxi Academy of Archaeology, Xi'an, China
| | - Xichen Zhao
- Shaanxi Academy of Archaeology, Xi'an, China
| | - Manli Sun
- School of Cultural Heritage, Northwest University, Xi'an, China
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63
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Sharma V, Vashishtha A, Jos ALM, Khosla A, Basu N, Yadav R, Bhatt A, Gulani A, Singh P, Lakhera S, Verma M. Phylogenomics of the Phylum Proteobacteria: Resolving the Complex Relationships. Curr Microbiol 2022; 79:224. [PMID: 35704242 DOI: 10.1007/s00284-022-02910-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 05/20/2022] [Indexed: 11/28/2022]
Abstract
Proteobacteria is one of the largest and phenotypically most diverse divisions within the domain bacteria. Due to the economic importance, this phylum demands an urgent need for a clear and scientifically sound classification system to streamline their characterization. The goal of our study was to carefully reevaluate the current system of classification and suggest changes wherein necessary. Phylogenetic trees of 84 Proteobacteria were constructed using single gene-based phylogeny involving 16S rRNA genes and protein sequences of 85 conserved genes, whole genome-based phylogenetic tree using CVtree3.0, amino acid Identity matrix tree, and concatenated tree with aforementioned conserved genes. The results of our study confirm the polyphyletic relationship between Desulfurella acetivorans, a Deltaproteobacteria with Epsilonproteobacteria. The group Syntrophobacterales was found to be polyphyletic with respect to Desulfarculus baarsii and the group Thiotrichales was found to be splitting in different phylogenetic trees. Placement of phylogenetic groups belonging to Rhodocyclales, Oceonospirilalles, and Chromatiales is controversial and requires further study and revisions. Based on our analysis, we strongly support reclassification of Magnetococcales as a separate class Etaproteobacteria. From our results, we conclude that concatenated trees of conserved proteins are a more accurate method for phylogenetic analysis, as compared to other methods used.
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Affiliation(s)
- Vaibhav Sharma
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Amit Vashishtha
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Arsha Liz M Jos
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Akshita Khosla
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Nirmegh Basu
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Rishabh Yadav
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Amit Bhatt
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Akshanshi Gulani
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Pushpa Singh
- Swami Shraddhanand College, University of Delhi, Alipur, New Delhi, Delhi, 110036, India
| | - Sanidhya Lakhera
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Mansi Verma
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India. .,Department of Zoology, Sri Venkateswara College, South Campus, University of Delhi, New Delhi, Delhi, 110021, India.
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64
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de Vries LP, van de Weijer MP, Bartels M. The human physiology of well-being: A systematic review on the association between neurotransmitters, hormones, inflammatory markers, the microbiome and well-being. Neurosci Biobehav Rev 2022; 139:104733. [PMID: 35697161 DOI: 10.1016/j.neubiorev.2022.104733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/09/2022] [Accepted: 06/07/2022] [Indexed: 02/08/2023]
Abstract
To understand the pathways through which well-being contributes to health, we performed a systematic review according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) guidelines on the association between well-being and physiological markers in four categories, neurotransmitters, hormones, inflammatory markers, and microbiome. We identified 91 studies. Neurotransmitter studies (knumber of studies=9) reported only a possible positive association between serotonin and well-being. For the hormone studies (k = 48), a lower momentary cortisol level was related to higher well-being (meta-analytic r = -0.06), and a steeper diurnal slope of cortisol levels. Inflammatory marker studies (k = 36) reported negative or non-significant relations with well-being, with meta-analytic estimates of respectively r = -0.07 and r = -0.05 for C-reactive protein and interleukin-6. Microbiome studies (k = 4) reported inconsistent associations between different bacteria abundance and well-being. The results indicate possible but small roles of serotonin, cortisol, and inflammatory markers in explaining differences in well-being. The inconsistent and limited results for other markers and microbiome require further research. Future directions for a complete picture of the physiological factors underlying well-being are proposed.
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Affiliation(s)
- Lianne P de Vries
- Department of Biological Psychology, Vrije Universiteit Amsterdam, the Netherlands; Amsterdam Public Health Research Institute, Amsterdam University Medical Centres, Amsterdam, the Netherlands.
| | - Margot P van de Weijer
- Department of Biological Psychology, Vrije Universiteit Amsterdam, the Netherlands; Amsterdam Public Health Research Institute, Amsterdam University Medical Centres, Amsterdam, the Netherlands
| | - Meike Bartels
- Department of Biological Psychology, Vrije Universiteit Amsterdam, the Netherlands; Amsterdam Public Health Research Institute, Amsterdam University Medical Centres, Amsterdam, the Netherlands
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65
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Crapitto AJ, Campbell A, Harris AJ, Goldman AD. A consensus view of the proteome of the last universal common ancestor. Ecol Evol 2022; 12:e8930. [PMID: 35784055 PMCID: PMC9165204 DOI: 10.1002/ece3.8930] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 12/30/2022] Open
Abstract
The availability of genomic and proteomic data from across the tree of life has made it possible to infer features of the genome and proteome of the last universal common ancestor (LUCA). A number of studies have done so, all using a unique set of methods and bioinformatics databases. Here, we compare predictions across eight such studies and measure both their agreement with one another and with the consensus predictions among them. We find that some LUCA genome studies show a strong agreement with the consensus predictions of the others, but that no individual study shares a high or even moderate degree of similarity with any other individual study. From these observations, we conclude that the consensus among studies provides a more accurate depiction of the core proteome of the LUCA and its functional repertoire. The set of consensus LUCA protein family predictions between all of these studies portrays a LUCA genome that, at minimum, encoded functions related to protein synthesis, amino acid metabolism, nucleotide metabolism, and the use of common, nucleotide‐derived organic cofactors.
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Affiliation(s)
| | - Amy Campbell
- Perelman School of Medicine University of Pennsylvania Philadelphia Pennsylvania USA
| | - AJ Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China
| | - Aaron D. Goldman
- Department of Biology Oberlin College Oberlin Ohio USA
- Blue Marble Space Institute of Science Seattle Washington USA
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66
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A Standardized Framework for Better Understanding of Phenotypic Differences within Bacterial Phyla Based on Protein Domain. J Bacteriol 2022; 204:e0014122. [PMID: 35652670 PMCID: PMC9210965 DOI: 10.1128/jb.00141-22] [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
We propose a standardized framework to classify target species based on their protein domains, which can be utilized in different contexts, like eukaryotes and prokaryotes. In this study, by applying the framework to the bacterial kingdom as an implementation example and comparing the results with the current taxonomy standards at the phylum level, we came to the conclusion that the sequence of domains rather than the content of domains in a protein and the presence of one domain rather than the number of occurrences of one domain play more important roles in deciding bacterial phenotypes as well as matching the current taxonomy. In addition, the comparison also helps us to better focus on the species that conflict with the current phylum category, as well as to further investigate their phenotypic or genotypic differences. IMPORTANCE A 3-step framework was designed which can be applied to clustering species based on their protein domains, and different candidate models are proposed in each step for better adaptation of various scenarios. We show its implementation for the bacterial kingdom as an example, which helps us to find the most appropriate model combination that will best reflect the relationship between domains and phenotypes in this context. In addition, identifying species that are distant in the results but should be closely related phylogenetically can help us to focus on the mismatch for better understanding of their key phenotypic or genotypic differences.
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67
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Schuster J, Tollefson GA, Zarate V, Agudelo A, Stabila J, Ragavendran A, Padbury J, Uzun A. Protein Network Analysis of Whole Exome Sequencing of Severe Preeclampsia. Front Genet 2022; 12:765985. [PMID: 35719905 PMCID: PMC9201216 DOI: 10.3389/fgene.2021.765985] [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: 08/28/2021] [Accepted: 11/03/2021] [Indexed: 11/13/2022] Open
Abstract
Preeclampsia is a hypertensive disorder of pregnancy, which complicates up to 15% of US deliveries. It is an idiopathic disorder associated with several different phenotypes. We sought to determine if the genetic architecture of preeclampsia can be described by clusters of patients with variants in genes in shared protein interaction networks. We performed a case-control study using whole exome sequencing on early onset preeclamptic mothers with severe clinical features and control mothers with uncomplicated pregnancies between 2016 and 2020. A total of 143 patients were enrolled, 61 women with early onset preeclampsia with severe features based on ACOG criteria, and 82 control women at term, matched for race and ethnicity. A network analysis and visualization tool, Proteinarium, was used to confirm there are clusters of patients with shared gene networks associated with severe preeclampsia. The majority of the sequenced patients appear in two significant clusters. We identified one case dominant and one control dominant cluster. Thirteen genes were unique to the case dominated cluster. Among these genes, LAMB2, PTK2, RAC1, QSOX1, FN1, and VCAM1 have known associations with the pathogenic mechanisms of preeclampsia. Using bioinformatic analysis, we were able to identify subsets of patients with shared protein interaction networks, thus confirming our hypothesis about the genetic architecture of preeclampsia.
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Affiliation(s)
- Jessica Schuster
- Pediatrics, Women and Infants Hospital, Providence, RI, United States
- Pediatrics, Warren Alpert Medical School, Brown University, Providence, RI, United States
| | | | - Valeria Zarate
- Pediatrics, Women and Infants Hospital, Providence, RI, United States
| | - Anthony Agudelo
- Pediatrics, Women and Infants Hospital, Providence, RI, United States
| | - Joan Stabila
- Pediatrics, Women and Infants Hospital, Providence, RI, United States
| | - Ashok Ragavendran
- Center for Computation and Visualization, Brown University, Providence, RI, United States
- Computational Biology of Human Disease, Brown University, Providence, RI, United States
| | - James Padbury
- Pediatrics, Women and Infants Hospital, Providence, RI, United States
- Pediatrics, Warren Alpert Medical School, Brown University, Providence, RI, United States
- Center for Computational Molecular Biology, Brown University, Providence, RI, United States
| | - Alper Uzun
- Pediatrics, Women and Infants Hospital, Providence, RI, United States
- Pediatrics, Warren Alpert Medical School, Brown University, Providence, RI, United States
- Computational Biology of Human Disease, Brown University, Providence, RI, United States
- Center for Computational Molecular Biology, Brown University, Providence, RI, United States
- *Correspondence: Alper Uzun,
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68
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Hu Y, Amir A, Huang X, Li Y, Huang S, Wolfe E, Weiss S, Knight R, Xu ZZ. Diurnal and eating-associated microbial patterns revealed via high-frequency saliva sampling. Genome Res 2022; 32:1112-1123. [PMID: 35688483 DOI: 10.1101/gr.276482.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 05/18/2022] [Indexed: 11/24/2022]
Abstract
The oral microbiome is linked to oral and systemic health, but its fluctuation under frequent daily activities remains elusive. Here, we sampled saliva at 10- to 60-min intervals to track the high-resolution microbiome dynamics during the course of human activities. This dense time series data showed that eating activity markedly perturbed the salivary microbiota, with tongue-specific Campylobacter concisus and Oribacterium sinus and dental plaque-specific Lautropia mirabilis, Rothia aeria, and Neisseria oralis increased after every meal in a temporal order. The observation was reproducible in multiple subjects and across an 11-mo period. The microbiome composition showed significant diurnal oscillation patterns at different taxonomy levels with Prevotella/Alloprevotella increased at night and Bergeyella HMT 206/Haemophilus slowly increased during the daytime. We also identified microbial co-occurring patterns in saliva that are associated with the intricate biogeography of the oral microbiome. Microbial source tracking analysis showed that the contributions of distinct oral niches to the salivary microbiome were dynamically affected by daily activities, reflecting the role of saliva in exchanging microbes with other oral sites. Collectively, our study provides insights into the temporal microbiome variation in saliva and highlights the need to consider daily activities and diurnal factors in design of oral microbiome studies.
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Affiliation(s)
- Yichen Hu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, PR China
| | - Amnon Amir
- Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA.,Sheba Medical Center, Ramat Gan 52621, Israel
| | - Xiaochang Huang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, PR China
| | - Yan Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, PR China
| | - Shi Huang
- Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA
| | - Elaine Wolfe
- Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA
| | - Sophie Weiss
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, California 92093, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA.,Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - Zhenjiang Zech Xu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, PR China.,Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen 518001, China.,Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China
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69
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Khan S. Conformational spread drives the evolution of the calcium-calmodulin protein kinase II. Sci Rep 2022; 12:8499. [PMID: 35589775 PMCID: PMC9120016 DOI: 10.1038/s41598-022-12090-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 05/03/2022] [Indexed: 11/17/2022] Open
Abstract
The calcium calmodulin (Ca2+/CaM) dependent protein kinase II (CaMKII) decodes Ca2+ frequency oscillations. The CaMKIIα isoform is predominantly expressed in the brain and has a central role in learning. I matched residue and organismal evolution with collective motions deduced from the atomic structure of the human CaMKIIα holoenzyme to learn how its ring architecture abets function. Protein dynamic simulations showed its peripheral kinase domains (KDs) are conformationally coupled via lateral spread along the central hub. The underlying β-sheet motions in the hub or association domain (AD) were deconvolved into dynamic couplings based on mutual information. They mapped onto a coevolved residue network to partition the AD into two distinct sectors. A second, energetically stressed sector was added to ancient bacterial enzyme dimers for assembly of the ringed hub. The continued evolution of the holoenzyme after AD–KD fusion targeted the sector’s ring contacts coupled to the KD. Among isoforms, the α isoform emerged last and, it alone, mutated rapidly after the poikilotherm–homeotherm jump to match the evolution of memory. The correlation between dynamics and evolution of the CaMKII AD argues single residue substitutions fine-tune hub conformational spread. The fine-tuning could increase CaMKIIα Ca2+ frequency response range for complex learning functions.
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Affiliation(s)
- Shahid Khan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,SBA School of Science and Engineering, LUMS, Lahore, Pakistan. .,Laboratory of Cell Biology, NINDS, NIH, Bethesda, MD, 20892, USA.
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70
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Wan L, Li H, Sun G, Zhang L, Xu H, Su F, He S, Xiao F. Mutational Pattern Induced by 5-Fluorouracil and Oxaliplatin in the Gut Microbiome. Front Microbiol 2022; 13:841458. [PMID: 35572679 PMCID: PMC9101311 DOI: 10.3389/fmicb.2022.841458] [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: 12/22/2021] [Accepted: 02/17/2022] [Indexed: 11/17/2022] Open
Abstract
Chemotherapeutic agents, such as 5-fluorouracil (5-FU) and oxaliplatin (Oxi), can not only kill the cancer cell but also influence the proliferation of gut microbiota; however, the interaction between these drugs and gut microbiota remains poorly understood. In this study, we developed a powerful framework for taxonomy composition and genomic variation analysis to investigate the mutagenesis effect and proliferation influence of chemotherapeutic agents, such as 5-FU and Oxi, on gut microbiota and the interaction between these drugs and gut microbiota during chemotherapy. Using the gut microbiome data, we detected 1.45 million variations among the chemotherapy groups and found the drugs significantly affected mutation signatures of gut microbiota. Oxi notably increased transversion rate, whereas 5-FU reduced the rate. Traits related to cell division and nutrient mobilization showed evidence of strong selection pressure from chemotherapeutic agents. In addition, drug-associated bacteriome shift patterns and functional alterations were found: the metabolism changes in the 5-FU group implied that gut microbiota could provide additional nicotinamide adenine dinucleotide (NAD+) to inhibit cancer cell autophagy; in the Oxi group, the ribosome and lysine biosynthesis genes were obviously enriched. Our study provides a blueprint for characterizing the role of microbes and drug–microbe interaction in the gut microbiota response to chemotherapy.
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Affiliation(s)
- Li Wan
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Beijing Institute of Geriatrics, Chinese Academy of Medical Sciences, Beijing, China
| | - Hexin Li
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Gaoyuan Sun
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Lili Zhang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Hongtao Xu
- Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Su
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fei Xiao
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Beijing Institute of Geriatrics, Chinese Academy of Medical Sciences, Beijing, China
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71
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Ancient Origins of Cytoskeletal Crosstalk: Spectraplakin-like Proteins Precede the Emergence of Cortical Microtubule Stabilization Complexes as Crosslinkers. Int J Mol Sci 2022; 23:ijms23105594. [PMID: 35628404 PMCID: PMC9145010 DOI: 10.3390/ijms23105594] [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: 03/28/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 11/17/2022] Open
Abstract
Adhesion between cells and the extracellular matrix (ECM) is one of the prerequisites for multicellularity, motility, and tissue specialization. Focal adhesions (FAs) are defined as protein complexes that mediate signals from the ECM to major components of the cytoskeleton (microtubules, actin, and intermediate filaments), and their mutual communication determines a variety of cellular processes. In this study, human cytoskeletal crosstalk proteins were identified by comparing datasets with experimentally determined cytoskeletal proteins. The spectraplakin dystonin was the only protein found in all datasets. Other proteins (FAK, RAC1, septin 9, MISP, and ezrin) were detected at the intersections of FAs, microtubules, and actin cytoskeleton. Homology searches for human crosstalk proteins as queries were performed against a predefined dataset of proteomes. This analysis highlighted the importance of FA communication with the actin and microtubule cytoskeleton, as these crosstalk proteins exhibit the highest degree of evolutionary conservation. Finally, phylogenetic analyses elucidated the early evolutionary history of spectraplakins and cortical microtubule stabilization complexes (CMSCs) as model representatives of the human cytoskeletal crosstalk. While spectraplakins probably arose at the onset of opisthokont evolution, the crosstalk between FAs and microtubules is associated with the emergence of metazoans. The multiprotein complexes contributing to cytoskeletal crosstalk in animals gradually gained in complexity from the onset of metazoan evolution.
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72
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DiGiacomo J, McKay C, Davila A. ThermoBase: A database of the phylogeny and physiology of thermophilic and hyperthermophilic organisms. PLoS One 2022; 17:e0268253. [PMID: 35536846 PMCID: PMC9089862 DOI: 10.1371/journal.pone.0268253] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/25/2022] [Indexed: 11/19/2022] Open
Abstract
Thermophiles and hyperthermophiles are those organisms which grow at high temperature (> 40°C). The unusual properties of these organisms have received interest in multiple fields of biological research, and have found applications in biotechnology, especially in industrial processes. However, there are few listings of thermophilic and hyperthermophilic organisms and their relevant environmental and physiological data. Such repositories can be used to standardize definitions of thermophile and hyperthermophile limits and tolerances and would mitigate the need for extracting organism data from diverse literature sources across multiple, sometimes loosely related, research fields. Therefore, we have developed ThermoBase, a web-based and freely available database which currently houses comprehensive descriptions for 1238 thermophilic or hyperthermophilic organisms. ThermoBase reports taxonomic, metabolic, environmental, experimental, and physiological information in addition to literature resources. This includes parameters such as coupling ions for chemiosmosis, optimal pH and range, optimal temperature and range, optimal pressure, and optimal salinity. The database interface allows for search features and sorting of parameters. As such, it is the goal of ThermoBase to facilitate and expedite hypothesis generation, literature research, and understanding relating to thermophiles and hyperthermophiles within the scientific community in an accessible and centralized repository. ThermoBase is freely available online at the Astrobiology Habitable Environments Database (AHED; https://ahed.nasa.gov), at the Database Center for Life Science (TogoDB; http://togodb.org/db/thermobase), and in the S1 File.
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Affiliation(s)
- Juliana DiGiacomo
- NASA Ames Research Center, Moffett Field, California, United States of America
- * E-mail:
| | - Christopher McKay
- NASA Ames Research Center, Moffett Field, California, United States of America
| | - Alfonso Davila
- NASA Ames Research Center, Moffett Field, California, United States of America
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73
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Ma T, Xue H, Piao C, Liu C, Yang M, Bian D, Li Y. Reclassification of 11 Members of the Family Rhodobacteraceae at Genus and Species Levels and Proposal of Pseudogemmobacter hezensis sp. nov. Front Microbiol 2022; 13:849695. [PMID: 35495672 PMCID: PMC9044078 DOI: 10.3389/fmicb.2022.849695] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, motile bacterial strain, D13-10-4-6T, was isolated from the bark sample of Populus × euramericana. The strain could grow at 15-35°C, at pH 6-10 and in 0-4% (w/v) NaCl, and the strain tested positive for oxidase and catalase activities. The main polar lipids were phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The main respiratory quinone was Q-10, and the predominant fatty acid was C18:1 ω7c. The phylogenetic analyses showed that the strain belonged to the genus Pseudogemmobacter of the family Rhodobacteraceae. The family Rhodobacteraceae is an ecologically diverse group that includes bacteria from aquatic to terrestrial ecosystems. As a consequence, the classification of the family Rhodobacteraceae is difficult, not least when the early taxonomy work relied heavily on 16S rRNA gene analysis. Recently, the taxonomic status of many members of the family has been revised based on the genome analysis; however, there are still some classification conflicts due to the lack of genome sequences and parallel publication time. In this study, phylogenetic trees based on 16S rRNA gene, gyrB gene, and 120 concatenated proteins, the average amino acid identity (AAI) and percentage of conserved proteins (POCP) have been used for the analysis of strain D13-10-4-6T and other members of 15 genera within the family to further clarify their taxonomic relationships. For the data of phylogeny, AAI, and POCP, the taxonomic proposals are (1) reclassification of Rhodobacter tardus as the type species of a novel genus, Stagnihabitans gen. nov., as Stagnihabitans tardus comb. nov.; (2) reclassification of Tabrizicola alkalilacus, Tabrizicola sediminis, Tabrizicola algicola into a novel genus, Pseudotabrizicola gen. nov., as Pseudotabrizicola alkalilacus comb. nov., Pseudotabrizicola sediminis comb. nov., Pseudotabrizicola algicola comb. nov.; (3) reclassification of Rhodobacter sediminicola into the genus Cereibacter as Cereibacter sediminicola comb. nov.; (4) reclassification of Rhodobacter flagellatus, Rhodobacter thermarum, and Xinfangfangia soli into the genus Tabrizicola as Tabrizicola flagellatus comb. nov., Tabrizicola thermarum comb. Nov., and Tabrizicola soli comb. nov.; (5) reclassification of Xinfangfangia humi into the genus Pseudogemmobacter as Pseudogemmobacter humicola comb. nov.; (6) classification of strain D13-10-4-6T as a novel species of the genus Pseudogemmobacter, for which the name P. hezensis sp. nov. is proposed, the type strain is D13-10-4-6T (= CFCC 12033T = KCTC 82215T).
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Affiliation(s)
- Tengfei Ma
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Han Xue
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Chungen Piao
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Chengyi Liu
- Panzhihua City Academy of Agricultural and Forest Sciences, Panzhihua, China
| | - Mei Yang
- Panzhihua City Academy of Agricultural and Forest Sciences, Panzhihua, China
| | - Danran Bian
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Yong Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
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74
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Cavender-Bares J, Schneider FD, Santos MJ, Armstrong A, Carnaval A, Dahlin KM, Fatoyinbo L, Hurtt GC, Schimel D, Townsend PA, Ustin SL, Wang Z, Wilson AM. Integrating remote sensing with ecology and evolution to advance biodiversity conservation. Nat Ecol Evol 2022; 6:506-519. [PMID: 35332280 DOI: 10.1038/s41559-022-01702-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 02/10/2022] [Indexed: 12/31/2022]
Abstract
Remote sensing has transformed the monitoring of life on Earth by revealing spatial and temporal dimensions of biological diversity through structural, compositional and functional measurements of ecosystems. Yet, many aspects of Earth's biodiversity are not directly quantified by reflected or emitted photons. Inclusive integration of remote sensing with field-based ecology and evolution is needed to fully understand and preserve Earth's biodiversity. In this Perspective, we argue that multiple data types are necessary for almost all draft targets set by the Convention on Biological Diversity. We examine five key topics in biodiversity science that can be advanced by integrating remote sensing with in situ data collection from field sampling, experiments and laboratory studies to benefit conservation. Lowering the barriers for bringing these approaches together will require global-scale collaboration.
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Affiliation(s)
| | - Fabian D Schneider
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | | | - Amanda Armstrong
- Biospheric Sciences Laboratory, NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - Ana Carnaval
- Department of Biology, Ph.D. Program in Biology, City University of New York and The Graduate Center of CUNY, New York City, NY, USA
| | - Kyla M Dahlin
- Department of Geography, Environment, and Spatial Sciences, Michigan State University, East Lansing, MI, USA
| | - Lola Fatoyinbo
- Biospheric Sciences Laboratory, NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - George C Hurtt
- Department of Geographical Sciences, University of Maryland, College Park, MD, USA
| | - David Schimel
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Philip A Townsend
- Department of Forest and Wildlife Ecology, Univ. of Wisconsin-Madison, Madison, WI, USA
| | - Susan L Ustin
- Department of Land, Air and Water Resources and the John Muir Institute of the Environment, University of California, Davis, CA, USA
| | - Zhihui Wang
- Key Lab of Guangdong for Utilization of Remote Sensing and Geographical Information System, Guangdong Open Laboratory of Geospatial Information Technology and Application, Guangzhou Institute of Geography, Guangdong Academy of Sciences, Guangzhou, China
| | - Adam M Wilson
- Department of Geography, University at Buffalo, Buffalo, NY, USA
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75
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Guo D, Duan H, Cheng Y, Wang Y, Hu J, Shi H. Omicron-included mutation-induced changes in epitopes of SARS-CoV-2 spike protein and effectiveness assessments of current antibodies. MOLECULAR BIOMEDICINE 2022; 3:12. [PMID: 35461370 PMCID: PMC9034971 DOI: 10.1186/s43556-022-00074-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/25/2022] [Indexed: 02/08/2023] Open
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is spreading globally and continues to rage, posing a serious threat to human health and life quality. Antibody therapy and vaccines both have shown great efficacy in the prevention and treatment of COVID-19, whose development progress and adaptation range have attracted wide attention. However, with the emergence of variant strains of SARS-CoV-2, the neutralization activity of therapeutic or vaccine-induced antibodies may be reduced, requiring long-term virus monitoring and drug upgrade in response to its evolution. In this paper, conformational changes including continuous epitopes (CPs), discontinuous epitopes (DPs) and recognition interfaces of the three representative SARS-CoV-2 spike protein (SP) mutants (i.e., the Delta (B.1.617.2), Mu (B.1.621) and Omicron (B.1.1.529) strains), were analyzed to evaluate the effectiveness of current mainstream antibodies. The results showed that the conformation of SP wild type (WT) and mutants both remained stable, while the local antigenic epitopes underwent significant changes. Sufficient flexibility of SP CPs is critical for effective antibody recognition. The DPs of Delta, Mu and Omicron variants have showed stronger binding to human angiotensin converting enzyme-2 (hACE2) than WT; the possible drug resistance mechanisms of antibodies against three different epitopes (i.e., NTD_DP, RBD1_DP and RBD2_DP) were also proposed, respectively; the RBD2 of Delta, NTD of Mu, NTD and RBD2 of Omicron are deserve more attention in the subsequent design of next-generation vaccines. The simulation results not only revealed structural characteristics of SP antigenic epitopes, but also provided guidance for antibody modification, vaccine design and effectiveness evaluation.
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Affiliation(s)
- Du Guo
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Huaichuan Duan
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, 610106, China
| | - Yan Cheng
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Yueteng Wang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, 610106, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, 610106, China.
| | - Hubing Shi
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China.
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76
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Khedkar S, Smyshlyaev G, Letunic I, Maistrenko OM, Coelho LP, Orakov A, Forslund SK, Hildebrand F, Luetge M, Schmidt TSB, Barabas O, Bork P. Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes. Nucleic Acids Res 2022; 50:3155-3168. [PMID: 35323968 PMCID: PMC8989519 DOI: 10.1093/nar/gkac163] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/30/2022] [Accepted: 03/11/2022] [Indexed: 12/02/2022] Open
Abstract
Prokaryotic Mobile Genetic Elements (MGEs) such as transposons, integrons, phages and plasmids, play important roles in prokaryotic evolution and in the dispersal of cargo functions like antibiotic resistance. However, each of these MGE types is usually annotated and analysed individually, hampering a global understanding of phylogenetic and environmental patterns of MGE dispersal. We thus developed a computational framework that captures diverse MGE types, their cargos and MGE-mediated horizontal transfer events, using recombinases as ubiquitous MGE marker genes and pangenome information for MGE boundary estimation. Applied to ∼84k genomes with habitat annotation, we mapped 2.8 million MGE-specific recombinases to six operational MGE types, which together contain on average 13% of all the genes in a genome. Transposable elements (TEs) dominated across all taxa (∼1.7 million occurrences), outnumbering phages and phage-like elements (<0.4 million). We recorded numerous MGE-mediated horizontal transfer events across diverse phyla and habitats involving all MGE types, disentangled and quantified the extent of hitchhiking of TEs (17%) and integrons (63%) with other MGE categories, and established TEs as dominant carriers of antibiotic resistance genes. We integrated all these findings into a resource (proMGE.embl.de), which should facilitate future studies on the large mobile part of genomes and its horizontal dispersal.
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Affiliation(s)
- Supriya Khedkar
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Georgy Smyshlyaev
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.,Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Ivica Letunic
- Biobyte solutions GmbH, Bothestr 142, 69117 Heidelberg, Germany
| | - Oleksandr M Maistrenko
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
| | - Askarbek Orakov
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Sofia K Forslund
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.,Max Delbrück Centre for Molecular Medicine, Berlin, Germany.,Experimental and Clinical Research Center, Charité-Universitätsmedizin and Max-Delbrück Center, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Falk Hildebrand
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Mechthild Luetge
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Thomas S B Schmidt
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Orsolya Barabas
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.,Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.,Max Delbrück Centre for Molecular Medicine, Berlin, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,Yonsei Frontier Lab (YFL), Yonsei University, Seoul 03722, South Korea
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77
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Hardin WR, Alas GCM, Taparia N, Thomas EB, Steele-Ogus MC, Hvorecny KL, Halpern AR, Tůmová P, Kollman JM, Vaughan JC, Sniadecki NJ, Paredez AR. The Giardia ventrolateral flange is a lamellar membrane protrusion that supports attachment. PLoS Pathog 2022; 18:e1010496. [PMID: 35482847 PMCID: PMC9089883 DOI: 10.1371/journal.ppat.1010496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/10/2022] [Accepted: 04/04/2022] [Indexed: 12/01/2022] Open
Abstract
Attachment to the intestinal epithelium is critical to the lifestyle of the ubiquitous parasite Giardia lamblia. The ventrolateral flange is a sheet-like membrane protrusion at the interface between parasites and attached surfaces. This structure has been implicated in attachment, but its role has been poorly defined. Here, we identified a novel actin associated protein with putative WH2-like actin binding domains we named Flangin. Flangin complexes with Giardia actin (GlActin) and is enriched in the ventrolateral flange making it a valuable marker for studying the flanges' role in Giardia biology. Live imaging revealed that the flange grows to around 1 μm in width after cytokinesis, then remains uniform in size during interphase, grows in mitosis, and is resorbed during cytokinesis. A flangin truncation mutant stabilizes the flange and blocks cytokinesis, indicating that flange disassembly is necessary for rapid myosin-independent cytokinesis in Giardia. Rho family GTPases are important regulators of membrane protrusions and GlRac, the sole Rho family GTPase in Giardia, was localized to the flange. Knockdown of Flangin, GlActin, and GlRac result in flange formation defects. This indicates a conserved role for GlRac and GlActin in forming membrane protrusions, despite the absence of canonical actin binding proteins that link Rho GTPase signaling to lamellipodia formation. Flangin-depleted parasites had reduced surface contact and when challenged with fluid shear force in flow chambers they had a reduced ability to remain attached, confirming a role for the flange in attachment. This secondary attachment mechanism complements the microtubule based adhesive ventral disc, a feature that may be particularly important during mitosis when the parental ventral disc disassembles in preparation for cytokinesis. This work supports the emerging view that Giardia's unconventional actin cytoskeleton has an important role in supporting parasite attachment.
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Affiliation(s)
- William R. Hardin
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Germain C. M. Alas
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Nikita Taparia
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Elizabeth B. Thomas
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Melissa C. Steele-Ogus
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Kelli L. Hvorecny
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Aaron R. Halpern
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Pavla Tůmová
- Institute of Immunology and Microbiology, 1 Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Justin M. Kollman
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, United States of America
| | - Nathan J. Sniadecki
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
- Bioengineering, University of Washington, Seattle, Washington, United States of America
- Lab Medicine & Pathology, University of Washington, Seattle, Washington, United States of America
- Center for Cardiovascular Biology, University of Washington, Seattle, Washington, United States of America
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Alexander R. Paredez
- Department of Biology, University of Washington, Seattle, Washington, United States of America
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78
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Revealing the microbial heritage of traditional Brazilian cheeses through metagenomics. Food Res Int 2022; 157:111265. [DOI: 10.1016/j.foodres.2022.111265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/13/2022] [Accepted: 04/17/2022] [Indexed: 01/02/2023]
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79
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Konno N, Kijima Y, Watano K, Ishiguro S, Ono K, Tanaka M, Mori H, Masuyama N, Pratt D, Ideker T, Iwasaki W, Yachie N. Deep distributed computing to reconstruct extremely large lineage trees. Nat Biotechnol 2022; 40:566-575. [PMID: 34992246 PMCID: PMC9934975 DOI: 10.1038/s41587-021-01111-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 10/01/2021] [Indexed: 02/07/2023]
Abstract
Phylogeny estimation (the reconstruction of evolutionary trees) has recently been applied to CRISPR-based cell lineage tracing, allowing the developmental history of an individual tissue or organism to be inferred from a large number of mutated sequences in somatic cells. However, current computational methods are not able to construct phylogenetic trees from extremely large numbers of input sequences. Here, we present a deep distributed computing framework to comprehensively trace accurate large lineages (FRACTAL) that substantially enhances the scalability of current lineage estimation software tools. FRACTAL first reconstructs only an upstream lineage of the input sequences and recursively iterates the same produce for its downstream lineages using independent computing nodes. We demonstrate the utility of FRACTAL by reconstructing lineages from >235 million simulated sequences and from >16 million cells from a simulated experiment with a CRISPR system that accumulates mutations during cell proliferation. We also successfully applied FRACTAL to evolutionary tree reconstructions and to an experiment using error-prone PCR (EP-PCR) for large-scale sequence diversification.
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Affiliation(s)
- Naoki Konno
- Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Yusuke Kijima
- Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.,Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada.,These authors contributed equally: Yusuke Kijima, Keito Watano, Soh Ishiguro
| | - Keito Watano
- Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.,These authors contributed equally: Yusuke Kijima, Keito Watano, Soh Ishiguro
| | - Soh Ishiguro
- Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.,School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada.,These authors contributed equally: Yusuke Kijima, Keito Watano, Soh Ishiguro
| | - Keiichiro Ono
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mamoru Tanaka
- Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Hideto Mori
- Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Nanami Masuyama
- Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.,School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Dexter Pratt
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Trey Ideker
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA.,Departments of Bioengineering and Computer Science, University of California San Diego, La Jolla, CA, USA
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Nozomu Yachie
- Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan. .,School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada. .,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan. .,Graduate School of Media and Governance, Keio University, Fujisawa, Japan.
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80
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Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome. Nat Commun 2022; 13:1445. [PMID: 35301310 PMCID: PMC8931123 DOI: 10.1038/s41467-022-29096-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/22/2022] [Indexed: 12/20/2022] Open
Abstract
Mobile genetic elements (MGEs) carrying antibiotic resistance genes (ARGs) disseminate ARGs when they mobilise into new bacterial hosts. The nature of such horizontal gene transfer (HGT) events between human gut commensals and pathogens remain poorly characterised. Here, we compare 1354 cultured commensal strains (540 species) to 45,403 pathogen strains (12 species) and find 64,188 MGE-mediated ARG transfer events between the two groups using established methods. Among the 5931 MGEs, we find 15 broad host range elements predicted to have crossed different bacterial phyla while also occurring in animal and environmental microbiomes. We experimentally demonstrate that predicted broad host range MGEs can mobilise from commensals Dorea longicatena and Hungatella hathewayi to pathogen Klebsiella oxytoca, crossing phyla simultaneously. Our work establishes the MGE-mediated ARG dissemination network between human gut commensals and pathogens and highlights broad host range MGEs as targets for future ARG dissemination management.
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81
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Evolutionary genomic relationships and coupling in MK-STYX and STYX pseudophosphatases. Sci Rep 2022; 12:4139. [PMID: 35264672 PMCID: PMC8907265 DOI: 10.1038/s41598-022-07943-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 02/28/2022] [Indexed: 11/08/2022] Open
Abstract
The dual specificity phosphatase (DUSP) family has catalytically inactive members, called pseudophosphatases. They have mutations in their catalytic motifs that render them enzymatically inactive. This study analyzes the significance of two pseudophosphatases, MK-STYX [MAPK (mitogen-activated protein kinase phosphoserine/threonine/tyrosine-binding protein]) and STYX (serine/threonine/tyrosine-interacting protein), throughout their evolution and provides measurements and comparison of their evolutionary conservation. Phylogenetic trees were constructed to show any deviation from various species evolutionary paths. Data was collected on a large set of proteins that have either one of the two domains of MK-STYX, the DUSP domain or the cdc-25 homology (CH2) /rhodanese-like domain. The distance between species pairs for MK-STYX or STYX and Ka/Ks ratio were calculated. In addition, both pseudophosphatases were ranked among a large set of related proteins, including the active homologs of MK-STYX, MKP (MAPK phosphatase)-1 and MKP-3. MK-STYX had one of the highest species-species protein distances and was under weaker purifying selection pressure than most proteins with its domains. In contrast, the protein distances of STYX were lower than 82% of the DUSP-containing proteins and was under one of the strongest purifying selection pressures. However, there was similar selection pressure on the N-terminal sequences of MK-STYX, STYX, MKP-1, and MKP-3. We next perform statistical coupling analysis, a process that reveals interconnected regions within the proteins. We find that while MKP-1,-3, and STYX all have 2 functional units (sectors), MK-STYX only has one, and that MK-STYX is similar to MKP-3 in the evolutionary coupling of the active site and KIM domain. Within those two domains, the mean coupling is also most similar for MK-STYX and MKP-3. This study reveals striking distinctions between the evolutionary patterns of MK-STYX and STYX, suggesting a very specific role for each pseudophosphatase, further highlighting the relevance of these atypical members of DUSP as signaling regulators. Therefore, our study provides computational evidence and evolutionary reasons to further explore the properties of pseudophosphatases, in particular MK-STYX and STYX.
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82
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Finney AG, Perry JM, Evans DR, Westbrook KJ, McElheny CL, Iovleva A, Doi Y, Shields RK, Van Tyne D. Isolation and Characterization of Lytic Bacteriophages Targeting Diverse Enterobacter spp. Clinical Isolates. PHAGE (NEW ROCHELLE, N.Y.) 2022; 3:50-58. [PMID: 36147219 PMCID: PMC9041515 DOI: 10.1089/phage.2021.0011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Background: Enterobacter spp. are opportunistic pathogens that cause nosocomial infections. Bacteriophages could be used to treat antibiotic-resistant Enterobacter infections. Materials and Methods: We used 10 genetically diverse clinical Enterobacter spp. isolates to identify lytic bacteriophages in hospital and municipal wastewater. Comparative genomics was performed on host bacterial isolates and isolated phages. Activity of each phage against all 10 host isolates was determined. We also tested phage activity against paired isolates from two patients who developed ceftazidime-avibactam resistance. Results: Bacteria belonged to three Enterobacter species and Klebsiella aerogenes. We isolated 12 bacteriophages, most of which belonged to the Myoviridae and Autographiviridae families. Most phages were able to lyse multiple bacterial isolates, and many lysed isolates of different species. Ceftazidime-avibactam-resistant isolates were still phage susceptible, and one isolate showed increased susceptibility compared with the parent isolate. Conclusion: The phages we isolated expand the diversity of Enterobacter-targeting phages, and could be useful for treating antibiotic-resistant Enterobacter infections.
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Affiliation(s)
- Amanda G. Finney
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jalyne M. Perry
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Daniel R. Evans
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kevin J. Westbrook
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Christi L. McElheny
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Alina Iovleva
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ryan K. Shields
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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83
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Henry D, Joselevitch C, Matthews GG, Wollmuth LP. Expression and distribution of synaptotagmin family members in the zebrafish retina. J Comp Neurol 2022; 530:705-728. [PMID: 34468021 PMCID: PMC8792163 DOI: 10.1002/cne.25238] [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: 06/15/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 11/10/2022]
Abstract
Synaptotagmins belong to a large family of proteins. Although various synaptotagmins have been implicated as Ca2+ sensors for vesicle replenishment and release at conventional synapses, their roles at retinal ribbon synapses remain incompletely understood. Zebrafish is a widely used experimental model for retinal research. We therefore investigated the homology between human, rat, mouse, and zebrafish synaptotagmins 1-10 using a bioinformatics approach. We also characterized the expression and distribution of various synaptotagmin (syt) genes in the zebrafish retina using RT-PCR, qPCR, and in situhybridization, focusing on the family members whose products likely underlie Ca2+ -dependent exocytosis in the central nervous system (synaptotagmins 1, 2, 5, and 7). Most zebrafish synaptotagmins are well conserved and can be grouped in the same classes as mammalian synaptotagmins, based on crucial amino acid residues needed for coordinating Ca2+ binding and determining phospholipid binding affinity. The only exception is synaptotagmin 1b, which lacks 34 amino acid residues in the C2B domain and is therefore unlikely to bind Ca2+ there. Additionally, the products of zebrafish syt5a and syt5b genes share identity with mammalian class 1 and 5 synaptotagmins. Zebrafish syt1, syt2, syt5, and syt7 paralogues are found in the zebrafish brain, eye, and retina, excepting syt1b, which is only present in the brain. The complementary expression pattern of the remaining paralogues in the retina suggests that syt1a and syt5a may underlie synchronous release and syt7a and syt7b may mediate asynchronous release or other Ca2+ -dependent processes in different retinal neurons.
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Affiliation(s)
- Diane Henry
- Department of Neurobiology & Behavior, Stony Brook University, Stony Brook, NY 11794-5230,Center for Nervous System Disorders, Stony Brook University, Stony Brook, NY 11794-5230
| | - Christina Joselevitch
- Department of Neurobiology & Behavior, Stony Brook University, Stony Brook, NY 11794-5230,Center for Nervous System Disorders, Stony Brook University, Stony Brook, NY 11794-5230
| | - Gary G. Matthews
- Department of Neurobiology & Behavior, Stony Brook University, Stony Brook, NY 11794-5230,Center for Nervous System Disorders, Stony Brook University, Stony Brook, NY 11794-5230
| | - Lonnie P. Wollmuth
- Department of Neurobiology & Behavior, Stony Brook University, Stony Brook, NY 11794-5230,Department of Biochemistry & Cell Biology, Stony Brook University, Stony Brook, NY 11794-5230,Center for Nervous System Disorders, Stony Brook University, Stony Brook, NY 11794-5230
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84
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Moody ERR, Mahendrarajah TA, Dombrowski N, Clark JW, Petitjean C, Offre P, Szöllősi GJ, Spang A, Williams TA. An estimate of the deepest branches of the tree of life from ancient vertically-evolving genes. eLife 2022; 11:66695. [PMID: 35190025 PMCID: PMC8890751 DOI: 10.7554/elife.66695] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/07/2022] [Indexed: 11/30/2022] Open
Abstract
Core gene phylogenies provide a window into early evolution, but different gene sets and analytical methods have yielded substantially different views of the tree of life. Trees inferred from a small set of universal core genes have typically supported a long branch separating the archaeal and bacterial domains. By contrast, recent analyses of a broader set of non-ribosomal genes have suggested that Archaea may be less divergent from Bacteria, and that estimates of inter-domain distance are inflated due to accelerated evolution of ribosomal proteins along the inter-domain branch. Resolving this debate is key to determining the diversity of the archaeal and bacterial domains, the shape of the tree of life, and our understanding of the early course of cellular evolution. Here, we investigate the evolutionary history of the marker genes key to the debate. We show that estimates of a reduced Archaea-Bacteria (AB) branch length result from inter-domain gene transfers and hidden paralogy in the expanded marker gene set. By contrast, analysis of a broad range of manually curated marker gene datasets from an evenly sampled set of 700 Archaea and Bacteria reveals that current methods likely underestimate the AB branch length due to substitutional saturation and poor model fit; that the best-performing phylogenetic markers tend to support longer inter-domain branch lengths; and that the AB branch lengths of ribosomal and non-ribosomal marker genes are statistically indistinguishable. Furthermore, our phylogeny inferred from the 27 highest-ranked marker genes recovers a clade of DPANN at the base of the Archaea and places the bacterial Candidate Phyla Radiation (CPR) within Bacteria as the sister group to the Chloroflexota.
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Affiliation(s)
- Edmund R R Moody
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - James W Clark
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Celine Petitjean
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Pierre Offre
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Gergely J Szöllősi
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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85
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Evseev P, Lukianova A, Tarakanov R, Tokmakova A, Shneider M, Ignatov A, Miroshnikov K. Curtobacterium spp. and Curtobacterium flaccumfaciens: Phylogeny, Genomics-Based Taxonomy, Pathogenicity, and Diagnostics. Curr Issues Mol Biol 2022; 44:889-927. [PMID: 35723345 PMCID: PMC8929003 DOI: 10.3390/cimb44020060] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/19/2022] [Accepted: 02/08/2022] [Indexed: 11/29/2022] Open
Abstract
The genus of Curtobacterium, belonging to the Microbacteriaceae family of the Actinomycetales order, includes economically significant pathogenic bacteria of soybeans and other agricultural crops. Thorough phylogenetic and full-genome analysis using the latest genomic data has demonstrated a complex and contradictory taxonomic picture within the group of organisms classified as the Curtobacterium species. Based on these data, it is possible to delineate about 50 new species and to reclassify a substantial part of the Curtobacterium strains. It is suggested that 53 strains, including most of the Curtobacterium flaccumfaciens pathovars, can compose a monophyletic group classified as C. flaccumfaciens. A genomic analysis using the most recent inventory of bacterial chromosomal and plasmid genomes deposited to GenBank confirmed the possible role of Microbacteriaceae plasmids in pathogenicity and demonstrated the existence of a group of related plasmids carrying virulence factors and possessing a gene distantly related to DNA polymerase found in bacteriophages and archaeal and eukaryotic viruses. A PCR diagnostic assay specific to the genus Curtobacterium was developed and tested. The presented results assist in the understanding of the evolutionary relations within the genus and can lay the foundation for further taxonomic updates.
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Affiliation(s)
- Peter Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia; (A.L.); (A.T.); (M.S.)
- Limnological Institute, Siberian Branch of Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia
- Correspondence: (P.E.); (K.M.)
| | - Anna Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia; (A.L.); (A.T.); (M.S.)
| | - Rashit Tarakanov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str., 49, 127434 Moscow, Russia;
| | - Anna Tokmakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia; (A.L.); (A.T.); (M.S.)
- Moscow Institute of Physics and Technology, Federal University, Institutskiy per., 9, 141701 Dolgoprudny, Moscow Oblast, Russia
| | - Mikhail Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia; (A.L.); (A.T.); (M.S.)
| | - Alexander Ignatov
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str., 6, 117198 Moscow, Russia;
| | - Konstantin Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia; (A.L.); (A.T.); (M.S.)
- Correspondence: (P.E.); (K.M.)
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86
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Ventolero MF, Wang S, Hu H, Li X. Computational analyses of bacterial strains from shotgun reads. Brief Bioinform 2022; 23:6524011. [PMID: 35136954 DOI: 10.1093/bib/bbac013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/21/2022] Open
Abstract
Shotgun sequencing is routinely employed to study bacteria in microbial communities. With the vast amount of shotgun sequencing reads generated in a metagenomic project, it is crucial to determine the microbial composition at the strain level. This study investigated 20 computational tools that attempt to infer bacterial strain genomes from shotgun reads. For the first time, we discussed the methodology behind these tools. We also systematically evaluated six novel-strain-targeting tools on the same datasets and found that BHap, mixtureS and StrainFinder performed better than other tools. Because the performance of the best tools is still suboptimal, we discussed future directions that may address the limitations.
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Affiliation(s)
| | - Saidi Wang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Haiyan Hu
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA.,Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816, USA
| | - Xiaoman Li
- Burnett School of Biomedical Science, University of Central Florida, Orlando, FL 32816, USA
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87
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Pierella Karlusich JJ, Pelletier E, Zinger L, Lombard F, Zingone A, Colin S, Gasol JM, Dorrell RG, Henry N, Scalco E, Acinas SG, Wincker P, de Vargas C, Bowler C. A robust approach to estimate relative phytoplankton cell abundances from metagenomes. Mol Ecol Resour 2022; 23:16-40. [PMID: 35108459 PMCID: PMC10078663 DOI: 10.1111/1755-0998.13592] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 01/09/2022] [Accepted: 01/25/2022] [Indexed: 11/28/2022]
Abstract
Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is universally and exclusively present in photosynthetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the size-fractionated marine samples collected by Tara Oceans, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these ecosystems, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular-based surveys, we compiled a curated database of >18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular-based evaluations of entire phytoplankton communities.
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Affiliation(s)
- Juan José Pierella Karlusich
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France.,CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Eric Pelletier
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France.,CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Fabien Lombard
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Océanographie de Villefranche (LOV), 06230, Villefranche-sur-Mer, France.,Institut Universitaire de France (IUF), Paris, France
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Sébastien Colin
- European Molecular Biology Laboratory, Heidelberg, Germany.,Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP, 29680, Roscoff, France.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Richard G Dorrell
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France
| | - Nicolas Henry
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Eleonora Scalco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Patrick Wincker
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Colomban de Vargas
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP, 29680, Roscoff, France
| | - Chris Bowler
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France.,CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
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88
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Wienkes H, Vilen K, Lorentz A, Gerlach D, Wang X, Saupe A, Danila R, Lynfield R, Smith K, Medus C. Transmission of and Infection With COVID-19 Among Vaccinated and Unvaccinated Attendees of an Indoor Wedding Reception in Minnesota. JAMA Netw Open 2022; 5:e220536. [PMID: 35212747 PMCID: PMC8881767 DOI: 10.1001/jamanetworkopen.2022.0536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
IMPORTANCE Characterizing rates of SARS-CoV-2 infection among vaccinated and unvaccinated persons with the same exposure is critical to understanding the association of vaccination with the risk of infection with the Delta variant. Additionally, evidence of Delta variant transmission by children to vaccinated adults has important public health implications. OBJECTIVE To characterize transmission and infection of SARS-CoV-2 among vaccinated and unvaccinated attendees of an indoor wedding reception. DESIGN, SETTING, AND PARTICIPANTS This cohort study included attendees at an indoor wedding reception in Minnesota in July 2021. Data were collected from REDCap surveys and routine surveillance interviews. The full list of attendees and a partial list of emails were obtained. Fifty-seven attendees completed the emailed survey. Eighteen additional attendees were identified from the state health department COVID-19 surveillance database. EXPOSURES Attendance at an indoor event. MAIN OUTCOMES AND MEASURES Risk of SARS-CoV-2 infection among vaccinated and unvaccinated attendees, identification of an index case, whole genome sequencing (WGS) to identify the COVID-19 variant, understanding of transmission patterns, and assessment of secondary transmission. The primary case definition was an individual with a positive SARS-CoV-2 test who attended the wedding in the 14 days prior to their illness. RESULTS Data were gathered for 75 attendees (mean [SE] age, 37.5 [13.7] years; 57 [76%] female individuals), of whom 56 (75%) were fully vaccinated, 4 (5%) were partially vaccinated, and 15 (20%) were unvaccinated. Of 62 attendees who were tested, 29 (47%) tested positive, including 16 of 46 fully vaccinated attendees (35%), 2 of 4 partially vaccinated attendees (50%), and 11 of 12 unvaccinated attendees (92%). Being unvaccinated was associated with a higher risk of infection compared with being vaccinated (risk ratio, 2.64; 95% CI, 1.71-4.06; P = .001). One unvaccinated adult required hospitalization. An unvaccinated child who was symptomatic on the event date was identified as the index case. Eleven specimens were available for WGS. All sequenced specimens were closely related and were identified as the Delta variant. WGS supported secondary transmission from a vaccinated individual with SARS-CoV-2. CONCLUSIONS AND RELEVANCE This cohort study identified a COVID-19 Delta variant outbreak at an indoor event despite a high proportion of vaccinated attendees. It found that vaccination was associated with a reduced risk of infection.
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Affiliation(s)
| | | | - Alexandra Lorentz
- Minnesota Department of Health, St Paul
- Association of Public Health Laboratories, Silver Spring, Maryland
| | | | | | - Amy Saupe
- Minnesota Department of Health, St Paul
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89
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Forde TL, Dennis TPW, Aminu OR, Harvey WT, Hassim A, Kiwelu I, Medvecky M, Mshanga D, Van Heerden H, Vogel A, Zadoks RN, Mmbaga BT, Lembo T, Biek R. Population genomics of Bacillus anthracis from an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity. Microb Genom 2022; 8:000759. [PMID: 35188453 PMCID: PMC8942019 DOI: 10.1099/mgen.0.000759] [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] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/10/2021] [Indexed: 11/18/2022] Open
Abstract
Genomic sequencing has revolutionized our understanding of bacterial disease epidemiology, but remains underutilized for zoonotic pathogens in remote endemic settings. Anthrax, caused by the spore-forming bacterium Bacillus anthracis, remains a threat to human and animal health and rural livelihoods in low- and middle-income countries. While the global genomic diversity of B. anthracis has been well-characterized, there is limited information on how its populations are genetically structured at the scale at which transmission occurs, critical for understanding the pathogen's evolution and transmission dynamics. Using a uniquely rich dataset, we quantified genome-wide SNPs among 73 B. anthracis isolates derived from 33 livestock carcasses sampled over 1 year throughout the Ngorongoro Conservation Area, Tanzania, a region hyperendemic for anthrax. Genome-wide SNPs distinguished 22 unique B. anthracis genotypes (i.e. SNP profiles) within the study area. However, phylogeographical structure was lacking, as identical SNP profiles were found throughout the study area, likely the result of the long and variable periods of spore dormancy and long-distance livestock movements. Significantly, divergent genotypes were obtained from spatio-temporally linked cases and even individual carcasses. The high number of SNPs distinguishing isolates from the same host is unlikely to have arisen during infection, as supported by our simulation models. This points to an unexpectedly wide transmission bottleneck for B. anthracis, with an inoculum comprising multiple variants being the norm. Our work highlights that inferring transmission patterns of B. anthracis from genomic data will require analytical approaches that account for extended and variable environmental persistence, as well as co-infection.
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Affiliation(s)
- Taya L. Forde
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Tristan P. W. Dennis
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - O. Rhoda Aminu
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - William T. Harvey
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Ayesha Hassim
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Ireen Kiwelu
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Matej Medvecky
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | | | - Henriette Van Heerden
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Adeline Vogel
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Ruth N. Zadoks
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
- Present address: Sydney School of Veterinary Science, University of Sydney, Sydney, Australia
| | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Tiziana Lembo
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
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90
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Chen R, Zhao L, Gan R, Feng Z, Cui C, Xie X, Hao F, Zhang Z, Wang L, Ran T, Wang W, Zhang S, Li Y, Zhang W, Pang M, Xiong Q, Shao G. Evidence for the Rapid and Divergent Evolution of Mycoplasmas: Structural and Phylogenetic Analysis of Enolases. Front Mol Biosci 2022; 8:811106. [PMID: 35145997 PMCID: PMC8822174 DOI: 10.3389/fmolb.2021.811106] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 12/29/2021] [Indexed: 12/21/2022] Open
Abstract
Mycoplasmas are a group of prokaryotes without cell walls that have evolved through several rounds of degenerative evolution. With a low cell DNA G + C content and definitively long genetic lineages, mycoplasmas are thought to be in a state of rapid evolution. However, little associated evidence has been provided. Enolase is a key enzyme in glycolysis that is widely found in all species from the three domains, and it is evolutionarily conserved. In our previous studies, enolase acted as a virulence factor and participated in cell-surface adhesion in Mycoplasma hyopneumoniae. Furthermore, unique loop regions were first found in the crystal structure of Mhp Eno. Here, enolase structures from Mycoplasma pneumoniae and Mycoplasma bovis were determined. An extra helix 7 is specific and conservatively found in almost all mycoplasma enolases, as confirmed by crystal structures and sequence alignment. Particular motifs for helix 7, which is composed of F-K/G-K-L/F-K-X-A-I, have been proposed and could be regarded as molecular markers. To our surprise, the genetic distances between any two mycoplasma enolases were obviously longer than those between the two corresponding species themselves, indicating divergent evolution of mycoplasma enolases, whereas no horizontal gene transfer was detected in mycoplasma enolase genens. Furthermore, different evolutionary patterns were adopted by different loop regions of mycoplasma enolase. Enolases from different Mycoplasma species also showed different affinities for PLG and fibronectin. Our results indicate the rapid and divergent evolution of mycoplasma enolase and mycoplasmas. This study will also aid understanding the independent evolution of Mycoplasma species after separation from their common ancestor.
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Affiliation(s)
- Rong Chen
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Lin Zhao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Rong Gan
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zhixin Feng
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Chenxi Cui
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xing Xie
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Fei Hao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zhenzhen Zhang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Li Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Tingting Ran
- Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Weiwu Wang
- Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Shuijun Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yufeng Li
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wei Zhang
- Key Lab of Animal Bacteriology of Ministry of Agriculture, OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Wei Zhang, ; Maoda Pang, ; Qiyan Xiong,
| | - Maoda Pang
- State Key Laboratory Cultivation Base of MOST, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- *Correspondence: Wei Zhang, ; Maoda Pang, ; Qiyan Xiong,
| | - Qiyan Xiong
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- *Correspondence: Wei Zhang, ; Maoda Pang, ; Qiyan Xiong,
| | - Guoqing Shao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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91
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Barbosa EP, Seraphim N, Valencia G, Maria L Azeredo-Espin A, V L Freitas A. Phylogenetic systematics of Yphthimoides Forster, 1964 and related taxa, with notes on the biogeographical history of Yphthimoides species. Mol Phylogenet Evol 2022; 168:107390. [PMID: 35031455 DOI: 10.1016/j.ympev.2022.107390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/03/2021] [Accepted: 12/07/2021] [Indexed: 10/19/2022]
Abstract
Species losses are increasing and may have an impact on our understanding of patterns of evolutionary pathways and phylogenetic relationships among the groups being lost. The knowledge of such patterns can contribute to preventing future losses by identifying which lineages have higher or lower diversification rates, thus informing conservation strategies. Recent years have seen a significant growth in studies of butterfly systematics, allowing a better understanding of evolutionary relationships among most groups and revealing significant taxonomic chaos in several groups. One of the latter groups is the nymphalid subtribe Euptychiina (Satyrinae), which has been shown to include a number of non-monophyletic genera based on recent molecular phylogenetic analyses. Among others, these genera include Yphthimoides, which is widespread throughout the Neotropical region but particularly diverse in the southeastern Neotropics, and a pair of related genera, Pharneuptychia Forster, 1964 and Moneuptychia Forster, 1964. Using molecular data, this study scope and aims was to provide a phylogenetic hypothesis that corroborates Yphthimoides as presently conceived being non-monophyletic, a result reinforced by a comparative study of the male genitalic morphology. Our results also show that Pharneuptychia and Moneuptychia, plus a species misplaced elsewhere in the Euptychiina, Euptychoides castrensis (Schaus, 1902), form a well supported clade, and that the latter 'species' is a complex of cryptic species. We therefore propose a number of taxonomic rearrangements in the present work to resolve these issues: Yphthimoides eriphule (A. Butler, 1867) will be moved to a new genus; Y. affinis (A. Butler, 1867), Y. maepius (Godart, [1824]), Y. mimula (Hayward, 1954), Y. neomaenas (Hayward, 1967) and Y. mythra (Weymer, 1911) are being transferred to Malaveria Viloria & Benmesbah, 2021; Pharneuptychia innocentia (Godart, [1824]) will be moved to another genus to be described; and Euptychoides castrensis, Pharneuptychia romanina (Bryk, 1953) and Yphthimoides viviana (Romieux, 1927) are being moved to Moneuptychia. The dating of divergences points to a split between the ancestral lineage of Yphthimoides and its sister group, Carminda Ebert and Dias, inDias 1998, during the last half of the Miocene, around 11.86 Mya, and to the diversification of the Pharneuptychia during the same time 11.35 (± 3.52) Mya. Biogeographic analysis showed that the most recent common ancestor of Yphthimoides started to diversify either in the the Brazilian Cerrado savannas or in a combined area of Cerrado and South Atlantic Forest, with a possible change in the ancestral habitat of Carminda. Furthermore, ancestral character mapping favors a savanna origin hypothesis over a forest origin hypothesis.
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Affiliation(s)
- Eduardo P Barbosa
- Depto de Biologia Animal and Museu de Zoologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
| | - Noemy Seraphim
- Instituto de Educação, Ciência e Tecnologia de São Paulo, câmpus Campinas CTI Renato Archer - Av. Comendador Aladino Selmi, s/n - Amarais, Campinas - SP, 13069-901.
| | - Gorky Valencia
- Museo de Biodiversidad del Perú and Museo de Historia Natural de la Universidad Nacional San Antonio Abad del Cusco, Peru.
| | - Ana Maria L Azeredo-Espin
- Departamento de Genética, Evolução, Microbiologia e Imunologia e Centro de Biologia Molecular e Engenharia Genética, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
| | - André V L Freitas
- Depto de Biologia Animal and Museu de Zoologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
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92
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Signorini L, Dolci M, Castelnuovo N, Crespi L, Incorvaia B, Bagnoli P, Parapini S, Basilico N, Galli C, Ambrogi F, Pariani E, Binda S, Ticozzi R, Ferrante P, Delbue S. Longitudinal, virological, and serological assessment of hospitalized COVID-19 patients. J Neurovirol 2022; 28:113-122. [PMID: 34997473 PMCID: PMC8740865 DOI: 10.1007/s13365-021-01029-0] [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: 09/02/2021] [Revised: 10/14/2021] [Accepted: 11/09/2021] [Indexed: 11/03/2022]
Abstract
Here we described the virological and serological assessment of 23 COVID-19 patients hospitalized and followed up in Milan, Italy, during the first wave of COVID-19 pandemic. Nasopharyngeal (NPS), anal swabs, and blood samples were collected from 23 COVID-19 patients, at hospital admission, and periodically up to discharge, for a median time of 20 days (3-83 days). RNA was isolated and tested for SARS-CoV-2 by qRT-PCR; anti-SARS-CoV-2 IgM and IgG antibody titers were evaluated in serum samples by ELISA. SARS-CoV-2 genome was detected in the NPS swabs of the 23 patients, at the admission, and 8/19 (42.1%) were still positive at the discharge. Anal swabs were positive to SARS-CoV-2 RNA detection in 20/23 (86.9%) patients; 6/19 (31.6%) were still positive at discharge. The mean time of RNA negative conversion was 17 days (4-36 days) and 33 days (4-77 days), for NPS and anal swabs, respectively. SARS-CoV-2-RNA was detected in the blood of 6/23 (26.1%) patients. Thirteen/23 (56.5%) and 17/23 (73.9%) patients were seropositive for IgM and IgG, respectively, at the admission, and the median IgM and IgG levels significantly (p < 0.05) increased after 13 days. Although the limited cohort size, our report provides evidence that SARS-CoV-2 is shed through multiple routes, with important implications in healthcare settings.
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Affiliation(s)
- Lucia Signorini
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Via Pascal 36, 20133, Milan, Italy
| | - Maria Dolci
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Via Pascal 36, 20133, Milan, Italy
| | - Nicolò Castelnuovo
- Istituto Clinico Città Studi (ICCS), Via Jommelli 17, 20133, Milan, Italy
| | - Luigia Crespi
- Istituto Clinico Città Studi (ICCS), Via Jommelli 17, 20133, Milan, Italy
| | - Barbara Incorvaia
- Istituto Clinico Città Studi (ICCS), Via Jommelli 17, 20133, Milan, Italy
| | - Pietro Bagnoli
- Istituto Clinico Città Studi (ICCS), Via Jommelli 17, 20133, Milan, Italy
| | - Silvia Parapini
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Nicoletta Basilico
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Via Pascal 36, 20133, Milan, Italy
| | - Cristina Galli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Federico Ambrogi
- Department of Clinical and Community Sciences, University of Milan, Milan, Italy.,Scientific Directorate, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Sandro Binda
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Rosalia Ticozzi
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Via Pascal 36, 20133, Milan, Italy
| | - Pasquale Ferrante
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Via Pascal 36, 20133, Milan, Italy. .,Istituto Clinico Città Studi (ICCS), Via Jommelli 17, 20133, Milan, Italy.
| | - Serena Delbue
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Via Pascal 36, 20133, Milan, Italy
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93
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Bansal MS. Deciphering Microbial Gene Family Evolution Using Duplication-Transfer-Loss Reconciliation and RANGER-DTL. Methods Mol Biol 2022; 2569:233-252. [PMID: 36083451 DOI: 10.1007/978-1-0716-2691-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Phylogenetic reconciliation has emerged as a principled, highly effective technique for investigating the origin, spread, and evolutionary history of microbial gene families. Proper application of phylogenetic reconciliation requires a clear understanding of potential pitfalls and sources of error, and knowledge of the most effective reconciliation-based tools and protocols to use to maximize accuracy. In this book chapter, we provide a brief overview of Duplication-Transfer-Loss (DTL) reconciliation, the standard reconciliation model used to study microbial gene families and provide a step-by-step computational protocol to maximize the accuracy of DTL reconciliation and minimize false-positive evolutionary inferences.
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Affiliation(s)
- Mukul S Bansal
- Department of Computer Science & Engineering, University of Connecticut, Storrs, CT, USA.
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94
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Martinez-Gutierrez CA, Aylward FO. Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea. Mol Biol Evol 2021; 38:5514-5527. [PMID: 34436605 PMCID: PMC8662615 DOI: 10.1093/molbev/msab254] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Reconstruction of the Tree of Life is a central goal in biology. Although numerous novel phyla of bacteria and archaea have recently been discovered, inconsistent phylogenetic relationships are routinely reported, and many inter-phylum and inter-domain evolutionary relationships remain unclear. Here, we benchmark different marker genes often used in constructing multidomain phylogenetic trees of bacteria and archaea and present a set of marker genes that perform best for multidomain trees constructed from concatenated alignments. We use recently-developed Tree Certainty metrics to assess the confidence of our results and to obviate the complications of traditional bootstrap-based metrics. Given the vastly disparate number of genomes available for different phyla of bacteria and archaea, we also assessed the impact of taxon sampling on multidomain tree construction. Our results demonstrate that biases between the representation of different taxonomic groups can dramatically impact the topology of resulting trees. Inspection of our highest-quality tree supports the division of most bacteria into Terrabacteria and Gracilicutes, with Thermatogota and Synergistota branching earlier from these superphyla. This tree also supports the inclusion of the Patescibacteria within the Terrabacteria as a sister group to the Chloroflexota instead of as a basal-branching lineage. For the Archaea, our tree supports three monophyletic lineages (DPANN, Euryarchaeota, and TACK/Asgard), although we note the basal placement of the DPANN may still represent an artifact caused by biased sequence composition. Our findings provide a robust and standardized framework for multidomain phylogenetic reconstruction that can be used to evaluate inter-phylum relationships and assess uncertainty in conflicting topologies of the Tree of Life.
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Affiliation(s)
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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95
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Ghassemi N, Poulhazan A, Deligey F, Mentink-Vigier F, Marcotte I, Wang T. Solid-State NMR Investigations of Extracellular Matrixes and Cell Walls of Algae, Bacteria, Fungi, and Plants. Chem Rev 2021; 122:10036-10086. [PMID: 34878762 DOI: 10.1021/acs.chemrev.1c00669] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Extracellular matrixes (ECMs), such as the cell walls and biofilms, are important for supporting cell integrity and function and regulating intercellular communication. These biomaterials are also of significant interest to the production of biofuels and the development of antimicrobial treatment. Solid-state nuclear magnetic resonance (ssNMR) and magic-angle spinning-dynamic nuclear polarization (MAS-DNP) are uniquely powerful for understanding the conformational structure, dynamical characteristics, and supramolecular assemblies of carbohydrates and other biomolecules in ECMs. This review highlights the recent high-resolution investigations of intact ECMs and native cells in many organisms spanning across plants, bacteria, fungi, and algae. We spotlight the structural principles identified in ECMs, discuss the current technical limitation and underexplored biochemical topics, and point out the promising opportunities enabled by the recent advances of the rapidly evolving ssNMR technology.
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Affiliation(s)
- Nader Ghassemi
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Alexandre Poulhazan
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States.,Department of Chemistry, Université du Québec à Montréal, Montreal H2X 2J6, Canada
| | - Fabien Deligey
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | | | - Isabelle Marcotte
- Department of Chemistry, Université du Québec à Montréal, Montreal H2X 2J6, Canada
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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96
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Real-time kinetic studies of Mycobacterium tuberculosis LexA-DNA interaction. Biosci Rep 2021; 41:230259. [PMID: 34792534 PMCID: PMC8607333 DOI: 10.1042/bsr20211419] [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: 06/11/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 11/18/2022] Open
Abstract
Transcriptional repressor, LexA, regulates the ‘SOS’ response, an indispensable bacterial DNA damage repair machinery. Compared with its Escherichia coli ortholog, LexA from Mycobacterium tuberculosis (Mtb) possesses a unique N-terminal extension of additional 24 amino acids in its DNA-binding domain (DBD) and 18 amino acids insertion at its hinge region that connects the DBD to the C-terminal dimerization/autoproteolysis domain. Despite the importance of LexA in ‘SOS’ regulation, Mtb LexA remains poorly characterized and the functional importance of its additional amino acids remained elusive. In addition, the lack of data on kinetic parameters of Mtb LexA–DNA interaction prompted us to perform kinetic analyses of Mtb LexA and its deletion variants using Bio-layer Interferometry (BLI). Mtb LexA is seen to bind to different ‘SOS’ boxes, DNA sequences present in the operator regions of damage-inducible genes, with comparable nanomolar affinity. Deletion of 18 amino acids from the linker region is found to affect DNA binding unlike the deletion of the N-terminal stretch of extra 24 amino acids. The conserved RKG motif has been found to be critical for DNA binding. Overall, the present study provides insights into the kinetics of the interaction between Mtb LexA and its target ‘SOS’ boxes. The kinetic parameters obtained for DNA binding of Mtb LexA would be instrumental to clearly understand the mechanism of ‘SOS’ regulation and activation in Mtb.
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97
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Tickner J, Hawas S, Totsika M, Kenyon JJ. The Wzi outer membrane protein mediates assembly of a tight capsular polysaccharide layer on the Acinetobacter baumannii cell surface. Sci Rep 2021; 11:21741. [PMID: 34741090 PMCID: PMC8571296 DOI: 10.1038/s41598-021-01206-5] [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: 09/20/2021] [Accepted: 10/19/2021] [Indexed: 11/30/2022] Open
Abstract
Identification of novel therapeutic targets is required for developing alternate strategies to treat infections caused by the extensively drug-resistant bacterial pathogen, Acinetobacter baumannii. As capsular polysaccharide (CPS) is a prime virulence determinant required for evasion of host immune defenses, understanding the pathways for synthesis and assembly of this discrete cell-surface barrier is important. In this study, we assess cell-bound and cell-free CPS material from A. baumannii AB5075 wildtype and transposon library mutants and demonstrate that the Wzi outer membrane protein is required for the proper assembly of the CPS layer on the cell surface. Loss of Wzi resulted in an estimated 4.4-fold reduction in cell-associated CPS with a reciprocal increase in CPS material shed in the extracellular surrounds. Transmission electron microscopy revealed a disrupted CPS layer with sparse patches of CPS on the external face of the outer membrane when Wzi function was lost. However, this genotype did not have a significant effect on biofilm formation. Genetic analysis demonstrated that the wzi gene is ubiquitous in the species, though the nucleotide sequences were surprisingly diverse. Though divergence was not concomitant with variation at the CPS biosynthesis K locus, an association between wzi type and the first sugar of the CPS representing the base of the structure most likely to interact with Wzi was observed.
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Affiliation(s)
- Jacob Tickner
- grid.1024.70000000089150953Centre of Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Sophia Hawas
- grid.1024.70000000089150953Centre of Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Makrina Totsika
- grid.1024.70000000089150953Centre of Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Johanna J. Kenyon
- grid.1024.70000000089150953Centre of Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia
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98
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Jha V, Narjala A, Basu D, T. N. S, Pachamuthu K, Chenna S, Nair A, Shivaprasad PV. Essential role of γ-clade RNA-dependent RNA polymerases in rice development and yield-related traits is linked to their atypical polymerase activities regulating specific genomic regions. THE NEW PHYTOLOGIST 2021; 232:1674-1691. [PMID: 34449900 PMCID: PMC9290346 DOI: 10.1111/nph.17700] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/14/2021] [Indexed: 05/31/2023]
Abstract
RNA-dependent RNA polymerases (RDR) generate double-stranded (ds)RNA triggers for RNA silencing across eukaryotes. Among the three clades, α-clade and β-clade members are key components of RNA silencing and mediators of stress responses across eukaryotes. However, γ-clade members are unusual in that they are represented in phylogenetically distant plants and fungi, and their functions are unknown. Using genetic, bioinformatic and biochemical methods, we show that γ-clade RDRs from Oryza sativa L. are involved in plant development as well as regulation of expression of coding and noncoding RNAs. Overexpression of γ-clade RDRs in transgenic rice and tobacco plants resulted in robust growth phenotype, whereas their silencing in rice displayed strong inhibition of growth. Small (s)RNA and RNA-seq analysis of OsRDR3 mis-expression lines suggested that it is specifically involved in the regulation of repeat-rich regions in the genome. Biochemical analysis confirmed that OsRDR3 has robust polymerase activities on both single stranded (ss)RNA and ssDNA templates similar to the activities reported for α-clade RDRs such as AtRDR6. Our results provide the first evidence of the importance of γ-clade RDRs in plant development, their atypical biochemical activities and their contribution to the regulation of gene expression.
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Affiliation(s)
- Vikram Jha
- National Centre for Biological SciencesGKVK CampusBangalore560065India
- BIOSS Centre for Biological Signaling StudiesFaculty of BiologyAlbert‐Ludwigs‐Universität FreiburgFreiburg im Breisgau79104Germany
| | - Anushree Narjala
- National Centre for Biological SciencesGKVK CampusBangalore560065India
- SASTRA UniversityThirumalaisamudram, Thanjavur613401India
| | - Debjani Basu
- National Centre for Biological SciencesGKVK CampusBangalore560065India
| | - Sujith T. N.
- National Centre for Biological SciencesGKVK CampusBangalore560065India
- University of Trans‐Disciplinary Health Sciences and TechnologyBengaluru560064India
| | - Kannan Pachamuthu
- National Centre for Biological SciencesGKVK CampusBangalore560065India
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersailles78000France
| | - Swetha Chenna
- National Centre for Biological SciencesGKVK CampusBangalore560065India
- SASTRA UniversityThirumalaisamudram, Thanjavur613401India
| | - Ashwin Nair
- National Centre for Biological SciencesGKVK CampusBangalore560065India
- SASTRA UniversityThirumalaisamudram, Thanjavur613401India
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99
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Torres‐Bacete J, Luís García J, Nogales J. A portable library of phosphate-depletion based synthetic promoters for customable and automata control of gene expression in bacteria. Microb Biotechnol 2021; 14:2643-2658. [PMID: 33783967 PMCID: PMC8601176 DOI: 10.1111/1751-7915.13808] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/14/2021] [Indexed: 12/14/2022] Open
Abstract
Industrial biotechnology gene expression systems relay on constitutive promoters compromising cellular growth from the start of the bioprocess, or on inducible devices, which require manual addition of cognate inducers. To overcome this shortcoming, we engineered an automata regulatory system based on cell-stress mechanisms. Specifically, we engineered a synthetic and highly portable phosphate-depletion library of promoters inspired by bacterial PHO starvation system (Pliar promoters). Furthermore, we fully characterized 10 synthetic promoters within the background of two well-known bacterial workhorses such as E. coli W and P. putida KT2440. The promoters displayed an interesting host-dependent performance and a wide strength spectrum ranging from 0.4- to 1.3-fold when compared to the wild-type phosphatase alkaline promoter (PphoA). By comparing with available gene expression systems, we proved the suitability of this new library for the automata and effective decoupling of growth from production in P. putida. Growth phase-dependent expression of these promoters could therefore be activated by fine tuning the initial concentration of phosphate in the medium. Finally, the Pliar library was implemented in the SEVA platform in a ready-to-use mode allowing its broad use by the scientific community.
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Affiliation(s)
- Jesús Torres‐Bacete
- Department of Systems BiologyCentro Nacional de Biotecnología (CSIC)Madrid28049Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC)MadridSpain
| | - José Luís García
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC)MadridSpain
- Department of Microbial and Plant BiotechnologyCentro de Investigaciones Biológicas (CIB)Centro Nacional de Biotecnología (CSIC)MadridSpain
| | - Juan Nogales
- Department of Systems BiologyCentro Nacional de Biotecnología (CSIC)Madrid28049Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC)MadridSpain
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100
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Abstract
Chemosensory pathways are among the most abundant prokaryotic signal transduction systems, allowing bacteria to sense and respond to environmental stimuli. Signaling is typically initiated by the binding of specific molecules to the ligand binding domain (LBD) of chemoreceptor proteins (CRs). Although CRs play a central role in plant-microbiome interactions such as colonization and infection, little is known about their phylogenetic and ecological specificity. Here, we analyzed 82,277 CR sequences from 11,806 representative microbial species covering the whole prokaryotic phylogeny, and we classified them according to their LBD type using a de novo homology clustering method. Through phylogenomic analysis, we identified hundreds of LBDs that are found predominantly in plant-associated bacteria, including several LBDs specific to phytopathogens and plant symbionts. Functional annotation of our catalogue showed that many of the LBD clusters identified might constitute unknown types of LBDs. Moreover, we found that the taxonomic distribution of most LBD types that are specific to plant-associated bacteria is only partially explained by phylogeny, suggesting that lifestyle and niche adaptation are important factors in their selection. Finally, our results show that the profile of LBD types in a given genome is related to the lifestyle specialization, with plant symbionts and phytopathogens showing the highest number of niche-specific LBDs. The LBD catalogue and information on how to profile novel genomes are available at https://github.com/compgenomicslab/CRs. IMPORTANCE Considering the enormous variety of LBDs at sensor proteins, an important question resides in establishing the forces that have driven their evolution and selection. We present here the first clear demonstration that environmental factors play an important role in the selection and evolution of LBDs. We were able to demonstrate the existence of LBD families that are highly enriched in plant-associated bacteria but show a wide phylogenetic spread. These findings offer a number of research opportunities in the field of single transduction, such as the exploration of similar relationships in chemoreceptors of bacteria with a different lifestyle, like those inhabiting or infecting the human intestine. Similarly, our results raise the question whether similar LBD types might be shared by members of different sensor protein families. Lastly, we provide a comprehensive catalogue of CRs classified by their LBD region that includes a large number of putative new LBD types.
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